bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extreme selective sweeps independently targeted the X chromosomes of the great apes
Authors: Nam Kiwoong , Munch Kasper , Hobolth Asger , Dutheil Julien Yann , Veeramah Krishna R. , Woerner August E. , Hammer Michael F. ,   Great Ape Genome Diversity Project, Mailund Thomas , Schierup Mikkel Heide , Prado-Martinez Javier , Sudmant Peter H. , Kidd Jeffrey M. , Li Heng , Kelley Joanna L. , Lorente-Galdos Belen , Veeramah Krishna R. , Woerner August E. , O’Connor Timothy D. , Santpere Gabriel , Cagan Alexander , Theunert Christoph , Casals Ferran , Laayouni Hafid , Munch Kasper , Hobolth Asger , Halager Anders E. , Malig Maika , Hernandez-Rodriguez Jessica , Hernando-Herraez Irene , Prüfer Kay , Pybus Marc , Johnstone Laurel , Lachmann Michael , Alkan Can , Twigg Dorina , Petit Natalia , Baker Carl , Hormozdiari Fereydoun , Fernandez-Callejo Marcos , Dabad Marc , Wilson Michael L. , Stevison Laurie , Camprubí Cristina , Carvalho Tiago , Ruiz-Herrera Aurora , Vives Laura , Mele Marta , Abello Teresa , Kondova Ivanela , Bontrop Ronald E. , Pusey Anne , Lankester Felix , Kiyang John A. , Bergl Richard A. , Lonsdorf Elizabeth , Myers Simon , Ventura Mario , Gagneux Pascal , Comas David , Siegismund Hans , Blanc Julie , Agueda-Calpena Lidia , Gut Marta , Fulton Lucinda , Tishkoff Sarah A. , Mullikin James C. , Wilson Richard K. , Gut Ivo G. , Gonder Mary Katherine , Ryder Oliver A. , Hahn Beatrice H. , Navarro Arcadi , Akey Joshua M. , Bertranpetit Jaume , Reich David , Mailund Thomas , Schierup Mikkel H. , Hvilsom Christina , Andrés Aida M. , Wall Jeffrey D. , Bustamante Carlos D. , Hammer Michael F. , Eichler Evan E. , Marques-Bonet Tomas 
Published: May 2015

Significance
The X chromosome has a different inheritance pattern from the autosomes, direct interaction and potential conflict with the Y chromosome, and fewer copies than the autosomes. Natural selection may, therefore, act differently on the X chromosome. We analyze polymorphism patterns in 10 great ape species using 87 high-coverage whole genomes. We find that the X chromosome contains megabase-sized regions that are almost without variation in most species. No such regions are found on the autosomes. We suggest that independent and very strong selective sweeps are the only plausible explanation for these observations, and we hypothesize that the targets of these sweeps are multicopy testis-expressed genes in a genetic conflict with the Y chromosome for transmission to the next generation.
Symbolic bones and interethnic violence in a frontier zone, northwest Mexico, ca. 500–900 C.E.
Authors: Nelson Ben A. , Martin Debra L. 
Published: May 2015

SignificancePersistent interethnic violence has affected some global regions for centuries. Recent research reveals that major outbreaks are often prevented or limited by creative social action. In the prehispanic Northern Frontier of Mesoamerica, approximately 500–900 C.E., people of different ethnic backgrounds struggled for standing in a shifting sociopolitical landscape. Evidence is consistent with long-term social violence, but also with the use of the dead to communicate a range of symbolic messages. Complex arrays of human skeletal material commemorated past physical conflicts, possibly discouraging their repetition, while also connecting the living symbolically with a metaphysical realm inhabited by ancestors and deities. This article highlights the postmortem agency of the dead and illustrates their roles in structuring social relations.
Specialization and integration of functional thalamocortical connectivity in the human infant
Authors: Toulmin Hilary , Beckmann Christian F. , O'Muircheartaigh Jonathan , Ball Gareth , Nongena Pumza , Makropoulos Antonios , Ederies Ashraf , Counsell Serena J. , Kennea Nigel , Arichi Tomoki , Tusor Nora , Rutherford Mary A. , Azzopardi Denis , Gonzalez-Cinca Nuria , Hajnal Joseph V. , Edwards A. David 
Published: May 2015

Significance
We investigated the way in which the human thalamus and cortex are functionally connected at the time of normal birth. We found the functional parcellation of the thalamus to be a good facsimile of that found in adult studies. However, although primary cortical regions were almost entirely connected to specific thalamic regions, heteromodal cortex was more widely connected to multiple thalamic regions, giving the potential for an integrative role for these circuits. Development seemed to have been modulated by the experience of premature extrauterine life, with an increase in connectivity to primary sensory cortex, but reduced connectivity between areas of the thalamus and heteromodal cortex known to support higher cognitive functions.
The phototransduction machinery in the rod outer segment has a strong efficacy gradient
Authors: Mazzolini Monica , Facchetti Giuseppe , Andolfi Laura , Proietti Zaccaria Remo , Tuccio Salvatore , Treu Johannes , Altafini Claudio , Di Fabrizio Enzo M. , Lazzarino Marco , Rapp Gert , Torre Vincent 
Published: May 2015

SignificancePhototransduction is now considered to be a quite thoroughly understood phenomenon. It is well known that new discs are continuously generated at the base of the outer segments (OSs) and old discs are shed at their tip, but the rod OSs are considered a well-stirred compartment with minor inhomogeneities. To verify this assumption and to better understand the machinery within the OS, we developed a new methodology to deliver highly localized lights. We found that, as the light stimulus is moved from the OS base toward its tip, the amplitude of saturating and single photon responses decreased by 5–10 times. This gradient of efficacy is attributed to a progressive loss of phosphodiesterase. Therefore, OSs are highly inhomogeneous compartments.
Single-cell mass spectrometry reveals small molecules that affect cell fates in the 16-cell embryo
Authors: Onjiko Rosemary M. , Moody Sally A. , Nemes Peter 
Published: May 2015

Significance
Spatiotemporal characterization of molecular expression during embryonic development is critical for understanding how cells become different and give rise to distinct tissues and organs. Technological advances enabled the measurement of RNAs and proteins in single cells of embryos, but there is very little information on small molecules, metabolites, that are the ultimate indication of the physiological state. To fill this knowledge gap, we developed and used a single-cell technology to find that embryonic cells that give rise to different tissues have characteristically different metabolic signatures that are not simply a reflection of cell pigmentation, yolk content, size, or position in the embryo, but also affect cell fate. This approach is likely to provide new mechanistic insights into early embryo development.
Lack of pairing during meiosis triggers multigenerational transgene silencing in
Caenorhabditis elegans
Authors: Leopold Luciana E. , Heestand Bree N. , Seong Soobin , Shtessel Ludmila , Ahmed Shawn 
Published: May 2015

Significance
Transgenes can be permanently silenced in a single generation via a previously described small RNA-induced epigenetic silencing (RNAe) mechanism, which is promoted by the presence of a perfect Piwi-interacting RNA (piRNA) target site. In this study, we identify a previously unidentified mechanism capable of silencing single-copy transgenes that lack perfect piRNA target sites and that is triggered by a lack of chromosomal pairing during meiosis for multiple generations. Multigenerational RNAe can lead to reversible or permanent transgene silencing and may provide insight into variability in the expression of single-copy transgenes or single-copy genomic insertions, which are commonly used in experimental biology. Our analysis of “multigenerational RNAe” also offers new insights into potentially common epigenetic silencing events relevant to genome expression in the germline and embryo.
Rational design of self-assembly pathways for complex multicomponent structures
Authors: Jacobs William M. , Reinhardt Aleks , Frenkel Daan 
Published: May 2015

Significance
Recent experiments have demonstrated that complex, three-dimensional nanostructures can be self-assembled out of thousands of short strands of preprogrammed DNA. However, the mechanism by which robust self-assembly occurs is poorly understood, and the same feat has not yet been achieved using any other molecular building block. Using a new theory of “addressable” self-assembly, we explain how the design of the target structure and the choice of interparticle interactions determine the self-assembly pathway, and, to our knowledge, for the first time predict that a time-dependent protocol, rather than merely a carefully tuned set of conditions, may be necessary to optimize the yield. With an understanding of these design principles, it should be possible to engineer addressable nanostructures using a much wider array of materials.
Differential effects of fructose versus glucose on brain and appetitive responses to food cues and decisions for food rewards
Authors: Luo Shan , Monterosso John R. , Sarpelleh Kayan , Page Kathleen A. 
Published: May 2015

Significance
Fructose compared with glucose may be a weaker suppressor of appetite. Here we sought to determine the effects of fructose versus glucose on brain, hormone, and appetitive responses to food cues and food-approach behavior. We show that the ingestion of fructose compared with glucose resulted in smaller increases in plasma insulin levels and greater brain responses to food cues in the visual cortex and left orbital frontal cortex. Ingestion of fructose versus glucose also led to greater hunger and desire for food and a greater willingness to give up long-term monetary rewards to obtain immediate high-calorie foods. These findings suggest that ingestion of fructose relative to glucose activates brain regions involved in attention and reward processing and may promote feeding behavior.
Stable long-range interhemispheric coordination is supported by direct anatomical projections
Authors: Shen Kelly , Mišić Bratislav , Cipollini Ben N. , Bezgin Gleb , Buschkuehl Martin , Hutchison R. Matthew , Jaeggi Susanne M. , Kross Ethan , Peltier Scott J. , Everling Stefan , Jonides John , McIntosh Anthony R. , Berman Marc G. 
Published: May 2015

Significance
We show that the functional coordination between the two hemispheres of the brain is maintained by strong and stable interactions of a specific subset of connections between homotopic regions. Our data suggest that the stability of those functional interactions is mediated in part by the direct anatomical projections of large, highly myelinated fibers that traverse the corpus callosum. These functional properties were evident in both humans and macaques, suggesting a preserved framework for interhemispheric communication despite an increase in functional lateralization in humans. These results contribute to our fundamental understanding of how dynamic functional interactions between the two hemispheres of the mammalian brain are supported by its underlying anatomical architecture.
Age-related changes in working memory and the ability to ignore distraction
Authors: McNab Fiona , Zeidman Peter , Rutledge Robb B. , Smittenaar Peter , Brown Harriet R. , Adams Rick A. , Dolan Raymond J. 
Published: May 2015

Significance
We reveal a novel and highly significant change in how items are held in mind in healthy aging. Using smartphones, data were collected from 29,631 participants, between the ages of 18–69 y. We compare the ability to exclude distractors when items are entered into working memory (WM) (encoding distraction, ED) and when items are held in mind (delay distraction, DD). In older adults, WM in the absence of distraction was more similar to ED exclusion than DD exclusion. A greater reliance on focused attention during encoding may reflect compensation for the more pronounced deterioration we observed in DD exclusion in older age. This can inform other areas of cognition and strategies to ameliorate or manage debilitating age-related cognitive decline.
Elastocapillary interactions on nematic films
Authors: Liu Iris B. , Gharbi Mohamed A. , Ngo Victor L. , Kamien Randall D. , Yang Shu , Stebe Kathleen J. 
Published: May 2015

SignificanceIn this research we demonstrate complementary roles for elastic and capillary interactions for particles on thin nematic liquid crystal films. A priori estimates would suggest that surface tension effects would dominate over those associated with bend, twist, or splay of nematic director fields. This work is the first to our knowledge to clearly demonstrate complementary roles for both effects and extends significantly the means for developing oriented anisotropic assemblies. Anisotropic particles create strong capillary interactions that can dictate assembly. These assemblies obey orientations dictated by director fields in oriented planar nematic films. Curved interfaces add another degree of freedom, because curvature capillary-driven alignment competes with elastic-driven orientations. Experimental results are supported by analysis.
Role of a ribosomal RNA phosphate oxygen during the EF-G–triggered GTP hydrolysis
Authors: Koch Miriam , Flür Sara , Kreutz Christoph , Ennifar Eric , Micura Ronald , Polacek Norbert 
Published: May 2015

Significance
Translational GTPases are key players in ribosomal protein synthesis. Their intrinsic GTPase activity is low and is stimulated by ribosome association. Although it has been shown by structural and biochemical studies that the sarcin-ricin loop of ribosomal RNA (rRNA) closely approaches the supposedly catalytic His of elongation factor (EF)-G and EF-Tu and thereby may contribute to GTP hydrolysis, the exact mechanism of activation remains unclear and is a matter of controversial debate. Using the atomic mutagenesis approach that allows incorporation of nonnatural 23S rRNA nucleotides into 70S particles, we show that a nonbridging phosphate oxygen of rRNA is key for GTP hydrolysis of translational GTPases. To date, this is only the second rRNA backbone residue shown to be critical in ribosome function.
Self-motion perception in autism is compromised by visual noise but integrated optimally across multiple senses
Authors: Zaidel Adam , Goin-Kochel Robin P. , Angelaki Dora E. 
Published: May 2015

Significance
Descriptions of impaired coherent motion perception in autism spectrum disorder (ASD) underlie theories that individuals with ASD have difficulty integrating local “parts” into a global percept. This notion maintains widespread influence and motivates recent theories of defective multisensory integration in ASD. However, heightened sensitivity to sensory noise, used to manipulate task difficulty in predominant visual motion stimuli, may provide an alternative explanation for impaired performance. Here we indeed found increased sensitivity in ASD to sensory noise. Noiseless motion perception and multisensory integration (even with noise) were unimpaired. These findings question prevalent theories of global and multisensory integration deficits in ASD. Rather, they suggest increased reliance on—and sensitivity to—incoming sensory information and less use of prior knowledge in ASD.
Nitrogen emissions from animal agricultural systems and strategies to protect the environment.
Authors: Kohn R. A. 
Published: May 2015

Abstract

Animal production systems are among the largest contributors of reactive nitrogen to the environment. Nitrogen (N) is lost from animal agriculture through volatilization to the atmosphere (NH3, N2O, NO) and runoff and leaching to water resources (NH4+, NO3-, organic N). Most N losses from agriculture are in a form (NH4+, NH3, NO3-) that does not directly affect climate change. However, these compounds have serious environmental consequences of their own, including contributing to haze, acidity of rain, eutrophication of surface water bodies and damage to forests. In addition, a significant amount of nitrous oxide (N2O) emissions result from animal agriculture because the ammonium and nitrates from agriculture are converted to N2O during manure storage and crop production. N2O is a potent greenhouse gas. Although animals emit very little nitrogen directly to the air, animal excreta (urine and faeces) contains environmentally reactive nitrogen, which begins moving to the air and water from the moment it leaves the animal, unless it is incorporated into a crop or converted to molecular nitrogen (N2). Nitrogen is lost from the barn floor or pen, storage facility and from cropland during manure application and crop growth. Additional nitrogen is lost to the environment when producing feeds for animals using nitrogen fertilizer. Strategies to control or mitigate nitrogen losses must simultaneously consider multiple forms of losses (e.g. NH4+, NH3, N2O and NOx) in various media (e.g. air, water) for multiple processes (e.g. animal feeding, crop production, manure storage). Otherwise, management practices merely shift the losses from one form or source to another. Fortunately, process-based models assist with estimating emissions and optimizing management choices. Increased nutrient utilization efficiency of animals and crops has had the greatest impact on decreasing reactive nitrogen losses to the environment of all management strategies employed to date. Nonetheless, increased demand for animal products has continued to present environmental challenges.
Proteomics in studying the molecular mechanism of fibre degradation.
Authors: Singh N. K. 
Published: May 2015

Abstract

The degradation of plant cell walls by ruminants is of major economic importance in the developed as well as the developing world. Rumen fermentation and degradation of cell wall relies on the cooperation between the microorganisms that produce fibrolytic enzymes and the host animal, which provides an anaerobic fermentation chamber. From the 19th century, the efficiency with which the rumen microbiota degrades fibre has been the subject of extensive research. In this chapter, we will discuss various proteomic approaches such as protein fractionation (chromatography, isoelectric focusing), protein separation (two-dimensional gel electrophoresis, SDS polyacrylamide gel electrophoresis), in-gel digestion to peptides (matrix-assisted laser desorption ionization, mass spectrometry or electrospray mass spectrometry), peptide separation (two-dimensional liquid chromatography), complex protein solution digestion to peptides (electrospray ionization or MALDI-tandem MS) and proteomics of fibrolytic bacteria, which can be used to improve our knowledge of the functional framework of plant cell wall degradation in the rumen.
Indigenous livestock resources in a changing climate: Indian perspective.
Authors: Ahlawat S. P. S. , Pushpendra Kumar Pushpendra Kumar , Kush Shrivastava Kush Shrivastava , Sahoo N. R. 
Published: May 2015

Abstract

Biological diversity, the variability of life on earth, exists in the form of different species and breeds within the animal kingdom. This diversity is created in the process of molecular/biochemical/metabolic reactions, and acts as a critical measure of adaptation in changing climatic conditions. Indigenous breeds have adapted to climatic variations since time immemorial, and hence have acquired unique traits that make them suitable in given agroclimatic zones; for example, the Indian cattle breeds, Tharparkar and Sahiwal, are heat and tick resistant. Similar cases have also been observed worldwide in Asia, Africa, Europe, Latin America, North America and the south-west Pacific region, having a total of 1144, 1300, 345, 104 and 108 breeds of major livestock species, respectively. Native breeds, namely N'Dama cattle, Red Massai sheep, etc., have developed trypanosomiasis resistance and gastrointestinal nematode tolerance by continuous natural selection. The overwhelming majority of indigenous livestock around the world are bred locally and kept by small-scale livestock keepers; hence, there is a need to promote local indigenous livestock species, as they represent a genetic resource that is relatively resilient to climate variability.
Thermodynamic and kinetic control of methane emissions from ruminants.
Authors: Kohn R. A. 
Published: May 2015

Abstract

CH4 emissions occur directly from animal digestion (enteric) and from animal waste that is stored under anaerobic conditions. In both regards, CH4 emissions depends on kinetic and thermodynamic factors. With kinetic control, the profile of products formed depends on the relative rates of the different competing reactions. In turn, the rates of reactions depend on substrate concentrations and enzyme activities, and these enzyme activities depend on microbial growth or enzyme synthesis. With thermodynamic control, which pathway branches are available and the direction of metabolite flow depends on the concentrations of reactants and products. Biologists have focused on controlling the kinetic elements of fermentation such as enzyme function, microbial activity, gene expression or provision of substrates. However, fermentation is often controlled by thermodynamics. In chemistry, thermodynamics is quantified using Gibbs energy calculations. Whether or not a reaction can proceed spontaneously in the forward direction is represented by the change in Gibbs energy (ΔG), which can be calculated based on the ratio of products and reactants in the system. Using this calculation, a strongly negative ΔG indicates that a reaction could proceed strongly in the forward direction without the addition of energy to the system. A strongly positive value of ΔG indicates the reaction cannot proceed in the forward direction without the addition of energy to the system, and it may even run in the reverse direction. The analysis of thermodynamics in different situations in the rumen or manure storage facility can identify when CH4 may be controlled kinetically by affecting the rates of reactions, or thermodynamically by affecting substrate or product concentrations.
Feed-based approaches in enteric methane amelioration.
Authors: Malik P. K. , Bhatta R. , Soren N. M. , Sejian V. , Mech A. , Prasad K. S. , Prasad C. S. 
Published: May 2015

Abstract

Mitigation of methane (CH4) emissions from ruminants is necessary not only from the global warming point of view but also for saving dietary energy. Livestock being the significant contributors to the anthropogenic CH4 pool have remained the prime target of global research for the past two decades, in order to find suitable, sustainable and economical possibilities of reducing enteric CH4 emission. The adoption of a particular strategy by the stakeholders depends on the input cost, economic status, toxicity to host/inhabiting microbes, mitigation potential and persistency in long run. Among all the available options, feed-based intervention seems remarkable, and can be tried anywhere by making little alterations to the available feed resources and prevailing feeding practices. This chapter deliberates the pros and cons of various nutritional interventions, along with their future prospects to reduce enteric CH4 emission. Issues like necessity of methanogenesis in the rumen, the feasibility of reducing livestock numbers and cutting down emissions, and the expected reimbursements that arise from this practically feasible reduction, are well debated in the chapter.