bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trajectories from Snapshots: Integrated proteomic and metabolic single-cell assays reveal multiple independent adaptive responses to drug tolerance in a BRAF-mutant melanoma cell line
Authors: Su Yapeng , Li Guideng , Ko Melissa E. , Cheng Hanjun , Zhu Ronghui , Xue Min , Wang Jessica , Lee Jihoon W. , Frankiw Luke , Xu Alexander , Wong Stephanie , Robert Lidia , Takata Kaitlyn , Huang Sui , Ribas Antoni , Levine Raphael , Nolan Garry P. , Wei Wei , Plevritis Sylvia K. , Baltimore David , Heath James R. 
Published: September 2019

AbstractThe determination of individual cell trajectories through a high-dimensional cell-state space is an outstanding challenge, with relevance towards understanding biological changes ranging from cellular differentiation to epigenetic (adaptive) responses of diseased cells to drugging. We report on a combined experimental and theoretic method for determining the trajectories that specific highly plastic BRAFV600E mutant patient-derived melanoma cancer cells take between drug-naïve and drug-tolerant states. Recent studies have implicated non-genetic, fast-acting resistance mechanisms are activated in these cells following BRAF inhibition. While single-cell highly multiplex omics tools can yield snapshots of the cell state space landscape sampled at any given time point, individual cell trajectories must be inferred from a kinetic series of snapshots, and that inference can be confounded by stochastic cell state switching. Using a microfludic-based single-cell integrated proteomic and metabolic assay, we assayed for a panel of signaling, phenotypic, and metabolic regulators at four time points during the first five days of drug treatment. Dimensional reduction of the resultant data set, coupled with information theoretic analysis, uncovered a complex cell state landscape and identified two distinct paths connecting drug-naïve and drug-tolerant states. Cells are shown to exclusively traverse one of the two pathways depending on the level of the lineage restricted transcription factor MITF in the drug-naïve cells. The two trajectories are associated with distinct signaling and metabolic susceptibilities, and are independently druggable. Our results update the paradigm of adaptive resistance development in an isogenic cell population and offer insight into the design of more effective combination therapies.
Signaling to TRP53 and TAp63 from CHK1/CHK2 is responsible for elimination of most oocytes defective for either chromosome synapsis or recombination
Authors: Rinaldi Vera D. , Bloom Jordana C. , Schimenti John C. 
Published: September 2019

ABSTRACTEukaryotic organisms have evolved mechanisms to prevent the accumulation of cells bearing genetic aberrations. This is especially crucial for the germline, because fecundity, and fitness of progeny would be adversely affected by an excessively high mutational incidence. The process of meiosis poses unique problems for mutation avoidance, due to the requirement for SPO11-induced programmed double strand breaks (DSBs) in recombination-driven pairing and segregation of homologous chromosomes. Mouse meiocytes bearing unrepaired meiotic DSBs or unsynapsed chromosomes are eliminated before completing meiotic prophase I. In previous work, we showed that checkpoint kinase 2 (CHK2; CHEK2), a canonical DNA damage response protein, is crucial for eliminating not only oocytes defective in meiotic DSB repair (e.g.Trip13Gtmutants), but also asynapticSpo11−/−oocytes that accumulate a threshold level of spontaneous DSBs. However, rescue of such oocytes byChk2deficiency was incomplete, raising the possibility that a parallel checkpoint pathway(s) exists. Here, we show that mouse oocytes lacking both TAp63 and TRP53 protects nearly allSpo11−/−andTrip13Gt/Gtoocytes from elimination. We present evidence that checkpoint kinase I (CHK1; CHEK1), which is known to signal to TRP53, also becomes activated by persistent DSBs in oocytes, and to an increased degree when CHK2 is absent. The combined data indicate that nearly all oocytes reaching a threshold level of unrepaired DSBs are eliminated by a semi-redundant pathway of CHK1/CHK2 signaling to TRP53/TAp63.
An approach for fault prediction in SOA-based systems using machine learning techniques
Authors: Bhandari Guru Prasad , Gupta Ratneshwer , Upadhyay Satyanshu Kumar 
Published: September 2019

Purpose
Software fault prediction is an important concept that can be applied at an early stage of the software life cycle. Effective prediction of faults may improve the reliability and testability of software systems. As service-oriented architecture (SOA)-based systems become more and more complex, the interaction between participating services increases frequently. The component services may generate enormous reports and fault information. Although considerable research has stressed on developing fault-proneness prediction models in service-oriented systems (SOS) using machine learning (ML) techniques, there has been little work on assessing how effective the source code metrics are for fault prediction. The paper aims to discuss this issue.

Design/methodology/approach
In this paper, the authors have proposed a fault prediction framework to investigate fault prediction in SOS using metrics of web services. The effectiveness of the model has been explored by applying six ML techniques, namely, Naïve Bayes, Artificial Networks (ANN), Adaptive Boosting (AdaBoost), decision tree, Random Forests and Support Vector Machine (SVM), along with five feature selection techniques to extract the essential metrics. The authors have explored accuracy, precision, recall, f-measure and receiver operating characteristic curves of the area under curve values as performance measures.

Findings
The experimental results show that the proposed system can classify the fault-proneness of web services, whether the service is faulty or non-faulty, as a binary-valued output automatically and effectively.

Research limitations/implications
One possible threat to internal validity in the study is the unknown effects of undiscovered faults. Specifically, the authors have injected possible faults into the classes using Java C3.0 tool and only fixed faults are injected into the classes. However, considering the Java C3.0 community of development, testing and use, the authors can generalize that the undiscovered faults should be few and have less impact on the results presented in this study, and that the results may be limited to the investigated complexity metrics and the used ML techniques.

Originality/value
In the literature, only few studies have been observed to directly concentrate on metrics-based fault-proneness prediction of SOS using ML techniques. However, most of the contributions are regarding the fault prediction of the general systems rather than SOS. A majority of them have considered reliability, changeability, maintainability using a logging/history-based approach and mathematical modeling rather than fault prediction in SOS using metrics. Thus, the authors have extended the above contributions further by applying supervised ML techniques over web services metrics and measured their capability by employing fault injection methods.
Employers’ preferences for IT-retrainees: evidence from a discrete choice experiment
Authors: Vooren Melvin , Haelermans Carla , Groot Wim , Maassen van den Brink Henriette 
Published: September 2019

PurposeThe purpose of this paper is to present the results of a discrete choice experiment (DCE) on the competencies of potential information technology (IT)-retrainees. The results give insights in the monetary value and relative returns to both soft and hard skills.Design/methodology/approachThe authors apply a DCE in which the authors propose seven pairs of hypothetical candidates to employers based in the municipality of Amsterdam, the Netherlands. These hypothetical candidates differ on six observable skill attributes and have different starting wages. The authors use the inference from the DCE to calculate the marginal rates of substitution (MRS). The MRS gives an indication of the monetary value of each skill attribute.FindingsEmployers prefer a candidate who possesses a degree in an exact field over a similar candidate from another discipline. Programming experience from previous jobs is the most highly valued characteristic for an IT-retrainee. Employers would pay a candidate with basic programming experience a 53 percent higher starting wage. The most high-valued soft skill is listening skills, for which employers are willing to pay a 46 percent higher wage. The results of this paper show that both hard and soft skills are important, but not all soft skills are equally important.Originality/valueThe results on the returns to skills provide guidelines to tailor IT training and retraining programs to the needs of the business environment. A key strength of this paper is that the authors have information on the preference orderings for different skills and kinds of experience.
Airport noise compensation: real estate perspective
Authors: Batóg Jacek , Foryś Iwona , Konowalczuk Jan 
Published: September 2019

Purpose
This study aims to present a problem of noise compensation related to the localization of single-family houses in the restricted use areas (RUA) created around airports. The authors presented different methodological approaches to the valuation of such amends and characterized distinct solutions applied in that area in chosen countries and cities.

Design/methodology/approach
To estimate the level of those indemnities, linear models including spatial and generalized linear models, were applied. The set of explanatory variables contains quantitative and qualitative attributes of real estates. The influence of outliers indicated by means of cluster analysis on the received results were also considered.

Findings
The results show that after accounting for noise level and house characteristics, houses in noisier areas were sold for less than houses subjected to less noise. Unit prices of houses located outside the RUA were on average 17.05 per cent higher than the prices observed in zone with noise level for the daytime of 60 dB and 8.95 per cent in zone characterized by noise level for the daytime of 55 dB.

Practical implications
Received results can be compared with results obtained by other authors, but its most important application is possibility of use the proposed methodology by judicial appraisers to assess the proper level of noise compensation for home owners or tenants.

Originality/value
An identification of real estate market heterogeneity and its considering in estimation of compensation related to airport noise evidence some novelty of the research.
Field measurements of comfort, seasonal performance and cold stress in cross-laminated timber (CLT) school buildings
Authors: Adekunle Timothy Oluseun 
Published: September 2019

Purpose
The purpose of this paper is to examine the seasonal performance, occupants’ comfort and cold stress in cross-laminated timber school buildings located in the USA (Northeast region).

Design/methodology/approach
The Fall survey was done from October–November 2017. In the Winter, it was considered from December 2017–February 2018. The study measured environmental parameters in the chosen spaces. The research applied the wet-bulb globe temperature (WBGT) model to determine the indexes in various seasons.

Findings
In the Fall, the average inside temperature was 21.2°C, the average RH was 50.7 per cent, and the mean dew-point was 9.3°C. The mean inside temperature was 20.5°C in the Winter while the mean RH was 23.9 per cent and the average dew-point was −1.9°C. The overall mean inside temperatures in both seasons were within the ASHRAE comfort temperature limits for cold seasons. During the surveys, higher average values of temperature, RH and dew-point were measured in the offices than the other spaces.

Practical implications
The research showed people might be subject to lower temperatures in the hall than the other spaces. Some design parameters and occupation hours may contribute to the lower temperatures reported in the hall than the different spaces.

Originality/value
The study proposes the WBGT of 16.0°C and 13.7°C as the stress indexes in the Fall and Winter seasons correspondingly. Last, the research suggests a WBGT of 14.9°C as the overall mean stress index within the spaces considered in this study.
Fire history and plant community composition outweigh decadal multi‐factor global change as drivers of microbial composition in an annual grassland
Authors: Qin Clara , Zhu Kai , Chiariello Nona R. , Field Christopher B. , Peay Kabir G. 
Published: September 2019

Abstract

Soil microbial communities regulate and respond to key biogeochemical cycles and influence plant community patterns. However, microbial communities also respond to disturbance events, motivating an assessment of the relative roles of decadal multi‐factor global change, disturbance and plant community structure on microbial community responses.

We used high‐throughput amplicon sequencing to characterize the diversity and composition of bacterial and fungal communities in bulk soil (0–7 cm) collected in 2014 from the Jasper Ridge Global Change Experiment, a full‐factorial field experiment in which ambient and elevated levels of nitrogen deposition (+7 g N m−2 yr−1 calcium nitrate), CO2 concentration (+275 ppm), temperature (+1–2°C) and precipitation (+50% volume with +3 weeks duration) were applied to a California annual grassland from 1998 to 2014. We used linear mixed‐effects modelling to test for the effects of global change on microbial diversity (observed richness, Shannon index). We also used generalized dissimilarity modelling (GDM) to study controls on compositional dissimilarity in fungal and bacterial communities.

Bacterial community composition was best explained by exposure to fires in 2003 and 2011, whereas fungal community composition was best explained by plant community composition. The richness of fungi increased under elevated nitrogen deposition; bacterial diversity metrics decreased under warmer temperatures. Interactions between global change factors were statistically insignificant or weak.

Synthesis. Our results indicate that even on decadal time‐scales, the effects of fire history and plant community composition on bacterial and fungal community composition, respectively, outweigh the effects of multi‐factor global change. Furthermore, global change factors have mostly additive effects on microbial diversity patterns. Our results show that highly variable mediators such as fire history and plant community composition limit the generalizability of soil microbial responses to long‐term global change.
Plant physical and chemical traits associated with herbivory in situ and under a warming treatment
Authors: Descombes Patrice , Kergunteuil Alan , Glauser Gaëtan , Rasmann Sergio , Pellissier Loïc 
Published: September 2019

AbstractPlants protect themselves against herbivore attacks with physical traits and toxic secondary metabolites. Levels of plant defences and herbivore performance might shift under climate warming, particularly in alpine habitats, where herbivore pressure is currently low. Plant responses to warming should be driven by species‐specific shifts in physical and chemical defence traits.We investigated the association between plant leaf physical and chemical traits and herbivory under current and warmer climates in three grasslands along a subalpine to alpine gradient. Specifically, we measured the rate of in situ natural herbivory, and performed bioassays to measure overall plant species‐level resistance using the extreme generalist non‐native caterpillarSpodoptera littoralis. We simulated warmer conditions by using open‐top chambers and assessed the effect of warming on leaf physical and chemical traits, and how trait changes affect caterpillar performance.Natural herbivory and caterpillar performance were associated with plant physical traits, including specific leaf area, and with ordination axes representing dimensions of the plant chemical profile. We found that the warming treatment independently decreased the number of distinct chemical compounds per species, and marginally increased specific leaf area. Changes in leaf functional traits were not systematically associated with changes in caterpillar performance.Synthesis. Plant physical traits and chemical profiles are both related to natural herbivory and plant resistance againstSpodoptera littoralis. While leaf physical and chemical traits of high elevation plants were modified by the warming treatment, these changes did not result in predictable effects on plant resistance against herbivores.
Getting the Sergeants on your side: the importance of interpersonal relationships and cultural interoperability for generating interagency collaboration between nurses and the police in custody suites
Authors: Rees Gethin 
Published: September 2019

AbstractIn this article, I contribute to the literature around interagency collaboration, especially between law enforcement and health care, by reconciling the previous work of Sarah Charman (2014) with the interprofessional teamwork literature. Drawing upon a semi‐structured interview‐based study with 20 custody nurses working in English police custody suites (analysed using Framework Analysis), I explore the ways they are able to achieve interagency collaboration with a particular police officer, the Desk Sergeant. I argue that nurses accomplish interagency interoperability by interacting regularly with the Desk Sergeant, anticipating their needs and limiting their own goals to those that are commensurate with the Desk Sergeant's, notably providing information and avoiding deaths in custody. Such practices are similar to the strategies of ‘Cultural Interoperability’ noted by Charman (2014); however, this study also identifies that such strategies are only available once a successful working relationship has formed between Desk Sergeant and nurse, and as a result, similarly to the findings of interprofessional teamwork studies, the success or failure of attempts to collaborate across agencies is underpinned by interpersonal relations. The paper concludes by commenting on the importance of analysing both the interpersonal and organisation levels when studying collaboration.
Algorithmic management and app‐work in the gig economy: A research agenda for employment relations and HRM
Authors: Duggan James , Sherman Ultan , Carbery Ronan , McDonnell Anthony 
Published: September 2019

AbstractCurrent understanding of what constitutes work in the growing gig economy is heavily conflated, ranging from conceptualisations of independent contracting to other forms of contingent labour. This article calls for a move away from problematic aggregations by proposing a classification of gig work into three variants, all based strongly upon key technological features: app‐work, crowdwork, and capital platform work. Focusing specifically on the app‐work variant, this article's more delineated focus on the textured dimensions of this work proposes new lines of enquiry into employment relationships and human resource management. Examining the crucial role of algorithmic management, we critically discuss the impact of this novel mediation tool used by gig organisations for the nature of employment relations within app‐work, work assignment processes, and performance management. In so doing, we propose a series of research questions that can serve as a guide for future research in this increasingly important field.
Individualized mating system estimation using genomic data
Authors: Colicchio Jack , Monnahan Patrick J. , Wessinger Carolyn A. , Brown Keely , Kern James Russell , Kelly John K. 
Published: September 2019

AbstractThe estimation of outcrossing rates in hermaphroditic species has been a major focus in the evolutionary study of reproductive strategies, and is also essential for plant breeding and conservation. Surprisingly, genomics has thus far minimally influenced outcrossing rate studies. In this article, we generalize a Bayesian inference method (BORICE) to accommodate genomic data from multiple subpopulations of a species. As an empirical demonstration, BORICE is applied to 115 maternal families of Mimulus guttatus. The analysis shows that low‐level whole genome sequencing of parents and offspring is sufficient for individualized mating system estimation: 208 offspring (88.5%) were definitively called as outcrossed, 23 (9.8%) as selfed. After mating system parameters are established (each offspring as outcrossed or selfed and the inbreeding level of maternal plants), BORICE outputs posterior genotype probabilities for each SNP genomewide. Individual SNP calls are often burdened with considerable uncertainty and distilling information from closely linked sites (within genomic windows) can be a useful strategy. For the Mimulus data, principal components based on window statistics were sufficient to diagnose inversion polymorphisms and estimate their effects on spatial structure, phenotypic and fitness measures. More generally, mating system estimation with BORICE can set the stage for population and quantitative genomic analyses, particularly researchers collect phenotypic or fitness data from maternal individuals.
Assessment of genetic diversity and population structure in cultured Australian Pacific oysters
Authors: Kijas J. W. , Gutierrez A. P. , Houston R. D. , McWilliam S. , Bean T. P. , Soyano K. , Symonds J. E. , King N. , Lind C. , Kube P. 
Published: September 2019

SummaryThe recent development of Pacific oyster (Crassostrea gigas) SNP genotyping arrays has allowed detailed characterisation of genetic diversity and population structure within and between oyster populations. It also raises the potential of harnessing genomic selection for genetic improvement in oyster breeding programmes. The aim of this study was to characterise a breeding population of Australian oysters through genotyping and analysis of 18 027 SNPs, followed by comparison with genotypes of oyster sampled from Europe and Asia. This revealed that the Australian populations had similar population diversity (HE) to oysters from New Zealand, the British Isles, France and Japan. Population divergence was assessed using PCA of genetic distance and revealed that Australian oysters were distinct from all other populations tested. Australian Pacific oysters originate from planned introductions sourced from three Japanese populations. Approximately 95% of these introductions were from geographically, and potentially genetically, distinct populations from the Nagasaki oysters assessed in this study. Finally, in preparation for the application of genomic selection in oyster breeding programmes, the strength of LD was evaluated and subsets of loci were tested for their ability to accurately infer relationships. Weak LD was observed on average; however, SNP subsets were shown to accurately reconstitute a genomic relationship matrix constructed using all loci. This suggests that low‐density SNP panels may have utility in the Australian population tested, and the findings represent an important first step towards the design and implementation of genomic approaches for applied breeding in Pacific oysters.