bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanopype: a modular and scalable nanopore data processing pipeline
Authors: Giesselmann Pay , Hetzel Sara , Müller Franz-Josef , Meissner Alexander , Kretzmer Helene 
Published: June 2019

Abstract

Summary
Long-read third-generation nanopore sequencing enables researchers to now address a range of questions that are difficult to tackle with short read approaches. The rapidly expanding user base and continuously increasing throughput have sparked the development of a growing number of specialized analysis tools. However, streamlined processing of nanopore datasets using reproducible and transparent workflows is still lacking. Here we present Nanopype, a nanopore data processing pipeline that integrates a diverse set of established bioinformatics software while maintaining consistent and standardized output formats. Seamless integration into compute cluster environments makes the framework suitable for high-throughput applications. As a result, Nanopype facilitates comparability of nanopore data analysis workflows and thereby should enhance the reproducibility of biological insights.

Availability and implementation
https://github.com/giesselmann/nanopype, https://nanopype.readthedocs.io.

Supplementary information
Supplementary data are available at Bioinformatics online.
VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations
Authors: Stephenson James D , Laskowski Roman A , Nightingale Andrew , Hurles Matthew E , Thornton Janet M 
Published: June 2019

Abstract

Motivation
Understanding the protein structural context and patterning on proteins of genomic variants can help to separate benign from pathogenic variants and reveal molecular consequences. However, mapping genomic coordinates to protein structures is non-trivial, complicated by alternative splicing and transcript evidence.

Results
Here we present VarMap, a web tool for mapping a list of chromosome coordinates to canonical UniProt sequences and associated protein 3D structures, including validation checks, and annotating them with structural information.

Availability and implementation
https://www.ebi.ac.uk/thornton-srv/databases/VarMap.

Supplementary information
Supplementary data are available at Bioinformatics online.
Role of activin, follistatin, and inhibin in the regulation of Kiss-1 gene expression in hypothalamic cell models†
Authors: Tumurgan Zolzaya , Kanasaki Haruhiko , Tumurbaatar Tuvshintugs , Oride Aki , Okada Hiroe , Hara Tomomi , Kyo Satoru 
Published: June 2019

Abstract
Kisspeptin (encoded by the Kiss-1 gene) in the arcuate nucleus (ARC) of the hypothalamus governs the hypothalamic-pituitary-gonadal (HPG) axis by regulating pulsatile release of gonadotropin-releasing hormone (GnRH). Meanwhile, kisspeptin in the anteroventral periventricular nucleus (AVPV) region has been implicated in estradiol (E2)-induced GnRH surges. Kiss-1–expressing cell model mHypoA-55 exhibits characteristics of Kiss-1 neurons in the ARC region. On the other hand, Kiss-1 expressing mHypoA-50 cells originate from the AVPV region. In the mHypoA-55 ARC cells, activin significantly increased Kiss-1 gene expression. Follistatin alone reduced Kiss-1 expression within these cells. Interestingly, activin-induced Kiss-1 gene expression was completely abolished by follistatin. Inhibin A, but not inhibin B reduced Kiss-1 expression. Activin-increased Kiss-1 expression was also abolished by inhibin A. Pretreatment of the cells with follistatin or inhibin A significantly inhibited kisspeptin- or GnRH-induced Kiss-1 gene expression in mHypoA-55 cells. In contrast, in the mHypoA-50 AVPV cell model, activin, follistatin, and inhibin A did not modulate Kiss-1 gene expression. The subunits that compose activin and inhibin, as well as follistatin were expressed in both mHypoA-55 and mHypoA-50 cells. Expression of inhibin βA and βB subunits and follistatin was much higher in mHypoA-55 ARC cells. Furthermore, we found that expression of the inhibin α subunit and follistatin genes was modulated in the presence of E2 in mHypoA-55 ARC cells. The results of this study suggest that activin, follistatin, and inhibin A within the ARC region participate in the regulation of the HPG axis under the influence of E2.
Completeness of digital accessible knowledge of the birds of western Africa: Priorities for survey
Authors: Freeman Benedictus , Peterson A Townsend 
Published: June 2019

AbstractOpen-source primary biodiversity data, or digital accessible knowledge (DAK), are widely used in biodiversity informatics to understand the status of global biodiversity, model species’ ecological niches and geographic distributions, and inform biodiversity conservation decisions. However, these datasets are often unavailable, incomplete, or unevenly distributed across regions. We examined DAK for the birds of western Africa, obtained from the Global Biodiversity Information Facility (GBIF) and eBird, to identify gaps in the current knowledge of birds of western Africa, which can be used to guide future avian surveys across the region. We cleaned and standardized the data, resulting in >430,000 records, with 91% from eBird. From these we calculated inventory completeness indices for all grid cells at 0.5°, 0.3°, and 0.1° spatial resolutions across the region. We defined well-surveyed grid cells as those with completeness indices >80% and with >200 associated DAK records. We found marked spatial, seasonal, environmental, and temporal (historical) biases and information gaps in coverage. We identified 59 well-surveyed cells at 0.1°, 55 at 0.3°, and 50 at 0.5° resolution, with well-surveyed sites clustered around points of access such as major cities and national reserves or parks. Our results identified remarkably distinct areas in environmental space with diverse climatic conditions to be given priority for future avian surveys and conservation. The distinctiveness in the climatic conditions of these areas compared to well-surveyed sites is an indication that these areas when sampled could provide new insights into western African bird diversity. Lastly, we show the underrepresentation of traditional biodiversity data (e.g., museums, herbaria collections) compared to citizen science–enabled data (e.g., eBird), which demonstrates the potential of citizen science in documenting and monitoring biodiversity in western Africa, and by extension other poorly known regions of the world.
Open peroral endoscopic myotomy for the treatment of achalasia: a case series of 82 cases
Authors: Liu W , Zeng X-H , Yuan X-L , Li C-H , Wu C-C , Ye L-S , Hu B 
Published: June 2019

SUMMARY
During peroral endoscopic myotomy (POEM), creation of the tunnel is highly technically demanding and mucosal injury is one of the most common potential complications. We explored a method without a submucosal tunnel, which we call open peroral endoscopic myotomy (O-POEM). This study aimed to assess the feasibility and safety of O-POEM. O-POEM was performed on 82 patients with achalasia. Treatment success was defined as an Eckardt score of less than or equal to 3 after the myotomy. Adverse events including operative and postoperative adverse events were recorded. Treatment success and procedure-related adverse events were analyzed. After a median follow-up of 18 months (range: 6–26 months), the treatment success (Eckhart score ≤3) was achieved in 96.3% of cases (mean score pre- vs. post-treatment (7.4 vs. 1.8); P &lt; 0.001) with a recurrence of 3 cases. Ten patients (12.2%) had adverse events consisting of 2 cases of mediastinitis, 1 case of post-O-POEM bleeding, 1 case of subcutaneous emphysema, 6 cases of pleural effusion. Two cases of mediastinitis required intraprocedural drainage, and other patients were managed by endoscopy and conservative medical treatment. There were no deaths. No patients required surgical conversion. Clinical reflux occurred in 15.9% of patients (13/82). O-POEM was reliable and effective for the treatment of achalasia. In addition, O-POEM might be a better option for patients with severe submucosal fibrosis.
Non-tariff measures, quality and exporting: evidence from microdata in food processing in Ukraine
Authors: Movchan Veronika , Shepotylo Oleksandr , Vakhitov Volodymyr 
Published: June 2019

Abstract
Domestic non-tariff measures (NTM) influence firm’s production and import decisions. We introduce NTMs into a model with heterogeneous firms. NTMs increase the cost of production and play a role of a positive demand shifter. Interplay of these two factors leads to ambiguous impact of NTMs on extensive and intensive margins of trade. We test predictions of the model by looking at food-processing firms in Ukraine in 2008–2013. Evidence shows that more SPS regulations on inputs in upstream industries lead to exports of better quality products. At the same time, mandatory certifications have a negative impact on quality by limiting access of domestic firms to new technologies and equipment.
Effects of crop insurance on farm disinvestment and exit decisions
Authors: Kim Youngjune , Yu Jisang , Pendell Dustin L 
Published: June 2019

AbstractOver the last two decades, the US federal crop insurance programme expanded rapidly. Despite growing importance of crop insurance programmes, little is known about the relationship between crop insurance and disinvestment and exit decisions of farms. Using a farm-level panel dataset, we parametrically and semi-parametrically estimate the effects of crop insurance on farm disinvestment and farm exits with carefully developed identification strategies. Our estimation results indicate that (i) crop insurance reduces the likelihood of farm exits and (ii) lowers the magnitude of farm disinvestment. The positive and significant effects of crop insurance on farm survival and disinvestment remain robust across different specifications.
Autophagosomes accumulation in the vacuoles of the fungus Ustilago maydis and the role of proteases in their digestion
Authors: Soberanes-Gutiérrez Cinthia V , Vázquez-Carrada Melissa , López-Villegas Edgar O , Vega-Arreguín Julio C , Villa-Tanaca Lourdes , Ruiz-Herrera José 
Published: June 2019

Abstract
In the present study we determined whether Ustilago maydis accumulates autophagosomes within vacuoles when the cells are exposed to nutritional stress conditions. We investigated whether proteinase B and proteinase A are involved in their degradation. To this effect, wild type and Δpep4 mutant were incubated in minimal medium lacking a carbon source. It was observed that after incubation in nutrient-deficient media, spherical bodies appeared within the Δpep4 mutant strains vacuoles. In addition, autophagosomes were accumulated in U. maydis WT cells incubated in the presence of the serine protease inhibitor PMSF and accumulation of large autophagosomes and electrodense structures in the Δpep4 mutant cell vacuoles took place. These results demonstrate that the homologues of both, the proteinase B and the protease A, are involved in the autophagosomes degradation process in U. maydis.
Cell wall peptidoglycan inMycobacterium tuberculosis: An Achilles’ heel for the TB-causing pathogen
Authors: Maitra Arundhati , Munshi Tulika , Healy Jess , Martin Liam T , Vollmer Waldemar , Keep Nicholas H , Bhakta Sanjib 
Published: June 2019

ABSTRACTTuberculosis (TB), caused by the intracellular pathogen Mycobacterium tuberculosis, remains one of the leading causes of mortality across the world. There is an urgent requirement to build a robust arsenal of effective antimicrobials, targeting novel molecular mechanisms to overcome the challenges posed by the increase of antibiotic resistance in TB. Mycobacterium tuberculosis has a unique cell envelope structure and composition, containing a peptidoglycan layer that is essential for maintaining cellular integrity and for virulence. The enzymes involved in the biosynthesis, degradation, remodelling and recycling of peptidoglycan have resurfaced as attractive targets for anti-infective drug discovery. Here, we review the importance of peptidoglycan, including the structure, function and regulation of key enzymes involved in its metabolism. We also discuss known inhibitors of ATP-dependent Mur ligases, and discuss the potential for the development of pan-enzyme inhibitors targeting multiple Mur ligases.
Temperature-Sensitive Reproduction and the Physiological and Evolutionary Potential for Mother’s Curse
Authors: Montooth Kristi L , Dhawanjewar Abhilesh S , Meiklejohn Colin D 
Published: June 2019

AbstractStrict maternal transmission of mitochondrial DNA (mtDNA) is hypothesized to permit the accumulation of mitochondrial variants that are deleterious to males but not females, a phenomenon called mother’s curse. However, direct evidence that mtDNA mutations exhibit such sexually antagonistic fitness effects is sparse. Male-specific mutational effects can occur when the physiological requirements of the mitochondria differ between the sexes. Such male-specific effects could potentially occur if sex-specific cell types or tissues have energy requirements that are differentially impacted by mutations affecting energy metabolism. Here we summarize findings from a model mitochondrial–nuclear incompatibility in the fruit fly Drosophila that demonstrates sex-biased effects, but with deleterious effects that are generally larger in females. We present new results showing that the mitochondrial–nuclear incompatibility does negatively affect male fertility, but only when males are developed at high temperatures. The temperature-dependent male sterility can be partially rescued by diet, suggesting an energetic basis. Finally, we discuss fruitful paths forward in understanding the physiological scope for sex-specific effects of mitochondrial mutations in the context of the recent discovery that many aspects of metabolism are sexually dimorphic and downstream of sex-determination pathways in Drosophila. A key parameter of these models that remains to be quantified is the fraction of mitochondrial mutations with truly male-limited fitness effects across extrinsic and intrinsic environments. Given the energy demands of reproduction in females, only a small fraction of the mitochondrial mutational spectrum may have the potential to contribute to mother’s curse in natural populations.
Combining scientific and fishers’ knowledge to co-create indicators of food web structure and function
Authors: Bentley Jacob W , Hines David E , Borrett Stuart R , Serpetti Natalia , Hernandez-Milian Gema , Fox Clive , Heymans Johanna J , Reid David G 
Published: June 2019

Abstract
In this study, we describe the approach taken by the International Council for the Exploration of the Seas Irish Sea benchmark working group (WKIrish), to co-create diet information for six commercial species using fishers' and scientists knowledge and incorporate it into an existing Ecopath food web model of the Irish Sea. To understand how the co-created diet information changed the model we compared a suite of food web indicators before and after the addition of fishers' knowledge (FK). Of the 80 predator–prey interactions suggested by fishers during workshops, 50 were already included in the model. Although the small number of changes made to the model structure had an insignificant impact on the ecosystem-level indicators, indicators of species hierarchical importance and mixed trophic impacts were significantly changed, particularly for commercial species. FK heightened the importance of discards as a source of food for rays, plaice, and whiting and reduced the importance of cod, toothed whales, and plaice as structural components of the food web. FK therefore led to changes which will influence pairwise advice derived from the model. We conclude by providing lessons from WKIrish which we believe were key to the positive co-production experience and development of integrated management.
All Hegemons Are Not the Same: The Role(s) of Relational Structures and Modes of Control
Authors: Nicholls Daniel Hywel 
Published: June 2019

AbstractIn this article I adopt a relational-structural approach to hegemonic order, setting out two distinct forms of consensual order, which differ in their modes of control. The central argument is that patterned structures of relational interaction determine the way in which roles are developed, and this, in turn, conditions structural power asymmetries, legitimacy, and authority. Within an elevated hegemonic order, intraperipheral ties are sparse, and a well-connected hegemon has been able to control flows of meanings and understandings. This relational domination leads to the hegemon role-making its own role and alter-casting roles onto its periphery. The resulting role-structures generate hegemonic privileges and pronounced structural power asymmetries within an order that exhibits authority but wherein legitimacy is either absent or exists in the form of “submission legitimacy,” even though consent is forthcoming. In an ensconced hegemonic order, the periphery is densely interconnected, allowing secondary actors to establish common aims and negotiate collectively with the hegemon. Here, the hegemon cannot control role-creation to a significant degree, and dynamics of role-taking predominate, both for hegemon and periphery. This plays out in reduced structural power disparities and an order based on legitimated roles and functions. This relational-structural approach moves us away from the consent-coercion dichotomy toward interpretations of subtler forms of control, blending a relational-constructivist focus on the production, reproduction, and modification of actor-roles into a schematic causal account of how and why roles matter for hierarchy. The two models are then woven into an analytical narrative that interprets forms of hegemonic order in the Western Hemisphere during the post–Cold War period.
How Knowledge Workers Manage Their Personal Information Spaces: Perceptions, Challenges and High-Level Strategies
Authors: Alon Lilach , Hardof-Jaffe Sharon , Nachmias Rafi 
Published: June 2019

AbstractThe study explored the personal information management (PIM) experiences of knowledge workers, defined as workers in professional fields where information is the essence of the work. It examined their perceptions of personal information spaces, challenges of managing personal information and the use of PIM strategies and looked for links between them. Qualitative data were collected in seven in-depth interviews with knowledge workers from education and industry. Content analysis included horizontal analysis and cluster of meanings analysis (Moustakas, 1994). Participants varied in the extent to which they sensed three factors: belonging to, dependence on and control of information spaces. They mentioned two specific challenges: the overloading of personal information spaces and the divergence of these spaces. Participants used a number of innovative high-level strategies for saving, managing and retrieving information. The strategies were linked to both perceptions and challenges of the personal space. The paper concludes with guidelines for managing information.RESEARCH HIGHLIGHTSA complex set of perceptions (belonging, dependence and control) characterizes the interaction between knowledge workers and their personal information spaces. High-level strategies for saving, managing and retrieving information are a useful way of coping with the PIM challenges of overloaded and divergent information spaces. Innovative thinking about PIM is an important aspect of knowledge workers’ ability to manage personal information in the digital era.
Review of Molecular Identification Techniques for Forensically Important Diptera
Authors: Gemmellaro M Denise , Hamilton George C , Ware Jessica L 
Published: June 2019

AbstractThe medico-legal section of forensic entomology focuses on the analysis of insects associated with a corpse. Such insects are identified, and their life history characteristics are evaluated to provide information related to the corpse, such as postmortem interval and time of colonization. Forensically important insects are commonly identified using dichotomous keys, which rely on morphological characteristics. Morphological identifications can pose a challenge as local keys are not always available and can be difficult to use, especially when identifying juvenile stages. If a specimen is damaged, certain keys cannot be used for identification. In contrast, molecular identification can be a better instrument to identify forensically important insects, regardless of life stage or specimen completeness. Despite more than 20 yr since the first use of molecular data for the identification of forensic insects, there is little overlap in gene selection or phylogenetic methodology among studies, and this inconsistency reduces efficiency. Several methods such as genetic distance, reciprocal monophyly, or character-based methods have been implemented in forensic identification studies. It can be difficult to compare the results of studies that employ these different methods. Here we present a comprehensive review of the published results for the molecular identification of Diptera of forensic interest, with an emphasis on evaluating variation among studies in gene selection and phylogenetic methodology.
THE SMALLEST SALABLE PATENT PRACTICING UNIT AND COMPONENT LICENSING: WHY $1 IS NOT $1
Authors: Gautier Axel , Petit Nicolas 
Published: June 2019

ABSTRACT
The smallest salable patent pricing unit (SSPPU) is a valuation method used as a preliminary step toward the calculation of fair, reasonable, and nondiscriminatory royalties for licenses over standard-essential patents (SEPs). Under SSPPU, royalties should reflect the value added to the smallest salable component implementing the patented invention. In this paper, we discuss policy-making proposals to convert SSPPU into a pricing rule that not only assists the assessment of SEPs’ added value but also forces the specification of royalties terms as a share of component costs in SEP licensing negotiations. We call this new rule SSPPU+ and we show that it distorts the distribution of surplus between SEP owners and implementers by laying down a revenue cap on standardized technologies. Therefore, a change in the royalty basis is not neutral and $1 is not $1. Furthermore, SSPPU+ imposes uniform pricing of SEPs across different industries and does not allow SEP owners to take advantage of complementarities between technologies. This pleads against a generalization of SSPPU+ at early standardization and negotiation stages.
Infectious-disease Screening and Vaccination for Refugees and Asylum Seekers Entering Europe in 2015–16: A Scoping Study of Six European Union Countries
Authors: Piselli Pierluca , Samuilova Mariya , Bozorgmehr Kayvan , Ippolito Giuseppe , Petrova-Benedict Roumyana , Kentikelenis Alexander , Girardi Enrico 
Published: June 2019

Abstract
In 2015, more than 1 million asylum seekers and refugees arrived in Europe. Information on how European countries addressed the prevention and control of infectious diseases among these populations during and after this period is limited. This study is based on 27 semi-structured interviews conducted with first-line staff and health officials in May–June 2016 in first-entry countries (Greece/Italy), transit countries (Croatia/Slovenia) and destination countries (Austria/Sweden). Characteristics of health-service provision for infectious diseases at each stage of reception, with a focus on tuberculosis, viral hepatitis, intestinal parasites and human immunodeficiency virus infections, were investigated. No major differences in the provision of services in accordance with migration status (asylum seekers vs refugees) were reported. At arrival, interventions were focused on addressing emerging health needs and no major barriers to accessing acute hospital care for infectious diseases were reported. There were shortcomings in interventions to tackle medium- to long-term needs with respect to infectious diseases, including screening for chronic treatable infections and adult vaccination. European evidence-based guidance highlighting the most relevant interventions for infectious diseases during the reception process is needed.