bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effective removal of mercury (Hg) from sediment by acid extraction
Authors: Nugraha W C , Jeong H , Dinh Q P , Ishibashi Y , Arizono K 
Published: November 2021

Abstract
Mercury (Hg) is a hazardous and toxic substance that is resistant to decomposition and can accumulate in sediment and enter the living organisms via food chain. Due to the status of level mercury in Indonesia has reached the warning level, the action should be taken to avoid any negative impact on the environment and human health. The purpose of this study to developed a simple, fast, and effective sediment washing method for Hg removal using acid extraction. The results showed that pollution level of sediment in Ciujung watershed and its tributaries was high, especially the pollution of Hg and Cd, according to geoaccumulation index (I
geo) and potential ecological risk index (PERI). By the proposed method, Hg-contaminated sediment can be extracted within 21 minutes with 99.5% of extraction rate. CRM ERM CC580 (estuarine sediment) was used for validating the results. The optimal conditions such as vortex time, acid concentration, sonication time were evaluated according to analytical parameters. The method is valuable for designing a remediation protocol for sediment washing in developing countries.
Seq-SetNet: directly exploiting multiple sequence alignment for protein secondary structure prediction
Authors: Ju Fusong , Zhu Jianwei , Zhang Qi , Wei Guozheng , Sun Shiwei , Zheng Wei-Mou , Bu Dongbo 
Published: November 2021

Abstract

Motivation
Accurate prediction of protein structure relies heavily on exploiting multiple sequence alignment (MSA) for residue mutations and correlations as this information specifies protein tertiary structure. The widely used prediction approaches usually transform MSA into inter-mediate models, say position-specific scoring matrix or profile hidden Markov model. These inter-mediate models, however, cannot fully represent residue mutations and correlations carried by MSA; hence, an effective way to directly exploit MSAs is highly desirable.

Results
Here, we report a novel sequence set network (called Seq-SetNet) to directly and effectively exploit MSA for protein structure prediction. Seq-SetNet uses an ‘encoding and aggregation’ strategy that consists of two key elements: (i) an encoding module that takes a component homologue in MSA as input, and encodes residue mutations and correlations into context-specific features for each residue; and (ii) an aggregation module to aggregate the features extracted from all component homologues, which are further transformed into structural properties for residues of the query protein. As Seq-SetNet encodes each homologue protein individually, it could consider both insertions and deletions, as well as long-distance correlations among residues, thus representing more information than the inter-mediate models. Moreover, the encoding module automatically learns effective features and thus avoids manual feature engineering. Using symmetric aggregation functions, Seq-SetNet processes the homologue proteins as a sequence set, making its prediction results invariable to the order of these proteins. On popular benchmark sets, we demonstrated the successful application of Seq-SetNet to predict secondary structure and torsion angles of residues with improved accuracy and efficiency.

Availability and implementation
The code and datasets are available through https://github.com/fusong-ju/Seq-SetNet.

Supplementary information
Supplementary data are available at Bioinformatics online.
Trust and mistrust in public services for people with disabilities: Analysing the gap between the perspectives of caseworkers and disabled people in Denmark
Authors: Kohl Katrine Syppli , Amilon Anna , Olsen Leif 
Published: November 2021

Abstract
This article explores a zone of conflict and a demonstrable gap in perceptions of casework and public services in Denmark between service users with disabilities and caseworkers. First, based on a descriptive analysis of responses from two surveys, one of service users with disabilities (N = 1,427) and one of caseworkers from four human services departments (N = 428): the ‘Job Centre’, ‘Adult Disability’, ‘Children & Families’ and ‘Health’, we find significantly different levels of trust in the services between the two groups. Second, drawing on semi-structured interviews with service users (N = 20) and municipal caseworkers (N = 10), we explain this difference through the identification of a series of intersecting dilemmas that create barriers and conflict. Overall, a thematic analysis of the interviews shows that the trust between caseworkers and people with disabilities is influenced by a complex interplay of individual, relational, situational and organisational factors. Knowledge gained from this study will help shape municipal service provision for people with disabilities, by supplementing the experiences and perspectives of caseworkers and service users and by directing attention to core dilemmas in social work that challenge trust and service user involvement.
Cycloserine and Linezolid for Tuberculosis Meningitis: Pharmacokinetic Evidence of Potential Usefulness
Authors: Kempker Russell R , Smith Alison G C , Avaliani Teona , Gujabidze Mariam , Bakuradze Tinatin , Sabanadze Shorena , Avaliani Zaza , Collins Jeffrey M , Blumberg Henry M , Alshaer Mohammad H , Peloquin Charles A , Kipiani Maia 
Published: November 2021

Abstract

Background
The ability of antituberculosis drugs to cross the blood–brain barrier and reach the central nervous system is critical to their effectiveness in treating tuberculosis meningitis (TBM). We sought to fill a critical knowledge gap by providing data on the ability of new and repurposed antituberculosis drugs to penetrate into the cerebrospinal fluid (CSF).

Methods
We conducted a clinical pharmacology study among patients treated for TBM in Tbilisi, Georgia, from January 2019 until January 2020. Serial serum and CSF samples were collected while patients were hospitalized. CSF was collected from routine lumbar punctures with the timing of the lumbar puncture alternating between 2 and 6 hours to capture early and late CSF penetration.

Results
A total of 17 patients treated for TBM (8 with confirmed disease) were included; all received linezolid, with a subset receiving cycloserine (5), clofazimine (5), delamanid (4), and bedaquiline (2). All CSF measurements of bedaquiline (12), clofazimine (24), and delamanid (19) were below the limit of detection. The median CSF concentrations of cycloserine at 2 and 6 hours were 15.90 and 15.10 µg/mL with adjusted CSF/serum ratios of 0.52 and 0.66. CSF concentrations of linezolid were 0.90 and 3.14 µg/mL at 2 and 6 hours, with adjusted CSF/serum ratios of 0.25 and 0.59, respectively. CSF serum linezolid concentrations were not affected by rifampin coadministration.

Conclusions
Based on moderate to high CSF penetration, linezolid and cycloserine may be effective drugs for TBM treatment, whereas the utility of bedaquiline, delamanid, and clofazimine is uncertain given their low CSF penetration.
From new kid on the block to leading journal: a review and reflection on the first 20 years of the European Journal of Cardiovascular Nursing
Authors: Fredericks Suzanne , Van Bulck Liesbet , Ski Chantal , Skibelund Anne Kathrine , Sanders Julie 
Published: November 2021

Abstract

Background
This year marks the 20th birthday of the European Journal of Cardiovascular Nursing (EJCN). The official journal of the Association of Cardiovascular Nursing and Allied Professionals, is now recognized as one of the leading nursing and allied professional journals.

Aims
This article reflects on the developments and impact of the journal over its 20-year lifespan.

Methods and results
We present a descriptive account of the journal from inception (2002) until present day (2021), using data provided by the EJCN editorial office and extracted from published and available information. In the last 20 years, the EJCN has published 20 volumes, 106 issues, and 1320 papers from 79 countries. The volume and quality of papers has been consistently increasing, culminating in a 2020 impact factor of 3.908, the highest in its history, ranking second for nursing science. Papers are predominantly patient focused with a range of research methods that cover an extensive range of cardiovascular conditions. Authors who contributed to the first issue continued their contribution; 293 articles in total.

Conclusion
The EJCN has evolved into a leading journal of cardiovascular care. As the journal enters its next era, with a new Editor-in-Chief, it is appropriate to have reflected on the phenomenal contribution of the outgoing Editor-in-Chief, and the editorial team, over the last 20 years.
Cell-Mediated Immune Responses After Administration of the Live or the Recombinant Zoster Vaccine: 5-Year Persistence
Authors: Johnson Michael J , Liu Cuining , Ghosh Debashis , Lang Nancy , Levin Myron J , Weinberg Adriana 
Published: November 2021

Abstract
We compared glycoprotein E (gE)- and varicella zoster virus (VZV)-specific Th1 immunity in 160 adults, aged 50–85 years, randomized to receive live or recombinant zoster vaccine (RZV). gE-specific responses measured by interferon-γ (IFN-γ) and interleukin 2 (IL-2) dual-color Fluorospot were significantly higher at all time points postimmunization in RZV recipients. VZV-specific IL-2+ memory, but not IFN-γ+ or IFN-γ+IL-2+ effector responses, were higher in RZV recipients at ≥3 months postimmunization. Only RZV recipients maintained higher postvaccination gE-specific IL-2+ and IFN-γ+ and VZV-specific IL-2+ responses for 5 years. The 5-year persistence of VZV-specific memory and gE-specific Th1 immunity may underlie superior RZV efficacy.
Clinical Trials Registration NCT02114333.
Defective Interferon-Gamma Production Is Common in Chronic Pulmonary Aspergillosis
Authors: Colombo Stefano A P , Hashad Rola , Denning David W , Kumararatne Dinakantha S , Ceron-Gutierrez Lourdes , Barcenas-Morales Gabriela , MacDonald Andrew S , Harris Chris , Doffinger Rainer , Kosmidis Chris 
Published: November 2021

AbstractBackgroundImmune defects in chronic pulmonary aspergillosis (CPA) are poorly characterized. We compared peripheral blood cytokine profiles in patients with CPA versus healthy controls and explored the relationship with disease severity.MethodsInterferon-gamma (IFNγ), interleukin (IL)-17, tumor necrosis factor-α, IL-6, IL-12, and IL-10 were measured after in vitro stimulation of whole blood with lipopolysaccharide (LPS), phytohemagglutinin, β-glucan, zymosan (ZYM), IL-12 or IL-18, and combinations. Clinical parameters and mortality were correlated with cytokine production.ResultsCytokine profiles were evaluated in 133 patients (57.1% male, mean age 61 years). In comparison to controls, patients with CPA had significantly reduced production of IFNγ in response to stimulation with β-glucan + IL-12 (312 vs 988 pg/mL), LPS + IL-12 (252 vs 1033 pg/mL), ZYM + IL-12 (996 vs 2347 pg/mL), and IL-18 + IL-12 (7193 vs 12 330 pg/mL). Age &gt;60 (hazard ratio [HR], 1.71; 95% confidence interval [CI], 1.00–2.91; P = .05) and chronic obstructive pulmonary disease (HR, 1.69; 95% CI, 1.03–2.78; P = .039) were associated with worse survival, whereas high IFNγ production in response to beta-glucan + IL-12 stimulation (HR, 0.48; 95% CI, .25–0.92; P = .026) was associated with reduced mortality.ConclusionsPatients with CPA show impaired IFNγ production in peripheral blood in response to stimuli. Defective IFNγ production ability correlates with worse outcomes. Immunotherapy with IFNγ could be beneficial for patients showing impaired IFNγ production in CPA.
Occurrence of a plasmid co-carrying cfr(D) and poxtA2 linezolid resistance genes in Enterococcus faecalis and Enterococcus casseliflavus from porcine manure, Italy
Authors: Cinthi Marzia , Coccitto Sonia Nina , Fioriti Simona , Morroni Gianluca , Simoni Serena , Vignaroli Carla , Magistrali Chiara Francesca , Albini Elisa , Brenciani Andrea , Giovanetti Eleonora 
Published: November 2021

Abstract

Objectives
To investigate the genetic elements and the transferability of linezolid resistance genes in three enterococci co-carrying cfr(D) and poxtA2 isolates from manure of a swine farm in central Italy.

Methods
Two Enterococcus faecalis isolates and one Enterococcus casseliflavus isolate carrying both cfr(D) and poxtA genes were tested for their susceptibility to florfenicol, chloramphenicol, linezolid, tedizolid, tetracycline and vancomycin. Linezolid resistance genes transfer (filter mating), localization (S1-PFGE/hybridization), genetic elements and relatedness between isolates (WGS) were analysed.

Results
Two E. faecalis isolates and one E. casseliflavus isolate carried the cfr(D) gene and the recently described poxtA2 variant. In the three enterococci, cfr(D) and poxtA2 were co-located on a 33 480 bp plasmid, pV386, 95%–100% identical (coverage 84%) to the Tn6349 transposon of Staphylococcus aureus AOUC-0915. In all isolates, both genes also showed a chromosomal location. Same sequence identities were found from the comparison with currently known poxtA2 genetic elements. In the plasmid pV386, poxtA2 gene was not bounded by two IS1216, as described in pIB-BOL, but closely associated to the cfr(D) and fexA genes. pV386 was always transferred by filter mating to Enterococcus faecium 64/3 recipient.

Conclusions
The occurrence of the pV386 plasmid in E. faecalis and E. casseliflavus from swine manure is of great concern and highlights the need for control measures to contain its spread to other enterococcal species.
Idiopathic hypopharyngeal perforation presenting as supraglottitis and parapharyngeal abscess: case report and literature review
Authors: Woodun Heerani , Woodun Heyrumb , Sethi Neeraj , Simons Anthony 
Published: November 2021

Abstract
A 75-year-old healthy male reported odynophagia and severe neck pain with radiation to chest and shoulders. Cardiac causes were excluded. After re-presenting with dysphonia and complete dysphagia, he was treated for supraglottitis. Imaging showed a left parapharyngeal and retropharyngeal space abscess with mediastinal emphysema. Progressive emphysema prompted contrast swallow test followed by left neck exploration and pan-endoscopy, which confirmed mucosal hypopharyngeal perforations. Histopathology reported inflammation. Autoimmune and gastroenterological aetiologies were excluded. Following conservative management, healing was demonstrated on repeat pan-endoscopy. Two months’ follow-up imaging showed complete resolution. Spontaneous hypopharyngeal perforation, atypical of Boerrhave’s syndrome and without risk factors (iatrogenic, oesophageal disease and foreign body ingestion), is rare and often misdiagnosed, including masquerading as supraglottitis. Nasoendoscopy should be complemented by radiological imaging. Presence of deep neck space collections and surgical emphysema should prompt diagnostic pan-endoscopy. Although most rupture cases require surgery, conservative management of hypopharyngeal perforations can be considered when clinically appropriate.
Tuning the lipophilic nature of pyclen-based 90Y3+ radiopharmaceuticals for β-radiotherapy
Authors: Le Fur Mariane , Fougère Olivier , Lepareur Nicolas , Rousseaux Olivier , Tripier Raphaël , Beyler Maryline 
Published: November 2021

Abstract
Pyclen-dipicolinate chelates proved to be very efficient chelators for the radiolabeling with β–-emitters such as 90Y. In this study, a pyclen-dipicolinate ligand functionalized with additional C12 alkyl chains was synthesized. The radiolabeling with 90Y proved that the addition of saturated carbon chains does not affect the efficiency of the radiolabeling, whereas a notable increase in lipophilicity of the resulting 90Y radiocomplex was observed. As a result, the compound could be extracted in Lipiodol® and encapsulated in biodegrable pegylated poly(malic acid) nanoparticles demonstrating the potential of lipophilic pyclen-dipicolinate derivatives as platforms for the design of radiopharmaceuticals for the treatment of liver or brain cancers by internal radiotherapy.
Reciprocal mutations of two multifunctional β-amyrin synthases fromBarbarea vulgarisshift α/β-amyrin ratios
Authors: Günther Jan , Erthmann Pernille Østerbye , Khakimov Bekzod , Bak Søren 
Published: November 2021

AbstractIn the wild cruciferous wintercress (Barbarea vulgaris), β-amyrin-derived saponins are involved in resistance against insect herbivores like the major agricultural pest diamondback moth (Plutella xylostella). Enzymes belonging to the 2,3-oxidosqualene cyclase family have been identified and characterized in B. vulgaris G-type and P-type plants that differ in their natural habitat, insect resistance and saponin content. Both G-type and P-type plants possess highly similar 2,3-oxidosqualene cyclase enzymes that mainly produce β-amyrin (Barbarea vulgaris Lupeol synthase 5 G-Type; BvLUP5-G) or α-amyrin (Barbarea vulgaris Lupeol synthase 5 P-Type; BvLUP5-P), respectively. Despite the difference in product formation, the two BvLUP5 enzymes are 98% identical at the amino acid level. This provides a unique opportunity to investigate determinants of product formation, using the B. vulgaris 2,3-oxidosqualene cyclase enzymes as a model for studying amino acid residues that determine differences in product formation. In this study, we identified two amino acid residues at position 121 and 735 that are responsible for the dominant changes in generated product ratios of β-amyrin and α-amyrin in both BvLUP5 enzymes. These amino acid residues have not previously been highlighted as directly involved in 2,3-oxidosqualene cyclase product specificity. Our results highlight the functional diversity and promiscuity of 2,3-oxidosqualene cyclase enzymes. These enzymes serve as important mediators of metabolic plasticity throughout plant evolution.
Speeding up dark matter with solar neutrinos
Authors: Zhang Yue 
Published: November 2021

Abstract
We present a novel mechanism of using solar neutrinos to speed up dark matter, inspired by the fact that neutrinos are the most energetic particles from the Sun with a well-understood spectrum. In a neutrino portal dark sector model, we show that dark matter with sub-GeV mass could be accelerated by pp neutrinos to velocities well above 10−3c and be capable of depositing large enough energy at direct detection experiments. A crucial ingredient of this mechanism is the dissociation of stable dark matter bound states that exist in nature. The resulting dark matter velocity distribution bears a strong resemblance in shape to the solar neutrino spectrum. As an application, we derive a leading limit on light dark matter interaction by reinterpreting a recent PICO experiment result.
Another Monoclonal Antibody Granted EUA to treat COVID-19
Authors: Aschenbrenner Diane S. 
Published: November 2021

The Food and Drug Administration has granted emergency use authorization to sotrovimab for the treatment of mild to moderate COVID-19 in patients at increased risk for progression to severe illness.Sotrovimab is a monoclonal antibody that works directly against the spike protein of SARS-CoV-2 to block its attachment and entry into a human cell.
Microvascular Ageing Links Metabolic Disease to Age-Related Disorders: The Role of Oxidative Stress and Inflammation in Promoting Microvascular Dysfunction
Authors: Mengozzi Alessandro , Pugliese Nicola Riccardo , Chiriacò Martina , Masi Stefano , Virdis Agostino , Taddei Stefano 
Published: November 2021

Abstract:
Longer life span and increased prevalence of chronic, noncommunicable, inflammatory diseases fuel cardiovascular mortality. The microcirculation is central in the cross talk between ageing, inflammation, cardiovascular, and metabolic diseases. Microvascular dysfunction, characterized by alteration in the microvascular endothelial function and wall structure, is described in an increasing number of chronic age-associated diseases, suggesting that it might be a marker of ageing superior to chronological age. The aim of this review is to thoroughly explore the connections between microvascular dysfunction, ageing, and metabolic disorders by detailing the major role played by inflammation and oxidative stress in their evolution. Older age, hypertension, nutrient abundance, and hyperglycemia concur in the induction of a persistent low-grade inflammatory response, defined as meta-inflammation or inflammageing. This increases the local generation of reactive oxygen species that further impairs endothelial function and amplifies the local inflammatory response. Mitochondrial dysfunction is a hallmark of many age-related diseases. The alterations of mitochondrial function promote irreversible modification in microvascular structure. The interest in the hypothesis of chronic inflammation at the center of the ageing process lies in its therapeutic implications. Inhibition of specific inflammatory pathways has been shown to lower the risk of many age-related diseases, including cardiovascular disease. However, the whole architecture of the inflammatory response underpinning the ageing process and its impact on the burden of age-related diseases remain to be fully elucidated. Additional studies are needed to unravel the connection between these biological pathways and to address their therapeutic power in terms of cardiovascular prevention.
C1q Tumor Necrosis Factor–Related Protein 1: A Promising Therapeutic Target for Atherosclerosis
Authors: Zhang Zi-Zhen , Wang Gang , Yin Shan-Hui , Yu Xiao-Hua 
Published: November 2021

Abstract:
Atherosclerosis serves as the pathological basis of most cardiovascular and cerebrovascular diseases. C1q tumor necrosis factor–related protein 1 (CTRP1) is a 35-kDa glycoprotein synthesized by various tissues and cells, such as adipose tissue and macrophages. As an adiponectin paralog, CTRP1 signals through adiponectin receptor 1 and participates in a variety of pathophysiological processes. Circulating CTRP1 levels are significantly increased in patients with coronary artery disease. Importantly, CTRP1 was shown to accelerate the development of atherosclerosis by promoting vascular inflammation, macrophage foam cell formation, and endothelial barrier dysfunction. This review focused on recent advances regarding the role of CTRP1 in atherogenesis with an emphasis on its potential as a novel biomarker and a promising therapeutic target for atherosclerosis-related diseases.
Unambiguous detection of SARS-CoV-2 subgenomic mRNAs with single cell RNA sequencing
Authors: Cohen Phillip , DeGrace Emma J , Danziger Oded , Patel Roosheel S , Barrall Erika A , Bobrowski Tesia , Kehrer Thomas , Cupic Anastasija , Miorin Lisa , García-Sastre Adolfo , Rosenberg Brad R 
Published: November 2021

AbstractSingle cell RNA sequencing (scRNA-Seq) studies have provided critical insight into the pathogenesis of Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2), the causative agent of COronaVIrus Disease 2019 (COVID-19). scRNA-Seq workflows are generally designed for the detection and quantification of eukaryotic host mRNAs and not viral RNAs. Here, we compare different scRNA-Seq methods for their ability to quantify and detect SARS-CoV-2 RNAs with a focus on subgenomic mRNAs (sgmRNAs). We present a data processing strategy, single cell CoronaVirus sequencing (scCoVseq), which quantifies reads unambiguously assigned to sgmRNAs or genomic RNA (gRNA). Compared to standard 10X Genomics Chromium Next GEM Single Cell 3′ (10X 3′) and Chromium Next GEM Single Cell V(D)J (10X 5′) sequencing, we find that 10X 5′ with an extended read 1 (R1) sequencing strategy maximizes the detection of sgmRNAs by increasing the number of unambiguous reads spanning leader-sgmRNA junction sites. Using this method, we show that viral gene expression is highly correlated across cells suggesting a relatively consistent proportion of viral sgmRNA production throughout infection. Our method allows for quantification of coronavirus sgmRNA expression at single-cell resolution, and thereby supports high resolution studies of the dynamics of coronavirus RNA synthesis.