bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish
Authors: Naftaly Alice S. , Pau Shana , White Michael A. 
Published: November 2020

AbstractAlternate isoforms contribute immensely to phenotypic diversity across eukaryotes. While short read RNA-sequencing has increased our understanding of isoform diversity, it is challenging to accurately detect full-length transcripts, preventing the identification of many alternate isoforms. Long-read sequencing technologies have made it possible to sequence full length alternative transcripts, accurately characterizing alternative splicing events, alternate transcription start and end sites, and differences in UTR regions. Here, we utilize PacBio long read RNA-sequencing (Iso-Seq) to examine the transcriptomes of five tissues in threespine stickleback fish (Gasterosteus aculeatus), a widely used genetic model species. The threespine stickleback fish has a refined genome assembly with gene annotations that are based on short-read RNA sequencing and predictions from coding sequence of other species. This suggests some of the existing annotations may be inaccurate or alternative transcripts may not be fully characterized. Using Iso-Seq we detected thousands of novel isoforms, indicating many isoforms are absent in the current Ensembl gene annotations. In addition, we refined many of the existing annotations within the genome. We noted many improperly positioned transcription start sites that were refined with long-read sequencing. The Iso-Seq predicted transcription start sites were more accurate, verified through ATAC-seq. We were also able to detect many alternative splicing events between sexes and across tissues. We found a substantial number of genes in both somatic and gonad tissue that had sex-specific isoforms. Our study highlights the power of long-read sequencing to study the complexity of transcriptomes, greatly improving genomic resources for the threespine stickleback fish.
Tracking the Movement of Electronic Cigarette Flavor Chemicals and Nicotine from Refill Fluids to Aerosol, Lungs and Exhale
Authors: Khachatoorian Careen , McWhirter Kevin J. , Luo Wentai , Pankow James F. , Talbot Prue 
Published: November 2020

SUMMARYElectronic cigarettes (ECs) have been linked to lung diseases, including COVID-19, with little understanding of exposure, retention, and exhalation of EC aerosol chemicals. Here, flavor chemicals and nicotine were quantified in two refill fluids, their transfer efficiency to EC aerosols was determined, exhalation by human participants was measured, and chemical retention was modeled. Nicotine transferred well to aerosols irrespective of topography; however, transfer efficiencies of flavor chemicals depended on the chemical, puff volume, puff duration, pump head, and EC power. Participants could be classified as “mouth inhalers” or “lung inhalers” based on their retention and exhale of flavor chemicals and nicotine. Only mouth inhalers exhaled sufficient concentrations of flavor chemicals and nicotine to contribute to chemical deposition on environmental surfaces. These data help distinguish two types of EC users, add to our knowledge of chemical exposure during vaping, and provide information useful in treating EC-related diseases and regulating EC use.
Flexible loans and access to agricultural credit for smallholder farmers in Kenya
Authors: Odhiambo Fredrick Onyango , Upadhyaya Radha 
Published: November 2020

PurposeThe purpose of this paper is to determine the level of flexibility in loan products offered to smallholder farmers in Siaya County in Kenya and to examine the effect of flexibility on access to credit.Design/methodology/approachThe paper uses primary survey data from a sample of smallholder farmers in Siaya County in Kenya who had borrowed from various lending institutions within the study area. The paper develops an index variable of loan flexibility using multiple correspondence analysis (MCA) technique. The model is estimated using both OLS and truncated regression analyses. Access to credit is measured as the amount of loan borrowed by each farmer.FindingsThe authors find that the level of flexibility of loans offered to farmers is low. Furthermore, the authors find that the level of flexibility is not significantly correlated to access to credit. Further analysis using individual components of flexible loans show that refinancing and lines of credit are more likely to improve access to credit when farmers are more educated and wealthier, respectively. The age of a farmer, the type of lender, the type of loan, education and household wealth are the main determinants of access to credit.Originality/valueThe paper adds to the debate on access to credit by showing that theoretically, while loan flexibility should lead to higher credit access, this is not a key determinant of access to credit in this context.
Employee strengths use and innovative behavior: a moderated mediation model
Authors: Ding He , Lin Xinqi , Su Weilin 
Published: November 2020

Purpose
This study aims to investigate the mediating role of positive affect and the moderating role of deficit correction in the relationship between employee strengths use and innovative behavior.

Design/methodology/approach
This study adopted a three-wave research design to gather data. A convenience sample of 189 employees working in diverse organizations in China was applied to examine the hypotheses.

Findings
The results indicated that employee strengths use was positively related to innovative behavior, and positive affect mediated the relationship between employee strengths use and innovative behavior. In addition, deficit correction enhanced the direct relationship of employee strengths use with positive affect and the indirect relationship of employee strengths use with innovative behavior through positive affect.

Originality/value
The current study contributes to the existing literature on employee strengths use-innovative behavior relationships by revealing positive affect as a mediator and deficit correction as a moderator between employee strengths use and innovative behavior.
Exploring preferences for affordable housing criteria importance among EWS in India
Authors: Ghumare Pavan Namdeo , Chauhan Krupesh A. , Yadav Sanjaykumar M. 
Published: November 2020

Purpose
The purpose of this paper is to provide affordable housing to economically weaker section (EWS). The enormity of India’s housing affordability problem has led the authors to study and analyze the criteria delaying an affordable housing for EWS. The issues affecting supply and demand for affordable housing in Indian urban areas for EWS are analyzed.

Design/methodology/approach
The judgment sampling is used among housing and planning experts working in five different sectors, including local authorities, housing developers, housing sectors, town planning and property/affordable housing consultants. The study has established the problem and acknowledged 30 factors behind it. A total of 349 questionnaires were administered among the housing experts in 4 states of India. Descriptive statistical method was used to determine the significance of criteria.

Findings
A complete structure of criteria signifying housing affordability, established by the authors, is validated and analyzed in this paper. The questionnaire surveys were conducted with housing and planning experts across the four states of India to determine household perceptions on the criteria contributing to housing affordability and to rank these criteria according to their importance. The study establishes that the experts’ views on this issue differ insignificantly across different states of India, while they differ in certain levels depending on the urban area.

Practical implications
To build successful societies for the future, the authors wish to draw closer on affordability issues for EWS. The suggestions prominent information to investors, and real estate firms, which could assistance ecological growth of housing projects that are affordable.

Originality/value
Based on the examination of the ranking and greatness of housing criteria, this paper further suggests possible developments for EWS in India.
Mapping geographic patterns in federal corporate agreements
Authors: Homer Emily M. , Higgins George E. 
Published: November 2020

Purpose
The purpose of this study is to use crime mapping techniques to examine geographic patterns of signed deferred and non-prosecution agreements across federal districts. The purpose is also to examine the variation in the number of agreements by the district since 1992.

Design/methodology/approach
This study uses data from the Corporate Prosecution Registry to examine geographic patterns in federal corporate agreements since 1992 (n = 534). Choropleth mapping techniques were used to create national crime maps displaying the geographic locations of signed corporate agreements.

Findings
The results showed that, overall, prosecutors in the District of Columbia have signed the most federal corporate agreements although there is some variation over time.

Research limitations/implications
This study is unable to determine the causes of changes in the geographic placement or number of agreements signed. It is also unable to determine the precise geographic locations of crimes, but only the location of the District Court that elected to pursue a federal agreement with the organization.

Practical implications
The wide discretion prosecutors have in the agreement process has led to an overall lack of transparency concerning prosecutors’ decision-making when signing agreements with organizations. This study helps to make the number and geographic location of agreements more transparent.

Originality/value
This study uses crime mapping techniques to visually depict the locations of signed agreements allowing for visual comparisons and analyzes for an extended period of time.
Mauritius as an offshore financial centre and laws relating to tax avoidance and evasion
Authors: Beebeejaun Ambareen 
Published: November 2020

Purpose
While Mauritius is ranked as the fastest growing financial centre in Africa and the second-fastest-growing offshore financial centre (OFC) in the word by the New World Health in 2019, the country is facing severe allegations that it is progressing at the expense of other developing countries. In this respect, this paper aims to assess the contribution of the Mauritius OFC, the robustness of tax avoidance and evasion laws, the endeavours undertaken by the Mauritius Government to promote Mauritius OFC and the alleged classification of Mauritius as a tax haven.

Design/methodology/approach
To achieve the above research objectives, this paper will adopt the black letter approach. That is, the relevant legislation and case laws will be scrutinised. Also, books, journal articles, newspaper articles, reports from international bodies amongst others will be used. The research methodology also comprising a critical analysis which implies that existing studies conducted on the subject matter of this research will be assessed and the extent to which the researcher agrees with the existing work will be weighed.

Findings
Based on the critical analysis, this paper recommends that the Mauritius Income Tax Act be amended to provide for punitive and corrective actions for those engaged in impermissible tax avoidance. Additionally, for transparency and clarity, it is suggested that the Mauritius Revenue Authority (MRA) clarifies in a practice note the factors that it considers when determining the tax liability that should have been payable or when detecting tax avoidance cases. Similarly, to discourage tax evasion, the fines and penalties for tax-evading offences should be more strict and a regulatory framework for tax practitioners need to be set up.

Originality/value
To the author’s knowledge, this paper is amongst the first academic research that emphasises the position of Mauritius as an OFC and critically analysed the related laws relating to the financial world.
High variation of mitochondrial DNA diversity as compared to nuclear microsatellites in mammalian populations
Authors: Saitoh Takashi 
Published: November 2020

AbstractThe effective gene number (the number of genes that can be inherited) of mitochondrial DNA (mtDNA) is one‐fourth of that of nuclear DNA (ncDNA) in idealized populations. Therefore, mtDNA haplotype diversity (h) is predicted to be lower than ncDNA heterozygosity (HE) because of the higher effect of genetic drift on mtDNA. This prediction has not yet been systematically tested. To this end, in this study, published data for 739 populations of 108 mammalian species (66 terrestrial and 42 marine species) revealed the following patterns: (a) h was higher than HE in 54.9% of populations, (b) the variance of h (0.097) was significantly higher than that of HE (0.018) and (c) the frequency distribution of h differed between terrestrial and marine species. The terrestrial species exhibited a U‐shaped distribution, whereas the marine species exhibited a right triangle shape. HE showed a unimodal distribution for both groups. (d) The mean of HE was similar between the terrestrial (0.668) and marine (0.672) species, whereas the mean of h was significantly lower for the terrestrial species (0.578) than for the marine species (0.740). Two hypotheses were considered to explain the above‐described patterns, one of which was based on the higher mutation rates of mtDNA, while the other was based on a nested subpopulation structure in which an ncDNA‐based population includes several mtDNA‐based subpopulations. Herein, the plausibility of these two hypotheses was discussed with a focus on the higher intraspecific variation of h.
Abiotic conditions outweigh microbial origin during bacterial assembly in soils
Authors: Kaminsky Laura M. , Esker Paul D. , Bell Terrence H. 
Published: November 2020

SummaryUnderstanding the processes guiding microbial community assembly in soils is essential for predicting microbiome structure and function following soil disturbance events like agricultural soil fumigation. However, assembly outcomes are complex and variable, being affected by both selective abiotic forces and by the history of colonizing microorganisms. To untangle the interactions between these factors, we conducted a controlled microcosm study tracking bacterial assembly in cleared soils over 7 weeks. We used mesh bags to connect five unsterilized source soils, differing in land use history (forested, agricultural, or fallow), with four sterile recipient soil treatments, differing in abiotic conditions (no soil additives, salt addition, urea addition, or mixed salt/urea addition). We found that 59%–96% of bacterial colonizers after 1 week were Firmicutes, but by 7 weeks Actinobacteria and Bacteroidetes were also dominant. Salt and nitrogen additions reshaped bacterial assembly by constraining alpha diversity by up to half and biomass accumulation by up to an order of magnitude. Within‐treatment dispersion was significantly lower for salt and nutrient addition microcosms, suggesting deterministic selective pressures. In contrast, source soil origin had little impact on assembly trajectories. These results suggest that abiotic conditions can overshadow microbial source history in shaping community assembly outcomes.
Public support for state surveillance
Authors: ZILLER CONRAD , HELBLING MARC 
Published: November 2020

AbstractThis study examines citizens’ support for state surveillance, contingent upon factors related to policy design and the context of implementation. While most people want to live in a secure environment, we argue in this study that the support of policies to reach this goal depends on their necessity, extensiveness and reliability. Results from survey experiments in four European countries show that citizens are ready to approve the introduction of far‐reaching state surveillance that includes measures of facial recognition and motion detection. Public support is further enhanced if these measures are to be targeted at potential criminals, rather than at all citizens (i.e., policy extensiveness), as well as if a safety threat is salient (i.e., policy necessity). Concerns about data security reduce support (i.e., policy reliability). While these conditions matter for the support of specific policies, they do not influence how trustworthy citizens consider government and other political authorities to be.
Whole genome sequencing of silver carp (Hypophthalmichthys molitrix) and bighead carp (Hypophthalmichthys nobilis) provide novel insights into their evolution and speciation
Authors: Jian Jianbo , Yang Liandong , Gan Xiaoni , Wu Bin , Gao Li , Zeng Honghui , Wang Xuzhen , Liang Zhiqiang , Wang Ying , Fang Lihua , Li Jie , Jiang Sanjie , Du Kang , Fu Beide , Bai Mingzhou , Chen Ming , Fang Xiaodong , Liu Huanzhang , He Shunping 
Published: November 2020

AbstractThe edible silver carp (Hypophthalmichthys molitrix) and bighead carp (H. nobilis), which are two of the “Four Domesticated Fish” of China, are cultivated intensively worldwide. Here, we constructed 837‐ and 845‐Mb draft genome assemblies for the silver carp and the bighead carp, respectively, including 24,571 and 24,229 annotated protein‐coding genes. Genetic maps, anchoring 71.7% and 83.8% of all scaffolds, were obtained for the silver and bighead carp, respectively. Phylogenetic analysis showed that the bighead carp formed a clade with the silver carp, with an estimated divergence time of 3.6 million years ago; the time of divergence between the silver carp and zebrafish was 50.7 million years ago. An East Asian cyprinid genome‐specific chromosome fusion took place ~9.2 million years after this clade diverged from the clade containing the common carp and Sinocyclocheilus. KEGG and GO analyses indicated that the expanded gene families in the silver and bighead carp were associated with diseases, the immune system and environmental adaptations. Genomic regions differentiating the silver and bighead carp populations were detected based on the whole‐genome sequences of 42 individuals. Genes associated with the divergent regions were associated with reproductive system development and the development of primary female sexual characteristics. Thus, our results provided a novel systematic genomic analysis of the East Asian cyprinids, as well as the evolution and speciation of the silver carp and bighead carp.
Sulfur assimilation in corals with aposymbiotic and symbiotic zooxanthellae
Authors: Higuchi Tomihiko , Tanaka Kentaro , Shirai Kotaro , Yuyama Ikuko , Mezaki Takuma , Takahata Naoto , Sano Yuji 
Published: November 2020

SummaryAlthough sulfate ions are the main form of sulfur in the ocean, there is limited knowledge on their use by living organisms. Stable isotope labelling and NanoSIMS analysis were used in this study to clarify how sulfate, in seawater, is assimilated by corals and zooxanthellae at the cellular level. Aposymbiotic and symbiotic coral juveniles from the genus Acropora were incubated for 2 days in filtered seawater with 34S‐labelled sulfate. Further, the labelled corals were incubated for additional 2 days in natural seawater. Mapping of sulfur isotopes (34S/32S) showed that the ‘hotspots’ were enriched in 34S on a sub‐micro level and were heterogeneously distributed in the coral soft tissues. Specifically, 34S hotspots were found in both the symbiotic zooxanthellae and coral host tissues. In aposymbiotic corals, 34S was detected in the tissues, indicating that the host corals directly assimilated the sulfate ions without any aid from the zooxanthellae. Even after 2 days in normal seawater, the 34S label was clearly seen in both symbiotic and aposymbiotic corals, indicating that the assimilated sulfur was retained for at least 2 days.
PSPManalysis: Steady‐state and bifurcation analysis of physiologically structured population models
Authors: de Roos André M. 
Published: November 2020

Abstract

How environmental conditions affect the life history of individuals and how these effects shape population and community dynamics on ecological and evolutionary time‐scales is a central question in many eco‐evolutionary studies.

Physiologically structured population models (PSPMs) allow to address this question theoretically as PSPMs are built on a function‐based life‐history model, which explicitly describes how life history depends on individual traits and environmental factors. PSPMs furthermore explicitly account for population feedback on these environmental factors, which translates into density‐dependent effects on life history.

PSPManalysis is an r package that allows to simulate ecological dynamics of PSPMs, compute their ecological steady states as a function of model parameters and detect bifurcation points in the computed curves where dynamics change drastically. It furthermore allows for analysing evolutionary dynamics and evolutionary singular states of PSPMs based on Adaptive Dynamics theory. The package only requires a relatively straightforward specification of the life‐history functions as input.

Compared to dynamic simulations alone, PSPManalysis uses methods from bifurcation analysis to gain a more complete and comprehensive understanding of model behaviour which is much less dependent on particular parameter values or initial model conditions. Given the central role of the individual life history in many studies, there is substantial scope for using PSPManalysis in fields as diverse as ecology, ecotoxicology, conservation biology and evolutionary biology.
Tumor mutation burden as a biomarker for lung cancer patients treated with pemetrexed and cisplatin (the JIPANG‐TR)
Authors: Sakai Kazuko , Tsuboi Masahiro , Kenmotsu Hirotsugu , Yamanaka Takeharu , Takahashi Toshiaki , Goto Koichi , Daga Haruko , Ohira Tatsuo , Ueno Tsuyoshi , Aoki Tadashi , Nakagawa Kazuhiko , Yamazaki Koji , Hosomi Yukio , Kawaguchi Koji , Okumura Norihito , Takiguchi Yuichi , Sekine Akimasa , Haruki Tomohiro , Yamamoto Hiromasa , Sato Yuki , Akamatsu Hiroaki , Seto Takashi , Saeki Sho , Sugio Kenji , Nishio Makoto , Okabe Kazunori , Yamamoto Nobuyuki , Nishio Kazuto 
Published: November 2020

AbstractThe JIPANG study is a randomized phase III study of pemetrexed/cisplatin (Pem/Cis) versus vinorelbine/cisplatin (Vnr/Cis) for completely resected stage II‐IIIA non‐squamous non‐small cell lung cancer (Ns‐NSCLC). This study did not meet the primary endpoint (recurrence‐free survival, RFS) but Pem/Cis had a similar efficacy to Vnr/Cis with a better tolerability. Tumor mutation burden (TMB) is thought to have a predictive value of immune checkpoint inhibitors. However, the relevance of TMB to cytotoxic chemotherapy remains unknown. This exploratory study investigates the relationship between tumor mutation profiles and clinical outcome of Pem/Cis. Formalin‐fixed, paraffin‐embedded tumor tissues (n = 389) were obtained from the patients. Mutation status of tissue DNA was analyzed by targeted deep sequencing. Epidermal growth factor receptor (EGFR) mutations were detected frequently in Ns‐NSCLC (139/374). Patients without any EGFR mutations experienced longer RFS in the Pem/Cis arm versus Vnr/Cis arms. Pem/Cis in patients with high TMB (≥12‐16 mut/Mb) tended to have improved survival. In patients with wild‐type EGFR, TMB ≥ 12 mut/Mb was significantly associated with improved RFS with Pem/Cis versus Vnr/Cis (not reached vs 52.5 months; hazard ratio (HR) 0.477). It could be proposed that TMB was predictive of RFS benefit with Pem/Cis versus Vnr/Cis in Ns‐NSCLC. Further investigation is required to determine whether TMB combined with EGFR mutation status could be used as a predictive biomarker.