Nestedness can contribute towards the robustness of a network. If species that share fewer interactions are the first to go extinct, the remaining mutualistic system have a greater chance of survival. The authors also calculate a coefficient as a parameter of a network’s robustness.

The phylogenetic or evolutionary relationship between species can predict the types and quantity of interaction patterns they exhibit in a network. Using a simulation of extinction events, the authors also demonstrated that the extinction of one species can result in the extinction of others species that are evolutionarily related.

The authors studied the feeding behaviors of birds in the Galapagos island. They discovered that these birds ate a not just a select few, but a wide variety of plants on the island. They called this behavior interaction release, a survival tactic where animals expand their niche.

In contrast to Foster, Chimera found that introduced birds in Hawaii dispersed predominately the seeds of non-native plants. Possible explanations could be that the non-native plants produce larger fruit, that are more abundant and have a smaller seed size. These qualities are more enticing to birds and enhance the plants’ chances of getting eaten and later deposited.

Foster and colleagues investigated how often introduced, fruit-eating birds on the islands of Hawaii consume and disperse seeds from native plants versus seeds from exotic plants. They found that seeds from native plants made up the majority of the introduced bird species’ diets. This supports the potential of introduced bird species playing a role in the conservation efforts of native habitats.

Bornscheuer discusses the various applications of biocatalysis. Biocatalysts offer a more practical and a green route to synthesis when compared to organometallic catalysts. Professor Arnold's work features the use of biocatalysis as a key step in C-Si bond formation.

This paper describes how Cu(OTf)2 can be used to catalyze asymmetric carbenoid insertion into a Si-H bond. 22 reactions were run and the product, alpha-silyl esters, was formed in high yields and up to 99% enantiomeric excess. When Professor Arnold's group ran the desired reaction with Cu(OTf)2, a complex mixture of products from Si-H, O-H and N-H insertion reactions was observed.

This paper discusses the use of rhodium catalysts in the asymmetric, intramolecular silylation reaction of cyclopropyl C-H bonds. The reaction proceeds with high enantiomeric excess. However, when Professor Arnold's group used Rh2(OAc)4 to catalyze C-Si bond formation, they observed that O-H and N-H insertions often dominated over the preferred silylation reactions.

Silicon, an isostere of carbon, has unique properties. Properties of silicon and application of organosilicon molecules in drug release technology, etc., are discussed. These properties can be used to enhance drug potency and improve pharmacological action.

Viboud and colleagues found a strong correlation between people's traveling rate between their workplace and home and the spread of infection. A gravity model can describe the workflow.

The authors used mobile phone data to depict the travel patterns of people in Kenya over a year. They found the exportation of malaria from specific regions to others. The finding suggested human mobility as an essential factor in the spread of malaria.

The authors conducted a correlational study using mobility data from Wuhan and case data from different regions of China.

The spatial distribution of confirmed cases of COVID-19 before the implementation of travel restrictions was found related to the human mobility data. Such correlation was diminished after the implementation, and the growth of COVID-19 in many areas turned to a decline.

Wang and co-workers synthesized the up-to-date understandings of COVID-19 by then. They summarized the time of the early-stage outbreak, the characteristics of infected patients, and control measures that had been taken by the time.

Lu and the team collected samples from nine patients presenting symptoms of viral pneumonia.

They then used the samples for DNA sequencing. The full-length sequence reported in this study confirmed the distinction of the newly reported coronavirus from the previously reported ones.

Zhu and colleagues isolated the virus that had caused the outbreak of an epidemic in Wuhan, China.

They captured images of the virus and performed DNA sequencing. Based on the results, they reported the identification of a new type of coronavirus.

I'm going to need some significant time delving into and mining this treasure trove of references.

Burke provides a sort of miniature commonplace book about journal articles and books on commonplaces!

A great resource for an overview of some of the more recent studies (since year TK?) on commonplace book research.

This paper discusses the directed evolution via mutation of the amino acids of myoglobin that lead to 49% enantiomeric excess. Engineered myoglobin catalysts are used to synthesize thioethers via a carbene S-H insertion reaction. Conversions as high as 99% and turnover numbers as high as 5400 were observed.

O'Brien and Herschlag discuss the evolution of a superfamily of enzymes and the diverse reactions they catalyze. Single point mutations can lead to the evolution of new enzymatic activities. Professor Arnold's work also involves mutations of the WT to alter the reactivity of the enzyme.

References for many of the pieces in this article.

Interesting to see that Jonathan Edwards cross referenced his commonplace book to his bible as well.

Iron compounds are found abundantly in nature and are cheap. The paper discusses the use of iron complexes as catalysts to add Si-H (hydrosilylation) across alkene double bonds. The catalysis proceeds with high regioselectivity, thereby eliminating the need for product purification.

The article presents a wealth of information about heme c and cytochrome c. This knowledge is essential for engineering enzymes to catalyze novel reactions.

Iron carbene complexes react with organosilanes leading to insertion of carbene in the Si-H bond. This is another example of the use of organometallic catalyst to carry out the insertion reaction.

This paper presents the crystal structure of cyt c. X-ray crystallography shows that cytochrome c consists of alpha helices wrapped around the compact heme core. In addition, there is a singular alpha helix that wraps around the back of the molecule.

This paper describes how silicon isosteres can be critical to drug discovery success. Professor Arnold's paper uses an approach whose benefits can be applied to drug design.

This paper describes how potassium tert-butoxide can catalyze the silylation of C-H bonds in aromatic heterocycles. The reaction is one step, occurs under mild conditions and is scalable to ~100 g. This methodology replaces the expensive route of using Rh or Ir complexes.

This article compares and contrasts solid waste management (SWM) practices in developed versus developing countries. SWM practices in industrialized countries are often affected by public health, the environment, resource scarcity, climate change, and public awareness and participation. However, urbanization, inequality, economic growth, and socioeconomic factors often complicate SWM in developing countries.

This research examined the sizes and locations of plastic particles found in the world's oceans. When plastic objects in the ocean are exposed to sunlight, they tend to break up into small particles because sunlight weakens the plastic structure and waves provide mechanical force. The small plastic particles are quite durable. Most of the plastic debris recovered and measured during this study was about 2 mm in diameter. The total amount of plastic in the ocean estimated by this study was less than predicted from plastics production and input rates. The "missing" plastics were hypothesized to be removed through one or more of the following processes: shore deposition (being deposited on shore somewhere), nano-fragmentation (breaking up into very small pieces), biofouling (small organisms grow on the plastic particles, and the plastics become heavy enough to sink), and ingestion (being consumed by marine life). The pathway and fate of the "missing" plastic is unknown.

When sea ice forms, it traps particulate matter from the water column such as microplastics. When sea ice melts, the particulate matter is released back into the ecosystem. This study examines the concentration of microplastics in Arctic Sea ice and finds that sea ice contains high concentrations of microplastics and other manmade particulates. Melting sea ice has the potential to release large amounts of microplastics back into the ocean.

Articles in Science are very brief. Supplementary materials available online can include text or images such as figures and graphs. Supplementary materials can provide additional information about how the research was conducted or additional evidence that supports the article's conclusions.

An ocean gyre is a circular ocean current formed by Earth’s wind patterns and rotation. The area in the center of a gyre tends to be very calm, and the circulation patterns of the currents draw debris into the stable center, where it becomes trapped. The debris is composed of objects both manmade and natural (i.e., driftwood). Many kinds of sea life live on and near the debris, such as gooseneck barnacles. Goldstein and Goodwin examined the digestive tracts of gooseneck barnacles to see if the barnacles consumed any plastics. One-third of the 385 barnacles examined had plastic particles present in their digestive tracts, and larger barnacles tended to contain more plastic particles. The effects of plastic particle ingestion on the ecosystem are still unknown.

Other than filling some space and giving a bit of quirky context, did the text even mention this image? There should have been something.

There was one later reference to parts of animals, but not specific to this image which could have been tied in better.

Waterhouse et al. investigate the effects of deleting CTLA-4 from mice. These "CTLA-4 deficient" mice had disorders of T cell proliferation and quickly died.

Gribben et al. show that CTLA-4 functions to induce cell death of T cells. In biology, many signaling events are also controlled by an off switch that prevents prolonged or out-of-control signaling. CTLA-4 fulfills this role for T cells.

Brunet et al. identify the sequence of the CTLA-4 receptor. They note that it is part of immunoglobulin and has hydrophobic flanking sequences reminiscent of a membrane-bound protein. They also show that its expression is restricted to activated lymphocytes (T cells and B cells).

Mueller, Jenkins, and Schwartz review the body of research on T cell costimulatory signaling pathways. In the few years after the discovery of the T-cell receptor, which directly binds the antigen to which a T cell is responding, researchers proposed that other signals are needed for T cells to become fully activated. This led to the two-signal model of T-cell activation described in this review.

I've done some bibliographical cards in the past myself, but find that I never used or revisited them or had great need to have them crosslinked myself. I've been moving away from doing this as well.

To add on wearable skin electronics, the created sweat glucose and pH sensors. The sensors were created out of carbon nanotubes combined with different polymers.

They have created a flexible pressure sensor which has the capability of non-invasive continuous radial artery pule monitoring. It is stated that this has the capability of being a breakthrough for wearable cardiovascular health monitoring.

They created an hemispherical optoelectronic device that can replicate the functions and characteristics of a human eye such as a wide field of view and low aberrations. This electronic device is based off of single-crystalline silicon and is compressible, which enables the hemispherical shape.

Here, biocompatable and stretchable materials were tested for implant use. Gold coated silver nanowires within a polymer were tested to see its conductivity. Using this material they were able to fabricate wearable and implantable soft bioelectronic devices that can be conformally integrated with human skin.

They reviewed materials that maintain proper electronic properties while having the ability to be stretched, compressed, twisted, bent, and deformed. They discussed different applications for these technologies and possible commercialization.

They used transistors with a floating gate embedded in hybrid dielectrics at a nanoscale of size, and created a flexible array of these floating gate transistors. They coupled this with a pressure sensitive rubber sheet, and the result was a matrix that was able to read mechanical pressure and store it as an image.

They test a high density, hemispherical image sensor array comprised of an atomically small MoS2 heterostructure that has the capability of releasing strain. They deem this device to be capable of being a soft retinal implant capable of various imaging elements.

Stiff-neural implants have very rare compatibility with soft-neural tissues. Therefore an soft-neural implant was configured that is elastic like dura matter (the protective membrane of the spinal cord).

An elastomeric camera was created in the likeness of ant and beetle eyes. These cameras have close to full hemispherical shapes, at around 160 degrees. This hopes to copy arthropods who have wide-angle field of view, low aberrations, high acuity to motion and an infinite depth of field which are all difficult to replicate.

A self-healing system was created that was capable of automatically repair damage from repeating events. They used a coating-substrate (a substance on which an enzyme acts) to deliver healing agents to cracks within the polymer.

They created a thin, comfortable device that can be laminated or stuck to the skin of a person to allow for the monitoring of physiological monitoring for the user. Examples of this could be heart rate or blood pressure. This is also a wireless device.

A non-invasive ultra-thin electronic interface was created what is capable of being mounted on tissue using a a protein called fibroin which can be obtained from silk. This protein is capable of being absorbed back into the tissue which results in the mounting of the device. These electronics are capable of neural mapping of the brain.

They created a wireless, battery free, touch based electronic system that is capable of being placed onto the skin. This technology has the capability of communicating information through vibrations. They also have the capability of being used for VR.

A multiple phase heat sensitive rubber like material was created. This substance is extremely tough and durable while also having the capability of self-healing.

An easily foldable and stretchable circuit was created using silicon, a good semi-conductive metal. They combined the silicon with rubber like plastic material to help create the flexibility of the circuit.

Wilson and Hastings discuss bioluminescence in this article. This is a very large overview and descriptor of bioluminescence, where it covers what it is and what it does.

The chemical way in which bioluminescence works is described in depth, and explained that the factors which control the intensity of this light can vary. Wilson and Hastings also touch on how this can be credited for some bacteria to sense their density and regulate specific genes through chemical communication.

Roger Hanlon discusses the use of dynamic camouflage, specifically applied to cephalopods.

Hanlon discusses that these animals are able to camouflage themselves against almost any background, which is a feat non mastered by any land animals. He also categorizes different camouflage patterns. These patterns help to allow the animals that possess them to stay alive.

This paper found that extended release devices, like the one described in this paper, add therapeutic and convenience benefits, without adding any risks.

This paper gave the authors the idea for the Leopard Tortoise shell shape to design this pill.

This paper showed the authors that microneedles increase bioavailability of a drug and can be safely excreted by the body as seen using a swine model.

This paper showed the authors that direct injection into the stomach lining leads to a more predictable delivery rate when compared to a small intestine injection.

This source showed that there were few injuries after multiple upper endoscopies, which are much more invasive. This was another source that showed the authors that injecting insulin into the GI tract is a safe way to deliver insulin, since it is less invasive than an upper endoscopy.

This source explains that the mucosal surface in the GI tract is quick healing, giving the authors a good place to inject insulin without causing damage to the GI tract.

This source shows that the bioavailability for even the most advanced drugs when taken orally is usually only 1-2%, meaning that very little drug is actually usable by the body, when a pill is taken orally. This led to the authors designing a pill that directly administered insulin directly into the GI tract.

This study was important to the authors to find proper coatings for successful treatments of diabetes via the GI tract.

This study explained that optimized treatment for Type II diabetes is delayed by, on average, 7.7 years. This meant that people with Type II diabetes were not well monitored or treated.

This paper found that intense regular treatments of diabetes led to a decreased rate of progression to diabetic retinopathy (a disease of the eye caused by diabetes).

This source describes the preference of people taking injections or tablets. The authors of that paper found that people preferred tablets over injections. This led the authors of this paper to design a tablet to treat diabetes as an alternative to insulin injections.

This paper details a technique that rivals conventional electrowetting techniques. Here liquid dispersion forces are used in order to pull colored oil out of a reservoir and into an observable area greatly increasing the ability to see color while enhancing contrast.

This paper describes the process of electrowetting. This process is a way of taking paper and using electric fields to manipulate water droplets that are found on the surface of the paper. In terms of application this paper uses electrowetting as a way of creating a reflective surface that can be altered.

This paper was published in 2003 and highlighted advances in the field of thermal imaging. Specifically advancements in infrared detection was made. Here the author highlights three new techniques to detecting infrared waves.

In this piece we start with a review detailing how different studies of color changing organisms has led to what we currently know about camouflage. The paper then goes onto describe how organisms do not only change color based on their background but potentially also the number of predators that are threatening them.

Stevens and Merilaita explain the importance of animal camouflage and their implications in science today.

While other authors focus on the how animal camouflage would work in general, there is more of a focus on defining camouflage strategies and crypsis, or features of physical appearance but also behavioral traits.

Robert Shephard, who is an author of this work, teamed up with several of his collages in order to help introduce soft robotics to the world. Here he defines what constitutes as soft robotics and how it can be useful to different fields of study.

Cott and Huxley describe general camouflage and warning coloration and mimicking which animals use.

This knowledge of camouflage can be utilized to be adapted towards soft machines and how to use dynamic coloration. The ability for this type of technology is not commonly used and replicated by using other technologies.

Shepherd and others describe the utilization of a soft robot that is exclusively made of soft polymers.

This soft quadrupedal robot is utilized as it can produce complex motions. Soft robotics can simplify the more mechanical structures and do not require a mechanically strong and rigid skeleton.

This word is exactly the point. What if this web page were a public thing within Roam? Then other people's notebooks could comment within their own, but using notifications (via Webmention) could be placed into a comments section at the bottom of one's page or even done inline on the portions they're commenting on using block references.

A flexible sensor device was created with the ability to analyze different elements/compounds found within sweat such as glucose and sodium while also monitoring skin temperature. All of this is fully integrated within the system so no outside analysis is needed.

Fatemifar et al. (2013) showed that HMGA2 is associated with craniofacial features such as the width of the eye region, the width of the lower part of the nose, and the height of the mid-brow prominence.

I hear this name and can't help but think about the potential influence on the name of the character from The Dead Poets Society

https://www.youtube.com/watch?v=LjHORRHXtyI

Weedon et al. concluded that the HMGA2 gene was one of several that has a role in influencing height in adult humans.

Zhou (1995) found that, in mice, mutant alleles sometimes arise from deleted DNA or from chromosomal inversions.

When these mutations cause the protein Hmgi-c to inactivate and not be expressed in mice, the result is dwarfism. This protein is associated with the HMGA2 gene.

Pfannkuche and colleagues (2009) found that HMGA2 is an important factor in embryonic stem cells and seems to magnify other factors, such as the regulation of body height in humans, the repression of certain genes, and several other functions.

The previous tree from Lamichhaney and colleagues in 2015 showed that the initial split between warbler finches and other finches happened 900,000 years ago. Rapid divergence of ground and tree finches occurred 100,000 – 300,000 years ago.

Abzhanov and colleagues (2004) analyzed various growth factors that were known to be expressed during craniofacial development of birds. When looking at Darwin's finch species, some factors showed simply showed no correlation whereas other factors showed a correlation with beak size, but not beak shape.

However, researchers did find that the expression of the Bmp4 molecule had strong association with both beak size and shape.

Grant and Grant (2006) reported that the finch species Geospiza fortis diverged in beak size from one of its competitors, G. magnirostris. This divergence happened on an isolated Galapagos island 22 years after G. magnirostris arrived to share a habitat with G. fortis.

This work is part of the foundation that the Wnt signaling pathway is well established chemical pathway in embyrogenesis. This is important, because embryos contain stem cells which require direction for migration and differentiation much the the regeneration in adult planarians.

This research was the first to identify the set of genes in C. elegans (a simple nematode invertebrate model) that were used in the experimental RNAi silencing by Alvarado and colleagues. Evidence was also provided that showed a potential role in early embryonic development.

The data confirm that β-catenin regulates cell fate in two very distant animal species, which suggest that β-catenin has an ancient metazoan origin.

The authors in this study show that β-catenin plays a role in cell adhesion and body plan development in sea urchins, a primitive invertebrate animal. This research provides additional evidence the β-catenin is an evolutionarily important molecule and its role has been maintained over time across the animal kingdom.

The authors used two vertebrate models, zebrafish and frogs, to identify that β-catenin via the Wnt signaling pathway plays a role in dorsal-ventral polarity. This research suggest that β-catenin is an important molecule because it has been found to play similar roles in both vertebrates and invertebrates.

The data provided insight into how the Wnt signaling pathway and β-catenin target gene activation. This foundational information provided understanding of how RNAi could be used to silence the genes associated with control of this pathway.

Some amphibian species have the ability to regenerate limbs. The data suggest that Wnt/β-catenin signaling plays an essential role in this process. These results again confirm that β-catenin is present across various animal species. A full understanding of regeneration in vertebrates may lead to potential treatments for human organ regeneration.

Morgan was a pioneer in the field of genetics. His theory that polarity, or development of two axes in animals was a direct result of the presence of a yet unidentified molecule. This theory has stood the test of time and provides the foundation of this research.

Earlier research by Alvarado and colleagues identified the types of tissue that are able to regenerate from a blastema that forms after tissue damage. Without previously identifying this role, the current research would not be possible.

The authors used Channelrhodopsin-2 to selectively photostimulate hypocretin-producing neurons in the lateral hypothalamus and showed a frequency-dependent effect on sleep-to-wakefulness transition. This paper supported optogenetics' ability to stimulate cells and elicit a physiological effect.

This paper discusses targeting strategies to selectively express opsins to certain regions or cell types as well as methods to read out expression and activity. Methods include electrophysiology, imaging, and behavior analysis.

A paper describing the first use of halorhodopsin—a chloride pump expressed in an archaeon named Natronomonas pharaonis that expressed temporal optical inhibition of neural activity. The investigators were then able to co-express both NpHR and ChR2 in the same cell and optically control its activity.

The authors engineered the NpHR from the F. Zhang et al. paper in 2007 to be better expressed at the cell membrane by inserting a membrane-insertion signal and an endoplasmic reticulum export signal. Both interventions created eNpHR (enhanced NpHR) that improved protein trafficking and membrane expression. This was a necessary modification for the current paper published by the same first author. Temporal precision is a key parameter when dealing with neural firing which can occur at millisecond resolution.

The authors investigated a red-shifted cation-conducting opsin variant from the algae species Volvox carteri that could be stimulated at a wavelength of 595nm. VChR1 can be stimulated by yellow light and offered a third class of microbial opsins.

Creswell et al. identified a physical reaction to stereotype threat and found that values affirmation reduces this reaction.

Cohen et al. performed a large-scale examination of the efficacy of values affirmation in an authentic classroom environment.

They found that having students complete a short writing exercise, in which they wrote about a value they found important (values affirmation), reduced the gap in performance between African American students and other students.

A full PDF copy of this research can be found in the Related content tab.

Good, Aronson, and Inzlicht assessed whether specific kinds of mentoring could reduce the effects of stereotype threat in female, minority, or low-income 7th graders.

They found that students paired with a college-student mentor who either 1) encouraged them to view intelligence as malleable, or 2) told them to attribute academic difficulties to the novelty of the educational setting, performed much better than students who did not get this framing.

Cohen et al. found that an initial values affirmation intervention could have long-lasting positive effects.

S. Burgess stresses that knowledge of the cause or causes of mass extinctions can inform understanding of how the biosphere responds to dramatic environmental change and can help to validate hypotheses about probable outcomes of anthropogenic changes. Both the asteroid impact and large-scale volcanic eruptions as the cause of the K-Pg extinction are credible. Now, with more accurate dating techniques, it appears that most of the large-scale eruptions occurred after the impact, delaying recovery.

Mass extinctions often result in the loss of entire branches of the tree of life. Pincelli Hull argues that macroevolution is shaped as much by the species that survive a mass extinction as by those that do not. He contends that more than 99% of all species that have ever lived are now extinct and that the losses have not been random.

Wilf et al. differentiate between climatic change and asteroid impact effects on biodiversity. They determined there was a cooling trend during the final 0.1 m.y. of the Cretaceous. This likely accounts for some loss of biodiversity from its peak during the earlier warm interval and makes inaccurate the observation that the asteroid impact alone resulted in the loss of 70%–90% of macrofossil species.

The authors tested the hypothesis that an impact winter following the asteroid impact selected against slow-growing evergreen species. Using fossil leaf collections crossing a 2-million-year interval spanning the K-Pg boundary, they assessed both carbon assimilation rate and carbon investment using leaf vein density and leaf mass per area as proxies. They learned that species that survived the K-Pg extinction had fast-growth strategies with high assimilation rates and low carbon investment.

Clyde et al. used several different dating techniques to more precisely determine the age of volcanic ash deposits across the K-Pg boundary in the Denver Basin. The results were compared to data derived from an analysis of fossil spores and pollen from deposits in the same region. They concluded that the interval between the extinction of the dinosaurs and the appearance of the earliest Cenozoic mammals in the Denver Basin lasted ∼185 k.y. and the "fern spike" lasted ∼1 k.y. after the K–Pg boundary layer was deposited, indicating rapid rates of biotic extinction and initial recovery in the Denver Basin.

Wilson’s research concludes that the richness of mammalian species remained relatively stable for most of the last ~1.9 m.y. of the Cretaceous. However, the relative abundance of mammals more closely related to marsupials than to placentals began declining ~500–600 k.y. before the Cretaceous-Paleogene boundary. Based on available fossil evidence, mammalian recovery occurred within ~600–700 k.y. of the Cretaceous-Paleogene event.

Prum and colleagues investigated avian phylogeny with a data set of >390,000 bases of genomic sequence from each of 198 species of living birds. This represents all major avian lineages, and two crocodilian outgroups. The results of their divergence time analyses are congruent with the paleontological record and support a major radiation of crown birds following the Cretaceous–Paleogene (K–Pg) mass extinction.

This paper reports the identification of the importance of the HMGA2 gene in affecting beak shape in Darwin's finches, especially during natural selection that occurred during a drought in 2004-05.

In this summary of genes and traits of hybridizing finches on Daphne Major, the authors established general patterns found in hybridization of the finches on this island: that hybrids are generally intermediate between parental species and often go on to mate with members of the parental species.

They discuss hybridization as a source of genetic variation within existing species and suggest that it can happen through new combinations of genes (additive genetic variance) as well as new patterns of dominance or co-dominance among known genes, or even the establishment of new combinations of genes on chromosomes.

They also note how rare it would be to see hybridization produce birds much larger than parent species, and how unusual occurrences might be necessary to provide the conditions for this to happen.

In this discussion of transgressive segregation, Riesenberg et al. review many studies and conclude that the genetic basis of transgressive segregation is through complementary alleles: new combinations of alleles that provide novel combinations of genotypes.

They find that transgressive segregation occurs most frequently in crosses between closely related species and that niche separation is the most important factor in favoring the establishment of hybrids.

Swarth's paper reorganized the classification of Darwin's finches slightly, particularly with regard to the Geospiza genus.

Lack's book recounts what he learned about Darwin's finches from a visit to the Galapagos in late 1938-39, one of the first visits to the island focused on the finches since Darwin's time. The work includes the classification of the finches as well as notes on speciation, adaptive radiation, and evolution.

Grant and Grant use genetic information to quantify the effects of the gene exchange between populations of birds. They explore two situations: genes that enter a population through mating with a bird of the same species (conspecific) but from a different population on another island; and genes that enter a population from a member of a different species (heterospecific). They conclude that while both types of gene flow are rare, they do occur and have measurable effects on the populations that are complex and change through time rather than being steady.

This paper presents the results of a whole genome study of 120 of Darwin's finches and identifies the ALX1 gene as important in determining beak shape. The study also helps revise the phylogenetic tree of the finches and provides evidence for hybridization as the finches evolved.

This book gives a complete evolutionary history of Darwin's finches. Grant and Grant explain the speciation that occurred and the mechanisms that underpin the formation of different species of finches in the Galapagos Islands.

In the article "How Common is Homoploid Hybrid Speciation?" Schumer et al. indicate that in the study of this topic future research needs to clarify the mechanisms of this type of event. They also propose criteria by which to judge the strength of evidence for this event, arguing that evidence for hybridization's role in speciation is somewhat limited.

Researchers at the Department of Genetics and Pathology in Rudbeck Laboratory studied three vascular endothelial growth-factor receptors (VEGF) responsible for regulating the cardiovascular system. VEGFR1, VEGFR2, and VEGFR3 all function slightly different but together produce cardiovascular development, control endothelial-cell function and the development and survival of blood vessels. They showed the importance of controlling angiogenetic-growth-factors (such as proangiogenic) that are responsible for the formation of blood vessels. Fibronectin is not mentioned by name but other glycoproteins are emphasized for their importance as receptors for VEGF.

Researchers at Harvard were the first to keep a 1cm thick vascularized tissue alive in lab conditions for longer than 6 weeks. They achieved this by co-printing a mixture of bioinks composed of human stem cells, skin cells, cells from umbilical cord vessels, and growth factors. The printed artificial tissue contained a network of embedded blood vessels used for perfusion to keep the tissue alive.

Jordan S. Miller at Rice University highlighted that more clinical trials, proper tissue fabrication sterilization, sufficient vasculature and quality assurance will lead to good manufacturing practice (GMP) and a standard regulatory process. Miller believes overcoming these obstacles will transition the use of 3D printed tissue from research and development to manufacturing and production.

Michael Potente, Holger Gerhardt, and Peter Carmeliet worked with endothelial cells in order to grow blood vessels in a scaffold smaller than any needle is capable of printing. The cells naturally line the inner surface of the vessel and are responsible for repair and growth of new vasculature. Under predetermined conditions the cell have genes that will be expressed to grow vasculature; a process known as angiogenesis.

Christian Frantz, Kathleen M. Stewart and Valerie M. Weaver compiled information on the extracellular matrix (ECM) and its application in tissue engineering

Dvir and colleagues used a specific type of stem cells called pluripotent stem cells that allowed them to grow and develop vascularization as an embryo would. They are the first to take cells from a patient to print a personalized full size and function heart using bioinks. Bioinks are the printing material that replicates the extracellular matrix and has living cells in it.

HW Kang and others at Wake Forest Institute for Regenerative Medicine used microchannels developed at University of Pennsylvania on an integrated tissue-organ printer (ITOP) so that they can produce human-scale mandible and calvarial bone, cartilage and skeletal muscle.

J.S. Miller and others in the Bioengineering Departmnet of University of Pennsylvenia were able to 3D print living cells together to form a tissue. The current problem is that blood and oxygen was unable to get to the center of the tissue leaving a large dead spot in the center called a necrotic core. They solved this problem by engineering in channels for blood to flow as they do through veins to keep a wide variety of cell types alive.

This paper describes the development of a self healing dielectric elastomer. The actuator contains a layer of oil which allows the actuator to maintain dimensional stability even after being punctured multiple times.

This paper describes self‐repairable, high permittivity dielectric elastomers with large actuation strains at low electric fields. The actuators can be operated repeatedly and reversibly at voltages below the first breakdown.

This paper demonstrates the fault-tolerant dielectric elastomer electrodes consisting of elastomers spray coated with carbon nanotubes. The electrodes allows for isolation of the fault after a dielectric breakdown increasing the reliability of the actuator.

This paper describes the change in characteristics of elastomers when pre-strained. The resulting elastomers feature double the strength and speed of previous actuators.

This paper describes the development of a quadrupedal soft robot that moves through fluid pressure.

This paper reviews a specific type of soft robot, elastomeric robots, that are powered by fluid pressure.

This paper defines the characteristics of many types of soft robots. The authors compile a benchmark of these characteristics for future research reference.

This article is a review of the current common designs and applications of "soft-robots". Soft-robots are robots modeled after things that occur in nature. For example, robotics would traditionally use gears and motors to move. .Soft-robotics use designs that mimic human or even insect muscle.

Liu and colleagues created "triggerable tough hydrogels," composed of novel materials that promote a prolonged stay in the gastric system.

The once-monthly smart birth control pill employs this concept of tough materials that will only disintegrate in the presence of chemical stimuli to ensure the contraceptive will stay in the digestive tract longer.

Bellinger and colleagues design a long-term drug delivery system for malaria. They accomplish this by designing an oral capsule that stays in the gastric cavity for up to 14 days.

The smart birth control pill presented in this work builds off of this research and the idea that reducing dosage frequency can be accomplished by increasing the time it stays in the stomach.

A study was performed to investigate scalable doses and the modulation of drug release in the gastrointestinal system.

The author's used most of the characteristics of these dosage forms in the manufacturing of the oral contraceptive.

Snoeck and colleagues determine the time it takes for a dosage form to pass through pigs. This information can help in the design of oral drug delivery methods.

The authors discuss the current alternative contraceptive forms that provide shorter-term protection (about 1 month).

Allen and colleagues discuss the use of contraceptives as a form of family planning in women over the age of 40. Due to being at the end of the reproductive age range, special attributes of the effects of contraceptives for women over 40 need to be considered.

The authors discuss that some contraceptive devices can be implanted outside of the uterus and release hormones for about 3 years, after which they are surgically removed.

The World Health Organization describes the vast impacts of contraceptives, ranging from its role in family planning to its involvement in protecting from sexually transmitted infections, as well as the many different forms of contraceptives that are available.

In this natural experiment, as a result of a hydroelectric dam flooding a rainforest in Venezuela, researchers were able to measure the results of predator removal in isolated communities. Top-down regulation of these communities were discovered and drastic trophic cascades were observed. 

This observational study of 153 sites demonstrated, over the course of 3-15 years, the importance of sea otters to the community structure of the kelp forests of the Aleutian Islands and Alaska. Without sea otters, the kelp forests collapsed due to overgrazing by urchins and other herbivores, leading to implications for numerous other organisms in the system. With sea otter predation on urchins, the kelp system was stable and supported a much higher diversity of organisms at all trophic levels (Fig 3).

The authors highlight 5 lines of reasoning to underscore the importance of predators as top-down controls:

1) the rate of planetary fossil fuel accumulation over time has not been minuscule as compared to the rate of photosynthesis in the same systems;

2) given this, decomposers must be food-limited; otherwise, fossil fuels would build up at higher rates;

3) in terrestrial systems, plants are typically not herbivore-controlled, nor are they regularly destroyed by weather, but are controlled by bottom-up factors such as light, water, and nutrients;

4) terrestrial herbivores are therefore typically not limited by their food supply, even in areas where the primary consumers are overabundant;

5) herbivore populations are therefore controlled by predators.

While ⁴He is formed as a result of radioactive decay, the origin of ³He has been traced to collision with meteorites. Thus a high ³He/⁴He ratio indicates that the rock sample has been collected from a region which has been undisturbed and very ancient. Hence it is expected that OIBs, which are conventionally identified as undegassed, primitive mantle sources, should show high concentrations of ³He. However, this conventional model fails in reality. This is also known as the "Helium Concentration Paradox". This paper aims at self-consistently explain the paradox by measuring the carbon dioxide in mid-ocean ridge basalts (MORBs) and ocean island basalts (OIBs).

This article reports the helium isotope data from ancient basalts located in three islands in the southern pacific ocean. The HIMU (high μ, where μ= U-238/Pb-204) sample collected from this area shows a relatively low and stable helium-3 to helium-4 ratio. While, other enriched samples show a variation in this isotope ratio.

This paper focuses on classifying the deformations of dielectric elastomers. The classification aims to better characterize properties of elastomers under deformation.

This paper is a review of dielectric elastomers, their characteristics and use.

This paper reviews the recent advancements in dielectric elastomers which allow for longer use before dielectric breakdown renders them unusable.

This paper describes a computational model that attempts to demonstrate of an actuator can be programmed to deform in a specific form.

This paper describes the characteristics of polymer actuators when serially stacked. Stacking actuators allows for significant unidirectional contraction.

This paper describes the development of a new type of artificial muscle constructed from high-strength polymer fibers, like fishing line or sewing thread. This new muscle is much more efficient than natural human muscle.

This paper is based on a 25-year review on the field of soft robotics. Actuators, sensors, and flexible energy harvesters are all reviewed.

This paper is the second of a two part series of papers studying and attempting to replicate an octopus tentacle in a soft robot model.

This article reviews the current findings and knowledge in the field of soft robotics.

This paper analyzes possible inspiration for soft-robot designs, such as elephant trunks or octopus tentacles. It also analyzes the benefits of soft-robot designs compared to more rigid traditional robotic designs.

This link does not seem to work, but the data resources of the United States Naval Observatory Astronomical Applications Department can be found at this website.

The Center for Disease Control and Prevention describes existing methods of contraception. In addition to oral pills, other methods include subcutaneous implants, intrauterine devices, vaginal rings, transdermal patches, and injectables.

Statistics show that "the chance of pregnancy in women using oral contraceptive pills is ~9% per year," signifying the need for improving oral contraceptives.

The authors discuss that intrauterine (within the uterus) hormone devices can serve as an alternative contraceptive form, providing protection for 3-6 years.

The authors conclude that the distribution of ejecta from the asteroid impact in Chicxulub around the globe provides evidence that the impact triggered the K-Pg mass extinction. The volcanic eruption hypotheses fail to explain the global distribution of ejecta, its composition, the timing of the extinction, and the scale of environmental changes.

The authors conducted a quantitative analysis of megafloral turnover across the K-Pg. They based their work on data from the Williston Basin located in southwestern North Dakota. They relied on previously recovered high-resolution palynological data. Their data confirm that a major plant extinction event occurred in conjunction with the asteroid impact. An estimate of plant extinction, based on species lost that were present in the uppermost 5 m of Cretaceous strata, is 57%.

The authors confirm that current rates of extinction are higher than expected based on the fossil record. He, and other scientists, suggest that a sixth mass extinction may be underway. Conservation efforts must be increased.

In this paper, the authors have shown that only the hottest hotspots with the slowest wave velocity draw from the ancient reservoirs formed during the early days of planet Earth.

There has been a lot of debate regarding the exact location of the chemical reservoirs containing superdeep diamonds. In this research, the authors have done carbon isotope analysis on these diamonds and concluded that the most likely origin is in the lower mantle of Earth.

This research article debunks the popular outcomes of previous geological models of Earth's interior. The author shows data to disprove the previous hypothesis of correlating high R in basalts with excess of helium-3 and existence of primitive gas-rich chemical reservoirs.

In this paper, the authors have performed a series of experiments on diamond samples in order to ascertain the chemical composition and isotope variability of diamonds from the Orapa kimberlite.

There are several existing models of the Earth's formation. In this research, the author points out the discrepancies in the preconceived models and highlights the fact that the chemical compositions of the upper and lower mantle are different.

The author reports a seismic study of old parts of southeast Brazil and provides no concrete evidence of metamorphic rocks which are commonly found in regions occupied by subducted oceanic plates.

In this research, the authors investigate the geochemical processes involving diamond formation within the Siberian cratonic lithosphere. They particularly study the halogen and noble gas geochemistry of fluids trapped in diamonds sampled from this region.

In this research paper, the author presents their data of helium isotope analysis of rock samples from the Yellowstone region. They conclude that the analysis shows no evidence of a deep mantle origin of the collected samples.

Krummel and Allison study the effect of CTLA-4 engagement. Their anti-CTLA-4 antibody blocks the receptor without engaging it. On its own, blocking the receptor does not have an effect on T-cell responses. Combined with an activation signal, anti-CTLA-4 allows for enhanced proliferation of T cells. The antibodies introduced here are the same ones used in the treatment of mice in this paper.

Walunas et al. show that CTLA-4 is an inhibitor of T cells. Their approach is to cross-link the receptors together, mimicking the cross-linking that would occur naturally upon receptor engagement. The effect of this is inhibition of T cell proliferation.

Linsley et al. study the differences between binding of CD28 and CTLA-4 to B7 molecules. Though they have similar avidities, they bind the B7 surface molecules using different conformations and kinetics.

Linsley et al. show that CTLA-4, like CD28, binds B7. Using a soluble version of CTLA-4, they show that it binds to B7 with an affinity of 12 nM.

Harper et al. present compelling evidence that CTLA-4 and CD28 share a similar function. They found that the receptors share similarities in structure, sequence, gene location, and expression patterns.

In this commentary, Linsley speculates on how the evidence for the roles of CD28 and CTLA-4 fits together. T-cell activation is more complex than scientists originally thought.

In this minireview, Bluestone summarizes the studies showing the nuances of CD28-mediated signaling. He discusses that different B7 molecules result in differing levels of activation, and that CTLA-4 has an inhibitory effect.

In this minireview, Jenkins summarizes the evidence for the role of CTLA-4. It was shown from multiple studies that CTLA-4 has an immunosuppressive effect.

Baskar et al. investigate the effect of B7 expression in tumor cells on the helper T cell immune response. They show that engineered tumor cells generate a helper T cell response and tumor rejection.

Townsend and Allison investigate whether expressing B7 on the surface of a tumor will enhance its rejection. They show that B7 expression results in a cytotoxic T cell immune response.

Chen et al. investigate whether expressing B7 on the surface of a tumor will enhance its rejection. They show a B7-dependent immune response by cytotoxic T cells.

June, Bluestone, Nadler, and Thompson review the research on B7 and CD28. Though they are the most commonly found members, each of these molecules is part of a larger receptor family of related molecules.

Linsley and Ledbetter summarize the research on CD28 and B7 molecules. The costimulatory signal needed for full T-cell activation is supplied through these surface molecules.

Votre référence est bien en bib, mais (hormis l'hyperlien), elle est totalement vide : si vou l'aviez exporté à partir de la bibliographie commune sur Zotero, elle aurait été plus fournie et les indices bib auraient alors fait sens.

c'est moins un article, qu'une partie d'un ouvrage commun

si c'est un chapitre, c'est un chapitre

les PUM sont ici la maison d'édition

référence qui aurait mérité d'être éditée dans la bibliographie

référence à intégrer dans la bibliographie

la référence est ici attendue

l'ajout de la référence aurait été nécessaire ici.

ces références auraient pu être intégrées au corps du texte avec les indices bib (sans appel de note)

il est conseillé de citer les revues en utilisant l'italique

Il s,agit davantage d'un billet de blog

vous avez ici placé la bibliographie du cours, ce qui vous génère une bibliographie immense avec des entrées doubles... Était davantage attendue une bibliographie présentant les ouvrages dont vous vous êtes inspirée pour créer le compte rendu (dont l'ouvrage de référence).

même remarque que pour la référence précédente, de plus un espace manquant entre la page et son numéro