bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of 12 cancer types through genome deep learning
Authors: Sun Yingshuai , Zhu Sitao , Ma Kailong , Liu Weiqing , Yue Yao , Hu Gang , Lu Huifang , Chen Wenbin 
Published: January 2019

AbstractMotivationCancer is a major cause of death worldwide, and an early diagnosis is required for a favorable prognosis. Histological examination is the gold standard for cancer identification; however, there is a large amount of inter-observer variability in histological diagnosis. Numerous studies have shown that cancer genesis is accompanied by an accumulation of harmful mutations within patients’ genome, potentiating the identification of cancer based on genomic information. We have proposed a method, GDL (genome deep learning), to study the relationship between genomic variations and traits based on deep neural networks with multiple hidden layers and nonlinear transformations.ResultWe analyzed 6,083 samples from 12 cancer types obtained from the TCGA (The Cancer Genome Atlas) and 1,991 healthy samples from the 1000 Genomes project(Genomes Project, et al., 2010). We constructed 12 specific models to distinguish between certain types of cancers and healthy tissues, a specific model that can identify healthy vs diseased tissues, and a mixture model to distinguish between all 12 types of cancer based on GDL. We present the success obtained with GDL when applied to the challenging problem of cancer based on genomic variations and demonstrate state-of-the-art results (97%, 70.08% and 94.70%) for cancer identification. The mixture model achieved a comparable performance. With the development of new molecular and sequencing technologies, we can now collect circulating tumor DNA (ctDNA) from blood and monitor the cancer risk in real time, and using our model, we can also target cancerous tissue that may develop in the future. We developed a new and efficient method for the identification of cancer based on genomic information that offers a new direction for disease diagnosis while providing a new method to predict traits based on that information.Contact:chenwenbin@genomics.cn
Bioshake: a Haskell EDSL for bioinformatics pipelines
Authors: Bedő Justin 
Published: January 2019

AbstractBackgroundTypical bioinformatics analysis comprise long running computational pipelines. An important part of producing reproducible research is the management and execution of these computational pipelines to allow robust execution and to minimise errors. Bioshake is an embedded domain specific language embedded in Haskell for specifying and executing computational pipelines in bioinformatics that significantly reduces the possibility of errors occurring.ResultsUnlike other pipeline frameworks, Bioshake raises many properties to the type level to allow the correctness of a pipeline to be statically checked during compilation, catching errors before any lengthy execution process. Bioshake builds on the Shake build tool to provide robust dependency tracking, parallel execution, reporting, and resumption capabilities. Finally, Bioshake abstracts execution so that jobs can either be executed directly or submitted to a cluster.ConclusionsBioshake is available at http://github.com/papenfusslab/bioshake.
3.5KJPNv2, An allele frequency panel of 3,552 Japanese Individuals
Authors: Tadaka Shu , Katsuoka Fumiki , Ueki Masao , Kojima Kaname , Makino Satoshi , Saito Sakae , Otsuki Akihito , Gocho Chinatsu , Sakurai-Yageta Mika , Danjoh Inaho , Motoike Ikuko N. , Yamaguchi-Kabata Yumi , Shirota Matsuyuki , Koshiba Seizo , Nagasaki Masao , Minegishi Naoko , Hozawa Atsushi , Kuriyama Shinichi , Shimizu Atsushi , Yasuda Jun , Fuse Nobuo ,   the Tohoku Medical Megabank Project Study Group, Tamiya Gen , Yamamoto Masayuki , Kinoshita Kengo 
Published: January 2019

AbstractThe first step towards realizing personalized healthcare is to catalog the genetic variations in a population. Since the dissemination of individual-level genomic information is strictly controlled, it will be useful to construct population-level allele frequency panels and to provide them through easy-to-use interfaces.In the Tohoku Medical Megabank Project, we have sequenced nearly 4,000 individuals from a Japanese population, and constructed an allele frequency panel of 3,552 individuals after removing related samples. The panel is called the 3.5KJPNv2. It was constructed by using a standard pipeline including the 1KGP and gnomAD algorithms to reduce technical biases and to allow comparisons to other populations. Our database is the first largescale panel providing the frequencies of variants present on the X chromosome and on the mitochondria in the Japanese population. All the data are available on our original database at https://jmorp.megabank.tohoku.ac.jp.
Huntington’s disease onset is determined by length of uninterrupted CAG, not encoded polyglutamine, and is modified by DNA maintenance mechanisms
Authors:   Genetic Modifiers of Huntington’s Disease (GeM-HD) Consortium, Lee Jong-Min , Correia Kevin , Loupe Jacob , Kim Kyung-Hee , Barker Douglas , Hong Eun Pyo , Chao Michael J , Long Jeffrey D. , Lucente Diane , Vonsattel Jean-Paul , Mouro Pinto Ricardo , Abu Elneel Kawther , Ramos Eliana Marisa , Mysore Jayalakshmi Srinidhi , Gillis Tammy , Wheeler Vanessa C. , MacDonald Marcy E. , Gusella James F , Massey Thomas , McAllister Branduff , Medway Christopher , Stone Timothy C , Hall Lynsey , Jones Lesley , Holmans Peter , Kwak Seung , Ehrhardt Anka , Sampaio Cristina , Ciosi Marc , Maxwell Alastair , Chatzi Afroditi , Monckton Darren G , Orth Michael , Landwehrmeyer G. Bernhard , Paulsen Jane S , Dorsey E. Ray , Shoulson Ira , Myers Richard H 
Published: January 2019

SUMMARYThe effects of variable, glutamine-encoding, CAA interruptions indicate that a property of the uninterrupted HTT CAG repeat sequence, distinct from huntingtin’s polyglutamine segment, dictates the rate at which HD develops. The timing of onset shows no significant association with HTT cis-eQTLs but is influenced, sometimes in a sex-specific manner, by polymorphic variation at multiple DNA maintenance genes, suggesting that the special onset-determining property of the uninterrupted CAG repeat is a propensity for length instability that leads to its somatic expansion. Additional naturally-occurring genetic modifier loci, defined by GWAS, may influence HD pathogenesis through other mechanisms. These findings have profound implications for the pathogenesis of HD and other repeat diseases and question a fundamental premise of the “polyglutamine disorders”.
Excess neuronal branching allows for innervation of specific dendritic compartments in cortex
Authors: Bird A D , Deters L H , Cuntz H 
Published: January 2019

AbstractThe connectivity of cortical microcircuits is a major determinant of brain function; defining how activity propagates between different cell types is key to scaling our understanding of individual neuronal behaviour to encompass functional networks. Furthermore, the integration of synaptic currents within a dendrite depends on the spatial organisation of inputs, both excitatory and inhibitory. We identify a simple equation to estimate the number of potential anatomical contacts between neurons; finding a linear increase in potential connectivity with cable length and maximum spine length, and a decrease with overlapping volume. This enables us to predict the mean number of candidate synapses for reconstructed cells, including those realistically arranged. We identify an excess of putative connections in cortical data, with densities of neurite higher than is necessary to reliably ensure the possible implementation of any given connection. We show that potential contacts allow the particular implementation of connectivity at a subcellular level.
RNA interactions with CTCF are essential for its proper function
Authors: Saldaña-Meyer Ricardo , Rodriguez-Hernaez Javier , Nishana Mayilaadumveettil , Jácome-López Karina , Nora Elphege P. , Bruneau Benoit G. , Furlan-Magaril Mayra , Skok Jane , Reinberg Danny 
Published: January 2019

SummaryThe function of the CCCTC-binding factor (CTCF) in the organization of the genome has become an important area of investigation, but the mechanisms of how CTCF dynamically contributes to genome organization is not clear. We previously discovered that CTCF binds to large numbers of endogenous RNAs; promoting its oligomerization. Here we found that inhibition of transcription or interfering with CTCF ability to bind RNA through mutations of two of its 11 zinc fingers that are not involved with CTCF binding to its cognate site in vitro, zinc finger-1 (ZF1) or −10 (ZF10), disrupt CTCF association to chromatin. These mutations alter gene expression profiles as CTCF mutants lose their ability to promote local insulation. Our results highlight the importance of RNA as a structural component of the genome, in part by affecting the association of CTCF with chromatin and likely its interaction with other factors.Transcriptional inhibition disrupts CTCF binding to chromatinRNA-binding regions (RBR) in CTCF are found within ZF1 and ZF10Local insulation is markedly decreased in ZF1∆ and ZF10∆ mutant rescuesGene expression and chromatin organization are disrupted by RBR mutants
Potential involvement of root auxins in drought tolerance by modulating nocturnal and daytime water use in wheat
Authors: Sadok Walid , Schoppach Rémy 
Published: January 2019

AbstractThe ability of wheat genotypes to save water by reducing their transpiration rate (TR) under times of the day with high vapour pressure deficit (VPD) has been linked to increasing yields in terminal drought environments. Further, recent evidence shows that reducing nocturnal transpiration (TRN) could amplify water-saving. Previous research indicates that such traits involve a root-based hydraulic limitation, but the contribution of hormones, particularly auxin and abscisic acid (ABA) has not been explored to explain the shoot-root link. In this investigation, based on physiological, genetic and molecular evidence gathered on a mapping population, we hypothesized that root auxin accumulation regulates whole-plant water use during both times of the day. Eight double-haploid lines were selected from a mapping population descending from two parents with contrasted water-saving strategies and root hydraulic properties. These spanned the entire range of slopes of TR responses to VPD and TRN encountered in the population. On those lines, we examined daytime/night-time auxin and ABA contents in the roots and the leaves in relation to hydraulic traits that included whole-plant TR, plant hydraulic conductance (KPlant), slopes of TR responses to VPD and leaf-level anatomical traits. Root auxin levels were consistently genotype-dependent in this group irrespective of experiments and times of the day. Daytime root auxin concentrations were found to be strongly and negatively correlated with daytime TR, KPlant and the slope of TR response to VPD. Night-time root auxin levels significantly and negatively correlated with TRN. In addition, daytime and night-time leaf auxin and ABA concentrations did not correlate with any of the examined traits. The above results indicate that accumulation of auxin in the root system reduces daytime and night-time water use and modulates plant hydraulic properties to enable the expression of water-saving traits that have been associated with enhanced yields under drought.
Gametic specialization of centromeric histone paralogs inDrosophila virilis
Authors: Kursel Lisa E. , Malik Harmit S. 
Published: January 2019

AbstractIn most eukaryotes, centromeric histone (CenH3) proteins mediate the highly conserved process of chromosome segregation as the foundational kinetochore assembly factor. However, in multicellular organisms, CenH3 proteins have to perform their essential functions in different chromatin environments. CenH3 proteins not only mediate mitosis and meiosis but also ensure epigenetic inheritance of centromere identity on sperm chromatin, which is highly compact and almost completely stripped of histones during spermiogenesis. We hypothesized that such disparate chromatin environments might impose different functional constraints on CenH3. If so, gene duplications could ameliorate the difficulty of encoding divergent and even potentially incompatible centromeric functions in the same gene. Here, we analyzed the cytological localization of two recently identified CenH3 paralogs, Cid1 and Cid5, inD. virilisusing specific antibodies and epitope-tagged transgenic strains. We find that only ancestral Cid1 is present in somatic cells, whereas both Cid1 and Cid5 are expressed in testes and ovaries. However, Cid1 and Cid5 are alternately retained in male and female gametes; Cid1 is lost in male meiosis but retained throughout oogenesis, whereas Cid5 is lost during female meiosis but retained in mature sperm. Following fertilization, maternally deposited Cid1 rapidly replaces paternal Cid5 during the protamine-to-histone transition. Our studies reveal mutually exclusive gametic specialization of two divergent CenH3 paralogs. We suggest that centromeric histone duplication and divergence may allow essential genes involved in chromosome segregation to specialize and thereby resolve an intralocus conflict between maternal and paternal centromeric histone requirements in many animal species.
Organizational readiness for change: an inherent concern for Indian small and medium enterprises (SMEs)
Authors: Budhiraja Sunil 
Published: January 2019

Purpose
This paper aims to discuss various determinants of organizational readiness to change for India small and medium enterprises (SMEs) and proposes a framework to strengthen the employees’ readiness to change which is integral to organizational readiness for change (ORC).

Design/methodology/approach
This paper is based upon the subjective viewpoint of the author.

Findings
The paper brings forward the opportunities and challenges of Indian SMEs with a suggestive framework on employee readiness for change (ERC).

Practical implications
The paper will help SMEs consider a framework to assess ERC before implementing a change.

Originality/value
The exists no framework for Indian SMEs to look-up as a benchmark to assess their ORC and ERC. Hence the paper will contribute to the literature and will be a handy reference for SMEs.
How can universities align bricks with modern learning?
Authors: van Sprang Hester , Driessen Jasper , Groen Brenda 
Published: January 2019

PurposeThis study aims to explore modern learning (ML) scenarios in Dutch higher education towards 2030 and corresponding consequences for facility management (FM) and corporate real estate strategies (CRES) of universities of applied sciences (UAS).Design/methodology/approachThe designing an accommodation strategy model is used to retrieve the match between demand and supply in real estate of Dutch UAS for both present and future. Application of this model resulted in a scenario-planning session with six education experts to determine future demand in education towards 2030. Subsequently, corporate real estate (CRE) managers of nine Dutch UAS were interviewed concerning this subject (one per UAS).FindingsThe results show that CRES of Dutch UAS is only partly aligned to consequences of ML scenarios towards 2030. Most UAS have real estate portfolios that are only partially flexible, so changes in qualitative and quantitative demand due to ML scenarios are not easy to adapt to. The consequences for FM and real estate of the ML scenarios “institute learning” and “mass customization” seem manageable for Dutch UAS, whereas the other ML scenarios, namely, “navigator” and “natural learning”, would create major portfolio problems.Originality/valueThere is an ongoing interest in developments in higher education combined with FM and CRES and its alignment with the corporate vision. Previous studies into modern ways of learning mainly focused on the past and present. However, this study is explorative and explores possible future ML scenarios. These scenarios can contribute to awareness amongst UAS in The Netherlands and abroad regarding their long-term vision. Moreover, these scenarios will help Dutch UAS facility and CRE managers to develop a more future-proof strategic real estate strategy aligned with the corporate vision.
Structural damage localization through multi-channel empirical mode decomposition
Authors: Salehi Mehdi , Azami Mansour 
Published: January 2019

Purpose
The purpose of this paper is to develop a new structural damage detection technique based on multi-channel empirical mode decomposition (MEMD) of vibrational response data.

Design/methodology/approach
Empirical mode decomposition (EMD) is an empirical data-based signal decomposition method which has been applied in many engineering problems. Utilizing classical EMD to reveal the damage-indicating features of structural vibration response encounters some difficulties due to the inconsistency of modes obtained from different data channels. To overcome this problem, MEMD has been employed. To this end, MEMD algorithm has been adopted to impulse response vector of measured DOFs. The proposed method has been carried out concerning both numerical and experimental beam models. Damage has been modeled by reducing the flexural rigidity in some predefined beam sections. The effects of various factors such as measurement grid density, damage severity and damage position are investigated.

Findings
The results of both numerical and experimental case studies have been promising. The method could determine the damage location in all cases. The efficiency of method gets better when damage is located far from inflation points of the corresponding mode. In such cases, utilizing higher modes can make up the efficiency.

Research limitations/implications
Since the present research is the first investigation of MEMD in damage localization, just one-dimensional structures have been studied. Extending the method to more complicated geometries needs further attempt.

Originality/value
Although a number of relevant studies have been carried out based on EMD, up to the author’s best knowledge, this is the first attempt to structural damage localization using MEMD.
Examining predictive factors and effects of in-class multitasking with mobile phones
Authors: Deng Liping , Ku Kelly Yee Lai , Kong Qiuyi 
Published: January 2019

Purpose
The study aims to give a descriptive account of university students’ engagement with non-learning-related activities during class time and explore the relationship between off-task multitasking and learning. The predictive factors for off-task multitasking from individual, social and class-related dimensions are also examined.

Design/methodology/approach
Contextualized in a comprehensive university in Hong Kong, the study adopts a survey design and involves 79 samples.

Findings
The data show that Hong Kong university students are avid users of mobile phones and heavily engage with digital devices. Off-task multitasking with mobile phones is a common phenomenon, yet not related to learning performance. Among the various media and apps on mobile phones, instant messenger stands out as the most frequently used app on a daily basis and inside the classroom. The individual device-use habit and classroom engagement are significant predictors for off-task multitasking during class time.

Practical implications
This paper will allow teachers and students to be more aware of the causes and effects of off-task multitasking behaviors during class time and derive practical guidance and strategies to pay heed to and resist the disruptive influence of technologies on learning.

Originality/value
The existing scholarly work show a mixed and incomplete picture regarding the effects and determining factors of students’ multitasking. This study includes three variables from individual, social and teaching/learning dimensions and seeks to evaluate their predictive strengths. The results of the study will deepen our understanding of the patterns of off-task multitasking.
Assessing the level of knowledge and practice of breastfeeding among factory working mothers in Kathmandu, Nepal
Authors: Sharma Ira , Khadka Arati 
Published: January 2019

Purpose
The purpose of this paper is to assess the level of knowledge and practice of breastfeeding among factory working mothers in Kathmandu who had a minimum of one child of less than two years of age.

Design/methodology/approach
A cross-sectional survey, with the help of a semi-structured questionnaire, was completed. χ2 or Fisher exact tests were applied for analysis using the SPSS program.

Findings
In total, 36.0 percent of the mothers had adequate knowledge, and 40.0 percent had an appropriate practice of breastfeeding (BF). Also, 30 percent of them were supplementing their BF with additional milk and 54.0 percent began to give additional food at less than six months of age, mainly due to insufficient breast milk. However, 40.0 percent of mothers practiced exclusive BF; 34.0 percent of mothers continued BF until their child reached two years of age. BF was initiated within an hour by 64.0 percent of mothers. Regarding knowledge, the majority of them (82 percent) knew about initiation time of the feed, 64.0 percent of mothers knew that breast milk had positive effects on a child’s health while 48.0 percent knew that it also had good effects on the mothers’ health. There was a positive association between available facilities and BF knowledge levels (p-value<0.00, χ2=4.25, df=1). The associations of knowledge levels against the education status of mothers (p-value=0.11, χ2=2.59, df=1) and practice level of initiation of breast milk (p-value=0.96, χ2=0.02, df=1) were not significant.

Originality/value
The knowledge and practices of BF among factory working mothers are not satisfactory. Hence, an effective way to encourage BF is to increase the availability of facilities for the practice of BF at a mother’s workplace.
Strategic choices of exploration and exploitation alliances under market uncertainty
Authors: Li Wan , Wang Liang 
Published: January 2019

PurposeThe purpose of this paper is to provide a better understanding of what drives firms’ choice between exploration alliances and exploitation alliances by examining the role of organizational slack and its interaction with market uncertainty.Design/methodology/approachAn empirical study is conducted based on 1,614 alliances formed by 581 US biotechnology firms, and the hypotheses are tested using a zero-inflated multilevel Poisson model.FindingsThe results indicate that firms’ strategic choice to pursue exploration or exploitation alliances is a reflection of organizational intention and adaptation to environmental turbulence. More specifically, firms with more financial slack tend to form more exploration alliances and fewer exploitation alliances. However, under high market uncertainty, firms with financial slack tend to establish more exploitative partnerships and avoid exploration collaborations.Originality/valueThis paper contributes to the literature on exploration–exploitation alliances, which tends to fall short of providing an understanding of why organizations pursue such alliances. By identifying the impact of organizational slack and its interaction with market uncertainty, this study shows that organizations are able to respond to environmental change, and those with capabilities are likely to craft their strategic choice configurations based on their own characteristics.