bluuebunny/crossref_metadata_2025_split huggingface dataset:
How much does reduced food intake contribute to cancer-associated weight loss?
Authors: Martin Lisa , Kubrak Catherine 
Published: August 2018

Purpose of review
An international consensus group defined cancer cachexia as a syndrome of involuntary weight loss, characterized by loss of skeletal muscle (with or without fat loss), which is driven by a variable combination of reduced food intake and altered metabolism.
This review presents recent studies that evaluated the contribution of reduced food intake to cancer-associated weight loss.

Recent findings
Four studies examined food intake in relation to weight loss. Heterogeneity among studies rendered aggregation and interpretation of results challenging. Despite these limitations, reduced food intake had consistent significant, independent associations with weight loss. However, reduced food intake did not explain all the variation in weight loss; and limited data suggests factors related to alterations in metabolism (e.g. increased resting energy expenditure, systemic inflammation) are also contributing to weight loss.

Summary
Reduced food intake is a significant contributor to cancer-associated weight loss. Understanding the magnitude of the association between food intake and weight loss may improve when it is possible to account for alterations in metabolism. Efforts to align clinical assessments of food intake to reduce heterogeneity are needed.
Adhesion to nanofibers drives cell membrane remodeling through 1D wetting
Authors: Charles-Orszag Arthur , Tsai Feng-Ching , Bonazzi Daria , Manriquez Valeria , Sachse Martin , Mallet Adeline , Salles Audrey , Melican Keira , Staneva Ralitza , Bertin Aurélie , Millien Corinne , Goussard Sylvie , Lafaye Pierre , Shorte Spencer , Piel Matthieu , Krijnse-Locker Jacomine , Brochard-Wyart Françoise , Bassereau Patricia , Duménil Guillaume 
Published: August 2018

AbstractThe shape of cellular membranes is highly regulated by a set of conserved mechanisms. These mechanisms can be manipulated by bacterial pathogens to infect cells. Human endothelial cell plasma membrane remodeling by the bacteriumNeisseria meningitidisis thought to be essential during the blood phase of meningococcal infection, but the underlying mechanisms are unknown. Here we show that plasma membrane remodeling occurs independently of F-actin, along meningococcal type IV pili fibers, by a novel physical mechanism we term “ onedimensional” membrane wetting. We provide a theoretical model that gives the physical basis of 1D wetting and show that this mechanism occurs in model membranes interacting with model nanofibers, and in human cells interacting with model extracellular matrices. It is thus a new general principle driving the interaction of cells with their environment at the nanoscale that is diverted by meningococcus during infection.
Novel small molecule agonists of anAedes aegyptineuropeptide Y receptor block mosquito biting behavior
Authors: Duvall Laura B. , Ramos-Espiritu Lavoisier , Barsoum Kyrollos E. , Glickman J. Fraser , Vosshall Leslie B. 
Published: August 2018

AbstractFemaleAedes aegyptimosquitoes bite humans to obtain a blood-meal to develop their eggs. Remarkably, strong attraction to humans is suppressed for several days after the blood-meal by an unknown mechanism. We investigated a role for neuropeptide Y (NPY)-related signaling in this long-term behavioral suppression, and discovered that drugs targeting human NPY receptors modulate mosquito host-seeking behavior. In a screen of all 49 predictedAe. aegyptipeptide receptors, we identified NPY-like receptor 7 (NPYLR7) as the sole target of these human drugs. To obtain small molecule agonists selective for NPYLR7, we carried out a high-throughput cell-based assay of 265,211 compounds, and isolated 6 highly selective NPYLR7 agonists that inhibit mosquito attraction to humans.NPYLR7CRISPR-Cas9 null mutants are defective in behavioral suppression, and resistant to these drugs. Finally, we show that these drugs are capable of inhibiting biting and blood-feeding on a live host, suggesting a novel approach to control infectious disease transmission by controlling mosquito behavior.
Correlation between the aberrant human testicular germ-cell gene expression and disruption of spermatogenesis leading to male infertility
Authors: Baksi Arka , Jain Ruchi , Manjithaya Ravi , S Vasan S , Kondaiah Paturu , Dighe Rajan R. 
Published: August 2018

AbstractSpermatogenesis is characterized by sequential gene-expression at precise stages in progression of differentiation of the germ cells. Any alteration in expression of the critical genes is responsible for arrest of spermatogenesis associated with infertility. Inspite of advances the differential gene expression accompanying spermatogenesis, the corresponding regulatory mechanisms and their correlation to human infertility have not been clearly established. This study aims to identify the gene expression pattern of the human testicular germ cells from the patients either with obstructive azoospermia with complete intra-testicular spermatogenesis or non-obstructive azoospermia with spermatogenesis arrested at different stages and correlate the same to infertility. The testicular transcriptomes of 3 OA and 8 NOA patients and pooled testicular RNA (commercial source) were analyzed for their differential gene expression to identify potential regulators of spermatogenesis and the results were further validated in all of the 44 patients clinically diagnosed with azoospermia undergoing sperm retrieval surgery over the study period and 4 control samples included in this study. Analyses of the differential transcriptome led to identification of genes enriched in a specific testicular cell type and subsequently, several regulators of the diploid-double-diploid-haploid transitions in the human spermatogenesis were identified. Perturbations in the expression of these genes were identified as the potential causes of the spermatogenic arrest seen in azoospermia and thus the potential mediators of human male infertility. Another interesting observation was the increased autophagy in the testes of patients with non-obstructive azoospermia. The present study suggests that the regulation of the diploid-double-diploid-haploid transition is multigenic with the tandem alteration of several genes resulting in infertility. In conclusion, this study identified some of the genetic regulators controlling spermatogenesis using comparative transcriptome analyses of testicular tissues from azoospremic individuals and showed how alterations in several genes results in disruption of spermatogenesis and subsequent infertility. This study also provides interesting insights into the gene expression patterns of the Indian population that were not available earlier.
Minor isozymes tailor yeast metabolism to carbon availability
Authors: Bradley Patrick H. , Gibney Patrick A. , Botstein David , Troyanskaya Olga G. , Rabinowitz Joshua D. 
Published: August 2018

AbstractIsozymes are enzymes that differ in sequence but catalyze the same chemical reactions. Despite their apparent redundancy, isozymes are often retained over evolutionary time for reasons that can be unclear. We find that, in yeast, isozymes are strongly enriched in central carbon metabolism. Using a gene expression compendium, we find that many isozyme pairs show anticorrelated expression during the respirofermentative shift, suggesting roles in adapting to changing carbon availability. Building on this observation, we assign function to two minor central carbon isozymes, aconitase 2 (ACO2) and pyruvate kinase 2 (PYK2).ACO2is expressed during fermentation and proves advantageous when glucose is limiting.PYK2is expressed during respiration and proves advantageous for growth on three-carbon substrates.PYK2’s deletion is rescued by expressing the major pyruvate kinase, but only if that enzyme carries mutations mirroringPYK2’s allosteric regulation. Thus, central carbon isozymes enable more precise tailoring of metabolism to changing nutrient availability.ImportanceGene duplication is one of the main evolutionary drivers of new protein function. However, some gene duplicates have nevertheless persisted long-term without apparent divergence in biochemical function. Further, under standard lab conditions, many isozymes have subtle or no knockout phenotypes. These factors make it hard to assess the unique contributions of individual isozymes to fitness. We therefore developed a method to identify experimental perturbations that could expose such contributions, and applied it to yeast gene expression data, revealing a potential role for a set of yeast isozymes in adapting to changing carbon sources. Our experimental confirmation of distinct roles for two “minor” yeast isozymes, including one with no previously described knockout phenotype, highlight that even apparently redundant paralogs can have important and unique functions, with implications for genome-scale metabolic modeling and systems-level studies of quantitative genetics.
P-TEFb activation by RBM7 shapes a pro-survival transcriptional response to genotoxic stress
Authors: Bugai Andrii , Quaresma Alexandre J.C. , Friedel Caroline C. , Lenasi Tina , Sibley Christopher R. , Kukanja Petra , Fujinaga Koh , Blasius Melanie , Hennig Thomas , Ule Jernej , Dölken Lars , Barboric Matjaz 
Published: August 2018

SUMMARYCellular DNA damage response (DDR) involves dramatic transcriptional alterations, the mechanisms of which remain ill-defined. Given the centrality of RNA polymerase II (Pol II) promoter-proximal pause release in transcriptional control, we evaluated its importance in DDR. Here we show that following genotoxic stress, the RNA-binding motif protein 7 (RBM7) stimulates Pol II elongation and promotes cell viability by activating the positive transcription elongation factor b (P-TEFb). This is mediated by genotoxic stress-enhanced binding of RBM7 to 7SK snRNA (7SK), the scaffold of the 7SK small nuclear ribonucleoprotein (7SK snRNP) which inhibits P-TEFb. In turn, P-TEFb relocates from 7SK snRNP to chromatin to induce transcription of short units including key DDR genes and multiple classes of non-coding RNAs. Critically, interfering with RBM7 or P-TEFb provokes cellular hypersensitivity to DNA damage-inducing agents through activation of apoptotic program. By alleviating the inhibition of P-TEFb, RBM7 thus facilitates Pol II elongation to enable a pro-survival transcriptional response that is crucial for cell fate upon genotoxic insult. Our work uncovers a new paradigm in stress-dependent control of Pol II pause release, and offers the promise for designing novel anti-cancer interventions using RBM7 and P-TEFb antagonists in combination with DNA-damaging chemotherapeutics.
Characterization of segmental duplications and large inversions using Linked-Reads
Authors: Karaoglanoglu Fatih , Ricketts Camir , Rasekh Marzieh Eslami , Ebren Ezgi , Hajirasouliha Iman , Alkan Can 
Published: August 2018

AbstractMany algorithms aimed at characterizing genomic structural variation (SV) have been developed since the inception of high-throughput sequencing. However, the full spectrum of SVs in the human genome is not yet assessed. Most of the existing methods focus on discovery and genotyping of deletions, insertions, and mobile elements. Detection of balanced SVs with no gain or loss of genomic segments (e.g., inversions) is particularly a challenging task. Long read sequencing has been leveraged to find short inversions but there is still a need to develop methods to detect large genomic inversions. Furthermore, currently there are no algorithms to predict the insertion locus of large interspersed segmental duplications.Here we propose novel algorithms to characterize large (>40Kbp) interspersed segmental duplications and (>80Kbp) inversions using Linked-Read sequencing data. Linked-Read sequencing provides long range information, where Illumina reads are tagged with barcodes that can be used to assign short reads to pools of larger (30-50 Kbp) molecules. Our methods rely on split molecule sequence signature that we have previously described [11]. Similar to the split read, split molecules refer to large segments of DNA that span an SV breakpoint. Therefore, when mapped to the reference genome, the mapping of these segments would be discontinuous. We redesign our earlier algorithm, VALOR, to specifically leverage Linked-Read sequencing data to discover large inversions and characterize interspersed segmental duplications. We implement our new algorithms in a new software package, called VALOR2.AvailabilityVALOR2 is available at https://github.com/BilkentCompGen/valor.
Dimensionality in recurrent spiking networks: global trends in activity and local origins in connectivity
Authors: Recanatesi Stefano , Ocker Gabriel Koch , Buice Michael A. , Shea-Brown Eric 
Published: August 2018

AbstractThe dimensionality of a network’s collective activity is of increasing interest in neuroscience. This is because dimensionality provides a compact measure of how coordinated network-wide activity is, in terms of the number of modes (or degrees of freedom) that it can independently explore. A low number of modes suggests a compressed low dimensional neural code and reveals interpretable dynamics [1], while findings of high dimension may suggest flexible computations [2, 3]. Here, we address the fundamental question of how dimensionality is related to connectivity, in both autonomous and stimulus-driven networks. Working with a simple spiking network model, we derive three main findings. First, the dimensionality of global activity patterns can be strongly, and systematically, regulated by local connectivity structures. Second, the dimensionality is a better indicator than average correlations in determining how constrained neural activity is. Third, stimulus evoked neural activity interacts systematically with neural connectivity patterns, leading to network responses of either greater or lesser dimensionality than the stimulus.Author summaryNew recording technologies are producing an amazing explosion of data on neural activity. These data reveal the simultaneous activity of hundreds or even thousands of neurons. In principle, the activity of these neurons could explore a vast space of possible patterns. This is what is meant by high-dimensional activity: the number of degrees of freedom (or “modes”) of multineuron activity is large, perhaps as large as the number of neurons themselves. In practice, estimates of dimensionality differ strongly from case to case, and do so in interesting ways across experiments, species, and brain areas. The outcome is important for much more than just accurately describing neural activity: findings of low dimension have been proposed to allow data compression, denoising, and easily readable neural codes, while findings of high dimension have been proposed as signatures of powerful and general computations. So what is it about a neural circuit that leads to one case or the other? Here, we derive a set of principles that inform how the connectivity of a spiking neural network determines the dimensionality of the activity that it produces. These show that, in some cases, highly localized features of connectivity have strong control over a network’s global dimensionality—an interesting finding in the context of, e.g., learning rules that occur locally. We also show how dimension can be much different than first meets the eye with typical “pairwise” measurements, and how stimuli and intrinsic connectivity interact in shaping the overall dimension of a network’s response.
Plasticity of Mitochondrial DNA Inheritance and its Impact on Nuclear Gene Transcription in Yeast Hybrids
Authors: Hewitt Sarah K. , Duangrattanalert Kobchai , Burgis Tim , Zeef Leo A.H. , Delneri Daniela 
Published: August 2018

AbstractMitochondrial DNA (mtDNA) in budding yeast is biparentally inherited, but colonies rapidly lose one type of parental mtDNA, becoming homoplasmic. Therefore, hybrids between different yeast species possess two homologous nuclear genomes, but only one type of mitochondrial DNA. We hypothesise that the choice of mtDNA retention is influenced by its contribution to hybrid fitness in different environments, and that the allelic expression of the two nuclear sub-genomes is affected by the presence of different mtDNAs in hybrids. Here, we crossedSaccharomyces cerevisiaewithS. uvarumunder different environmental conditions and examined the plasticity of the retention of mtDNA in each hybrid. We showed that on fermentable carbon sources at warm temperatures each parental mtDNA was equally likely to be retained, while at colder temperatures, hybrids preferentially retained mtDNA derived fromS. uvarum. On a non-fermentable carbon source, hybrids retainedS. cerevisiaemtDNA, independent of temperature. By acquiring transcriptome data and co-expression profiles for hybrids harbouring different mtDNA in a selection of environments, we found a clear pattern of concerted allelic transcription of one or the other sub-genome for specific biological pathways, supporting the notion that the hybrid cell works preferentially with one set of parental alleles or the other according to specific cellular functions. We argue that the type of mtDNA retained in hybrids affects the expression of the nuclear genome and the organism fitness in different environments, and therefore may have a role in driving the evolution of the hybrid nuclear genome in terms of gene retention and loss.
Incremental solidification (toward 3D-printing) of magnetically-confined metal-powder by localized microwave heating
Authors: Fugenfirov Mihael , Meir Yehuda , Shelef Amir , Nerovny Yuri , Aharoni Eli , Jerby Eli 
Published: August 2018

Purpose
This paper aims to present an experimental and theoretical study oriented to investigate the potential use of localized microwave-heating (LMH) in 3D-printing and additive-manufacturing (AM) processes.

Design/methodology/approach
Following a previous study by the authors, a magnetic confinement technique is developed here as a non-contact support for the incremental solidification by LMH of small metal-powder batches. This approach, which saves the need for a mechanic support in contact with the powder-batch during the microwave heating, may significantly simplify the LMH–AM process.

Findings
The powder properties are characterized, and a theoretical LMH model is used to simulate the LMH mechanism dominated here by magnetic eddy currents.

Originality/value
The experimental products are analyzed, and their hardness, porosity and oxidation are evaluated. Practical considerations and further improvements of the non-contact LMH–AM process are discussed.
Analysis of an iron-core and ironless railguns powered sequentially
Authors: Waindok Andrzej , Piekielny Pawel 
Published: August 2018

Purpose
The purpose of this paper is to calculate and measure transients for two different constructions of electrodynamic accelerators (ironless and iron-core) supplied by a three-section power system (three capacitor banks). The optimization of power supply parameters (switch-on times and capacitances of individual sections) in terms of system efficiency has been carried out.

Design/methodology/approach
Calculations have been carried out using a field-circuit model. For three-dimensional magnetostatic analysis, the Maxwell software and finite element method (FEM) were used, while for circuit model, the Matlab/Simulink software was implemented. For optimization of the supply system parameters, the genetic algorithm was used. The mathematical models were verified experimentally by using the original laboratory stand.

Findings
The efficiency of the system is much higher in case of iron-core accelerator. In both cases, the results obtained for optimized supply settings are only slightly better than those obtained by simultaneously switching on the thyristors and for symmetrical capacity division.

Research limitations/implications
Due to the presented field-circuit model, eddy currents in rails have been neglected. In the field model, there was no possibility to combine current flow calculations with moving of the projectile.

Originality/value
Using the presented filed-circuit model, both electrical and mechanical transients could be calculated with sufficient precision. Thus, it could be used in the optimization of supply system. The solution time is low compared with the solution time of the transient field model.
Topological and topical characterisation of Twitter user communities
Authors: Gadek Guillaume , Pauchet Alexandre , Malandain Nicolas , Vercouter Laurent , Khelif Khaled , Brunessaux Stéphan , Grilhères Bruno 
Published: August 2018

Purpose
Most of the existing literature on online social networks (OSNs) either focuses on community detection in graphs without considering the topic of the messages exchanged, or concentrates exclusively on the messages without taking into account the social links. The purpose of this paper is to characterise the semantic cohesion of such groups through the introduction of new measures.

Design/methodology/approach
A theoretical model for social links and salient topics on Twitter is proposed. Also, measures to evaluate the topical cohesiveness of a group are introduced. Inspired from precision and recall, the proposed measures, called expertise and representativeness, assess how a set of groups match the topic distribution. An adapted measure is also introduced when a topic similarity can be computed. Finally, a topic relevance measure is defined, similar to tf.idf (term-frequency, inverse document frequency).

Findings
The measures yield interesting results, notably on a large tweet corpus: the metrics accurately describe the topics discussed in the tweets and enable to identify topic-focused groups. Combined with topological measures, they provide a global and concise view of the detected groups.

Originality/value
Many algorithms, applied on OSN, detect communities which often lack of meaning and internal semantic cohesion. This paper is among the first to quantify this aspect, and more precisely the topical cohesion and topical relevance of a group. Moreover, the proposed indicators can be exploited for social media monitoring, to investigate the impact of a group of people: for instance, they could be used for journalism, marketing and security purposes.
Blinded by the sand of its burrowing? Examining fans’ intentions to follow one-day cricket on TV with a moderating effect of social influence
Authors: Kashif Muhammad , Fernando P.M.P , Wijenayake S.I. 
Published: August 2018

PurposeThe purpose of this paper is to investigate the effect of patriotism, nostalgia, drama and excitement of the game, and interest in star players to predict fans’ intentions to follow one-day cricket in near future. Furthermore, social influence is positioned as a moderator to enrich the understanding of fans’ motives to follow one-day cricket.Design/methodology/approachThe data are collected by means of a cross-sectional survey conducted among 609 university students enroled in Pakistani and Sri Lankan universities. The collected data are analysed by employing a structural equation modelling procedures to reach meaningful conclusions.FindingsThe variables of patriotism, nostalgic associations, excitement and drama of the game, and interest in star players are found to positively relate to the fans’ intentions to follow one-day cricket in near future. However, the moderating effects of social influence only moderated with interest in star players, which has practical and theoretical implications.Originality/valueThe study is an original contribution to the field of sports marketing. The proposed relationships are based on social identity theory paradigm. Furthermore, the moderating effects of social influence and a multi-country data are unique to this study. Finally, in previous studies, football fans’ motivation and test-match cricket fans’ motivations are studied, hence one-day cricket as a context is also unique to this study.