bluuebunny/crossref_metadata_2025_split huggingface dataset:
The sperm of aging male bustards retards their offspring’s development
Authors: Preston Brian T. , Saint Jalme Michel , Hingrat Yves , Lacroix Frederic , Sorci Gabriele 
Published: February 2015

AbstractUnderstanding whether the sperm of older males has a diminished capacity to produce successful offspring is a key challenge in evolutionary biology. We investigate this issue using 10 years of reproductive data on captive long-lived houbara bustards (Chlamydotis undulata), where the use of artificial insemination techniques means parents can only influence offspring quality via their gametes. Here we show that paternal aging reduces both the likelihood that eggs hatch and the rate at which chicks grow, with older males producing the lightest offspring after the first month. Surprisingly, this cost of paternal aging on offspring development is of a similar scale to that associated with maternal aging. Fitting with predictions on germline aging, the sperm of immature males produce the fastest growing offspring. Our findings thus indicate that any good genes benefit that might be offered by older ‘proven’ males will be eroded by aging of their germline DNA.
Toll-like receptor ligands sensitize B-cell receptor signalling by reducing actin-dependent spatial confinement of the receptor
Authors: Freeman Spencer A. , Jaumouillé Valentin , Choi Kate , Hsu Brian E. , Wong Harikesh S. , Abraham Libin , Graves Marcia L. , Coombs Daniel , Roskelley Calvin D. , Das Raibatak , Grinstein Sergio , Gold Michael R. 
Published: February 2015

AbstractIntegrating signals from multiple receptors allows cells to interpret the physiological context in which a signal is received. Here we describe a mechanism for receptor crosstalk in which receptor-induced increases in actin dynamics lower the threshold for signalling by another receptor. We show that the Toll-like receptor ligands lipopolysaccharide and CpG DNA, which are conserved microbial molecules, enhance signalling by the B-cell antigen receptor (BCR) by activating the actin-severing protein cofilin. Single-particle tracking reveals that increased severing of actin filaments reduces the spatial confinement of the BCR within the plasma membrane and increases BCR mobility. This allows more frequent collisions between BCRs and greater signalling in response to low densities of membrane-bound antigen. These findings implicate actin dynamics as a means of tuning receptor signalling and as a mechanism by which B cells distinguish inert antigens from those that are accompanied by indicators of microbial infection.
Quantum Hooke's Law to Classify Pulse Laser Induced Ultrafast Melting
Authors: Hu Hao , Ding Hepeng , Liu Feng 
Published: February 2015

AbstractUltrafast crystal-to-liquid phase transition induced by femtosecond pulse laser excitation is an interesting material's behavior manifesting the complexity of light-matter interaction. There exist two types of such phase transitions: one occurs at a time scale shorter than a picosecond via a nonthermal process mediated by electron-hole plasma formation; the other at a longer time scale via a thermal melting process mediated by electron-phonon interaction. However, it remains unclear what material would undergo which process and why? Here, by exploiting the property of quantum electronic stress (QES) governed by quantum Hooke's law, we classify the transitions by two distinct classes of materials: the faster nonthermal process can only occur in materials like ice having an anomalous phase diagram characterized with dTm/dP < 0, where Tm is the melting temperature and P is pressure, above a high threshold laser fluence; while the slower thermal process may occur in all materials. Especially, the nonthermal transition is shown to be induced by the QES, acting like a negative internal pressure, which drives the crystal into a “super pressing” state to spontaneously transform into a higher-density liquid phase. Our findings significantly advance fundamental understanding of ultrafast crystal-to-liquid phase transitions, enabling quantitative a priori predictions.
Hydrostatic pressure: A very effective approach to significantly enhance critical current density in granular iron pnictide superconductors
Authors: Shabbir Babar , Wang Xiaolin , Ghorbani S. R. , Shekhar Chandra , Dou Shixue , Srivastava O. N. 
Published: February 2015

AbstractPressure is well known to significantly raise the superconducting transition temperature, Tc, in both iron pnictides and cuprate based superconductors. Little work has been done, however, on how pressure can affect the flux pinning and critical current density in the Fe-based superconductors. Here, we propose to use hydrostatic pressure to significantly enhance flux pinning and Tc in polycrystalline pnictide bulks. We have chosen Sr4V2O6Fe2As2 polycrystalline samples as a case study. We demonstrate that the hydrostatic pressure up to 1.2 GPa can not only significantly increase Tc from 15 K (underdoped) to 22 K, but also significantly enhance the irreversibility field, Hirr, by a factor of 4 at 7 K, as well as the critical current density, Jc, by up to 30 times at both low and high fields. It was found that pressure can induce more point defects, which are mainly responsible for the Jc enhancement. Our findings provide an effective method to significantly enhance Tc, Jc, Hirr and the upper critical field, Hc2, for other families of Fe-based superconductors in the forms of wires/tapes, films and single crystal and polycrystalline bulks.
Spectrally Shaped DP-16QAM Super-Channel Transmission with Multi-Channel Digital Back-Propagation
Authors: Maher Robert , Xu Tianhua , Galdino Lidia , Sato Masaki , Alvarado Alex , Shi Kai , Savory Seb J. , Thomsen Benn C. , Killey Robert I. , Bayvel Polina 
Published: February 2015

AbstractThe achievable transmission capacity of conventional optical fibre communication systems is limited by nonlinear distortions due to the Kerr effect and the difficulty in modulating the optical field to effectively use the available fibre bandwidth. In order to achieve a high information spectral density (ISD), while simultaneously maintaining transmission reach, multi-channel fibre nonlinearity compensation and spectrally efficient data encoding must be utilised. In this work, we use a single coherent super-receiver to simultaneously receive a DP-16QAM super-channel, consisting of seven spectrally shaped 10GBd sub-carriers spaced at the Nyquist frequency. Effective nonlinearity mitigation is achieved using multi-channel digital back-propagation (MC-DBP) and this technique is combined with an optimised forward error correction implementation to demonstrate a record gain in transmission reach of 85%; increasing the maximum transmission distance from 3190 km to 5890 km, with an ISD of 6.60 b/s/Hz. In addition, this report outlines for the first time, the sensitivity of MC-DBP gain to linear transmission line impairments and defines a trade-off between performance and complexity.
Aged insulin granules display reduced microtubule-dependent mobility and are disposed within actin-positive multigranular bodies
Authors: Hoboth Peter , Müller Andreas , Ivanova Anna , Mziaut Hassan , Dehghany Jaber , Sönmez Anke , Lachnit Martina , Meyer-Hermann Michael , Kalaidzidis Yannis , Solimena Michele 
Published: February 2015

SignificanceInsulin is key for control of glucose homeostasis in vertebrates. Insufficient insulin secretion relative to metabolic needs causes diabetes. Pancreatic beta cells store insulin into secretory granules (SGs), which release insulin extracellularly upon fusion with the plasma membrane. SGs exist in different functional pools, with newly generated SGs being preferentially secreted. Here we show that aged SGs display reduced competence for glucose-stimulated microtubule-mediated transport and are disposed within actin-positive multigranular bodies. These data highlight the link between SG age and mobility and thus are relevant for better understanding insulin secretion in health and diabetes.
Matching times of leading and following suggest cooperation through direct reciprocity during V-formation flight in ibis
Authors: Voelkl Bernhard , Portugal Steven J. , Unsöld Markus , Usherwood James R. , Wilson Alan M. , Fritz Johannes 
Published: February 2015

SignificanceCooperation in animals is an enigma because it contravenes the basic notion that evolution favors selfish genes that promote only their own well-being. Bird migration in organized V-shaped or echelon formations constitutes such a cooperation dilemma. We show that juvenile Northern bald ibis (Geronticus eremita) cooperate by taking turns and precisely matching times they spend in the advantageous trailing position and in the disadvantageous front position. This time matching is done on a pairwise level. Furthermore, we found evidence that the animals' propensity to reciprocate in leading has a substantial influence on the size and cohesion of the flight formations. This study shows that direct reciprocation can enable cooperation between animals in a natural context.
Adipogenesis and epicardial adipose tissue: A novel fate of the epicardium induced by mesenchymal transformation and PPARγ activation
Authors: Yamaguchi Yukiko , Cavallero Susana , Patterson Michaela , Shen Hua , Xu Jian , Kumar S. Ram , Sucov Henry M. 
Published: February 2015

Significance
A layer of fat surrounds the heart in most mammals, including humans. The biology of this tissue has been speculated for centuries, but never subjected to experimental analysis because common experimental model species are thought to not have this tissue. In this study, we show that rodents have cardiac fat, albeit in a very specific location in the heart. We implicate the origin of this tissue from the epicardium (the outer epithelium of the heart) and the underlying mechanisms that account for its derivation. By comparing human and mouse epicardial cells, we provide an explanation for the prominent species differences in the presence and amount of cardiac adipose tissue.
Adverse childhood experiences and physiological wear-and-tear in midlife: Findings from the 1958 British birth cohort
Authors: Barboza Solís Cristina , Kelly-Irving Michelle , Fantin Romain , Darnaudéry Muriel , Torrisani Jérôme , Lang Thierry , Delpierre Cyrille 
Published: February 2015

Significance
The role of early life experiences on health is of major concern to research. Recent studies have shown that chronic stress may “get under the skin” to alter human developmental processes and impact later health. Our findings suggest that early negative circumstances during childhood, collected prospectively in a British birth cohort, could be associated with physiological wear-and-tear in midlife as measured by allostatic load. This relationship was largely explained by health behaviors, body mass index, and socioeconomic status in adulthood, but not entirely. These results suggest that a biological link between adverse childhood exposures and adult health may be plausible. Our findings contribute to the development of more adapted public health interventions, both at a societal and individual level.
NADPH oxidase 4 is a critical mediator in Ataxia telangiectasia disease
Authors: Weyemi Urbain , Redon Christophe E. , Aziz Towqir , Choudhuri Rohini , Maeda Daisuke , Parekh Palak R. , Bonner Michael Y. , Arbiser Jack L. , Bonner William M. 
Published: February 2015

Significance
Ataxia telangiectasia (A-T) is a rare, autosomal recessive disorder characterized by progressive cerebellar degeneration. Oxidative stress is one cause of the symptoms of A-T disease. We report that inactivation of NADPH oxidase 4 (NOX4) reduced ROS, oxidative DNA damage, DNA double-strand breaks and replicative senescence in A-T primary cells. Analyses of A-T patients revealed elevated levels of NOX4 in the cerebellum that also correlated with increased levels of DNA damage and apoptosis. These observations were substantiated by the absence of abnormal NOX4 cerebellar expression in mouse models of A-T disease which do not display cerebellar degeneration. However, injecting A-T mice with NOX4 inhibitor decreased their elevated cancer incidence. Therefore, NOX4 appears as a critical mediator in A-T disease.
Absence of knots in known RNA structures
Authors: Micheletti Cristian , Di Stefano Marco , Orland Henri 
Published: February 2015

Significance
Biopolymers have arguably evolved to be free of entanglements that could impair their folding or function. This selection mechanism is, however, opposed by the general physical principle that sufficiently long and densely packed polymers are inevitably entangled. This competition is nowadays well-documented for proteins and viral DNA, which can be knotted and yet, functionally viable. By contrast, the incidence of knots in RNA is still virtually unexplored. To fill this gap, we topologically profiled thousands of RNA structures, finding only three deeply knotted chains. Comparison with higher-resolution homologs further suggests that these instances may actually be unknotted as well. The practical absence of knots indicates that thermodynamic or kinetic mechanisms are likely at play for minimizing the entanglement of biologically viable structured RNAs.
The spontaneous emergence of conventions: An experimental study of cultural evolution
Authors: Centola Damon , Baronchelli Andrea 
Published: February 2015

Significance
Social conventions shape every aspect of our lives, from how we greet each other to the languages we speak. Yet their origins have been a topic of theoretical speculation since the time of Aristotle. Most approaches assume that institutions are necessary to organize large populations, but the simplest explanation is that universally accepted conventions are the unintended consequence of individuals’ efforts to coordinate locally with one another. Although this hypothesis is compelling, it lacks conclusive empirical support. Here, we present results from controlled experiments demonstrating that changes in network connectivity can cause global social conventions to spontaneously emerge from local interactions, even though people have no knowledge about the population, or that they are coordinating at a global scale.
Rate of language evolution is affected by population size
Authors: Bromham Lindell , Hua Xia , Fitzpatrick Thomas G. , Greenhill Simon J. 
Published: February 2015

Significance
Evolutionary methods are increasingly being applied to investigating linguistic change. But does language change conform to the predictions of evolutionary theory? Here, we use data from closely related pairs of languages to show that a key prediction of evolutionary theory is met: rates of gain of new words are higher in larger populations whereas rates of word loss are greater in small populations. Our analysis provides, to our knowledge, the first statistically robust evidence of an influence of population size on rate of language change. These results demonstrate the potential for demographic factors to influence language evolution.
Dynamic phototuning of 3D hydrogel stiffness
Authors: Stowers Ryan S. , Allen Shane C. , Suggs Laura J. 
Published: February 2015

Significance
Extracellular matrix (ECM) stiffness is an influential factor in many biological processes. Temporal changes in ECM stiffness are observed in cancer, cardiovascular disease, and wound healing, and are likely involved in disease progression. However, no cell culture systems exist to appropriately model temporal changes in ECM stiffness to determine the biological relevance and mechanisms involved. Here, we present a 3D hydrogel cell culture system in which the matrix stiffness can be tuned by light. Our approach offers both spatial and temporal control of stiffness, is compatible with cell culture, and can be used transdermally for in vivo applications. This system is amenable to many applications to investigate the influence of matrix stiffness on cell behavior and fate.
Thioredoxin, a master regulator of the tricarboxylic acid cycle in plant mitochondria
Authors: Daloso Danilo M. , Müller Karolin , Obata Toshihiro , Florian Alexandra , Tohge Takayuki , Bottcher Alexandra , Riondet Christophe , Bariat Laetitia , Carrari Fernando , Nunes-Nesi Adriano , Buchanan Bob B. , Reichheld Jean-Philippe , Araújo Wagner L. , Fernie Alisdair R. 
Published: February 2015

SignificanceThe present work extends redox-based change in enzyme activity to the TCA cycle of plant mitochondria. Thioredoxin (TRX) was found to regulate the activity of enzymes of the mitochondrial cycle (succinate dehydrogenase and fumarase) and of an enzyme associated with it (ATP-citrate lyase) by modulating thiol redox status. A combination of experiments based on mutant and carbon isotope labeling analyses provides evidence that flux through this pathway is coordinately modulated by TRX at the enzyme level of both mitochondria and cytosol. The results provide in vivo confirmation of earlier in vitro results and further show that mitochondria resemble plastids in using TRX and redox status to regulate the main carbon flux pathway of the organelle.
Spoken Grammar: Where Are We and Where Are We Going?
Authors: Carter Ronald , McCarthy Michael 
Published: February 2015

AbstractThis article synthesises progress made in the description of spoken (especially conversational) grammar over the 20 years since the authors published a paper in this journal arguing for a re-thinking of grammatical description and pedagogy based on spoken corpus evidence. We begin with a glance back at the 16th century and the teaching of Latin grammar in England, with its emphasis on speaking the target language. Later grammars were dominated by written standards, a situation that persisted till the 20th century, when recording technology and spoken corpora enabled new insights into the grammar of everyday speaking. We highlight those insights which especially challenge grammars derived only or mainly from written sources. We evidence the view that conversational grammar is non-sentence-based, co-constructed and highly interactive, and that it poses questions concerning metalanguage. We briefly review debates concerning spoken grammar and ELT/ESL pedagogy. We then consider 21st-century Internet technologies and e-communication, and implications for the spoken/written grammar distinction, arguing that description and pedagogy may need to undergo further re-thinking in light of the multi-modality which characterises e-language.
Message from the ISCB: ISCB Ebola award for important future research on the computational biology of Ebola virus
Authors: Karp Peter D. , Berger Bonnie , Kovats Diane , Lengauer Thomas , Linial Michal , Sabeti Pardis , Hide Winston , Rost Burkhard 
Published: February 2015

Abstract
Speed is of the essence in combating Ebola; thus, computational approaches should form a significant component of Ebola research. As for the development of any modern drug, computational biology is uniquely positioned to contribute through comparative analysis of the genome sequences of Ebola strains and three-dimensional protein modeling. Other computational approaches to Ebola may include large-scale docking studies of Ebola proteins with human proteins and with small-molecule libraries, computational modeling of the spread of the virus, computational mining of the Ebola literature and creation of a curated Ebola database. Taken together, such computational efforts could significantly accelerate traditional scientific approaches. In recognition of the need for important and immediate solutions from the field of computational biology against Ebola, the International Society for Computational Biology (ISCB) announces a prize for an important computational advance in fighting the Ebola virus. ISCB will confer the ISCB Fight against Ebola Award, along with a prize of US$2000, at its July 2016 annual meeting (ISCB Intelligent Systems for Molecular Biology 2016, Orlando, FL).
Contact: dkovats@iscb.org or rost@in.tum.de
Starcode: sequence clustering based on all-pairs search
Authors: Zorita Eduard , Cuscó Pol , Filion Guillaume J. 
Published: February 2015

Abstract
Motivation: The increasing throughput of sequencing technologies offers new applications and challenges for computational biology. In many of those applications, sequencing errors need to be corrected. This is particularly important when sequencing reads from an unknown reference such as random DNA barcodes. In this case, error correction can be done by performing a pairwise comparison of all the barcodes, which is a computationally complex problem.
Results: Here, we address this challenge and describe an exact algorithm to determine which pairs of sequences lie within a given Levenshtein distance. For error correction or redundancy reduction purposes, matched pairs are then merged into clusters of similar sequences. The efficiency of starcode is attributable to the poucet search, a novel implementation of the Needleman–Wunsch algorithm performed on the nodes of a trie. On the task of matching random barcodes, starcode outperforms sequence clustering algorithms in both speed and precision.
Availability and implementation: The C source code is available at http://github.com/gui11aume/starcode.
Contact: guillaume.filion@gmail.com
Learning HMMs for nucleotide sequences from amino acid alignments
Authors: Fischer Carlos N. , Carareto Claudia M. A. , dos Santos Renato A. C. , Cerri Ricardo , Costa Eduardo , Schietgat Leander , Vens Celine 
Published: February 2015

Abstract
Profile hidden Markov models (profile HMMs) are known to efficiently predict whether an amino acid (AA) sequence belongs to a specific protein family. Profile HMMs can also be used to search for protein domains in genome sequences. In this case, HMMs are typically learned from AA sequences and then used to search on the six-frame translation of nucleotide (NT) sequences. However, this approach demands additional processing of the original data and search results. Here, we propose an alternative and more direct method which converts an AA alignment into an NT one, after which an NT-based HMM is trained to be applied directly on a genome.
Contact : carlos@rc.unesp.br
Supplementary information: Supplementary data are available at Bioinformatics online.