text:
\section{Introduction}
Two different  models for the formation of  gas giant planets in a disk
of gas and dust are under discussion.
Both are subject to major difficulties. A gravitational  instability
 in a disk (Boss 1997) would be a fast process but probably
is not achievable, except in the outer regions of a disk (beyond
$\approx 30$ AU; see \S 2.1),
 because of the requirement that the cooling rate
by radiation be comparable to or shorter than the orbital time scale
(Gammie 2001; Rice et al. 2003).
The core accretion model,  on the other hand,  explains a number of
observed properties of the giant planets in the solar system,  but for
standard low-mass disk parameters it  requires a time scale that is
longer than the expected lifetime of
the solar nebula. In order to explain the formation of Jupiter
within 3 million years or less (Hubickyj, Bodenheimer, \& Lissauer 2005),
one has to postulate an enhancement in the surface density of solid
particles in the disk well above (by a factor of $\sim 3$)
 that in the minimum mass solar nebula (MMSN; Weidenschilling 1977, Hayashi 1981).
Other detailed studies of the accretion
of the core of Jupiter (Weidenschilling 1998;
Inaba, Wetherill, \& Ikoma 2003; Thommes, Duncan, \& Levison
2003) suggest that the
disk has to have up to 10 times the mass of the MMSN.
Formation of the Oort cloud and the outward migration of Uranus and Neptune
imply the removal from that region of about 50 M$_\oplus$ of condensed
material, which is comparable to the core masses of all four
giant planets combined. Thus a more realistic minimum mass would be
about twice the classical value, which, however, is still insufficient
according to the recent simulations.
The discussion of an acceleration mechanism is the main point of this paper.
We wish to show that even in a MMSN it could be possible to form
Jupiter in the required time, just to show how efficient the mechanism
proposed in this paper can be.

\subsection{Formation of vortices}
   The vortices can either form primordially by perturbations
induced by matter infalling onto the disk (Barranco \& Marcus 2000),
or result from a hydrodynamical instability, such as  the Rossby wave
instability (Lovelace et al. 1999; Li et al. 2001)
or a global baroclinic instability (Klahr \& Bodenheimer 2003a,b).
Entropy gradients
in rotating systems can produce Rossby waves, which can eventually break into
vortices, as is known to occur near planetary surfaces in the solar system, and
in the atmospheres of giant planets.

{Until recently anti-cyclonic vortices were thought to
be excluded by the action of magnetohydrodynamics (MHD) and
that the magnetorotational instability (MRI) would destroy any
large scale vortices.
Recent simulations by Fromang \& Nelson (2005) showed the opposite.
They performed three-dimensional global MHD simulations of
protoplanetary disks in a cylindrical potential, very similar to previous studies by Armitage (1998), Hawley (2001) and Steinacker \& Papaloizou (2002).
But Fromang \& Nelson (2005) measured for the first time the vorticity
distribution of the flow and found that large-scale and long-lived
anti-cyclonic vortices formed.
These extended vorticity minima are easy to miss as
the short-lived and small-scale vorticity fluctuations
are stronger in amplitude.
They also found that up to 75$\%$ of all
meter sized objects  (referred to here as ``boulders")
randomly placed into the disk radially outside of the vortex
were captured in those vortices for
 a simulation which ran for a time of 200 orbits at the inner edge of the disk.
Less than half the boulders got lost and migrated off the grid,
potentially into the star.
We will again refer to this very important result for the discussion
of the capture probability of boulders by vortices.}

\subsection{Stability of vortices}

   Two-dimensional anti-cyclonic vortices can survive in protoplanetary disks
without strong turbulence,  that is, with low viscosity, for many orbits
 (Godon \& Livio 1999a,b).
The analytic solutions for large three-dimensional  vortices (Goodman, Narayan \& Goldreich 1987)
 have recently been numerically
tested for stability by Johansen, Andersen \& Brandenburg (2004).
They find that the lifetime of the  3-D  vortex is inversely
proportional to an artificially imposed  background viscosity.

{ Recently, Barranco \& Marcus (2005) studied the
stability of three-dimensional
vortices in stratified disks using an anelastic approximation.
They find that an analytic vortex solution
to the anelastic equations
is not hydrodynamically stable if placed in the midplane of a disk.
But these small subsonic\footnote{The anelastic approach can only handle
subsonic flows.}
vortices are quite different from the large
azimuthally extended vortices that show
up in Klahr \& Bodenheimer (2003a) and in Fromang \& Nelson (2005).
The vortex used by Barranco \& Marcus (2005) was placed into
the midplane,  but it decayed and reappeared in the stratified atmosphere
away from the midplane.
This indicates that stratification is actually
benefitial for the stability of the vortex.
In fact a vortex seems to be stable if it is flat, e.g.\ the vertical
extent is smaller than the radial and horiziontal extent. Stratification
is such an agent to keep vortices flat. Another possibility to allow for
flat vortices is to use global models beyond the limits of a shearing sheet box.
Fromang \& Nelson (2005) showed that a three-dimensional
vortex does survive in a global non-stratified disk.
Thus, it is possible that the instability in Barranco \& Marcus (2005)
results from the limitations of the anelastic and of the local approach,
while global and fully compressible
hydrodynamics and MHD indicate a certain stability for three-dimensional
anticylonic vortices.}

\subsection{Vortices in planet formation}
It has already been suggested that anti-cyclonic vortices can be beneficial
for the planetary formation process (Adams \& Watkins 1995, Barge \& Sommeria 1995;
Tanga et al. 1996; Godon \& Livio 1999b).
In general the vortices can be regarded as preferred
 formation sites of planets because they
tend to collect solid particles from the surrounding disk.
If one invokes a three-phase model for the planetary formation process (Klahr 2003; Klahr \& Bodenheimer 2003b,c)
one can regard the formation of vortices as phase one. Phase two is characterized by
the accumulation of solids in the center of vortices and by the growth of a
planetary core,  and phase three  by the accretion of gas onto the core.
In this paper we investigate the latter two
phases in the framework of the core accretion model (Pollack et al. 1996).
This model allows us to quantify the
reduction in formation time of Jupiter by accelerated solid accretion into vortices,
a radial expansion of the feeding zone,  and  a relatively efficient process of
 emptying the feeding zone.

We do not claim  that planetesimals cannot form without
a vortex, but vortices
accelerate the planetesimal formation. For giant planets there
is a time scale problem, to form the entire planet before the
disappearance of the gas,  which can be overcome by this mechanism.
For terrestrial planets that particular time scale  problem does not
exist, and we do not deal in this paper with the numerous
other problems of terrestrial planet formation.

Section 2  gives  an overview of the current formation scenarios
under discussion and shows  how the new scenario fits into the old
framework.
In Section 3 we derive the accretion rate of solid material
as  an input parameter for the core accretion model. This model
is then analyzed, in Section 4,
through numerical simulations, as a possible way to form Jupiter rapidly.
Section 5  summarizes and discusses  our results and
gives an outlook  for  future work.

\section{Planet Formation Models}
We introduce  the new three-phase planet formation scenario
 because we think that the current models under discussion have
substantial physical problems. The new model is not a revolutionary
approach,  but more a merging of the fundamental ideas from the
existing models plus some vortex theory from geophysical fluid dynamics.
Before we explain the new model we briefly describe the
existing models and elucidate in more detail what the difficulties are.
Further discussion of these models can be found in a review by
Bodenheimer \& Lin (2002).

\subsection{Disk Instability Model}
Boss (1997,\ 2001) proposed a model in which a
cool  protoplanetary disk, with roughly 10\% of the mass of
the star,  fragments  as a consequence of its
self gravity and spontaneously forms multiple
giant planets within a few orbital periods.
 Mayer et al. (2002) showed, in a numerical simulation with simple
assumptions regarding cooling, that fragments can form and survive
if the Toomre $Q$ parameter is low enough, in their case about 1.4.
The fundamental problem with this model is that it needs an almost
isothermal gas to allow for the collapse and to keep the Toomre parameter
low. Gammie (2001, see also Rice et al. 2003) shows that
the cooling time $t_{\rm cool}$ has to be smaller than
an orbital period $t_{\rm orb}$.
\begin{equation}
t_{\rm cool} < \frac{1}{2} t_{\rm orb}.
\end{equation}
Radiative diffusion within a dust-rich disk as well as in a self-gravitating
blob is
too inefficient to allow for such high cooling rates. Also
the recently invoked thermal convection can only slightly increase the
efficiency of the cooling (Bell et al. 1997); they show that
the maximum fraction of the energy carried vertically outward
through a disk  by convection is about 20\%.
Convection  in itself does not result in energy loss from the
 disk; it  only transports the
heat to the surface where it still has to be radiated away.
Even if strong convection would be able
to transport energy in the interior of the disk (Boss 2004)
the gas would still have to radiate at the surface as a black body, at a
maximum rate  proportional to $T^4$, where $T$ is the central
temperature in the disk.
The cooling time would then be longer than an orbital period for
radii out to 33 AU:
\begin{equation}
t_{\rm cool} \approx \frac{\Sigma c_v}{2 \sigma} T^{-3} =
 \frac{\Sigma}{10^3~{\rm g~cm}^{-2}} \left(\frac{T}{50 {\rm K}}\right)^{-3} \times 190 {\rm~yrs}.
\end{equation}
Here we used typical  surface densities $\Sigma$ and temperatures $T$ from the Boss model (Boss 2001);
$c_v$ is the specific heat and $\sigma$ is the Stefan-Boltzmann
constant. Note that for even only slightly smaller temperatures the
cooling time increases dramatically.
We argue  on the basis of  this estimate that it is possible
to form brown dwarf companions out of an extended
circumstellar disk at large radii but not planets
at the distances of Jupiter or Saturn.
Basically one can conclude that the conditions needed for planet formation
by gravitational instability are unlikely to occur in disks.

\subsection{Core Accretion}
In the other formation model
(e.g.\ Pollack et al. 1996; Wuchterl, Guillot \& Lissauer 2000),  first
a solid core of at least 5-10 $M_{\oplus}$ is  built
up via successive collisions of planetesimals.
Starting from this mass the core can accrete gas
from the disk. The  gas accretion rate is determined by
the cooling of the protoplanet. This means that as long
as there are still planetesimals plunging into the
planetary atmosphere and releasing their potential energy
 within, the planet  contracts only slowly and  can not accrete gas efficiently.
Only after the mass of the gaseous envelope approaches that of
the solid core  can the contraction of
the envelope take place fast enough to provide a runaway
gas accretion.  Even for massive
disks with three times the solid surface density  of the MMSN,
 it takes roughly 6 Myr to form Jupiter (Hubickyj et al. 2005), if the grain
opacity in the planetary envelope is based on an interstellar size
distribution.
However, their calculations also show that  by
artificially stopping the accretion of solids at an early
time after the core is established,  or by reducing the grain  opacity in
the envelope of the protoplanet  below the interstellar value, it is
possible
to start the runaway phase earlier. The reduction in grain opacity
is consistent with the detailed calculations of Podolak (2003).
 Also a modest  enhancement of
solids in the nebula, above three times that in the MMSN,
  can reduce the growth time substantially.

    This model contains another so far unsolved problem. Dust can efficiently
 coagulate to build boulders up to a size of tens of centimeters (Blum \& Wurm
 2000).
 Sedimentation and radial drift due to gas drag and the sub-Keplerian rotation of the disk
 provide high enough relative velocities for
 efficient capture of smaller particles. At the same time the impact
 velocities are low enough so that the surface of the boulder is not destroyed
 by sputtering and fragmentation (e.g.\ Leinhardt, Richardson, \& Quinn 2000) faster
 than it is supplied with mass.

 But by the time the boulder reaches meter size,
it will drift with velocity up to 100 m s$^{-1}$ at 1 AU  (Weidenschilling \& Cuzzi 1993),
 or 22 m s$^{-1}$
at 7.5 AU (which is the case we consider in \S 3.2).
 At velocities above 10  m s$^{-1}$  the boulder gets eroded
 by the many impacts of smaller grains due to the high relative velocity
 with respect to the smaller objects. If this would not be a problem on its own,
 there is another effect. At a velocity of 100 m s$^{-1}$ the boulder
 will drift
 into the sun faster than it can grow to a large enough size to be beyond the
regime  of high radial drift velocities.
Thus the mechanism for forming kilometer-sized planetesimals is still an open
question.

 To be fair,   in general there is no strong observational evidence
that distinguishes between core accretion models and gravitational
instability models, except that the correlation of the incidence of extrasolar
planets with metallicity of the host star
 (Santos et al. 2003; Fischer \& Valenti 2005) does favor core accretion models somewhat.

\subsection{The Role of Vortices}
Vortices combine the previous models in the following sense:
anti-cyclonic vortices stabilize mass concentrations
 in the protoplanetary disk,
for example the blobs in the Boss model,  against shear.  In this case the
stabilizing effect is not
gravity but the action of Coriolis forces.
The resulting flow is in a so-called geostrophic balance, between
pressure effects and Coriolis effects.
The vortices are stable flow features
even without cooling,  and  they do not need self gravity to
stay bound (Goodman et al. 1987). This is the same effect that stabilizes
hurricanes on earth or the giant red spot on Jupiter.

We suggest three reasons why vortices may be important  for planet formation.
In contrast to the sub-Keplerian gaseous
disk,  (1) at least the centers of vortices orbit at the Keplerian rate,
(2)  they have no vertical shear, and (3)
they have  no radial shear and thus  will not generate (MHD)-turbulence.
The following  subsections amplify these points briefly.

\subsubsection{Vortices move at Keplerian speed}
First one has to define the center of the vortex, which we take to
be given by the maximum in pressure, and which we refer to as the ``eye".
At a local pressure maximum the radial and azimuthal
pressure gradients vanish. Thus the only forces
determining the motion of the gas at the eye of the
vortex are gravity and centrifugal force. Thus the eye
must move on a Keplerian orbit and is not bound to the
sub-Keplerian motion of the gas outside the vortex.

For the vortex to generate a local pressure maximum
in the disk, it must exceed some minimum strength, or
amplitude, in terms of vorticity.
 While all cyclones are low-pressure regions
and all anticyclones high-pressure regions, just
as in the earth's  atmosphere, a weak vortex will not
generate a local pressure maximum in the radially
falling pressure profile in a disk.
However    the anticyclones  reported in the numerical simulations of
 Klahr \& Bodenheimer (2003a)
are between 30 \% to 100 \% higher in pressure than the ambient
gas, and they have a chance
to decouple from the gas with the eye on a Keplerian orbit.

   What are the consequences of this? Once  small solid particles  have
accumulated in the eye of the vortex and have grown to kilometer size,
they will decouple from the gas and no longer actively
be bound to the vortex eye by the vortical gas motion. However they
also will be in Keplerian motion, along with the eye.
Thus,   as long as there are no additional effects scattering
them out of the vortex eye,  the planetesimals may well stay in co-orbit with
the vortex for many, many orbits.

{Simulations by Klahr \& Bodenheimer (2003c) and Fromang \& Nelson (2005) have
shown that meter-sized boulders stay captured once they are inside a vortex for
hundreds of orbits even if the overall disk flow is strongly turbulent.
Yet it is still to be shown what happens to objects large enough to
decouple from the gas flow. They might  drift out of the vortex due
to some residual non-Keplerian drift of the vortex or even be scattered out
of the vortex by the gravitational torques of the disk gas (Fromang \& Nelson 2005).
The fate of kilometer sized and larger objects definitively needs
 further investigation.}

\subsubsection{Vortices have no vertical shear}

The vertical shear in an accretion disk
is purely an effect of the stronger sub-Keplerian motion
of the gas in the midplane than in the upper layers of the
disk, because the pressure is the highest in the midplane
and thus the radial pressure support the strongest.
In contrast,  all  the way through the vertical extent
of the vortex eye, the gas will move at the
Keplerian frequency. Of course this vertical direction
is not the vertical direction of a cylindrical
coordinate system but is  given by the local effective gravity
in the  system co-rotating with the vortex eye, which means
that the  rotational axis of the vortex bends
slightly towards the rotational axis of the accretion disk with
increasing height above the midplane.
In a thin accretion disk this  effect may well be unobservable.

   The effect of the non-existence of a vertical shear is very
interesting.
It means that solids can sediment to the midplane and
concentrate  to a density higher than the  critical value where
 self-gravitational effects become important,
without generating a shear layer instability (Cuzzi et al. 1993).

\subsubsection{Inside a vortex there is potentially no (MHD)-turbulence}
As is known for hurricanes on earth, the eye of
a (anti-) cyclone is quiet. There is probably
little or no turbulence acting in the center of
a vortex, because  shear is required for the generation of,
for instance, the magnetorotational instability.
This radial shear is not present in a giant vortex.
   The vortices are also likely to be in a thermodynamical
equilibrium owing to their relatively small dimensions, so  that
a baroclinic instability is also unlikely.

    As a result of this absence of turbulence there
will be very small RMS velocities between the
boulders. Also,
 collisions will be gentle, and the likelihood
of scattering out of the vortex is small.

It was already suggested that vortices
could be the direct precursors of planetary formation.
The planets could form either by concentration of dust in the centers of
the vortices, as was suggested by Barge \& Sommeria (1995),
or by sufficient gas accretion onto a vortex so that it undergoes
gravitational collapse (Adams \&  Watkins 1995).
The latter possibility seems unlikely in the light of our observation
(Klahr \& Bodenheimer 2003a)
that the vortices are still far away from a critical Jeans mass.

   Basically we think that there are three possibilities concerning  what
happens to the solids once they are captured in the eye of
the anti-cyclone.
\begin{enumerate}
\item{}The naive picture assumes that all
captured solids will contribute to one single growing
core. This picture has the possibly significant problem that
the core
might actually leave the vortex  once it  grows to kilometer size
and decouples from the gas.
Even though  we stated that a strong geostrophic vortex will
orbit at the Keplerian rate, as will the kilometer-size planetesimal,
there are two sources of danger.
First,   the vortex is a dynamical feature, and it could migrate in the
radial direction
by interaction with the ambient disk.  Second, even when the core
forms from material with basically the same angular momentum
as the vortex eye, a small variation in the specific kinetic
energy in the azimuthal direction can lead to a  slow azimuthal
drift of the core out of the eye of the vortex. This problem
might be overcome once one starts to investigate the feedback
of the core on the gas, via gravity as well as via friction.
These effects might stabilize once more the gas around the core.

\item{}In a second model one can assume that the boulders (meter size)
that accrete into the vortex interior do  not
accumulate in the center and  form one giant core, but that they
form a ``core zone", enriched in solid mass but still containing some gas.
This particle layer could then eventually undergo gravitational collapse (Goldreich \& Ward 1973),
which in this case will not be prevented by vertical shear. The precise conditions
 for this instability  will have to be derived elsewhere;
in particular, the velocity dispersion of the accumulated particles
has to  be investigated in detail.
{A similar study for solids immersed in local MHD turbulence has been
performed by Johansen, Klahr \& Henning (2006),  who discuss the
possibility of gravoturbulent formation of planetesimals in small-scale
short-lived vortices.
This study should be expanded to a global simulation.}

   This picture has the benefit that all boulders might stay actually captured
by the vortex until the core forms in one single collapse. Thus even if
 the vortex is not 100 percent precisely  Keplerian,  or if it radially migrates.
the solids would follow the vortex and not get ejected.

\item{}In any case we do not expect the physical capturing process to be
perfect. Thus probably a smaller or larger fraction of planetesimals that
have decoupled from the gas may get ejected from   the vortex.
If this is a minor effect, then this is a wonderful way to
produce planetesimals in vortices and then scatter them to other
regions of the disk, where they could be used in
the formation of other planets, that form
independently of a vortex.

   If this scattering of the planetesimals out of the
cyclone is more the rule than the exception, then it
will become unlikely to form a planetary core mass inside the vortex.
Nevertheless the process would produce 100 m to 1 km planetesimals
which are difficult to form by any other means because of the effects
of gas drag.
Once  scattered out of the vortex, the planetesimals
will stay at about the same radius. These planetesimals, whose total mass
would be 10--20 M$_\oplus$ or more,
would thus still be in a radially confined and strongly enriched feeding-zone
and could  accumulate to a core by collisions and gravitational focussing, as
is assumed in the classical picture (Pollack et al.\ 1996).
 Thus the formation of a core for  a giant planet is  more likely at the
radial position of a vortex, as the formation time for the core
becomes reasonably small. Thus even if a planetary core does not
form in a vortex, the presence of the vortex may be
 very beneficial for planet formation.
\end{enumerate}

The third idea will have to be elaborated elsewhere.
For this paper we will follow pictures one and two or
an arbitrary mixture of both. For our model it is
not important how the core forms, as long as the mass
of the solids inside the core zone starts to gravitationally act on
the surrounding gas in the eye of the vortex. Thus we simply
assume that sooner or later the accreted solids will provide
the potential well for the giant planet formation.

We propose that the formation of planets is probably characterized by three phases,
that depend directly on each other:
\begin{itemize}
\item{Phase 1: Formation of anti-cyclonic vortices as pre-protoplanetary condensations}
\item{Phase 2: Accumulation of solids into the vortices  to form
 protoplanetary cores}
\item{Phase 3: Accretion of gas onto  the protoplanetary cores}
\end{itemize}
The following section will quantify phase 2, while
section 4 will make predictions on both phases  2 and 3.

\section{Accretion Rate of Solid Material}
The accretion rate of solid material $\dot M_s$ onto the planetary
core depends on the available mass $M_{s}$ in solid material
in the feeding zone of the planetary embryo,
the time scale for particle production $\tau_p$, the time scale
for radial drift $\tau_d$,{  and the capture probability $q_c$. }
\begin{equation}
\dot M_s = \frac{q_c M_s}{{\rm max}\left\{\tau_d, \tau_p\right\}}
\end{equation}
Whatever time scale is longer determines
the accretion rate.

{ The capture probability $q_c$ has shown to be between 50$\%$ and 75$\%$
(Fromang \& Nelson 2005; see also Klahr \& Bodenheimer 2003c).
The high capture rate  can be explained in the following way. The vortex is not a
completely isolated entity in the disk. Even if it stretches only over 45 to 60 degrees
in the azimuthal direction,
the rotational profile is also changed in the rest of the disk.    The
remaining 300 degrees of the disk at the radial  location of the anti-cyclone
can be interpreted as a large and thus weak cyclone. This cyclone
expels particles and therefore hinders their inward passage.
It eventually transports them towards the anti-cyclone. It can be observed in the
relevant simulations (Fromang \& Nelson 2005) that
particles randomly distributed in the disk radially outside of
the vortex first  drift to the radial location
of the vortex and then drift azimuthally towards the center of the vortex.
In the following we simply use the symbol  $M_{s}$ to represent $ q_c M_{s} $.
The consequence is that the minimum mass disk required to form Jupiter will
be increased by $q_c^{-1}$ which is probably less than 2.}

\subsection{Mass of Solid Material}
In the standard core accretion model only mass in
the vicinity of the core, in an annulus extending outward in both
directions  from the planet to about
4 Hill sphere radii,
can be swept up via gravitational attraction and accreted onto the core.
The Hill sphere  radius is
\begin{equation}
R_H = R \left(\frac{M_p}{3 M_\ast} \right) ^ {\frac{1}{3}}
\end{equation}
where $R$ is the distance to the central star and $M_p$ and $M_\ast$ are
the masses of the planet and the central star, respectively. The value
during planet formation
is relatively small, leading to the need of a high surface density in
solids and gas for the disk.         It also grows
only slowly with the mass of the planetary embryo, which makes
the initial growth from less than an earth mass a long process.
The formation process is also held up by the slow contraction
rate of the gaseous envelope, once the core has swept up most of
the available solid material.
Models without an anti-cyclonic vortex need a surface density in
solid material about three times that of the MMSN
to form Jupiter at 5 AU  in less than $10^7$ years,
which  is the maximum accepted lifetime of the nebula itself.

   If there are anti-cyclonic vortices in the disk, then the
accumulation of solids is no longer driven by gravity but
by gas drag. Thus, the reservoir of solids that can be accreted
is not given by the Hill radius,
 but simply by the radial separation
of the vortices in the solar nebula. Simulations (Klahr \& Bodenheimer 2003c, Fromang \& Nelson 2005)
have shown that mobile solids are accreted into their closest inner
vortex in a short time at a 50-75 $\%$  percent efficiency.
For this paper we consider
the inner (Jupiter) vortex to be located at 5 AU and the outer (Saturn) vortex
at 10 AU. We adopt a reasonable solar nebula model (Bell et al. 1997)
with a total surface density of $250~{\rm g}~{\rm cm}^{-2}$ on the average from 5 AU out to 10 AU.
These parameters correspond to a disk with an effective viscosity
of $\alpha = 10^{-3}$ and a mean accretion rate of the disk gas onto
the star of  $\dot M = 10^{-8}$ M$_\odot$ yr$^{-1}$.
With these parameters one is close to the MMSN
and also in good agreement with the currently accepted accretion disk theory.
For a conservative solid to gas fraction of $1:100$ this corresponds to
a surface density of  $\Sigma_d = 2.5{\rm~g~cm}^{-2}$ in solid material.
 The total solid  mass between 5 and 10 AU is then:
\begin{equation}
M_{s} = 2 \pi \Sigma_d R_{mean} dR  = 1.33 \times 10^{29} {\rm g} = 22 M_\earth.
\end{equation}
This is enough mass to form a core for Jupiter, even if the
growth and capture processes   are not 100 percent efficient,
and also to explain its  mean  metallicity.
{ If the capture probability is as low as 50 $\%$ (Fromang \& Nelson 2005),
then one can still compensate for  this effect by a two times larger mass
in the nebula, which is still less than the 10 times MMSN required by
previous work (Weidenschilling 1998;
Inaba, Wetherill, \& Ikoma 2003; Thommes, Duncan, \& Levison
2003).}

\subsection{Particle Drift}
The radial drift velocity $v_r$ of particles with friction time
$\tau_f$ sets a lower limit to the aggregation time
of a core in the anti-cyclonic vortex:
\begin{equation}
\tau_d = dR / v_r(R_{mean}).
\end{equation}
The actual time a particle of radius $a \sim 30~{\rm cm}$ needs inside the vortex to spiral to its center is
only one orbital time ($10~{\rm yr}$) (Chavanis 2000) and thus can be neglected, as we
will see later. Chavanis (2000) also calculated the escape probability due to stochastic
motion for the
boulders and found that  30 cm particles have no chance to escape
from the vortex in the time needed for the planet formation process.

The radial drift velocity for the relevant objects, up to meter size,  is given by
 Weidenschilling \& Cuzzi (1993):
\begin{equation}
v_r = 2 dV \Omega \tau_f,
\end{equation}
where  $\Omega$ is the orbital frequency and
$dV$ is the deviation of the rotational velocity of the gas from the Keplerian value,
which is an effect of the radial pressure gradient in the gas.
This deviation can be estimated to be
\begin{equation}
dV = \frac{c_s^2}{\Omega R}.
\end{equation}
The sound speed at $R_{mean} = 7.5 AU$ in our model is
 $c_s = 4 \times 10^4~{\rm cm/s}$,
and the Keplerian velocity is $V_{Kep} = 1.1  \times 10^6~{\rm cm/s}$. Thus
the deviation from Keplerian velocity is
\begin{equation}
dV = 1.5 \times 10^3~ {\rm cm/s}.
\end{equation}
The dimensionless friction time ($\tau_f \Omega$) for particles of radius $a$
 and density $\rho_d$
in the Epstein regime is  determined by
\begin{equation}
\tau_f \Omega = \frac{a \rho_d}{c_s \rho} \Omega \approx \frac{a \rho_d}{\Sigma},
\end{equation}
for gas of density $\rho$  and  surface density $\Sigma$.
The maximum drift velocity will occur for $\tau_f \Omega = 1$ particles with $\rho_d = 1.39~{\rm g/cm}^3$
at the size of $180~{\rm cm}$.
We can then define:
\begin{equation}
v_r = dV \frac{a}{90 {\rm cm}} {{\rm cm}/{\rm sec}},
\end{equation}
which holds for boulders of up to $90~{\rm cm}$ in radius.
The drift time for $dR = 2.5$ AU is a function of particle size:
\begin{equation}
\tau_d = 8 \times 10^2 \frac{90~{\rm cm}}{a}~{\rm yr}.
\end{equation}
So even for bowling-ball-sized boulders ($a = 10.8~{\rm cm}$)
the radial drift time is less than $8000~{\rm yr}$.
In Figure \ 1 we  compare the radial drift time as a function of
particle size to the characteristic growth time.

\subsection{Particle Growth}
The weakest point of our estimate is the growth time $\tau_p$ for
$1~{\rm cm}$ to $1~{\rm m}$ sized boulders starting from
micron sized dust, or, to be more precise,
the production rate of those objects $\dot M_p = M_{s} / \tau_p$.
Smaller objects do not decouple sufficiently  from
the gas to reach a vortex in less than the lifetime of the protoplanetary disk.
Based on simulations of particle growth (e.g.\ Weidenschilling \&  Cuzzi 1993)
 and experiments by Blum \& Wurm (2000)
we assume the following scenario: particles grow first by Brownian
motion which takes only a couple of thousand years at $7.5$ AU.
This initial growth  can occur while the vortex at 5 AU is still forming, which
also will take a few times $10^4$ years (Klahr \& Bodenheimer 2003a).
Afterwards particles sediment and grow owing to sedimentation,
which is also a fast process. Then they drift radially inward and sweep up smaller particles
until the collision velocity exceeds the fragmentation velocity of about $10^3$ cm/s.
This part of the growth  takes the  longest time,  and thus we neglect the time
used in the previous stages.
During the radial drift, the mass gain per boulder $\dot m$ is given by
\begin{equation}
\dot m = v_r \sigma_d n_s m_s.
\end{equation}
This means the accumulation of mass $\dot m$ is proportional to the relative
velocity $v_r$ between the boulder and smaller particles, the cross section
of the boulder $\sigma_d$, the number density $n_s$ of the smaller particles in the
path of the boulder and their mass per particle $m_s$.
This expression can be simplified and leads to an differential equation for the
particles' mass ($m$)
as a function of the reference particle size $a_0 = 90$ cm and of the ratio between the density
of the boulder $\rho_d$ to the density of the small dust material
$\rho_s = \Sigma_s / H = 6 \times 10^{-13}~{\rm g}~{\rm cm}^{-3}$ in the gas:
\begin{equation}
\dot m = m \left(\frac{6 dV}{4 a_0} \frac{\rho_s}{\rho_d}\right).
\end{equation}
This equation  indicates exponential growth with the typical
time $\tau_g$ at 7.5 AU of
\begin{equation}
\tau_g = \frac{90}{1.1 \times 10^3} \frac{\rho_d}{\rho_s} {\rm sec}= 6 \times 10^3 {\rm yr}.
\end{equation}
The entire growth time $\tau_e$ for particles from micron to
10 cm sized objects, e.g.\ fifteen orders of magnitude
in mass,
should be about $\tau_e = 10^5~{\rm yr}$, as a rough
estimate with the assumed physics.
{ This gives only an upper limit to the growth time. Any settling would
decrease the growth time.}

  From Figure \ 1 we see that the drift time scale $\tau_d$ is shorter than the
growth time scale $\tau_g$ for particles larger than $10$ cm.
This means after they reach a size of $10$ cm they will drift
into the next vortex  before they  can  grow by an order of magnitude in size.
Thus, the boulders grow on the average in $\tau_e = 10^5$ yrs to the critical size, and then
they become accreted within $4 \times 10^3~{\rm yr}$ into the center of the vortex to form the core.

  It is more complicated to estimate the production rate $\sim \tau_p$ of $10$ cm solids.
Theoretically, all boulders could grow simultaneously and reach the critical size at the
same time. Then the production rate would be infinite and the drift time scale the
only limiting factor.
On the other hand there is a spread in the particle size distribution (see Weidenschilling \& Cuzzi 1993). This translates into a spread in the time that particles need to grow to the critical size
of maybe $\pm \frac{1}{2} \tau_e$.
Thus, we can conservatively estimate an
accretion rate of solids of
$\dot M_s = 2.2 \times 10^{-4} M_\earth / {\rm yr}$.
 In  case our estimate is still wrong by one order of magnitude
we also consider a model of $\dot M_s = 2.2 \times 10^{-5} M_\earth / {\rm yr}$ and compare the results.

It is interesting to note that the drift time will be smaller than
the growth time for particles of about $a = 10~{\rm cm}$ (see Fig.\ 1),
which means that no significant number of larger particles can probably form
outside the vortices and thus, the critical velocities for
fragmentation of particles which occurs for $a = 90~{\rm cm}$ sized
boulders will not be reached. This fragmentation was so far considered to be
the end of planetesimal growth (e.g.\ Leinhardt, Richardson, \& Quinn 2000), and the formation
of larger objects an unsolved problem. We conclude that vortices are
not only helpful to form gas giants but also to build up planetesimals,
which will be either scattered out of the vortex later on or set free
after the vortex has dispersed.

\section{Time Scales for Gas Accretion}

The assumed mechanism for planet formation is the
core accretion -- gas capture process. The vortex is assumed
to have been formed at 5 AU from the central object.  Particles
in the 10 cm size range  migrate inward in the disk
as a result of gas drag and accumulate in the vortex
where they quickly spiral toward its center. The
vortex is assumed to last long enough so that all the
solid particles originally  between 5 and 10 AU are
captured by it.

The procedure for numerically calculating the formation of
a planet is described by Pollack et al. (1996).  There
are three main elements of the calculation: 1) the determination
of $\dot M_{\rm s}$ by accretion of planetesimals, 2)
the calculation of the interaction of accreting planetesimals
with the gaseous envelope through which they fall, to determine
where they dissolve in the envelope or whether they reach the
core, and 3) the calculation of the evolution of the
envelope. Steps 1 and 2 are simplified in the current
calculations.

Although Pollack et al. (1996) made a detailed calculation
of the variable accretion rate of planetesimals onto a
planetary core, in this case we simply assume that small
particles are accreted at a constant rate by the vortex,
and that they quickly fall to the center to join the
planetary core. The accretion rate stays constant until all
the available solid material has been accreted by the vortex,
after which time $\dot M_{\rm s}$ is set to zero. This
last assumption also differs from those of Pollack et al.
(1996) in that they assume that solid accretion continues
even during the gas accretion phase. In our picture there are
no further solids available to accrete. The core is set to a
constant density of 3.2 g cm$^{-3}$.

\begin{table}%
\begin{tabular}{l|l|r|r|r|l|l|l|l}
 Case & $\dot M_{\rm s} (M_\odot yr^{-1})$ &$  M_{\rm core,final} (M_\earth)$ &          Opacity & Formation Time (yrs)\\
\hline
{I}   &$2.2 \times 10^{-4}$ & 22 & high &$0.3 \times 10^{6}$\\
{II}  &$2.2 \times 10^{-5}$ & 15 & high &$1.3 \times 10^{6}$\\
{III} &$2.2 \times 10^{-5}$ & 15 & low  &$0.8 \times 10^{6}$

\end{tabular}
\caption{\label{tab1} Parameters chosen in the different
models and resulting formation time for Jupiter. }
\end{table}
\clearpage

The planetesimal interaction with the gaseous envelope is not
calculated. Planetesimals are assumed to fall through the envelope
and hit the core, or, if they become dissolved in the envelope,
to settle to the core. These assumptions do not give results
significantly different from those of Pollack et al. (1996).
Thus the energy liberated at the boundary of the core by planetesimals
falling onto it is approximately
\begin{equation}
L_{\rm acc} ={{ G M_{\rm core} \dot M_{\rm s}} \over {R_{\rm core}}}
\end{equation}

The calculation of the envelope is carried out through an
implicit numerical solution of the spherically symmetric stellar
structure equations as given by Bodenheimer \& Pollack (1986). The
energy sources are planetesimal  accretion and gravitational contraction
of the gas. The outer edge of the planet at a radius $R_{\rm p}$
 is assumed to be the smaller of
the Hill sphere radius (eq. 4) or the Bondi accretion radius
\begin{equation}
R_b \approx {{G M_{\rm p}} \over {c^2}}
\end{equation}
where $c$ is the sound speed in the disk just outside the planet.
The surface boundary conditions at   $R_{\rm p}$  are taken to be
a constant density and temperature taken from a standard disk
model (Bell et al.\ 1997). In the cases presented here the outer
temperature $T_{\rm neb} = 150$ K, and the outer density
$\rho_{\rm neb}= 5 \times 10^{-11}$  g cm$^{-3}$. The mass accretion
rate for the envelope $\dot M_{\rm gas}$  is determined by the requirement that
$R_{\rm p} = {\rm min}(R_H, R_b)$.
These radii expand as the planet gains mass, and especially at later
stages the planet tends to contract, so  mass is added until
the above requirement is satisfied.

  The equation of state of the
envelope, which is assumed to have solar composition, is provided
by the tables of  Saumon, Chabrier, \& Van Horn (1995).   The opacities
are provided by grains at low temperatures, and by molecules and other
sources at temperatures above about 1800 K, where the most refractory
grains evaporate. The highest temperatures that are encountered are in
the range 20,000 K. The  Rosseland mean
 opacities in the range 800--20,000 K are
provided by the table of Alexander \& Ferguson (1994), while those
in the lower temperature range are obtained from Pollack, McKay,
\& Christofferson (1985). These opacities in the grain regime are
based on the assumption that they have an interstellar size distribution.
In the absence of detailed calculations, we assume that the grains
in the vortex in the gas outside the planetary core have those
properties. However we do one calculation in which the opacity in the
grain regime (only) is reduced by a factor of 100. This assumption
is justified  by the work of Podolak (2003), who did a calculation of
grain coagulation, settling, and evaporation in the envelope of a
protoplanet, redid the opacity calculation on the basis of the
modified size distribution that he found, and concluded that the
opacities are roughly two or more orders of magnitude reduced from
the interstellar values.

The initial condition for the simulation of the evolution of the
envelope is taken to be a core mass of 1 M$_\oplus$. The hydrostatic
solution for the value of the envelope mass at that point gives
a value of $1 \times 10^{-4}$ M$_\oplus$. During the course of the
calculation the envelope mass remains small until the core mass
has reached its limiting value, after which time the envelope mass
grows at an accelerating rate. When the envelope mass equals the
core mass, the rapid gas accretion phase begins,  during which the
total mass builds up to the final planet mass, as determined by
disk clearing or gap formation, on a time scale of only $10^4$ yr.
Since the main point of the calculation is to determine the
formation time of the planet, we stop the calculation when the
envelope mass is slightly larger than the core mass. We note that
a standard core accretion process, without the presence of the
vortex, in a disk at 5 AU with a solid surface density of 2.5
g  cm$^{-2}$, would have a formation time much longer than the
typical half-life of a disk, 3 Myr (Haisch et al. 2001).

The parameters of the three cases are listed in Table I.  Case I
is the standard case discussed above. In Case II the assumed
accretion rate is decreased by a factor of 10, and it is assumed
that the final core mass is only 15 M$_\oplus$. Both of these
changes tend to increase the formation time, so these parameters
give a rather unfavorable case for planet formation. Case III is
identical to Case II, except the grain opacities are reduced
by a factor of 100. This change tends to speed up planet
formation during the phase of relatively slow gas accretion
(Pollack et al. 1996).

As discussed above the evolution separates fairly neatly into
a core accretion phase and an envelope accretion phase.
The masses of the core and envelope, as well as the luminosity
radiated at the planet's surface, are  plotted as a function of
time for Case I in Figure  \ref{fig1.ref}.  During the first
20000 yr the value of $\dot M_s$ is gradually increased from an initial
value of $1.4 \times 10^{-5}$ M$_\oplus$ yr$^{-1}$ to its final
constant value of $2.2 \times 10^{-4}$ M$_\oplus$ yr$^{-1}$, which it
reaches when the core mass is 2  M$_\oplus$. The luminosity at this
point is $10^{-5}  $ L$_\odot$. Thereafter
the core mass grows linearly with time, the envelope mass is negligibly
small, and the luminosity grows as $M_{\rm core}^{2/3}$.
Starting at about $10^5$ yr, $\dot M_s$ is smoothly reduced to zero.
The envelope mass at this time is about 0.2  M$_\oplus$. As the energy
source arising from accretion of planetesimals is cut off, the
luminosity rapidly falls, since the only remaining source is the
gravitational contraction of the low-mass envelope. The luminosity
levels off at just above  $10^{-6}  $ L$_\odot$.
As the envelope contracts rapidly to supply the radiated luminosity,
its mass increases according to the requirement that the outer
edge of the planet be at $R_{\rm p}$.          As the envelope mass
increases, the luminosity increases as well. At about $3 \times 10^5$
yr the core mass and envelope mass are the same, the so-called
crossover mass. Thereafter the envelope mass increases extremely
rapidly until gas accretion is terminated by gap opening or by
the dissipation of the disk. This later stage is not followed
because the total formation time will be only slightly longer than
the time to crossover. Essentially planet formation is complete
at  $3 \times 10^5$ yr, a factor of 20 faster than the standard
core accretion model would need with a considerably higher (factor 4)
solid surface density and with the same opacity.

A plot of the same quantities is shown in Figure  \ref{fig2.ref}
for Case II. The core accretion rate is a factor 10 slower than in
Case I and the accretion time for the core is $ 6 \times 10^5$ yr,
less than a factor of 10 longer than in Case I because the final core
mass is only 14.7   M$_\oplus$ rather than 22 M$_\oplus$.
At  a core mass  of 2  M$_\oplus$, the luminosity is  $10^{-6}  $ L$_\odot$,
a factor of 10 lower than that in Case I at the same core mass.
Again the luminosity drops by about an order of magnitude just after the
core accretion is cut off, then begins to climb again as the envelope mass
approaches that of the core. The luminosity during most of the envelope
accretion phase is about a factor 5 less than that in Case 1, mainly
as a result of the smaller core mass, as explained in Pollack et al. (1996).
Thus the contraction rate, and the accretion rate of the gas, are slower
by a similar factor. The gas accretion phase lasts $7 \times 10^5$ yr,
compared to  $1.8 \times 10^5$ yr in Case I. The overall evolution time
is $1.3 \times 10^6$ yr, a factor of 4.3 longer than that in Case I,
but still shorter than typical disk lifetimes.

 The only difference between Case II and  Case III (Figure \ref{fig3.ref})
is the reduction of the opacity in the envelope. The core accretion phase is
unaffected, so the time scale and luminosity are the same as in Case II.
The reduction in the envelope opacity results in an increase in the
average envelope luminosity by about a factor of 3 in comparison with
Case II. The envelope accretion phase lasts $2.2 \times 10^5$ yr,
and the total formation time is $8.2 \times 10^5$ yr.
Note that if the same opacity reduction had been applied to Case I,
which has the standard core accretion rate, the overall evolution time
would have been  only $2 \times 10^5$ yr, which is the most likely estimate
of the planetary formation time in a vortex, since it incorporates the
most reasonable values of parameters.

\section{Conclusion}
We present a new formation model for gas giants.
The general idea is that a giant vortex can accelerate
the core formation considerably, even in a low-mass disk.
The envelope accretion phase is speeded up also, because once
the core has accreted all available solid material, the only energy
source available for the gaseous envelope is its own contraction.
The main reason for the long formation times for Jupiter  in the earlier
models of Pollack et al. (1996) was the additional contribution
of planetesimal accretion to the energy supply  of the envelope,
during the first part of the gas accretion phase.
We determine approximately,   for the first time, the resulting
time scales of such a scenario for the case of Jupiter's formation in a MMSN,
{ (or twice MMSN, if the capture probability is as low as 50$\%$)}.
If  a vortex  had been
responsible for the formation of Jupiter, the formation time
would fall in  the range $2 \times 10^5$  -- $1.3 \times 10^6$ yr.

   The major drawback of our model is that there are no direct  observations
of giant vortices in protoplanetary disks so far. But observations
are planned to look for giant vortices with future instruments such as
ALMA (Wolf \& Klahr 2002).
A vortex can be observed with ALMA because
it is usually a region of higher gas surface density and thus also more
dust is available to emit radiation.
The boulders that
become trapped in the vortices are not observable, but if they collide
then some micron sized debris could enhance the dust to gas ratio and
increase the opacity in the vortex region. But again, in Wolf \& Klahr (2002)
we show that the vortex can be
observed even without accumulating more dust.

This paper concentrates on the second and third  of the phases
outlined in \S 2.3. It
still needs to be proved that (1) conditions necessary for vortex
formation actually commonly occur in disks, and (2) that a vortex actually
survives long enough so that a planetary core of 10--20 M$_\oplus$ can form
in it. Initial studies by Li et al. (2001) and Klahr \& Bodenheimer (2003a,b)
and most recently for the case of MHD by Fromang \& Nelson (2005)
indicate that vortices can form, and work by Adams \& Watkins (1995)
and Johansen et al.\ (2004) shows that vortices
can survive,  at least  up to several $10^4$ yr at 5 AU (Godon
\& Livio 1999a,b).
A linear stability analysis shows that vorticity can be generated
from entropy gradients in the disk (Klahr 2004; Johnson \& Gammie 2005),
which is  a necessary condition to form large scale vortices.
Johansen \& Klahr (2005) showed that in local MHD simulations
one can find anti-cyclonic vortices to form and concentrate
particles, but those small vortices which are
part of the turbulent flow, do only survive a few orbits, before they
decay.
{ Even more convincing are the global simulations by Fromang \& Nelson (2005)
which find the formation of long-lived anti-cyclonic vortices
in MHD turbulence. Thus, it seems that vortex formation
is a generic feature to any kind of turbulence in
accretion disks.}

Further work is required to show how robust the vortex production process is.
Assuming that the above conditions are satisfied, the  main
 benefits of the vortex-core planet formation model are:
\begin{itemize}
\item{No need for a solar nebula much more massive than minimum mass.}
\item{Diminished loss of boulders as a result of drift into the central object.}
\item{No fragmentation of boulders as a result of   high impact velocities.}
\item{Gentle aggregation of a core in the quiet eye of the vortex, which need not be
self-gravitating.}
\item{A formation time far less than the lifetime of the nebula.}
\end{itemize}

{ We conclude that  this model is able to solve outstanding problems in the theory
of planet formation, and that further work on the difficult problem of vortex
generation, through  MHD
simulations  including radiation transport,  transport and feedback effects
 of the
solid boulders, and self gravity in three space dimensions, is warranted.}

\acknowledgments
We want to thank our referee Stuart Weidenschilling
for his constructive criticism, and
Doug Lin and Norm Murray for fruitful discussions.
This research
has been supported in part by the NSF through grant AST-9987417,
by NASA through grants NAG5-4610,  NAG5-9661,  and NAG5-13285, and by a
special NASA astrophysics theory program which supports a joint
Center for Star Formation Studies at NASA-Ames Research Center, UC
Berkeley, and UC Santa Cruz. The
work was  supported in part by the European Community's Human Potential
Programme under contract HPRN-CT-2002-00308, PLANETS.

redpajama_set_name: RedPajamaArXiv


text:
Hepatitis C mutations 'outrun' immune systems, lab study shows
Hep C virus exposed to attack
"We're redirecting the focus of the immune response away from regions of the virus that generate antibodies that are not only ineffective, but which block the effectiveness of the desirable antibodies.
"It's the first time this has been demonstrated in HCV that you can actually re-engineer the surface protein to generate a profoundly different immune response that is now cross-reactive and blocks the virus from entering cells.
"That gives us a lead that we can work with to produce a vaccine candidate that's going to be amenable for a clinical trial."
Study identifies mutations outside of traditional vaccine targets as barrier to vaccine development
Unlike its viral cousins hepatitis A and B, hepatitis C virus (HCV) has eluded the development of a vaccine and infected more than 170 million people worldwide. Now, researchers at Johns Hopkins Medicine report that a novel laboratory tool that lets them find virus mutations faster and more efficiently than ever before has identified a biological mechanism that appears to play a big role in helping HCV evade both the natural immune system and vaccines.
For their study, described March 8 in PLOS Pathogens, the researchers used one of the largest libraries of naturally occurring HCV to rapidly sort out which mutations allow HCV to evade immune responses and found that mutations that occur outside of the viral sites typically targeted by such antibody responses play a major role in the virus' resistance.
"We think those mutations could account for the difficulty of making an effective vaccine," says Justin Bailey, M.D., Ph.D., assistant professor of medicine at the Johns Hopkins University School of Medicine.
All told, the researchers compiled a library of 113 HCV strains from 27 patients with HCV infections followed at The Johns Hopkins Hospital. The researchers then tested each strain of the virus for susceptibility to two potent and commonly used antibodies in vaccine development experiments for HCV, HC33.4 and AR4A.
Because natural HCVs do not thrive in the lab, the researchers first created pseudo-viruses using the contents and capsule of HIV, a virus that grows easily in the lab. Then, by placing surface proteins of each HCV virus onto these pseudoviruses, the researchers were able to efficiently infect human cells with the HCV strains in tissue culture.
One-third of the cells infected with each strain received treatment with HC33.4 antibodies, one-third received treatment with AR4A antibodies and a final third (the control group) received no treatment. The researchers then compared the level of infection in the treated cells against the untreated cells.
The investigators observed that HC33.4 and AR4A neutralized only 88 percent and 85.8 percent of the virus, respectively. "We discovered that there was a lot of naturally occurring resistance, meaning we may need to greatly expand the set of viruses we use to evaluate potential vaccines," says Ramy El-Diwany, a student at the Johns Hopkins University School of Medicine and first author of the study.
The team also found that the effectiveness of the antibodies varied, with some viral strains very inhibited by the antibodies and others hardly affected at all. To find out what was causing the variation, the researchers next tapped into the HCV genomes.
Using a program that compared the genetic sequences of each viral strain, the researchers were able to analyze which mutations conferred resistance to each strain of the virus. They found that despite wide-ranging levels of resistance to HC33.4 and AR4A, the areas that allow these antibodies to bind to the virus barely varied. The HC33.4 binding site mutated at only one location, for example, and the AR4A binding site was the same across all viral strains.
The researchers then expanded their search to the proteins on the surface of HCV. They found that while mutations in the binding site were not associated with resistance, other mutations in the surface proteins away from the binding site correlated with viruses that persisted despite antibody treatment.
"These are the mutations we believe may allow the viruses to avoid being blocked by antibodies altogether. If you think of it like a race, the antibody is trying to bind to the virus before it can enter the cell. We think this mutation may allow the virus to get into the cell before it even encounters the immune system," says Bailey.
HCV is spread from person to person through contact with the blood of an infected person. Some patients are able to fight off the infection naturally, but for 70 to 85 percent of people, the infection becomes chronic.
A new HCV infection is effectively treated with direct-acting antiviral drugs, but the researchers say a preventive vaccine is needed to control what they call an HCV pandemic because as many as 50 percent of people infected are unaware that they carry the virus, putting others at risk of infection. Treatment does not protect those at risk from future infection by HCV. "HCV is very unlikely to be eliminated by treatment alone," says El-Diwany.
Other researchers involved in this study include Valerie Cohen, Madeleine Mankowski, Lisa Wasilewski, Jilian Brady, Anna Snider, William Osburn and Stuart Ray of the Johns Hopkins University School of Medicine, and Ben Murrell of the University of California, San Diego.
Extra-epitopic hepatitis C virus polymorphisms confer resistance to broadly neutralizing antibodies by modulating binding to scavenger receptor B1
This research was funded by the National Institute of Allergy and Infectious Diseases Extramural Activities (1K08 AI102761, U19 AI088791), the National Institute of Drug Abuse (R37 DA013806), and the Johns Hopkins University Center for AIDS Research (1P30AI094189).
https://www.eurekalert.org/pub_releases/2017-03/jhm-hcm031417.php
Posted by HCV New Drugs at Wednesday, March 15, 2017
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redpajama_set_name: RedPajamaCommonCrawl


Basis of the artwork by Korean artist Kyungwoo Chun, is the public power supply for water, current and gas in Bremen.
The power- and water supply lines are lifelines of a city. They form a complex network that unites the different households. Generally the pipes and cables are not visible for the city's inhabitants. Only in case of a supply disruption they are perceived negatively.
Kyungwoo Chun's intention is to raise the public's awareness of the invisible network of pipes and cables. He gives participants as well as the interested public the possibility to think over the importance of energy in their lifes regardless of their everyday work.
Apart from the material connection between households, the artproject "The invisible words" also create a spiritual connection between people. Together several participants form an artwork that spread everywhere in the city. Just as the supply lines, the "invisible words" are not visible, but take effect in the thoughts and conversations of the people. And maybe one day, the words will be found and redefined.


What the case is about- was a landmark United States Supreme Court case in which the Court formed the basis for the exercise of judicial review in the United States under Article III of the Constitution.
Constitutional principle- That case established the power of judicial review, the power of the Supreme Court (and other federal courts) to rule that a law passed by Congress is unconstitutional and therefore invalid.
Significance- court case established the concept of Judicial Review or the ability of the Judiciary Branch to declare a law unconstitutional.
significance- it made the way for the government to rule a law unconstitutional.
What the case is about- Martin concerned competing claims to land in Virginia owned by Lord Fairfax. Virginia seized the land from Fairfax during the war.
Constitutional principle- the Supreme Court asserted its authority under section 25 of the judiciary act of 1789 to review state court decisions dealing with federal law.
significance- first confronted the argument that federal judicial power came from the states, therefore that the Supreme Court had no right to overrule a state's interpretation of the treaty without the state consent.
What the case is about- Supreme Court decision most noted for the courts assertion of its power to review state Supreme Court decisions in criminal law matters when the defendant claims that their constitutional rights have been violated.
Constitutional principle- it gave power to the federal government over the states It also allowed the practice if restricting the state legislature.


An insert sleeve for aluminum post installation on the SafeWaze Mobile Safelink Horizontal Lifeline System. A 3" OD plastic pipe with a 12" depth. The unit is inserted during the forming and puring process.


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text:
Muhammad Ali lost everything in opposing the Vietnam War. But in 1968, he triumphed
Muhammad Ali lost everything in opposing the war
Author: Andrew Wolfson (Courier Journal)
Updated: 9:27 AM MST March 2, 2018
Credit: Charles Harrity, AP
FILE - In this May 11, 1967, file photo, Muhammad Ali speaks at an anti-war rally at the University of Chicago. The day before his star-studded funeral, members of Muhammad Ali's Islamic faith will get their chance to say a traditional goodbye to the Champ. Bob Gunnell, a spokesman for Ali's family, announced Monday, June 6, 2016, that a Jenazah, a traditional Muslim funeral service, will be held at Freedom Hall at noon Thursday. (AP Photo/Charles Harrity, File)
It was a sad sight: Stripped of his crown, the former heavyweight champion of the world was reduced to making a paid appearance at a boat show in his hometown of Louisville, Ky.
"I am not allowed to work in America and I'm not allowed to leave America," Muhammad Ali said in February 1968, at the start of his first full year of exile from boxing. "I'm just about broke."
Married a year with his first child on the way, Ali was so desperate his manager tried to arrange a bout in Arizona on an Indian reservation – outside the reach of state boxing commissions that wouldn't let him fight. But the Pima tribe rejected the proposal, saying it would defile the memory of Indian veterans who'd fought for their country.
The previous April, Ali had declared himself a conscientious objector and refused induction into the U.S. Army, famously saying, "I ain't got no quarrel with them Viet Cong."
By 1968, 19,560 Americans had died in the Vietnam War and another 16,502 would die that year alone. It was the year the Viet Cong and North Vietnamese army mounted the Tet Offensive, an ambitious campaign that helped persuade the American public that the war wasn't going as well as the generals and politicians had led them to believe.
The war was escalating, as was opposition to it. Just a few weeks before Ali said no to his draft board, Martin Luther King Jr., had denounced the war. He later quoted Ali in support of his position: "As "Muhammad Ali puts it, we are all — black and brown and poor — victims of the same system of oppression."
Credit: MICHAEL COERS/Louisville Courier Journal
The Rev. A.D. Williams King, right, chats with another minister, Cassius Clay, former heavyweight boxing champion, now Black Muslim preacher. Both attended a rally at Freedom Hall for about 600 participants in the Poor People's march on Washington who spent the night at the fairgrounds. May 8, 1968
Ali was already one of America's greatest heavyweights ever. He'd won an Olympic gold medal for the United States in Rome when he was just 18 and four years later, against all odds, defeated Sonny Liston to win his first title as world champion.
And in an era when most fighters let their managers do the talking, Ali thrived in the spotlight. He was the master of "rhyming prediction and derision," as biographer David Remnick would later write. He was already "the greatest," as he proclaimed himself, not just for his skills in the ring, but for talking trash – and doing it in verse.
It wasn't just what he said, but how he said it, poet Maya Angelou later put it.
"'Float like a butterfly, sting like a bee' – I mean, as a poet, I like that," she once said. "If he hadn't put his name on it, I might have chosen to use that."
Now Ali was paying the price for refusing to serve. Convicted of violating selective service laws and sentenced to five years in prison, he was free on bail. But his passport had been taken away, along with his ability to make a living.
More Black History Month Stories
Credit: Len Trievnor, Getty Images
American Heavyweight boxer Cassius Clay (later known as Muhammad Ali) is seen lying on his hotel bed in London. He holds up five fingers in a prediction of how many rounds it will take him to knock out British boxer Henry Cooper in 1963.
Finding his strength
With his characteristic bluster, he insisted he didn't ache for the money or the ring. Asked during a television appearance if he missed being heavyweight champion, he deadpanned, "No, they miss me."
But sportswriter Dave Kindred, who interviewed Ali at the boat show for the Courier-Journal, wrote that the more Ali talked about not missing the ring, the more you realized he did.
"It was his identity," Kindred said recently. "Boxing gave him his sense of self."
Credit: Associated Press
Students at Notre Dame listen to Muhammad Ali as he advocated the establishment of a separate state for blacks, either in the United States or in another country. May 20, 1968
Without it, recalled New York Times sportswriter Robert Lipsyte, who traveled with Ali in 1968, "He could get moody and down." Without boxing, Lipsyte said, Ali was often alone – and he was "not a guy who liked to be alone."
In the decades to come, his country and the world would come to embrace him as an ambassador of peace and goodwill. And after his death in 2016, his legacy grew larger still.
So it is easy to forget that 50 years ago, in the tumult of 1968, Ali didn't know how things would turn out, or if he'd ever fight again, said Bill Siegel, whose 2013 film, The Trials of Muhammad Ali, documented Ali's four years away from the ring.
It's easy, Siegel said, to forget that Ali "was willing to sacrifice everything on principle."
Refusing induction, Ali cited religious reasons, specifically, the Quran's ban on Muslims fighting Christian wars, but his objection was far broader.
"My conscience won't let me go shoot my brother, or some darker people, or some poor hungry people in the mud for big powerful America," he said. "And shoot them for what? They never called me nigger, they never lynched me, they didn't put no dogs on me, they didn't rob me of my nationality, rape and kill my mother and father. … Shoot them for what? How can I shoot them poor people?"
It was a humbling year for Ali, but also one of remarkable growth. Exiled from boxing, he grew bigger than the sport.
Yet he was still widely reviled.
Popular black athletes such as Jackie Robinson and Joe Louis denounced him. Time magazine, ripping him for his opposition to the war and his embrace of the Nation of Islam, called him "Gaseous Cassius," a reference to what he called his slave name, Cassius Clay.
Muhammad Ali spoke to a gathering at a Black Muslim convention in Chicago. Feb. 25, 1968
In Chicago, where he spent much of his banishment, Mayor Richard Daley refused to call him by his Muslim name, and Illinois Gov. Otto Kerner called him "unpatriotic."
On British television, famed talk show host David Susskind excoriated Ali as "a disgrace to his country, his race and what he laughingly describes as his profession." Ali, Susskind said, was a "simplistic pawn and a fool."
To pay the bills and help support his wife, Khalilah, and their child, Ali embarked on a college speaking tour, earning pennies on the dollar compared to his time in the ring.
His first lecture, at Philadelphia's Temple University, paid $1,000. The next, at Cheney State College in Pennsylvania, half that.
He ended his appearance at Union College in New York with a poem: "I like your school and admire your style, but your pay is so small, I won't be back for a while."
At first he was a terrible speaker, Lipsyte and others recalled. He spewed religious dogma from Nation of Islam, which he had joined four years earlier, regurgitating the words of its leader, Elijah Muhammad.
At University of Wisconsin, students booed when he denounced interracial marriage as "a trick to keep us with the white man," as they did the next day in San Francisco when he complained about the marijuana smell wafting from the crowd and insisted no "intelligent so-called Negro would allow his daughter to marry a white man."
He distanced himself from the Civil Rights Movement, telling 400 men and women he wouldn't join them in the Poor People's Campaign "because I don't believe in turning the other cheek."
"I don't say we shall overcome," he said at another appearance, "because I done overcame."
But Ali's speeches got better. He warmed to the crowds, and they to him. Lipsyte said Ali, though poorly educated, was a quick study.
"He had a real intellectual growth spurt," Lipsyte said.
Ali developed his own consciousness, moving away from Nation of Islam orthodoxy. He delivered lengthy soliloquies on his objection to the war and his experience with racism in America.
Verbally sparring with students forced him to become an independent thinker, said Kindred, who later wrote Sound and Fury: Two Powerful Lives, Fateful Friendship, a dual biography of Ali and sportscaster Howard Cosell,
And as the anti-war movement grew, Ali became a hero.
"Anti-war activists didn't care what he said about Elijah or the Nation, they cared only that the most famous man on Earth shared their opposition to that war," Kindred said.
"He became a man," Spiegel said.
Ali also helped move black radicalism into the mainstream, Harvard professor Henry Louis Gates Jr. later wrote.
He forged an unlikely alliance with King, who on the face of it had no grounds for common cause or friendship. The Nation of Islam bitterly opposed integration. Malcolm X had derided King's seminal 1963 "March on Washington" as "the Farce on Washington."
But King and Ali found common bond through their opposition to the war – and the hatred they both faced. Dave Zirin, sports editor of The Nation, wrote that famed 1968 Olympian and protester John Carlos once told him, "If there was an Olympic sport for the number of death threats received, King and Ali would be fighting for the gold."
King, hoping Ali's story would inspire others to refuse to serve in the war, singled out the boxer for praise in a sermon.
"He is giving up his fame," King said. "He is giving up millions of dollars in order to stand for what his conscience tells him is right. No matter what you think of his religion, you have to admire his courage."
Explainer iframe
Credit: JSJ, ASSOCIATED PRESS
Squelching a rumor that he had hurt a hand during training challenger (Muhammad Ali) Cassius Clay uses bare knuckles on the light punching bag on Saturday, Feb. 24, 1964 in Miami Beach, Fla., during his final workout for Tuesday night's title fight with champion Sonny Liston.
Exile turns to triumph
In May 1968, a federal appeals court affirmed Ali's conviction, saying "Clay had been fairly accorded due process of law, without discrimination."
But Ali's popularity was soaring, and he knew it. While he was driving in the San Francisco Bay Area, a black man on a bicycle spotted Ali and thrust his hand through an open window, Lipsyte wrote in a column.
"Let me shake the hand of the only real heavyweight champion of the world," the man said.
Ali was overjoyed.
"They made me bigger by taking my title," he told Lipsyte. "Before, that chap on the street couldn't identify with me. He'd say, 'You not with me, you up on the hill with whitey.'
"There are only two kinds of men," Ali continued, "those who compromise and those who take a stand."
Ali told Pacifica Radio he was "proud to say that I am the first man in the history of all America, athlete and entertainer-wise, who gave up all the white man's money, looked the white man in the eye, and told him the truth, and stayed with his people."
If he had ever lost his mojo, by October 1968 it was back.
Striding down West 52nd Street in New York, he hummed a song in the cold evening air, walking with the "bright swagger of a champion," Pete Hamill wrote in LIFE magazine. "People stepped out of a steak house to watch him go by. Auto horns beeped in salute. A middle-aged lady asked him to autograph her newspaper.
"Look at me,'" Ali said softly, "Bigger than boxing. As big as all history."
As Ali's consciousness grew, so did the nation's.
"The speeches were important, not just for Ali but for everyone who heard them," Lipsyte said.
Muhammad Ali through the years
The Courier-Journal, USA TODAY Sports
Ali shaving at his home in Louisville in 1978.
Policeman and mentor Joe Martin Ali as he admires his golden gloves ring in 1959.
Ali relaxes ringside at the 5th Street Gym in Miami Beach prior to his training workout for his world heavyweight title bout with Joe Frazier in 1971.
The Courier-Journal, The Courier-Journal-USA TODAY Sports
Ali takes a drink as he trains at the 5th Street Gym in Miami Beach for his world heavyweight title bout with Joe Frazier in 1971.
Ali gave a victory sign as he posed behind the wheel of his 1963 convertible after winning his driver's license back in 1963.
Ali addresses the media during an interview session at the 5th Street Gym in Miami Beach following his training workout for his world heavyweight title bout with Joe Frazier in 1971.
Ali relaxes at his hotel in Miami Beach while in town training workout for his world heavyweight title bout with Joe Frazier in 1971.
Keith Williams, The Courier-Journal-USA TODAY Sports
Ali signs autographs in his training room during his training for his bout with Leon Spinks at the Superdome in 1978.
Ali poses in a portrait session before making his singing debut in 1960 at the Louisville fairgrounds. Clay sang in the special chorus during his high school days at Central High School.
Ali punches the speed bag at Bruner's Headline Gym as he prepares for his first professional fight in 1960.
entral High students crowd around Ali and his brother Rudy Clay (holding Ali's hand up) after returning home with a gold medal in the 1960 Summer Olympics.
Ali works with a jump rope during a training session in 1971.
Ali embraces ABC sportscaster Howard Cosell in 1975.
Ali embraces his daughter Rasheda Ali after a boxing match in 1981.
Ali signs pictures of himself in his hotel room before a fight against Larry Holmes at Caesars Palace in 1980.
Ali shadow boxes while watching film of his upcoming opponent Larry Holmes in 1980.
Ali (left) interacts with fans prior to his fight against Trevor Berbick in 1981.
Ali talks on a car phone in 1964.
Ali address the media at a local selective service board facility in his hometown of Louisville in 1966.
Ali trains on the fast bag at the 5th Street Gym in Miami Beach during his training for his world heavyweight title bout with Joe Frazier in 1971.
Ali takes his daily three-mile run along a Pennsylvania country road shrouded in early morning fog near his Deer Lake training camp in 1978.
Ali is greeted by then-senator Barack Obama at the Muhammad Ali Center in 2006.
Ali punches the double-end bag at Bruner's Headline Gym as Jimmy Ellis (right) watches in background in 1961.
Ali chats with Joe Frazier in his training room during his training for his bout with Leon Spinks in 1978.
Ali shares a laugh with Joe Frazier in his training room during his training for his bout with Leon Spinks in 1978.
Ali shows off a new pink Cadillac to his mother Odessa Clay in 1960. He bought the automobile for his parents following his first professional fight.
Ali waves to the crowd at a Louisville Cardinals basketball game in 1988.
Ali signs autographs for fans in 1986.
Ali speaks speaks at a rally at the Quinn Chapel AME church in 1967.
Ali appears on NBC's celebrity roast with Dean Martin in 1976.
Ali eats breakfast while watching "Mohammad Messenger of God" in his hotel room before his fight against Larry Holmes in 1980.
Ali prepares for his fight against Trevor Berbick (not pictured) with his brother Rahman Ali in 1981.
Ali (right) fights Trevor Berbick (left) at the Queen Elizabeth Sports Centre. Berwick defeated Ali in ten rounds by unanimous decision and was Ali's last professional fight.
John Rooney, AP
Muhammad Ali stands over fallen challenger Sonny Liston, shouting and gesturing shortly after dropping Liston with a short hard right to the jaw on May 25, 1965.
Eileen Blass, USA TODAY Sports
Ali photographed in the gym at his Michigan home in 1999. The photograph behind him is from 1963.
Elieen Blass, USA TODAY Sports
Ali photographed in the gym at his Michigan home.
Dave Pickoff, AP
This historic picture shows five American heavyweight boxers who have at one time or another worn the crown of World Heavyweight Champion, Sept. 23, 1976. From left to right: Joe Frazier, Jimmy Ellis, Ali, Joe Louis and Floyd Patterson.
Ali chops down a tree with an ax in a forest near Frankfurt, Germany on Sept. 1, 1966.
Gerald Herbert, AP
Ali, left, and Floyd Patterson, center, meet former President Richard M. Nixon on Oct. 4, 1988 in New York.
Ric Feld, AP
Ali embraces Coretta Scott King, widow of Dr. Martin Luther King, Jr., at a news conference in Atlanta, Ga., launching a celebration for the first national holiday honoring Dr. King, Jan. 10, 1986.
Mario Cabrera, AP
Ali before reporters prior to checking out of a New York hospital on Sept. 21, 1984 after being diagnosed with Parkinson's syndrome.
Reed Saxon, AP
Ali delivers a friendly punch to his father Cassius Clay, Sr. on Jan. 4, 1980.
Ali gives a kiss to his newborn daughter Laila after she was born in Dec. 1977.
Ali with his third wife, Veronica Porsche, on their wedding day, Aug. 19, 1977.
Marty Lederhandler, AP
Joe Frazier tries to stop the torrent of words coming from  Ali during a signing in 1970 before their fight on March 8, 1971.
Ali smashes a right into the jaw of challenger Brian London of Britain, Aug. 6, 1966, in London. Ali knocked out his opponent in the third round.
Peter Kemp, AP
Two-year-old Shelley Obermuller tugs for the attention of Ali as he signs autographs during a training session in London on May 17, 1966.
Julien's Auctions / Rex Features via AP
A Muhammad Ali training-worn fight robe robe with satin letters on the back spelling out "Muhammad Ali" worn by Ali while training for his third fight with Ken Norton. That fight took place on September 28, 1976 and was the last championship fight ever held at Yankee Stadium.
Sal Veder, AP
Ali, holds the "Muhammad Speaks" newspaper with his picture as he and followers of the Muslim sect leave the Las Vegas convention center after weigh-in before his fight against Floyd Patterson on Nov. 22, 1965.
Ali arm wrestles with novelist Norman Mailer on Aug. 1, 1965.
Dan Grossi, AP
Ali with his trainer Angelo Dundee at City Parks Gym in New York, Feb. 8, 1962.
Al Blunk, The Courier-Journal
Ali in 1958.
Muhammad Ali during training for his fight with Al 'Blue' Lewis held in Dublin, Republic of Ireland in 1972.
AFP/Getty Images
Ali and George Foreman fight in "The Match of the Century" on Oct. 30, 1974 in Kinshasa, Congo.
Amanda Edwards, Getty Images
Ali jokes on stage with Howard Bingham and Magic Johnson during the 20th Annual "Midsummer Night's Magic Awards Dinner" on July 13, 2005 in Los Angeles.
Curtis Compton, AFP/Getty Images
Ali lights the first Olympic torch for the Salt Lake 2002 Olympic Winter Games at Centennial Olympic Park in Atlanta in Dec. 2001.
Kevin Winter, Getty Images
Director Michael Mann, Ali and actor Tom Cruise arrive at the premiere of "Collateral" in Los Angeles in 2004.
Ezra Shaw, Getty Images
Ali greets the crowd before he unveils a new wallscape for adidas with his daughter Laila on Feb. 5, 2003 in Harlem.
Ralph Orlowski, AFP/Getty Images
Ali kisses his wife Lonnie during the presentation of his book: "Greatest of All Time" at the Frankfurt Book Fair in Oct. 2003.
Linda Spillers, AP
Ali and his daughter, Rasheda Ali-Walsh in 2000.
Jim Winn, The Courier-Journal
Prince Turki Al-Faisal of Saudi Arabia, right, watched as Shawn Geary held up Hunter Geary, 2, for a kiss from Ali in 2006.
Lucy Nicholson, AFP
US former world heavyweight boxing champion Muhammad Ali (L) jokes with US actor Will Smith (R) who portrays him in new film "Ali," at the movie's premiere in Hollywood, CA, 12 December 2001. AFP PHOTO/Lucy NICHOLSON ORG XMIT: LAX01
A trio of U.S. boxers wear gold medals at the Olympic village in Rome, September 6, 1960. From the left are: Wilbert McClure of Toledo, Ohio, light middleweight; Cassius Clay of Louisville, KY, light heavyweight; and Edward Crook of Fort Campbell, KY, middleweight. (AP Photo) ORG XMIT: APHS200 (Via MerlinFTP Drop)
Angelo Dundee with Muhammad Ali, then named Cassius Clay, in Louisville in 1961 after his sixth straight pro win.
Al Hixenbaught, The Courier-Journal
Home from the 1960 Olympics, where he was a gold medalist in boxing. Muhammad Ali paid visit to physically challenged children at Kosair Hospital in Louisville, Ky. Photo by Al Hixenbaugh Oct 20, 1960 (Via MerlinFTP Drop)
Nick Elgar, Getty Images
Billy Crystal & Muhammad Ali at Audemars Piguet's Time To Give Celebrity Watch Auction For Charity, held at Christie's Auction House in New York City. 10/23/00 ( Nick Elgar/ImageDirect ) (Via MerlinFTP Drop)
Michael Kappeler, AFP/Getty Images
Ali shadow boxes during a press conference in Berlin in 2005, before being awarded the Otto Hahn Medal for Peace.
Chrystna Czjawkowsky, AP
Ali, left, smiles at fans while photographer Howard L. Bingham autographs a copy of his book in 1993.
Abder Raouf, AP
Ali intones prayers with a class of Muslim boys at Dafaalah el Sa'em Mosque in Khartoum, Sudan in 1988.
Frank Gunn, AP
Lennox Lewis greets Ali at a Parkinson's Disease fundraiser in 2002.
Ron Frehm, AP
Ali, left, and golfer Tiger Woods pose together before Sports Illustrated's 20th Century Sports Awards Thursday on Dec. 2, 1999.
Israel Leal, AP
Ali is crowned "King of Boxing" while accompanied by his wife, Lonnie, right, and Argentine boxer Sergio "Maravilla" Martinez during the 50th convention of the World Boxing Council in Cancun on Dec. 3, 2012.
George Burns, AP
Actors Jada Pinkett Smith, left, and her husband Will Smith, talk with boxing great Ali, and Oprah Winfrey during a taping of "The Oprah Winfrey Show," on Nov. 16, 2001.
Kathy Willens, AP
NBA commissioner David Stern, left, talks with at commencement exercises for Columbia University in New York where Ali was one of several people to receive an honorary degree in 1999.
Ali, right, gives Larry Holmes a wide-eyed look during their WBC championship title fight on Oct. 2, 1980, which Holmes won when Ali failed to answer the bell at the start of the 11th round.
Lennox McLendon, AP
Ali and Mike Tyson chat during a special tribute honoring Ali in 1996. Ali was once asked whether Tyson could have beaten him. "Don't make me laugh," he said. "Tyson don't have it. He don't have it,'' said Ali, pointing to his head.
Stan Honda, AFP
Ali gestures to photographers as he sits at ringside before his daughter Laila's fight in April 1999.
Ali training pm Oct. 9, 1974 for his fight in Zaire.
Ed Reinke, AP
Ali is joined by daughters Jamillah, left, and Rasheda Ali, and his wife Lonnie, right, as they appear before the crowd gathered to celebrate the dedication of the Muhammad Ali Center in 2005.
Eric Draper, AP
Ali poses with 1996 Dream Team members from left: Scottie Pippen, Hakeem Olajuwon, Reggie Miller, Shaquille O'Neal, Karl Malone and Gary Payton after receiving the gold medal, which replaces the 1960 gold medal he lost.
Michael Probst, AP
American swimmer Janet Evans looks on as Ali lights the Olympic flame during the 1996 Summer Olympic Games opening ceremony in Atlanta.
The Beatles pretend to be knocked out by a fake blow from Ali while visiting his training camp in Miami Beach in 1964.
Ali tries to evade kicks by wrestler Antonio Inoki during their 15-round World Martial Arts in 1976.
Ali and Joe Frazier in the 12-round non-title fight at Madison Square Garden on Jan. 28, 1974.
Cleveland Williams is spreadeagled on the canvas as referee Harry Kessler sends Ali to a corner during their heavyweight bout at the Astrodome on Nov. 14, 1966.
Andy Warhol, left, is shown photographing Ali, his infant daughter, Hanna, and wife, Veronica on Aug. 18, 1977.
Ali is cheered by Zaire admirers as he drives in downtown Kinshasa for a sightseeing trip in 1974.
Bill Ingraham, AP
Muhammad Ali and his family walk in front of their apartment building in Cherry Hill, N.J., on Aug. 24, 1974.
Ali, left, greets Joe Frazier on Jan. 29, 1974 after Ali won their fight at Madison Square Garden.
Ali crashes a right to the side of Ken Norton's head on Sept. 10, 1973.
Ali jogs along a snow-covered road in Stateline, Nev. on Nov. 21, 1972.
Joe Frazier is directed to the ropes by referee Arthur Marcante after knocking down Ali during the 15th round of the title bout at Madison Square Garden on March 8, 1971. Frazier won the bout by decision.
Joe Migon, AP
Ali, in a jovial mood before his 1971 bout with Joe Frazier, is seen speaking on the phone and wearing a king's crown.
John Lindsay, AP
Keith Green, a nine-year-old fourth grader from P.S. 175 in Manhattan, is shown striking a victorious pose after "flooring" Ali at Madison Square Garden in 1967.
Johnny Carson watches Ali hamming it up for a photographer in New York on Feb. 10, 1967.
Ali works out on the light punching bag at his training camp before his title bout against Sonny Liston on May 13, 1965.
Frank C. Curtin, AP
Ali holds a large collar and rope which he says he is going to fasten around "the Bear," his name for Sonny Liston, Nov. 9, 1964.
Ali and his wife Sonji pose in a nearby hotel after landing at Logan Airport in 1964.
Ali waves as he leaves Kennedy Airport in New York City for Ghana on May 15, 1964.
Ali with Malcolm X, outside the Trans-Lux Newsreel Theater on Broadway in 1964.
Muhammad Ali, then known as Cassius Clay, celebrates after winning the heavyweight championship with a knockout of Sonny Liston in the seventh round on Feb. 25, 1964 in Miami Beach, Fla.
Jack Kanthal, AP
Ali signs autographsin 1964 beside Malcolm X in New York.
Harry Harris, AP
Ali thrusts his fist out Feb. 19, 1964, as he tells a crowd at Surfside, Fla., how he'll hit Sonny Liston.
The Beatles, from right to left, Paul McCartney, John Lennon, George Harrison and Ringo Starr pretend to be knocked out by Ali.
Harold P. Matosian, AP
Ali points to a sign he wrote on a chalk board in his dressing room before his fight against Archie Moore in Los Angeles, on Nov. 15, 1962.
Ali in action during the Olympic bout against Z. Pietrzykowski of Poland in Rome on Sept. 5, 1960. Ali won the gold medal.
Ali squares off with Tony Madigan of Australia during the Olympic semifinals in 1960.
Ali during a training session in Rome during the 1960 Olympics.
Pablo Martinez Monsivais, AP
Bill Clinton, left, holds onto boxing great Ali during awards presentation an award ceremony in 2000.
Cort Best, The Courier-Journal
Ali signs a professional contract in 1960.
Ali returns to Louisville after the 1960 Olympics.
Mark Wilson, Getty Images
Michael J. Fox and Ali pretend to spar prior to giving testimony before the Senate Appropriations Subcommittee on Health and Human Services in 2002.
Ali throws a punch at Joe Frazier in the 12th round of their fight at Madison Square Garden on Jan. 28, 1974.
Ali and Joe Frazier in action during their fight at Madison Square Garden on March 8, 1971. Frazier won in the 15th round.
Joe Caneva, AP
Ali toys with the finely-combed hair of television sports commentator Howard Cosell before the start of the Olympic boxing trials in 1972.
Ali training for his May 25, 1965 fight with Sonny Liston.
Ali is escorted from the Armed Forces Examining and Entrance Station in Houston in 1967.
Tom Easterling
Joe Frazier stands over Ali after knocking him down in the 15th round of their heavyweight title fight at Madison Square Garden on March 8, 1971.
H. Darr Beiser, USA TODAY Sports
Ali in 1994 at Miami Beach Convention Center, where he beat Sonny Liston.
Ali particularly influenced black athletes, as dramatically seen at the 1968 Summer Olympics when medalists John Carlos and Tommie Smith raised their fists in the Black Power salute Smith later called an endorsement of all human rights.
African-American athletes today continue that tradition as they kneel during the National Anthem to protest mistreatment by police.
But his story inspired all athletes to stand up for equality in their sport, and beyond. Baseball players fought for free agency; track stars to end the sham of amateurism; and women for equal tennis prize money.
"I really believe if Ali hadn't done what he did, Smith and Carlos wouldn't have raised their fists," Arthur Ashe, the pioneering black tennis star who protested apartheid and raised awareness about AIDS, said in the 1995 oral history Muhammad Ali: The People's Champ.
"He was largely responsible for it becoming an expected part of the black athlete's responsibility to get involved," Ashe said. "He put it all on the line for what he believed in. And if Ali did that, who were the rest of us lesser athlete mortals not to do it?"
With his Supreme Court appeal still pending, Ali's promoter arranged a fight in Georgia, which had no state boxing commission. Despite the objections of segregationist Gov. Lester Maddox, Ali took on Jerry Quarry in Atlanta on Oct. 26, 1970, and beat him in the third round.
His lawyers also won a court order forcing the New York State Athletic Commission to let him fight. The following March he lost the 15-round "Fight of the Century" to Joe Frazier.
But on June 28, 1971, he won his biggest victory: The Supreme Court unanimously overturned his conviction, saying his draft board failed to specify why his conscientious objector application was denied. Throughout the war, Selective Service granted more than 170,000 men C.O. status.
Ali twice reclaimed his heavyweight championship – and the hearts of some who supported the war. In 2005, wracked by Parkinson's, his hands shaking, he accepted the nation's highest civilian honor, the Medal of Freedom, at a White House ceremony.
"The American people," said President George W. Bush, "are proud to call Muhammad Ali one of our own."
Follow Andrew Wolfson on Twitter: @adwolfson. For more stories in the 1968 project, visit 1968.usatoday.com
Credit: EVAN VUCCI, AP
President Bush presents the Presidential Medal of Freedom to boxer Muhammad Ali in the East Room of the White House. Ali, the magnificent heavyweight champion whose fast fists and irrepressible personality transcended sports and captivated the world, has died according to a statement released by his family Friday, June 3, 2016. He was 74.
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