bluuebunny/crossref_metadata_2025 huggingface dataset:
Neural network for calculating direct and inverse nonlinear Fourier transform
Authors: Sedov E.V. , Chekhovskoy I.S. , Prilepsky J.E.
Published: November 2021

A neural network architecture is proposed that allows a continuous nonlinear spectrum of optical signals to be predicted and an inverse nonlinear Fourier transform (NFT) to be performed for signal modulation. The average value of the relative error in predicting the continuous spectrum by the neural network when calculating the direct NFT is found to be 2.68 × 10−3, and the average value of the relative error in predicting the signal for the inverse NFT is 1.62 × 10−4.
Multicore optical fibre embedded Fabry–Perot sensing element of a bend sensor
Authors: Egorova O.N. , Zhuravlev S.G. , Pustovoy V.I. , Semjonov S.L.
Published: November 2021

We propose a new type of a sensing element of a sensor for measuring the bending direction and magnitude, based on fibre Fabry–Perot interferometers embedded in the cores of multicore optical fibre. The measured sensitivity to the bend radius is 81 pm/m−1. It is found that this sensitivity can be increased by varying the diameters of the optical fibres forming the sensing element.
Correlation between optical fibre diameter and characteristics of tilted fibre Bragg grating-assisted sensors
Authors: Tomyshev K.A. , Dolzhenko E.I. , Butov O.V.
Published: November 2021

We report the results of a study on the influence of the fibre cladding diameter on the accuracy and resolution of tilted fibre Bragg grating-assisted refractometers. Tilted fibre Bragg gratings are an essential element used to develop high-precision fibre sensors for environmental monitoring. Comparative research was performed using one of comprehensive processing algorithms employing spectral envelope analysis. It was shown that the sensor accuracy decreases with decreasign fibre cladding diameter. At the same time, an increase in the diameter deteriorates the spectral pattern contrast, thus impeding the development of high-efficiency sensor elements.
Factors associated with transactional sex among a cohort of gay, bisexual, and other men who have sex with men in Vancouver, Canada
Authors: Armstrong Heather L. , Sang Jordan M. , Skala Ales , Wang Lu , Zhu Julia , Lachowsky Nathan J. , Card Kiffer G. , Benoit Cecilia , Olarewaju Gbolahan , Hogg Robert S. , Moore David M. , Roth Eric A.
Published: November 2021

Background Gay, bisexual, and other men who have sex with men (GBM) who engage in transactional sex (sex in exchange for drugs, money, or goods) experience increased risk of sexually transmitted infections (STI), including HIV. This study explored additional psychosocial and health-related factors associated with transactional sex among GBM. Methods Respondent-driven sampling was used to recruit GBM in Vancouver, Canada, from 2012 to 2015, with follow up every 6 months until July 2019. We examined factors associated with transactional sex using multivariable three-level mixed-effects modelling. Results Among 698 GBM, 22.1% reported ever receiving drugs, money, or goods for sex. Transactional sex was more likely to be reported by GBM who were younger (<30 years) and who had lower incomes, less education, and insecure housing. GBM reporting transactional sex were more likely to report substance use (i.e. crystal methamphetamine, poppers, GHB, and non-steroid injection drugs) and higher risk sexual behaviours (i.e. more sex partners, sex party attendance, and condomless anal sex with serodifferent or unknown HIV status partners); however, they were no more likely to be living with HIV or to report a recent bacterial STI diagnosis. GBM who reported higher loneliness, anxiety, and cognitive escape were also more likely to report transactional sex. Conclusions More than one-fifth of GBM in Vancouver reported transactional sex and those who did were more likely to also experience psychosocial stressors, increased substance use, and higher risk sexual behaviours. Programs which consider the interconnections of personal, social, and structural challenges faced by GBM engaging in transactional sex are necessary to support improved mental, physical, and sexual health for these men.
A Kalirin missense mutation enhances dendritic RhoA signaling and leads to regression of cortical dendritic arbors across development
Authors: Grubisha Melanie J. , Sun Tao , Eisenman Leanna , Erickson Susan L. , Chou Shinnyi , Helmer Cassandra D. , Trudgen Melody T. , Ding Ying , Homanics Gregg E. , Penzes Peter , Wills Zachary P. , Sweet Robert A.
Published: November 2021

Significance

Dendrites are long branching processes on neurons that contain small processes called spines that are the site of connections with other neurons, establishing cortical circuitry. Dendrites have long been considered stable structures, with rapid growth prior to adolescence followed by maintenance of size into adulthood. However, schizophrenia is characterized by accelerated reductions of cortical gray matter volume and onset of clinical symptoms during adolescence, with reductions in dendritic length present when examined after death. We show that dendrites retain the capacity for regression and that a mild genetic vulnerability in a regression pathway leads to onset of structural impairments in previously formed dendrites across adolescence. This suggests that targeting specific regression pathways could potentially lead to new therapeutics for schizophrenia.
Temporal self-compression: Behavioral and neural evidence that past and future selves are compressed as they move away from the present
Authors: Brietzke Sasha , Meyer Meghan L.
Published: November 2021

Significance

For centuries, great thinkers have struggled to understand how people represent a personal identity that changes over time. Insight may come from a basic principle of perception: as objects become distant, they also become less discriminable or “compressed.” In Studies 1–3, we demonstrate that people’s ratings of their own personality become increasingly less differentiated as they consider more distant past and future selves. In Study 4, we found neural evidence that the brain compresses self-representations with time as well. When we peer out a window, objects close to us are in clear view, whereas distant objects are hard to tell apart. We provide evidence that self-perception may operate similarly, with the nuance of distant selves increasingly harder to perceive.
Fragility indices for only sufficiently likely modifications
Authors: Baer Benjamin R. , Gaudino Mario , Charlson Mary , Fremes Stephen E. , Wells Martin T.
Published: November 2021

Significance

In frequentist hypothesis testing,
P
values are used to establish statistical significance. Currently, there is an active movement to use alternative metrics, such as the fragility index, which measures how many outcome modifications in a clinical trial are required to reverse statistical significance. The fragility index approach compares to alternative outcomes that could have arisen from the same clinical trial. However, the existing fragility index does not take into account the likelihood of the outcomes and is defined only for 2 × 2 tables. We introduce methods that provide intuitive remedies to these problems.
Structural basis for substrate specificity of heteromeric transporters of neutral amino acids
Authors: Rodriguez Carlos F. , Escudero-Bravo Paloma , Díaz Lucía , Bartoccioni Paola , García-Martín Carmen , Gilabert Joan G. , Boskovic Jasminka , Guallar Víctor , Errasti-Murugarren Ekaitz , Llorca Oscar , Palacín Manuel
Published: November 2021

Significance

The transport of amino acids across the plasma membrane plays a central role in physiology. The heteromeric amino acid transporters (HATs) of neutral amino acids (LAT1/CD98hc, LAT2/CD98hc, and Asc1/CD98hc) participate in a variety of processes such as modulation of glutamatergic neurotransmission and synaptic plasticity, auditory function, and promotion of brain development and tumor growth by supporting mTORC1 activity. We identify substrate specificity determinants of neutral amino acids HATs within the substrate-binding cavity and in a nearby region that holds the conformation of the substrate-binding site. LAT2 mutations in this scaffold region are associated with human diseases, and our results pave the way to understand the molecular mechanisms of these pathologies.
Reconsidering theshi…(de)construction in spoken Mandarin
Authors: Cook Angela
Published: November 2021

This paper revisits the use of theshi…deconstruction, based on the analysis of structures with predicative adjectives in a 500,000-character corpus of spoken Mandarin assembled from transcripts of a popular Chinese chat show. Overall,dewas omitted more than 40% of the time with a predicative adjective, a significantly higher rate than that found in previous studies. The data reveal a number of factors that may all play a role in determining the likelihood ofdeomission or retention: the time dependency of the adjective, the particular intensifier chosen to modify the adjective, the discourse function of the utterance and the presence of certain markers of epistemic modality. The findings also lend support to the hypothesis thatshiis grammaticalizing to a bound morpheme in some so-called ‘conventionalised forms’ involving epistemic and evidentiality markers.
Revisions to the Siraya lexicon based on the original Utrecht Manuscript
Authors: Joby Christopher
Published: November 2021

Linguistic historiography analyzes how linguistic knowledge has been acquired, stored, used and diffused. This article examines what can happen if linguists rely on copies of source data rather than the source data itself. It takes as a case study linguistic data from Siraya, a now-extinct Formosan language. Documents compiled in the seventeenth century by Dutch missionaries in Taiwan form a significant source of data for Siraya. One such document, a wordlist known as the Utrecht Manuscript (UM), is the principal source for the lexicon of one variety of Siraya, “Siraya Proper”. It has been published three times. Each edition, however, contains many errors. These editions, rather than the manuscript, have been used by scholars investigating Siraya. This article aims to correct errors in the editions and secondary literature on the UM with my readings of the manuscript itself. It therefore presents a more accurate record of the lexicon of “Siraya Proper” as well as illustrating the importance of using primary rather than secondary sources of linguistic data. Finally, it introduces an online edition of the UM, which will provide scholars and language revivalists with a useful resource for this lexicon.
Discoursal representation of masculine parenting in Arabic and English websites
Authors: Al-Ali Mohammed Nahar , Shatat Hanan A.
Published: November 2021

The purpose of this study is to investigate the differences and similarities between Arabic and English parents’ role in
Arabic and English parenting website texts and the linguistic exponents used to address parents and signal their roles, and to find out the
socio-cultural ideologies that have given rise to variations in gender roles. To this end, a corpus of 40 articles targeting gender-neutral
titles and father related ones were selected equally from English and Arabic websites. Drawing on Van
Leeuwen’s (2008) framework on critical discourse analysis (CDA) and Sunderland’s (2000,
2006) framework of analysis, the data were analysed and contrasted. The English texts reflected the prevalence of ‘shared parenting’
discourse, whereas the Arabic ones revealed a ‘very traditional parenthood’ discourse. These differences can be attributed to variation in
the socio-cultural practices dominant in Arab and Western societies. Such findings will hopefully provide some useful insights for family
life educators and parents who resort to such websites.
L2 Theme development in Discursive and Experimental undergraduate student writing
Authors: Chen Xiao , Gardner Sheena
Published: November 2021

To complement earlier studies of writing development in the BAWE corpus of successful student writing (Nesi & Gardner 2012; Staples et al. 2016), we examine the Systemic Functional Linguistics notion of Theme as used by L2 writers across first- and third-year and in two distinctive discourse types: persuasive/argumentative Discursive writing of assignments in the soft disciplines and Experimental report writing of assignments in the hard sciences. Theme analysis reveals more substantial differences across the two discourse types than between first- and third-year L2 undergraduate writing. Textual Themes are consistently more frequent than interpersonal Themes, and some variance is found within subcategories of each. Significant differences in lexical density occur across third-year discourse types and between first- and third-year Experimental writing where a predominance of N+N topical Themes is also found. These findings are important as previous research has tended to focus on L1 Discursive writing.
A growth factor–expressing macrophage subpopulation orchestrates regenerative inflammation via GDF-15
Authors: Patsalos Andreas , Halasz Laszlo , Medina-Serpas Miguel A. , Berger Wilhelm K. , Daniel Bence , Tzerpos Petros , Kiss Máté , Nagy Gergely , Fischer Cornelius , Simandi Zoltan , Varga Tamas , Nagy Laszlo
Published: November 2021

Muscle regeneration is the result of the concerted action of multiple cell types driven by the temporarily controlled phenotype switches of infiltrating monocyte–derived macrophages. Pro-inflammatory macrophages transition into a phenotype that drives tissue repair through the production of effectors such as growth factors. This orchestrated sequence of regenerative inflammatory events, which we termed regeneration-promoting program (RPP), is essential for proper repair. However, it is not well understood how specialized repair-macrophage identity develops in the RPP at the transcriptional level and how induced macrophage–derived factors coordinate tissue repair. Gene expression kinetics–based clustering of blood circulating Ly6Chigh, infiltrating inflammatory Ly6Chigh, and reparative Ly6Clow macrophages, isolated from injured muscle, identified the TGF-β superfamily member, GDF-15, as a component of the RPP. Myeloid GDF-15 is required for proper muscle regeneration following acute sterile injury, as revealed by gain- and loss-of-function studies. Mechanistically, GDF-15 acts both on proliferating myoblasts and on muscle-infiltrating myeloid cells. Epigenomic analyses of upstream regulators of Gdf15 expression identified that it is under the control of nuclear receptors RXR/PPARγ. Finally, immune single-cell RNA-seq profiling revealed that Gdf15 is coexpressed with other known muscle regeneration–associated growth factors, and their expression is limited to a unique subpopulation of repair-type macrophages (growth factor–expressing macrophages [GFEMs]).
Predicting the multi-label protein subcellular localization through multi-information fusion and MLSI dimensionality reduction based on MLFE classifier
Authors: Liu Yushuang , Jin Shuping , Gao Hongli , Wang Xue , Wang Congjing , Zhou Weifeng , Yu Bin
Published: November 2021

Motivation

Multi-label (ML) protein subcellular localization (SCL) is an indispensable way to study protein function. It can locate a certain protein (such as the human transmembrane protein that promotes the invasion of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)) or expression product at a specific location in a cell, which can provide a reference for clinical treatment of diseases such as coronavirus disease 2019 (COVID-19).

Results

The article proposes a novel method named ML-locMLFE. First of all, six feature extraction methods are adopted to obtain protein effective information. These methods include pseudo amino acid composition, encoding based on grouped weight, gene ontology, multi-scale continuous and discontinuous, residue probing transformation and evolutionary distance transformation. In the next part, we utilize the ML information latent semantic index method to avoid the interference of redundant information. In the end, ML learning with feature-induced labeling information enrichment is adopted to predict the ML protein SCL. The Gram-positive bacteria dataset is chosen as a training set, while the Gram-negative bacteria dataset, virus dataset, newPlant dataset and SARS-CoV-2 dataset as the test sets. The overall actual accuracy of the first four datasets are 99.23%, 93.82%, 93.24% and 96.72% by the leave-one-out cross validation. It is worth mentioning that the overall actual accuracy prediction result of our predictor on the SARS-CoV-2 dataset is 72.73%. The results indicate that the ML-locMLFE method has obvious advantages in predicting the SCL of ML protein, which provides new ideas for further research on the SCL of ML protein.

Availability and implementation

The source codes and datasets are publicly available at https://github.com/QUST-AIBBDRC/ML-locMLFE/.

Supplementary information

Supplementary data are available at Bioinformatics online.
RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB
Authors: Bittrich Sebastian , Rose Yana , Segura Joan , Lowe Robert , Westbrook John D , Duarte Jose M , Burley Stephen K
Published: November 2021

Motivation

Membrane proteins are encoded by approximately one fifth of human genes but account for more than half of all US FDA approved drug targets. Thanks to new technological advances, the number of membrane proteins archived in the PDB is growing rapidly. However, automatic identification of membrane proteins or inference of membrane location is not a trivial task.

Results

We present recent improvements to the RCSB Protein Data Bank web portal (RCSB PDB, rcsb.org) that provide a wealth of new membrane protein annotations integrated from four external resources: OPM, PDBTM, MemProtMD and mpstruc. We have substantially enhanced the presentation of data on membrane proteins. The number of membrane proteins with annotations available on rcsb.org was increased by ∼80%. Users can search for these annotations, explore corresponding tree hierarchies, display membrane segments at the 1D amino acid sequence level, and visualize the predicted location of the membrane layer in 3D.

Availability and implementation

Annotations, search, tree data and visualization are available at our rcsb.org web portal. Membrane visualization is supported by the open-source Mol* viewer (molstar.org and github.com/molstar/molstar).

Supplementary information

Supplementary data are available at Bioinformatics online.
Identification, semantic annotation and comparison of combinations of functional elements in multiple biological conditions
Authors: Leone Michele , Galeota Eugenia , Masseroli Marco , Pelizzola Mattia
Published: November 2021

Motivation

Approaches such as chromatin immunoprecipitation followed by sequencing (ChIP-seq) represent the standard for the identification of binding sites of DNA-associated proteins, including transcription factors and histone marks. Public repositories of omics data contain a huge number of experimental ChIP-seq data, but their reuse and integrative analysis across multiple conditions remain a daunting task.

Results

We present the Combinatorial and Semantic Analysis of Functional Elements (CombSAFE), an efficient computational method able to integrate and take advantage of the valuable and numerous, but heterogeneous, ChIP-seq data publicly available in big data repositories. Leveraging natural language processing techniques, it integrates omics data samples with semantic annotations from selected biomedical ontologies; then, using hidden Markov models, it identifies combinations of static and dynamic functional elements throughout the genome for the corresponding samples. CombSAFE allows analyzing the whole genome, by clustering patterns of regions with similar functional elements and through enrichment analyses to discover ontological terms significantly associated with them. Moreover, it allows comparing functional states of a specific genomic region to analyze their different behavior throughout the various semantic annotations. Such findings can provide novel insights by identifying unexpected combinations of functional elements in different biological conditions.

Availability and implementation

The Python implementation of the CombSAFE pipeline is freely available for non-commercial use at: https://github.com/DEIB-GECO/CombSAFE.

Supplementary information

Supplementary data are available at Bioinformatics online.
springD2A: capturing uncertainty in disease–drug association prediction with model integration
Authors: Wang Weiwen , Zhang Xiwen , Dai Dao-Qing
Published: November 2021

Motivation

Drug repositioning that aims to find new indications for existing drugs has been an efficient strategy for drug discovery. In the scenario where we only have confirmed disease–drug associations as positive pairs, a negative set of disease–drug pairs is usually constructed from the unknown disease–drug pairs in previous studies, where we do not know whether drugs and diseases can be associated, to train a model for disease–drug association prediction (drug repositioning). Drugs and diseases in these negative pairs can potentially be associated, but most studies have ignored them.

Results

We present a method, springD2A, to capture the uncertainty in the negative pairs, and to discriminate between positive and unknown pairs because the former are more reliable. In springD2A, we introduce a spring-like penalty for the loss of negative pairs, which is strong if they are too close in a unit sphere, but mild if they are at a moderate distance. We also design a sequential sampling in which the probability of an unknown disease–drug pair sampled as negative is proportional to its score predicted as positive. Multiple models are learned during sequential sampling, and we adopt parameter- and feature-based ensemble schemes to boost performance. Experiments show springD2A is an effective tool for drug-repositioning.

Availability and implementation

A python implementation of springD2A and datasets used in this study are available at https://github.com/wangyuanhao/springD2A.

Supplementary information

Supplementary data are available at Bioinformatics online.
HDMC: a novel deep learning-based framework for removing batch effects in single-cell RNA-seq data
Authors: Wang Xiao , Wang Jia , Zhang Han , Huang Shenwei , Yin Yanbin
Published: November 2021

Motivation

With the development of single-cell RNA sequencing (scRNA-seq) techniques, increasingly more large-scale gene expression datasets become available. However, to analyze datasets produced by different experiments, batch effects among different datasets must be considered. Although several methods have been recently published to remove batch effects in scRNA-seq data, two problems remain to be challenging and not completely solved: (i) how to reduce the distribution differences of different batches more accurately; and (ii) how to align samples from different batches to recover the cell type clusters.

Results

We proposed a novel deep-learning approach, which is a hierarchical distribution-matching framework assisted with contrastive learning to address these two problems. Firstly, we design a hierarchical framework for distribution matching based on a deep autoencoder. This framework employs an adversarial training strategy to match the global distribution of different batches. This provides an improved foundation to further match the local distributions with a maximum mean discrepancy-based loss. For local matching, we divide cells in each batch into clusters and develop a contrastive learning mechanism to simultaneously align similar cluster pairs and keep noisy pairs apart from each other. This allows to obtain clusters with all cells of the same type (true positives), and avoid clusters with cells of different type (false positives). We demonstrate the effectiveness of our method on both simulated and real datasets. Results show that our new method significantly outperforms the state-of-the-art methods and has the ability to prevent overcorrection.

Availability and implementation

The python code to generate results and figures in this article is available at https://github.com/zhanglabNKU/HDMC, the data underlying this article is also available at this github repository.

Supplementary information

Supplementary data are available at Bioinformatics online.
Personalized subcutaneous implantable cardioverter-defibrillator sensing vectors generated by mathematical rotation increase device eligibility whilst preserving device performance
Authors: Wiles Benedict M , Roberts Paul R , Allavatam Venugopal , Acharyya Amit , Vemishetty Naresh , ElRefai Mohamed , Wilson David G , Maharatna Koushik , Chen Hanjie , Morgan John M
Published: November 2021

Aims

Approximately 5.7% of potential subcutaneous implantable cardioverter-defibrillator (S-ICD) recipients are ineligible by virtue of their vector morphology, with higher rates of ineligibility observed in some at-risk groups. Mathematical vector rotation is a novel technique that can generate a personalized sensing vector, one with maximal R:T ratio, using electrocardiogram (ECG) signal recorded from the present S-ICD location.

Methods and results

A cohort of S-ICD ineligible patients were identified through ECG screening of ICD patients with no ventricular pacing requirement and their personalized vectors were generated using ECG signal from a Holter monitor. Subcutaneous ICD eligibility in this cohort was then recalculated. In a separate cohort, episodes of arrhythmia were recorded in patients undergoing arrhythmia induction, and arrhythmia detection in standard S-ICD vectors was compared to rotated vectors using an S-ICD simulator. Ninety-two participants (mean age 64.9 ± 2.7 years) underwent screening and 5.4% were found to be S-ICD ineligible. Personalized vector generation increased the R:T ratio in these vectors from 2.21 to 7.21 (4.54–9.88, P < 0.001) increasing the cohort eligibility from 94.6% to 100%. Rotated S-ICD vectors also showed high ventricular fibrillation (VF) detection sensitivity (97.8%), low time to VF detection (6.1 s), and excellent tachycardia discrimination (sensitivity 96%, specificity 88%), with no significant differences between rotated and standard vectors.

Conclusion

In S-ICD ineligible patients, mathematical vector rotation can generate a personalized vector that is associated with a significant increase in R:T ratio, resulting in universal device eligibility in our cohort. Ventricular fibrillation detection efficacy, time to VF detection, and tachycardia discrimination were not affected by vector rotation.
Hybridization Dynamics and Extensive Introgression in theDaphnia longispinaSpecies Complex: New Insights from a High-QualityDaphnia galeataReference Genome
Authors: Nickel Jana , Schell Tilman , Holtzem Tania , Thielsch Anne , Dennis Stuart R , Schlick-Steiner Birgit C , Steiner Florian M , Möst Markus , Pfenninger Markus , Schwenk Klaus , Cordellier Mathilde
Published: November 2021

Hybridization and introgression are recognized as an important source of variation that influence adaptive processes; both phenomena are frequent in the genus Daphnia, a keystone zooplankton taxon in freshwater ecosystems that comprises several species complexes. To investigate genome-wide consequences of introgression between species, we provide here the first high-quality genome assembly for a member of the Daphnia longispina species complex, Daphnia galeata. We further resequenced 49 whole genomes of three species of the complex and their interspecific hybrids both from genotypes sampled in the water column and from single resting eggs extracted from sediment cores. Populations from habitats with diverse ecological conditions offered an opportunity to study the dynamics of hybridization linked to ecological changes and revealed a high prevalence of hybrids. Using phylogenetic and population genomic approaches, we provide first insights into the intra- and interspecific genome-wide variability in this species complex and identify regions of high divergence. Finally, we assess the length of ancestry tracts in hybrids to characterize introgression patterns across the genome. Our analyses uncover a complex history of hybridization and introgression reflecting multiple generations of hybridization and backcrossing in the Daphnia longispina species complex. Overall, this study and the new resources presented here pave the way for a better understanding of ancient and contemporary gene flow in the species complex and facilitate future studies on resting egg banks accumulating in lake sediment.
Regulation of bla system in ST59-related oxacillin-susceptible mecA-positive Staphylococcus aureus
Authors: Jian Ying , Li Tianming , Zhao Lin , Zhao Na , Liu Yao , Lv Huiying , Wang Ya’nan , Liu Qian , Li Min
Published: November 2021

Objectives

Oxacillin-susceptible mecA-positive Staphylococcus aureus (OS-MRSA) is clinically significant and isolated globally but the mechanism of its occurrence remains indistinct. We sought to assess the mechanism of regulating oxacillin susceptibility in OS-MRSA isolates by evaluating the evolutionary dynamics of OS-MRSA and the discrepancies of mecA-regulating genes in OS-MRSA and oxacillin-resistant MRSA (OR-MRSA).

Methods

Nine OS-MRSA isolates and 77 OR-MRSA isolates were sequenced using next-generation sequencing (NGS) platforms. Two representative OS-MRSA isolates (ET-13, ET-16) were induced to be oxacillin resistant and sequenced also. OS-MRSA ET-16 and its counterpart isolate with induced oxacillin resistance, ET-16I, and their mutants were used to confirm the role of the bla system in regulating methicillin susceptibility. Oxacillin MICs were determined using Etests. Expression of mecA and blaR1 was quantified by quantitative RT–PCR.

Results

A deletion in blaR1 in most OS-MRSA isolates (7/9; 77.78%) was found using NGS data, and overexpression of OR-blaR1 in OS-MRSA isolate ET-16 restored its oxacillin resistance. OS-MRSA could be induced to be oxacillin resistant, while growth was suppressed in the induced isolates. Plasmid containing the bla locus was lost in most induced isolates during the induction process and complementation of blaR1-blaI from OS-MRSA ET-16 to the induced isolate ET-16I converted its oxacillin susceptibility.

Conclusions

Deletion in blaR1 resulted in oxacillin susceptibility in OS-MRSA, and loss of the bla regulator in OS-MRSA restored oxacillin resistance. The bla system played a crucial role in regulating oxacillin susceptibility in OS-MRSA isolates.
Clinical Trial Endpoints in Metastatic Cancer: Using Individual Participant Data to Inform Future Trials Methodology
Authors: Goldberg Richard M , Adams Richard , Buyse Marc , Eng Cathy , Grothey Axel , André Thierry , Sobrero Alberto F , Lichtman Stuart M , Benson Al B , Punt Cornelis J A , Maughan Tim , Burzykowski Tomasz , Sommeijer Dirkje , Saad Everardo D , Shi Qian , Coart Elisabeth , Chibaudel Benoist , Koopman Miriam , Schmoll Hans-Joachim , Yoshino Takayuki , Taieb Julien , Tebbutt Niall C , Zalcberg John , Tabernero Josep , Van Cutsem Eric , Matheson Alastair , de Gramont Aimery
Published: November 2021

Meta-analysis based on individual participant data (IPD) is a powerful methodology for synthesizing evidence by combining information drawn from multiple trials. Hitherto, its principal application has been in questions of clinical management, but an increasingly important use is in clarifying trials methodology, for instance in the selection of endpoints, as discussed in this review. In oncology, the Aide et Recherche en Cancérologie Digestive (ARCAD) Metastatic Colorectal Cancer Database is a leader in the use of IPD-based meta-analysis in methodological research. The ARCAD database contains IPD from more than 38 000 patients enrolled in 46 studies and continues to collect phase III trial data. Here, we review the principal findings of the ARCAD project in respect of endpoint selection and examine their implications for cancer trials. Analysis of the database has confirmed that progression-free survival (PFS) is no longer a valid surrogate endpoint predictive of overall survival in the first-line treatment of colorectal cancer. Nonetheless, PFS remains an endpoint of choice for most first-line trials in metastatic colorectal cancer and other solid tumors. Only substantial PFS effects are likely to translate into clinically meaningful benefits, and accordingly, we advocate an oncology research model designed to identify highly effective treatments in carefully defined patient groups. We also review the use of the ARCAD database in assessing clinical response including novel response metrics and prognostic markers. These studies demonstrate the value of IPD as a tool for methodological studies and provide a reference point for the expansion of this approach within clinical cancer research.
Meningioma-associated abscess: an unusual case report and review of the literature
Authors: Rashed Sami , Vassiliou Anna , Ogborne Rosalie , McKenna Gráinne
Published: November 2021

Central nervous system (CNS) infection and neoplasm occur most often independently. Their concomitant presentation has been noted across different CNS tumours but is considered a rare entity. The phenomenon is mostly seen in relation to direct seeding of infection via frontal air sinuses. Here, we present an unusual case of an occipital meningioma associated with intraparenchymal paratumoural abscess formation. It is also the second documented to culture methicillin-susceptible Staphylococcus aureus. We then review and surmise the relevant literature of meningioma-associated abscess. We discuss the clinical presentations, aetiology, suspected pathogenesis, management and outcomes reported.
Involvement of α-galactosidase OmAGAL2 in planteose hydrolysis during seed germination of Orobanche minor
Authors: Okazawa Atsushi , Baba Atsuya , Okano Hikaru , Tokunaga Tomoya , Nakaue Tsubasa , Ogawa Takumi , Shimma Shuichi , Sugimoto Yukihiro , Ohta Daisaku
Published: November 2021

Root parasitic weeds of the Orobanchaceae, such as witchweeds (Striga spp.) and broomrapes (Orobanche and Phelipanche spp.), cause serious losses in agriculture worldwide, and efforts have been made to control these parasitic weeds. Understanding the characteristic physiological processes in the life cycle of root parasitic weeds is particularly important to identify specific targets for growth modulators. In our previous study, planteose metabolism was revealed to be activated soon after the perception of strigolactones in germinating seeds of O. minor. Nojirimycin inhibited planteose metabolism and impeded seed germination of O. minor, indicating a possible target for root parasitic weed control. In the present study, we investigated the distribution of planteose in dry seeds of O. minor by matrix-assisted laser desorption/ionization–mass spectrometry imaging. Planteose was detected in tissues surrounding—but not within—the embryo, supporting its suggested role as a storage carbohydrate. Biochemical assays and molecular characterization of an α-galactosidase family member, OmAGAL2, indicated that the enzyme is involved in planteose hydrolysis in the apoplast around the embryo after the perception of strigolactones, to provide the embryo with essential hexoses for germination. These results indicate that OmAGAL2 is a potential molecular target for root parasitic weed control.
Chandra revisits WR 48a: testing colliding wind models in massive binaries
Authors: Zhekov Svetozar A , Gagné Marc , Skinner Stephen L
Published: November 2021

We present results of new Chandra High-Energy Transmission Grating (HETG) observations (2019 November–December) of the massive Wolf–Rayet binary WR 48a. Analysis of these high-quality data showed that the spectral lines in this massive binary are broadened (full width at half-maximum, FWHM  = 1400 km s−1) and marginally blueshifted (∼−100 km s−1). A direct modelling of these high-resolution spectra in the framework of the standard colliding stellar wind (CSW) picture provided a very good correspondence between the shape of the theoretical and observed spectra. Also, the theoretical line profiles are in most cases an acceptable representation of the observed ones. We applied the CSW model to the X-ray spectra of WR 48a from previous observations: Chandra-HETG (2012 October) and XMM–Newton (2008 January). From this expanded analysis, we find that the observed X-ray emission from WR 48a is variable on the long time-scale (years) and the same is valid for its intrinsic X-ray emission. This requires variable mass-loss rates over the binary orbital period. The X-ray absorption (in excess of that from the stellar winds in the binary) is variable as well. We note that lower intrinsic X-ray emission is accompanied by higher X-ray absorption. A qualitative explanation could be that the presence of clumpy and non-spherically symmetric stellar winds may play a role.
Low-frequency quasi-periodic oscillations and shocks in accretion on to black hole
Authors: Singh Chandra B , Mondal Santanu , Garofalo David
Published: November 2021

Low-frequency quasi-periodic oscillations (LFQPOs) have been routinely observed in black hole X-ray binaries (BHXRBs). These LFQPOs can be explained by axisymmetric shock oscillation in accretion flow around a rotating black hole. We address the physical origin of Type-C LFQPOs in BHXRBs observed by the Rossi X-ray Timing Explorer satellite considering a minimum number of free parameters, namely, specific energy and specific angular momentum of the infalling matter for a given set of BH mass and spin parameter. We apply the solution for a large number of BH candidates to further strengthen the scenario of an anticorrelation between the QPO frequency and the location of the shock. Our study also confirms that Compton cooling can be sufficient to explain the observed QPOs.
Satellite quenching was not important for z ∼ 1 clusters: most quenching occurred during infall
Authors: Werner S V , Hatch N A , Muzzin A , van der Burg R F J , Balogh M L , Rudnick G , Wilson G
Published: November 2021

We quantify the relative importance of environmental quenching versus pre-processing in z ∼ 1 clusters by analysing the infalling galaxy population in the outskirts of 15 galaxy clusters at 0.8 < z < 1.4 drawn from the GOGREEN and GCLASS surveys. We find significant differences between the infalling galaxies and a control sample; in particular, an excess of massive quiescent galaxies in the infalling region. These massive infalling galaxies likely reside in larger dark matter haloes than similar-mass control galaxies because they have twice as many satellite galaxies. Furthermore, these satellite galaxies are distributed in an NFW profile with a larger scale radius compared to the satellites of the control galaxies. Based on these findings, we conclude that it may not be appropriate to use ‘field’ galaxies as a substitute for infalling pre-cluster galaxies when calculating the efficiency and mass dependence of environmental quenching in high-redshift clusters. By comparing the quiescent fraction of infalling galaxies at 1 < R/R200<3 to the cluster sample (R/R200<1) we find that almost all quiescent galaxies with masses >1011 M⊙ were quenched prior to infall, while up to half of lower mass galaxies were environmentally quenched after passing the virial radius. This means most of the massive quiescent galaxies in z ∼ 1 clusters were self-quenched or pre-processed prior to infall.
Revised event rates for extreme and extremely large mass-ratio inspirals
Authors: Vázquez-Aceves Verónica , Zwick Lorenz , Bortolas Elisa , Capelo Pedro R , Amaro Seoane Pau , Mayer Lucio , Chen Xian
Published: November 2021

One of the main targets of the Laser Interferometer Space Antenna (LISA) is the detection of extreme mass-ratio inspirals (EMRIs) and extremely large mass-ratio inspirals (X-MRIs). Their orbits are expected to be highly eccentric and relativistic when entering the LISA band. Under these circumstances, the inspiral time-scale given by Peters’ formula loses precision and the shift of the last-stable orbit (LSO) caused by the massive black hole spin could influence the event rates estimate. We re-derive EMRIs and X-MRIs event rates by implementing two different versions of a Kerr loss-cone angle that includes the shift in the LSO, and a corrected version of Peters’ time-scale that accounts for eccentricity evolution, 1.5 post-Newtonian hereditary fluxes, and spin-orbit coupling. The main findings of our study are summarized as follows: (1) implementing a Kerr loss-cone changes the event rates by a factor ranging between 0.9 and 1.1; (2) the high-eccentricity limit of Peters’ formula offers a reliable inspiral time-scale for EMRIs and X-MRIs, resulting in an event-rate estimate that deviates by a factor of about 0.9–3 when compared to event rates computed with the corrected version of Peters’ time-scale and the usual loss-cone definition. (3) Event-rate estimates for systems with a wide range of eccentricities should be revised. Peters’ formula overestimates the inspiral rates of highly eccentric systems by a factor of about 8–30 compared to the corrected values. Besides, for e0 ≲ 0.8, implementing the corrected version of Peters’ formula is necessary to obtain accurate estimates.
The viewing angle in AGN SED models: a data-driven analysis
Authors: Ramos Padilla Andrés F , Wang Lingyu , Małek Katarzyna , Efstathiou Andreas , Yang (杨光) Guang
Published: November 2021

The validity of the unified active galactic nuclei (AGNs) model has been challenged in the last decade, especially when different types of AGNs are considered to only differ in the viewing angle to the torus. We aim to assess the importance of the viewing angle in classifying different types of Seyfert galaxies in spectral energy distribution (SED) modelling. We retrieve photometric data from publicly available astronomical data bases: CDS and NED, to model SEDs with x-cigale in a sample of 13 173 Seyfert galaxies located at redshift range from z = 0 to 3.5, with a median redshift of z ≈ 0.2. We assess whether the estimated viewing angle from the SED models reflects different Seyfert classifications. Two AGN models with either a smooth or clumpy torus structure are adopted in this paper. We find that the viewing angle in Type-1 AGNs is better constrained than in Type-2 AGNs. Limiting the viewing angles representing these two types of AGNs does not affect the physical parameter estimates such as star formation rate (SFR) or AGN fractional contribution (fAGN). In addition, the viewing angle is not the most discriminating physical parameter to differentiate Seyfert types. We suggest that the observed and intrinsic AGN disc luminosity can (i) be used in z < 0.5 studies to distinguish between Type-1 and Type-2 AGNs, and (ii) explain the probable evolutionary path between these AGN types. Finally, we propose the use of x-cigale for AGN galaxy classification tasks. All data from the 13 173 SED fits are available at Zenodo1.
Uncovering the chemical structure of the pulsating low-mass white dwarf SDSS J115219.99+024814.4
Authors: Romero A D , Lauffer G R , Istrate A G , Parsons S G
Published: November 2021

Pulsating low-mass white dwarf (WD) stars are WDs with stellar masses between 0.30 and 0.45 M⊙ that show photometric variability due to gravity-mode pulsations. Within this mass range, they can harbour both a helium core and hybrid core, depending if the progenitor experienced helium-core burning during the pre-WD evolution. SDSS J115219.99+024814.4 is an eclipsing binary system where both components are low-mass WDs, with stellar masses of 0.362 ± 0.014 M⊙ and 0.325 ± 0.013 M⊙. In particular, the less-massive component is a pulsating star, showing at least three pulsation periods of ∼1314, ∼1069, and ∼582.9 s. This opens the way to use asteroseismology as a tool to uncover its inner chemical structure, in combination with the information obtained using the light-curve modelling of the eclipses. To this end, using binary evolutionary models leading to helium- and hybrid-core WDs, we compute adiabatic pulsations for ℓ = 1 and ℓ = 2 gravity modes with Gyre. We found that the pulsating component of the SDSS J115219.99+024814.4 system must have a hydrogen envelope thinner than the value obtained from binary evolution computations, independently of the inner composition. Finally, from our asteroseismological study, we find a best-fitting model characterized by T$_{\rm eff}=10\,917$ K, M = 0.338 M⊙, and MH = 10−6 M⊙ with the inner composition of a hybrid WD.
No need for dark matter: resolved kinematics of the ultra-diffuse galaxy AGC 114905
Authors: Mancera Piña Pavel E , Fraternali Filippo , Oosterloo Tom , Adams Elizabeth A K , Oman Kyle A , Leisman Lukas
Published: November 2021

We present new H i interferometric observations of the gas-rich ultra-diffuse galaxy AGC 114905, which previous work, based on low-resolution data, identified as an outlier of the baryonic Tully–Fisher relation. The new observations, at a spatial resolution ∼2.5 times higher than before, reveal a regular H i disc rotating at about 23 km s−1. Our kinematic parameters, recovered with a robust 3D kinematic modelling fitting technique, show that the flat part of the rotation curve is reached. Intriguingly, the rotation curve can be explained almost entirely by the baryonic mass distribution alone. We show that a standard cold dark matter halo that follows the concentration–halo mass relation fails to reproduce the amplitude of the rotation curve by a large margin. Only a halo with an extremely (and arguably unfeasible) low concentration reaches agreement with the data. We also find that the rotation curve of AGC 114905 deviates strongly from the predictions of modified Newtonian dynamics. The inclination of the galaxy, which is measured independently from our modelling, remains the largest uncertainty in our analysis, but the associated errors are not large enough to reconcile the galaxy with the expectations of cold dark matter or modified Newtonian dynamics.
Current-driven kink instabilities in relativistic jets: dissipation properties
Authors: Bodo G , Mamatsashvili G , Rossi P , Mignone A
Published: November 2021

We analyse the evolution of current-driven kink instabilities of a highly magnetized relativistic plasma column, focusing in particular on its dissipation properties. The instability evolution leads to the formation of thin current sheets where the magnetic energy is dissipated. We find that the total amount of dissipated magnetic energy is independent of the dissipation properties. Dissipation occurs in two stages: a peak when the instability saturates that is characterized by the formation of a helicoidal current sheet at the boundary of the deformed plasma column, followed by a weaker almost flat phase, in which turbulence develops. The detailed properties of these two phases depend on the equilibrium configuration and other parameters, in particular on the steepness of the pitch radial profile, on the presence of an external axial magnetic field and on the amount of magnetization. These results are relevant for high energy astrophysical sources, since current sheets can be the sites of magnetic reconnection where particles can be accelerated to relativistic energies and give rise to the observed radiation.