bluuebunny/crossref_metadata_2025_split huggingface dataset:
Observations of interplanetary scintillation of the 2005 May 13 coronal mass ejection: numerical models
Authors: Chang O , González R F , Bisi M M , Fallows R A 
Published: September 2021

ABSTRACT
The 2005 May 13 eruption was an Earth-directed coronal mass ejection (CME) observed using the Multi-Element Radio-Linked Interferometer Network telescope system in the UK as it traversed the Interplanetary Medium on 2005 May 14. Observations of interplanetary scintillation (IPS) provide information on the solar wind conditions, which include velocities and density. In addition, it is also possible to calculate other parameters related to the turbulence and geometry of density irregularities in the solar wind from observations of IPS. Previous analyses have shown that IPS information can be difficult to interpret when a complex structure is crossing the line of sight since the physical properties of the plasma may change quite drastically with distance from the Sun. In order to compare and relate the internal structure of a CME and its physical changes, with the results from observations of IPS obtained previously, we carried out a numerical simulation of the 2005 May 13 eruptive event as it propagates into the IPM, adapting the geometrical properties derived by IPS analysis. In this work, we give a possible explanation of some signatures of CME sub-structure from the point of view of the IPS technique combined with what the modelling reveals.
Thermonuclear X-ray bursts from 4U 1636 − 536 observed withAstroSat
Authors: Roy Pinaki , Beri Aru , Bhattacharyya Sudip 
Published: September 2021

ABSTRACTWe report results obtained from the study of 12 thermonuclear X-ray bursts in six AstroSat observations of a neutron star X-ray binary and well-known X-ray burster, 4U 1636 − 536. Burst oscillations (BOs) at ∼ 581 Hz are observed with 4–5σ confidence in three of these X-ray bursts. The rising phase BOs show a decreasing trend of the fractional rms amplitude at 3σ confidence, by far the strongest evidence of thermonuclear flame spreading observed with AstroSat. During the initial 0.25 s of the rise a very high value ($34.0\pm 6.7{{{\ \rm per\ cent}}}$) is observed. The concave shape of the fractional amplitude profile provides a strong evidence of latitude-dependent flame speeds, possibly due to the effects of the Coriolis force. We observe decay phase oscillations with amplitudes comparable to that observed during the rising phase, plausibly due to the combined effect of both surface modes, as well as the cooling wake. The Doppler shifts due to the rapid rotation of the neutron star might cause hard pulses to precede the soft pulses, resulting in a soft lag. The distance to the source estimated using the photospheric radius expansion bursts is consistent with the known value of ∼6 kpc.
Butyrate Production Pathway Abundances Are Similar in Human and Nonhuman Primate Gut Microbiomes
Authors: Mallott Elizabeth K , Amato Katherine R 
Published: September 2021

Abstract
Over the course of human evolution, shifts in dietary practices such as meat-eating and cooking, have resulted in reduced fiber intake, a trend that has been exaggerated more recently in industrialized populations. Reduced fiber consumption is associated with a loss of gut microbial taxa that degrade fiber, particularly butyrate. Therefore, this dietary shift in humans may have altered the abundance of microbial genes involved in butyrate production. This study uses a gene-targeted alignment approach to quantify the abundance of butyrate production pathway genes from published wild nonhuman primate and human gut metagenomes. Surprisingly, humans have higher diversity and relative abundances of butyrate production pathways compared with all groups of nonhuman primates except cercopithecoids. Industrialized populations of humans also differ only slightly in butyrate pathway abundance from nonindustrialized populations. This apparent resilience of butyrate production pathways to shifts in human diet across both evolutionary and modern populations may signal an evolutionary shift in host–microbe interactions in humans that increased SCFA production. Such a shift could have contributed to meeting the increased energy requirements of humans relative to nonhuman primates.
Active site characterization and activity of the human aspartyl (asparaginyl) β-hydroxylase
Authors: Greve Jenna M , Pinkham Andrew M , Thompson Zechariah , Cowan J A 
Published: September 2021

Abstract
Human aspartyl/asparaginyl beta-hydroxylase (HAAH) is a member of the superfamily of nonheme Fe2+/α-ketoglutarate (αKG) dependent oxygenase enzymes with a noncanonical active site. HAAH hydroxylates epidermal growth factor (EGF) like domains to form the β-hydroxylated product from substrate asparagine or aspartic acid and has been suggested to have a negative impact in a variety of cancers. In addition to iron, HAAH also binds divalent calcium, although the role of the latter is not understood. Herein, the metal binding chemistry and influence on enzyme stability and activity have been evaluated by a combined biochemical and biophysical approach. Metal binding parameters for the HAAH active site were determined by use of isothermal titration calorimetry, demonstrating a high-affinity regulatory binding site for Ca2+ in the catalytic domain in addition to the catalytic Fe2+ cofactor. We have analyzed various active site derivatives, utilizing LC-MS and a new HPLC technique to determine the role of metal binding and the second coordination sphere in enzyme activity, discovering a previously unreported residue as vital for HAAH turnover. This analysis of the in vitro biochemical function of HAAH furthers the understanding of its importance to cellular biochemistry and metabolic pathways.
Bacteriophage Twort protein Gp168 is a β-clamp inhibitor by occupying the DNA sliding channel
Authors: Liu Bing , Li Shanshan , Liu Yang , Chen Huan , Hu Zhenyue , Wang Zhihao , Zhao Yimin , Zhang Lei , Ma Biyun , Wang Hongliang , Matthews Steve , Wang Yawen , Zhang Kaiming 
Published: September 2021

Abstract
Bacterial chromosome replication is mainly catalyzed by DNA polymerase III, whose beta subunits enable rapid processive DNA replication. Enabled by the clamp-loading complex, the two beta subunits form a ring-like clamp around DNA and keep the polymerase sliding along. Given the essential role of β-clamp, its inhibitors have been explored for antibacterial purposes. Similarly, β-clamp is an ideal target for bacteriophages to shut off host DNA synthesis during host takeover. The Gp168 protein of phage Twort is such an example, which binds to the β-clamp of Staphylococcus aureus and prevents it from loading onto DNA causing replication arrest. Here, we report a cryo-EM structure of the clamp–Gp168 complex at 3.2-Å resolution. In the structure of the complex, the Gp168 dimer occupies the DNA sliding channel of β-clamp and blocks its loading onto DNA, which represents a new inhibitory mechanism against β-clamp function. Interestingly, the key residues responsible for this interaction on the β-clamp are well conserved among bacteria. We therefore demonstrate that Gp168 is potentially a cross-species β-clamp inhibitor, as it forms complex with the Bacillus subtilis β-clamp. Our findings reveal an alternative mechanism for bacteriophages to inhibit β-clamp and provide a new strategy to combat bacterial drug resistance.
Regulatory roles of RNA modifications in breast cancer
Authors: Kumari Kanchan , Groza Paula , Aguilo Francesca 
Published: September 2021

Abstract
Collectively referred to as the epitranscriptome, RNA modifications play important roles in gene expression control regulating relevant cellular processes. In the last few decades, growing numbers of RNA modifications have been identified not only in abundant ribosomal (rRNA) and transfer RNA (tRNA) but also in messenger RNA (mRNA). In addition, many writers, erasers and readers that dynamically regulate the chemical marks have also been characterized. Correct deposition of RNA modifications is prerequisite for cellular homeostasis, and its alteration results in aberrant transcriptional programs that dictate human disease, including breast cancer, the most frequent female malignancy, and the leading cause of cancer-related death in women. In this review, we emphasize the major RNA modifications that are present in tRNA, rRNA and mRNA. We have categorized breast cancer-associated chemical marks and summarize their contribution to breast tumorigenesis. In addition, we describe less abundant tRNA modifications with related pathways implicated in breast cancer. Finally, we discuss current limitations and perspectives on epitranscriptomics for use in therapeutic strategies against breast and other cancers.
Evolutionary and functional lessons from human-specific amino acid substitution matrices
Authors: Shauli Tair , Brandes Nadav , Linial Michal 
Published: September 2021

Abstract
Human genetic variation in coding regions is fundamental to the study of protein structure and function. Most methods for interpreting missense variants consider substitution measures derived from homologous proteins across different species. In this study, we introduce human-specific amino acid (AA) substitution matrices that are based on genetic variations in the modern human population. We analyzed the frequencies of &gt;4.8M single nucleotide variants (SNVs) at codon and AA resolution and compiled human-centric substitution matrices that are fundamentally different from classic cross-species matrices (e.g. BLOSUM, PAM). Our matrices are asymmetric, with some AA replacements showing significant directional preference. Moreover, these AA matrices are only partly predicted by nucleotide substitution rates. We further test the utility of our matrices in exposing functional signals of experimentally-validated protein annotations. A significant reduction in AA transition frequencies was observed across nine post-translational modification (PTM) types and four ion-binding sites. Our results propose a purifying selection signal in the human proteome across a diverse set of functional protein annotations and provide an empirical baseline for interpreting human genetic variation in coding regions.
Allele-specific assembly of a eukaryotic genome corrects apparent frameshifts and reveals a lack of nonsense-mediated mRNA decay
Authors: Cosentino Raúl O , Brink Benedikt G , Siegel T Nicolai 
Published: September 2021

Abstract
To date, most reference genomes represent a mosaic consensus sequence in which the homologous chromosomes are collapsed into one sequence. This approach produces sequence artefacts and impedes analyses of allele-specific mechanisms. Here, we report an allele-specific genome assembly of the diploid parasite Trypanosoma brucei and reveal allelic variants affecting gene expression. Using long-read sequencing and chromosome conformation capture data, we could assign 99.5% of all heterozygote variants to a specific homologous chromosome and build a 66 Mb long allele-specific genome assembly. The phasing of haplotypes allowed us to resolve hundreds of artefacts present in the previous mosaic consensus assembly. In addition, it revealed allelic recombination events, visible as regions of low allelic heterozygosity, enabling the lineage tracing of T. brucei isolates. Interestingly, analyses of transcriptome and translatome data of genes with allele-specific premature termination codons point to the absence of a nonsense-mediated decay mechanism in trypanosomes. Taken together, this study delivers a reference quality allele-specific genome assembly of T. brucei and demonstrates the importance of such assemblies for the study of gene expression control. We expect the new genome assembly will increase the awareness of allele-specific phenomena and provide a platform to investigate them.
Effectiveness of a Multicomponent Strategy for Implementing Guidelines for Treating Tobacco Use in Vietnam Commune Health Centers
Authors: Shelley Donna , Cleland Charles M , Nguyen Trang , VanDevanter Nancy , Siman Nina , Van Minh Hoang , Nguyen Nam 
Published: September 2021

Abstract

Introduction
Strategies are needed to increase implementation of evidence-based tobacco dependence treatment (TDT) in health care systems in low-and middle-income countries (LMICs).

Aims and Methods
We conducted a two-arm cluster randomized controlled trial to compare the effectiveness of two strategies for implementing TDT guidelines in community health centers (n = 26) in Vietnam. Arm 1 included training and a tool kit (eg, reminder system) to promote and support delivery of the 4As (Ask about tobacco use, Advise to quit, Assess readiness, Assist with brief counseling) (Arm 1). Arm 2 included Arm 1 components plus a system to refer smokers to a community health worker (CHW) for more intensive counseling (4As + R). Provider surveys were conducted at baseline, 6 months, and 12 months to assess the hypothesized effect of the strategies on provider and organizational-level factors. The primary outcome was provider adoption of the 4As.

Results
Adoption of the 4As increased significantly across both study arms (all p &lt; .001). Perceived organizational priority for TDT, compatibility with current workflow, and provider attitudes, norms, and self-efficacy related to TDT also improved significantly across both arms. In Arm 2 sites, 41% of smokers were referred to a CHW for additional counseling.

Conclusions
The study demonstrated the effectiveness of a multicomponent and multilevel strategy (ie, provider and system) for implementing evidence-based TDT in the Vietnam public health system. Combining provider-delivered brief counseling with opportunities for more in-depth counseling offered by a trained CHW may optimize outcomes and offers a potentially scalable model for increasing access to TDT in health care systems like Vietnam.

Implications
Improving implementation of evidence-based TDT guidelines is a necessary step toward reducing the growing burden of noncommunicable diseases and premature death in LMICs. The findings provide new evidence on the effectiveness of multilevel strategies for adapting and implementing TDT into routine care in Vietnam and offer a potentially scalable model for meeting Framework Convention on Tobacco Control Article 14 goals in other LMICs with comparable public health systems. The study also demonstrates that combining provider-delivered brief counseling with referral to a CHW for more in-depth counseling and support can optimize access to evidence-based treatment for tobacco use.
Clinical trials number: NCT01967654.
Mesozooplankton trait distribution in relation to environmental conditions and the presence of krill and salps along the northern Antarctic Peninsula
Authors: Plum Christoph , Cornils Astrid , Driscoll Ryan , Wenta Philipp , Badewien Thomas H , Niggemann Jutta , Moorthi Stefanie 
Published: September 2021

AbstractZooplankton community structure is often characterized by using traits as a function of environmental conditions. However, trait-based knowledge on Southern Ocean mesozooplankton is limited, particularly regarding size and elemental composition. Nine stations around the northern Antarctic Peninsula were sampled during austral autumn to investigate the spatial variability in mesozooplankton taxonomic composition, size structure and stoichiometry in relation to environmental predictors, but also to the abundance of Antarctic krill and salps. The mesozooplankton communities around the South Shetland Islands were dominated by small copepods, mainly Oithonidae and Oncaeidae, while stations along the frontal zones and the Weddell Sea revealed a higher proportion of larger organisms. Spatial differences in taxonomic composition and size structure were significantly altered by salp abundance, with stronger impact on small-sized copepods. Furthermore, taxonomic composition was significantly related to temperature and total carbon but not chlorophyll a, indicating reduced relevance of phytoplankton derived food during autumn. Bulk mesozooplankton stoichiometry, however, showed no significant relation to environmental conditions, mesozooplankton size structure or dominant taxa. Our results indicate that aside from bottom-up related drivers, top-down effects of salps may lead to mesozooplankton communities that are more dominated by larger size classes with potential consequences for trophic interactions and nutrient fluxes.
X-ray microscopy enables multiscale high-resolution 3D imaging of plant cells, tissues, and organs
Authors: Duncan Keith E , Czymmek Kirk J , Jiang Ni , Thies August C , Topp Christopher N 
Published: September 2021

AbstractCapturing complete internal anatomies of plant organs and tissues within their relevant morphological context remains a key challenge in plant science. While plant growth and development are inherently multiscale, conventional light, fluorescence, and electron microscopy platforms are typically limited to imaging of plant microstructure from small flat samples that lack a direct spatial context to, and represent only a small portion of, the relevant plant macrostructures. We demonstrate technical advances with a lab-based X-ray microscope (XRM) that bridge the imaging gap by providing multiscale high-resolution three-dimensional (3D) volumes of intact plant samples from the cell to the whole plant level. Serial imaging of a single sample is shown to provide sub-micron 3D volumes co-registered with lower magnification scans for explicit contextual reference. High-quality 3D volume data from our enhanced methods facilitate sophisticated and effective computational segmentation. Advances in sample preparation make multimodal correlative imaging workflows possible, where a single resin-embedded plant sample is scanned via XRM to generate a 3D cell-level map, and then used to identify and zoom in on sub-cellular regions of interest for high-resolution scanning electron microscopy. In total, we present the methodologies for use of XRM in the multiscale and multimodal analysis of 3D plant features using numerous economically and scientifically important plant systems.
Repetitive Transcranial Magnetic Stimulation for Patients with Fibromyalgia: A Systematic Review with Meta-Analysis
Authors: Sun Pingping , Fang Lei , Zhang Jianzhong , Liu Yang , Wang Guodong , Qi Rui 
Published: September 2021

Abstract

Objective
Fibromyalgia is a poorly understood pain syndrome. Repetitive transcranial magnetic stimulation (rTMS) is a noninvasive brain stimulation therapy and is commonly applied for the management of fibromyalgia. However, controversy about its efficacy remains. Therefore, a meta-analysis was conducted to evaluate the effectiveness of rTMS for fibromyalgia syndrome.

Methods
Four medical databases and one physiotherapy database were screened for randomized controlled trials. A systematic review and meta-analysis was performed. Numerical Pain Rating Scale (NPRS) score, Beck Depression Inventory (BDI) score, Hospital Anxiety and Depression Scale (HADS) anxiety score, Pain Catastrophizing Scale (PCS) score, Fatigue Severity Scale (FSS) score, Short Form-36 General Health Survey mental score, and Fibromyalgia Impact Questionnaire (FIQ) score were set as outcome measures.

Results
Analysis of 14 studies and 433 participants indicated that rTMS exerted more favorable effects than did sham rTMS after treatment on the NPRS (standardized mean difference = −0.49, 95% confidence interval = −0.86 to −0.13, P = 0.008, I2 = 68%) and the FIQ (standardized mean difference = −0.50, 95% confidence interval = −0.75 to −0.25, P = 0.0001, I2 = 28%). However, the BDI, FSS, PCS, mood index, and HADS scores showed no significant difference compared with sham rTMS after treatment. The mean methodological quality of the included studies was an acceptable score of 8.5 based on the PEDro scale, suggesting the validity of our conclusions.

Conclusion
This study demonstrated that rTMS relieved pain and enhanced the quality of life of patients with fibromyalgia; however, on the basis of current reports, it did not improve anxiety, depression, or other symptoms.
Health-care utilization and costs in adults with systemic lupus erythematosus in the United Kingdom: a real-world observational retrospective cohort analysis
Authors: Samnaliev Mihail , Barut Volkan , Weir Sharada , Langham Julia , Langham Sue , Wang Xia , Desta Barnabas , Hammond Edward 
Published: September 2021

Abstract

Objective
The aim was to describe direct health-care costs for adults with SLE in the UK over time and by disease severity and encounter type.

Methods
Patients aged ≥18 years with SLE were identified using the linked Clinical Practice Research Datalink–Hospital Episode Statistics database from January 2005 to December 2017. Patients were classified as having mild, moderate or severe disease using an adapted claims-based algorithm based on prescriptions and co-morbid conditions. We estimated all-cause health-care costs and incremental costs associated with each year of follow-up compared with a baseline year, adjusting for age, sex, disease severity and co-morbid conditions (2017 UK pounds).

Results
We identified 802 patients; 369 (46.0%) with mild, 345 (43.0%) moderate and 88 (11.0%) severe disease. The mean all-cause cost increased in the 3 years before diagnosis, peaked in the first year after diagnosis and remained high. The adjusted total mean annual increase in costs per patient was £4476 (95% CI: £3809, £5143) greater in the year of diagnosis compared with the baseline year (P &lt; 0.0001). The increase in costs per year was 4.7- and 1.6-fold higher among patients with severe SLE compared with those with mild and moderate SLE, respectively. Primary care utilization was the leading component of costs during the first year after diagnosis.

Conclusion
The health-care costs for patients with SLE in the UK are substantial, remain high after diagnosis and increase with increasing severity. Future research should assess whether earlier diagnosis and treatment might reduce disease severity and associated high health-care costs.
Fabrication and evaluation of an optimized xenogenic decellularized costal cartilage graft: preclinical studies of a novel biocompatible prosthesis for rhinoplasty
Authors: Lin Shuang , He Yuanjia , Tao Meihan , Wang Aijun , Ao Qiang 
Published: September 2021

Abstract
On account of the poor biocompatibility of synthetic prosthesis, millions of rhinoplasty recipients have been forced to choose autologous costal cartilage as grafts, which suffer from limited availability, morbidity at the donor site and prolonged operation time. Here, as a promising alternative to autologous costal cartilage, we developed a novel xenogeneic costal cartilage and explored its feasibility as a rhinoplasty graft for the first time. Adopting an improved decellularization protocol, in which the ionic detergent was substituted by trypsin, the resulting decellularized graft was confirmed to preserve more structural components and better mechanics, and eliminate cellular components effectively. The in vitro and in vivo compatibility experiments demonstrated that the decellularized graft showed excellent biocompatibility and biosecurity. Additionally, the functionality assessment of rhinoplasty was performed in a rabbit model, and the condition of grafts after implantation was comprehensively evaluated. The optimized graft exhibited better capacity to reduce the degradation rate and maintain the morphology, in comparison to the decellularized costal cartilage prepared by conventional protocol. These findings indicate that this optimized graft derived from decellularized xenogeneic costal cartilage provides a new prospective for future investigations of rhinoplasty prosthesis and has great potential for clinical application.