bluuebunny/crossref_metadata_2025_split huggingface dataset:
MARS-Net: Deep learning-based segmentation pipeline for profiling cellular morphodynamics from multiple types of live cell microscopy
Authors: Jang Junbong , Wang Chuangqi , Zhang Xitong , Choi Hee June , Pan Xiang , Lin Bolun , Yu Yudong , Whittle Carly , Ryan Madison , Chen Yenyu , Lee Kwonmoo 
Published: September 2017

AbstractQuantitative studies of cellular morphodynamics rely on extracting leading-edge velocity time-series based on accurate cell segmentation from live cell imaging. However, live cell imaging has numerous challenging issues about accurate edge localization. Here, we develop a deep learning-based pipeline, termed MARS-Net (Multiple-microscopy- type-based Accurate and Robust Segmentation Network), that utilizes transfer learning and the datasets from multiple types of microscopy to localize cell edges with high accuracy, allowing quantitative profiling of cellular morphodynamics. For effective training with the datasets from multiple types of live cell microscopy, we integrated the pretrained VGG-19 encoder with U-Net decoder and added dropout layers. Using this structure, we were able to train one neural network model that can accurately segment various live cell movies from phase contrast, spinning disk confocal, and total internal reflection fluorescence microscopes. Intriguingly, MARS-Net produced more accurate edge localization than the neural network models trained with single microscopy type datasets, whereas the standard U-Net could not increase the overall accuracy. We expect that MARS-Net can accelerate the studies of cellular morphodynamics by providing accurate segmentation of challenging live cell images.
A space and time-efficient index for the compacted colored de Bruijn graph
Authors: Almodaresi Fatemeh , Sarkar Hirak , Patro Rob 
Published: September 2017

AbstractWe present a novel data structure for representing and indexing the compacted colored de Bruijn graph, which allows for efficient pattern matching and retrieval of the reference information associated with each k-mer. As the popularity of the de Bruijn graph as an index has increased over the past few years, so have the number of proposed representations of this structure. Existing structures typically fall into two categories; those that are hashing-based and provide very fast access to the underlying k-mer information, and those that are space-frugal and provide asymptotically efficient but practically slower pattern search.Our representation achieves a compromise between these two extremes. By building upon minimum perfect hashing, carefully organizing our data structure, and making use of succinct representations where applicable, our data structure provides practically fast k-mer lookup while greatly reducing the space compared to traditional hashing-based implementations. Further, we describe a sampling scheme built on the same underlying representation, which provides the ability to trade off k-mer query speed for a reduction in the de Bruijn graph index size. We believe this representation strikes a desirable balance between speed and space usage, and it will allow for fast search on large reference sequences.Pufferfish is developed in C++11, is open source (GPL v3), and is available athttps://github.com/COMBINE-lab/Pufferfish. The scripts used to generate the results in this manuscript are available athttps://github.com/COMBINE-lab/pufferfish_experiments.
Modeling the schizophrenias: subunit-specific NMDAR antagonism dissociates frontalδand hippocampalθmodulation of ~140 Hz oscillations
Authors: Pittman-Polletta Benjamin , Hu Kun , Kocsis Bernat 
Published: September 2017

ABSTRACTNMDAR antagonism alters mesolimbic, hippocampal, and cortical function, acutely reproducing the positive, cognitive, and negative symptoms of schizophrenia. These physiological and behavioral effects may depend differentially on NMDAR subtype-and region-specific effects. The dramatic electrophysiological signatures of NMDAR blockade in rodents include potentiated high frequency oscillations (HFOs, ~140 Hz), likely generated in mesolimbic structures, and increased HFO phase-amplitude coupling (PAC), a phenomenon related to goal-directed behavior and dopaminergic tone. This study examined the impact of subtype-specific NMDAR antagonism on HFOs and PAC. We found that positive-symptom-associated NR2A-preferring antagonism (NVP-AAM077), but not NR2B-specific antagonism (Ro25-6985) or saline control, replicated increases in HFO power seen with nonspecific antagonism (MK-801). However, PAC following NR2A-preferring antagonism was distinct from all other conditions. Whileθ-HFO PAC was prominent or potentiated in other conditions, NVP-AAM077 increasedδ-HFO PAC and decreasedθ-HFO PAC. Furthermore, active wake epochs exhibiting narrowband frontalδoscillations, and not broadband sleep-associatedδ, selectively exhibitedδ-HFO coupling, while paradoxical sleep epochs having a high CA1θto frontalδratio selectively exhibitedθ-HFO coupling. Our results suggest: (1) NR2A-preferring antagonism induces oscillopathies reﬂecting frontal hyperfunction and hippocampal hypofunction; and (2) HFO PAC indexes cortical vs. hippocampal control of mesolimbic circuits.
Prediction of residue-residue contacts in CASP12 targets from its predicted tertiary structures
Authors: Agrawal Piyush , Singh Sandeep , Nagpal Gandharva , Sethi Deepti , Raghava Gajendra P.S. 
Published: September 2017

AbstractOne of the challenges in the field of structural proteomics is to predict residue-residue contacts in a protein. It is an integral part of CASP competitions due to its importance in the field of structural biology. This manuscript describes RRCPred 2.0 a method participated in CASP12 and predicted residue-residue contact in targets with high precision. In this approach, firstly 150 predicted protein structures were obtained from CASP12 Stage 2 tarball and ranked using clustering-based quality assessment software. Secondly, residue-residue contacts were assigned in top 10 protein structures based on distance between residues. Finally, residue-residue contacts were predicted in target protein based on consensus/average in top 10 predicted structures. This simple approach performs better than most of CASP12 methods in the categories of TBM and TBM/FM. It ranked 1stin following categories; i) TBM domain on list size L/5, ii) TBM/FM domain on list size L/5 and iii) TBM/FM domain on Top 10. These observations indicate that predicted tertiary structure of a protein can be used for predicting residue-residue contacts in protein with high accuracy.
Updating the 97% identity threshold for 16S ribosomal RNA OTUs
Authors: Edgar Robert C. 
Published: September 2017

AbstractThe 16S ribosomal RNA (rRNA) gene is widely used to survey microbial communities. Sequences are often clustered into Operational Taxonomic Units (OTUs) as proxies for species. The canonical clustering threshold is 97% identity, which was proposed in 1994 when few 16S rRNA sequences were available, motivating a reassessment on current data. Using a large set of high-quality 16S rRNA sequences from finished genomes, I assessed the correspondence of OTUs to species for five representative clustering algorithms using four accuracy metrics. All algorithms had comparable accuracy when tuned to a given metric. Optimal identity thresholds that best approximated species were ∼99% for full-length sequences and ∼100% for the V4 hypervariable region.
Incorporating trait-based mechanisms, alternative interaction modes and forbidden links increases the minimum trait dimensionality of ecological networks
Authors: Kiziridis Diogenis A. , Boddy Lynne , Eastwood Daniel C. , Yuan Chenggui , Fowler Mike S. 
Published: September 2017

ABSTRACTSpecies’ traits mediate ecological interaction outcomes and community structure. It is important, therefore, to identify the minimum number of traits required to characterise observed networks, i.e. the ‘minimum dimensionality’. Existing methods for estimating minimum dimensionality often lack three features commonly associated with a higher numbers of traits: a mechanistic description of observed interactions, alternative interaction modes (e.g. different feeding strategies such as activevssit-and-wait feeding), and trait-mediated ‘forbidden links’. Omitting these features can lead to underestimation of the trait numbers involved, and therefore, minimum dimensionality. Here, we develop a ‘minimum mechanistic dimensionality’ measure, accounting for these three features.The only input required by our method is the observed network of interaction outcomes. We then assume how traits are mechanistically involved in alternative interaction modes. These unidentified traits are contrasted using pairwise performance inequalities between the interacting species. E.g. if a predator feeds upon a prey species via a typical predation mode, in each step of the predation sequence the predator’s performance must be greater than the prey’s. We construct a system of inequalities from all observed outcomes, which we attempt to solve with mixed integer linear programming. The minimum number of traits required for a feasible system of inequalities provides our dimensionality estimate.We applied our method to 658 published empirical ecological networks including animal dominance, predator–prey, primary consumption, pollination, parasitism and seed dispersal networks, to compare with minimum dimensionality estimates when the three focal features are missing. Minimum dimensionality was typically higher when including alternative interaction modes (54% of empirical networks), ‘forbidden interactions’ as trait-mediated interaction outcomes (92%), or a mechanistic perspective (81%), compared to network dimensionality estimates missing these features.Our method can reduce the risk of omitting essential traits that are involved mechanistically, in different interaction modes, or in failure outcomes. More accurate estimates will allow us to parameterise models to generate theoretical networks with a more realistic structure at the interaction outcome level. Thus, we hope our method can improve predictions of community structure and structure-dependent dynamics.
The Parasite Extinction Assessment & Red List: an open-source, online biodiversity database for neglected symbionts
Authors: Carlson Colin J. , Muellerklein Oliver C. , Phillips Anna J. , Burgio Kevin R. , Castaldo Giovanni , Cizauskas Carrie A. , Cumming Graeme S. , Dallas Tad A. , Doña Jorge , Harris Nyeema , Jovani Roger , Miao Zhongqi , Proctor Heather , Yoon Hyun Seok , Getz Wayne M. 
Published: September 2017

AbstractParasite conservation is a rapidly growing field at the intersection of ecology, epidemiology, parasitology, and public health. The overwhelming diversity of parasitic life on earth, and recent work showing that parasites and other symbionts face severe extinction risk, necessitates infrastructure for parasite conservation assessments. Here, we describe the release of the Parasite Extinction Assessment & Red List (PEARL) version 1.0, an open-access database of conservation assessments and distributional data for almost 500 macroparasitic invertebrates. The current approach to vulnerability assessment is based on range shifts and loss from climate change, and will be expanded as additional data (e.g., host-parasite associations and coextinction risk) is consolidated in PEARL. The web architecture is also open-source, scalable, and extensible, making PEARL a template for more eZcient red listing for other high-diversity, data-de1cient groups. Future iterations will also include new functionality, including a user-friendly open data pository and automated assessment and re-listing.
Empirical patterns of time value decay in options
Authors: McKeon Ryan 
Published: September 2017

Purpose
The purpose of this paper is to conduct an empirical analysis of the pattern of time value decay in listed equity options, considering both call and put options and different moneyness and maturity levels.

Design/methodology/approach
The research design is empirical, with great attention paid to creating a standardized measure of time value that can be both tracked over time for an individual option contract and meaningfully compared across two or more different option contracts.

Findings
The author finds that moneyness classification at the beginning of the holding period is the key determinant of the pattern of subsequent time decay. The type of option, call or put, and the maturity of the contract have surprisingly little relevance to the pattern of time decay “out-the-money contracts having similar patterns on average, regardless of whether they are calls or puts, 30-day or 60-day contracts.” More detailed analysis reveals that In-the-money and out-the-money contracts have slow time decay for most of the contract life, with a significant percentage of the time decay concentrated on the final day of the option. At-the-money contracts experience strong decay early in the life of the option.

Research limitations/implications
The study is limited by not having intra-day data included to analyze more frequent price movements.

Practical implications
The results reported in the paper provide insight into issues of active management facing options traders, specifically choices such as the initial maturity of the option contract and rollover frequency.

Originality/value
Very few studies examine the important issue of how option time value behaves. Time value is the subjective part of the option contract value, and therefore very difficult to predict and understand. This paper provides insight into typical empirical patterns of time value behavior.
Extent of employee turnover in Nigerian SMEs
Authors: Siyanbola Tejumade Omowumi , Gilman Mark W. 
Published: September 2017

PurposeThe purpose of this paper is to assess the magnitude of employee turnover (E-turnover) in Nigerian small- and medium-sized enterprises (SMEs) with particular focus on the manufacturing and service firms adjudged as central to the growth and development of Nigerian economy.Design/methodology/approachData from 602 employees and 94 owner/managers of SMEs located in three Southwestern Nigerian states were collected through survey questionnaire and analysed quantitatively.FindingsEmployees’ and management’s responses indicated that E-turnover still pervades the Nigerian SMEs surveyed with most employees leaving their jobs in less than a year of employment. Multiple exits also occurred; additionally, employees were more prone to exiting if they were male, older, had a smaller family size and/or worked in the manufacturing rather than service SMEs.Research limitations/implicationsMore needs to be done to comprehend owner-managers’ apparent deliberate disguise of employee over-casualisation in the SMEs studied, an act that appeared to limit the interpretation of status-related turnover extent among employees.Practical implicationsTwenty-first century businesses need to stimulate sustainable cost-effective employment relationship capable of thwarting the threat accompanying high E-turnover in businesses.Originality/valueThrough this research, extant global E-turnover literature (largely on western businesses) is enriched by dedicated empirical data on Nigerian SMEs that this study offers.
Pay reductions and work attitudes: the moderating effect of employee involvement practices
Authors: Wang Wen , Seifert Roger 
Published: September 2017

PurposeSince the 2008 financial crisis, the UK workforce in general has experienced a period of stagnant and falling wages in both nominal and real terms. The main parties involved remain unsure of the consequences from such a historically unusual phenomenon. The purpose of this paper is twofold: first, to explore the main effect on job satisfaction and organizational commitment of those employees who had experienced pay reductions (nominal wage cuts or pay freezes under a positive inflation rate) as compared with those who experienced nominal pay rises during the recent recession; and second, to examine the moderating effect of employee involvement (EI) practices on that relationship. This was done by using aggregated employee perception data to measure organizational EI practices.Design/methodology/approachEmployee-employer matched data were used, involving 8,489 employees and their associated 497 organizations (medium or large sized). The number of employees from each organization was between 15 and 25. The data used were extracted from the 2011 Workplace Employment Relations Study in the UK to which the authors applied hierarchical linear regression in STATA 13.FindingsThe results indicate that when compared with those employees who had nominal pay rises during the recession, employees who had wage cuts or freezes (with 5 percent inflation rate) are significantly and negatively associated with their job satisfaction and organizational commitment, even when controlling for important variables such as perception of job insecurity and the degree of adverse impact caused by recession on the organization studied. That is to say, facing the same perception of job loss, those who experienced pay reductions are significantly unhappier and less committed than those who had pay rises. However, the adverse effect of pay reductions on employees’ work attitudes is much less in workplaces characterized by a high, as opposed to a low level, of EI practices.Research limitations/implicationsImplications, limitations, and further research issues are discussed in light of current employment relations’ practices.Originality/valueThe intention is to extend the current debate on employment relations under adverse changes such as pay reductions. Thus, the unique contribution of this study is to examine the value of EI in modifying extreme employee reactions to adverse changes.
German temporary agency workers’ SWB: the impact of POS provided by agencies
Authors: Imhof Susanne , Andresen Maike 
Published: September 2017

PurposeThe purpose of this paper is to focus on the specific relationship between temporary agency workers (TAWs) and their employing temporary work agencies in Germany that is characterized – in contrast to other European countries – by agencies’ central role in employment and the prevalence of permanent contracts. The study addresses a research gap in understanding the mediating role of perceived organizational support (POS) provided by temporary work agencies in the relationship between employment-specific antecedents and TAWs’ subjective well-being (SWB).Design/methodology/approachBased on a sample of 350 TAWs in Germany, the mediating role of POS provided by agencies is analyzed using structural equation modeling.FindingsThe authors show that procedural justice, performance feedback and social network availability positively relate to POS while perceived job insecurity shows the expected negative influence and distributive justice has no impact on POS. POS, in turn, positively relates to SWB. The partially mediating effect of POS between employment-specific antecedents and SWB is also confirmed.Research limitations/implicationsThe study is based on cross-sectional data and self-reported measures; this may limit causal inferences.Practical implicationsThe results highlight the importance of agencies creating POS and reducing perceived job insecurity for improving TAWs’ SWB.Originality/valueThe study contributes to previous POS research by focusing on the agencies’ role and by showing the mediating effect of POS on TAWs’ SWB in Germany.
Do multinational subsidiaries demonstrate a convergence across their HRM practices in a less developed host-country?
Authors: Ayentimi Desmond Tutu , Burgess John , Dayaram Kantha 
Published: September 2017

PurposeUsing an institutionalist perspective, and through a case study analysis, the purpose of this paper is to examine whether subsidiaries of MNEs demonstrate a convergence across their HRM practices in a less developed host-country context.Design/methodology/approachThis paper reports on an exploratory qualitative study involving five MNEs subsidiaries that operate in Ghana and originate from the UK, France, Germany, and India. The authors applied thematic and cross-case analysis techniques to explore similarities and differences in their HRM practices by drawing data from in-depth face-to-face interviews and document analyses.FindingsFindings suggest that MNE subsidiaries demonstrate more convergence across their HRM practices as well as other HRM characteristics. Despite the similarities in their HRM practices, the evidence suggests that MNE subsidiaries’ HRM practices were similar to corporate headquarters HRM practices. It appears that the host-country has less influence in driving their convergence but rather the country-of-origin effect; competitive isomorphic pressure and global integration benefits were driving their convergence across their HRM practices.Originality/valueThis study makes a contribution to the convergence-divergence literature in the international HRM (IHRM) domain with specific focus on addressing an under-researched context of less developed host-countries. One of the puzzles in comparative and IHRM literature yet to be resolved is the convergence-divergence thesis of firms’ HRM practices.
Organizational support
Authors: Ye Xiaoqian , Li Ling , Tan Xuejun 
Published: September 2017

Purpose
Drawing on recent literature and empirical data, the purpose of this paper is to explore the relationships between perceived organizational support (POS), perceived overqualification (POQ) and turnover intentions (TI) in repatriates working in multinational corporations (MNCs).

Design/methodology/approach
Survey data were collected from 145 repatriates who had been contacted beforehand from MNCs in China. Structural equation modeling and hierarchical regression are used to examine the data.

Findings
It is shown that POQ and POS both affect repatriates TI, with POQ having the stronger effect, while POS plays a mediatory role between POQ and TI. Specifically, under the same POQ, repatriates TI will decrease as the POS increases.

Research limitations/implications
The study design is cross-sectional and based on self-reporting, which makes causal explanations of the results difficult.

Practical implications
POQ and POS are both shown to influence TI, with POQ having the greater effect. This means managers can offset the effect of repatriates POQ on TI by providing better support and assistance, which can help MNCs reduce repatriates TI and retain employees.

Originality/value
This paper examines the antecedents of TI, and adds valuable new insights to the literature on repatriation through its research data, offering further evidence that managers in transnational corporations should pay more attention to organizational support policy on repatriates in order to reduce their turnover.
Onboarding is a change
Authors: Karambelkar Mohan , Bhattacharya Shubhasheesh 
Published: September 2017

Purpose
The purpose of this paper is to examine the onboarding process with reference to the change management model ADKAR to improve effectiveness.

Design/methodology/approach
Change management phases and project management phases of the ADKAR model are applied to onboarding process, and onboarding activities are analyzed.

Findings
The change management approach and project management approach provide a systematic design and implementation plan for onboarding.

Originality/value
HR professionals can plan a customized, systematic, and holistic onboarding program covering technical and non-technical aspects in terms of knowledge, skills, abilities, and behavior.