text:
Specialization of the HOG pathway and its impact on differentiation and virulence of Cryptococcus neoformans
Yong Sun Bahn, Kaihei Kojima, Gary M. Cox, Joseph Heitman
The human pathogenic fungus Cryptococcus neoformans has diverged from a common ancestor into three biologically distinct varieties or sibling species over the past 10-40 million years. During evolution of these divergent forms, serotype A C. neoformans var. grubii has emerged as the most virulent and cosmopolitan pathogenic clade. Therefore, understanding how serotype A C. neoformans is distinguished from less successful pathogenic serotypes will provide insights into the evolution of fungal virulence. Here we report that the structurally conserved Pbs2-Hog1 MAP kinase cascade has been specifically recruited as a global regulator to control morphological differentiation and virulence factors in the highly virulent serotype A H99 clinical isolate, but not in the laboratory-generated and less virulent serotype D strain JEC21. The mechanisms of Hog1 regulation are strikingly different between the two strains, and the phosphorylation kinetics and localization pattern of Hog1 are opposite in H99 compared with JEC21 and other yeasts. The unique Hog1 regulatory pattern observed in the H99 clinical isolate is widespread in serotype A strains and is also present in some clinical serotype D isolates. Serotype A hog1Δ and pbs2Δ mutants are attenuated in virulence, further underscoring the role of the Pbs2-Hog1 MAPK cascade in the pathogenesis of cryptococcosis.
Molecular Biology of the Cell
https://doi.org/10.1091/mbc.E04-11-0987
Published - 2005 May
10.1091/mbc.E04-11-0987
Dive into the research topics of 'Specialization of the HOG pathway and its impact on differentiation and virulence of Cryptococcus neoformans'. Together they form a unique fingerprint.
Cryptococcus neoformans Medicine & Life Sciences 100%
Serogroup Medicine & Life Sciences 72%
Cryptococcosis Medicine & Life Sciences 12%
MAP Kinase Signaling System Medicine & Life Sciences 10%
Virulence Factors Medicine & Life Sciences 10%
Fungi Medicine & Life Sciences 8%
Yeasts Medicine & Life Sciences 7%
Bahn, Y. S., Kojima, K., Cox, G. M., & Heitman, J. (2005). Specialization of the HOG pathway and its impact on differentiation and virulence of Cryptococcus neoformans. Molecular Biology of the Cell, 16(5), 2285-2300. https://doi.org/10.1091/mbc.E04-11-0987
Bahn, Yong Sun ; Kojima, Kaihei ; Cox, Gary M. ; Heitman, Joseph. / Specialization of the HOG pathway and its impact on differentiation and virulence of Cryptococcus neoformans. In: Molecular Biology of the Cell. 2005 ; Vol. 16, No. 5. pp. 2285-2300.
@article{a8ca0f9de23e467fb98c81b16c1c1794,
title = "Specialization of the HOG pathway and its impact on differentiation and virulence of Cryptococcus neoformans",
abstract = "The human pathogenic fungus Cryptococcus neoformans has diverged from a common ancestor into three biologically distinct varieties or sibling species over the past 10-40 million years. During evolution of these divergent forms, serotype A C. neoformans var. grubii has emerged as the most virulent and cosmopolitan pathogenic clade. Therefore, understanding how serotype A C. neoformans is distinguished from less successful pathogenic serotypes will provide insights into the evolution of fungal virulence. Here we report that the structurally conserved Pbs2-Hog1 MAP kinase cascade has been specifically recruited as a global regulator to control morphological differentiation and virulence factors in the highly virulent serotype A H99 clinical isolate, but not in the laboratory-generated and less virulent serotype D strain JEC21. The mechanisms of Hog1 regulation are strikingly different between the two strains, and the phosphorylation kinetics and localization pattern of Hog1 are opposite in H99 compared with JEC21 and other yeasts. The unique Hog1 regulatory pattern observed in the H99 clinical isolate is widespread in serotype A strains and is also present in some clinical serotype D isolates. Serotype A hog1Δ and pbs2Δ mutants are attenuated in virulence, further underscoring the role of the Pbs2-Hog1 MAPK cascade in the pathogenesis of cryptococcosis.",
author = "Bahn, {Yong Sun} and Kaihei Kojima and Cox, {Gary M.} and Joseph Heitman",
doi = "10.1091/mbc.E04-11-0987",
journal = "Molecular Biology of the Cell",
publisher = "American Society for Cell Biology",
Bahn, YS, Kojima, K, Cox, GM & Heitman, J 2005, 'Specialization of the HOG pathway and its impact on differentiation and virulence of Cryptococcus neoformans', Molecular Biology of the Cell, vol. 16, no. 5, pp. 2285-2300. https://doi.org/10.1091/mbc.E04-11-0987
Specialization of the HOG pathway and its impact on differentiation and virulence of Cryptococcus neoformans. / Bahn, Yong Sun; Kojima, Kaihei; Cox, Gary M.; Heitman, Joseph.
In: Molecular Biology of the Cell, Vol. 16, No. 5, 05.2005, p. 2285-2300.
T1 - Specialization of the HOG pathway and its impact on differentiation and virulence of Cryptococcus neoformans
AU - Bahn, Yong Sun
AU - Kojima, Kaihei
AU - Cox, Gary M.
AU - Heitman, Joseph
N2 - The human pathogenic fungus Cryptococcus neoformans has diverged from a common ancestor into three biologically distinct varieties or sibling species over the past 10-40 million years. During evolution of these divergent forms, serotype A C. neoformans var. grubii has emerged as the most virulent and cosmopolitan pathogenic clade. Therefore, understanding how serotype A C. neoformans is distinguished from less successful pathogenic serotypes will provide insights into the evolution of fungal virulence. Here we report that the structurally conserved Pbs2-Hog1 MAP kinase cascade has been specifically recruited as a global regulator to control morphological differentiation and virulence factors in the highly virulent serotype A H99 clinical isolate, but not in the laboratory-generated and less virulent serotype D strain JEC21. The mechanisms of Hog1 regulation are strikingly different between the two strains, and the phosphorylation kinetics and localization pattern of Hog1 are opposite in H99 compared with JEC21 and other yeasts. The unique Hog1 regulatory pattern observed in the H99 clinical isolate is widespread in serotype A strains and is also present in some clinical serotype D isolates. Serotype A hog1Δ and pbs2Δ mutants are attenuated in virulence, further underscoring the role of the Pbs2-Hog1 MAPK cascade in the pathogenesis of cryptococcosis.
AB - The human pathogenic fungus Cryptococcus neoformans has diverged from a common ancestor into three biologically distinct varieties or sibling species over the past 10-40 million years. During evolution of these divergent forms, serotype A C. neoformans var. grubii has emerged as the most virulent and cosmopolitan pathogenic clade. Therefore, understanding how serotype A C. neoformans is distinguished from less successful pathogenic serotypes will provide insights into the evolution of fungal virulence. Here we report that the structurally conserved Pbs2-Hog1 MAP kinase cascade has been specifically recruited as a global regulator to control morphological differentiation and virulence factors in the highly virulent serotype A H99 clinical isolate, but not in the laboratory-generated and less virulent serotype D strain JEC21. The mechanisms of Hog1 regulation are strikingly different between the two strains, and the phosphorylation kinetics and localization pattern of Hog1 are opposite in H99 compared with JEC21 and other yeasts. The unique Hog1 regulatory pattern observed in the H99 clinical isolate is widespread in serotype A strains and is also present in some clinical serotype D isolates. Serotype A hog1Δ and pbs2Δ mutants are attenuated in virulence, further underscoring the role of the Pbs2-Hog1 MAPK cascade in the pathogenesis of cryptococcosis.
U2 - 10.1091/mbc.E04-11-0987
DO - 10.1091/mbc.E04-11-0987
JO - Molecular Biology of the Cell
JF - Molecular Biology of the Cell
Bahn YS, Kojima K, Cox GM, Heitman J. Specialization of the HOG pathway and its impact on differentiation and virulence of Cryptococcus neoformans. Molecular Biology of the Cell. 2005 May;16(5):2285-2300. https://doi.org/10.1091/mbc.E04-11-0987


text:
Toto Riina Admitted to Meeting PM Andreotti in the 1990s
By Ed Scarpo Wednesday, August 27, 2014
Andreotti died having been
cleansed of Mafia-related crimes.
"Riina changed Cosa Nostra from having a democratic, federal organisation to an authoritarian management style – and that's a euphemism given that he would murder colleagues for making the wrong hand gesture at meetings."
Toto Riina, the jailed 'boss of bosses' of the Sicilian Mafia, for the first time, claimed he met with seven-time Italian prime minister Giulio Andreotti.
This revelation is released mere days before the Venice premier of La Trattativa, an Italian documentary about secret talks allegedly held between Cosa Nostra and the Italian government in the 1990s.
According to the Telegraph Riina has long been accused of meeting the former Christian Democrat leader.
Andreotti (January 1919 – May 2013) was the 41st Prime Minister of Italy and leader of the Christian Democracy party -- which clung to power for decades by being the only alternative to communism in the turbulent decades of the Cold War. Of all the Western powers, it was long feared that Italy would most likely be the first democracy to fall under the Eastern Bloc's flag.
Mob watchers have suggested that the mafia's murder of magistrate Paolo Borsellino in 1992 was assisted by secret service agents because Borsellino had stumbled onto evidence of
mafia-state talks.
Andreotti, occupying all the major offices of state over a forty-year political career, reassured the civil service, business community, and the Vatican and also helped to further integrate Italy into the European Union. In foreign policy, he established closer relations with the Arab world.
Andreotti was subjected to criminal prosecutions -- and was acquitted following trial in Palermo of collaborating with the Mafia. Many of his close Sicilian allies had known links to Sicily's Cosa Nostra.
The Telegraph noted: "Prosecutors in Perugia charged him with ordering the murder of a journalist. In 2002 he was found guilty, which led to complaints that the justice system had "gone mad."
He was later definitively acquitted by the supreme court. Andreotti remarked "Apart from the Punic Wars, for which I was too young, I have been blamed for everything."
He wouldn't be so flippant right now, with what Riina has been saying.
Riina on tria
Riina was allegedly trying to broker a deal with the Italian government to reduce jail time for imprisoned mob bosses, even as the mob mounted a series of murderous bomb attacks up and down Italy. Riina has been held in a maximum security prison since his 1993 capture.
Now, police have revealed that Riina admitted the meeting did take place.
"With an escort, I met him," Riina told Puglian crime boss Alberto Lorusso in a prison exercise yard, where police had installed secret microphones, La Repubblica reported.
The admission actually was made last year, but only now was placed in evidence in an ongoing trial in Palermo of senior Italian politicians accused of bargaining with Riina's men to get the mob to stop its bombing campaign.
The probe is central to La Trattativa, comedian and actress Sabina Guzzanti's new film, which combines documentary interviews with actors playing mobsters and politicians.
"Riina changed Cosa Nostra from a having a democratic, federal organisation to an authoritarian management style – and that's a euphemism given that he would murder colleagues for making the wrong hand gesture at meetings," she told the Telegraph.
"What followed were the senseless murder of hundreds, strange contacts with the Italian secret services and the bombings," said Guzzanti.
Guzzanti said allegations of shadowy talks were just as relevant today as they were two decades ago.
"We are not just talking about bombs and concessions made by politicians to the mafia, but the idea that the mafia was receiving help from elements within the Italian army, the secret services and the government."
Mob watchers have suggested that the mafia's murder of a magistrate, Paolo Borsellino, in 1992, was assisted by secret service agents because Borsellino had stumbled onto evidence of mafia-state talks.
"This film is also relevant because the mob went on to give its backing to Silvio Belusconi's newly formed Forza Italia party in 1994 after the fall of Andreotti's Christian Democrats," said Guzzanti.
Guzzanti said Riina may be attempting to flex what muscle he has left. "After years of rotting in jail, these statements could be a threat made in order to get something in return for his silence."
Salvatore "Toto" Riina

redpajama_set_name: RedPajamaCommonCrawl


text:
package psidev.psi.mi.jami.enricher.impl.full;

import psidev.psi.mi.jami.bridges.fetcher.InteractorFetcher;
import psidev.psi.mi.jami.enricher.ComplexEnricher;
import psidev.psi.mi.jami.enricher.CvTermEnricher;
import psidev.psi.mi.jami.enricher.OrganismEnricher;
import psidev.psi.mi.jami.enricher.exception.EnricherException;
import psidev.psi.mi.jami.enricher.listener.InteractorEnricherListener;
import psidev.psi.mi.jami.model.Complex;

/**
 * Full enricher for complexes
 *
 * @author Gabriel Aldam (galdam@ebi.ac.uk)
 * @since 13/08/13

 */
public class FullComplexUpdater extends FullModelledInteractionUpdater<Complex> implements ComplexEnricher {

    private FullInteractorBaseUpdater<Complex> interactorEnricher = null;

    /**
     *
Constructor for FullComplexUpdater.

     */
    public FullComplexUpdater(){
        super();
        this.interactorEnricher = new FullInteractorBaseUpdater<Complex>();
    }

    /**
     *
Constructor for FullComplexUpdater.

     *
     * @param interactorEnricher a {@link psidev.psi.mi.jami.enricher.impl.full.FullInteractorBaseUpdater} object.
     */
    protected FullComplexUpdater(FullInteractorBaseUpdater<Complex> interactorEnricher){
        super();
        this.interactorEnricher = interactorEnricher != null ? interactorEnricher : new FullInteractorBaseUpdater<Complex>();
    }

    /**
     * Strategy for the Interaction enrichment.
     * This method can be overwritten to change how the interaction is enriched.
     *
     * @param interactionToEnrich   The interaction to be enriched.
     * @throws psidev.psi.mi.jami.enricher.exception.EnricherException if any.
     */
    protected void processOtherProperties(Complex interactionToEnrich) throws EnricherException {
        super.processOtherProperties(interactionToEnrich);

        // interactor properties

        // Interactor type
        this.interactorEnricher.processInteractorType(interactionToEnrich, null);

        // Organism
        this.interactorEnricher.processOrganism(interactionToEnrich, null);

    }

    /** {@inheritDoc} */
    @Override
    protected void processOtherProperties(Complex objectToEnrich, Complex objectSource) throws EnricherException {
        super.processOtherProperties(objectToEnrich, objectSource);

        // interactor properties

        // Interactor type
        this.interactorEnricher.processInteractorType(objectToEnrich, objectSource);

        // Organism
        this.interactorEnricher.processOrganism(objectToEnrich, objectSource);

        // FULL NAME
        this.interactorEnricher.processFullName(objectToEnrich, objectSource);

        //ALIASES
        this.interactorEnricher.processAliases(objectToEnrich, objectSource);
    }

    /**
     *
getInteractorFetcher.

     *
     * @return a {@link psidev.psi.mi.jami.bridges.fetcher.InteractorFetcher} object.
     */
    public InteractorFetcher<Complex> getInteractorFetcher() {
        return this.interactorEnricher.getInteractorFetcher();
    }

    /** {@inheritDoc} */
    public void setListener(InteractorEnricherListener<Complex> listener) {
        this.interactorEnricher.setListener(listener);
    }

    /**
     *
getListener.

     *
     * @return a {@link psidev.psi.mi.jami.enricher.listener.InteractorEnricherListener} object.
     */
    public InteractorEnricherListener<Complex> getListener() {
        return this.interactorEnricher.getListener();
    }

    /** {@inheritDoc} */
    public void setCvTermEnricher(CvTermEnricher cvTermEnricher) {
        this.interactorEnricher.setCvTermEnricher(cvTermEnricher);
    }

    /** {@inheritDoc} */
    public void setOrganismEnricher(OrganismEnricher organismEnricher) {
        this.interactorEnricher.setOrganismEnricher(organismEnricher);
    }

    /**
     *
getOrganismEnricher.

     *
     * @return a {@link psidev.psi.mi.jami.enricher.OrganismEnricher} object.
     */
    public OrganismEnricher getOrganismEnricher() {
        return this.interactorEnricher.getOrganismEnricher();
    }

    /**
     *
Getter for the field interactorEnricher.

     *
     * @return a {@link psidev.psi.mi.jami.enricher.impl.full.FullInteractorBaseUpdater} object.
     */
    protected FullInteractorBaseUpdater<Complex> getInteractorEnricher() {
        return interactorEnricher;
    }
}

redpajama_set_name: RedPajamaGithub


The USDA became a Money Smart Week National Champion in 2011 as part of the expansion of Money Smart Week® to a national campain. The National Institute of Food and Agriculture (NIFA) is an agency within the US. Department of Agriculture (USDA), part of the executive branch of the Federal Government.
United States Department of Agriculture (USDA) - The National Institute of Food and Agriculture (NIFA), Division of Family and Consumer Sciences strengthens families, farms, communities and the economy as a division of USDA - NIFA. The Division of Family and Consumer Sciences integrates education, research, and the Cooperative Extension System to enhance Family and Consumer Economics. The purpose of the USDA -NIFA Family and Consumer Economics is to establish educational and research priorities for local communities, states, multi-state, and national work on emerging issues germane to the economic well-being of individuals and families. Priority issues include financial instability across the lifespan, helping rural and urban individuals and families maintain economic stability in a changing economy, and supporting community development in increasingly complex and diverse environments.
Created by Dr. Barbara O'Neill, to provide insightful and fun videos for people to learn financial literacy.


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» Danielle Steel
1) The Whittiers: a novel
Steel, Danielle
15 copies, 7 people are on the wait list.
[2022] Delacorte Press
1 audio media player (6.5 hr.) : digital, HD audio ; 3 3/8 x 2 1/8 in.
"Preston and Constance Whittier have built a happy life together, with a brood of six children raised in a beautiful historic Manhattan mansion. Now, with a nearly empty nest, it's easier than ever for the Whittiers to maintain their tradition of a solo romantic "Wintermoon" ski trip. But with this year's trip comes tragedy, and suddenly the Whittier's adult children find themselves reuniting in the family home without their parents for the first...
2) The high notes: a novel
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Iris Cooper has been singing ever since she can remember, hitting the high notes like no one else. When she is twelve, her father convinces the owner of a bar in Lake City, Texas, to let her perform, and she stuns the audience. In the ensuing years, never staying anywhere for long, father and daughter move from one dusty town to the next, her passion for music growing every time she takes the mike in another roadhouse. But it is not an easy life for...
3) Without a trace
NYT - Hardcover Fiction
15 copies, 18 people are on the wait list.
Charles Vincent seems to have it all a beautiful wife, two successful children, and a well-paying career. Yet happiness remains out of reach. He is trapped in a loveless marriage and his job is simply a paycheck. But his life changes forever one night as he drives along the Normandy coast, heading to their lavish château for the weekend. In one terrifying moment, Charles falls asleep at the wheel and veers off the road, plunging thirty feet down...
4) The challenge: a novel
1 audio media player : digital, HD audio ; 3 3/8 x 2 1/8 in.
In this thrilling novel from #1 New York Times bestselling author Danielle Steel, a small community is tested when their children go missing while exploring a dangerous local peak, forcing them to band together during the crisis. Fishtail, Montana, is home to Anne and Pitt Pollock, local royalty, high school sweethearts, and owners of the successful Pollock ranch. The sprawling foothills of the Beartooth Mountains surround the town, overlooking the...
5) The right time: a novel
Book, CD audio book, eAudiobook, eBook, Kindle, Large Print, Playaway
2017 Recorded Books, Llc
8 audio discs (9 hr.) : digital ; 4 3/4 in.
[2017], p2017 Findaway World, LLC
1 sound media player (9 hr.) : digital, HD audio ; 3 3/8 x 2 1/8 in.
"Abandoned by her mother at age seven, Alexandra Winslow took solace in the mystery stories she read with her devoted father--and soon she was writing them herself, slowly graduating to dark, violent, complex crime stories that reflected skill and imagination far beyond her years. After her father's early death, at fourteen Alex is taken in by the nuns of a local convent, where she finds twenty-six mothers to take the place of the one she lost, and...
6) Turning point
2019. Delacorte Press
[2019] Recorded Books, LLC
1 audio media player ( : digital, HD audio ; 3 3/8 x 2 1/8 in.
Bill Browning heads the trauma unit at San Francisco's busiest emergency room, SF General. With his ex-wife and daughters in London, he immerses himself in his work and lives for rare visits with his children. A rising star at her teaching hospital, UCSF at Mission Bay, Stephanie Lawrence has two young sons, a frustrated stay-at-home husband, and not enough time for any of them. Harvard-educated Wendy Jones is a dedicated trauma doctor at Stanford,...
7) Accidental heroes: a novel
Book, CD audio book, eBook, Kindle, Large Print, Playaway
1 sound media player (6 hr., 45 min.) : digital, HD audio ; 3 1/2 x 2 1/4 in. + 1 AAA battery.
"A decorated former Air Force pilot. A pregnant flight attendant. A dedicated TSA agent. The fates of these three, and many others, converge in Danielle Steel's gripping new novel--a heart-stopping thriller that engagesordinary men and women in the fight of their lives during a flight from New York to San Francisco. On a beautiful May morning at New York's John F. Kennedy airport, two planes have just departed for San Francisco--one a 757, another...
8) Suspects: a novel
Theodora Morgan is fashion royalty. Founder of a wildly popular online shopping service, she is one of the most successful businesswomen in the world, although she prefers to keep a low profile, especially in recent months. It was a year ago when the unthinkable struck her family: her husband, industry mogul Matthieu Pasquier, and their son were kidnapped and held for ransom -- a nightmare that ended in tragedy. The case has gone cold, despite evidence...
9) Silent night: a novel
First large print edition
1 sound media player (7 hr., 25 min.) : digital, HD audio ; 3 3/8 x 2 1/8 in.
"Paige Watts is the ultimate stage mother. The daughter of Hollywood royalty, Paige channels her own acting dreams into making her daughter, Emma, a star. By the age of nine, Emma is playing a central role in a hit TV show. Then everything is shattered by unforeseeable tragedy. Now Emma is living with her aunt Whitney, who had chosen a very different path than her sister. Whitney was always the studious older sister, hating the cult of celebrity that...
10) Blue: a novel
2015. Brilliance Audio
Ginny Carter was once a rising star in TV news, married to a top anchorman, with a three-year-old son and a full and happy life in Beverly Hills-until her whole world dissolved in a single instant on the freeway two days before Christmas. In the aftermath, she pieces her life back together and tries to find meaning in her existence as a human rights worker in the worst areas around the globe. Then, on the anniversary of the fateful accident-and wrestling...
11) Fairytale: a novel
Book, CD audio book, eAudiobook, eBook, Kindle, Large Print
℗2017. Recorded Books
Camille Lammenais has grown up in the beauty of the Napa Valley, surrounded by acres of her family's vineyards. Her parents, Christophe and Joy, still deeply in love after two decades of marriage, have built a renowned winery and château modeled after Christophe's ancient family estate in his native Bordeaux. Camille has had a perfect childhood, safe in her parents' love. After graduating from Stanford, she returns to help manage Château Joy,...
12) Child's play: a novel
1 sound media player ( hr., min.) : digital, HD audio ; 3 3/8 x 2 1/8 in.
"A senior partner at a prestigious New York law firm, Kate Morgan couldn't be prouder of her three grown children. Tamara, Anthony, and Claire all went to great schools, chose wonderful career paths, and would have made their father proud. A single mother for years after the death of her husband, Kate keeps a tight rein on her family, her career, and even her own emotions, never once asking herself if she truly knows her children . . . or if her hopes...
13) Rushing waters: a novel
1 audio media player (approximately 8 hr.) : digital ; 3 3/8 x 2 1/8 in.
"A 38-year-old American interior designer based in London and her independent-minded 74-year-old architect mother; a British investment banker in New York to see his ex-wife and young children; a resident ER doctor who experienced Hurricane Sandy when she was a medical student; two young men, 21-year-old NYU students; their friends; and others are thrust together when a major hurricane descends upon New York City and wreaks unimaginable chaos and...
14) Fall from grace: a novel
[2018]. Recorded Books
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"From #1 New York Times bestselling author Danielle Steel comes the gripping story of a woman who loses everything--her husband, her home, her sense of self and safety, and her freedom. Sydney Wells's perfect life with her wealthy, devoted husband vanishes when he dies suddenly in an accident. Widowed at forty-nine, she discovers he has failed to include her in his will. With Andrew's vicious daughters in control of his estate, and no home or money,...
15) Beauchamp Hall
6 audio discs (435 min.) : CD audio, digital ; 4 3/4 in.
[2018]. Findaway World, LLC
Winona Farmington once dreamed of graduating from college, moving to New York City, and pursuing a career in publishing. Then real life got in the way when she left college and returned to her small Michigan hometown to care for her sick mother. Years later, stuck in a dead-end job and an unsatisfying relationship, Winnie has concluded that dreams were meant for others. She consoles herself with binge-watching the British television series that she...
16) The good fight: a novel
7 audio disc (8 hr.) : digital, stereo ; 4 3/4 in.
"Against the electrifying backdrop of the 1960s, Danielle Steel unveils the gripping chronicle of a young woman discovering a passion for justice and of the unsung heroes she encounters on her quest to fight the good fight. The daughter and granddaughter of prominent Manhattan lawyers, Meredith McKenzie is destined for the best of everything: top schools, elite social circles, the perfect marriage. Spending her childhood in Germany as her father prosecutes...
17) High stakes: a novel
[2022] Recorded Books, Inc
"Jane Addison is an ambitious young woman with big dreams of owning her own company someday. At twenty-eight, she arrives in New York to start a job at Fletcher and Benson, a prestigious talent agency. Eager to impress her new colleagues, Jane jumps right in as an assistant to Hailey West, one of the agents in the literary department. Hailey is dedicated to the authors she represents, but her home life is chaotic and challenging. After her husband's...
18) Country
Available at another branch (library use only)
[Large print edition]
After the death of her husband, Stephanie Adams, a devoted stay-at-home mother, meets country music megastar Chase Taylor, who opens his whole world to her.
19) Invisible: a novel
NYT - Mass Market
Antonia Adams is the product of a loveless marriage between a beautiful young model and an aristocrat. Unprotected and unloved, she learns that the only way to feel safe is to hide from the dangers around her. Her love of the movies turns into a dream to become a screenwriter, and a summer job at a Hollywood studio. There, a famous British filmmaker notices her, and suddenly she can remain invisible no longer. He wants to put her in a movie and make...
20) The cast: a novel
"Kait Whittier has built her magazine column into a hugely respected read followed by fans across the country. She loves her work and adores her grown children, treasuring the time they spend together. But after two marriages, she prefers to avoid the complications and uncertainties of a new love. Then, after a chance meeting with Zack Winter, a television producer visiting Manhattan from Los Angeles, everything changes. Inspired by the true story...
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Stakeholder-Partnered Implementation Research and Innovation Translation (SPIRIT) program
Ong, Michael K. Gould, Michael K.
University of California Los Angeles, Los Angeles, CA, United States
Search 6 grants from Michael Ong
Search 145 grants from Michael Gould
Search grants from University of California Los Angeles
Neural Circuits Balancing Reward-Approaching with Threat-Avoidance
A Cul5 E3 ubiquitin ligase complex that prevents allergic asthma
MrgprC, A New Target for the Treatment of Neuropathic Pain
Anti-HIV-1 Effect of TALL-104 Cells
DPC4 function in human pancreatic cancer
Production of Pedigreed SPF Rhesus Macaques
South Africa-Pittsburgh Public Health Genomic Epidemiology Research Training Program (SAPPHGenE)
Interdisciplinary and multi-level approach to estimate the disease burden and outcomes of childhood tuberculous meningitis.
Electronic cigarettes in Latin America: Evaluation of impacts and policy options
As a collaboration among UCLA, Kaiser Permanente Southern California, the VA Greater Los Angeles Healthcare System, and the LA County Department of Health Services, the proposed new AHRQ-PCORI K12 program, Stakeholder-Partnered Implementation Research and Innovation Translation (SPIRIT), is designed to prepare outstanding postdoctoral scholars (including MD, PhD, MD/PhD, ScD, DrPH, and PharmD) for academic research careers focused on rapid and sustainable uptake of new scientific discoveries and innovations that improve the design, delivery, and outcomes of care for chronic diseases at the individual, population, and health care system levels. In the current era of declining numbers of health scientists nationwide, particularly among clinical providers, and of expanding need to bridge research and practice across diverse real-world settings of health services and systems as well as demographically diverse populations, SPIRIT will fill a critical need for research on a broad range of issues in the generation, dissemination, and implementation of clinical evidence and will advance the goals of increasing the pace and volume of innovation in the diagnosis, treatment, and prevention of chronic diseases to facilitate and advance learning health systems. In response to the challenges of better understanding variation in practice and outcomes and the barriers of T4 translation, the interdisciplinary curriculum and mentored hands-on research opportunities of the new K12 program interweave the scientific expertise and mentoring experience of 24 high-quality multidisciplinary investigators who are committed to collaborative, team-based cross-training and research in health services and patient-centered outcomes, clinical epidemiology, and dissemination and implementation. SPIRIT will leverage topically germane resources of education, training, and career development programs extant among the four partners for the core curriculum and protected time, foremost, the UCLA National Clinician Scholars Program, to achieve the following specific aims: (1) expand the multidisciplinary knowledge base of evidence- based practice and learning health systems as it relates to different aspects of chronic disease care across the clinical spectrum; (2) provide didactic and hands-on research training/career development in the intellectual and philosophical foundation of rapid translation of evidence into practice within the broader research enterprise of translational medicine; (3) develop scholars' scientific writing skills for presentations, publications, and grants; (4) provide an academic environment that enables development of the research skills and experience needed for successful, independent scientific careers as members and leaders of interdisciplinary teams dedicated to improving patient and population outcomes and health system performance; and (5) model research-empowering teaching and mentoring skills for scholars' development, including their eventual replication of research education, training, and career development programs in health system stakeholder- partnered improvements of chronic disease care as their careers evolve into stable, scientific independence.
Through mentored research career development of the next generation of interdisciplinary team members, leaders, and innovators in dissemination and implementation science and learning health systems, the Stakeholder-Partnered Implementation Research and Innovation Translation (SPIRIT) K12 Program will advance our knowledge of delivery and implementation strategies for proven interventions in real-world practice and community settings. In closing the gap between evidence-based interventions and their uptake across diverse settings and populations, including historically underserved populations who manifest wide disparities in health status, SPIRIT will contribute to improved health system performance as well as patient outcomes and overall quality of life of adults and children, and their families, who live and often struggle with a broad range of chronic conditions.
Physician Scientist Award (Program) (PSA) (K12)
5K12HS026407-02
Special Emphasis Panel (ZHS1)
Hsieh, Chinghui
Internal Medicine/Medicine
K12 HS PA-20-072 Stakeholder-Partnered Implementation Research and Innovation Translation (SPIRIT) Program: Vulnerable Populations Cared for by Learning Health Systems During the COVID-19 Pandemic
Ong, Michael K.; Gould, Michael K. / University of California Los Angeles
K12 HS Stakeholder-Partnered Implementation Research and Innovation Translation (SPIRIT) program
Be the first to comment on Michael Ong's grant


Kids love experimenting; this is how they learn about the world. Therefore, science experiments with kids are a perfect family activity. Simple science experiments you can do at home with your kids are a fun way to introduce children of all ages to basic scientific concepts.
One of the easiest ways to impress them is by demonstrating kitchen chemistry science using some simple foods and by letting them explore everyday foods.
Because it turns to a particular color if you add different foods to it, red cabbage juice is an excellent pH indicator. The easiest way to impress a young scientist is to use baking soda and vinegar. Most importantly, you can find these in every kitchen.
Just let them experiment with everything they can see around. And finally, enjoy the time spent together.


text:
The Big Read foi uma pesquisa sobre livros realizada pela BBC no Reino Unido em 2003, onde mais de três quartos de milhão de votos foram recebidos do público britânico para encontrar o romance mais querido de todos os tempos da nação. A pesquisa de um ano foi o maior teste de leitura pública até à data e culminou com vários programas organizados por celebridades, defendendo seus livros favoritos.

200 romances principais

 The Lord of the Rings por J. R. R. Tolkien
 Pride and Prejudice por Jane Austen
 His Dark Materials por Philip Pullman
 The Hitchhiker's Guide to the Galaxy by Douglas Adams
 Harry Potter and the Goblet of Fire por J. K. Rowling
 To Kill a Mockingbird por Harper Lee
 Winnie-the-Pooh por A. A. Milne
 Nineteen Eighty-Four por George Orwell
 The Lion, the Witch and the Wardrobe por C. S. Lewis
 Jane Eyre por Charlotte Brontë
 Catch-22 por Joseph Heller
 Wuthering Heights por Emily Brontë
 Birdsong por Sebastian Faulks
 Rebecca por Daphne du Maurier
 The Catcher in the Rye por J. D. Salinger
 The Wind in the Willows por Kenneth Grahame
 Great Expectations por Charles Dickens
 Little Women por Louisa May Alcott
 Captain Corelli's Mandolin por Louis de Bernières
 War and Peace por Leo Tolstoy
 Gone with the Wind por Margaret Mitchell
 Harry Potter and the Philosopher's Stone por Rowling
 Harry Potter and the Chamber of Secrets por Rowling
 Harry Potter and the Prisoner of Azkaban por Rowling
 The Hobbit por Tolkien
 Tess of the d'Urbervilles por Thomas Hardy
 Middlemarch por George Eliot
 A Prayer for Owen Meany por John Irving
 The Grapes of Wrath por John Steinbeck
 Alice's Adventures in Wonderland por Lewis Carroll
 The Story of Tracy Beaker por Jacqueline Wilson
 Cem Anos de Solidão por Gabriel García Márquez
 The Pillars of the Earth por Ken Follett
 David Copperfield por Dickens
 Charlie and the Chocolate Factory por Roald Dahl
 Treasure Island por Robert Louis Stevenson
 A Town Like Alice por Nevil Shute
 Persuasion por Austen
 Dune (romance) por Frank Herbert
 Emma por Austen
 Anne of Green Gables por Lucy Maud Montgomery
 Watership Down por Richard Adams
 The Great Gatsby por F. Scott Fitzgerald
 The Count of Monte Cristo por Alexandre Dumas
 Brideshead Revisited por Evelyn Waugh
 Animal Farm por Orwell
 A Christmas Carol por Dickens
 Far from the Madding Crowd por Hardy
 Goodnight Mister Tom por Michelle Magorian
 The Shell Seekers por Rosamunde Pilcher
 The Secret Garden por Frances Hodgson Burnett
 Of Mice and Men por Steinbeck
 The Stand por Stephen King
 Anna Karenina por Tolstoy
 A Suitable Boy por Vikram Seth
 The BFG por Dahl
 Swallows and Amazons por Arthur Ransome
 Black Beauty por Anna Sewell
 Artemis Fowl por Eoin Colfer
 Crime and Punishment por Fyodor Dostoyevsky
 Noughts & Crosses por Malorie Blackman
 Memoirs of a Geisha por Arthur Golden
 A Tale of Two Cities por Dickens
 The Thorn Birds por Colleen McCullough
 Mort por Terry Pratchett
 The Magic Faraway Tree por Enid Blyton
 The Magus por John Fowles
 Good Omens por Neil Gaiman e Pratchett
 Guards! Guards! por Pratchett
 Lord of the Flies por William Golding
 Perfume por Patrick Süskind
 The Ragged-Trousered Philanthropists por Robert Tressell
 Night Watch por Pratchett
 Matilda por Dahl
 Bridget Jones's Diary por Helen Fielding
 The Secret History por Donna Tartt
 The Woman in White por Wilkie Collins
 Ulysses por James Joyce
 Bleak House por Dickens
 Double Act por Wilson
 The Twits por Dahl
 I Capture the Castle por Dodie Smith
 Holes por Louis Sachar
 Gormenghast por Mervyn Peake
 The God of Small Things por Arundhati Roy
 Vicky Angel por Wilson
 Brave New World por Aldous Huxley
 Cold Comfort Farm por Stella Gibbons
 Magician por Raymond E. Feist
 On the Road por Jack Kerouac
 The Godfather por Mario Puzo
 The Clan of the Cave Bear por Jean M. Auel
 The Colour of Magic por Pratchett
 O Alquimista por Paulo Coelho
 Katherine por Anya Seton
 Kane and Abel por Jeffrey Archer
 Love in the Time of Cholera por García Márquez
 Girls in Love por Wilson
 The Princess Diaries por Meg Cabot
 Midnight's Children por Salman Rushdie
 Three Men in a Boat por Jerome K. Jerome
 Small Gods por Pratchett
 The Beach por Alex Garland
 Dracula por Bram Stoker
 Point Blanc por Anthony Horowitz
 The Pickwick Papers por Dickens
 Stormbreaker por Horowitz
 The Wasp Factory por Iain Banks
 The Day of the Jackal por Frederick Forsyth
 The Illustrated Mum por Wilson
 Jude the Obscure por Hardy
 The Secret Diary of Adrian Mole, Aged 13¾ por Sue Townsend
 The Cruel Sea por Nicholas Monsarrat
 Les Misérables por Victor Hugo
 The Mayor of Casterbridge por Hardy
 The Dare Game por Wilson
 Bad Girls por Wilson
 The Picture of Dorian Gray por Oscar Wilde
 Shōgun por James Clavell
 The Day of the Triffids por John Wyndham
 Lola Rose por Wilson
 Vanity Fair por William Makepeace Thackeray
 The Forsyte Saga por John Galsworthy
 House of Leaves por Mark Z. Danielewski
 The Poisonwood Bible por Barbara Kingsolver
 Reaper Man por Pratchett
 Angus, Thongs and Full-Frontal Snogging por Louise Rennison
 The Hound of the Baskervilles por Arthur Conan Doyle
 Possession: A Romance por A. S. Byatt
 The Master and Margarita por Mikhail Bulgakov
 The Handmaid's Tale por Margaret Atwood
 Danny, the Champion of the World por Dahl
 East of Eden por Steinbeck
 George's Marvellous Medicine por Dahl
 Wyrd Sisters por Pratchett
 The Color Purple por Alice Walker
 Hogfather por Pratchett
 The Thirty-Nine Steps por John Buchan
 Girls in Tears por Wilson
 Sleepovers por Wilson
 All Quiet on the Western Front por Erich Maria Remarque
 Behind the Scenes at the Museum por Kate Atkinson
 High Fidelity por Nick Hornby
 It por King
 James and the Giant Peach por Dahl
 The Green Mile por King
 Papillon por Henri Charrière
 Men at Arms por Pratchett
 Master and Commander por Patrick O'Brian
 Skeleton Key por Horowitz
 Soul Music por Pratchett
 Thief of Time por Pratchett
 The Fifth Elephant por Pratchett
 Atonement por Ian McEwan
 Secrets por Wilson
 The Silver Sword por Ian Serraillier
 One Flew Over the Cuckoo's Nest por Ken Kesey
 Heart of Darkness por Joseph Conrad
 Kim por Rudyard Kipling
 Outlander por Diana Gabaldon
 Moby-Dick por Herman Melville
 River God por Wilbur Smith
 Sunset Song por Lewis Grassic Gibbon
 The Shipping News por E. Annie Proulx
 The World According to Garp por Irving
 Lorna Doone por R. D. Blackmore
 Girls Out Late por Wilson
 The Far Pavilions por M. M. Kaye
 The Witches por Dahl
 Charlotte's Web por E. B. White
 Frankenstein por Mary Shelley
 They Used to Play on Grass por Terry Venables and Gordon Williams
 The Old Man and the Sea por Ernest Hemingway
 The Name of the Rose por Umberto Eco
 Sophie's World por Jostein Gaarder
 Dustbin Baby por Wilson
 Fantastic Mr Fox por Dahl
 Lolita por Vladimir Nabokov
 Jonathan Livingston Seagull por Richard Bach
 The Little Prince por Antoine de Saint-Exupéry
 The Suitcase Kid por Wilson
 Oliver Twist por Dickens
 The Power of One por Bryce Courtenay
 Silas Marner por Eliot
 American Psycho por Bret Easton Ellis
 The Diary of a Nobody por George e Weedon Grossmith
 Trainspotting por Irvine Welsh
 Goosebumps por R. L. Stine
 Heidi por Johanna Spyri
 Sons and Lovers por D. H. Lawrence
 The Unbearable Lightness of Being por Milan Kundera
 Man and Boy por Tony Parsons
 The Truth por Pratchett
 The War of the Worlds por H. G. Wells
 The Horse Whisperer por Nicholas Evans
 A Fine Balance por Rohinton Mistry
 Witches Abroad por Pratchett
 The Once and Future King por T. H. White
 The Very Hungry Caterpillar por Eric Carle
 Flowers in the Attic por V. C. Andrews

Ligações externas

Prémios literários do Reino Unido
BBC

redpajama_set_name: RedPajamaWikipedia


text:
Q: Is this RESTful? Using Tonic I'm trying to create a REST service which shows/adds/deletes/edits soccer data in a database.
I've made a design of how I could achieve this, but it becomes quite complicated.
For example, when a goal is scored, what URL should I call?
So the question is, am I going in the right direction or do you advice something way different?

A: *

*I agree with Abhiniav's answer except on the fact that PUT should not always be used for editing.  It should only be used when you are sending the new complete resource.  If you are sending a modification or partial, use POST, or the lesser known PATCH.

*Reading up on Safe and Idempotent methods should be useful.

*You would most likely use POST or PATCH to update the goal count: /{country}/team/{team_id}/goals.

*The biggest reason something isn't REST is because services are not discoverable. Read up on HATEOAS.

A: Everything seems fine in your structure except that you should switch PUT and POST.
PUT can be used for both updating/creating records. In case you know the resource ID before hand, you can use PUT.
POST is used when you would be creating new resources whose IDs you would not know.
Stackoverflow has a pretty detailed discussion here:
PUT vs POST in REST

redpajama_set_name: RedPajamaStackExchange


text:
Home > In the News > Closed code threatens science
Closed code threatens science
Thom Holwerda 2012-04-16 In the News 32 Comments
"Modern science relies upon researchers sharing their work so that their peers can check and verify success or failure. But most scientists still don't share one crucial piece of information – the source codes of the computer programs driving much of today's scientific progress." Pretty crazy this isn't the norm yet.
Thom Holwerda
Follow me on Twitter @thomholwerda
kwan_e
There is a danger that by releasing the source code, other scientists would use the source code with all the bugs which causes errors to propagate undetectably in derived research.
Ostensibly, scientists can check the source code to find bugs, but it's never going to be complete.
There is something to be said about scientists having to recreate source code in a clean room environment because errors in either code or hypothesis is easier to expose.
cyrilleberger
Instead of that, they should write their own implementation with its own set of bugs… right? Instead of fixing the bugs in the original implementation and bringing improvements…
Instead of that, they should write their own implementation with its own set of bugs… right?
Yes. It's another way to check that the theories in the original code are correctly implemented.
Say you want to write some code to verify the Hockey Stick Graph is correct. If you use the original source code, chances are, you're not going to spot all the bugs in the implementation and you'll likely end up with the same graph, which does not fulfil the goal of independent verification.
We're talking scientific formulae, not a Linux desktop environment here. The most important thing is the data.
Instead of fixing the bugs in the original implementation and bringing improvements…
The only useful improvements for scientific research are corrections to formulae and theories. That can be done outside of code, and probably better served by being outside of code.
Do you seriously think it is a good idea for logic bugs to propagate through hundreds of research projects derived from the same code?
j-kidd
The alternative is to have hundreds of research projects derived from hundreds of different codebases, each with its own bag of logic bugs. All code are inherently buggy, and scientists, due to lack of basic training in software engineering (e.g. code reuse, unit test, etc), tend to write buggier code.
Last year, I had to do some data deduplication work using string metric such as Jaro–Winkler distance. I found 3 open source libraries, one in Java, two in Python. And the three of them implement the formula differently, resulting in significantly different metrics. The good thing is that, because the code is open, I submitted patches to the maintainers. Some got fixed, some did not (but the bug report is publicly available nevertheless).
One of these libraries, Febrl (Freely Extensible Biomedical Record Linkage), was released by Australia National University as part of research. I owe greatly to the authors, in particularly their willingness to put the code out for scrutiny.
Yes, that's the point.
If you have multiple independent implementations of the same formula, the more chance you have of finding problems with the actual formula.
You do understand that there is a development methodology that's used for designing and writing robust code by implementing with different languages, don't you?
In fact, many modern CPUs have a similar thing where a calculation takes place twice and the results are compared at the end to verify the calculation was correct. What I'm suggesting is that it's analogous to having multiple cleanroom implementations of formula.
looncraz
During peer review, the code would be checked to verify any unexpected results.
With open code, any meaningful problem would be found and solved, and old studies could be easily re-run and verified or discarded.
With closed code, the bugs are never found, and the authors have no reason to repair it if they get what they think are sound results.
–The loon
It doesn't matter because it's the published results that matter, and if the results are wrong, someone can verify it independently when its published. If you use the original source code, to verify, it's no longer independent.
In a research organization where there are hundreds of people pulling in open source code, you cannot guarantee someone did not pull code from the original base, leading to a compromised verification of the data.
thomasg76
Well, it can also work quite easily in the opposite. The source code is taken, with little or no review, and new data are run through it, confirming the original result.
I am sure that this happens. Not too long ago I run in to this issue while looking at studies done in the field of psychology. They run most there studies through SPSS to make a factor analysis, do get something out of the data. Everybody using the same software the same way of conducting the study, of course they confirm the result of others. Most of the conclusions drawn are just simply wrong, because less than half of the data is actually supporting the result.
Now since most psychologist aren't statisticians, they just take the work of others as template for their own. And you propagate a wrong method / software.
The same is going to happen with opening the source code for all research. If the code is critical to the research than it should be implemented independently to confirm the results, based on the same data. If the code is auxiliary to the problem, then who cares anyway.
Also I know of Professors that stopped publishing all together because of that requirement. Now what do you gain?
The good thing from all the published work is, we KNOW that certain things work/exist, so they can be re-discovered and independently verified.
renox
I'm not so sure: there was a time where a popular idea to produce safe code (for avionics or things like that) was to have several independant teams coding the same software to have different bugs.
A study discovered then that independants teams had quite a few identical bugs, so it became much less popular!
Yes, but with scientific research spread all over the world, we can afford to have more teams than any single organization can afford.
And again, I refer people to the Climategate non-scandal. What if it turns out everyone who verified the data were using the same code, or at least derived versions of the same code? Think about the fallout from that. Even if the bugs were mostly identical, do we want to risk being wrong?
moondevil
But if the code becomes available how can you patent it?
(I'm being sarcastic)
Neolander
Well, sure, others can take a copy of my source code anytime they want. I wrote it with a focus on readability by future lab members anyway. But… It's written using proprietary software and a nonstandard programming language, so I can hardly see them doing anything with it without the closed-source software I used, unless they feel highly motivated.
Also, it would take them quite a lot of time to get familiar with the codebase, whereas if they asked me about the core measurement algorithm I could likely explain it on half a page of text, skipping all the annoying details of hardware initialization, GUI code, and so on.
So, I'm not sure that source code would be much more useful than what you find in your typical scientific paper in the end.
Edited 2012-04-16 07:12 UTC
Alfman
Neolander,
Well I don't read many scientific papers these days, but I would think whether or not source code is useful depends on how instrumental the source code is in making the case for the paper's conclusions.
For example, if the data speaks for itself and doesn't need complex software processing to be understood, then providing source code is more about convenience than an instrumental part of the paper.
If the data were transformed using atypical algorithms and there is no way to understand it directly without software analysis, then of course other scientists would be at a loss to validate the work unless they actually re-implemented the software from scratch. Even if they do, they might be left to guess about implementation details and not be able to validate the paper directly.
lucas_maximus
This is a little simplistic.
Knowing the algorithm and having access to the data should be sufficient for replication, having the original code is not necessary.
In fact, being able to reproduce the algorithm yourself, i.e. writing your own code, is a better test than merely inspecting
However this doesn't scale for larger programs.
Science isn't an economic endeavour. Accuracy should be preferred over scale or efficiency.
no but if you have a sufficiently large program it might not be feasible to recreate.
You can say that about every sufficiently important scientific study. Yet researchers still must verify the results independently, and they used to do it for complex studies without source code.
Oh right.
Well that is interesting from a development prospective because I know that certain fortran code is particularly well debugged and I wonder how they recreate the accuracy of some numerical results.
l3v1
Demanding souce code has nothing to do with verification of results.
A lot of researchers provide either sources (mostly proof-of-concept Matlab code, or sometimes regular sources under some license) or executable code along with some publications. To verify results – which is almost never done, mind you – noone requires sources, a simple executable, a binary library, or a Matlab basic code would be quite enought for all intents and purposes.
And, surprise surprise, a lot of researchers will provide you with either an executable, or a library if you ask for it, others will run their algorithm on your data and give it to you. And yes, there are people who don't, but that's their prerogative.
Demangind sources for all the algorithms is much more than any of the above, and in almost all cases you just simply couldn't justify your need for it, besides saying that you want it. Well, not every day is Christmas.
What's the reason behind it? Multiple. Research and creation of proof-of-concept code for an article is _not_ software development, and it shouldn't be – unless of course the article deals with software development Also, producing such code is often a result of a lot of blood and sweat, and sometimes one requires more reason to share sources, than kindness of the heart (still, it happens from time to time). Also, some (a lot of) researchers can't afford to patent results, thus keeping the sources is a fairly good way to make stealers' work harder.
Not everything is black and white here, and most people can't see that. And the title saying "Closed source threatens science" is just plain untrue. I mean come on, it threatens it now? Didn't it threaten for decades? What is the exact nature of that thread (beacuse the simple unavailability of sources is simply not a threat)?
Also, about:
If I knew there was a publication requirement for my code, I probably would have done things like comment it better, kept better track of it, and generally put a bit more thought and effort into my code
…yes, and that's exactly what I don't want to do in a lot of cases. More often than not, the idea is far more important than the code that provides a method to test it. Implementation (yes, the code) is not the science (unless we're in algirithm design and software implementation science), an implementation is just one way of realizing the presented idea.
Also, another important issue, sometimes the software implementation of a presented method, algorithm or idea is simply not public, restircted, sometimes it can be even confidential – in such cases, demainding pubication of the sources is just simply not an option. And you'd be willing to send away good papers because of that? Right, good luck being a high impact journal.
And if an idea is so good, and there's real marketability in it, then a lot of times it evolves into a distributable software and everyone can get their hands on it.
Really? ABSOLUTELY nothing?
tidux
Yes, absolutely all source code relevant to published science should be freely available. Otherwise, how do we know there isn't some magic constant hidden in there compensating for systemic error? How do we even know the data's being analyzed at all? If research that relies on computation doesn't provide source code, it's basically unreproducible over the long term, since no OS or hardware platform lasts forever.
The algorithm and any formulas used will be part of the paper. Someone with significant understanding can reproduce and verify the results.
I don't think it is too different than working against a well written software specification.
Without the source code, how do you know that's the formula they used? For all you know, their RNGs could have always returned 3.
Because they must publish papers describing their research and results. Then other people can reimplement parts of the paper and if the results don't match what the paper has, then you know something is wrong.
If analyzing source code can really prove or disprove scientific results, we would already have this whole software business completely automated with software that writes itself.
kwan_e,
"If analyzing source code can really prove or disprove scientific results,"
Why should we assume that it cannot? If we have an accurate mathematical model of a scientific process, then software can reveal insight and even proofs for scientific processes that wouldn't otherwise be conceived. However in order for an implementation's results to be valid, the authors source code ought to be peer reviewed.
It's true that one might get away with publishing pseudo code or even logic charts instead of real code. But if the goal is to reduce errors and encourage 3rd parties to validate the work, the inclusion of real code is nice.
"we would already have this whole software business completely automated with software that writes itself."
At an abstract level, I'd argue that's what a compiler does already: it takes a specification written in one language and builds binary software implementing that specification. I guess you might have been thinking compiling software from an English spec, but there are at least two obstacles with that.
1 – English is ambiguous and it takes a lot of words to exactly describe a process that computer languages can nail down exactly. A thought experiment would be to stick 10 qualified programmers in 10 black boxes, give them an english spec, and see how different their work is. Now if we give those same programmers specs written in one computer language, and force them to translate them into another computer language, with any luck they'd still end up with functionally identical work because computer languages are so concise. (We should play the "telephone game" with computer languages!)
2 – English speakers have shared knowledge due to shared human experiences and contextual knowledge. This enables them to gloss over a great deal of information that would otherwise lead to holes in an english spec.
Sorry my response has gone way off topic, but the point is the lack of english language compilers is no reason to negate the scientific merit of computer source code proofs.
Do you know what sort of effort it required to prove that a computer program is mathematically correct?
We are going into the Vienna Developer Method territory. Which is totally irrelevant anyway.
The whole point is that the information in the paper should be sufficient to reproduce the results, … you are putting the cart before the horse.
If formulae and relevant parts of the algorithm are described (pseudo-code is pretty good IMHO, and I write my proper code first as pseudo code) is more than sufficient.
jburnett
My academic background is computer science. I didn't publish any papers that had algorithms so complex they could not reimplemented. Some of the visualization and driver code was a pain, but the core algorithm I was describing was pretty tight and neat. All of computer science was that way, you almost never see a paper with an algorithm that is difficult to reproduce (aside from the really complicated math). When you do see such a paper, it was generally a hardware specific way of doing something where the specific hardware was annoying to program. But I always thought of those as more marketing than science.
So, what is so complex in biology, chemistry, physics, psychology, etc… that it cannot be reimplemented fairly easily when given the core algorithm?
Speaking for physics, not much… Except that the people who do numerical simulations may like to use open-source highly optimized math libraries, because those take a lot of time to mature.
I have heard that CERN scientists still use Fortran a lot, simply because they have gigabytes of highly optimized Fortran code around and can't bother to rewrite it in something more modern like C.
jburnett,
As long as it's described well enough (and perhaps even if it's not) then anything can be reimplemented – that is not a point of contention.
I just think it's more work to do so, that's all. If the scientific community has been doing it without source code all these years, then maybe it's not such a big deal. The main issue I have is when someone reads the paper thinking "gee, I would like to play with the numbers myself but I don't have the time/skill to write my own software from scratch".
Yamin
Academia tends to have formal specifications for formula. They express things in mathematical formulas or specialized scientific notation.
To most scientists, software is just a tool. They're really not interested in the program. Chances are it is messy, sporadic… they might even be embarrassed to release it.
So the output is the formula… that is what they release.
Others have mentioned, but I personally think it increases scientific accuracy if they don't release their test software. It would be far too easy to copy that code or just run their program to validate the formula.
Let's remember the output is the scientific formula… not the program itself.
It is actually better if someone else codes their own test system and validates it.
It's kind of life making you buy your measuring equipment from a different source than your vendor. Would you buy a Cisco router tester from Cisco? Nope, you'd want something independent from a company like Ixia or something.
As a side note, I happen to think this line should blur. That is to say, it should be possible to have the scientist write their formula in whatever academic language they want and tools should be able to output that into a library for a common language or even their own compilers.
Software / formal academic specifications do the same thing. They express algorithms….
From reading the comments since my last post it seems there are two main arguments for requiring the release of source code.
1. Authors do not fully disclose their method, making their work unreproducible. I thought this was the whole point of peer review. Journal editors are supposed to review the work to make sure that, at a minimum, it could be reproduced, even if they don't reproduce the work themselves. Otherwise you have a SCIgen http://pdos.csail.mit.edu/scigen/ situation. (sorry, I don't know how to embed links in comments)
2. Scientists have gotten so lazy or incompetent that they are unable to reproduce results when given everything that a skilled scientist requires. Having gone to public school in the US I can believe this.
Fortunately, science is mostly merit based, so these people will quickly fall out of the ranks and go on to stimulating careers writing about science and politics, where they won't take up any more valuable peer review time.
I agree on your first point.
I have to take issue with your second though, not everyone who qualifies as a competent scientist is a competent programmer. And even those who are might be too busy to spend their time reimplementing other's work.
So including source code has some merit, but the bigger question is to what degree. The overall consensus here is that it's not terribly important, and that's fine.
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The average rent for an apartment in Holland is $896, a 7% increase compared to the previous year, when the average rent was $837.
$896 7% 871 sq. ft.
The average size for a Holland, MI apartment is 871 square feet, but this number varies greatly depending on apartment type. Studio apartments are the smallest and most affordable, 1-bedroom apartments are closer to the average, while 2-bedroom apartments and 3-bedroom apartments offer a more generous square footage.
The rental statistics on this page were compiled using data provided by our sister company, Yardi Matrix, an apartment market intelligence solution which offers comprehensive information on all Holland apartment buildings 50 units or larger. Yardi Matrix covers ~80% of the U.S. metro area population, including over 80,000 properties and 15.2 million apartments across 124 U.S. markets.


parrot had a bad attitude and an even worse vocabulary.
think of to 'clean up' the bird's vocabulary.
Finally, John was fed up and he yelled at the parrot.
everything I can to correct my rude and unforgivable behavior."
softly and said, "May I ask what the turkey did?"
When the trooper asked the driver why he was speeding, the driver said he was a Magician and Juggler and was on his way to Beckley, WV to do a show at the Shrine Circus. He didn't want to be late.
While the man was juggling, a car pulled in behind the patrol car. A drunken good old boy from West Virginia got out, watched the performance briefly, then went over to the patrol car, opened the rear door and got in. The trooper observed him and went over to the patrol car and opened the door asking the drunk what he thought he was doing.
The drunk replied, "You might as well take my *** to jail, because there ain't no way I can pass that test."
I guess I'll post a collection.
Here's some that I made up during bible class.
You know the story of Absalom? Well, it's perfect example of what one should not do. You see, Absalom decided to jump ahead, instead of waiting for his turn to become king. He started a revolution, gathered and army, and attempted to oust David from the throne. He met his end when his hair was tangled up in a tree. The general decided to have him killed for his treachery.
So what's the moral of the story? Be careful. Absalom attempted to use goto, and it cost him his life. The other moral? Your tangled spaghetti code can get you caught on the wrong side of a binary search tree.
2+2 != 4. Why? Because I use base 4, silly.
Argon walks into a bar. The bartender says "We only serve noble gas here!" Argon doesn't react.
Cats are made up of Iron, Lithium, and Neon. FeLiNe.
Math tells us the saddest love stories ever. Parallel lines, who travel side by side but are destined to never meet. Tangent lines, who cross paths once and never see each other again. Asymptotic lines, who get closer and closer but never meet. Derivatives, which attempt to mimic someone they see as better, but always remain a shadow of the original.
Yes, all I really know are nerd jokes. Get over it.
A doctor, a reporter and an engineer are out golfing.
Right about the 5th hole they notice the man playing ahead of them is playing extremely slowly, taking forever to finally sink the ball. The three friends become extremely frustrated and annoyed at the delays. Upon looking closer, they realize this man is blind.
The doctor turns to the caddy and asks "What's the deal? Why is this blind man playing golf here?"
The caddy explains "Well, last year the clubhouse caught fire. That man was one of the firefighters who responded to the call. He saved the lives of eight people, including the entire staff. Unfortunately he was injured in the rescue, and was rendered permanently blind. In gratitude he's allowed to play here for free, whenever he likes.
The doctor is overwhelmed by the story. "You know, from now on I'm going to dedicate my career to finding a way to help this man see again." The reporter is similarly overcome. "I'm going to write a book, and it's going to be all about the life of this courageous man." The engineer simply asks "Why can't he just play at night?"
A Scotsman paying his first visit to a zoo stopped by one of the cages "An' whut animal would that be ?" he asked the keeper.
"That's a moose from Canada", came the reply.
"A moose!!", exclaimed the Scotsman. "Hoots, mon, if that's a moose then they must ha' rats the size of elephants over there!"
I think it's time for another computer joke!
A programmer is out on his back porch with his wife. He pulls out a cigarette, and lights it up. His wife says "Those things are dangerous for you! Didn't you notice the warning label?" The man replies "I'm a programmer. I worry about errors, not warnings."
Here come the chemistry jokes.
A sign outside the hotel read, "Great morning rates! Even better NO3's!".
What did the dipole say to the other dipole? "Hey, you got a moment?"
What did the chemist say when he found two new isotopes of helium? Hehe.
What kind of weapon can you make with Iron, Nickel and Potassium? A KNiFe.
What's the compound CH2O? Seawater.
and he was getting thirsty. He thought maybe he knew the direction back, now that he'd paid attention to the sun and thought he'd figured out which way was north, so he decided to start walking. He figured he only had to go about 30 miles or so and he'd be back to the small town he'd gotten gas in last.
town. But he doesn't recognize any of this. He had to cross a dry creek bed a mile or two back, and he doesn't remember coming through it in the SUV. He figures that maybe he got his direction off just a little and that the dry creek bed was just off to one side of his path. He tells himself that he's close, and that after dark he'll start seeing the town lights over one of these hills, and that'll be all he needs.
sure that whatever substance they denature the fluid with is just designed to make you sick - their way of keeping winos from buying cheap wiper fluid for the ethanol content. He can handle throwing up, if it comes to that.
stroke finally catching him, or maybe he was wrong and the denaturing of the wiper fluid was worse than he thought. He tries to steady himself, and keep going.
shake the sand out, and a good wash, and they'd be wearable again. He wishes his throat were wet enough to laugh. He coughs a little instead, and it hurts.
dunes, more sand. This isn't where he drove his SUV. This is Hell. Or close enough.
After a few steps, he realizes that he's in trouble - he's not going to be able to keep his balance. After a couple of more sliding, tottering steps, he falls and starts to roll down the dune. The sand it so hot when his body hits it that for a minute he thinks he's caught fire on the way down - like a movie car wreck flashing into flames as it goes over the cliff, before it ever even hits the ground. He closes his eyes and mouth, covers his face with his hands, and waits to stop rolling.
have that chance - to see the world. Before he becomes bound here like I have been.
Shouting to Sammy as he pulled the steering wheel, "BETTER NATE THAN LEVER," he ran over the snake.
What did the Turkey say on Thanksgiving?
FATHER?! NO!!!!! CURSE YOU, YOU MONSTERS! I WILL HAVE MY VENGEANCE!!!!


Dark Blue Beverage Napkins - 20 Ct.
1 package of 9" blue plastic plates. Each pack has 10 plates. These heavy duty blue plastic plates are beautiful and have vibrant coloring. They will make any event look special. These colors are the most vibrant we have come across in any line we have dealt with to day!


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