bluuebunny/crossref_metadata_2025_split huggingface dataset:
First detection of low field microwave absorption in the disordered multiferroic double perovskite BiFe0.5Mn0.5O3
Authors: Sibanda Brian , Mahule Tebogo Sfiso , Delmonte Davide , Sala Andrea , Gilioli Edmondo , Srinivasu V V 
Published: June 2021

Abstract
BiFe0.5Mn0.5O3 (BFMO) is an intriguing magnetic double perovskite, only obtainable through high pressure-high temperature synthesis. It shows bulk multiferroic properties, namely the coexistence between a spin canted antiferromagnetic structure superimposed to an externally induced electric polarization at least from 77 K. In particular, the system is characterized by a significant weak ferromagnetic hysteresis loop and by a very rare phenomenon: the spontaneous magnetization reversal (MRV) versus temperature in the low field regime. To clarify the BFMO exotic magnetic phase in the low field regime, the Electron Spin Resonance (ESR) and the low field microwave absorption (LFMA) techniques were used, providing the first observation of LFMA in the bulk BFMO as an additional functionality of this material. A striking feature is that the hysteresis in LFMA signals vanishes above 45 K, while the bulk M-H loop hysteresis, measured in the same field range of LFMA, persists till room temperature. The temperature at which LFMA hysteresis vanishes qualitatively matches the position of the magnetic susceptibility’s second derivative peak, corresponding to the temperature at which the local second order mechanism responsible for MRV is maximum. The line shape of LFMA completely changes above 45 K and the ESR linewidth starts decreasing above this temperature, indicating the role of defect/disorder induced inhomogeneity. The temperature evolution of LFMA hysteresis and line shapes as a measure of the competition between Fe- and Mn-rich clusters suggests a sort of local frustration at the microscopic scale, responsible for the peculiar magnetization reversal of this system.
PDBe aggregated API: programmatic access to an integrative knowledge graph of molecular structure data
Authors: Nair Sreenath , Váradi Mihály , Nadzirin Nurul , Pravda Lukáš , Anyango Stephen , Mir Saqib , Berrisford John , Armstrong David , Gutmanas Aleksandras , Velankar Sameer 
Published: June 2021

Abstract

Summary
The PDBe aggregated API is an open-access and open-source RESTful API that provides programmatic access to a wealth of macromolecular structural data and their functional and biophysical annotations through 80+ API endpoints. The API is powered by the PDBe graph database (https://pdbe.org/graph-schema), an open-access integrative knowledge graph that can be used as a discovery tool to answer complex biological questions.

Availability and implementation
The PDBe aggregated API provides up-to-date access to the PDBe graph database, which has weekly releases with the latest data from the Protein Data Bank, integrated with updated annotations from UniProt, Pfam, CATH, SCOP and the PDBe-KB partner resources. The complete list of all the available API endpoints and their descriptions are available at https://pdbe.org/graph-api. The source code of the Python 3.6+ API application is publicly available at https://gitlab.ebi.ac.uk/pdbe-kb/services/pdbe-graph-api.

Supplementary information
Supplementary data are available at Bioinformatics online.
A low-dimensional structure of neurological impairment in stroke
Authors: Bisogno Antonio Luigi , Favaretto Chiara , Zangrossi Andrea , Monai Elena , Facchini Silvia , De Pellegrin Serena , Pini Lorenzo , Castellaro Marco , Basile Anna Maria , Baracchini Claudio , Corbetta Maurizio 
Published: June 2021

AbstractNeurological deficits following stroke are traditionally described as syndromes related to damage of a specific area or vascular territory. Recent studies indicate that, at the population level, post-stroke neurological impairments cluster in three sets of correlated deficits across different behavioural domains. To examine the reproducibility and specificity of this structure, we prospectively studied first-time stroke patients (n = 237) using a bedside, clinically applicable, neuropsychological assessment and compared the behavioural and anatomical results with those obtained from a different prospective cohort studied with an extensive neuropsychological battery. The behavioural assessment at 1-week post-stroke included the Oxford Cognitive Screen and the National Institutes of Health Stroke Scale. A principal component analysis was used to reduce variables and describe behavioural variance across patients. Lesions were manually segmented on structural scans. The relationship between anatomy and behaviour was analysed using multivariate regression models. Three principal components explained ≈50% of the behavioural variance across subjects. PC1 loaded on language, calculation, praxis, right side neglect and memory deficits; PC2 loaded on left motor, visual and spatial neglect deficits; PC3 loaded on right motor deficits. These components matched those obtained with a more extensive battery. The underlying lesion anatomy was also similar. Neurological deficits following stroke are correlated in a low-dimensional structure of impairment, related neither to the damage of a specific area or vascular territory. Rather they reflect widespread network impairment caused by focal lesions. These factors showed consistency across different populations, neurobehavioural batteries and, most importantly, can be described using a combination of clinically applicable batteries (National Institutes of Health Stroke Scale and Oxford Cognitive Screen). They represent robust behavioural biomarkers for future stroke population studies.
Reassessment of the Fiscal Multiplier in Developing Countries: Regime-Switching Model
Authors: Hlaváček Michal , Ismayilov Ilgar , Zeynalov Ayaz 
Published: June 2021

Abstract
The existing literature on fiscal policy has mainly employed linear models that found a small fiscal multiplier in developing economies. These findings challenge the importance and effectiveness of fiscal policy for these countries. However, linear models are not capable of distinguishing the size of a fiscal multiplier in the different phases of economic cycles. Responding to previous studies that confirm the regime dependency of a fiscal multiplier, we develop a non-linear panel threshold vector autoregression model to measure the size of the fiscal multiplier for developing countries. Our findings confirm asymmetry in the response of GDP to government expenditure shock during periods of recovery and downturn. Our main result shows that the response of GDP to government expenditure shock during a recovery period in developing countries is double that for developed ones. Our results also confirm a significantly larger fiscal multiplier during recovery than in an economic downturn. (JEL codes: E32, E62, G15, and C54)
Effect of scan angle on ALS metrics and area-based predictions of forest attributes for balsam fir dominated stands
Authors: van Lier Olivier R , Luther Joan E , White Joanne C , Fournier Richard A , Côté Jean-François 
Published: June 2021

Abstract
In this study, we assessed the effect of airborne laser scanning (ALS) scan angle on point cloud metrics and the estimation of forest attributes in balsam fir (Abies balsamea (L.) Mill.) dominated forests of western Newfoundland, Canada. We collected calibration data from ground plot locations representing varying scan angles from two flight lines: within 4° of nadir in one flight line, and either 11–20° from nadir (low scan angle plots: L), or 21–30° from nadir (high scan angle plots: H) in an adjacent flight line. We computed three sets of ALS point cloud metrics for each ground plot using ALS data from: individual flight lines (near-nadir and off-nadir) and data from all available flight lines (up to 4) combined (aggregated, as commonly used in an operational inventory context). We generated three sets of models for each of the L and H plots using the ALS metric sets, and applied the models to independent validation data. We analysed the effect of scan angle on both the ALS metrics and performance statistics for area-based models generated using the L and H datasets. Our results demonstrate that off-nadir scan angles significantly affected (P &lt; 0.05) specific metrics from both L (i.e. coefficient of variation (COVAR)) and H (i.e. maximum height, 95th percentile of height, mean height) plots, although the effects were trivial (mean absolute differences were ≤ 0.01 for COVAR and &lt; 0.3 m for the height metrics). Forest attribute predictions using these and other metrics were also significantly affected (P &lt; 0.05), namely gross merchantable volume (GMV), total volume (TVOL) and aboveground tree biomass (AGB) from L; and Lorey’s mean height (HGT), mean diameter at breast height (DBH), and GMV from H. We further demonstrated that combining ALS data from all available flight lines significantly increased errors for the predictions of HGT, GMV, and TVOL using L, and significantly reduced errors of HGT using H when compared to errors resulting from models developed with near-nadir data. While the differences in prediction errors were significant, they were small, with differences in mean absolute prediction errors all &lt;1.3 per cent. Based on our results, we concluded that the effects of large scan angles, up to 30° off-nadir, on area-based forest attribute predictions were minimal in this study, which used ALS metrics calculated from ALS returns with a height above ground &gt;2 m for balsam fir-dominated forests. This result may provide for operational efficiencies in implementing enhanced forest inventories in this particular forest environment.
Defining the consequences of endogenous genetic variation within a novel family of Schizosaccharomyces pombe heterochromatin nucleating sequences
Authors: Joshi Arati , Musicante Meryl J , Wheeler Bayly S 
Published: June 2021

Abstract
Centromeres are essential for genetic inheritance—they prevent aneuploidy by providing a physical link between DNA and chromosome segregation machinery. In many organisms, centromeres form at sites of repetitive DNAs that help establish the chromatin architecture required for centromere function. These repeats are often rapidly evolving and subject to homogenization, which causes the expansion of novel repeats and sequence turnover. Thus, centromere sequence varies between individuals and across species. This variation can affect centromere function. We utilized Schizosaccharomyces pombe to assess the relationship between centromere sequence and chromatin structure and determine how sensitive this relationship is to genetic variation. In S. pombe, nucleating sequences within centromere repeats recruit heterochromatin via multiple mechanisms, which include RNA-interference (RNAi) . Heterochromatin, in turn, contributes to centromere function through its participation in three essential processes; establishment of a kinetochore, cohesion of sister chromatids, and suppression of recombination. Here, we show that a centromere element containing RevCen, a target of the RNAi pathway, establishes heterochromatin and gene silencing when relocated to a chromosome arm. Within this RevCen-containing element (RCE), a highly conserved domain is necessary for full heterochromatin nucleation but cannot establish heterochromatin independently. We characterize the 10 unique RCEs in the S. pombe centromere assembly, which range from 60% to 99.6% identical, and show that all are sufficient to establish heterochromatin. These data affirm the importance of centromere repeats in establishing heterochromatin and suggest there is flexibility within the sequences that mediate this process. Such flexibility may preserve centromere function despite the rapid evolution of centromere repeats.
Codon usage bias and dinucleotide preference in 29 Drosophila species
Authors: Kokate Prajakta P , Techtmann Stephen M , Werner Thomas 
Published: June 2021

Abstract
Codon usage bias, where certain codons are used more frequently than their synonymous counterparts, is an interesting phenomenon influenced by three evolutionary forces: mutation, selection, and genetic drift. To better understand how these evolutionary forces affect codon usage bias, an extensive study to detect how codon usage patterns change across species is required. This study investigated 668 single-copy orthologous genes independently in 29 Drosophila species to determine how the codon usage patterns change with phylogenetic distance. We found a strong correlation between phylogenetic distance and codon usage bias and observed striking differences in codon preferences between the two subgenera Drosophila and Sophophora. As compared to the subgenus Sophophora, species of the subgenus Drosophila showed reduced codon usage bias and a reduced preference specifically for codons ending with C, except for codons with G in the second position. We found that codon usage patterns in all species were influenced by the nucleotides in the codon’s 2nd and 3rd positions rather than the biochemical properties of the amino acids encoded. We detected a concordance between preferred codons and preferred dinucleotides (at positions 2 and 3 of codons). Furthermore, we observed an association between speciation, codon preferences, and dinucleotide preferences. Our study provides the foundation to understand how selection acts on dinucleotides to influence codon usage bias.
Mantis: flexible and consensus-driven genome annotation
Authors: Queirós Pedro , Delogu Francesco , Hickl Oskar , May Patrick , Wilmes Paul 
Published: June 2021

Abstract

Background
The rapid development of the (meta-)omics fields has produced an unprecedented amount of high-resolution and high-fidelity data. Through the use of these datasets we can infer the role of previously functionally unannotated proteins from single organisms and consortia. In this context, protein function annotation can be described as the identification of regions of interest (i.e., domains) in protein sequences and the assignment of biological functions. Despite the existence of numerous tools, challenges remain in terms of speed, flexibility, and reproducibility. In the big data era, it is also increasingly important to cease limiting our findings to a single reference, coalescing knowledge from different data sources, and thus overcoming some limitations in overly relying on computationally generated data from single sources.

Results
We implemented a protein annotation tool, Mantis, which uses database identifiers intersection and text mining to integrate knowledge from multiple reference data sources into a single consensus-driven output. Mantis is flexible, allowing for the customization of reference data and execution parameters, and is reproducible across different research goals and user environments. We implemented a depth-first search algorithm for domain-specific annotation, which significantly improved annotation performance compared to sequence-wide annotation. The parallelized implementation of Mantis results in short runtimes while also outputting high coverage and high-quality protein function annotations.

Conclusions
Mantis is a protein function annotation tool that produces high-quality consensus-driven protein annotations. It is easy to set up, customize, and use, scaling from single genomes to large metagenomes. Mantis is available under the MIT license at https://github.com/PedroMTQ/mantis.
A qualitative examination of responses from a survey of pharmacy staff in Georgia regarding access to Narcan®
Authors: Griner Thomas , Strasser Sheryl 
Published: June 2021

Abstract
Georgia state lawmakers enacted legislation designed to reduce opioid overdose deaths by increasing public access to rescue products, such as Narcan®. This article explores whether pharmacy employees have effectively adopted such changes into pharmacy practice. We analyzed unsolicited remarks noted during a parent telephone survey of 120 Georgia pharmacy staff regarding price, availability and barriers to layperson purchase of Narcan®. Comments regarding dispensing requirements and challenges in obtaining inventory and changes in communication style were recorded. Around 15% were unfamiliar with Narcan® as an opioid overdose reversal agent or were unaware of their pharmacy’s policies governing its sale. Nearly half of those contacted did not have Narcan® in stock with some reporting that receiving Narcan® would take several days after placing an order. Over half specified requirements for purchasing Narcan® not required by law. Fewer than 15% had Narcan® available and imposed no unnecessary requirements for its purchase. During approximately 10% of the survey calls, respondents used a tone of voice or made comments suggestive of bias. We conclude that non-compliance with current laws, lack of familiarity with Narcan® and negative communication tendencies that suggest implicit bias and stigmatizing behaviors could ultimately inhibit access to opioid overdose treatment.
Impact of cardiac fibrosis and collagens on right ventricular failure and acute kidney injury in patients after continuous-flow left ventricular assist devices
Authors: Tie Hongtao , Welp Henryk , Martens Sven , Seiler Martina , Albers Petra , Mueller Klaus-Michael , Li Zhenhan , Martens Sabrina 
Published: June 2021

Abstract

OBJECTIVES
We aim to investigate the impact of cardiac fibrosis and collagens on right ventricular failure (RVF) and acute kidney injury (AKI) in patients receiving continuous flow left ventricular assist devices.

METHODS
Heart tissues from 34 patients were obtained from continuous flow left ventricular assist device insertion sites and corresponding clinical data were collected. The participants were divided into 2 groups according to the extent of the cardiac fibrosis or collagens.

RESULTS
Overall, 18 patients developed RVF with 14 receiving right ventricular assist device (RVAD), and 22 patients developed AKI with 12 needing new-onset renal replacement therapy. Higher collagen I (Col1) was significantly associated with increased incidences of RVF (76.5% vs 29.4%, P = 0.015), RVAD support (64.7% vs 17.6%, P = 0.013) and stage 3 AKI (58.8% vs 17.6%, P = 0.032), and patients with higher Col1 were more prone to renal replacement therapy (52.9% vs 17.6%, P = 0.071). Receiver operating characteristic curves showed that Col1 had good predictive effects on RVF [area under the curve (AUC) = 0.806, P = 0.002], RVAD support (AUC = 0.789, P = 0.005), stage 3 AKI (AUC = 0.740, P = 0.020) and renal replacement therapy (AUC = 0.731, P = 0.028) after continuous-flow left ventricular assist device. Moreover, patients with higher Col1 had significantly longer postoperative duration of mechanical ventilation, duration of intensive care unit stay and hospital length of stay (all P &lt; 0.05). Cardiac fibrosis, collagen III (Col3) and Col1/Col3 shared similar results or trends with Col1.

CONCLUSIONS
Cardiac fibrosis and related collagens in the apical left ventricular tissue are associated with increased risks of RVF, RVAD use and worse renal function. Further study is warranted owing to the small sample size.
Type 2 immunity is maintained during cancer-associated adipose tissue wasting
Authors: Lenehan Patrick J , Cirella Assunta , Uchida Amiko M , Crowley Stephanie J , Sharova Tatyana , Boland Genevieve , Dougan Michael , Dougan Stephanie K , Heckler Max 
Published: June 2021

Summary
Objectives: Cachexia is a systemic metabolic disorder characterized by loss of fat and muscle mass, which disproportionately impacts patients with gastrointestinal malignancies such as pancreatic cancer. While the immunologic shifts contributing to the development of other adipose tissue (AT) pathologies such as obesity have been well described, the immune microenvironment has not been studied in the context of cachexia.
Methods: We performed bulk RNA-sequencing, cytokine arrays, and flow cytometry to characterize the immune landscape of visceral AT (VAT) in the setting of pancreatic and colorectal cancers.
Results: The cachexia inducing factor IL-6 is strongly elevated in the wasting VAT of cancer bearing mice, but the regulatory type 2 immune landscape which characterizes healthy VAT is maintained. Pathologic skewing toward Th1 and Th17 inflammation is absent. Similarly, the VAT of patients with colorectal cancer is characterized by a Th2 signature with abundant IL-33 and eotaxin-2, albeit also with high levels of IL-6.
Conclusions: Wasting AT during the development of cachexia may not undergo drastic changes in immune composition like those seen in obese AT. Our approach provides a framework for future immunologic analyses of cancer associated cachexia.
Risk Is Relative: Heterogeneous Responses to Institutional Risks for Foreign Investment
Authors: Beazer Quintin H , Blake Daniel J 
Published: June 2021

Abstract
Are economic actors equally sensitive to institutional conditions? While existing research recognizes that institutions can have varying effects on actors’ interests, the implicit assumption is that actors are homogeneous in how sensitive they are to their institutional environment. We investigate this assumption in the context of foreign direct investment, arguing that actors from countries with weaker institutions will be less affected by information about host country institutional conditions—both good and bad. We test this argument using survey data from a diverse group of managers-in-training at an international business school. We find that when asked to evaluate a potential foreign investment location, respondents from developing countries are significantly less sensitive to information about the host country’s courts than their counterparts from developed economies. In contrast, we find that economic actors from both developed and developing countries respond similarly to information about the stability of economic policies. The findings suggest that sensitivity to the risks and safeguards of certain institutional conditions vary systematically across actors, depending on both the home environment to which economic actors have been exposed and the type of host institution.
Bioethics in China’s Biosecurity Law: forms, effects, and unsettled issues
Authors: Wang Leifan , Wang Fangzhong , Zhang Weiwen 
Published: June 2021

Abstract
The Biosecurity Law has laid down a regulatory framework on bioethics in China, from raising awareness through education, requiring researchers to conform to ethical principles and conduct ethical reviews on biomedical research, to giving special attention to human genetic resources. The law constructively leaves a wide range of discretion to medical institutions and professionals in ethical decision-making, adaptive to the biotechnology-ethics-regulation dynamics. This regulatory strategy poses crucial institutional challenges in its implementation, particularly on how to safeguard institutional review boards (IRB), a core mechanism in the governance, to effectively protect human subjects but not unnecessarily hinder the progress of biomedical research. Further measures need to clarify important issues on the IRB-based governance, including legal status of the IRB review decision, potential liabilities, and protections of the IRB members.