bluuebunny/crossref_metadata_2025_split huggingface dataset:
Why cooperation is not running away
Authors: Geoffroy Félix , Baumard Nicolas , André Jean-Baptiste 
Published: May 2018

AbstractA growing number of experimental and theoretical studies show the importance of partner choice as a mechanism to promote the evolution of cooperation, especially in humans. In this paper, we focus on the question of the precise quantitative level of cooperation that should evolve under this mechanism. When individuals compete to be chosen by others, their level of investment in cooperation evolves towards higher values, a process called competitive altruism, or runaway cooperation. Using a classic adaptive dynamics model, we first show that, when the cost of changing partner is low, this runaway process can lead to a profitless escalation of cooperation. In the extreme, when partner choice is entirely frictionless, cooperation even increases up to a level where its cost entirely cancels out its benefit. That is, at evolutionary equilibrium, individuals gain the same payoff than if they had not cooperated at all. Second, importing models from matching theory in economics we, however, show that, when individuals can plastically modulate their choosiness in function of their own cooperation level, partner choice stops being a runaway competition to outbid others, and becomes a competition to form the most optimal partnerships. In this case, when the cost of changing partner tends toward zero partner choice leads to the evolution of the socially optimum level of cooperation. This last result could explain the observation that human cooperation seems to be often constrained by considerations of social efficiency.
Microbial Biomarkers of Intestinal Barrier Maturation in Preterm Infants
Authors: Ma Bing , McComb Elias , Gajer Pawel , Yang Hongqiu , Humphrys Mike , Okogbule-Wonodi Adora C. , Fasano Alessio , Ravel Jacques , Viscardi Rose M 
Published: May 2018

ABSTRACTIntestinal barrier immaturity, or “leaky gut,” is the proximate cause of susceptibility to necrotizing enterocolitis in preterm neonates. However, the impact of intestinal microbiota development on intestinal mucosal barrier maturation has not been evaluated in this population. In this study, we investigated a longitudinally sampled cohort of 38 preterm infants monitored for intestinal permeability (IP) and fecal microbiota during the first two weeks of life. Rapid decrease in IP indicating intestinal barrier function maturation correlated with significant increase in community diversity. In particular, members of the Clostridiales and Bifidobacterium were highly transcriptionally active, and progressively increasing abundance in Clostridiales was significantly associated with decreased gut permeability. Further, neonatal factors previously identified to promote intestinal barrier maturation, including early exclusive breastmilk feeding and low antibiotic exposure, favor the early colonization of the gut microbiota by members of the Clostridiales, which altogether are associated with improved intestinal barrier function in preterm infants.
Link Between Short tandem Repeats and Translation Initiation Site Selection
Authors: Arabfard M , Kavousi K , Delbari A , Ohadi M 
Published: May 2018

AbstractRecent work in yeast and humans suggest that evolutionary divergence incis-regulatory sequences impact translation initiation sites (TISs).Cis-elements can also affect the efficacy and amount of protein synthesis. Despite their vast biological implication, the landscape and relevance of short tandem repeats (STRs)/microsatellites to the human protein-coding gene TISs remain largely unknown. Here we characterized the STR distribution at the 120 bp cDNA sequence upstream of all annotated human protein-coding gene TISs based on the Ensembl database. Furthermore, we performed a comparative genomics study of all annotated orthologous TIS-flanking sequences across 47 vertebrate species (755,956 transcripts), aimed at identifying human-specific STRs in this interval. We also hypothesized that STRs may be used as genetic codes for the initiation of translation. The initial five amino acid sequences (excluding the initial methionine) that were flanked by STRs in human were BLASTed against the initial orthologous five amino acids in other vertebrate species (2,025,817 pair-wise TIS comparisons) in order to compare the number of events in which human-specific and non-specific STRs occurred with homologous and non-homologous TISs (i.e. ≥50% and <50% similarity of the five amino acids). We characterized human-specific STRs and a bias of this compartment in comparison to the overall (human-specific and non-specific) distribution of STRs (Mann Whitney p=1.4 × 10−11). We also found significant enrichment of non-homologous TISs flanked by human-specific STRs (p<0.00001). In conclusion, our data indicate a link between STRs and TIS selection, which is supported by differential evolution of the human-specific STRs in the TIS upstream flanking sequence.AbbreviationscDNAComplementary DNACDSCoding DNA sequenceSTRShort Tandem RepeatTISTranslation Initiation SiteTSSTranscription Start Site
Increased excitation-inhibition ratio stabilizes synapse and circuit excitability in four autism mouse models
Authors: Antoine Michelle W. , Schnepel Philipp , Langberg Tomer , Feldman Daniel E. 
Published: May 2018

SummaryDistinct genetic forms of autism are hypothesized to share a common increase in excitation-inhibition (E-I) ratio in cerebral cortex, causing hyperexcitability and excess spiking. We provide the first systematic test of this hypothesis across 4 mouse models (Fmr1−/y,Cntnap2−/-,16p11.2del/+,Tsc2+/-), focusing on somatosensory cortex. All autism mutants showed reduced feedforward inhibition in layer 2/3 coupled with more modest, variable reductions in feedforward excitation, driving a common increase in E-I conductance ratio. Despite this, feedforward spiking, synaptic depolarization and spontaneous spiking were essentially normal. Modeling revealed that E and I conductance changes in each mutant were quantitatively matched to yield stable, not increased, synaptic depolarization for cells near spike threshold. Correspondingly, whisker-evoked spiking was not increasedin vivo, despite detectably reduced inhibition. Thus, elevated E-I ratio is a common circuit phenotype, but appears to reflect homeostatic stabilization of synaptic drive, rather than driving network hyperexcitability in autism.
Functional degradation: a mechanism of NLRP1 inflammasome activation by diverse pathogen enzymes
Authors: Sandstrom Andrew , Mitchell Patrick S. , Goers Lisa , Mu Edward W. , Lesser Cammie F. , Vance Russell E. 
Published: May 2018

AbstractInflammasomes are multi-protein platforms that initiate innate immunity by recruitment and activation of Caspase-1. The NLRP1B inflammasome is activated upon direct cleavage by the anthrax lethal toxin protease. However, the mechanism by which cleavage results in NLRP1B activation is unknown. Here we find that cleavage results in proteasome-mediated degradation of the N-terminal domains of NLRP1B, liberating a C-terminal fragment that is a potent Caspase-1 activator. Proteasome-mediated degradation of NLRP1B is both necessary and sufficient for NLRP1B activation. Consistent with our new ‘functional degradation’ model, we identify IpaH7.8, aShigella flexneriubiquitin ligase secreted effector, as an enzyme that induces NLRP1B degradation and activation. Our results provide a unified mechanism for NLRP1B activation by diverse pathogen-encoded enzymatic activities.One Sentence SummaryTwo distinct pathogen enzymes activate an innate immune sensor called NLRP1B by a mechanism that requires proteasome-mediated degradation of NLRP1B.
Color depth MIP mask search: a new tool to expedite Split-GAL4 creation
Authors: Otsuna Hideo , Ito Masayoshi , Kawase Takashi 
Published: May 2018

AbstractThe GAL4-UAS system has proven its versatility in studying the function and expression patterns of neurons theDrosophilacentral nervous system. Although the GAL4 system has been used for 25 years, recent genetic intersectional tools have enabled genetic targeting of very small numbers of neurons aiding in the understanding of their function. This split-GAL4 system is extremely powerful for studying neuronal morphology and the neural basis of animal behavior. However, choosing lines to intersect that have overlapping patterns restricted to one to a few neurons has been cumbersome. This challenge is now growing as the collections of GAL4 driver lines has increased. Here we present a new method and software plug-in for Fiji to dramatically improve the speed of querying large databases of potential lines to intersect and aid in the split-GAL4 creation. We also provide pre-computed datasets for the Janelia GAL4 (5,738 lines) and VT GAL4 (7,429 lines) of the Drosophila central nervous system (CNS). The tool reduced our split-GAL4 creation effort dramatically.
AnIn SilicoModel of DNA Repair for Investigation of Mechanisms in Non-Homologous End Joining
Authors: Warmenhoven John W. , Henthorn Nicholas T. , Sotiropoulos Marios , Korabel Nickolay , Fedotov Sergei , Mackay Ranald I. , Kirkby Karen J. , Merchant Michael J. 
Published: May 2018

AbstractIn human cells, non-homologous end joining is the preferred process to repair radiation induced DNA double strand breaks. The complex nature of such biological systems involves many individual actions that combine to produce an overall behaviour. As such, experimentally determining the mechanisms involved, their individual roles, and how they interact is challenging. An in silico approach to radiobiology is uniquely suited for detailed exploration of these complex interactions and the unknown effects of specific mechanisms on overall behaviour. We detail the construction of a mechanistic model by combination of several, experimentally supported, hypothesised mechanisms. Compatibility of these mechanisms was tested by fitting to results reported in the literature. To avoid over fitting, individual mechanisms within this pathway were sequentially fitted. We demonstrate that using this approach the model is capable of reproducing published protein kinetics and overall repair trends. This process highlighted specific biological mechanisms which are not clearly defined experimentally, and showed that the assumed motion of individual double strand break ends plays a crucial role in determining overall system behaviour.
Genetic basis of variation in heat and ethanol tolerance in Saccharomyces cerevisiae
Authors: Riles Linda , Fay Justin C. 
Published: May 2018

ABSTRACTSaccharomyces cerevisiae has the capability of fermenting sugar to produce concentrations of ethanol that are toxic to most organisms. Other Saccharomyces species also have a strong fermentative capacity, but some are specialized to low temperatures, whereas S. cerevisiae is the most thermotolerant. Although S. cerevisiae has been extensively used to study the genetic basis of ethanol tolerance, much less is known about temperature dependent ethanol tolerance. In this study, we examined the genetic basis of ethanol tolerance at high temperature among strains of S. cerevisiae. We identified two amino acid polymorphisms in SEC24 that cause strong sensitivity to ethanol at high temperature and more limited sensitivity to temperature in the absence of ethanol. We also identified a single amino acid polymorphism in PSD1 that causes sensitivity to high temperature in a strain dependent fashion. The genes we identified provide further insight into genetic variation in ethanol and temperature tolerance and the interdependent nature of these two traits in S. cerevisiae.
Genetic Dissection of Haploid Male Fertility in Maize (Zea mays L.)
Authors: Yang Jiwei , Li Haochuan , Qu Yanzhi , Chen Qiong , Tang Jihua , lübberstedt Thomas , Liu Zonghua 
Published: May 2018

AbstractHaploid genome doubling is a key limiting step of haploid breeding in maize. Spontaneous restoration of haploid male fertility (HMF) provides a method by which costs can be saved and which does not require the use of toxic chemicals, in contrast to the artificial doubling process. To reveal the genetic basis of HMF, haploids were obtained from the offspring of 285 F2:3 families, derived from the cross Zheng58× K22. The F2:3 families were used as female donor and YHI-1 as the male inducer line. The rates of HMF from each family line were evaluated at two field sites over two planting seasons. Quantitative trait loci (QTL) for HMF were identified using a genetic linkage map containing 157 simple sequence repeat (SSR) markers. QTL for HMF displayed incomplete dominance. Transgressive segregation of haploids from F2:3 families was observed relative to haploids derived from the two parents of the mapping population. A total of nine QTL were detected, which were distributed on chromosomes 1, 3, 4, 7, and 8. Three QTL, qHMF3b, qHMF7a, and qHMF7b were detected in both locations, respectively. In our mapping population, HMF was controlled by three major QTL. These QTL could be useful to predict the ability of spontaneous haploid genome doubling in related breeding materials, and to accelerate the haploid breeding process by introgression or aggregation of those QTL.
The Effect of Berberine on the Transcriptome and Proteome ofE. coli
Authors: Shilei Zhang , Ze Jia , Xianghe Zhai , Chunguang Wang , Tie Zhang 
Published: May 2018

AbstractBerberine is commonly used to treat diarrhea in China, and the antibacterial properties of berberine have been confirmed. High-throughput sequencing technology was used to explore the changes induced inE. coliby berberine. After treatment with berberine, the expression of RstA and YbjG were found to be significantly different by RNA-seq and quantitative proteomics. However, the levels of MdtA, PmrA, LolD, LptG, MlaB, RcsF, and DppB were found to be significantly different by quantitative proteomics. Transcriptome sequencing did not yield as many results as proteome sequencing. The results of small RNA prediction showed increased sRNA00002 levels. The study showed that the differentially expressed mRNAs and proteins were associated with multidrug-resistant efflux systems. It can be inferred that berberine reducesE. coliantibiotic resistance. The results of this study are undoubtedly valuable to other researchers.
Multiple functions for the catenin family member plakoglobin in cadherin-dependent adhesion, fibronectin matrix assembly andXenopusgastrulation movements
Authors: Hirsh Glen D. , Dzamba Bette J. , Sonavane Pooja R. , Shook David R. , Allen Claire M. , DeSimone Douglas W. 
Published: May 2018

AbstractShaping an embryo requires tissue-scale cell rearrangements known as morphogenetic events. These force-dependent processes require cells to adhere to their neighbors, through cadherin-catenin complexes, and to their extracellular matrix substrates, through integrin-based focal contacts. Integrin receptors are not only important for attachment to the extracellular matrix, but also for its fibrillar assembly. Fibrillogenesis requires actomyosin contractility, regulated in part by cadherin-catenin complexes. One such catenin, plakoglobin, mediates the attachment of actin stress fibers to cadherin cytoplasmic tails through its interactions with actin-binding proteins. InXenopusgastrulae, plakoglobin has been identified as an essential member in the force-induced collective migration of the mesendoderm tissue. In the current study, we have further characterized the role of plakoglobin in two additional morphogenetic processes, epiboly and convergent extension. Plakoglobin-deficient tadpoles are 40% shorter and gastrulae contain notochords that are 60% wider than stage-matched controls, indicating convergent extension defects. The radially intercalating ectoderm of morphant animal caps is nearly twice as thick as controls. Furthermore, morphant embryos exhibit a failure to assemble a fibronectin matrix at the notochord-somite-boundary or along the blastocoel roof. The loss of the fibronectin matrix, while not due to changes in overall patterning, is a result of a failure to assemble the soluble dimers into long fibrils. The force of attachment to a cadherin or fibronectin substrate is reduced in plakoglobin morphants, indicating defects in adhesion to both cadherin and fibronectin. These data suggest that plakoglobin regulates morphogenesis and fibronectin assembly through cell-cell and cell-matrix adhesion.
Comprehensive Glycoproteomic Analysis of Chinese Hamster Ovary Cells
Authors: Yang Ganglong , Hu Yingwei , Sun Shisheng , Ouyang Chuanzi , Yang Weiming , Betenbaugh Michael , Zhang Hui 
Published: May 2018

AbstractThe Chinese hamster ovary (CHO) cell line is a major expression system for the production of therapeutic proteins, the majority of which are glycoproteins, such as antibodies and erythropoietin (EPO). The characterization of the glycosylation profiles is critical to understand the important role of glycosylation on therapeutic glycoproteins from CHO cells. In this study, a large scale glycoproteomic workflow was established and applied to CHO-K1 cells expressing EPO. The workflow includes enrichment of intact glycopeptides from CHO-K1 cell lysate and medium using hydrophilic enrichment, fractionation of the obtained intact glycopeptides (IGPs) by basic reversed phase liquid chromatography (bRPLC), analyzing the glycopeptides using LC-MS/MS, and annotating the results by GPQuest 2.0. A total of 10,338 N-linked glycosite-containing IGPs were identified, representing 1,162 unique glycosites in 530 glycoproteins, including 71 unique atypical N-linked IGPs on 18 atypical N-glycosylation sequons with an overrepresentation of the N-X-C motifs. Moreover, we compared the glycoproteins from CHO cell lysate with those from medium using the in-depth N-linked glycoproteome data. The obtained large scale glycoproteomic data from intact N-linked glycopeptides in this study is complementary to the genomic, proteomic, and N-linked glycomic data previously reported for CHO cells. Our method has the potential to accelerate the production of recombinant therapeutic glycoproteins.
Factors for the adoption of green building specifications in China
Authors: Wang Wei , Zhang Shoujian , Pasquire Christine 
Published: May 2018

PurposeGreen specifications are some of the most important strategies for energy saving and describe the best practice in the field of sustainable construction. They have great effects on resource saving and environmental protection. The demand of sustainable construction has spurred the emerging and development of green specifications. However, there are many factors that affect the adoption of green specifications in China. Therefore, the purpose of this paper is to investigate the factors that affect the adoption of green specifications in China.Design/methodology/approachBased on the comprehensive literature review, a questionnaire survey has been conducted to with major stakeholders in construction area to identify issues concerning the adoption of green specifications in China. In total, 18 variables that affect the adoption of green specifications in were summarized. Then this study uses factor analysis and mean score method to analyze 18 variables which the authors get from the questionnaire.FindingsUsing the rank analysis and factor analysis, the variables have been ranked, analyzed and categorized into five independent factors. They are summarized as: green technology and techniques; awareness and attitude; policies and regulations; market; and economics. This study provides a variable reference for policy makers to put forward focused policies and incentives for green specifications implementation and industry practitioners to better understand of green specifications adoption in China.Originality/valueThis paper makes a contribution to the understanding of the factors that affect the adoption of the green specifications in China. The results can also contribute to better adoption of green specifications in other developing countries.
How does emotional conflict affect innovation behavior?
Authors: Wu Weiwei , Liu Yexin , Kim Yanggi , Gao Pengbin 
Published: May 2018

PurposeThis study aims to offer insights regarding the impact of emotional conflict on innovation behavior. This study also explores the boundary conditions by examining the moderating effects of leader-member exchange (LMX) and team-member exchange (TMX) on the relationship between emotional conflict and innovation behavior.Design/methodology/approachThis study used a questionnaire survey to collect data in China. Hypotheses were tested using hierarchical regression analysis. To test for inverted U-shaped relationship between emotional conflict and innovation behavior, the authors computed the squared term for emotional conflict. To investigate moderating roles of LMX and TMX, the authors carried out an interaction term between the main effect variables (emotional conflict and emotional conflict2) and the moderating variables (LMX and TMX).FindingsThe empirical findings indicated that emotional conflict had an inverted U-shaped relationship with innovation behavior. Furthermore, LMX and TMX moderated the inverted U-shaped relationship between the emotional conflict and innovation behavior in such a way that the inverted U-shaped relationship was flatter in high-quality LMX and TMX than in low-quality LMX and TMX. That is to say, LMX and TMX may dampen the positive effects of lower levels of emotional conflict on innovation behavior; yet, it may also weaken the negative effects of higher levels of emotional conflict on innovation behavior.Research limitations/implicationsThis research can be extended in several ways. First, future research can investigate the impact mechanism of emotional conflict on innovation behavior. Second, future research can analyze other types of moderators at different levels. The last but not the least, future research can test the results using heterogeneous samples. Despite these potential limitations, this study provides an elaborate understanding of the conflict–creativity relationship by outlining the inverted U-shaped relationship between emotional conflict and innovation behavior under the LMX and TMX contexts, which can make important contributions to the conflict management literature.Practical implicationsThe findings of this study offer some guidance on how to stimulate innovation behavior through emotional conflict. It suggests that managers should maintain the emotional conflict at the moderate level. Furthermore, managers can strengthen the LMX and TMX to avoid the negative effects of high levels of emotional conflict, and several practices are provided as well.Originality/valueThis study develops an exhaustive understanding of the conflict–creativity relationship by figuring the curvilinear relationship between emotional conflict and innovation behavior, which is the response to the call of Posthuma to focus on the outcomes of conflict management. The findings further provide an empirical evidence of the conceptual argument that the consequences of conflict depend on the situational context by pointing out the important contingency factors of LMX and TMX.