bluuebunny/crossref_metadata_2025_split huggingface dataset:
DenVar: Density-based Variation analysis of multiplex imaging data
Authors: Seal Souvik , Vu Thao , Ghosh Tusharkanti , Wrobel Julia , Ghosh Debashis 
Published: September 2021

AbstractMultiplex immunohistochemistry (mIHC) and multiplexed ion beam imaging (MIBI) platforms have become increasingly popular for studying complex single-cell biology in the tumor microenvironment (TME) of cancer subjects. Studying the intensity of the proteins that regulate important cell-functions, often known as functional markers, in the TME becomes extremely crucial for subject-specific assessment of risks, such as risk of recurrence and risk of death. The conventional approach requires selection of two thresholds, one to define the cells of the TME as positive or negative for a particular functional marker, and the other to classify the subjects based on the proportion of the positive cells. The selection of the thresholds has a large impact on the results and an arbitrary selection can lead to an incomprehensible conclusion. In light of this problem, we present a threshold-free distance between the subjects based on the probability densities of the functional markers. The distance can be used to classify the subjects into meaningful groups or can be used in a linear mixed model setup for testing association with clinical outcomes. The method gets rid of the subjectivity bias of the thresholding-based approach, enabling an easier but interpretable analysis of these types of data. With the proposed method, we analyze a lung cancer dataset from an mIHC platform, finding the difference in the density of functional marker HLA-DR to be significantly associated with the overall survival. The approach is also applied on an MIBI triple-negative breast cancer dataset to analyze effects of multiple functional markers. Finally, we demonstrate the reliability of our method through extensive simulation studies.
An ensemble deep learning framework to refine large deletions in linked-reads
Authors: Hu Yunfei , Mangal Sanidhya V , Zhang Lu , Zhou Xin 
Published: September 2021

AbstractThe detection of structural variants (SVs) remains challenging due to inconsistencies in detected breakpoints and biological complexity of some rearrangements. Linked-reads have demonstrated their superiority in diploid genome assembly and SV detection. Recently developed tools Aquila and Aquila_stLFR use a reference sequence and linked-reads to generate a high quality diploid genome assembly, using which they then detect and phase personal genetic variations. However, they both produce a substantial proportion of false positive deletion SV calls. To take full advantage of linked-reads, an effective downstream filtering and refinement framework is needed pressingly. In this work, we propose AquilaDeepFilter to filter large deletion SVs from Aquila and Aquila_stLFR. AquilaDeepFilter relies on a deep learning ensemble approach by integrating six state-of-the-art CNN backbones. The filtering of deletion SVs is formulated as a binary classification task on image data that are generated through the extraction of multiple alignment signals, including read depth, split reads and discordant read pairs. Three linked-reads libraries sequenced from the well-studied sample NA24385 and the gold standard of GiaB benchmark were used to perform thorough experiments on our proposed method. The results demonstrated that AquilaDeepFilter could increase the precision rate of Aquila while the recall rate of Aquila decreased only slightly, and the overall F1 improved by 20%. Furthermore, AquilaDeepFilter outperformed another deep learning based method for SV filtering, DeepSVFilter. Even though we designed AquilaDeepFilter for linked-reads, the framework could also be used to improve SV detection on short reads.
Risk scores for predicting HIV incidence among adult heterosexual populations in sub-Saharan Africa: a systematic review and meta-analysis
Authors: Jia Katherine M. , Eilerts Hallie , Edun Olanrewaju , Lam Kevin , Howes Adam , Thomas Matthew L. , Eaton Jeffrey W. 
Published: September 2021

AbstractIntroductionSeveral HIV risk scores have been developed to identify individuals for prioritised HIV prevention in sub-Saharan Africa. We systematically reviewed HIV risk scores to: (i) identify factors that consistently predicted incident HIV infection, (ii) review inclusion of community-level HIV risk in predictive models, and (iii) examine predictive performance.MethodsWe searched nine databases from inception until February 15, 2021 for studies developing and/or validating HIV risk scores among the heterosexual adult population in sub-Saharan Africa. Studies not prospectively observing seroconversion or recruiting only key populations were excluded. Record screening, data extraction, and critical appraisal were conducted in duplicate. We used random-effects meta-analysis to summarise hazard ratios and the area under the receiver-operating characteristic curve (AUC-ROC).ResultsFrom 1563 initial search records, we identified 14 risk scores in 13 studies. Seven studies were among sexually active women using contraceptives enrolled in randomised-controlled trials, three among adolescent girls and young women (AGYW), and three among cohorts enrolling both men and women. Consistently identified HIV prognostic factors among women were younger age (pooled adjusted hazard ratio: 1.62 [95% Confidence Interval: 1.17, 2.23], compared to above-25), single/not cohabiting with primary partners (2.33 [1.73, 3.13]) and having sexually transmitted infections (STIs) at baseline (HSV-2: 1.67 [1.34, 2.09]; curable STIs: 1.45 [1.17; 1.79]). Among AGYW only STIs were consistently associated with higher incidence, but studies were limited (n=3). Community-level HIV prevalence or unsuppressed viral load strongly predicted incidence but were only considered in three of 11 multi-site studies. The AUC-ROC ranged from 0.56 to 0.79 on the model development sets. Only the VOICE score was externally validated by multiple studies, with pooled AUC-ROC 0.626 [0.588, 0.663] (I2: 64.02%).ConclusionsYounger age, non-cohabiting, and recent STIs were consistently identified as predicting future HIV infection. Both community HIV burden and individual factors should be considered to quantify HIV risk. However, HIV risk scores had only low-to-moderate discriminatory ability and uncertain generalisability, limiting their programmatic utility.Further evidence on the relative value of specific risk factors, studies populations not restricted to ‘at-risk’ individuals, and data outside South Africa will improve the evidence base for risk differentiation in HIV prevention programmes.PROSPERO NumberCRD42021236367
Pollutants corrupt resilience pathways of aging in the nematode C. elegans
Authors: Scharf Andrea , Limke Annette , Guehrs Karl-Heinz , von Mikecz Anna 
Published: September 2021

AbstractDelaying aging while prolonging health and lifespan is a major goal in aging research. While many resources have been allocated to find positive interventions with promising results, negative interventions such as pollution and their accelerating effect on age-related degeneration and disease have been mostly neglected. Here, we used the short-lived model organism C. elegans to analyze whether two candidate pollutants interfere with positive interventions by corrupting general aging pathways. We took advantage of the immense data sets describing the age-related remodeling of the proteome including increased protein insolubilities to complement our analysis. We show that the emergent pollutant silica nanoparticles (NP) and the classic xenobiotic inorganic mercury reduce lifespan and cause a premature protein aggregation phenotype. Silica NPs rescaled the longevity effect of genetic interventions targeting the IGF-1/insulin-like signaling pathway. Comparative mass spectrometry revealed that increased insolubility of proteins with important functions in proteostasis is a shared phenotype of intrinsic- and pollution-induced aging supporting the hypothesis that proteostasis is a central resilience pathway controlling lifespan and aging. The presented data demonstrate that pollutants corrupt intrinsic aging pathways, which results in premature aging phenotypes. Reducing pollution is therefore an important step to increase healthy aging and prolong life expectancies on a population level in humans and animals.
Distinct Expansion of Group II Introns Depends on the Type of Intron-encoded Protein and Genomic Signatures in Prokaryotes
Authors: Miura Masahiro C. , Nagata Shohei , Tamaki Satoshi , Tomita Masaru , Kanai Akio 
Published: September 2021

AbstractGroup II introns (G2Is) are self-splicing ribozymes that have retroelement characteristics in prokaryotes. Although G2Is are considered an important factor in the evolution of prokaryotes, comprehensive analyses of these introns among the tens of thousands of prokaryotic genomes currently available are still limited. Here, we developed a bioinformatic pipeline that systematically collects G2Is and applied it to prokaryotic genomes. We found that in bacteria, 25% (447 of 1,790) of the total representative species had an average of 5.3 G2Is, and in archaea, 9% (28 of 296) of the total representative species had an average of 3.0 G2Is. The greatest number of G2Is per species was 101 in Arthrospira platensis (phylum Cyanobacteriota). A comprehensive sequence analysis of the intron-encoded protein (IEP) in each G2I sequence was conducted and resulted in the addition of three new IEP classes (U1–U3) to the previous classification. This analysis suggested that about 30% of all IEPs are noncanonical IEPs. The number of G2Is per species was defined almost at the phylum level, and the type of IEP was associated as a factor in the G2I increase, i.e. there was an explosive increase in G2Is with bacterial C-type IEPs in the phylum Firmicutes and in G2Is with CL-type IEPs in the phylum Cyanobacteriota. We also systematically analyzed the relationship between genomic signatures and the mechanism of these increases in G2Is. This is the first study to systematically characterize G2Is in the prokaryotic phylogenies.
CNpare: matching DNA copy number profiles
Authors: Chaves-Urbano Blas , Hernando Bárbara , Garcia Maria J , Macintyre Geoff 
Published: September 2021

AbstractSelecting the optimal cancer cell line for an experiment can be challenging given the diversity of lines available. Cell lines are often chosen based on their tissue of origin, however, the results of large-scale pan-cancer studies suggest that matching lines based on molecular features may be more appropriate. Existing approaches are available for matching lines based on gene expression, DNA methylation or low resolution DNA copy number features. However, a specific tool for computing similarity based on high resolution genome-wide copy number profiles is lacking. Here, we present CNpare, which identifies similar cell line models based on genome-wide DNA copy number. CNpare compares copy number profiles using four different similarity metrics, quantifies the extent of genome differences between pairs, and facilitates comparison based on copy number signatures. CNpare incorporates a precomputed database of 1,170 human cancer cell line profiles for comparison. In an analysis of separate cultures of 304 cell line pairs, CNpare identified the matched lines in all cases. CNpare provides a powerful solution to the problem of selecting the best cell line models for cancer research, especially in the context of studying chromosomal instability.
Critical role of DNA unwinding and Cas9 conformational changes in modelling off-target effects
Authors: Khakimzhan Aset , Noireaux Vincent 
Published: September 2021

AbstractCRISPR-Cas9 off-target effects interfere with the ability to accurately perform genetic edits. To predict off-target effects CRISPR-Cas9 researchers perform high throughput guide RNA mismatch and bulge experiments and then use the data to fit thermodynamic binding models. While impactful from an engineering perspective such models are not based on the experimentally observed target interrogation process and thus incorrectly measure the energetic effects mismatches have on the system. In this work we convert an experimentally deduced qualitive model of target interrogation to a linear ODE model and demonstrate that the mismatch tolerance patterns observed in experiments do not need to be caused by differences in energetic penalties of mismatches but rather are emergent effects of the timing and coordination of target DNA unwinding and Cas9 conformational changes.
Microbiological quality assessment of five common foods sold at different points of sale in Burkina-Faso
Authors: Compaore Muller K. A , Kpoda Dissinviel Stéphane , Bazie Bazoin S. R. , Ouedraogo Marcelline , Yakoro Alphonse , Nikiema Fulbert , Belemlougri Asseto , Meda Romaric , Bande Moumouni , Barro Nicolas , Kabre Elie 
Published: September 2021

AbstractThe aim of the present study was to assess the microbial quality of five different types of food such as bread, pasta, rice with sauce, beans and milk sold in five localities of Burkina Faso. One hundred and one (101) samples were collected and microbial quality were assessed by evaluating the food hygiene indicators such as total aerobic mesophilic flora, total coliforms, thermotolerant coliforms, yeast and mould. Food safety indicators such as Escherichia coli, Salmonella, coagulase-positive staphylococci, Clostridium perfringens and Bacillus cereus were checked too. All samples were analyzed under ISO methods.The results showed that 73.27% of samples were satisfactory while 14.85% were acceptable and 11.88% were not satisfactory according to international standards. Among the food safety indicators sought, Escherichia coli was detected in two samples and Bacillus cereus in four samples. Most of the analyzed food exhibited good hygiene behavior within the acceptable limits and the highest of not satisfactory rate was observed in milk powder and rice with sauce. Ouagadougou samples record the highest number of not satisfactory samples.Despite the general quality was satisfactory, the presence of specific microorganisms such as coliforms is indicative of the poor hygiene surrounded these foods. It is therefore necessary to train and follow up the vendors in the handling of equipment, hand-washing practices and selling environment hygiene for better improvement of the quality of the street foods.
Laboratory exploration of mineral precipitates from Europa's subsurface ocean
Authors: Thompson Stephen P. , Kennedy Hilary , Butler Benjamin M. , Day Sarah J. , Safi Emmal , Evans Aneurin 
Published: September 2021

The precipitation of hydrated phases from a chondrite-like Na–Mg–Ca–SO4–Cl solution is studied usingin situsynchrotron X-ray powder diffraction, under rapid- (360 K h−1,T= 250–80 K,t= 3 h) and ultra-slow-freezing (0.3 K day−1,T = 273–245 K,t= 242 days) conditions. The precipitation sequence under slow cooling initially follows the predictions of equilibrium thermodynamics models. However, after ∼50 days at 245 K, the formation of the highly hydrated sulfate phase Na2Mg(SO4)2·16H2O, a relatively recent discovery in the Na2Mg(SO4)2–H2O system, was observed. Rapid freezing, on the other hand, produced an assemblage of multiple phases which formed within a very short timescale (≤4 min, ΔT= 2 K) and, although remaining present throughout, varied in their relative proportions with decreasing temperature. Mirabilite and meridianiite were the major phases, with pentahydrite, epsomite, hydrohalite, gypsum, blödite, konyaite and loweite also observed. Na2Mg(SO4)2·16H2O was again found to be present and increased in proportion relative to other phases as the temperature decreased. The results are discussed in relation to possible implications for life on Europa and application to other icy ocean worlds.
Development of career capital during expatriation: partners' perspectives
Authors: Kanstrén Kaisu , Suutari Vesa 
Published: September 2021

PurposeThe purpose of this qualitative study is to examine the effects of expatriation on the development of career capital among the partners of expatriates.Design/methodology/approachThe study draws on in-depth interviews with 30 Finnish partners of expatriates.FindingsThe results reflect the various learning experiences reported by partners of expatriates that developed their career capital during expatriation. The learning experiences related to the experience of living abroad itself and to the specific activities undertaken when abroad. The extent to which partners developed knowing-why, knowing-how and knowing-whom career capital was found to partly reflect their situation abroad as stay-at-home partners or as employees in less-demanding or more-demanding jobs. Though the experiences were developmental for all partners as have been reported among expatriates, the authors also identified several aspects in which partners' experiences differed from the typical developmental experiences of expatriates.Practical implicationsThe results also highlight the influence of initiative, an active role and career self-management skills in partners' career capital development.Originality/valueThis paper advances the understanding of how expatriation affects expatriate partners' career capital, a topic that has not previously been studied in-depth.
Human resources, organizational learning and due diligence: avoiding the honeymoon hangover effect in mergers & acquisitions
Authors: Lattuch Frank , Ruppert Enno 
Published: September 2021

Purpose
Mergers & acquisitions (M&As) can be an effective way to expand into new markets or business opportunities. Yet, a considerable number of failed M&As can be attributed to disregarded human resource (HR) concerns. In particular, an organization’s leadership tends to hail the advantages of a merger or acquisition during the early stages, raising employees’ expectations (honeymoon effect). Many documented failures in such corporate transactions indicate organizational members’ declining satisfaction following a deal (hangover effect).

Design/methodology/approach
Drawing on in-depth interviews with senior M&A experts (n = 12) at a global big-four accountancy firm and focus group sessions with their respective clients, this study investigates in two cases the interplay between HR issues and M&A transactions and infers effective risk management actions.

Findings
A honeymoon hangover after a transaction may appear in organizations if HR issues are neglected. Study results provide notable implications for HR departments and HR professionals facing a merger or acquisition. These implications include (1) focusing on HR risks, (2) involving HR executives to manage the HR due diligence efforts, (3) setting up transition teams that communicate well, (4) creating policies for learning and knowledge sharing, (5) developing new competencies for the NewCo, (6) being sensitive to cultural differences and (7) considering legal aspects.

Research limitations/implications
The two transactions studied revealed patterns that are important for successful change. However, we should not underestimate the individual perspective in M&As. Further studies with interview data directly from stakeholders are important to analyze further the relationships between HR due diligence, organizational learning, effective knowledge transfer, and culture. Due to our research approach, we cannot claim that the results can be generalizable to all major M&As. Further research is needed to measure the impact of the HR Due Diligence aspects outlined on M&A success.

Originality/value
Although M&As have been much researched, relatively little has been written on practical managerial adaptation from a human resource perspective and its implications for organizational learning. This article helps address this imbalance by providing a people-oriented approach for effectively managing M&As from beginning to integration.
Exploration of employability perceptions with blended multi-criteria decision-making methods
Authors: Castro-Lopez Adrian , Monteiro Sílvia , Bernardo Ana B. , Almeida Leandro S. 
Published: September 2021

PurposeThe purpose of this paper is to explore employment perception of students as a relevant indicator of higher education quality, using blended multi-criteria decision-making methods.Design/methodology/approachThe differential impact of these variables was analyzed in this paper taking a sample of 641 students and six higher education lecturers identified as experts on young vocational careers. The traditional study of student behavior and perceptions of employability does not incorporate the uncertainty associated with multi-criteria decision processes and is therefore less adapted to the human reasoning process. This research applies traditional techniques together with fuzzy techniques capable of managing more effectively the uncertainty associated with student actions and behaviors.FindingsThis research shows that it is important to consider previous work experience, academic achievement and soft skills developed during education experiences. In this way, this research shows the lecturers how to adapt their pedagogical practices according to students' perceptions of employability and assess their students' perceptions of employability. In addition, lecturers will be able to incorporate the uncertainty associated with decision-making processes to optimize employability perception.Originality/valueHigher education-related research on uncertainty environments as multi-criteria decision problems is still in early stages. The incorporation of the uncertainty associated with decision-making processes to this field allows to optimize employability perception thanks to its adaptation to real human behavior in the adoption of decisions.
Developing human capital 4.0 in emerging economies: an industry 4.0 perspective
Authors: Singh Rohit Kumar , Agrawal Soni , Modgil Sachin 
Published: September 2021

PurposeThe present study is an attempt of identifying the human capital skills and HR-related challenges faced by top management in the perspective of industry 4.0 in emerging economies. In addition, the importance or key resources related to human assets that help in attaining competitive advantages while adopting newer digital technologies are also identified.Design/methodology/approachFor identifying the dimensions of human capital skills in the perspective of industry 4.0, an extensive review of literature was performed. Along with that, feedback from the expert was used to conceptualize the importance and relationship of the skills in the context of industry 4.0. After that, a qualitative survey was launched and triangulate method was applied for identifying the skills. AHP and DEMATEL was used to analyze the relationship among the skills and subskills and to rank them based on their importance.FindingsThe qualitative survey resulted in skills such as “Cognitive, Emotional and Behavioural skills” and subskills of them. AHP results indicated that “Cognitive skills” was found as the most important skill followed by “Emotional skills” and “Behavioural skills”. In addition to this, DEMATEL was applied for seeking the inter-relationship and identifying the “Cause” and “Effect” relationship of skills and sub-skills.Originality/valueThis study prioritizes factors in a coordinated manner and also finds the relative importance in the context of industry 4.0. It will help further in identifying and deploying human capital with the right skills and will play a significant role at the time of formulating organizational and HR level strategies.