bluuebunny/crossref_metadata_2025_split huggingface dataset:
The European Genome-phenome Archive in 2021
Authors: Freeberg Mallory Ann , Fromont Lauren A , D’Altri Teresa , Romero Anna Foix , Ciges Jorge Izquierdo , Jene Aina , Kerry Giselle , Moldes Mauricio , Ariosa Roberto , Bahena Silvia , Barrowdale Daniel , Barbero Marcos Casado , Fernandez-Orth Dietmar , Garcia-Linares Carles , Garcia-Rios Emilio , Haziza Frédéric , Juhasz Bela , Llobet Oscar Martinez , Milla Gemma , Mohan Anand , Rueda Manuel , Sankar Aravind , Shaju Dona , Shimpi Ashutosh , Singh Babita , Thomas Coline , de la Torre Sabela , Uyan Umuthan , Vasallo Claudia , Flicek Paul , Guigo Roderic , Navarro Arcadi , Parkinson Helen , Keane Thomas , Rambla Jordi 
Published: October 2021

Abstract
The European Genome-phenome Archive (EGA - https://ega-archive.org/) is a resource for long term secure archiving of all types of potentially identifiable genetic, phenotypic, and clinical data resulting from biomedical research projects. Its mission is to foster hosted data reuse, enable reproducibility, and accelerate biomedical and translational research in line with the FAIR principles. Launched in 2008, the EGA has grown quickly, currently archiving over 4,500 studies from nearly one thousand institutions. The EGA operates a distributed data access model in which requests are made to the data controller, not to the EGA, therefore, the submitter keeps control on who has access to the data and under which conditions. Given the size and value of data hosted, the EGA is constantly improving its value chain, that is, how the EGA can contribute to enhancing the value of human health data by facilitating its submission, discovery, access, and distribution, as well as leading the design and implementation of standards and methods necessary to deliver the value chain. The EGA has become a key GA4GH Driver Project, leading multiple development efforts and implementing new standards and tools, and has been appointed as an ELIXIR Core Data Resource.
iProX in 2021: connecting proteomics data sharing with big data
Authors: Chen Tao , Ma Jie , Liu Yi , Chen Zhiguang , Xiao Nong , Lu Yutong , Fu Yinjin , Yang Chunyuan , Li Mansheng , Wu Songfeng , Wang Xue , Li Dongsheng , He Fuchu , Hermjakob Henning , Zhu Yunping 
Published: October 2021

Abstract
The rapid development of proteomics studies has resulted in large volumes of experimental data. The emergence of big data platform provides the opportunity to handle these large amounts of data. The integrated proteome resource, iProX (https://www.iprox.cn), which was initiated in 2017, has been greatly improved with an up-to-date big data platform implemented in 2021. Here, we describe the main iProX developments since its first publication in Nucleic Acids Research in 2019. First, a hyper-converged architecture with high scalability supports the submission process. A hadoop cluster can store large amounts of proteomics datasets, and a distributed, RESTful-styled Elastic Search engine can query millions of records within one second. Also, several new features, including the Universal Spectrum Identifier (USI) mechanism proposed by ProteomeXchange, RESTful Web Service API, and a high-efficiency reanalysis pipeline, have been added to iProX for better open data sharing. By the end of August 2021, 1526 datasets had been submitted to iProX, reaching a total data volume of 92.42TB. With the implementation of the big data platform, iProX can support PB-level data storage, hundreds of billions of spectra records, and second-level latency service capabilities that meet the requirements of the fast growing field of proteomics.
G-quadruplex RNA motifs influence gene expression in the malaria parasite Plasmodium falciparum
Authors: Dumetz Franck , Chow Eugene Yui-Ching , Harris Lynne M , Liew Shiau Wei , Jensen Anders , Umar Mubarak I , Chung Betty , Chan Ting Fung , Merrick Catherine J , Kwok Chun Kit 
Published: October 2021

Abstract
G-quadruplexes are non-helical secondary structures that can fold in vivo in both DNA and RNA. In human cells, they can influence replication, transcription and telomere maintenance in DNA, or translation, transcript processing and stability of RNA. We have previously showed that G-quadruplexes are detectable in the DNA of the malaria parasite Plasmodium falciparum, despite a very highly A/T-biased genome with unusually few guanine-rich sequences. Here, we show that RNA G-quadruplexes can also form in P. falciparum RNA, using rG4-seq for transcriptome-wide structure-specific RNA probing. Many of the motifs, detected here via the rG4seeker pipeline, have non-canonical forms and would not be predicted by standard in silico algorithms. However, in vitro biophysical assays verified formation of non-canonical motifs. The G-quadruplexes in the P. falciparum transcriptome are frequently clustered in certain genes and associated with regions encoding low-complexity peptide repeats. They are overrepresented in particular classes of genes, notably those that encode PfEMP1 virulence factors, stress response genes and DNA binding proteins. In vitro translation experiments and in vivo measures of translation efficiency showed that G-quadruplexes can influence the translation of P. falciparum mRNAs. Thus, the G-quadruplex is a novel player in post-transcriptional regulation of gene expression in this major human pathogen.
PLSDB: advancing a comprehensive database of bacterial plasmids
Authors: Schmartz Georges P , Hartung Anna , Hirsch Pascal , Kern Fabian , Fehlmann Tobias , Müller Rolf , Keller Andreas 
Published: October 2021

AbstractPlasmids are known to contain genes encoding for virulence factors and antibiotic resistance mechanisms. Their relevance in metagenomic data processing is steadily growing. However, with the increasing popularity and scale of metagenomics experiments, the number of reported plasmids is rapidly growing as well, amassing a considerable number of false positives due to undetected misassembles. Here, our previously published database PLSDB provides a reliable resource for researchers to quickly compare their sequences against selected and annotated previous findings. Within two years, the size of this resource has more than doubled from the initial 13,789 to now 34,513 entries over the course of eight regular data updates. For this update, we aggregated community feedback for major changes to the database featuring new analysis functionality as well as performance, quality, and accessibility improvements. New filtering steps, annotations, and preprocessing of existing records improve the quality of the provided data. Additionally, new features implemented in the web-server ease user interaction and allow for a deeper understanding of custom uploaded sequences, by visualizing similarity information. Lastly, an application programming interface was implemented along with a python library, to allow remote database queries in automated workflows. The latest release of PLSDB is freely accessible under https://www.ccb.uni-saarland.de/plsdb.
A randomized phase II trial of efficacy and safety of the immunotherapy ALECSAT as an adjunct to radiotherapy and temozolomide for newly diagnosed glioblastoma
Authors: Werlenius Katja , Stragliotto Giuseppe , Strandeus Michael , Blomstrand Malin , Carén Helena , Jakola Asgeir S , Rydenhag Bertil , Dyregaard Dorte , Dzhandzhugazyan Karine N , Kirkin Alexei F , Raida Martin K , Smits Anja , Kinhult Sara 
Published: October 2021

Abstract

Background
There is an urgent need for effective treatments against glioblastoma (GBM). In this trial, we investigated the efficacy and safety of an adoptive cell-based immunotherapy.

Methods
Patients with newly diagnosed GBM were recruited at 4 study sites in Sweden. The patients were randomized 1:2 to receive either radiotherapy (RT), 60 Gy/30 fractions, with concomitant and adjuvant temozolomide (TMZ) only, or RT and TMZ with the addition of Autologous Lymphoid Effector Cells Specific Against Tumor (ALECSAT) in an open-label phase II trial. The primary endpoint was investigator-assessed progression-free survival (PFS). The secondary endpoints were survival and safety of ALECSAT.

Results
Sixty-two patients were randomized to either standard of care (SOC) with RT and TMZ alone (n = 22) or SOC with ALECSAT (n = 40). Median age was 57 years (range 38–69), 95% of the patients were in good performance status (WHO 0–1). There was no significant difference between the study arms (SOC vs ALECSAT + SOC) in PFS (7.9 vs 7.8 months; hazard ratio [HR] 1.28; 95% confidence interval [CI] 0.70–2.36; P = .42) or in median overall survival (OS) (18.3 vs 19.2 months; HR 1.16, 95% CI 0.58–2.31; P = .67). The treatment groups were balanced in terms of serious adverse events (52.4% vs 52.5%), but adverse events ≥grade 3 were more common in the experimental arm (81.0% vs 92.5%).

Conclusion
Addition of ALECSAT immunotherapy to standard treatment with radiochemotherapy was well tolerated but did not improve PFS or OS for patients with newly diagnosed GBM.
A review of West African monsoon penetration during Green Sahara periods; implications for human evolution and dispersals over the last three million years
Authors: Larrasoaña Juan Cruz 
Published: October 2021

Abstract
Green Sahara periods (GSPs) represent episodes during which the present-day Sahara was transformed into a savannah in response to intensification of the West African monsoon (WAM). Although GSPs might have dramatically altered the size, structure, and connectivity of human populations in Africa and nearby regions of Asia, their significance for human evolution remains unknown due to the problems involved in gauging the penetration of the WAM over the Sahara at evolutionary timescales. Here I reanalyse monsoon run-off and dust records back to 3 million years ago from Eastern Mediterranean ODP Site 967, and assimilate them with North African palaeoenvironmental data to substantiate penetration of the WAM front during GSPs to latitudes beyond 28°N. These results, coupled with demographic and ecological data for modern hunter-gatherers, point to a significant expansion of human populations during GSPs compared with background desert conditions. Given the clustering of GSPs around long-term maxima in the eccentricity of the Earth’s orbit, I propose that recurrent periods of human population expansion driven by GSPs led to an increased number of favourable mutations. Along with environmental factors favourable for triggering epigenetic changes, this might have led to the rise in enhanced phenotypic plasticity that underpins the speciation of hominin lineages at times of high climate variability envisaged by the variability selection hypothesis. Clustering of GSPs around the Pliocene/Pleistocene boundary, simultaneously with a protracted period of wetter conditions in East Africa and the Sinai Peninsula, further suggests that the initial colonization of Eurasia by hominins occurred circa 2.6 Ma, much earlier than typically considered.
Abnormal paraoxonase-1 (PON1) enzyme activity in idiopathic inflammatory myopathies
Authors: Bae Sangmee Sharon , Shahbazian Ani , Wang Jennifer , Golub Ilana , Oganesian Buzand , Dowd Tyler , Vayngortin Beata , Wang Ryan , Elashoff David , Reddy Srinivasa T , Charles-Schoeman Christina 
Published: October 2021

Abstract

Objectives
Patients with idiopathic inflammatory myopathies (IIM) have severe vascular involvement, which contributes to disease morbidity and mortality. Paraoxonase-1 (PON1) is a high-density lipoprotein (HDL) associated protein that protects the vascular endothelium from oxidative injury and damage. The current work assessed the functional and genetic determinants of PON1 activity in IIM patients.

Methods
A total of 184 IIM patients and 112 healthy controls (HC) were included. PON1 enzyme activity was assessed by paraoxonase, arylesterase and lactonase assays, and the Q192R PON1 single nucleotide polymorphism (SNP) was analysed. Multivariate regression models examined associations of PON1 activity with IIM diagnosis and myositis disease outcomes.

Results
The arylesterase and lactonase activities of PON1 were significantly lower in IIM patients compared with HC. Higher myositis disease activity, the presence of severe IIM-associated interstitial lung disease (ILD), and the presence of MDA5 or anti-synthetase antibodies were significantly associated with lower PON1 activity. The PON1 Q192R polymorphism was strongly linked to the paraoxonase activity of PON1 in IIM, and patients with the PON1 QQ genotype had better IIM disease outcomes compared with patients with the QR or RR genotypes.

Conclusions
The arylesterase and lactonase activities of PON1 are significantly impaired in IIM patients compared with HC, and inversely associate with IIM disease activity and the presence of severe ILD. The PON1 QQ genotype associates with more favourable disease outcomes in IIM patients. Large prospective studies are needed to further evaluate the role of PON1 and PON1 genetic polymorphisms in the development and propagation of IIM and IIM-ILD.
Accountability in Humanitarian Action
Authors: Hilhorst Dorothea , Melis Samantha , Mena Rodrigo , van Voorst Roanne 
Published: October 2021

Abstract
Although a growing number of NGOs are combining humanitarian and development activities, it was long the case that humanitarian action was isolated from discussions and practices in the world of development. The work of saving lives was deemed to be guided solely by the humanitarian principles, and discussions on accountability were rare. In the 1990s, humanitarian standards initiatives arose in recognition that humanitarian organisations were not accountable to affected populations. This article aims to take stock of accountability initiatives and practices in the sector. It builds on accountability theory in distinguishing upward, sideways, and downward accountability, and incorporates formal and informal forms of accountability. It is based on empirical research in Myanmar, Afghanistan, and Sierra Leone. The first part of the article outlines the history of accountability in the humanitarian sector, including an accountability timeline, and discusses current trends in performances around accountability towards displaced people, minorities, and other recipients of aid. It then presents the findings from the three countries. The article concludes by calling attention to the everyday politics of accountability, the widening accountability arena, the differential accountability demands on international and national aid providers, and the crucial importance of sideways accountability to bring accountability to a next level.
The Globalization of an Interaction Ritual Chain: “Clapping for Carers” During the Conflict Against COVID-19
Authors: Rigal Alexandre , Joseph-Goteiner David 
Published: October 2021

AbstractSociologists have long been interested in the theoretical possibility of a universal ritual. Despite a growing number of indicators of world society and globalization, there have not been attempts to observe and analyze the international reach of particular rituals. We propose an extension of the “interaction ritual chain” by theorizing how an interaction ritual might be created and diffused internationally. We look at the case of the COVID-19 pandemic, which created shared conditions of social distancing and emotional distress. We analyze a discontinuous chain of urban and national interaction rituals that focused attention on the efforts of healthcare workers fighting the virus. We count clapping and noise-making in 101 countries and 26 global cities. While we find similar ritual forms and international symbols of solidarity, there was also substantial evidence of conflict and particularism.
Chronic Benzene Exposure Aggravates Pressure Overload-Induced Cardiac Dysfunction
Authors: Zelko Igor N , Dassanayaka Sujith , Malovichko Marina V , Howard Caitlin M , Garrett Lauren F , Uchida Shizuka , Brittian Kenneth R , Conklin Daniel J , Jones Steven P , Srivastava Sanjay 
Published: October 2021

AbstractBenzene is a ubiquitous environmental pollutant abundant in household products, petrochemicals, and cigarette smoke. Benzene is a well-known carcinogen in humans and experimental animals; however, little is known about the cardiovascular toxicity of benzene. Recent population-based studies indicate that benzene exposure is associated with an increased risk for heart failure. Nonetheless, it is unclear whether benzene exposure is sufficient to induce and/or exacerbate heart failure. We examined the effects of benzene (50 ppm, 6 h/day, 5 days/week, and 6 weeks) or high-efficiency particulate absorbing-filtered air exposure on transverse aortic constriction (TAC)-induced pressure overload in male C57BL/6J mice. Our data show that benzene exposure had no effect on cardiac function in the Sham group; however, it significantly compromised cardiac function as depicted by a significant decrease in fractional shortening and ejection fraction, as compared with TAC/Air-exposed mice. RNA-seq analysis of the cardiac tissue from the TAC/benzene-exposed mice showed a significant increase in several genes associated with adhesion molecules, cell-cell adhesion, inflammation, and stress response. In particular, neutrophils were implicated in our unbiased analyses. Indeed, immunofluorescence studies showed that TAC/benzene exposure promotes infiltration of CD11b+/S100A8+/myeloperoxidase+-positive neutrophils in the hearts by 3-fold. In vitro, the benzene metabolites, hydroquinone, and catechol, induced the expression of P-selectin in cardiac microvascular endothelial cells by 5-fold and increased the adhesion of neutrophils to these endothelial cells by 1.5- to 2.0-fold. Benzene metabolite-induced adhesion of neutrophils to the endothelial cells was attenuated by anti-P-selectin antibody. Together, these data suggest that benzene exacerbates heart failure by promoting endothelial activation and neutrophil recruitment.
Advances in Assessing Hazard and Risk to Emerging Threats and Emergency Response: Comparing and Contrasting Efforts of 3 Federal Agencies
Authors: Mumtaz Moiz M , Nickle Rich A , Lambert Jason C , Johnson Mark S 
Published: October 2021

Abstract
Federal statutes authorize several agencies to protect human populations from chemical emergencies and provide guidance to evacuate, clean, and reoccupy affected areas. Each of the authorized federal agencies has developed programs to provide managers, public health officials, and regulators, with a rapid assessment of potential hazards and risks associated with chemical emergencies. Emergency responses vary based on exposure scenarios, routes, temporal considerations, and the substance(s) present. Traditional chemical assessments and derivation of toxicity values are time-intensive, typically requiring large amounts of human epidemiological and experimental animal data. When a rapid assessment of health effects is needed, an integrated computational approach of augmenting extant toxicity data with in vitro (new alternative toxicity testing methods) data can provide a quick, evidence-based solution. In so doing, multiple streams of data can be used, including literature searches, hazard, dose-response, physicochemical, environmental fate, transport property data, in vitro cell bioactivity testing, and toxicogenomics. The field of toxicology is moving, towards increased use of this approach as it transforms from observational to predictive science. The challenge is to objectively and transparently derive toxicity values using this approach to protect human health and the environment. Presented here are examples and efforts toward rapid risk assessment that demonstrate unified, parallel, and complementary work to provide timely protection in times of chemical emergency.
Detection of Mycobacterium leprae infection in family clusters from six leprosy-endemic regions in Colombia
Authors: Serrano-Coll Héctor , Osorio-Leal Yuliana , Escobar-Builes María Victoria , Cardona-Castro Nora 
Published: October 2021

Abstract

Background
Leprosy is a chronic infectious disease caused by Mycobacterium leprae, which continues to be endemic in tropical countries, making it necessary to implement strategies for its elimination. The objective of the current article was to detect M. leprae infection and associated factors through serological and epidemiological evaluation in family clusters of leprosy patients.

Methods
Mycobacterium leprae infection was determined in 50 family clusters of leprosy patients from the departments of Bolívar, Atlántico, Santander, Boyacá, Chocó and Antioquia through the detection of antibodies (protein A, IgM, IgG) against anti-natural octyl disacharide-leprosy IDRI diagnostic (NDO-LID).

Results
Higher seroconversion and elevated titers of these antibodies against NDO-LID were observed in the population of Chocó and Atlántico (p&lt;0.05). Additionally, a higher frequency of infection was observed in large family groups that consumed armadillo meat and belonged to a low socioeconomic stratum (p&lt;0.05). Multivariate analysis established that the main associated factors for a family cluster experiencing this infection were belonging to a vulnerable economic stratum and a large family group.

Conclusions
This study found that the set of social and demographic variables (i.e. armadillo consumption, geographic area, low socioeconomic status and belonging to a large family cluster) are related to the promotion of seropositivity in family clusters.
Clinical Outcome of Nerve Decompression Surgery for Migraine Improves with Nerve Wrap
Authors: Alizadeh Kaveh , Kreinces Jason B. , Smiley Abbas , Gachabayov Mahir 
Published: October 2021

Background:
Chronic migraine headaches affect nearly 30 million Americans every year and are responsible for roughly 1.2 million emergency department visits annually. Many of the standard therapies commonly used to treat migraines are often unsuccessful and may furthermore introduce unwanted side effects. The purpose of this study was to identify independent predictors of clinical improvement in patients undergoing surgical nerve decompression for migraine.

Methods:
A retrospective chart review between 2010 and 2020 was conducted. The primary endpoint was clinical improvement at 1-year follow-up, defined as an independence from prescription medications. Patients were stratified into two groups: clinical improvement and treatment failure. Backward multivariable logistic regression was used to examine the associations between migraine improvement and different patient characteristics.

Results:
A total of 153 patients were included. In total, 129 (84.3%) patients improved and 24 (15.7%) did not. Significant associations with clinical improvement at multivariable logistic regression were found with acellular dermal matrix nerve wrap (OR = 10.80, 95%CI: 6.18–16.27), and operation of trigger sites four (OR = 37.96, 95%CI: 2.16–73.10) and five (OR = 159, 95%CI: 10–299).

Conclusion:
The use of acellular dermal matrix nerve wraps in surgery was significantly associated with clinical migraine improvement, as was operation at trigger sites four and five.