bluuebunny/crossref_metadata_2025_split huggingface dataset:
nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
Authors: Rieder Dietmar , Fotakis Georgios , Ausserhofer Markus , René Geyeregger , Paster Wolfgang , Trajanoski Zlatko , Finotello Francesca 
Published: November 2021

Abstract

Summary
Somatic mutations and gene fusions can produce immunogenic neoantigens mediating anticancer immune responses. However, their computational prediction from sequencing data requires complex computational workflows to identify tumor-specific aberrations, derive the resulting peptides, infer patients’ Human Leukocyte Antigen types and predict neoepitopes binding to them, together with a set of features underlying their immunogenicity. Here, we present nextNEOpi (nextflow NEOantigen prediction pipeline) a comprehensive and fully automated bioinformatic pipeline to predict tumor neoantigens from raw DNA and RNA sequencing data. In addition, nextNEOpi quantifies neoepitope- and patient-specific features associated with tumor immunogenicity and response to immunotherapy.

Availability and implementation
nextNEOpi source code and documentation are available at https://github.com/icbi-lab/nextNEOpi

Contact
dietmar.rieder@i-med.ac.at or francesca.finotello@uibk.ac.at

Supplementary information
Supplementary data are available at Bioinformatics online.
A2Sign: Agnostic Algorithms for Signatures—a universal method for identifying molecular signatures from transcriptomic datasets prior to cell-type deconvolution
Authors: Boldina Galina , Fogel Paul , Rocher Corinne , Bettembourg Charles , Luta George , Augé Franck 
Published: November 2021

Abstract

Motivation
Molecular signatures are critical for inferring the proportions of cell types from bulk transcriptomics data. However, the identification of these signatures is based on a methodology that relies on prior biological knowledge of the cell types being studied. When working with less known biological material, a data-driven approach is required to uncover the underlying classes and generate ad hoc signatures from healthy or pathogenic tissue.

Results
We present a new approach, A2Sign: Agnostic Algorithms for Signatures, based on a non-negative tensor factorization (NTF) strategy that allows us to identify cell-type-specific molecular signatures, greatly reduce collinearities and also account for inter-individual variability. We propose a global framework that can be applied to uncover molecular signatures for cell-type deconvolution in arbitrary tissues using bulk transcriptome data. We also present two new molecular signatures for deconvolution of up to 16 immune cell types using microarray or RNA-seq data.

Availability and implementation
All steps of our analysis were implemented in annotated Python notebooks (https://github.com/paulfogel/A2SIGN). To perform NTF, we used the NMTF package, which can be downloaded using Python pip install.

Supplementary information
Supplementary data are available at Bioinformatics online.
Scientists from Minority-Serving Institutions and Their Participation in Grant Peer Review
Authors: Gallo Stephen A , Sullivan Joanne H , Croslan DaJoie R 
Published: November 2021

ABSTRACT
Funding disparities currently exist across racial groups for grant applicants and between minority-serving institutions (MSIs) and traditionally White institutions (TWIs), with implicit bias in grant review a likely source of these differences. A survey examining grant review participation was disseminated to thousands of MSI-based scientists, and their responses were compared with those in a previous study of predominantly TWI-based scientists. Despite similar levels of grant submission, only 45% of the MSI-based scientists had recently participated in grant review, which is much lower than the rate reported in the previous study. MSI-based scientists indicated not being invited and a general lack of time (largely because of teaching and service responsibilities) as barriers. Nevertheless, the majority of the MSI-based respondents were interested in reviewing and in training in grant reviewing. These results serve as a call to action for research funders to increase both invitations to review and training opportunities for MSI-based scientists.
Healthy, happy places—a more integrated approach to creating health and well-being through the built environment?
Authors: Turnbull Rachel 
Published: November 2021

Abstract

Introduction
This paper explores how the built environment impacts upon health and well-being and suggests that there are opportunities for more integrated working between professionals and citizens to create healthier, happier places.

Sources of data
Policy and practice guidance is presented from the urban planning and design fields. Evidence and data are presented from a range of disciplines on housing, green infrastructure and mental well-being.

Areas of agreement
There is an overwhelming agreement around the principles and rationale of incorporating health in planning and design processes.

Areas of controversy
These principles are not always implemented in practice. Challenges also exist around how different disciplines create and use evidence.

Growing points
More innovative ways of working which incorporates health, public health, planners, designers and citizens, which responds to the needs of communities, should be tested.

Areas timely for developing research
Health and public health professionals can contribute to the evidence base using objective measures to assess the impact of the built environment on mental health and well-being.
Improving Bitcoin Transaction Propagation Efficiency through Local Clique Network
Authors: Yan Kailun , Zhang Jilian , Wu Yongdong 
Published: November 2021

AbstractBitcoin is a popular decentralized cryptocurrency, and the Bitcoin network is essentially an unstructured peer-to-peer (P2P) network that can synchronize distributed database of replicated ledgers through message broadcasting. In the Bitcoin network, the average clustering coefficient of nodes is very high, resulting in low message propagation efficiency. In addition, average node degree in the Bitcoin network is also considerably large, causing high message redundancy when nodes use the gossip protocol to broadcast messages. These may affect message propagation speed, hindering Bitcoin from being applied to scenarios of high transactional throughputs. To illustrate, we have collected single-hop propagation data of transactions of 366 blocks from Bitcoin Core. The analysis results show that transaction verification and network delay are two major causes of low transaction propagation efficiency. In this paper, we propose a novel P2P network structure, called local clique network (LCN), for message broadcasting in the Bitcoin network. Specifically, to reduce transaction validation latency and message redundancy, in LCN local nodes (logically) form cliques, and only a few nodes in a clique broadcast messages to the other cliques, instead of each node sending messages to its neighboring nodes. We have conducted extensive experiments, and the results show that message redundancy is low in LCN, and message propagation speed increases significantly. Meanwhile, LCN exhibits excellent robustness when average node degree remains high in the Bitcoin network.
Prototheca-ID: a web-based application for molecular identification of Prototheca species
Authors: Dziurzyński Mikołaj , Decewicz Przemyslaw , Iskra Mateusz , Bakuła Zofia , Jagielski Tomasz 
Published: November 2021

Abstract
The genus Prototheca houses unicellular, achlorophyllous, yeast-like algae, widely distributed in the environment. Protothecae are the only known plants that have repeatedly been reported to infect vertebrates, including humans. Although rare, protothecosis can be clinically demanding, with an unpredictable and treatment-resistant behavior. Accurate identification of Prototheca species relies upon DNA sequence-based typing of the mitochondrially encoded CYTB gene. However, no bioinformatic tool for the processing and analyzing of protothecal sequence data exists. Moreover, currently available sequence databases suffer from a limited number of records and lack of or flawed sequence annotations, making Prototheca identification challenging and often inconclusive. This report introduces the Prototheca-ID, a user-friendly, web-based application providing fast and reliable speciation of Prototheca isolates. In addition, the application offers the users the possibility of depositing their sequences and associated metadata in a fully open Prototheca-ID database, developed to enhance research integrity and quality in the field of Protothecae and protothecosis.
Database URL: The Prototheca-ID application is available at https://prototheca-id.org
Cardiac magnetic resonance imaging improves prognostic stratification of patients with ST-elevation myocardial infarction and preserved ejection fraction
Authors: Reindl Martin , Stiermaier Thomas , Lechner Ivan , Tiller Christina , Holzknecht Magdalena , Mayr Agnes , Schwaiger Johannes P , Brenner Christoph , Klug Gert , Bauer Axel , Thiele Holger , Feistritzer Hans-Josef , Metzler Bernhard , Eitel Ingo , Reinstadler Sebastian J 
Published: November 2021

AbstractAimsTo evaluate the prognostic validity of clinical risk factors as well as infarct characterization and myocardial deformation by cardiac magnetic resonance (CMR) in ST-elevation myocardial infarction (STEMI) patients with preserved left ventricular ejection fraction (LVEF) following primary percutaneous coronary intervention (PCI).Methods and resultsThis multicentre, individual patient-data analysis from two large CMR trials included 1247 STEMI patients. Cardiac magnetic resonance examinations were conducted 3 [interquartile range (IQR) 2–4] days after PCI. LVEF, infarct size, microvascular obstruction (MVO), and myocardial strain values were measured. Primary endpoint was defined as composite of major adverse cardiovascular events (MACE) including death, re-infarction, and congestive heart failure. A preserved LVEF (defined as LVEF ≥50%) was observed in 724 patients (=58%). In the overall cohort, 97 patients experienced a MACE event [follow-up time 12 (IQR 12–13) months], and 34 MACE events occurred in the group with preserved LVEF (5% vs. 12% incidence rate in patients with LVEF &lt; 50%). TIMI risk score [hazard ratio (HR) 1.28, 95% confidence interval (CI) 1.02–1.59; P = 0.03] and female gender (HR 2.24, 95% CI 1.10–4.57; P = 0.03) emerged as independent clinical determinants of MACE in the patient group with preserved LVEF. Among CMR parameters, the presence of MVO (HR 2.39, 95% CI 1.05–5.46; P = 0.04) and reduced global longitudinal strain (GLS; HR 1.12, 95% CI 1.02–1.23; P = 0.02) independently predicted MACE in the LVEF-preserved population. The addition of MVO and GLS to the clinical prognostic markers (TIMI risk score, female gender) increased (P = 0.02) the prognostic validity [AUC 0.76 (95% CI 0.73–0.79)] compared to the clinical markers alone [AUC 0.65 (0.62–0.69)].ConclusionIn contemporary treated STEMI patients showing preserved LVEF, a CMR-based risk prediction approach assessing MVO and GLS provided strong prognostic value that was incremental to clinical outcome parameters.
The value of perioperative biomarker release for the assessment of myocardial injury or infarction in cardiac surgery
Authors: Schneider Ulrich , Mukharyamov Murat , Beyersdorf Friedhelm , Dewald Oliver , Liebold Andreas , Gaudino Mario , Fremes Stephen , Doenst Torsten 
Published: November 2021

Abstract

OBJECTIVES
Cardiac biomarkers are indicators of irreversible cell damage. Current myocardial infarction (MI) definitions require concomitant clinical characteristics. For perioperative MI, a correlation of biomarker elevations and mortality has been suggested. Definitions emerged relying on cardiac biomarker release only. This approach is questionable as several clinical and experimental scenarios exist where relevant biomarker release can occur apart from MI.

METHODS
We reviewed the clinical and basic science literature and revealed important aspects regarding the use and interpretation of cardiac biomarker release with special focus on their interpretation in the perioperative setting.

RESULTS
Ischaemic biomarkers may be released without cell death in multiple conditions, such as after endurance runs in athletes, temporary inotropic stimulation in animal models and flow variations in in vitro cell models. In addition, access through atrial tissue during cannulation or concomitant valve procedures adds sources of enzyme release that may not be related to ventricular ischaemia (i.e. MI). Such non-cell death-related mechanisms may explain the lack of poor correlations of enzyme release and long-term outcomes in recent trials. In addition, the 3 main biomarkers, troponin T, I and creatine kinase myocardial band, differ in their release kinetics, which may differentially trigger MI events in trial patients.

CONCLUSIONS
The identification of irreversible myocardial injury in cardiac surgery based only on biomarker release is unreliable. Cell death- and non-cell death-related mechanisms create a mix in the perioperative setting that requires additional markers for proper identification of MI. In addition, the 3 most common ischaemic biomarkers display different release kinetics adding to the confusion. We review the topic.
Discerning Josquin
Authors: Milsom John 
Published: November 2021

Abstract
This study describes and evaluates some newly identified polyphonic phenomena in Josquin’s most securely attributed works for five and six voices. By examining some characteristic touches of Josquin’s hand, it aims to shed new light on the later style of this celebrated yet enigmatic composer, and contributes to the debate about what makes Josquin sound like Josquin. Specifically, it looks at how Josquin sometimes interlocked passages of canon and stretto fuga against bass motion along the chain of 5ths, and then evolved this aspect of craft to the point where it contributes to the perceived tonality, modality and form of individual works. Extracts from nine pieces by Josquin are examined: five motets, three chansons, and the Credo of the Missa De beata virgine. Closest attention is paid to passages from Pater noster, Nimphes napées, Preter rerum seriem, Douleur me bat and Plaine de deuil.
Domains of spirituality and their importance to the health of 75 533 adolescents in 12 countries
Authors: Michaelson V , Šmigelskas K , King N , Inchley J , Malinowska-Cieślik M , Pickett W ,   for the HBSC Spiritual Health Writing Group, Michaelson V , Pickett W , Trothen T , Davison C , Kalman M , Jirásek I , Brooks F , Walsh S , Harel-Fisch Y , Smigelskas K , Pudule I , Gobina I , Mazur J , Malinowska-Cieslik M , Lesco G , Matochkina A , Inchley J , Whitehead R , Kolarcik P , Roberts C 
Published: November 2021

Summary
Spirituality is an ancient concept with many contemporary applications to the field of health promotion. While recognized in the UN Convention on the Rights of the Child as a basic human right, definitional misunderstandings about what spirituality is, and is not, and the mechanisms by which it affects the health of young people, remain. In this cross-national analysis involving &gt;75 000 adolescents from 12 countries, we examined the relative importance of each of four spiritual health domains (connections to self, others, nature and the transcendent) in the lives of young people, and how these connections relate to a standard indicator of positive mental health status. Descriptive and applied regression analyses confirmed two major findings: (i) boys and girls in all 12 countries ranked the importance of each of the four domains in the same order, with ‘connections to self’ identified as most important; and (ii) both direct and indirect pathways are evident that connect the remaining three domains to positive mental health status, but through strong connections to self. Based on our scale items, fostering a strong connection to self, which involves cultivating a sense of meaning, purpose and joy in the lives of adolescents, appears most fundamental to fostering optimal mental health. This may be achieved directly or, dependent upon context and culture, indirectly with emphasis on the connections afforded by the other three domains. Such findings provide important insights to guide the content of adolescent health promotion interventions.
Automatic discard registration in cluttered environments using deep learning and object tracking: class imbalance, occlusion, and a comparison to human review
Authors: van Essen Rick , Mencarelli Angelo , van Helmond Aloysius , Nguyen Linh , Batsleer Jurgen , Poos Jan-Jaap , Kootstra Gert 
Published: November 2021

Abstract
This paper presents and evaluates a method for detecting and counting demersal fish species in complex, cluttered, and occluded environments that can be installed on the conveyor belts of fishing vessels. Fishes on the conveyor belt were recorded using a colour camera and were detected using a deep neural network. To improve the detection, synthetic data were generated for rare fish species. The fishes were tracked over the consecutive images using a multi-object tracking algorithm, and based on multiple observations, the fish species was determined. The effect of the synthetic data, the amount of occlusion, and the observed dorsal or ventral fish side were investigated and a comparison with human electronic monitoring (EM) review was made. Using the presented method, a weighted counting error of 20% was achieved, compared to a counting error of 7% for human EM review on the same recordings.
Associations between residential proximity to oil and gas extraction and hypertensive conditions during pregnancy: a difference-in-differences analysis in Texas, 1996–2009
Authors: Willis Mary D , Hill Elaine L , Kile Molly L , Carozza Susan , Hystad Perry 
Published: November 2021

Abstract

Background
Oil and gas extraction produces air pollutants that are associated with increased risks of hypertension. To date, no study has examined residential proximity to oil and gas extraction and hypertensive conditions during pregnancy. This study quantifies associations between residential proximity to oil and gas development on gestational hypertension and eclampsia.

Methods
We utilized a population-based retrospective birth cohort in Texas (1996–2009), where mothers reside &lt;10 km from an active or future drilling site (n = 2 845 144.) Using full-address data, we linked each maternal residence at delivery to assign exposure and evaluate this exposure with respect to gestational hypertension and eclampsia. In a difference-in-differences framework, we model the interaction between maternal health before (unexposed) or after (exposed) the start of drilling activity (exposed) and residential proximity near (0–1, &gt;1–2 or &gt;2–3 km) or far (≥3–10 km) from an active or future drilling site.

Results
Among pregnant women residing 0–1 km from an active oil or gas extraction site, we estimate 5% increased odds of gestational hypertension [95% confidence interval (CI): 1.00, 1.10] and 26% increased odds of eclampsia (95% CI: 1.05, 1.51) in adjusted models. This association dissipates in the 1- to 3-km buffer zones. In restricted models, we find elevated odds ratios among maternal ages ≤35 years at delivery, maternal non-Hispanic White race, ≥30 lbs gained during pregnancy, nulliparous mothers and maternal educational attainment beyond high school.

Conclusions
Living within 1 km of an oil or gas extraction site during pregnancy is associated with increased odds of hypertensive conditions during pregnancy.
Hedonic adaptation and conscious consumption in the civil engineering market: corporate reputation and user behavior strategies for sustainable development
Authors: Su Haiyang , Ahmadov Miragha , Tkachenko Daria , Danshina Svetlana 
Published: November 2021

AbstractThe purpose of this study is to identify changes in consumption strategies in the civil engineering market in a hedonic context. To assess the attitude of consumers to a certain type of civil engineering technology, a multicomponent methodological approach to the characterization of goods based on a survey of consumers was used. The key trends in the development of the European Union, Chinese and Russian civil engineering market for 2010–19 are analyzed. The designation of four ‘green’ strategies for the behavior of end consumers regarding hedonic adaptation in the civil engineering market is proposed: eco-efficient, environmentally friendly, energy-saving and intellectual-content one.
The Permutahedral Variety, Mixed Eulerian Numbers, and Principal Specializations of Schubert Polynomials
Authors: Nadeau Philippe , Tewari Vasu 
Published: November 2021

AbstractWe compute the expansion of the cohomology class of the permutahedral variety in the basis of Schubert classes. The resulting structure constants $a_w$ are expressed as a sum of normalized mixed Eulerian numbers indexed naturally by reduced words of $w$. The description implies that the $a_w$ are positive for all permutations $w\in S_n$ of length $n-1$, thereby answering a question of Harada, Horiguchi, Masuda, and Park. We use the same expression to establish the invariance of $a_w$ under taking inverses and conjugation by the longest word and subsequently establish an intriguing cyclic sum rule for the numbers. We then move toward a deeper combinatorial understanding for the $a_w$ by exploiting in addition the relation to Postnikov’s divided symmetrization. Finally, we are able to give a combinatorial interpretation for $a_w$ when $w$ is vexillary, in terms of certain tableau descents. It is based in part on a relation between the $a_w$ and principal specializations of Schubert polynomials. Along the way, we prove results and raise questions of independent interest about the combinatorics of permutations, Schubert polynomials, and related objects. We also sketch how to extend our approach to other Lie types, highlighting an identity of Klyachko in particular.
Asylum, Borders, and the Politics of Violence: From Suspicion to Cruelty
Authors: Aradau Claudia , Canzutti Lucrezia 
Published: November 2021

AbstractCritical scholarship in international relations, border, and migration studies has analyzed the cultures of suspicion that underpin border practices and have increasingly reshaped the politics of asylum globally. They have highlighted either the generalization of suspicion through the securitization of asylum or racialized and gendered continuities of colonial violence. We propose to understand the entanglements of continuity and discontinuity in the politics of asylum through “technologies of cruelty.” To conceptualize technologies of cruelty, we draw on Etienne Balibar's “topographies of cruelty” and Rita Laura Segato's “pedagogies of cruelty.” Empirically, the article argues that technologies of cruelty minimize, erase, undo, splinter, and devalue asylum seekers’ claims for protection in ways that objectify and dehumanize them. Methodologically, the argument is developed through an analysis of a corpus of asylum appeal decisions in the United Kingdom. Asylum appeals are a particularly important archive for the diagnosis of cruelty internationally, as they are both inscriptions of dominant knowledge and contestations over knowledge and claims to protection. They also allow us to trace how the politics of asylum is situated within global topographies of cruelty, shaped by technologies of cruelty and the deactivation of empathy.