bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polarization signaling in swordtails alters female mate preference
Authors: Calabrese Gina M. , Brady Parrish C. , Gruev Viktor , Cummings Molly E. 
Published: September 2014

Significance
Polarization, the alignment of light waves in a plane, is a property that many nonhuman animals can detect. Polarized body patterning on some animals has prompted research into polarization as a signaling modality, but experimental evidence is lacking. We found evidence for sexual selection on polarization ornamentation in a swordtail fish: sexually dimorphic polarization patterning with higher polarization contrast in males and females exhibiting a mate preference for this ornamentation. We manipulated male polarization properties in a mate choice experiment and found that females prefer males with polarized over depolarized ornamentation and that males may increase polarization contrast in social environments. Polarization signaling may provide enhanced display detection, along with privatized communication, due to the directional component of polarized light.
Preferential infection of human Ad5-specific CD4 T cells by HIV in Ad5 naturally exposed and recombinant Ad5-HIV vaccinated individuals
Authors: Hu Haitao , Eller Michael A. , Zafar Shah , Zhou Yu , Gu Mengnan , Wei Zhi , Currier Jeffrey R. , Marovich Mary A. , Kibuuka Hannah N. , Bailer Robert T. , Koup Richard A. , Robb Merlin L. , Michael Nelson L. , Kim Jerome H. , Ratto-Kim Silvia 
Published: September 2014

Significance
Efforts to develop an efficacious HIV vaccine have been unsuccessful to date. Efficacy trials have reported that recombinant Ad5 (rAd5)-HIV vaccines were not efficacious and unexpectedly associated with excess HIV infection in vaccine recipients. Understanding the underlying mechanisms is urgent and will further HIV vaccine design. By comparing human CD4 T cells specific to Ad5 and CMV, we report that natural exposure- or vaccine-induced Ad5-specific CD4 T cells are highly susceptible to HIV compared with CMV-specific CD4 T cells and selectively manifest a Th17-like proinflammatory phenotype. Our findings suggest a potential mechanism for rAd5-associated excess HIV infections in vaccine recipients and highlight that testing HIV susceptibility of vaccine-generated CD4 T cells may have utility before vaccine evaluation in human trials.
Combined fluorescent and electron microscopic imaging unveils the specific properties of two classes of meiotic crossovers
Authors: Anderson Lorinda K. , Lohmiller Leslie D. , Tang Xiaomin , Hammond D. Boyd , Javernick Lauren , Shearer Lindsay , Basu-Roy Sayantani , Martin Olivier C. , Falque Matthieu 
Published: September 2014

Significance
In many eukaryotes, two types of meiotic crossovers (COs) coexist: class I COs that show CO interference and class II COs that do not show interference. Little is known about the separate properties of these two CO pathways or their interaction in wild-type organisms because individual COs cannot be assigned by class using marker segregation. We present an improved cytogenetic approach to identify COs from each class simultaneously on tomato meiotic chromosomes to reveal that the two CO classes have different distributions, with class II COs enriched in short arms and heterochromatin. Although class II CO distributions are consistent with no interference, interference between the two pathways was detected, with suppression of close class I and class II COs.
Complement activation by ligand-driven juxtaposition of discrete pattern recognition complexes
Authors: Degn Søren E. , Kjaer Troels R. , Kidmose Rune T. , Jensen Lisbeth , Hansen Annette G. , Tekin Mustafa , Jensenius Jens C. , Andersen Gregers R. , Thiel Steffen 
Published: September 2014

Significance
A salient feature of the immune system is its ability to discriminate self from nonself. We define the molecular mechanism governing activation of an ancient and central component: the lectin pathway of complement. The basis is the association of two proteases in distinct complexes with at least five pattern recognition molecules. Clustering of these complexes on ligand surfaces allows cross-activation of the proteases, which subsequently activate downstream factors to initiate a proteolytic cascade. This is conceptually similar to signaling by cellular receptors and could be viewed as cellular signaling turned inside out. Different pattern recognition complexes “talk to each other” to coordinate immune activation, which may impart differential activation based on recognition of simple vs. complex ligand patterns.
Genetic erosion in maize’s center of origin
Authors: Dyer George A. , López-Feldman Alejandro , Yúnez-Naude Antonio , Taylor J. Edward 
Published: September 2014

Significance
Unlike germplasm banks, on-farm conservation allows crops to evolve continuously in response to changing conditions. Agricultural adaptation to climate change, emerging pests, and diseases thus depends on conserving crop genetic diversity in situ. However, increasing awareness of these issues has not translated into effective conservation policies. We find that previous assessments of on-farm maize diversity in Mexico are flawed and conceal widespread genetic erosion that could thwart current food security strategies for climate adaptation. Unable to mitigate declining yields by recourse to diversity, farmers might abandon agriculture, leading to a vicious cycle of yield and diversity losses. A reassessment of the conservation status in other centers of crop diversity is similarly urgent but could take a decade given data requirements.
Structural basis for the mutual antagonism of cAMP and TRIP8b in regulating HCN channel function
Authors: Saponaro Andrea , Pauleta Sofia R. , Cantini Francesca , Matzapetakis Manolis , Hammann Christian , Donadoni Chiara , Hu Lei , Thiel Gerhard , Banci Lucia , Santoro Bina , Moroni Anna 
Published: September 2014

Significance
cAMP regulation of ion channels controls higher brain functions, such as sleep, memory, and cognition. Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are activated by the direct binding of cAMP to their cytoplasmic tail and inhibited by the neuronal β-subunit tetratricopeptide repeat-containing Rab8b interacting protein (TRIP8b), which prevents cAMP binding. Understanding the molecular mechanisms of regulation of this family of ion channels is critical because it pertains to the physiological processes and diseases associated with dysfunctions in the HCN current. Here, we explain the dual regulatory system of HCN2 channels in atomic detail. cAMP and TRIP8b do not compete for the same binding site on the HCN2 cytoplasmic tail; rather, they exert their mutual competition by promoting and stabilizing two different conformational states of the protein.
Primed 3D injectable microniches enabling low-dosage cell therapy for critical limb ischemia
Authors: Li Yaqian , Liu Wei , Liu Fei , Zeng Yang , Zuo Simin , Feng Siyu , Qi Chunxiao , Wang Bingjie , Yan Xiaojun , Khademhosseini Ali , Bai Jing , Du Yanan 
Published: September 2014

Significance
Optimal cell delivery strategies are in urgent need to enhance the specificity, efficacy, and reproducibility of cell therapy leading to minimized cell dosage and side effects. Here, we addressed this unmet need by developing injectable 3D microscale cellular niches (microniches) based on biocompatible and biodegradable gelatin microcryogels. Dramatic improvement in cell retention, survival, and therapeutic effects enabled by the primed 3D microniches was demonstrated in treatment of critical limb ischemia (CLI) in mouse models compared with the free cell-based therapy. To the best of our knowledge, this is the first convincing demonstration of injectable and primed cell delivery strategy realizing superior therapeutic efficacy with the lowest cell dosage for treating CLI in mouse model.
A rock engraving made by Neanderthals in Gibraltar
Authors: Rodríguez-Vidal Joaquín , d’Errico Francesco , Pacheco Francisco Giles , Blasco Ruth , Rosell Jordi , Jennings Richard P. , Queffelec Alain , Finlayson Geraldine , Fa Darren A. , Gutiérrez López José María , Carrión José S. , Negro Juan José , Finlayson Stewart , Cáceres Luís M. , Bernal Marco A. , Fernández Jiménez Santiago , Finlayson Clive 
Published: September 2014

Significance
The production of purposely made painted or engraved designs on cave walls is recognized as a major cognitive step in human evolution, considered exclusive to modern humans. Here we present the first known example of an abstract pattern engraved by Neanderthals, from Gorham’s Cave in Gibraltar. It consists of a deeply impressed cross-hatching carved into the bedrock of the cave older than 39 cal kyr. The engraving was made before the accumulation of Mousterian layer IV. Most of the lines composing the design were made by repeatedly and carefully passing a pointed lithic tool into the grooves, excluding the possibility of an unintentional or utilitarian origin. This discovery demonstrates the Neanderthals’ capacity for abstract thought and expression.
C-terminal domain small phosphatase 1 and MAP kinase reciprocally control REST stability and neuronal differentiation
Authors: Nesti Edmund , Corson Glen M. , McCleskey Maxwell , Oyer Jon A. , Mandel Gail 
Published: September 2014

Significance
A fundamental process involved in nervous-system formation is the conversion of stem cells into mature neurons. A key transcription factor in this regard is repressor element 1 (RE1) silencing transcription factor (REST), which suppresses the neuronal phenotype in stem cells and must be eliminated to promote the expression of neuronal genes in postmitotic neurons. We find that a phosphatase, C-terminal domain small phosphatase 1, coexpressed with REST in stem cells, dephosphorylates a newly identified site on REST and promotes REST stability. Conversely, we find that epidermal growth factor, an extracellular signaling molecule that promotes neurogenesis, induces phosphorylation by extracellular signal-regulated (ERK/MAP) kinases at the same site on REST. The phosphorylation facilitates elimination of REST during the transition to neurons. Our mechanism helps explain the timing of REST degradation during neuronal differentiation.
Single cell sequencing reveals low levels of aneuploidy across mammalian tissues
Authors: Knouse Kristin A. , Wu Jie , Whittaker Charles A. , Amon Angelika 
Published: September 2014

Significance
Aneuploidy refers to the gain or loss of individual chromosomes within a cell. Typically, aneuploidy is associated with detrimental consequences at both the cellular and organismal levels. However, reports of high levels of aneuploidy in the brain and liver suggested that aneuploidy might play a positive role in these organs. Here we use single cell sequencing to determine the prevalence of aneuploidy in somatic tissues. We find that aneuploidy is a rare occurrence in the liver and brain and is no more prevalent in these tissues than in skin. Our results demonstrate high karyotypic stability in somatic tissues, arguing against a role for aneuploidy in organ function and reinforcing its adverse effects at the cellular and organismal levels.
Valuation of Hospital Bed-Days Released by Infection Control Programs: A Comparison of Methods
Authors: Stewardson Andrew J. , Harbarth Stephan , Graves Nicholas ,   on behalf of the TIMBER Study Group
Published: September 2014

We performed a contingent valuation survey to elicit the opportunity cost of bed-days consumed by healthcare-associated infections in 11 European hospitals. The opportunity cost of a bed-day was significantly lower than the accounting cost; median values were €72 and €929, respectively (P < .001). Accounting methods overestimate the opportunity cost of bed-days.Infect Control Hosp Epidemiol 2014;35(10):1294–1297
Over-representation of correlation analysis (ORCA): a method for identifying associations between variable sets
Authors: Pomyen Yotsawat , Segura Marcelo , Ebbels Timothy M. D. , Keun Hector C. 
Published: September 2014

AbstractMotivation: Often during the analysis of biological data, it is of importance to interpret the correlation structure that exists between variables. Such correlations may reveal patterns of co-regulation that are indicative of biochemical pathways or common mechanisms of response to a related set of treatments. However, analyses of correlations are usually conducted by either subjective interpretation of the univariate covariance matrix or by applying multivariate modeling techniques, which do not take prior biological knowledge into account. Over-representation analysis (ORA) is a simple method for objectively deciding whether a set of variables of known or suspected biological relevance, such as a gene set or pathway, is more prevalent in a set of variables of interest than we expect by chance. However, ORA is usually applied to a set of variables differentiating a single experimental variable and does not take into account correlations.Results: Over-representation of correlation analysis (ORCA) is a novel combination of ORA and correlation analysis that provides a means to test whether more associations exist between two specific groups of variables than expected by chance. The method is exemplified by application to drug sensitivity and microRNA expression data from a panel of cancer cell lines (NCI60). ORCA highlighted a previously reported correlation between sensitivity to alkylating anticancer agents and topoisomerase inhibitors. We also used this approach to validate microRNA clusters predicted by mRNA correlations. These observations suggest that ORCA has the potential to reveal novel insights from these data, which are not readily apparent using classical ORA.Availability and implementation: The R code of the method is available at https://github.com/ORCABioinfo/ORCAcodeSupplementary information: Supplementary data are available at Bioinformatics online.
CCharPPI web server: computational characterization of protein–protein interactions from structure
Authors: Moal Iain H. , Jiménez-García Brian , Fernández-Recio Juan 
Published: September 2014

Abstract
Summary: The atomic structures of protein–protein interactions are central to understanding their role in biological systems, and a wide variety of biophysical functions and potentials have been developed for their characterization and the construction of predictive models. These tools are scattered across a multitude of stand-alone programs, and are often available only as model parameters requiring reimplementation. This acts as a significant barrier to their widespread adoption. CCharPPI integrates many of these tools into a single web server. It calculates up to 108 parameters, including models of electrostatics, desolvation and hydrogen bonding, as well as interface packing and complementarity scores, empirical potentials at various resolutions, docking potentials and composite scoring functions.
Availability and implementation: The server does not require registration by the user and is freely available for non-commercial academic use at http://life.bsc.es/pid/ccharppi
Contact: juanf@bsc.com
Risk assessment of the environmental impact of Norwegian Atlantic salmon farming
Authors: Taranger Geir Lasse , Karlsen Ørjan , Bannister Raymond John , Glover Kevin Alan , Husa Vivian , Karlsbakk Egil , Kvamme Bjørn Olav , Boxaspen Karin Kroon , Bjørn Pål Arne , Finstad Bengt , Madhun Abdullah Sami , Morton H. Craig , Svåsand Terje 
Published: September 2014

Abstract
Norwegian aquaculture has grown from its pioneering days in the 1970s to be a major industry. It is primarily based on culturing Atlantic salmon and rainbow trout and has the potential to influence the surrounding environment and wild populations. To evaluate these potential hazards, the Institute of Marine Research initiated a risk assessment of Norwegian salmon farming in 2011. This assessment has been repeated annually since. Here, we describe the background, methods and limitations of the risk assessment for the following hazards: genetic introgression of farmed salmon in wild populations, regulatory effects of salmon lice and viral diseases on wild salmonid populations, local and regional impact of nutrients and organic load. The main findings are as follows: (i) 21 of the 34 wild salmon populations investigated indicated moderate-to-high risk for genetic introgression from farmed escaped salmon. (ii) of 109 stations investigated along the Norwegian coast for salmon lice infection, 27 indicated moderate-to-high likelihood of mortality for salmon smolts while 67 stations indicated moderate-to-high mortality of wild sea trout. (iii) Viral disease outbreaks (pancreas disease, infectious pancreatic necrosis, heart and skeletal muscle inflammation, and cardiomyopathy syndrome) in Norwegian salmon farming suggest extensive release of viruses in many areas. However, screening of wild salmonids revealed low to very low prevalence of the causal viruses. (iv) From ∼500 yearly investigations of local organic loading under fish farms, only 2% of them displayed unacceptable conditions in 2013. The risk of eutrophication and organic load beyond the production area of the farm is considered low. Despite several limitations, especially limited monitoring data, this work represents one of the world’s first risk assessment of aquaculture. This has provided the Norwegian government with the basis upon which to take decisions for further development of the Norwegian aquaculture industry.
Evaluation of the Functionality of Five Different Soybean Proteins in Hot‐Press Wheat Flour Tortillas
Authors: Perez‐Carrillo Esther , Chew‐Guevara Ana A. , Heredia‐Olea Erick , Chuck‐Hernández Cristina , Serna‐Saldivar Sergio O. 
Published: September 2014

ABSTRACTFive different soybean protein sources were added to wheat flour to increase the protein content by 15–25%, and the resulting composite flours were optimally processed into hot‐press tortillas in a pilot plant. The rheological properties of composite flours were evaluated with the farinograph, alveograph, and other wheat quality tests. Tortilla‐making qualities of the control and soybean‐fortified flours were evaluated during dough handling, hot pressing, and baking. The resulting tortillas were tested in terms of yield, physical and chemical parameters, sensory properties, color, and objective and subjective texture. The soybean‐fortified tortillas had increased yields because of the higher dough water absorption and enhanced essential amino acid scores. Among the five different soybean proteins, the defatted soybean flour (SBM1) with the lowest fat absorption index and protein dispersibility index (PDI) and the soybean concentrate produced the best fortified tortillas. The protein meals with high PDI and relatively lower water absorption index (SBM3 and SBM4) produced sticky doughs, lower alveograph P/L values, and defective tortillas. All soybean proteins produced higher yields of tortillas with an enhanced protein quality and amount of dietary fiber.
Modeling End‐Use Quality in U.S. Soft Wheat Germplasm
Authors: Kiszonas Alecia M. , Fuerst E. Patrick , Morris Craig F. 
Published: September 2014

ABSTRACTEnd‐use quality in soft wheat (Triticum aestivum L.) can be assessed by a wide array of measurements, generally categorized into grain, milling, and baking characteristics. Samples were obtained from four U.S. regional nurseries. Selected parameters included test weight, kernel hardness, kernel size, kernel diameter, wheat protein, polyphenol oxidase activity, flour yield, break flour yield, flour ash content, milling score, flour protein content, flour SDS sedimentation volume, flour swelling volume, Rapid Visco Analyzer peak paste viscosity, solvent retention capacity (SRC) parameters, total and water‐extractable arabinoxylan (TAX and WEAX, respectively), and cookie diameter. The objectives were to model cookie diameter and lactic acid SRC as well as to compare exceptionally performing varieties for each quality parameter. Cookie diameter and lactic acid SRC were modeled by using multiple regression analyses and all of the aforementioned quality parameters. Cookie diameter was positively associated with peak paste viscosity and was negatively associated with or modeled by kernel hardness, flour protein content, sodium carbonate SRC, lactic acid SRC, and water SRC. Lactic acid SRC was positively modeled by break flour yield, milling score, flour SDS sedimentation volume, and sucrose SRC and was negatively modeled by flour protein content. Exceptionally high‐ and low‐performing varieties were selected on the basis of their responses to the aforementioned characteristics in each nursery. High‐ and low‐performing varieties exhibited notably wide variation in kernel hardness, break flour yield, milling score, sodium carbonate SRC, sucrose SRC, water SRC, TAX content, and cookie diameter. This high level of variation in variety performance can facilitate selection for improved quality based on exceptional performance in one or more of these traits. The models described allow a more focused approach toward predicting soft wheat quality.
Observational Outcome Results Following a Randomized Controlled Trial of Early Amino Acid Administration in Preterm Infants
Authors: van den Akker Chris H.P. , te Braake Frans W.J. , Weisglas‐Kuperus Nynke , van Goudoever Johannes B. 
Published: September 2014

ABSTRACTObjective:Several reports have investigated amino acid administration in premature infants during the early postnatal phase. Most of these previous studies, however, have only evaluated short‐term in‐hospital outcomes. Our aim was to describe long‐term outcomes in premature infants previously subjected to different nutritional regimens in a randomized controlled trial. The primary outcome was survival without major disabilities, and the secondary outcomes included anthropometry and mental development.Methods:Infants born <32 weeks' gestation and <1500 g were randomized to receive glucose (n = 69) or glucose with 2.4 g · kg−1 · day−1 amino acids (n = 63) from birth. From postnatal day 3 onward, the nutritional intake was similar. At 2 years of corrected age, the surviving infants were assessed for neurodevelopmental outcome and anthropometry.Results:Ninety‐seven percent of the surviving infants were examined at follow‐up, with no overall effect on survival without major disabilities. Boys, however, had a normal outcome significantly more often if amino acids were administered from birth onward (crude odds ratio 3.8, 95% confidence interval 1.3–11.4) and following adjustment for confounders (odds ratio 6.2, 95% confidence interval 1.0–38.0). The secondary outcomes exhibited no differences in anthropometric data. The mental developmental index was lower in the small number of girls who survived without major disabilities following the early administration of amino acids.Conclusions:In this hypothesis‐generating outcome study, premature boys, but not girls, benefited from amino acid administration directly following birth. The observed lower mental developmental index in a subgroup of girls, however, warrants further studies.