bluuebunny/crossref_metadata_2025_split huggingface dataset:
Precise, pan-cancer discovery of gene fusions reveals a signature of selection in primary tumors
Authors: Freeman Donald Eric , Hsieh Gillian Lee , Howard Jonathan Michael , Lehnert Erik , Salzman Julia 
Published: August 2017

Short AbstractThe extent to which gene fusions function as drivers of cancer remains a critical open question in cancer biology. In principle, transcriptome sequencing provided by The Cancer Genome Atlas (TCGA) enables unbiased discovery of gene fusions and post-analysis that informs the answer to this question. To date, such an analysis has been impossible because of performance limitations in fusion detection algorithms. By engineering a new, more precise, algorithm and statistical approaches to post-analysis of fusions called in TCGA data, we report new recurrent gene fusions, including those that could be druggable; new candidate pan-cancer oncogenes based on their profiles in fusions; and prevalent, previously overlooked, candidate oncogenic gene fusions in ovarian cancer, a disease with minimal treatment advances in recent decades. The novel and reproducible statistical algorithms and, more importantly, the biological conclusions open the door for increased attention to gene fusions as drivers of cancer and for future research into using fusions for targeted therapy.
Deep learning: Using machine learning to study biological vision
Authors: Majaj Najib J. , Pelli Denis G. 
Published: August 2017

ABSTRACTToday many vision-science presentations employ machine learning, especially the version called “deep learning”. Many neuroscientists use machine learning to decode neural responses. Many perception scientists try to understand how living organisms recognize objects. To them, deep neural networks offer benchmark accuracies for recognition of learned stimuli. Originally machine learning was inspired by the brain. Today, machine learning is used as a statistical tool to decode brain activity. Tomorrow, deep neural networks might become our best model of brain function. This brief overview of the use of machine learning in biological vision touches on its strengths, weaknesses, milestones, controversies, and current directions. Here, we hope to help vision scientists assess what role machine learning should play in their research.
RNA editing of CAPS1 regulates synaptic vesicle organization, release and retrieval
Authors: Ulbricht Randi J. , Sun Sarah J. , DelBove Claire E. , Kitko Kristina E. , Rehman Saad C. , Wang Michelle Y. , Lazarenko Roman M. , Zhang Qi , Emeson Ronald B. 
Published: August 2017

ABSTRACTCalcium-dependent activator protein for secretion 1 (CAPS1) facilitates the docking and priming of synaptic and dense core vesicles. A conserved hairpin structure in the CAPS1 pre-mRNA allows an post-transcriptional adenosine-to-inosine RNA editing event to alter a genomically-encoded glutamate to a glycine codon. Functional comparisons of CAPS1 protein isoforms in primary hippocampal neurons show that elevation of edited CAPS1 isoforms facilitates presynaptic vesicle clustering and turnover. Conversely, non-edited CAPS1 isoforms slow evoked release, increase spontaneous fusion, and loosen the clustering of synaptic vesicles. Therefore, CAPS1 editing promotes organization of the vesicle pool in a way that is beneficial for evoked release, while non-edited isoforms promote more lax vesicle organization that widens distribution, attenuates evoked release and eases the control of spontaneous fusion. Overall, RNA editing of CAPS1 is a mechanism to fine tune neurotransmitter release.IMPACT STATEMENTPost-transcriptional RNA editing of CAPS1 is a mechanism to regulate neurotransmitter release from synaptic vesicles.
The Anti-Epileptic Ketogenic Diet Alters Hippocampal Transporter Levels and Reduces Adiposity in Aged Rats
Authors: Hernandez Abbi R. , Hernandez Caesar M. , Campos Keila T. , Truckenbrod Leah M. , Sakarya Yasemin , McQuail Joseph A. , Carter Christy S. , Bizon Jennifer L. , Maurer Andrew P. , Burke Sara N. 
Published: August 2017

AbstractNutritional ketosis is induced by high fat/low carbohydrate dietary regimens, which produce high levels of circulating ketone bodies, shifting metabolism away from glucose utilization. While ketogenic diets (KD) were initially introduced to suppress seizures, they are garnering attention for their potential to treat a myriad of neurodegenerative and metabolic disorders that are associated with advanced age. The feasibility and physiological impact of implementing a long-term KD in old animals, however, has not been systematically examined. In this study, young and aged rats consumed a calorically- and nutritionally-matched KD or control diet for 12 weeks. All KD-fed rats maintained higher levels of β-hydroxybutyrate (BHB) and lower levels of glucose relative to controls. However, it took the aged rats longer to reach asymptotic levels of BHB compared to young animals. Moreover, KD-fed rats had significantly less visceral white and brown adipose tissue than controls without a loss of lean mass. Interestingly, the KD lead to significant alterations in protein levels of hippocampal transporters for monocarboxylates, glucose and vesicular glutamate and GABA. Most notably, the age-related decline in vesicular glutamate transporter expression was reversed by the KD. These data demonstrate the feasibility and potential benefits of KDs for treating age-associated neural dysfunction.
Behavioral and neural indices of affective coloring for neutral social stimuli
Authors: Grupe Daniel W. , Schaefer Stacey M. , Lapate Regina C. , Schoen Andrew J. , Gresham Lauren K. , Mumford Jeanette A. , Davidson Richard J. 
Published: August 2017

AbstractEmotional processing often continues beyond the presentation of emotionally evocative stimuli, which can result in affective biasing or coloring of subsequently encountered events. Here, we describe neural correlates of affective coloring and examine how individual differences in affective style impact the magnitude of affective coloring. We conducted functional magnetic resonance imaging in 117 adults who passively viewed negative, neutral, and positive pictures presented 2s prior to neutral faces. Brain responses to neutral faces were modulated by the valence of preceding pictures, with greater activation for faces following negative (vs. positive) pictures in the amygdala, dorsomedial and lateral prefrontal cortex, ventral visual cortices, posterior superior temporal sulcus, and angular gyrus. Three days after the MRI scan, participants rated their memory and liking of previously encountered neutral faces. Individuals higher in trait positive affect and emotional reappraisal rated faces as more likable when preceded by emotionally arousing (negative or positive) pictures. Additionally, greater amygdala responses to neutral faces preceded by positively valenced pictures were associated with greater memory for these faces three days later. Collectively, these results reveal individual differences in how emotions spill over onto the processing of unrelated social stimuli, resulting in persistent and affectively biased evaluations of such stimuli.
Current geography masks dynamic history of gene flow during speciation in northern Australian birds
Authors: Peñalba Joshua V. , Joseph Leo , Moritz Craig 
Published: August 2017

AbstractDuring early stages of speciation, genome divergence is greatly influenced by gene flow. As populations diverge, geography can allow or restrict gene flow in the form of barriers. Current geography, e.g. whether sister species are allopatric or parapatric, is often used to predict the potential for gene flow during the divergence process. We test the validity of this assumption in eight meliphagoid bird species codistributed across four regions. These regions are separated by known biogeographic barriers within and between northern Australia and Papua New Guinea. We find that bird populations across the same barrier have a range of divergence levels and probability of gene flow regardless of range connectivity. Geographic distance and maximum range connectivity over time can better predict divergence and probability of gene flow than whether populations are currently allopatric or parapatric. We also find support for a nonlinear decrease of the probability of gene flow during the divergence process. This implies that although gene flow influences divergence early in speciation, other factors associated with higher divergence restrict gene flow later in speciation. Current geography may then mislead inferences regarding potential for gene flow during speciation under a complex and dynamic history of geographic and reproductive isolation.
Inferring propensity amongst lung and breast carcinomas via overlapped gene expression profiles
Authors: Jaiswal Rajni , Dhakal Sabin , Jauhari Shaurya 
Published: August 2017

ABSTRACTReconstruction of biological networks for topological analyses helps in correlation identification between various types of biomarkers. These networks have been vital components of System Biology in present era. Genes are the basic physical and structural unit of heredity. Genes act as instructions to make molecules called proteins. Alterations in the normal sequence of these genes are the root cause of various diseases and cancer is the prominent example disease caused by gene alteration or mutation. These slight alterations can be detected by microarray analysis. The high throughput data obtained by microarray experiments aid scientists in reconstructing cancer specific gene regulatory networks. The purpose of experiment performed is to find out the overlapping of the gene expression profiles of breast and lung cancer data, so that the common hub genes can be sifted and utilized as drug targets which could be used for the treatment of diseased conditions. In this study, first the differentially expressed genes have been identified (lung cancer and breast cancer), followed by a filtration approach and most significant genes are chosen using paired t-test and gene regulatory network construction. The obtained result has been checked and validated with the available databases and literature.
WDR88,CCDC11, andARPP21genes indulge profoundly in the desmoplastic retort to prostate and breast cancer metastasis
Authors: Jaiswal Rajni , Jauhari Shaurya , Rizvi S.A.M. 
Published: August 2017

Abstract.Microarray technology has unlocked doors to a multitude of open analysis problems that if conceived with efficacy may uncover varied genotypic and phenotypic traits. Algorithms belonging to different cultures in computer science have been applied to gene expression data to derive correlation and stratification parameters. While most outcomes are subject to clinical validation, majority of which get declined, the search for the precisely targeted therapeutic agents is still on. This paper is an effort in the similar direction and strives to delineate genes with significant stromal signatures. We suggest a corroborative indulgence of a human laterality disorder gene, CCDC11 in the metastasis, in addition to the role ofWDR88andARPP21genes has been further materialized in the analysis. Another standout aspect of the study has been the associated implications of the genes in rare disorders of male breast and female prostate cancers. There is also a threshold proposal that stratifies “safe” expression space for genes. Complimentarily, the manuscript serves as an expedient protocol for anyone seeking microarray data analysis, particularly in R.
Genes relocated betweenDrosophila chromosomearms evolve under relaxed selective constraints relative to non-relocated genes
Authors: Hart Margaret L. I. , Vu Ban L. , Bolden Quinten , Chen Keith T. , Oakes Casey L. , Zoronjic Lejla , Meisel Richard P. 
Published: August 2017

AbstractGene duplication creates a second copy of a gene either in tandem to the ancestral locus or dispersed to another chromosomal location. When the ancestral copy of a dispersed duplicate is lost from the genome, it creates the appearance that the gene was “relocated” from the ancestral locus to the derived location. Gene relocations may be as common as canonical dispersed duplications in which both the ancestral and derived copies are retained. Relocated genes appear to be under more selective constraints than the derived copies of canonical duplications, and they are possibly as conserved as single-copy non-relocated genes. To test this hypothesis, we combined comparative genomics, population genetics, gene expression, and functional analyses to assess the selection pressures acting on relocated, duplicated, and non-relocated single-copy genes inDrosophilagenomes. We find that relocated genes evolve faster than single-copy non-relocated genes, and there is no evidence that this faster evolution is driven by positive selection. In addition, relocated genes are less essential for viability and male fertility than single-copy non-relocated genes, suggesting that relocated genes evolve fast because of relaxed selective constraints. However, relocated genes evolve slower than the derived copies of canonical dispersed duplicated genes. We therefore conclude that relocated genes are under more selective constraints than canonical duplicates, but are not as conserved as single-copy non-relocated genes.
RNA-dependent intergenerational inheritance of enhanced synaptic plasticity after environmental enrichment
Authors: Benito Eva , Kerimoglu Cemil , Ramachandran Binu , Zhou Qihui , Pena Tonatiuh , Capece Vincenzo , Jain Gaurav , Burkhardt Susanne , Stilling Roman , Edbauer Dieter , Dean Camin , Fischer André 
Published: August 2017

ABSTRACTPhysical exercise in combination with cognitive training is known to enhance synaptic plasticity, learning & memory and lower the risk for various complex diseases including Alzheimer’s disease. Here we show that exposure of adult male mice to an environmental enrichment paradigm leads to enhancement of synaptic plasticity and cognition also in the next generation. We show that the effect is mediated through sperm RNA and is explained by microRNAs 212/132. In conclusion, our study reports intergenerational inheritance of an acquired cognitive benefit and points to specific microRNAs as candidates mechanistically involved in this type of transmission.
Abnormal cell sorting underlies the unique X-linked inheritance ofPCDH19Epilepsy
Authors: Pederick Daniel T. , Richards Kay L. , Piltz Sandra G. , Mandelstam Simone A. , Dale Russell C. , Scheffer Ingrid E. , Gecz Jozef , Petrou Steve , Hughes James N. , Thomas Paul Q. 
Published: August 2017

SummaryX-linked diseases typically exhibit more severe phenotypes in males than females. In contrast,Protocadherin 19(PCDH19) mutations cause epilepsy in heterozygous females but spare hemizygous males. The cellular mechanism responsible for this unique pattern of X-linked inheritance is unknown. We show that PCDH19 contributes to highly specific combinatorial adhesion codes such that mosaic expression ofPcdh19in heterozygous female mice leads to striking sorting between WT PCDH19- and null PCDH19-expressing cells in the developing cortex, correlating with altered network activity. Complete deletion of PCDH19 in heterozygous mice abolishes abnormal cell sorting and restores normal network activity. Furthermore, we identify variable cortical malformations in PCDH19 epilepsy patients. Our results highlight the role of PCDH19 in determining specific adhesion codes during cortical development and how disruption of these codes is associated with the unique X-linked inheritance ofPCDH19epilepsy.
The impact of global operations on product architecture: an exploratory study
Authors: Pashaei Sebastian , Olhager Jan 
Published: August 2017

Purpose
The purpose of this paper is to explore how global operations of manufacturing companies influence the choice of product architecture decisions, ranging from integral to modular product designs.

Design/methodology/approach
The authors perform a multiple-case study of three global manufacturing companies with integral and modular product architectures.

Findings
The authors find that the internal network capabilities, the number of capable plants, the focus of component plants, the focus of assembly plants, the distances from key suppliers to internal plants, and the number of market segments significantly influence the choice of integral vs modular architecture.

Research limitations/implications
This study is limited to three large manufacturing companies with global operations. However, the authors investigate both integral and modular products. The authors develop propositions that can be tested in further survey research.

Practical implications
The findings show that the type of global operations network influences the decision on product architecture, such that certain global operations characteristics support integral product designs, while other characteristics support modular designs.

Originality/value
To the best of the authors’ knowledge this paper is the first study on the explicit impact of global operations on product architecture, rather than the other way around.
A multi-dimensional approach for managing open innovation in NPD
Authors: Bahemia Hanna , Squire Brian , Cousins Paul 
Published: August 2017

Purpose
This paper explores openness within new product development (NPD) projects. The purpose of this paper is to examine the impact of breadth, depth and partner newness on product innovativeness and product competitive advantage. The authors also seek to examine the contingent effects of the appropriability regime. The authors make suggestions to academics and practitioners based on the findings.

Design/methodology/approach
The authors use a structured survey instrument producing an empirical analysis of 205 NPD projects in the manufacturing sector in the UK. The authors use an ordinary least squares regression model to test hypothesised relationships between openness (breadth, depth and partner newness), product innovativeness, product competitive advantage and the appropriability regime.

Findings
The authors find that each of the three dimensions of openness, depth, breadth and partner newness, have a significant but differing impact on product innovativeness. Specifically, the study indicates that breadth has a positive effect but only in the presence of a strong appropriability regime, partner newness has a direct positive effect, and depth a direct negative effect. The authors also find that product innovativeness has a positive impact on product competitive advantage.

Research limitations/implications
Further research should focus on replicating the findings in other countries, search for further moderating factors, such as the stage of the NPD process, and analyse the longitudinal impact of openness within NPD projects.

Practical implications
Organisations are encouraging managers to be more open in their approach to NPD. The authors’ findings suggest that managers need to think about the three dimensions of openness, breadth, depth and partner newness. Their engagement with each of these dimensions depends on the desired outcomes of the innovation project and the strength of patents.

Originality/value
The research extends the extant supplier involvement in new product development literature to examine the effect of up to 11 types of external actor in NPD projects. The authors test a new multi-dimensional measurement scale for the openness construct. The authors show that each dimension has a different relationship with product innovativeness.
Evaluating the effects of supply chain quality management on food firms’ performance
Authors: Song Hua , Turson Rabia , Ganguly Anirban , Yu Kangkang 
Published: August 2017

PurposeThe purpose of this paper is to identify the two kinds of supply chain quality management (SCQM) capabilities: intra-SCQM and inter-SCQM, and explore the effect of intra- and inter-food SCQM on food safety and quality, and the effect of food SCQM on domestic and export performance through food certification and corporate reputation.Design/methodology/approachSecondary data on food selling or processing firms in Western China were collected to test all the hypotheses. The data were then analyzed using the statistical technique of stepwise regression and inference was drawn based on the result.FindingsThrough utilizing secondary data sources, it is found that intra-SCQM promotes sales in domestics market with mediating role of corporate reputation, while the realization of overseas performance depend both on intra- and inter-SCQM with mediating role of food certification.Practical implicationsThe paper study on food supply chain quality problem, the suggested approaches can be easily realized by agro-food companies to achieve international competitiveness by implementing both intra- and inter-SCQM. Meanwhile to Chinese domestic companies, it is important to strengthen inter-SCQM and food certification in order to achieve competitive advantage.Originality/valueReview of literature indicated that there is a dearth of open literature that discusses food safety from the perspective of inter- and intra-organizational management. Furthermore, it was also observed that there has been no study that has taken the safety signaling perspective. The current research tires to shed some light on this important, but sparely discussed issue.
An approach for speed limit determination for vehicle tracking in case of GID ambiguity and lack of information in navigation maps
Authors: Haliti Nusret , Kadriu Arbana , Jusufi Mensur 
Published: August 2017

Purpose
The purpose of the research presented in this paper is about an algorithm used for speed limit determination, in cases when there is ambiguity in determining the correct road data for a tracked vehicle. This algorithm resolves the glitch that happens when emitted global positioning system (GPS) data are ambiguous regarding roads that are very near to each other. Furthermore, we give a solution for other difficulties regarding the speed limit involving accuracy of emitted data and lack of information in navigation maps.

Design/methodology/approach
Our vehicle tracking system parses all GPS data from different vehicles to a single centralized database. It uses balancers and parsers to parse these data. Balancers use algorithms like round-robin to choose between different parsers. Information gained by the GPS unit is parsed, and then sent to a central server at regular intervals. For the gained data, we try to analyze the speed limit problem when tracking vehicles, analyze the challenges that are linked with speed limit problem, define a solution for the above discussed drawbacks and measure the driving performance.

Findings
We have already developed a fully functioning tracking system, which uses the above-described algorithm in tracking of few hundred vehicles, which makes approximately 1,300,000 requests per day, resulting in more than 4,000,000 tracking records gained in six months. The system monitors the motion of different vehicles using the gained GPS data from the first hand. This monitoring is done by developing web and mobile applications for third-party actors. This monitoring regards not only to the raw-produced data but also to new metrics that are derived from the raw one.

Originality/value
To our knowledge, there is not a similar algorithm/technology that can be of help in case of geographical identifier (GID) ambiguity. This research presents a solution to a real problem that we faced and which could not be answered by any of the current algorithms and technologies regarding the speed limit. Therefore, we consider this paper as highly original, which brings value in the field of pervasive computing and machine-to-machine communication.