bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gaussian Light Model in Brightfield Optical Projection Tomography
Authors: Koskela Olli , Montonen Toni , Belay Birhanu , Figueiras Edite , Pursiainen Sampsa , Hyttinen Jari 
Published: September 2019

AbstractThis study focuses on improving the reconstruction process of the brightfield optical projection tomography (OPT). OPT is often described as the optical equivalent of X-ray computed tomography, but based on visible light. The detection optics used to collect light in OPT focus on a certain distance and induce blurring in those features out of focus. However, the conventionally used inverse Radon transform assumes an absolute focus throughout the propagation axis. In this study, we model the focusing properties of the detection by coupling Gaussian beam model (GBM) with the Radon transform. The GBM enables the construction of a projection operator that includes modeling of the blurring caused by the light beam. We also introduce the concept of a stretched GBM (SGBM) in which the Gaussian beam is scaled in order to avoid the modeling errors related to the determination of the focal plane. Furthermore, a thresholding approach is used to compress memory usage. We tested the GBM and SGBM approaches using simulated and experimental data in mono- and multifocal modes. When compared with the traditionally used filtered backprojection algorithm, the iteratively computed reconstructions, including the Gaussian models GBM and SGBM, provided smoother images with higher contrast.
„Freude pflegen“
Authors: Maier Julia 
Published: September 2019

ZusammenfassungZu viele Patienten, zu wenig Personal, zu wenig Zeit – das desillusioniert oft
schon junge Pflegende. Mit Humor und Achtsamkeit will ein
Kooperationsprojekt hier gegensteuern, was auch dem Pflegemanagement nutzen
kann.
Signo ecográfico de las capas de cebolla en el testículo
Authors: Aguilera Guillermo , Skoknic Velimir , Mora Mario 
Published: September 2019

ResumenLos quistes epidermoides del testículo son tumores benignos que representarían aproximadamente el 1% de todas las masas testiculares. Clínicamente es una patología poco sintomática, que se presenta como un aumento de volumen testicular o es detectado en exámenes de rutina. La ecografía demuestra una lesión focal del testículo, ovalada, heterogénea, con múltiples capas lineales hiperecogénicas concéntricas que da el signo clásico de "capas de cebolla" o con morfología de "anillo", y que no presenta flujo al Doppler color (Figuras 1
2
3). Cabe señalar también que se ha descrito la presencia de calcificaciones murales o una imagen hiperecogenica central como forma de presentación. Es necesario tener en cuenta que existen algunas publicaciones que describen casos aislados en que esta apariencia ecográfica característica podría también estar presente en teratomas, el cual sería su principal diagnóstico diferencial. La importancia del conocimiento de esa lesión radica en la alta probabilidad de ser una lesión benigna, que puede ser tratada con enucleación y no necesariamente requerir orquiectomia extendida, ya que hasta ahora, no existen reportes de malignización, diseminación ni recurrencia.
Survey of Global Health Education and Training in Pathology Residency Programs in the United States
Authors: Glynn Emily H , Guarner Jeannette , Hall Allison , Nelson Ann M , Andiric Linda R , Milner Dan A , Eichbaum Quentin 
Published: September 2019

Abstract

Objectives
This study assessed the prevalence, general interest, and barriers to implementing global health curricula in pathology residency programs.

Methods
We conducted a survey of 166 US pathology residency programs.

Results
Thirty-two (195) of 166 programs responded. Of these, 13% have a formalized global health program (n = 4), and the majority indicated at least some general interest in global health among trainees (88%, n = 28) and faculty (94%, n = 30), albeit at a low to moderate level. Funding limitations, regulatory constraints, and insufficient knowledge of global health were frequently cited barriers to developing a global health program.

Conclusions
Few US pathology departments incorporate global health education into postgraduate training. The importance of pathology in global health has been underappreciated, despite its critical role in the delivery of health care in resource-limited settings. One solution is for pathology departments to expand global health educational opportunities for trainees.
Low-Grade Ductal Carcinoma In Situ
Authors: Alghamdi Sarah A , Krishnamurthy Kritika , Garces Narvaez Sofia A , Algashaamy Khaled J , Aoun Jessica , Reis Isildinha M , Recine Monica A , Jorda Merce , Poppiti Robert J , Gomez-Fernandez Carmen R 
Published: September 2019

AbstractObjectivesWe aimed to determine the interobserver reproducibility in diagnosing low-grade ductal carcinoma in situ (DCIS). We also aimed to compare the interobserver variability using a proposed two-tiered grading system as opposed to the current three-tiered system.MethodsThree expert breast pathologists and one junior pathologist identified low-grade DCIS from a set of 300 DCIS slides. Months later, participants were asked to grade the 300 cases using the standard three-tiered system.ResultsUsing the two-tiered system, interobserver agreement among breast pathologists was considered moderate (κ = 0.575). The agreement was similar (κ = 0.532) with the junior pathologist included. Using the three-tiered system, pathologists’ agreement was poor (κ = 0.235).ConclusionsPathologists’ reproducibility on diagnosing low-grade DCIS showed moderate agreement. Experience does not seem to influence reproducibility. Our proposed two-tiered system of low vs nonlow grade, where the intermediate grade is grouped in the nonlow category has shown improved concordance.
EvolClust: automated inference of evolutionary conserved gene clusters in eukaryotes
Authors: Marcet-Houben Marina , Gabaldón Toni 
Published: September 2019

Abstract

Motivation
The evolution and role of gene clusters in eukaryotes is poorly understood. Currently, most studies and computational prediction programs limit their focus to specific types of clusters, such as those involved in secondary metabolism.

Results
We present EvolClust, a python-based tool for the inference of evolutionary conserved gene clusters from genome comparisons, independently of the function or gene composition of the cluster. EvolClust predicts conserved gene clusters from pairwise genome comparisons and infers families of related clusters from multiple (all versus all) genome comparisons.

Availability and implementation
https://github.com/Gabaldonlab/EvolClust/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Towards next-generation diagnostics for tuberculosis: identification of novel molecular targets by large-scale comparative genomics
Authors: Goig Galo A , Torres-Puente Manuela , Mariner-Llicer Carla , Villamayor Luis M , Chiner-Oms Álvaro , Gil-Brusola Ana , Borrás Rafael , Comas Espadas Iñaki 
Published: September 2019

Abstract

Motivation
Tuberculosis (TB) remains one of the main causes of death worldwide. The long and cumbersome process of culturing Mycobacterium tuberculosis complex (MTBC) bacteria has encouraged the development of specific molecular tools for detecting the pathogen. Most of these tools aim to become novel TB diagnostics, and big efforts and resources are invested in their development, looking for the endorsement of the main public health agencies. Surprisingly, no study has been conducted where the vast amount of genomic data available is used to identify the best MTBC diagnostic markers.

Results
In this work, we used large-scale comparative genomics to identify 40 MTBC-specific loci. We assessed their genetic diversity and physiological features to select 30 that are good targets for diagnostic purposes. Some of these markers could be used to assess the physiological status of the bacilli. Remarkably, none of the most used MTBC markers is in our catalog. Illustrating the translational potential of our work, we develop a specific qPCR assay for quantification and identification of MTBC DNA. Our rational design of targeted molecular assays for TB could be used in many other fields of clinical and basic research.

Availability and implementation
The database of non-tuberculous mycobacteria assemblies can be accessed at: 10.5281/zenodo.3374377.

Supplementary information
Supplementary data are available at Bioinformatics online.
Evaluation of bottom-up and top-down mass spectrum identifications with different customized protein sequences databases
Authors: Li Ziwei , He Bo , Feng Weixing 
Published: September 2019

AbstractMotivationGenerally, bottom-up and top-down are two complementary approaches for proteoforms identification. The inference of proteoforms relies on searching mass spectra against an accurate proteoform sequence database. A customized protein sequence database derived by RNA-Seq data can be used to better identify the proteoform existed in a studied species. However, the quality of sequences in customized databases which constructed by different strategies affect the performances of mass spectrometry (MS) identification. Additionally, performances of identifications between bottom-up and top-down using customized databases are also needed to be evaluatedResultsThree customized databases were constructed with different strategies separately. Two of them were based on translating assembled transcripts with or without genomic annotation, and the third one is a variant-extending protein database. By testing with bottom-up and top-down MS data separately, a variant-extending protein database could identify not only the most number of spectra but also the alleles expressed at the same time in diploid cells. An assembled database could identify the spectrum missed in reference database and amino acid (AA) alterations existed in studied species.Availability and implementationExperimental results demonstrated that the proteoform sequences in an annotated database are more suitable for identifying AA alterations and peptide sequences missed in reference database. An unannotated database instead of a reference proteome database gets an enough high sensitivity of identifying mass spectra. The variant-extending reference database is the most sensitive to identify mass spectra and single AA variantsSupplementary informationSupplementary data are available at Bioinformatics online.
simurg: simulate bacterial pangenomes in R
Authors: Ferrés Ignacio , Fresia Pablo , Iraola Gregorio 
Published: September 2019

Abstract

Motivation
The pangenome concept describes genetic variability as the union of genes shared in a set of genomes and constitutes the current paradigm for comparative analysis of bacterial populations. However, there is a lack of tools to simulate pangenome variability and structure using defined evolutionary models.

Results
We developed simurg, an R package that allows to simulate bacterial pangenomes using different combinations of evolutionary constraints such as gene gain, gene loss and mutation rates. Our tool allows the straightforward and reproducible simulation of bacterial pangenomes using real sequence data, providing a valuable tool for benchmarking of pangenome software or comparing evolutionary hypotheses.

Availability and implementation
The simurg package is released under the GPL-3 license, and is freely available for download from GitHub (https://github.com/iferres/simurg).

Supplementary information
Supplementary data are available at Bioinformatics online.
Meltos: multi-sample tumor phylogeny reconstruction for structural variants
Authors: Ricketts Camir , Seidman Daniel , Popic Victoria , Hormozdiari Fereydoun , Batzoglou Serafim , Hajirasouliha Iman 
Published: September 2019

Abstract

Motivation
We propose Meltos, a novel computational framework to address the challenging problem of building tumor phylogeny trees using somatic structural variants (SVs) among multiple samples. Meltos leverages the tumor phylogeny tree built on somatic single nucleotide variants (SNVs) to identify high confidence SVs and produce a comprehensive tumor lineage tree, using a novel optimization formulation. While we do not assume the evolutionary progression of SVs is necessarily the same as SNVs, we show that a tumor phylogeny tree using high-quality somatic SNVs can act as a guide for calling and assigning somatic SVs on a tree. Meltos utilizes multiple genomic read signals for potential SV breakpoints in whole genome sequencing data and proposes a probabilistic formulation for estimating variant allele fractions (VAFs) of SV events.

Results
In order to assess the ability of Meltos to correctly refine SNV trees with SV information, we tested Meltos on two simulated datasets with five genomes in both. We also assessed Meltos on two real cancer datasets. We tested Meltos on multiple samples from a liposarcoma tumor and on a multi-sample breast cancer data (Yates et al., 2015), where the authors provide validated structural variation events together with deep, targeted sequencing for a collection of somatic SNVs. We show Meltos has the ability to place high confidence validated SV calls on a refined tumor phylogeny tree. We also showed the flexibility of Meltos to either estimate VAFs directly from genomic data or to use copy number corrected estimates.

Availability and implementation
Meltos is available at https://github.com/ih-lab/Meltos.

Supplementary information
Supplementary data are available at Bioinformatics online.
Late Miocene origin and recent population collapse of the Malagasy savanna olive tree (Noronhia lowryi)
Authors: Salmona Jordi , Olofsson Jill K , Hong-Wa Cynthia , Razanatsoa Jacqueline , Rakotonasolo Franck , Ralimanana Hélène , Randriamboavonjy Tianjanahary , Suescun Uxue , Vorontsova Maria S , Besnard Guillaume 
Published: September 2019

Abstract
Debates regarding the origin of tropical savannas have attempted to disentangle the role of human, biotic and abiotic factors. Understanding the origins of savanna remains essential to identifying processes that gave rise to habitat mosaics, particularly those found in the Central Plateau of Madagascar. Documenting the evolutionary history and demography of native trees occurring in open habitats may reveal footprints left by past and recent environmental changes. We conducted a population genetic analysis of an endangered Malagasy shrub (Noronhia lowryi, Oleaceae) of the Central Plateau. Seventy-seven individuals were sampled from three sites and genotyped at 14 nuclear and 24 chloroplast microsatellites. We found a highly contrasting nuclear and plastid genetic structure, suggesting that pollen-mediated gene flow allows panmixia, while seed-based dispersal may rarely exceed tens of metres. From a phylogeny based on full plastomes, we dated the surprisingly old crown age of maternal lineages back to ~6.2 Mya, perhaps co-occurring with the global expansion of savanna. In contrast, recent demographic history inferred from nuclear data shows a bottleneck signature ~350 generations ago, probably reflecting an environmental shift during the Late Pleistocene or the Holocene. Ancient in situ adaptation and recent demographic collapse of an endangered woody plant highlight the unique value and vulnerability of the Malagasy savannas.
The History of Foreseeability
Authors: Scott Helen 
Published: September 2019

Abstract
The factual component of the duty of care inquiry—that harm to the claimant as a result of the defendant’s conduct was reasonably foreseeable by the defendant—has been entrenched in English law since Donoghue v Stevenson. Both indigenous and comparative (specifically South African) evidence suggests that Lord Atkin’s formulation of the duty of care test was influenced by a particular fragment contained in Title 9.2 of Justinian’s Digest, ‘On the lex Aquilia’. Interrogation of the foreseeability principle in its original setting shows, however, that its role there was rather circumscribed. Derived perhaps from the account of wrongdoing offered by Aristotle, for whom the fact that harm had occurred contrary to expectation (paralogos) served to demonstrate that it had been unintentionally inflicted, in the context of Roman culpa foreseeability functioned as a technique for determining the avoidability of the harm—essentially a causal inquiry. This historical insight serves to illuminate the limits of foreseeability in the context of the modern test for duty of care. As a principle which generates liability, it may be that reasonable foreseeability cannot bear the normative weight assigned to it. Thus the history of foreseeability furnishes the material for a further critique of the duty concept, adding an historical dimension to contemporary calls to abandon the factual component of the duty of care entirely.
The Value of Communication Practices for Comparative Law: Exploring the Relationship Between Scotland and England
Authors: Braun Alexandra 
Published: September 2019

Abstract
This article explores the relationship between the Scottish and the English legal traditions through the lens of communication practices. ‘Communication practices’ are conceived of as the multiple ways in which legal traditions interact with one another by a combination of the circulation of legal ideas and the activities of legal actors. The article argues that greater attention should be paid in comparative legal literature to communication practices as they evolve over time and space, being especially mindful of the language used and the labels employed. By exploring different shapes of temporality and space, this article demonstrates the importance of looking beyond both discrete events and moments of transplantation, and the immediate geographical space. It also shows that the focus on language and what is explicitly said, but also on what is not said, generates insights both into the various techniques and practices involved in communication, as well as the factors that play a role. By examining concrete examples of communication involving both judges and legislatures, drawn from across different areas of law and different time periods, this article argues that contrary to the prevailing narrative, communication practices between Scotland and England are much richer and more dynamic than we tend to assume. Ultimately, the article questions the narrative and construction of the Scottish legal tradition, and of mixed legal systems more generally, as systems that primarily adopt ideas from abroad, rather than generating ideas capable of stimulating and shaping developments elsewhere.
Associations of six common functional polymorphisms in interleukins with tuberculosis: evidence from a meta-analysis
Authors: Yu Zhen , Wit Wichaidit , Xiong Lifen , Cheng Ying 
Published: September 2019

ABSTRACT

Background
Associations of polymorphisms in interleukin-6 (IL-6), IL-8 and IL-10 with tuberculosis (TB) susceptibility were already reported by many publications. The aim of this meta-analysis was to more precisely clarify associations between polymorphisms in IL-6/IL-8/IL-10 and TB by combing the results of all relevant publications.

Methods
Eligible publications were searched from PubMed, Embase, Web of Science and CNKI. We used Review Manager to combine the results of individual studies.

Results
A total of 47 publications were included in this study. IL-6 rs1800795 (1750 cases and 2335 controls, dominant, recessive and allele comparisons), IL-8 rs4073 (1125 cases and 1188 controls, dominant, recessive and allele comparisons), IL-10 rs1800871 (5528 cases and 7671 controls, dominant, recessive and allele comparisons), IL-10 rs1800872 (5269 cases and 7013 controls, dominant and allele comparisons) and IL-10 rs1800896 (7564 cases and 8952 controls, recessive comparison) polymorphisms were all significantly associated with TB in overall combined analyses. In subgroup analyses, we found that the positive results were mainly driven by the pulmonary tuberculosis and Asian subgroups.

Conclusions
Collectively, this meta-analysis proved that IL-6 rs1800795, IL-8 rs4073, IL-10 rs1800871, IL-10 rs1800872 and IL-10 rs1800896 may confer susceptibility to TB.
Machine-Learning Classification Suggests That Many Alphaproteobacterial Prophages May Instead Be Gene Transfer Agents
Authors: Kogay Roman , Neely Taylor B , Birnbaum Daniel P , Hankel Camille R , Shakya Migun , Zhaxybayeva Olga 
Published: September 2019

Abstract
Many of the sequenced bacterial and archaeal genomes encode regions of viral provenance. Yet, not all of these regions encode bona fide viruses. Gene transfer agents (GTAs) are thought to be former viruses that are now maintained in genomes of some bacteria and archaea and are hypothesized to enable exchange of DNA within bacterial populations. In Alphaproteobacteria, genes homologous to the “head–tail” gene cluster that encodes structural components of the Rhodobacter capsulatus GTA (RcGTA) are found in many taxa, even if they are only distantly related to Rhodobacter capsulatus. Yet, in most genomes available in GenBank RcGTA-like genes have annotations of typical viral proteins, and therefore are not easily distinguished from their viral homologs without additional analyses. Here, we report a “support vector machine” classifier that quickly and accurately distinguishes RcGTA-like genes from their viral homologs by capturing the differences in the amino acid composition of the encoded proteins. Our open-source classifier is implemented in Python and can be used to scan homologs of the RcGTA genes in newly sequenced genomes. The classifier can also be trained to identify other types of GTAs, or even to detect other elements of viral ancestry. Using the classifier trained on a manually curated set of homologous viruses and GTAs, we detected RcGTA-like “head–tail” gene clusters in 57.5% of the 1,423 examined alphaproteobacterial genomes. We also demonstrated that more than half of the in silico prophage predictions are instead likely to be GTAs, suggesting that in many alphaproteobacterial genomes the RcGTA-like elements remain unrecognized.
The Competition Law and Institutions of the European Union
Authors: Jones Alison , Sufrin Brenda , Dunne Niamh 
Published: September 2019

Abstract
This chapter sketches the history and functions of the EU and its institutions in order to set the EU competition rules in context. It then describes the competition provisions themselves and outlines the way in which the rules are applied and enforced, including the public enforcement of Articles 101 and 102 under Regulation 1/2003, the control of mergers with a European dimension under Regulation 139/2004, public enforcement by the national competition authorities of the Member States, and the role of private enforcement. It discusses the position and powers of the European Commission, particularly the role of the Competition Directorate General (DG Comp); the powers of the EU Courts; the significance of fundamental rights and the general principles of EU law in competition cases; the application of competition rules to particular sectors of the economy; and the application of the EU rules to the EEA.
Article 101 TFEU: The Elements
Authors: Jones Alison , Sufrin Brenda , Dunne Niamh 
Published: September 2019

Abstract
This chapter discusses the text and scheme of Article 101 which prohibits agreements, decisions and concerted practices which restrict competition and may affect trade between Member States. It explains the terms employed in Article 101(1) and how they are interpreted and applied. This entails a discussion of the meaning of ‘undertaking’ and ‘association of undertakings’, including the concepts of ‘economic activities’ and of a ‘single economic entity’; the meaning of ‘agreement’ including the coverage of both horizontal and vertical agreements; the meaning of ‘concerted practice’; the meaning of ‘decisions by associations of undertakings’; the application of Article 101(1) to complex arrangements and single continuous infringements; and the meaning of an appreciable effect on trade between Member States.