bluuebunny/crossref_metadata_2025_split huggingface dataset:
TransLnc: a comprehensive resource for translatable lncRNAs extends immunopeptidome
Authors: Lv Dezhong , Chang Zhenghong , Cai Yangyang , Li Junyi , Wang Liping , Jiang Qiushuang , Xu Kang , Ding Na , Li Xia , Xu Juan , Li Yongsheng 
Published: September 2021

Abstract
LncRNAs are not only well-known as non-coding elements, but also serve as templates for peptide translation, playing important roles in fundamental cellular processes and diseases. Here, we describe a database, TransLnc (http://bio-bigdata.hrbmu.edu.cn/TransLnc/), which aims to provide comprehensive experimentally supported and predicted lncRNA peptides in multiple species. TransLnc currently documents approximate 583 840 peptides encoded by 33 094 lncRNAs. Six types of direct and indirect evidences supporting the coding potential of lncRNAs were integrated, and 65.28% peptides entries were with at least one type of evidence. Considering the strong tissue-specific expression of lncRNAs, TransLnc allows users to access lncRNA peptides in any of the 34 tissues involved in. In addition, both the unique characteristic and homology relationship were also predicted and provided. Importantly, TransLnc provides computationally predicted tumour neoantigens from peptides encoded by lncRNAs, which would provide novel insights into cancer immunotherapy. There were 220 791 and 237 915 candidate neoantigens binding by major histocompatibility complex (MHC) class I or II molecules, respectively. Several flexible tools were developed to aid retrieve and analyse, particularly lncRNAs tissue expression patterns, clinical relevance across cancer types. TransLnc will serve as a valuable resource for investigating the translation capacity of lncRNAs and greatly extends the cancer immunopeptidome.
Assessment of pre-donation glomerular filtration rate: going back to basics
Authors: Mariat Christophe , Mjøen Geir , Watschinger Bruno , Sever Mehmet Sukru , Crespo Marta , Peruzzi Licia , Oniscu Gabriel C , Abramowicz Daniel , Hilbrands Luuk , Maggiore Umberto 
Published: September 2021

Abstract
The 2017 version of the Kidney Disease: Improving Global Outcomes (KDIGO) guidelines is the most recent international framework for the evaluation and care of living kidneys donors. Along with the call for an integrative approach evaluating the long-term end-stage kidney disease risk for the future potential donor, several recommendations are formulated regarding the pre-donation glomerular filtration rate (GFR) adequacy with no or little consideration for the donor candidate’s age or for the importance of using reference methods of GFR measurements. Herein, we question the position of the KDIGO guidelines and discuss the rationale and modalities for a more basic, but no less demanding GFR evaluation enabling a more efficient selection of potential kidney donors.
Self-energy dynamics and the mode-specific phonon threshold effect in Kekulé-ordered graphene
Authors: Zhang Hongyun , Bao Changhua , Schüler Michael , Zhou Shaohua , Li Qian , Luo Laipeng , Yao Wei , Wang Zhong , Devereaux Thomas P , Zhou Shuyun 
Published: September 2021

Abstract
Electron-phonon interaction and related self-energy are fundamental to both the equilibrium properties and non-equilibrium relaxation dynamics of solids. Although electron-phonon interaction has been suggested by various time-resolved measurements to be important for the relaxation dynamics of graphene, the lack of energy- and momentum-resolved self-energy dynamics prohibits direct identification of the role of specific phonon modes in the relaxation dynamics. Here, by performing time- and angle-resolved photoemission spectroscopy measurements on Kekulé-ordered graphene with folded Dirac cones at the Γ point, we have succeeded in resolving the self-energy effect induced by the coupling of electrons to two phonons at Ω1 = 177 meV and Ω2 = 54 meV, and revealing its dynamical change in the time domain. Moreover, these strongly coupled phonons define energy thresholds, which separate the hierarchical relaxation dynamics from ultrafast, fast to slow, thereby providing direct experimental evidence for the dominant role of mode-specific phonons in the relaxation dynamics.
Physiological Characteristics and Transcriptomic Dissection in Two Root Segments with Contrasting Net Fluxes of Ammonium and Nitrate of Poplar Under Low Nitrogen Availability
Authors: Lu Yan , Deng Shurong , Li Zhuorong , Wu Jiangting , Zhu Dongyue , Shi Wenguang , Zhou Jing , Fayyaz Payam , Luo Zhi-Bin 
Published: September 2021

AbstractTo investigate physiological and transcriptomic regulation mechanisms underlying the distinct net fluxes of NH4+ and NO3− in different root segments of Populus species under low nitrogen (N) conditions, we used saplings of Populus × canescens supplied with either 500 (normal N) or 50 (low N) μM NH4NO3. The net fluxes of NH4+ and NO3−, the concentrations of NH4+, amino acids and organic acids and the enzymatic activities of nitrite reductase (NiR) and glutamine synthetase (GS) in root segment II (SII, 35–70 mm to the apex) were lower than those in root segment I (SI, 0–35 mm to the apex). The net NH4+ influxes and the concentrations of organic acids were elevated, whereas the concentrations of NH4+ and NO3− and the activities of NiR and GS were reduced in SI and SII in response to low N. A number of genes were significantly differentially expressed in SII vs SI and in both segments grown under low vs normal N conditions, and these genes were mainly involved in the transport of NH4+ and NO3−, N metabolism and adenosine triphosphate synthesis. Moreover, the hub gene coexpression networks were dissected and correlated with N physiological processes in SI and SII under normal and low N conditions. These results suggest that the hub gene coexpression networks play pivotal roles in regulating N uptake and assimilation, amino acid metabolism and the levels of organic acids from the tricarboxylic acid cycle in the two root segments of poplars in acclimation to low N availability.
Myosin XI drives polarized growth by vesicle focusing and local enrichment of F-actin inPhyscomitrium patens
Authors: Galotto Giulia , Wisanpitayakorn Pattipong , Bibeau Jeffrey P , Liu Yen-Chun , Furt Fabienne , Pierce Ellen C , Simpson Parker J , Tüzel Erkan , Vidali Luis 
Published: September 2021

AbstractIn tip-growing plant cells, growth results from myosin XI and F-actin-mediated deposition of cell wall polysaccharides contained in secretory vesicles. Previous evidence showed that myosin XI anticipates F-actin accumulation at the cell’s tip, suggesting a mechanism where vesicle clustering via myosin XI increases F-actin polymerization. To evaluate this model, we used a conditional loss-of-function strategy by generating moss (Physcomitrium patens) plants harboring a myosin XI temperature-sensitive allele. We found that loss of myosin XI function alters tip cell morphology, vacuolar homeostasis, and cell viability but not following F-actin depolymerization. Importantly, our conditional loss-of-function analysis shows that myosin XI focuses and directs vesicles at the tip of the cell, which induces formin-dependent F-actin polymerization, increasing F-actin’s local concentration. Our findings support the role of myosin XI in vesicle focusing, possibly via clustering and F-actin organization, necessary for tip growth, and deepen our understanding of additional myosin XI functions.
‘All disease begins in the gut’—the role of the intestinal microbiome in ankylosing spondylitis
Authors: Harkins Patricia , Burke Eoghan , Swales Catherine , Silman Alan 
Published: September 2021

AbstractAnkylosing spondylitis is a chronic, debilitating arthritis with a predilection for the axial skeleton. It has a strong genetic predisposition, but the precise pathogenetic mechanisms involved in its development have not yet been fully elucidated. This has implications both for early diagnosis and for effective management. Recently, alterations in the intestinal microbiome have been implicated in disease pathogenesis. In this review, we summarize studies assessing the intestinal microbiome in AS pathogenesis, in addition to synthesizing the literature exploring the postulated mechanisms by which it exerts it pathogenic potential. Finally, we review studies analysing manipulation of the microbiome as a potential therapeutic avenue in AS management.
Long-term efficacy and safety of canakinumab in patients with mevalonate kinase deficiency: results from the randomised Phase 3 CLUSTER trial
Authors: Jeyaratnam Jerold , Simon Anna , Calvo Inmaculada , Constantin Tamas , Shcherbina Anna , Hofer Michael , Gattorno Marco , Martini Alberto , Bader-Meunier Brigitte , Vastert Bas , Levy Jeremy , Dekker Elise , de Benedetti Fabrizio , Frenkel Joost 
Published: September 2021

Abstract

Objectives
To evaluate the long-term efficacy and safety of canakinumab in patients with mevalonate kinase deficiency during the open label extension (weeks 41–113) of the randomized controlled CLUSTER trial.

Methods
During a 72-week period, patients received open-label canakinumab 150 or 300 mg, every 4 or 8 weeks. The disease activity was evaluated every 8 weeks using physician global assessment and counting the number of flares. Concentrations of CRP and serum amyloid A protein were measured. The safety was studied by determination and classification of observed adverse events. The safety and efficacy were analysed separately in three subgroups of patients receiving a cumulative dose of less than &lt;35 mg/kg, ≥35 to &lt;70 mg/kg or ≥70 mg/kg.

Results
Of the 74 patients who started the CLUSTER study, 66 entered Epoch 4 and 65 completed it. During the 72-week period, 42 (64%) patients experienced no flares, while 13 (20%) had one flare, as compared with a median of 12 flares per year reported at baseline. Low physician global assessment scores were seen at the end of the study for all groups with &gt;90% reporting minimal disease activity or none at all. Median CRP concentrations were consistently equal or lower than 10 mg/l, while median serum amyloid A concentrations remained only slightly above the normal range of 10 mg/l. The study showed no new or unexpected adverse events.

Conclusion
Canakinumab proved effective to control disease activity and prevent flares in mevalonate kinase deficiency during the 72-week study period. No new safety concerns were reported.

Trial registration
NCT02059291. https://clinicaltrials.gov.
Biofoundry-assisted expression and characterization of plant proteins
Authors: Dudley Quentin M , Cai Yao-Min , Kallam Kalyani , Debreyne Hubert , Carrasco Lopez Jose A , Patron Nicola J 
Published: September 2021

Abstract
Many goals in synthetic biology, including the elucidation and refactoring of biosynthetic pathways and the engineering of regulatory circuits and networks, require knowledge of protein function. In plants, the prevalence of large gene families means it can be particularly challenging to link specific functions to individual proteins. However, protein characterization has remained a technical bottleneck, often requiring significant effort to optimize expression and purification protocols. To leverage the ability of biofoundries to accelerate design–built–test–learn cycles, we present a workflow for automated DNA assembly and cell-free expression of plant proteins that accelerates optimization and enables rapid screening of enzyme activity. First, we developed a phytobrick-compatible Golden Gate DNA assembly toolbox containing plasmid acceptors for cell-free expression using Escherichiacoli or wheat germ lysates as well as a set of N- and C-terminal tag parts for detection, purification and improved expression/folding. We next optimized automated assembly of miniaturized cell-free reactions using an acoustic liquid handling platform and then compared tag configurations to identify those that increase expression. We additionally developed a luciferase-based system for rapid quantification that requires a minimal 11–amino acid tag and demonstrate facile removal of tags following synthesis. Finally, we show that several functional assays can be performed with cell-free protein synthesis reactions without the need for protein purification. Together, the combination of automated assembly of DNA parts and cell-free expression reactions should significantly increase the throughput of experiments to test and understand plant protein function and enable the direct reuse of DNA parts in downstream plant engineering workflows.
Review and prospect of maintenance technology for traction system of high-speed train
Authors: Xu Shaolong , Chen Chunyang , Lin Zhenjun , Zhang Xiao , Dai Jisheng , Liu Liangjie 
Published: September 2021

AbstractIn the past few decades, high-speed trains have witnessed tremendous and vigorous development with the appearance of the oil crisis and industrialization, which became a significant trend in the transportation industry the world over. With the increase of high-speed railway mileage, the amount of high-speed train has grown sharply, the service life of the trains has increased gradually and the components of the vehicle traction system have become worn and aged as a result. Therefore, advanced maintenance technology and its application are key factors to reduce maintenance cost, human resource input and ensure safe, stable and reliable operation of trains. This paper summarizes and discusses the development, application mode, maintenance management and maintenance technology of high-speed railways of the major countries in the world, especially discusses the condition-based maintenance and the key technology of the traction electrical system, and offers the prospect of research direction and the development of traction maintenance technology.
Unraveling gene content variation across eukaryotic giant viruses based on network analyses and host associations
Authors: Sun Tsu-Wang , Ku Chuan 
Published: September 2021

Abstract
The nucleocytoplasmic large DNA viruses (NCLDVs, phylum Nucleocytoviricota) infect vertebrates, invertebrates, algae, amoebae, and other unicellular organisms across supergroups of eukaryotes and in various ecosystems. The expanding collection of their genome sequences has revolutionized our view of virus genome size and coding capacity. Phylogenetic trees based on a few core genes are commonly used as a model to understand their evolution. However, the tree topology can differ between analyses, and the vast majority of encoded genes might not share a common evolutionary history. To explore the whole-genome variation and evolution of NCLDVs, we dissected their gene contents using clustering, network, and comparative analyses. Our updated core-gene tree served as a framework to classify NCLDVs into families and intrafamilial lineages, but networks of individual genomes and family pangenomes showed patterns of gene sharing that contradict with the tree topology, in particular at higher taxonomic levels. Clustering of NCLDV genomes revealed variable granularity and degrees of gene sharing within each family, which cannot be inferred from the tree. At the level of NCLDV families, a correlation exists between gene content variation, but not core-gene sequence divergence, and host supergroup diversity. In addition, there is significantly higher gene sharing between divergent viruses that infect similar host types. The identified shared genes would be a useful resource for further functional analyses of NCLDV–host interactions. Overall this study provides a comprehensive view of gene repertoire variation in NCLDVs at different taxonomic levels, as well as a novel approach to studying the extremely diverse giant virus genomes.
Trends in Mortality Due to Stimulants Use in Adolescents and Young Adults
Authors: Walia Namrata , Lat Jessica O. , Tariq Rabeet , Tyagi Surbhi , Qazi Adam M. , Salari Syeda W. , Jafar Amina , Kousar Tasneem , Renzu Mahvish , Leszkowitz David , Abreu Rafael , Rodriguez Ivan 
Published: September 2021

Objectives:
Stimulant medications including illegal use of Methamphetamine (MA) continues to rise in adolescents and young adults. This study aims to examine mortality trends because of the stimulant overdose in this age group (15 to 34 years).

Methods:
Age-adjusted mortality data, including 95% confidence intervals and standard errors, were extracted using publicly available multiple causes of death files from the United States Centers for Disease Control Wide-ranging ONline Data for Epidemiologic Research (WONDER). The data was filtered using International Classification of Disease (ICD-10) codes: F15.0 (Mental and behavioral disorders because of use of other stimulants, acute intoxication), F15.1 (Mental and behavioral disorders because of use of other stimulants, harmful use), T43.6 (Psychostimulants with abuse potential). The trends analysis for 1999 to 2019 was conducted using Joinpoint regression statistical software.

Results:
The mortality rate has been consistently increasing in the last decade across all races and ethnicities in adolescents and young adults. Non-Hispanic White population had the highest mortality rates (7.6 per 100,000 in 2019) compared with non-Hispanic Black (3.08 per 100,000 in 2019) and Hispanic population (3.33 per 100,000 in 2019). But the annual percent change in mortality was shown to be highest in non-Hispanic Black population (34.3% between 2009 and 2019).

Conclusion:
The increase in overall mortality rate because of stimulants use reflects the increase of MA use in this age group. The difference in the rate of change shows worsening racial inequality. Public health policies should be implemented to include evidence-based strategies to prevent MA misuse or overdose.
Cardiotoxic Effects of the Antineoplastic Doxorubicin in a Model of Metabolic Syndrome: Oxidative Stress and Transporter Expression in the Heart
Authors: Ogonowski Natalia , Rukavina Mikusic Natalia Lucía , Kouyoumdzian Nicolás Martín , Choi Marcelo Roberto , Fellet Andrea , Balaszczuk Ana María , Celuch Stella Maris 
Published: September 2021

Abstract:
The aim of the present work was to examine whether metabolic syndrome–like conditions in rats with fructose (F) overload modify the cardiotoxic effects induced by doxorubicin (DOX) and whether the treatment altered the expression of P-gp, breast cancer resistance protein, and organic cation/carnitine transporters in the heart. Male Sprague–Dawley rats received either tap water (control group [C]; n = 16) or water with F 10% wt/vol (n = 16) during 8 weeks. Three days before being killed, the animals received a single dose of DOX (6 mg/kg, ip, md) (C-DOX and F-DOX groups) or vehicle (VEH; ISS 1 mL/kg BW; ip) (C-VEH and F-VEH groups) (n = 8 per group). F overload enhanced thiobarbituric acid–reactive substance levels in the left ventricle, and DOX injection further increased those values. DOX did not alter thiobarbituric acid–reactive substance production in C animals. DOX caused a decrease of 30% in the ejection fraction and a nearly 40% reduction in the fractional shortening in F animals, but not in C rats. Cardiac tissue levels of P-gp decreased by about 30% in F rats compared with the C groups. DOX did not modify cardiac P-gp expression. Breast cancer resistance protein and organic cation/carnitine transporter (OCTN 1/2/3) protein levels did not change with either F or DOX. It is suggested that DOX could cause greater cardiotoxicity in rats receiving F, probably due to enhanced cardiac lipid peroxidation and lower expression of cardiac P-gp. These results support the hypothesis that the cardiotoxicity of DOX could be increased under metabolic syndrome–like conditions or in other health disorders that involve cardiovascular risk factors.
Catheter-based therapies in acute and chronic pulmonary embolism
Authors: Michaud Erinleigh , Pan Michael , Aggarwal Vikas 
Published: September 2021

Purpose of review
The aim of this study is to summarize currently available catheter-based therapies in acute and chronic pulmonary embolic disease.

Recent findings
Catheter-based therapies to treat acute pulmonary embolism and its sequelae such as chronic thromboembolic pulmonary hypertension (CTEPH) are emerging as the next frontier within interventional cardiology. However, the true benefit of these catheter-based therapies in intermediate-risk and high-risk pulmonary embolism and CTEPH remains unclear. The current evidence supporting such interventions comes primarily from small single-arm studies in acute pulmonary embolism and case series in CTEPH.

Summary
Appropriately powered randomized controlled trials with meaningful clinical outcomes as endpoints are needed to elucidate the true benefit of catheter-based therapies in pulmonary embolism compared with other treatment modalities such as anticoagulation and systemic thrombolysis in acute pulmonary embolism and riociguat and pulmonary endarterectomy in CTEPH.
Intensive Cardiac Rehabilitation Is Markedly Underutilized by Medicare Beneficiaries
Authors: Husaini Mustafa , Deych Elena , Racette Susan B. , Rich Michael W. , Joynt Maddox Karen E. , Peterson Linda R. 
Published: September 2021

Purpose:
Intensive cardiac rehabilitation (ICR) was developed to enhance traditional cardiac rehabilitation (CR) by adding sessions focused on nutrition, lifestyle behaviors, and stress management. Intensive CR has been Medicare-approved since 2010, yet little is known about national utilization rates of ICR in the Medicare population or characteristics associated with its use.

Methods:
A 5% sample of Medicare claims data from 2012 to 2016 was used to identify beneficiaries with a qualifying indication for ICR/CR and to quantify utilization of ICR or CR within 1 yr of the qualifying diagnosis.

Results:
From 2012 to 2015, there were 107 246 patients with a qualifying indication. Overall, only 0.1% of qualifying patients participated in ICR and 16.2% in CR from 2012 to 2016, though utilization rates of both ICR and CR increased during this period (ICR 0.06 to 0.17%, CR 14.3 to 18.2%). The number of ICR centers increased from 15 to 50 over the same period. There were no differences between ICR and CR enrollees with respect to age, sex, race, discharge location, median income, dual enrollment, or number of comorbidities. Compared with eligible beneficiaries who did not attend ICR or CR, those who attended either program were younger, more likely to be male and White, and had higher median income.

Conclusions:
Although ICR and CR have a class 1 indication for the treatment of cardiovascular disease and the number of ICR centers has increased, ICR is not widely available and remains markedly underutilized. Continued research is needed to understand the barriers to program development and patient participation.