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ECTOMYCORRHIZA'S INFLUENCE ON SEEDLING GROWTH
Abstract: Mycorrhizae play an important role in forest ecosystems through their symbiotic relationship with trees and root systems. Of the mycorrhizae, ectomycorrhiza (EM), specifically targets softwood species and some hardwoods. In this experiment, the results of a powdered EM inoculum and red oak (Quercus rubra L.), pitch pine (Pinus rigida Mill.), and red spruce (Picea rubens Sarg.) were evaluated during one growing season. The study compared a control of no EM and treatment with EM in seed grown trees in containers. Difference between heights of the treatment and control were recorded to see if the inoculum impacted seedling growth of the host species. Throughout this capstone the hypothesis states: An ectomycorrhizae (EM) powdered inoculum would influence pitch pine, red spruce, and red oak seedlings height and biomass for the duration of one growing season (April-Late August). Red oak control exceeded treatment in biomass but not height, and pitch pine and red spruce treatment exceeded control in height and biomass.
File Attachments: finalreport_slinger.docx
Authors: Samantha L. Slingerland
Coarse Woody Debris Volume Following Conventional and Whole-Tree Harvesting
Abstract: Coarse woody debris (CWD) affects important ecological patterns and processes in the forest, including nutrient cycling, carbon stocks, wildlife habitat, regeneration dynamics, and hydrology. Timber harvesting practices have been shown to affect the abundance and distribution of CWD in forest stands. This study separates timber harvesting practices into two categories: conventional harvesting (CH), where only the main stem of trees and possibly some large branches are harvested, leaving branches, twigs, leaves, buds, and other plant parts to decompose on the forest floor, and whole-tree harvesting (WTH), which removes the entire aboveground portion of trees. I measured post-harvest CWD volume within recent patch clear cuts in Vermont, comparing results between CH and WTH. Conventional harvesting sites contained significantly more (p = 0.04) CWD volume (954ft^3/ac) than WTH sites (422 ft^3/ac). In other words, CH resulted in a post-harvest CWD volume 126% greater than the volume resulting from WTH. The most important difference was a wide discrepancy between treatments in decay class 2, which contained 66% of the total CWD volume. The increased reduction of CWD through WTH, especially when carried out over multiple rotations, may have negative effects on future site productivity, as well as richness and abundance of wildlife. The choice to employ CH or WTH may also affect the carbon balance, regeneration dynamics, and hydrology of forest stands.
File Attachments: Bill_Musson_Final_Capstone_Report_12.4.18.docx
Authors: William (Bill) Musson
Antifungal activity of propolis, neem oil, and cedarwood oil against the white-rot fungus Trametes versicolor on American beech
Abstract: Fungi are often considered the most destructive organisms to attack wood that has gone through the milling process, so developing compounds to resist decay are extremely important. Copper chromated arsenic (CCA) was an industry standard until 2003 when its use was restricted due to environmental concerns. Thus, research into environmentally friendly compounds has become more common. This study investigated which compound, propolis extract, neem oil, or cedarwood oil, would best preserve beech wood exposed to Trametes versicolor. Extracts for each of the compounds were prepared using denatured ethanol, and infused into wood blocks using a vacuum pump. Blocks were made of American beech (Fagus grandifolia Ehrh.) and were 10mm x 20mm x 5mm in size. The blocks were subjected to a common white-rot fungal strain, Trametes (= Coriolus) versicolor (L.) Lloyd (1920), for six weeks. Overall, propolis and cedarwood oil treated blocks lost significantly less mass than both neem and control blocks, suggesting they have potential for use as natural wood preservatives, and could be used as cobiocides.
File Attachments: Final Capstone Report.docx
Authors: Adam Milenkowic, Timothy Otis
Engaging Visitors Of Glenview Preserve With Interpretive Signage
Abstract: Glenview Preserve is a Lowland forest and Field property that boarders the Bloomingdale Bog. Implementing an educational system at the preserve would lead to more public interaction that would guarantee support for the Adirondack Land Trust's mission objectives. This approach would involve the development of an interpretive day-use site, interpretive programs and signs, and an outdoor education space. For my portion I will be investigating how the Adirondack Land Trust can construct interpretive signage that is weather resistant and provides valuable content. The quality of the content will be evaluated using the National Association of Interpretation principles of POETRY. These signs will promote ALT's mission objectives by encouraging people to make a difference after their visit through well-constructed and entertaining information. Visitors will donate money to ensure that having an educational system at the preserve is a leading concern of the Adirondack Land Trust's management plan for Glenview Preserve.
Major: Integrative Studies, Natural Resources Conservation and Management, Recreation, Adventure Education and Leisure Management, Parks and Conservation Management
File Attachments: How Can the Adirondack land trust use interpretive signs to conserve the treasures of Glenview Preserve
Authors: Tiffany Elizabeth Marie Clark
Student of Natural Resources and Conservation Management
Fall 2018 graduate of Paul Smith's College
PROPOSED DAY-USE SITE AT THE ADIRONDACK LAND TRUST GLENVIEW PRESERVE
Abstract: Glenview Preserve is a lowland mix deciduous forest that boarders the Bloomingdale Bog. The property would be a quintessential location for public engagement through a day-use site, which in turn would ensure future use and elevation of the Adirondack Land Trust and their mission objectives. Through the determined design goals and the predetermined ALT goals for the property a comprehensive blueprint has been presented. The proposed day-use site is predicted to increase the three essential services that communities in the Adirondacks thrive off of. Their economic value, health and environmental benefits, and their social importance streamlines with the ALT's management practices and goals to provide a beneficial educational and recreational space for the community.
Major: Parks and Conservation Management
File Attachments: Capstone Paper Web Version.docx
Authors: Nathan Smith
Changes in aquatic communities resulting from interactions between climate change and invasive aquatic plants in the Adirondacks.
Abstract: Global climate change can act synergistically with invasive species leading to shifts in ecosystem structure and function. We assessed how a rise in water temperature influenced the potential competitive advantage of an invasive aquatic plant, Eurasian watermilfoil, (Myriophyllum spicatum) over a co-occurring native species northern watermilfoil (M. sibiricum). We also examined the interrelationship between water temperature, watermilfoil, and the aquatic ecosystem including periphyton growth and zooplankton abundance. The study was conducted using replicated mesocosms (3785-liter), with water heaters used to provide a range of temperatures. We found that increasing water temperature promoted the likely competitive advantage of the invasive species, M. spicatum: Survival of M. sibiricum plants was lower than that of M. spicatum across all temperature treatments with a mean survival rate of 24% and 96% respectively. M. sibiricum also showed significantly slower rates of plant growth (mean growth of 3.3 cm compared to 7.6 cm for M. spicatum) and reduced vigor compared to M. spicatum, with an average of less than half the number of growing meristems. Zooplankton densities averaged over 20 times higher in mesocosms with M. sibiricum compared to those with the invasive M. spicatum. Periphyton biomass was best explained by water temperature with an increase in growth in warmer water. Our study confirms that in the face of global climate change, the invasive M. spicatum will continue to exert dominance over its native counterpart. Our results also provide compelling evidence that the combined effects of climate change and invasive aquatic plants can dramatically alter aquatic ecosystems.
Major: Environmental Sciences, Fisheries and Wildlife Science, Forestry, Natural Resources Management and Policy
File Attachments: Climate change and milfoil draft FINAL.doc
Authors: Nicholas Boudreau, Zachary Bozic, Geoffrey S. Carpenter, David M. Langdon, Spencer R. LeMay, Shaun M. Martin, Reid M. Mourse, Sarah L. Prince, Kelli M. Quinn, David A. Patrick


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Employers / Norton Rose Fulbright / Get the inside view from graduates at Norton Rose Fulbright
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"The firm works with underprivileged schools in Southwark; gives them work experience. I felt that my interview was very much geared against my public school background, unlike many other firms, nepotism doesn't fly here and almost everyone from my intake went to state or grammar schools. I am in a minority in that sense, not because of prejudice against private schools either, I just think it is really meritocratic."
"The firm does lots of work with local schools and charities, with the aim of helping potential applicants from less privileged backgrounds to develop and strengthen their chances of obtaining a job in law and the City generally."
"The firm is involved in a number of schemes to promote the firm to applicants from less privileged backgrounds, help them understand the profession and attract their application. We run a great mentoring scheme."
"Trainees and other fee earners and support staff are encouraged to take part in mentoring programmes and networking events with young people that want to gain an insight into legal work and get some work experience. We work with SEO and PRIME, amongst others."
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Between Two Evils Series
Thanks to Jan over at JT Twissel for the fun interview questions!
(If you enjoy this interview, please visit her (very fun!) blog and subscribe.)
Today in my When I Get it Together (WIGIT) semi-regular series on meeting other writers, please welcome DL Orton whose sci-fi debut novel CROSSING IN TIME (first in a series) was recently released and is free on Amazon May 25, 2015 (which I hope is today unless my talents using WordPress are total crap). This fast paced novel envisions a world on the brink of extinction where two star-crossed lovers may hold the key to survival. However, they must go back in time. A very risky business. From my reading of her book, DL has researched quantum physics, climate change, and – dare I say it? – Masters and Johnson's studies on sex.
JTT: Hi Deb, thanks for agreeing to be featured on WIGIT. Let's assume you've come from either the future or past (which is probably the truth). Which is it and why?
DLO: My pleasure, Jan! I'm from the future, of course. Come to the dark side; we have time machines. Unfortunately, if I told you why, I'd have to shoot you. And yes, a woman DOES eventually get elected President, gays DO have a constitutional right to marry, and Florida IS going under. If you want to know how Game of Thrones ends, sign up for my newsletter. (PS: If you'd like to win a special prize, guess the news headline for May 4th, 2050, and include your email address written backwards e.g. moc.notrold@old in the comments. I'll send you a telepathic message if you win. Or perhaps I'll arrive in your bathroom with the news!)
JTT: Wow, well I'll have to sign up. In your book, Crossing in Time, you address two issues which psychologists believe are more strongly related that most people would think: parallel universes and the gender gap. Your response?
DLO: A shower curtain, an ant, and a bowling ball.
JTT: What?
DLO: Start with the shower curtain: a two-dimensional object in a 3-dimensional world. Imagine that you, gentle reader, are an ant, walking, talking, and having sex (do ants do that??) on a thin, flexible membrane (or a "brane" in physics-speak). Layered beneath you are a million other shower curtains, all of them with their own allotment of ants (some of which get paid 78 cents on the dollar due to slight differences in their copulatory organs). In a very real sense, those other ant universes are close to you in space (and time), but still seemingly undetectable — until someone drops a red-hot bowling ball on those piled up plastic sheets and makes the real-world equivalent of a black hole. Mind the gap.
JTT: Okay you're officially too smart for me. I saw strong similarities between your female protagonist, Isabel, and Sarah Connor of the Terminator Series. Why is it that female protagonists in sci-fi series such as the Terminator, Alien and Avatar are much more formidable than the protagonists of erotica such as Fifty Shades of Grey? Can the sci-fi and erotica genres unite to gain an audience?
DLO: Well, if the reviews I've been getting are any indication, then no. 😉
Although my book is not erotica, I expect some women will be turned off by the sex (because my protagonist is the antithesis of the ditzy woman in 50 Shades, and Isabel's lover is no demigod with a helicopter, handcuffs, and expensive taste in high heels. Sorry.)
JTT: No reason to be sorry. I think a lot of women fantasize about being an Isabel. I hate to ask this question because it is so hackneyed in writer interviews, but as a reader I really am interested to know, what motivated you to write this series?
DLO: When it comes to fiction, I find Frankenstein's monster very appealing. I'm drawn to an author who tosses together eclectic body parts and then sews them into something cool and unexpected. Books with character-driven sci-fi, lots of action, good (real!) sex, dark humor, strong female leads, a bit of a mystery, and an edgy love story are great reads, but there aren't many out there. So I wrote one. And once I got started, the monster took on a life of his own.
JTT: That's an interesting answer! My book – the Monster! Just one last question: What do you wished I'd asked you and why?
DLO: "What did you do with the $500,000 advance you got for the book?" But I'll settle for: "Any advice for unpublished writers?"
I once googled "how to get rid of a dead body" as part of my book research. The browser ads I started getting after that were downright scary, and I began to wonder if the NSA was going to coming knocking on my door. (I can't imagine what would have happened if I googled "how much fertilizer does it take to blow up a building.") I have since learned about "private browsing," and I highly recommend it.
My second best tip is: Keep writing, but also keep reading! Lots of the unpublished writers I meet have stopped reading because they don't feel they have the time for it, and I think that's a mistake. Reading is an excellent way to keep your writing tools sharp, and hey, it's damn good way to come up with unsavory phrases to google!
And my final tip: Murder the hero, maim the children, rip the clothes off the intrepid heroine, bestow fame and riches on the villain, and set the whole damn city on fire, but whatever you do, don't draw cartoons of bearded dead guys, and don't shoot the dog!
JTT: Great advice! Best of luck with the book.
DL ORTON lives in the foothills of the Rockies where she and her husband are raising three boys, a golden retriever, two Siberian cats, and an extremely long-lived Triops. Her future plans include completing the books in the BETWEEN TWO EVILS SERIES followed by an extended vacation on a remote tropical island (with a Starbucks). When she's not writing, playing tennis, or helping with algebra, she's building a time machine so that someone can go back and do the laundry.
Read the full interview here: Author Interview: DL Orton with JT Twissel.
Crossing In Time (Between Two Evils #1) on April 21, 2015
Genres: Post-Apocalyptic, romance, science fiction
I have never been a big reader on time traveling as it has never appealed to me, but when I read the blurb of this book I figured I would jump out of my norm of reading and give it a go.
Now I wasn't disappointed in the book as it was good, but I felt it had more romance in the book than anything and maybe this is what was intended. We start off with the story in a post-apocalyptic world where our main character Isabel is buying a gun and it makes us wonder oh what caused this scene. After that chapter of the buying of the gun we are then thrown into the present world where we meet Diego and him saving Isabel after a fire has started. Now these two have a past and a future together to where when going back in the past Isabel has to work on her relationship with Diego when he is twenty something years old. Because of these fires something was uncovered which has caused the government to kidnap people who might know about it, one of the characters being Matt then later on Diego because his name is mentioned.
There are some sex scenes that I wasn't too impressed with as it was going back and forth between Diego and Isabel when she went back into the past. It didn't feel real in a way I guess you could say along with all the puns though at times they were funny sometimes they seemed over used but that is my opinion.
We start each chapter with a different P.O.V. it is either Isabel's, Diego's or Matt's which it wasn't hard to understand what was going on with three different views as it went together very well and it was not confusing.
With the help of different people Diego and Matt are able to build a time machine to go back in time to fix the world before it is gone to hell in a hand basket, though the question is will it work? I see this book is part of a series so I can only hope in the other books we learn if it works or not and what exactly does the relationship between Diego and Isabel have to do with saving the world. The characters are okay I did enjoy them until the future Isabel came back into the past to see Diego. Just the way they acted and talked bothered me, only thing I can guess is because of the ages? I honestly can not put my finger on it. I do plan on reading the rest in this series to see if we get some answers to the world being saved by love.
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dc:title="Review: Crossing In Time: The 1st Disaster (Between Two Evils #1) by D.L. Orton"
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Source: Review: Crossing In Time by DL Orton – A Little Bit of R&R
Crossing in Time: The First Disaster is D. L. Orton's first book in the Between Two Evils series.
In short, Isabelle needs to go back in time to rescue her failed relationship with Diego to save the world. It's not difficult to see where Crossing in Time has its two focuses; a science fiction element encompassing time travel, and the relationship between Isabelle and Diego.
We're not allowed to judge a book by its cover, but I'll give a brief heads-up to the chapter header pages; some think the following might be a small point but I like it; they have a hand drawn picture on them which is slightly descriptive (as is the chapter title) and helps to give the book a feel of real craftsmanship.
There's also an indication of the subject of the first person who varies between three or four main characters. It's sort of obvious from the reading, but the chapter heading makes it clear right from the start and you can get straight into the mindset of the first person character without that frustrating initial who is this? moment.
D. L. Orton is clearly well versed in science fiction from literature and movies, and this percolates throughout the novel. This comes in the form of various quotes and references or parallels drawn in similar circumstances and again makes me feel that I'm reading a well crafted product.
Woven within the plot itself is subtle humour; it's really well done because it doesn't negate or lower the tone which D. L. Orton has skillfully set into place but enhances feelings and emotions felt by the characters. This isn't a comedy novel, rather comedy is used as a tool within it.
In addition to the scientific placing and the developed characters, there's the shifting point of view with multiple first person characters who give differing angles and views on events (and other characters). The final concoction is a well thought out novel with interesting characters, situations and a fascinating underlying plot!
There are some brilliant time travel and related science fiction ideas in Crossing in Time. At times though I felt that they could have been introduced or explained a little more instead of simply mentioned in passing. It's not that it was too complicated; I just thought there were some missed opportunities to expand on some fantastic ideas where other areas of the novel seemed to attract a huge amount of (unnecessary) attention.
Diego is the first to time travel. Actually, this is after much testing – though some may argue not enough! ? A team of scientists develops theories into the worlds of parallel universes and timelines, as well as instrumentation such as peepers to gain insights into them.
Through these scientific tests and discussions over the results, we learn more behind the mechanics of the time travel element. The ubiquitous bureaucracy, red tape, and village idiots inject a certain amount of realism and credibility to the saga.
Whereas Diego's trip in time has huge question marks hanging over it, things are a bit clearer for Isabelle, and indeed we follow Isabelle back in time to when she was with Diego in their early years together. Isabelle now has a younger body back in this history, that is to say, a body commensurate with the date. I immediately questioned whether she'd taken her old self's place, or whether she was the second version, and if so, where was the 'original'? Just as I was starting to think a hole was developing, clarity came in the text!
Actually, this happens quite frequently in Crossing in Time – I'd think there was a discrepancy or something vital missing only to read the explanation moments later. Note this is just me – it's my own weakness that I ask too many questions, and in this case, I slowly learned that D. L. Orton would answer my questions at the proper time!
Isabelle and Diego
I'm giving this a separate section as it's an important part of the novel, though I've only got three main things to say about it.
I thought that D. L. Orton captures really well an older Isabelle in a younger body meeting her boyfriend again. She retains memory and wisdom from the older self and still has the excitement from the early days.
A mysterious man in a Panama hat buys lunch for Diego and Isabella. I'm always suspicious of "mysterious" people in time travel novels as more often than not they turn out to be a key character from the future. Hopefully, I'm wrong here!
I was saddened that Isabelle thought that the best way to keep her and Diego together in the future was to teach him primarily how to respond to her sexual desires. Marriage is deeper than that.
Apart from these observations, I can't think of much else to say about it. Just lovey dovey stuff and erotica.
D.L. Orton 'warned' me beforehand that there was erotica in Crossing in Time and was curious to know what I thought about it from a male perspective. That comes as a relief, because for me to give a female perspective would be either impossible or painful. So here it is.
I didn't like it.
To be honest, it wasn't as explicit as I was expecting, in fact, it struck me as being done quite tastefully, but yes, it was graphic.
I've nothing against erotica being in a novel – it's what couples do. We also wait for buses and do the laundry but the point is that I'm just not interested in reading about it. Isabelle and Diego may as well have planted some grass seeds and watched them grow, or painted walls and watched them dry. So what?
In fairness to them, sex seems to be the crux of their relationship (see the last bullet point above) and of course, that's up to them, but that's not really my issue.
But that's just subjective personal preference. My main gripe in its inclusion isn't the content. It's how it drags on and on, adding nothing to the depth of character (please don't take that the wrong way…) or obstinately not taking the plot forwards. I simply felt awkward reading it (for the reasons I mentioned above) and I gained nothing from it.
A volcano with no eruption
Crossing in Time is not self-complete. Perhaps this is an unfair thing to comment on in a review of a book which quite clearly says "Book 1" on the cover, but I feel especially cheated because for the last quarter of the novel I was wasting my time reading about the physical relationship whilst the plot stagnated.
I was reminded of a recent visit to Mount Etna.
Flashback: A little while ago I went on an organised tour up Mount Etna. It was a really early start (4:15 am) and on the way, we stopped for a bite to eat. It took 3 hours. We also stopped off to be pressured into buying some tourist crap. For an hour.
Eventually, we got to Mount Etna and took a cable car to take us 500 m higher. Excellent stuff! At the top were off road vehicles which could take us right to the smoking rumbling crater rim; the stuff we'd come for!
But we'd arrived at the site too late; there was only half an hour before the last cable car left to take us back down. I was gutted. The whole purpose of the trip was to get to the top of an active volcano but too much time was wasted beforehand. Instead, we could only rumble around the barren rocky landscape.
And it's the same with this novel. Pages and pages of leg caressing and touching inner thighs…and then…the book ends. There's no off-roader to move the story line on.
*Growl*
So is this a teaser for Book 2? Maybe, but I'd fear that Book 2, and subsequent books until the last one, will end similarly.
But the story line is strong and ultimately I'd love to read the whole series to see how it pans out.
A little while ago a friend asked whether I read predominantly male-written books. I'd never really thought about it before; to be honest I go straight for the book descriptions and things. Judging a book by its cover is quoted for being bad, judging one by the sex of its author I think is insane.
But that said…it turns out that most books on my read list are written by men. That's not me deliberately picking out male books, and equally, I hope that it's not that I have a natural preference for male-written books. Or come to think of it, I hope it's also that there aren't enough science fiction books out there written by women (or girls).
So somehow that makes Crossing in Time special in that somehow it's made its way from the mind of a female author through my eyeballs and onto my retina, tumbling into my brain and providing me with much enjoyment.
Because it's written by a woman?
No. Because it's a great novel with some brilliant science fiction written against a knowledgeable (and humourous) backdrop!
Rating * * * *
Crossing in Time has a foot in two camps – romance (actually, sexual attraction) and science fiction. The trouble is that almost literally the legs are split too far between these camps.
The story line is strong and engaging, and there's a wealth of juicy time travel ideas and gadgetry in there. I'd love to read the whole series, so for these reasons I'm giving Crossing in Time 4 stars, losing a star due to the prolonged and unnecessary slushy stuff. I'm cautious, though, because focusing on this single book is like judging a meal by the way the waitress walks when she brings you the starter.
(And in this case, the waitress wrote the menu pretty well too! ? )
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Disclaimer: A copy of "Crossing in Time" was sent to me free of charge to read and review. This it!
Star ratings:
| 5* Excellent! | 4* Good | 3* OK | 2* Not good | 1* Crud |
Paul Wandason
Crossing in Time by D. L. Orton
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Review: Crossing in Time by D. L. Orton – time2timetravel.
Between Two Evils Series: The First Disaster
(Between Two Evils Book 1)
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Crossing In Time is the first book in the Between Two Evils series and D.L. Orton's debut novel. That is difficult to believe because her style of writing is extremely fluid and wonderfully immersive. She has a fantastic command of language, and I loved the subtle humor throughout the book.
Crossing In Time can't be classified as belonging to one single genre. This is science-fiction, it is romance, it is action and adventure. There is something here for everyone.
It is the story of the relationship between Isabel and Diego and how this relationship could prevent world annihilation. It is told from three different perspectives: Isabel's, Diego's and Matt's. Matt is a British scientist who is recruited with a bunch of other interesting characters to develop a time machine which enables Isabel to travel back into the past to work on her future relationship with Diego.
The characters feel very real and are easy to relate to. There are no one dimensional alpha males or damsels in distress here; these are your average people next-door type of characters that are properly fleshed out and authentic.
The romantic relationship between Isabel and Diego was endearing and sweet. There are some sex scenes, which I found fairly mild and tastefully done, but I have noticed that other reviewers felt they were steamy and explicit. So I guess it depends what you are used to reading. My only criticism would be that the sexual relationship took over a bit towards the end of the book. The stroking and caressing could have been condensed.
What I particularly enjoyed were the scenes of Isabel coping with survival in the bleak and dangerous dystopian future. Some of those descriptions got my heart pumping more than the love scenes. Overall, the story kept me thoroughly entertained and engrossed.
The ending leaves you with the frantic need to find out more about Isabel and Diego's as well as Matt's future, and I will certainly look out for part 2.
As far as the narration is concerned: I would give more than 5 stars if I could.
Having two narrators can be very tricky. The way that it was done here was absolutely impressive. Noah Michael Levine and Erin de Ward were a fantastic team. They had perfect timing and the narration was incredibly fluid. Noah Michael Levine did an amazing job switching effortlessly between the characters of Matt and Diego and keeping the accents straight. It felt like being at the movies. Outstanding performance! This is the sort of audiobook you want to give to people who don't do audiobooks to show them what they are missing. There were no issues with the production.
Crossing In Time should appeal to a wide audience because of its mix of genres and because of the exceptional narration.
If you did please follow this link to Audible and click the yes button on the "was this review helpful".
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10+ hrs, 2015, Action & Adventure, Alternate History, audio book, audio book reviews, audiobook, audiobook reviews, audiobookreviewer, Between Two Evils, Book 1, book one, book reviews, Contemporary Fiction, D. L. Orton, dystopian, Erin deWard, Literary, Noah Michael Levine, Post Apocalyptic, Rocky Mountain Press, science fiction, Unabridged
Crossing In Time (Between Two Evils Book 1) by D. L. Orton | Audio Book Reviewer.


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An Absolutely Remarkable Thing , by Hank Green
In his much-anticipated debut novel, Hank Green--cocreator of Crash Course, Vlogbrothers, and SciShow--spins a sweeping, cinematic tale about a young woman who becomes an overnight celebrity before realizing she's part of something bigger, and stranger, than anyone could have possibly imagined.
The Carls just appeared. Coming home from work at three a.m., twenty-three-year-old April May stumbles across a giant sculpture. Delighted by its appearance and craftsmanship--like a ten-foot-tall Transformer wearing a suit of samurai armor--April and her friend Andy make a video with it, which Andy uploads to YouTube. The next day April wakes up to a viral video and a new life. News quickly spreads that there are Carls in dozens of cities around the world--everywhere from Beijing to Buenos Aires--and April, as their first documentarian, finds herself at the center of an intense international media spotlight.
Now April has to deal with the pressure on her relationships, her identity, and her safety that this new position brings, all while being on the front lines of the quest to find out not just what the Carls are, but what they want from us.
Compulsively entertaining and powerfully relevant, An Absolutely Remarkable Thing grapples with big themes, including how the social internet is changing fame, rhetoric, and radicalization; how our culture deals with fear and uncertainty; and how vilification and adoration spring from the same dehumanization that follows a life in the public eye.
Criss Cross , by James Patterson
A killer with all the skills of a master detective has made Alex Cross the subject of his deranged "investigation."
In a Virginia penitentiary, Alex Cross and his partner, John Sampson, witness the execution of a killer they helped convict. Hours later, they are called to the scene of a copycat crime. A note signed "M" rests on the corpse. "You messed up big time, Dr. Cross."
Was an innocent man just put to death? Alex soon realizes he may have much to answer for, as "M" lures the detective out of the capital to the sites of multiple homicides, all marked with distressingly familiar details -- details that conjure up decades-old cases. Details that conjure up Cross family secrets. Details that make clear that M is after a prize so dear that -- were the killer to attain it -- Alex's heart would no longer have reason to beat.
Certain Liberties , by Sidney S Stark
CERTAIN LIBERTIES is an historical novel about a gifted young musician who defies 19th-century models of womanhood by trying to succeed in a man's world. It was said that she had 'male courage, feminine fortitude and the soul of an artist.' Challenging cultural bias against playing the 'masculine' violin and performing in public in an 'unladylike position', she incited censure for her views on everything from politics to the shackles of women's underwear, only to find there were more serious threats to her personal freedom. Running from a life of prescribed expectations and a controlling father, she was recruited to work for the Underground Railroad, which she did to reunite with a cherished childhood friend. Only then did she learn about freedom in its literal sense, the most important part of the Founding Fathers' Declaration of Independence, the right to life.
The Grave's a Fine and Private Place , by Alan Bradley
In the wake of an unthinkable family tragedy, twelve-year-old Flavia de Luce is struggling to fill her empty days. For a needed escape, Dogger, the loyal family servant, suggests a boating trip for Flavia and her two older sisters. As their punt drifts past the church where a notorious vicar had recently dispatched three of his female parishioners by spiking their communion wine with cyanide, Flavia, an expert chemist with a passion for poisons, is ecstatic. Suddenly something grazes her fingers as she dangles them in the water. She clamps down on the object, imagining herself Ernest Hemingway battling a marlin, and pulls up what she expects will be a giant fish. But in Flavia's grip is something far better: a human head, attached to a human body. If anything could take Flavia's mind off sorrow, it is solving a murder—although one that may lead the young sleuth to an early grave.
Sword of Kings , by Bernard Cornwell
The twelfth installment of Bernard Cornwell's New York Times bestselling series chronicling the epic saga of the making of England—"superior entertainment that is both engaging and enlightening" (Washington Post), and the basis for The Last Kingdom, the hit Netflix series.
It is a time of political turmoil once more as the fading King Edward begins to lose control over his successors and their supporters. There are two potential heirs—possibly more—and doubt over whether the once separate states of Wessex and Mercia will hold together . Despite attempts at pulling him into the political fray, Uhtred of Bebbanburg cares solely about his beloved Northumbria and its continuing independence from southern control.
But an oath is a strong, almost sacred commitment and such a promise had been exchanged between Uhtred and Aethelstan, his onetime companion in arms and now a potential king. Uhtred was tempted to ignore the demands of the oath and stay in his northern fastness, leaving the quarrelling Anglo-Saxons to sort out their own issues. But an attack on him by a leading supporter of one of the candidates and an unexpected appeal for help from another, drives Uhtred with a small band of warriors south, into the battle for kingship—and England's fate.
Tell Me No Lies , by Shelley Noble
Miss Fisher meets Downton Abbey in Tell Me No Lies, part of the critically acclaimed Lady Dunbridge Mystery series from New York Times bestselling author Shelley Noble.
Rise and shine, Countess, you're about to have a visitor.
Lady Dunbridge was not about to let a little thing like the death of her husband ruin her social life. She's come to New York City, ready to take the dazzling world of Gilded Age Manhattan by storm. The social events of the summer have been amusing but Lady Phil is searching for more excitement---and she finds it, when an early morning visitor arrives, begging for her help. After all, Lady Phil has been known to be useful in a crisis. Especially when the crisis involves the untimely death of a handsome young business tycoon.
His death could send another financial panic through Wall Street and beyond.
With the elegant Plaza Hotel, Metropolitan Museum of Art and the opulent mansions of Long Island's Gold Coast as the backdrop, romance, murder, and scandals abound. Someone simply must do something. And Lady Dunbridge is happy to oblige.
The Rise of Magicks , by Nora Roberts
The #1 New York Times bestselling author of Year One and Of Blood and Bone concludes her stunning new trilogy praised as "A match for end-of-the-world classics like Stephen King's The Stand."
After the sickness known as the Doom destroyed civilization, magick has become commonplace, and Fallon Swift has spent her young years learning its ways. Fallon cannot live in peace until she frees those who have been preyed upon by the government or the fanatical Purity Warriors, endlessly hunted or locked up in laboratories, brutalized for years on end. She is determined to save even those who have been complicit with this evil out of fear or weakness―if, indeed, they can be saved.
Strengthened by the bond she shares with her fellow warrior, Duncan, Fallon has already succeeded in rescuing countless shifters and elves and ordinary humans. Now she must help them heal―and rediscover the light and faith within themselves. For although from the time of her birth, she has been The One, she is still only one. And as she faces down an old nemesis, sets her sights on the enemy's stronghold, and pursues her destiny―to finally restore the mystical shield that once protected them all―she will need an army behind her…
Scarlet Fever , by Rita Mae Brown
Winter blizzards bring a flurry of cases to solve in this riveting new foxhunting mystery featuring "Sister" Jane Arnold and her incorrigible hounds from New York Times bestselling author Rita Mae Brown.
Frigid February air has settled into the bones of the Blue Ridge Mountains, making for a slow foxhunting season, though "Sister" Jane Arnold's enthusiasm is not so easily deterred. With the winter chill come tweed coats, blazing fireplaces—and perhaps another to share the warmth with, as the bold hunting scarlets worn by the men in Sister Jane's hunting club make the hearts of women flutter—until someone's stops entirely.
Harry Dunbar, a member of the Jefferson Hunt club with a penchant for antique furniture, is found with his skull cracked at the bottom of the stairs to a local store. There are no telltale signs of foul play—save for the priceless (and stolen) Erté fox ring in his pocket. Sister and her hounds set out to uncover the truth: was this simply an accident—a case of bad luck—or something much more sinister?
Steeped in the deep traditions of Virginia horse country and featuring a colorful cast of characters both two- and four-legged, Scarlet Fever is another spirited mystery from Rita Mae Brown.
Grit & Grace , by Tim McGraw
From Grammy-Award winning music superstar and actor Tim McGraw comes a one-of-a kind lifestyle book that melds his personal fitness transformation story with practical advice to inspire healthy changes in readers' lives.
Tim McGraw is as well-known for his unparalleled accomplishments in the entertainment industry as he is for his boundless energy—he is the embodiment of vitality and success. But only a decade ago, he found himself struggling with his health. The demands of his meteoric career and life on the road had taken a toll. McGraw came to a crossroads where knew that unless he made his physical health a priority, he would put his personal happiness and professional success at risk. In Grit & Grace, McGraw shares his transformation story along with encouragement, inspiration, and real-life, practical advice to help readers become healthy, strong and fit in mind and body.
For the first time, McGraw will share the details of the mental and physical routine that got him in the best shape of his life. He suggests that there is no magic formula to getting stronger and healthier: it is about making a commitment to do and be better, and holding yourself accountable each day. McGraw didn't follow a playbook or have a squad of trainers overseeing his every step. He describes his way of getting into shape as more "maverick"--tuning into a vision of what you personally want to achieve, staying focused, and putting in the work.
McGraw says his physical transformation has ignited a whole-life transformation. "My mind is clearer, my sense of purpose is sharper, and my relationships are deeper. Consistent physical exercise helps me bring focus to my life and to the people who mean the most to me." In Grit & Grace, McGraw makes this transformation accessible to anyone, sharing with readers the physical and mental tools they can use to create the life they deserve.
The Pioneer Woman Cooks: The New Frontier , by Ree Drummond
Welcome to Ree's new frontier! So much has happened on Drummond Ranch over the last couple of years: The kids are growing up, another left for college, Ree's schedule is crazier than ever…and through it all, her cooking has evolved. While she and her family still love all the hearty comfort foods they're accustomed to, Ree's been cooking up some incredible new dishes that reflect the flavors, colors, and texture she's craving these days.
The Pioneer Woman Cooks: The New Frontier features 112 brand new step-by-step recipes that bring fresh, exciting elements into your everyday meals. From super-scrumptious breakfasts, to satisfying soups and sandwiches, to deliciously doable suppers and sides—and, of course, a collection of irresistible sweets you'll want to make immediately!—these pages will deliver a big list of fabulous new dishes for you to add to your repertoire.
A wife of a cowboy, mother of growing kids, and a businesswoman with a packed work schedule, Ree knows exactly what it means to juggle life's numerous demands simultaneously. The recipes in this book use everything from a skillet to a Dutch oven to an Instant Pot, so you'll have a mix of options to suit your own timeframe. And to reflect her own occasional adventures in carb cutting, Ree shares dozens of luscious lower-carb options for those days you want to eat a little lighter without sacrificing flavor. In The Pioneer Woman Cooks: The New Frontier you can explore an amazing and eclectic mix of traditional and new.
Catch and Kill , by Ronan Farrow
In this instant New York Times bestselling account of violence and espionage, Pulitzer Prize-winning investigative reporter Ronan Farrow exposes serial abusers and a cabal of powerful interests hell-bent on covering up the truth, at any cost.
In 2017, a routine network television investigation led Ronan Farrow to a story only whispered about: one of Hollywood's most powerful producers was a predator, protected by fear, wealth, and a conspiracy of silence. As Farrow drew closer to the truth, shadowy operatives, from high-priced lawyers to elite war-hardened spies, mounted a secret campaign of intimidation, threatening his career, following his every move, and weaponizing an account of abuse in his own family.
All the while, Farrow and his producer faced a degree of resistance they could not explain -- until now. And a trail of clues revealed corruption and cover-ups from Hollywood to Washington and beyond.
This is the untold story of the exotic tactics of surveillance and intimidation deployed by wealthy and connected men to threaten journalists, evade accountability, and silence victims of abuse. And it's the story of the women who risked everything to expose the truth and spark a global movement.
Both a spy thriller and a meticulous work of investigative journalism, Catch and Kill breaks devastating new stories about the rampant abuse of power and sheds far-reaching light on investigations that shook our culture.
Stewartville Public Library - 110 2nd Street SE - Stewartville, MN 55976 - 507-533-4902 www.librarywebsites.com


text:
Q: check text file content with perl I am seeking some feedback as to the efficiency of this code and also how to remove the qualifying file from the @FilesToUse array if it is moved.
I am loading all files in a directory to the @FilesToUse array. I then need to check each file and see if line 7 says 'BATCH' if it does i would like to move the file and then also remove the filename from the @FilesToUse array so when i use that array later on it doesnt have the BATCH file name in it. I hope I stated this question clearly.
The text files are approx 10Mb and i typically have 2 files to process per day.
Thanks in advance for any assistance.
 #Loop thru the files that were found and delete the one that is BATCH

       foreach $FileToUse (@FilesToUse)    #Loop at the file level
       {

open (FH, $TheInputDir . $FileToUse) or $MailMsg = $MailMsg . "ERROR: Could not open input file: $FileToUse \n";

          while (<FH>)                     # Loop at the line level within each file
          {
             $TheLine = $_;
             chomp($TheLine);
             $LineCnt++;

             if ( $LineCnt == 7 and substr( $TheLine, 1, 6 ) =~ /BATCH/ ) {

                move( "$TheInputDir$FileToUse", "$TheBatchMoveDir" )
                   or $MoveFail = 1;

                if ( $MoveFail == 1 ) {
                   $MailMsg = $MailMsg
                      . "ERROR: Failed to move $FileToUse to Batch folder!\n";
                }
                else {
                   $MailMsg
                      = $MailMsg . "Moved BATCH file $FileToUse to Batch folder\n";
                }
             }

             last if $. == 7;
          }
       }

A:
how to remove the qualifying file from the @FilesToUse array

We can remove an element from an array with splice, but we need the array index for this.
You could change the outer loop to

       foreach $findex (-$#FilesToUse..0)  #Loop at the file level
       {
           $FileToUse = $FilesToUse[-$findex];

and insert
                splice @FilesToUse, -$findex, 1;

where you want to remove the file element.
(The array is processed from last to first element to avoid the "missing element syndrome" when an index is deleted - see also How do I completely remove an element from an array?)

A: I would clean up the semantics:
         $LineCnt = $.;

         if ( $LineCnt == 7 ) {
            close FH;

            if ( substr( $TheLine, 1, 6 ) =~ /BATCH/ ) {

               move( "$TheInputDir$FileToUse", "$TheBatchMoveDir" )
                  or $MoveFail = 1;

               if ( $MoveFail == 1 ) {
                  $MailMsg = $MailMsg
                     . "ERROR: Failed to move $FileToUse to Batch folder!\n";
               }
               else {
                  $MailMsg
                     = $MailMsg . "Moved BATCH file $FileToUse to Batch folder\n";
               }
            }

            last;
         }

redpajama_set_name: RedPajamaStackExchange


text:
Micrurus remotus est une espèce de serpents de la famille des Elapidae.

Répartition
Cette espèce se rencontre :
 dans le sud-est de la Colombie ;
 au Venezuela en Amazonas ;
 au Brésil en Amazonas.

Publication originale
 Roze, 1987 : Summary of coral snakes (Elapidae) from Cerro de la Neblina, Venezuela, with description of a new subspecies. Revue Française d'Aquariologie-Herpétologie, , n. 3 .

Notes et références

Liens externes

Elapidae
Serpent (nom scientifique)

redpajama_set_name: RedPajamaWikipedia


text:
\section{Introduction}
\label{sec:intro}

In 1996, Monique Tirion showed that the low-frequency normal modes of a protein (see section \ref{ssec:nma}) are not significantly altered when Lennard-Jones and electrostatic interactions are replaced by Hookean (harmonic) springs, for all atom pairs whose distance is smaller than a given cutoff value~\cite{Tirion:96}. In the case of biological macromolecules, this seminal work happened to be the first study of an Elastic Network Model (ENM). The ENM considered was an all-atom one, chemical bonds and angles being kept fixed through the use of internal coordinates, as often done in previous standard normal mode studies of proteins~\cite{Go:82,Go:83,Levitt:83}.

Soon afterwards, several coarse-grained versions of Tirion's ENM were proposed, in which each protein amino-acid residue is usually represented as a single bead and where most, if not all, chemical "details" are disregarded~\cite{Bahar:97,Hinsen:98}, including atom types and amino-acid masses.

Since then, it has been shown that such highly simplified protein models are able to provide fair insights on the dynamical properties of biological macromolecules~\cite{Bahar:97,Maritan:02,Phillips:07,NMA}, including those involved in their largest amplitude functional motions~\cite{Tama:01,Gerstein:02}, even in the case of large assemblies like RNA polymerase II~\cite{Delarue:02}, transmembrane channels~\cite{Helene:03,Elnemo2}, whole virus capsids~\cite{Tama:02v} or even the ribosome~\cite{Tama:03}. As a consequence, numerous applications have been proposed, noteworthy for exploiting fiber diffraction data~\cite{Tirion:95}, solving difficult molecular replacement problems~\cite{Elnemo1,Delarue:04}, or for fitting atomic structures into low-resolution electron density maps~\cite{Delarue:04,Tama:04,Hinsen:05, Tama:05, Norma}.

However, the idea that simple models can prove enough for capturing major properties of objects as complex as proteins had been put forward well before Tirion's introduction of ENMs in the realm of molecular biophysics. In the following, after a brief account of previous results supporting this claim (section \ref{sec:back}), theoretical tools required for studying an ENM are described (section \ref{sec:meth}), focusing on practical issues and, in particular, on possible artifacts. Then, an overview of typical results that have been obtained by studying protein ENMs is given (section \ref{sec:emp}).

\section{Background}
\label{sec:back}

Indeed, coarse-grained models of proteins had been considered twenty years before M. Tirion's work, for studying what may well be the most complex phenomenon known at the molecular scale, namely, protein folding. Indeed, as soon as 1975, Michael Levitt and Arieh Warshel proposed to model a protein as a chain of beads, each bead corresponding to the C$_{\alpha}$ atom of an amino-acid residue, the centroid of each amino-acid sidechain being taken into account with another bead grafted onto the chain~\cite{Levitt:75}. That same year, Nobuhiro Go and his collaborators proposed an even simpler model in which the chain of beads is mounted on a two-dimensional lattice, each bead corresponding either to a single residue or, more likely, to a secondary structure element (e.g., an $\alpha$-helix) of a protein~\cite{Go:75}. Moreover, while the Levitt-Warshel model had been designed so as to study a specific protein, that is, a polypeptidic chain with a given sequence of amino-acid residues,  the Go model focuses on the conformation of the chain, more precisely, on the set of pairs of amino-acids that are interacting together in the chosen (native) structure.

\begin{svgraybox}
So, it is fair to view protein ENMs as off-lattice versions of the Go model.
\end{svgraybox}

Lattice models of proteins have been studied extensively since then so as to gain, for instance, a better understanding of the sequence-structure relationship. Noteworthy, if the chain is short enough, all possible conformations on the lattice can be enumerated, allowing for accurate calculations of thermodynamic quantities and univoqual determination of the free energy minimum. Moreover, if the number of different amino-acids is small enough, then the whole sequence space can also be addressed. For instance, in the case of the tridimensional cubic lattice, a 27-mer chain has 103346 self-avoiding compact (i.e. cubic) conformations~\cite{Gutin:90}. On the other hand,  if only two kinds of amino-acids are retained, that is, if only their hydrophobic or hydrophilic nature is assumed to be relevant for the understanding of protein stability, then a 27-mer has $2^{27}$ different possible sequences. This is a large number, but it remains small enough so that for each sequence the lowest-energy compact conformation can be determined and, when a nearly-additive interaction energy is considered~\cite{Wingreen:97}, the conclusion of such a systematic study happens to be an amazing one. Indeed, it was found that a few conformations (1\% of them) are "preferred" by large sets of sequences~\cite{Wingreen:96}. Moreover, although each of these sets forms a neutral net in the sequence space, it is often possible to "jump" from a preferred conformation to another, as a consequence of single-point mutations~\cite{Trinquier:99}.

While the former property is indeed expected to be a protein-like one, allowing to understand why proteins are able to accomodate so many different single-point mutations without significant loss of both their structure and function, it is only during the last few years that the latter one has been exhibited. In particular, using sequence design techniques, a pair of proteins with 95\% sequence identity, but different folds and functions, was recently obtained~\cite{Orban:08}.
If generic enough, such a property would help to understand how the various protein folds nowadays found on earth may have been "discovered" during the earliest phases of life evolution (e.g. prebiotic ones), since discovering a first fold could have proved enough for having access to many other ones, a single-point mutation after another.

\begin{svgraybox}
In any case, this example shows how the study of simple models can help to think about, and maybe to understand better, major protein properties, in particular because such models can be studied on a much larger scale than actual proteins.
\end{svgraybox}

\section{Theoretical foundations}
\label{sec:meth}

The vast majority of protein ENM studies rely on Normal Mode Analysis (NMA)~\cite{NMA}. Moreover, the hypotheses underlying this kind of analysis probably inspired the design of the first ENM. Actually, in her seminal work, M. Tirion performed NMA in order to show that similar results can be obtained by studying an ENM or a protein described at a standard, semi-empirical, level~\cite{Tirion:96}.
So, hereafter, the principles of NMA are briefly recalled (more details can be found in classic textbooks~\cite{Goldstein:50,Wilson:55}). Next, the close relationship between NMA and the different types of ENMs is underlined.

\subsection{Normal Mode Analysis}
\label{ssec:nma}

Newton's equations of motion for a set of $N$ atoms can not be solved analytically when $N$ is large (namely, $ N > 2$),
except in rare instances like the following, rather general, one. Indeed, for small enough displacements of the atoms in the vicinity
of their equilibrium positions, $V$, the potential energy of the studied system, can be approximated by the first terms of a Taylor series:
\begin{equation}
\label{taylor}
V = V_0 + \sum_{i=1}^{3N} \left(\frac{\partial V}{\partial r_i}\right)_0 (r_i - r_i^0) +
  \frac{1}{2} \sum_{i=1}^{3N} \sum_{j=1}^{3N} \left(\frac{\partial^2 V}
  {\partial r_i \partial r_j}\right)_0 (r_i - r_i^0) (r_j - r_j^0)
\end{equation}
where $r_i$ is the $i^{th}$ coordinate,  $r_i^0$, its equilibrium value, and $V_0$,
the potential energy of the system at equilibrium.

Since, within the frame of classical physics, the exact value of $V$ is meaningless (only potential energy differences are expected to play a physical role),
$V_0$ can be zeroed.  Moreover, since $V_0$ is a minimum of $V$, for each coordinate:
\begin{equation}
\notag
\left(\frac{\partial V}{\partial r_i}\right)_0 = 0
\end{equation}
This yields:
\begin{equation}
\label{quad}
V = \frac{1}{2} \sum_{i=1}^{3N} \sum_{j=1}^{3N} \left(\frac{\partial^2 V}
  {\partial r_i \partial r_j}\right)_0 (r_i - r_i^0) (r_j - r_j^0)
\end{equation}

\noindent
In other words, if the atomic displacements around an equilibrium configuration are small enough,
then the potential energy of a system can be approximated by a quadratic form.

On the other hand,
if the system is {\it not} under any constraint with an {\it explicit} time-dependence, then
its kinetic energy can also be written as a quadratic form~\cite{Goldstein:50} and
it is straightforward to show that, when both potential and kinetic energy functions are quadratic forms, then
the equations of atomic motion have the following, analytical, solutions~\cite{Goldstein:50,Wilson:55,Sanejouand:Phd}:
\begin{equation}
\label{nma:solution}
r_i(t) = r_i^0 + \frac{1}{\sqrt{m_i}}
       \sum_{k=1}^{3N} C_k a_{ik} cos( 2 \pi \nu_k t + \Phi_k )
\end{equation}
where $m_i$ is the atomic mass and where $C_k$ and $\Phi_k$, the amplitude and phasis of the so-called normal mode of vibration $k$,
depend upon the initial conditions, that is, upon atomic positions and velocities at time $t=0$. Noteworthy,
$C_k$ is a simple function of $E_k$, the total energy of mode $k$. In particular, if all modes have identical total energies,
then:
\begin{equation}
\label{qampl}
C_k = \frac{\sqrt{2 k_B T}}{2 \pi \nu_k}
\end{equation}
where $T$ is the temperature and $k_B$ the Boltzmann constant.
This means that the amplitude of mode $k$ goes as the inverse of its frequency, $\nu_k$.
As a matter of fact, when NMA is performed in the case of proteins, using standard all-atom force-fields,
it can be shown that modes with frequencies below 30-100 cm$^{-1}$ are responsible
for 90-95\% of the atomic displacements~\cite{Levy:82}.

\begin{svgraybox}
Note that such analytical solutions can provide various
thermodynamic quantities like entropy, enthalpy, etc, and this, even at a quantum mechanical level of description~\cite{Levy:82}.
\end{svgraybox}

In practice, the $a_{ik}$'s involved in eq.~\ref{nma:solution}, which give the coordinate contributions to mode $k$, are
obtained as the $k^{th}$ eigenvector of ${\bf H}$, the mass-weighted Hessian of the potential energy,
that is, the matrix whose element $i j$ is:
\begin{equation}
\label{secder}
 \left(\frac{\partial^2 V} {\sqrt{m_i m_j} \partial r_i \partial r_j}\right)_0
\end{equation}
By definition, the $3N$ eigenvectors of a matrix like ${\bf H}$ form an orthogonal basis set. This means that, when $k \ne l$:
\begin{equation}
\notag
 \left(\frac{\partial^2 V} {\partial q_k \partial q_l}\right)_0 = 0
\end{equation}
where $q_k$ is the so-called normal coordinate, obtained by projecting the $3N$ mass-weighted cartesian coordinates onto eigenvector $k$, namely:
\begin{equation}
\label{qr}
q_k = \sum_i^{3N} a_{ik} \sqrt{m_i} ( r_i - r_i^0 )
\end{equation}

Moreover, the eigenvalues of ${\bf H}$, that is,
the diagonal elements of the matrix obtained by expressing ${\bf H}$ in this new basis set,
provide the $3N$ frequencies of the system since, for each mode $k$:
\begin{equation}
\notag
 \left(\frac{\partial^2 V} {\partial^2 q_k}\right)_0 = (2 \pi \nu_k)^2
\end{equation}

The eigenvalues and eigenvectors of a matrix are obtained by an operation called a diagonalization.
In principle, for a real and symmetrical matrix like ${\bf H}$, such an operation is always possible.
At a practical level, when the matrix size is not too large, that is, if the matrix can be stored in the computer memory,
algorithms and methods available in standard mathematical packages allow to get its eigenvalues and eigenvectors
at a CPU cost raising as $n N^2$, where $n$ is the number of requested eigensolutions.
In other words,  it is rather straightforward to obtain analytical solutions for the atomic motions, as long as
small-amplitude displacements around a given, well-defined,
equilibrium configuration are considered.
Note that for a tridimensional system at equilibrium, at least six zero eigenvalues have to be obtained
(except if the system is linear, in which case there are five of them), corresponding to the six possible rigid-body motions  (translations or rotations)
of the entire system. However, if the system is {\it not} at equilibrium, negative eigenvalues are usually observed. Moreover, significant mixing
between rotation modes and some others can occur, leaving three zero eigenvalues only, that is, those corresponding to the
three translation modes of the system~\cite{Sanejouand:Phd}.

\begin{svgraybox}
The main drawback of NMA is obvious: the actual dynamics of a protein is much more complicated than assumed above.
As a matter of fact, even on the short timescales considered within the frame of standard molecular dynamics simulations,
a protein is able to jump from the attraction basin of an equilibrium configuration to another~\cite{Elber:87}, and the number of these
equilibrium configurations is so huge that it is unlikely for a nanosecond trajectory to visit one of them twice.
In other words, while NMA focuses on protein dynamics at the level of a single minimum of the potential energy surface (PES),
it is well known that for proteins at room temperature the relevant PES is a higly complex, multi-minima, one.
\end{svgraybox}

NMA has several other drawbacks.
For instance, starting from a given protein structure, e.g., as found in the Protein Databank (PDB), an equilibrium configuration
has to be reached. This is usually done using energy-minimization techniques. As a consequence, the structure
studied with NMA and a standard force field is always a distorted one, the C$_{\alpha}$ root-mean-square deviation (C$_{\alpha}$-r.m.s.d) from the initial structure
being typically of 1-2{\AA}~\cite{NMA}.

More importantly, within the frame of NMA, it is not obvious to take solvent effects into account, as the meaning
of an equilibrium configuration in the case of an ensemble of molecules in the liquid state is unclear. As a matter of fact, the first
NMA studies of proteins were performed {\it in vacuo}~\cite{Go:82,Go:83,Levitt:83,Brooks:83}. Note that, nowadays, the availability of implicit solvent
models, like EEF1~\cite{EEF1}, offers a more satisfactory alternative.

However, as shown below, the main idea underlying the design of protein ENMs is not only to ignore the well-known drawbacks of NMA but, building upon its empirical successes, to add a few more on top of them.

\subsection{The Elastic Network Model}
\label{ssec:enm}

In essence, there are two different types of ENMs, which differ by their dimensionality. The Gaussian Network Model (GNM), proposed by Ivet Bahar, Burak Erman and Turkan Haliloglu in 1997~\cite{Bahar:97,Erman:97}, is a one-dimension model while Tirion's model, later called the Anisotropic Network Model~\cite{Bahar:01} (ANM), is a tridimensional one.

\subsubsection{The Anisotropic Network Model}

Although eq.~\ref{quad} may look simple, it relies on a large number of parameters, namely, the elements of the Hessian matrix (eq.~\ref{secder}).
In order to make it even simpler, M. Tirion proposed to replace eq.~\ref{quad} by another quadratic form, namely:
\begin{equation}
  \label{eqenm}
  V=\frac{1}{2} k_{enm} \sum_{d_{ij}^0 < R_c} (d_{ij}-d_{ij}^0)^2
\end{equation}
where $d_{ij}$ is the actual distance between atoms $i$ and $j$, $d_{ij}^0$ being their
distance in the studied structure~\cite{Tirion:96}. This amounts to set Hookean springs between all pairs
of atoms less than $R_c$ {\AA}ngstr\"oms  away from each other. Note that in Tirion's work, as well as in
most ANM studies (there are notable exceptions~\cite{Kneller:99}), $k_{enm}$, the spring force
constant, is the same for all atom pairs. When it is so, the role of $k_{enm}$ is just
to specify which system of units is used,  $R_c$ being the only physically relevant parameter of the model.
In other words, when studying an ENM, the major drawback added with respect to standard NMA is that
most atomic details are simply ignored.

However, considering eq.~\ref{eqenm} instead of eq.~\ref{quad} has several practical advantages.
First, an energy minimization is not required any more, since the configuration whose energy is the absolute minimum one
($V=0$) is known: it is the studied one. As a corollary, results obtained by studying ENMs are
easier to reproduce. Indeed, an energy minimization not only introduces unwanted distortions in a structure,
but it does it in a way that strongly depends upon the most tiny details of the protocole used, this, also as a consequence
of the huge number of minima of a realistic PES for a biological macromolecule.
Last but not least, as a straightforward consequence of eq.~\ref{eqenm}, the elements of the Hessian matrix (see eq.~\ref{secder}) are as simple as):
\begin{equation}
\label{eq:aij}
h_{ij} = - k_{enm} \frac{(x_i - x_j)(y_i - y_j)}{\sqrt{m_i m_j} d_{ij}^2}
\end{equation}
where $h_{ij}$ is the element corresponding to the $x$ and $y$ coordinates of atoms $i$ and $j$.

\subsubsection{The Gaussian Network Model}
\label{sec:gnm}

Because $R_c$, the cutoff value of an ANM, is usually rather small (see section~\ref{sec:cutoff}),
the corresponding Hessian matrix is sparse, that is, most of its elements (eq.~\ref{eq:aij}) are zeroes. So, as proposed by
I. Bahar, B. Erman and T. Haliloglu~\cite{Bahar:97}, it is tempting to go another step further into
the simplification process and to consider the corresponding adjacency matrix, that is, the matrix whose elements
are:
\begin{equation}
h_{ij} = - k_{enm}
\end{equation}
when residues $i$ and $j$ are interacting ($h_{ij} = 0$ otherwise). Note that in the case of an adjacency matrix,
as well as for the Hessian matrix of an ANM, $h_{ii}$, the diagonal element $i$, is so that:
\begin{equation}
h_{ii} = - \sum_{i \ne j}  h_{ij}
\end{equation}

\begin{svgraybox}
Of course, with an adjacency matrix, information about directionality is missing. This is a major drawback of GNMs
since this means that studying a GNM can only provide informations about motion amplitudes.
\end{svgraybox}

Note that GNMs are usually, if not always, set up at the residue level, while ANMs are
sometimes studied at the atomic level, like in the seminal study of M. Tirion~\cite{Tirion:96}.
From now on, to underline such (not so common) cases, these latter models will be coined "all-atom ANMs".

\subsubsection{The cutoff issue}
\label{sec:cutoff}

The main, if not the only, parameter of an ENM is $R_c$. Although several studies have tried
to justify the choice of a particular value for this parameter, typically by comparing calculated and experimental quantities,
cutoff values over a wide range are still of common use, varying between 7~\cite{Phillips:02} and 16{\AA}~\cite{Phillips:07}.

For the most part, this probably reflects the
fact the lowest-frequency modes of an ENM are usually "robust"~\cite{Nicolay:06}, that is, little sensitive to the way the model is built.
However, it is obvious that to be meaningful the
value of $R_c$ has to be on the small side. Putting it to an extreme: in the case of a GNM (see section~\ref{sec:gnm}), if $R_c$ is so large that the adjacency matrix
is completely filled with non-zero elements, its eigenvalues and eigenvectors, apart from being degenerate, will only depend upon $N$, the size
of the system, and not upon its topology or its shape. As a consequence, they can for sure not provide any useful information. On the other
hand, if $R_c$ is too small, then the network of interacting residues is split into sub-networks, either free to rotate with respect to another one (in the case of an ANM)
or completely independant from each other (in both ANM and GNM cases). Such dynamical properties are certainly not among those expected for a macromolecule,
and this is why, in ANM studies, the smallest cutoff values used are of the order of 8-10{\AA}~\cite{Tama:01,Delarue:02}, that is, larger than the
typical distance between two interacting amino-acid residues in a protein, namely 6-7{\AA}~\cite{Miyazawa:85,Miyazawa:96}.

\begin{svgraybox}
In practice, choosing a too small value for $R_c$ yields additional zero eigenvalues.
\end{svgraybox}

So, if more than one (for a GNM) or six (for an ANM)
zero eigenvalues are obtained, then it is highly recommanded to increase $R_c$.
Note that GNMs allow for the use of smaller values of $R_c$ (a value of 7.3{\AA} is often chosen~\cite{Phillips:02})
since in the case of a mono-dimensional model a single connection is enough for avoiding any free translation of a group of atoms with respect to another.
As a consequence, when a GNM is built with C$_{\alpha}$  atoms picked from a single protein chain, that is, when all amino-acid residues are chemically bonded
to each other through peptidic bonds, a value of $R_c$ as low as 4{\AA} (the typical distance between two consecutive C$_{\alpha}$  atoms) can be used.

At first sight, it may seem that problems with small cutoff values could be solved with a distance-dependant spring force constant, as early
proposed by Konrad Hinsen~\cite{Hinsen:98}.
However, it is clear that an exponential term, for instance, introduces a typical length which, when too small, yields similar artifacts.
Indeed, in such a case, the additional free rigid-body motions obtained with a too small value for $R_c$ are expected to be replaced by low-frequency
motions involving the same too little-connected groups of atoms.

Note that with ENMs other kinds of spurious low-frequency motions can be observed. For instance,
in crystal structures, protein N- and C-terminal ends are often found to extend away from the rest of the structure. As a consequence, large amplitude, usually
meaningless, motions of these (almost) free ends can be found among the lowest-frequency modes. So, in order to obtain
significant and clear-cut results, it is highly recommanded to begin an ENM study by "cleaning" the studied structure, namely, by removing such free ends.

A similar kind of spurious low-frequency motion can be observed with all-atom ANMs, in which groups of little-connected atoms are involved,
typically those at the end of long sidechains~\cite{Tama:Phd}. Note that an elegant way to cure such artifacts is to use the RTB approximation~\cite{Durand:94,Tama:00},
which allows to remove from the Hessian matrix all contributions associated to motions occuring inside each "block" the system is split into
(RTB stands for Rotation-Translation of Blocks). In most cases, a block corresponds to a given amino-acid residue but, while atom-atom
interactions are taken into account when the atoms belong to different blocks, each block can also correspond to a whole protein subunit, allowing for the
study of systems as large as entire virus capsids~\cite{Tama:02v}.

\section{Empirical foundations}
\label{sec:emp}

As illustrated above, ENMs and NMA are closely related. As a consequence, the theoretical foundations of ENMs are for the most part those of NMA.
However, when applied to complex molecular systems, NMA is known to have obvious drawbacks (see section~\ref{ssec:nma}). So,
if NMA is still widely performed it is because of its empirical, sometimes unexpected, successes. As recalled below, most of these successes
can also be achieved by studying ENMs.

\subsection{B-factors}

From eq.~\ref{nma:solution} and eq.~\ref{qampl}, it is straightforward to show that $<\Delta r_i^2>$, the
fluctuation of coordinate $i$ with respect to its equilibrium value, is so that:
\begin{equation}
\label{fluct}
<\Delta r_i^2> = \frac{k_B T}{m_i} \sum_{k=1}^{n_{nz}} \frac{a_{ik}^2}{4 \pi^2 \nu_k^2}
\end{equation}
$n_{nz}$ being the number of non-zero frequency normal modes of the system, namely,
$n_{nz}=N-1$ when a GNM is considered and $n_{nz}=3N-6$ when it is an ANM. However, in practice,
since such fluctuations scale as the inverse of $\nu_k$, the $k^{th}$ mode frequency, a sum over
the lowest-frequency normal modes of the system is usually enough for obtaining a fair approximation~\cite{Levy:82}.

On the other hand, $B_i$, the crystallographic Debye-Waller factor (the so-called isotropic B-factors) of atom $i$,
is expected to be related to the fluctuations of its atomic coordinates through:
\begin{equation}
\label{eqbf}
B_i = \frac{8 \pi^2}{3} <\Delta x_i^2 + \Delta y_i^2 + \Delta z_i^2>
\end{equation}
Although other physical factors are involved, like crystal disorder or lattice phonons, as well as non-physical ones,
like the number of water molecules included in the structure refinment process by crystallographers,
significant correlations between B-factor values predicted using eq.~\ref{fluct}-\ref{eqbf} and experimentally obtained ones
have been reported in numerous cases.

\vskip 0.5 cm
For instance, in a study of 30 protein GNMs ($R_c=7.5${\AA}), a mean value of $0.62 \pm 0.13$ for this correlation coefficient was found~\cite{Maritan:02}.
Interestingly, in the same study, 26 other proteins were considered, for which accurate relaxation measurements had been measured by NMR,
and the mean correlation between the corresponding fluctuations and those obtained using eq.~\ref{fluct} was found to be significantly higher, namely,
$0.76 \pm 0.04$,
a remarkable agreement with the experimental data being achieved in several cases, with a correlation coefficient over 0.9 for four of them~\cite{Maritan:02}.
Amazingly,  ANMs do not perform significantly better. For instance, in a study of 83 proteins ($R_c=16${\AA}), a mean value for the correlation coefficient of $0.68 \pm 0.11$ between
predicted and isotropic B-factors was obtained~\cite{Phillips:07} while, using the all-atom ANM ($R_c=5${\AA}) implemented in the Eln\'emo webserver~\cite{Elnemo2},
which makes use of the RTB approximation~\cite{Durand:94,Tama:00}, a very similar value of  $0.68 \pm 0.13$ was found~\cite{Phillips:07}.

\vskip 0.5 cm
Note that in both studies mentioned above, when eq.~\ref{fluct} was used, overall translations or rotations of the entire protein within the crystal cell were excluded from
the calculation, while it is well known that such motions are able to provide by themselves good correlations with experimental values~\cite{Kuriyan:91}.
In other words, much better correlations with experimental B-factors can be obtained by mixing NMA predictions with protein rigid-body motions,
the latters accounting partly for crystal disorder, but mostly for the phonon modes of the whole crystal. Interestingly, these latter modes can be taken into
account within the frame of ENM studies, simply by including all crystal cell symmetries in the model~\cite{Simonson:92,Hinsen:08,Phillips:09}.

Of course,  such significant correlations with experimental data can only be obtained because the amplitude of atomic thermal fluctuations scales
as the inverse of mode frequencies (see eq.~\ref{fluct}). Indeed, with crude models like ENMs, the actual high-frequency modes of a protein can not be predicted,
 because such modes strongly depend upon the chemical details of the structure, only a few neighboring atoms (e.g., covalently bonded ones) being involved
in the highest-frequency modes.  This does not mean, though, that the high-frequency modes of an ENM can not bring any useful information.
Indeed, they correspond to local motions occurring within the parts of the structure whose density is the highest~\cite{Erman:97}. Moreover, it has been shown that
such regions often ly nearby enzyme active sites~\cite{Juanico:07,Lavery:07}.

On the other hand, the B-factor values themselves can not directly be obtained by studying ENMs, since their average is proportional to $k_{enm}$.
Indeed, it is customary to choose $k_{enm}$ so as to match average experimental B-factor values~\cite{NMA}. Another common way is to choose $k_{enm}$ so as to reproduce
the lowest-frequency of the system, as obtained using all-atom force-fields~\cite{Juanico:07}.

\begin{figure}[t]
\includegraphics[scale=.65]{Fig_mbpenm_r8.ps}
\caption{Left: the open (ligand-free) form of maltodextrin binding protein (PDB identifier 1OMP). Right: the corresponding Elastic Network Model. Pairs of C$_{\alpha}$ atoms
are linked by springs (plain lines) when they are less than 8{\AA} from each other. Drawn with Molscript~\cite{Molscript}.}
\label{fig:mbp}
\end{figure}

\subsection{The relationship with protein functional motions}

The seminal paper of M. Tirion ends with the statement that~\cite{Tirion:96}:
\begin{quotation}
Tests performed on a periplasmic maltodextrin binding
protein (MBP) indicate that the slowest modes do indeed closely map the open
form into the closed form (Tirion, in preparation).
\end{quotation}
The next paper of M. Tirion never came out but her result was confirmed a few years later,
as part of a study of 20 protein ENMs ($R_c=8${\AA}) in both their ligand-free (open) and ligand-bound (closed) forms~\cite{Tama:01}. Indeed, for MBP, it was found that the
overlap between its second lowest-frequency mode and its functional conformational change is close to 0.9.
This means that 80\% of the functional motion
of MBP can be described by varying the normal coordinate associated to a single of its modes. Indeed, $O_k$, the overlap with mode $k$, is given by:
\begin{eqnarray}
\label{overlap}
O_k =
\frac {\sum_i \Delta r_i a_{ik}}
{\sqrt{\sum \Delta r_i^2}}
\end{eqnarray}
where $\Delta r_i$ is the variation of coordinate $i$ between the open and the closed form
after both structures have been superimposed~\cite{Marques:95}. On the other hand, since the modes of MBP form
an orthogonal basis set, the following property holds:
\begin{eqnarray}
\sum_{k=1}^{n_{nz}} O_k^2 = 1
\end{eqnarray}

More generally, it was found that when the conformational change of a protein upon ligand binding happens to be highly collective, one of its low-frequency normal modes
often compares well with the experimental motion (overlap over 0.5~\cite{Tama:01}).
Since then, a study of nearly 4,000 cases has confirmed this result~\cite{Gerstein:02}, while another study of a set of proteins with similar functions and shapes, but various
folds, namely DNA-dependant polymerases~\cite{Delarue:02}, has shown that the low-frequency modes of a protein, and hence the nature of its
large amplitude motions, are likely to be determined by its shape~\cite{Tama:01,Ma:05b,Tama:06}.

\vskip 0.5 cm
Indeed, this latter point has recently been confirmed in a rather direct way, by considering ENMs built in such a way that each amino-acid interacts with a given
number of neighbors (the closest ones). Then, at variance with cutoff-based ENMs, the rigidity of the system is fairly constant from a site to another.
However,  the relationship between the lowest-frequency modes of a protein and its functional motion is preserved. Specifically,
it was found that the subspace defined by up to the 10-12 lowest-frequency modes of a protein is conserved, whatever model is used.
Moreover, when no such, so-called robust, subspace exists, the fonctional motion of the protein is found to be either localized and/or of
small amplitude (typically: less than 2-3{\AA} of C$_{\alpha}$-r.m.s.d)~\cite{Nicolay:06}.

\vskip 0.5 cm
In retrospect, these results make sense. First, a strong relationship between low-frequency modes and protein fonctional motions
was first observed within the frame of NMA studies performed at a highly detailed, atomic level of description, noteworthy in the cases
of lysozyme~\cite{Karplus:76}, hexokinase~\cite{Harrison:84}, citrate synthase~\cite{Marques:95} and hemoglobin~\cite{Perahia:95}.
Since, as recalled above, it was later found that such a relationship also holds when most chemical details are removed, it is clear that the property captured by NMA has to be
a very general one. On the other hand, K. Hinsen has convincingly shown that the low-frequency modes of a protein can be used
to split its structure into well-defined domains~\cite{Hinsen:98}, with the additional advantage of a smooth, almost continuous, description of their boundaries.
So, since it is well known that most large amplitude protein functional motions
can be well described as combinations of almost rigid-body motions of entire structural domains~\cite{Branden:91,Gerstein:98}, the relationship
found between these motions and the low-frequency modes of ENMs is just another demonstration that whole quasi-rigid domain motions
are involved in such modes. On the other hand, it is not that difficult to admit that the spatial clustering of amino-acids into domains
can be revealed by studying protein dynamical properties, even at a crude level of description. A corollary of this line of thought is that
ENMs should perform better, as far as low-frequency and large amplitude motions are concerned, in the case of large, multi-domain systems.

\subsection{Applications}

As illustrated above, NMA of ENMs seems to have a clear predictive power.
So, given both the simplicity of these models and their coarse-grained nature, many applications have been proposed.
For instance, as early suggested, being able to guess the pattern of atomic fluctuations through eq.~\ref{fluct}
may prove useful for refining crystal structures~\cite{Diamond:90,Kidera:90}.

However, most applications take advantage of the possibility to predict atomic displacements through the reciproqual of eq.~\ref{qr}, namely:
\begin{equation}
\label{rq}
r_i = r_i^0 + \frac{1}{\sqrt{m_i}} \sum_k^{n_{sub}} a_{ik} q_k
\end{equation}
where $n_{sub}$ is the number of low-frequency modes considered to be enough for performing an accurate prediction.
In the simplest case, mode amplitudes can be varied arbitrarily, one mode after the other. Indeed, in the light of enough experimental data, the analysis of such trajectories
can prove enough for getting insights about the nature of the functional motion of a protein~\cite{Helene:03,Sanejouand:96}.
Some of the conformations thus obtained can also allow for solving difficult molecular-replacement problems, although
it is often necessary to explore at least a couple of modes in order to reach a useful conformation~\cite{Elnemo1}. More generally,
eq.~\ref{rq} can be used so as to reduce the dimensionality of the system and, thus, to find more easily protein conformations
fulfiling a given set of constraints. For instance, it has been used for fitting known structures into low-resolution electron density maps~\cite{Delarue:04,Tama:04,Hinsen:05, Norma}
providing, for instance, more detailled structural data for systems of major interest, like the ribosome~\cite{Tama:05}.

\begin{svgraybox}
Note that eq.~\ref{rq} is linear. As a consequence, atom motions follow straight lines and local distorsions (of most chemical bonds, valence angles, etc) can
not be avoided. So, for many applications, as well as for obtaining well-behaved normal mode trajectories, the conformations thus
generated need to be "regularized"~\cite{Elnemo1}, using for instance a detailled all-atom force-field and standard energy-minimization techniques.
\end{svgraybox}

\section{Conclusion}

Fifteen years after their introduction in the realm of molecular biophysics~\cite{Tirion:96}, thanks to their simplicity as well as to their coarse-grained nature, Elastic Network Models are
becoming more and more popular. Indeed, many applications have been proposed, noteworthy within the frame of various structural biology techniques.

From a theoretical point
of view, their relationship with Normal Mode Analysis is obvious, since both approaches rely on a quadratic form for the energy function, the former, {\it par d\'efinition},
the latter, as a consequence of a small displacement, so-called harmonic (or linear) approximation.

From an empirical point of view, it has been extensively shown
that normal mode studies of Elastic Network Models yield low-frequency, large amplitude and collective, motions which prove often similar
to those obtained with an all-atom model and a standard empirical force-field.

This is likely to be a consequence of the robusteness of these motions~\cite{Nicolay:06}.
Moreover, such motions
often provide fair predictions for the pattern of thermal atomic fluctuations (e.g. the crystallographic B-factors) or for the kind of functional motion a given protein can perform (e.g.
its conformational change upon ligand binding).

redpajama_set_name: RedPajamaArXiv


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