bluuebunny/crossref_metadata_2025_split huggingface dataset:
Indicative bacterial communities and taxa of disease-suppressing and growth-promoting composts and their associations to the rhizoplane
Authors: Mayerhofer Johanna , Thuerig Barbara , Oberhaensli Thomas , Enderle Eileen , Lutz Stefanie , Ahrens Christian H , Fuchs Jacques G , Widmer Franco 
Published: September 2021

ABSTRACTCompost applications vary in their plant growth promotion and plant disease suppression, likely due to differences in physico-chemical and biological parameters. Our hypothesis was that bacteria are important for plant growth promotion and disease suppression of composts and, therefore, composts having these traits would contain similar sets of indicative bacterial taxa. Seventeen composts prepared from five different commercial providers and different starting materials were classified accordingly with bioassays using cress plants and the pathogen Pythium ultimum. Using a metabarcoding approach, bacterial communities were assessed in bulk composts and cress rhizoplanes. Six and nine composts showed significant disease suppression or growth promotion, respectively, but these traits did not correlate. Growth promotion correlated positively with nitrate content of composts, whereas disease suppression correlated negatively with factors representing compost age. Growth promotion and disease suppression explained significant portions of variation in bacterial community structures, i.e. 11.5% and 14.7%, respectively. Among the sequence variants (SVs) associated with growth promotion, Microvirga, Acinetobacter, Streptomyces, Bradyrhizobium and Bacillus were highly promising, while in suppressive composts, Ureibacillus,Thermogutta and Sphingopyxis were most promising. Associated SVs represent the basis for developing prediction tools for growth promotion and disease suppression, a highly desired goal for targeted compost production and application.
Developing critical appraisal and evidence synthesis skills in future microbiologists
Authors: Flynn Matthew F 
Published: September 2021

ABSTRACT
The Covid-19 pandemic has demanded modifications to undergraduates’ learning experiences and promised a more challenging scientific world in which they will live. Bespoke evidence synthesis and critical appraisal skills modules are an opportunity to utilize our information-saturated world to our advantage. This program of study made use of a virtual journal club, structured literature searches, scoping review methods and a variety of online research tools to navigate and critique the literature. The program design is here outlined with sample learning objectives and reference to the resources used.
Limosilactobacillus caccaesp. nov., a new bacterial species isolated from the human gut microbiota
Authors: Lo Cheikh Ibrahima , Dione Niokhor , Mbaye Aminata , Gómez Patricia Fernández-Mellado , Ngom Issa Isaac , Valles Camille , Alibar Stéphane , Lagier Jean-Christophe , Fenollar Florence , Fournier Pierre-Edouard , Raoult Didier , Diene Seydina M 
Published: September 2021

ABSTRACTStrain Marseille-P3519T isolated from the fecal flora of a 25-year-old healthy French woman was a Gram-positive anaerobic bacterium, non-motile and non-spore forming. The 16S rRNA gene sequence of Marseille-P3519 showed 97.73% of sequence similarity with Limosilactobacillus reuteri DSM 20016, the closest species, phylogenetically. Furthermore, the average nucleotide identity of strain Marseille-3519 with its closest related species was 75.8% that was very below the recommended threshold (&gt;95–96%). Its genome had 2 237 367 bp with 45.42 mol% of G + C content. Major fatty acids were C16:0 (50.8%), C18:1n9 (18.0%), C18:2n6 (9.8%) and C19:1n9 (8.9%). It was catalase negative and fermented glycerol, glucose, fructose, D-maltose, lactose and mannose. These findings support that strain Marseille-P3519 ( = CSURP3519 = CECT 30110) is a new member of the genus Limosilactobacillus for which the name Limosilactobacillus caccae sp. nov., is proposed.
Impact of a training session for prescribers on the relative prescription of cefotaxime over ceftriaxone in elderly patients
Authors: Durand Amaury , Cayeux Sarah , Bloch Frédéric , Dupont Hervé , El Samad Youssef , Mary Aurélien , Hamdad Farida 
Published: September 2021

Abstract

Background
The prescription of ceftriaxone should be limited to patients with biliary tract infections and those lacking intravenous access. A specific training session for prescribers about the clinical relevance and economic value of prescribing cefotaxime instead of ceftriaxone might decrease the use of the latter in geriatric medicine.

Objectives
To determine the clinical and economic impact of a training session for prescribers on the subsequent prescription of third-generation cephalosporin, that is, the percentage of appropriate prescriptions and the cost of third-generation cephalosporin administration before and after the training session.

Methods
In a preliminary observational quasi-experimental, open-label study, appropriateness of cefotaxime and ceftriaxone prescription over a 4-week period immediately before the training session were compared with those during a 4-week period immediately afterwards.

Key findings
For 46 patients (29 before the training session and 17 afterwards), the proportion of cefotaxime prescriptions increased (from 3% to 35%; P = 0.007), and the proportion of appropriate prescriptions increased at the start of treatment (from 45% to 76%; P = 0.064) and at the end (from 76% to 88%; P = 0.450). The daily per-patient cost of treatment was €8 for cefotaxime and from €1.63 to €3.42 for ceftriaxone, depending on the administration route.

Conclusions
A training session for prescribers was associated with a decrease in ceftriaxone prescriptions encouraging further studies to improve the training session and then evaluate medico-economic impact through randomized clinical trials.
Highly Potent SARS-CoV-2 Neutralization by Intravenous Immunoglobulins manufactured from Post-COVID-19 and COVID-19-Vaccinated Plasma Donations
Authors: Karbiener Michael , Farcet Maria R , Schwaiger Julia , Powers Nicholas , Lenart James , Stewart Joseph M , Tallman Hema , Kreil Thomas R 
Published: September 2021

Abstract
From September 2020, some immunoglobulin lots from US plasma contained neutralizing antibodies against the newly emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Paralleled by the increasing numbers of post–coronavirus disease 2019 (COVID-19) donors, immunoglobulin lot antibody positivity increased to 93% by January 2021, at a mean titer of approximately 30 IU/mL. The correlation predicted that anti–SARS-CoV-2 potency would reach 345 IU/mL by July 2021. In addition to post–COVID-19 donors, the rapidly increasing number of plasma donors vaccinated against COVID-19 resulted in a mean antibody titer of &gt;600 IU/mL in July 2021 immunoglobulin lots, with SARS-CoV-2 antibody titers for several lots even higher than those of earlier produced hyperimmune globulin products.
Host cells with transient overexpression of MDR1 as a novel in vitro model for evaluating on-target effect for activity against the epicellular Cryptosporidium parasite
Authors: Yang Bo , Wang Dongqiang , Liu Mingxiao , Wu Xiaodong , Yin Jigang , Zhu Guan 
Published: September 2021

Abstract

Objectives
To rapidly generate host cells with resistance to multiple compounds for differentiating drug action on parasite target or the host cell target (i.e. on-target or off-target effect) against the zoonotic enteric parasite Cryptosporidium parvum.

Methods
Transient overexpression of a multidrug resistance protein 1 (MDR1) gene in host cells (HCT-8 cell line) was explored to increase drug tolerance of the host cells to selected anti-cryptosporidial leads. In vitro cytotoxicity and anti-cryptosporidial efficacy of selected compounds were evaluated on the parasite grown in WT parental and transiently transfected HCT-8 cells. The approach was based on the theory that, for an epicellular parasite receiving consistent exposure to compounds in culture medium, overexpressing MDR1 in HCT-8 cells would increase drug tolerance of host cells to selected compounds but would not affect the anti-cryptosporidial efficacy if the compounds acted solely on the parasite target and the drug action on host cell target played no role on the antiparasitic efficacy.

Results
Six known anti-cryptosporidial leads were tested. Transient overexpression of MDR1 increased drug tolerance of HCT-8 cells on paclitaxel, doxorubicin HCl and vincristine sulphate (2.11- to 2.27-fold increase), but not on cyclosporin A, daunorubicin HCl and nitazoxanide. Increased drug tolerance in host cells had no effect on antiparasitic efficacy of paclitaxel, but affected that of doxorubicin HCl.

Conclusions
Data confirmed that, at efficacious concentrations, paclitaxel acted mainly on the parasite target, while doxorubicin might act on both parasite and host cell targets. This model can be employed for studying the action of additional anti-cryptosporidial leads, and adapted to studying drug action in other epicellular pathogens. The limitation of the model is that the anti-cryptosporidial leads/hits need to be MDR1 substrates.
Nucleosome assembly protein 1 is a regulator of histone H1 acetylation
Authors: Yoneda Mitsuhiro , Yasui Kiyoshi , Nakagawa Takeya , Hattori Naoko , Ito Takashi 
Published: September 2021

Abstract
Acetylation of histone H1 is generally considered to activate transcription, whereas deacetylation of H1 represses transcription. However, the precise mechanism of the acetylation is unknown. Here, using chromatography, we identified nucleosome assembly protein 1 (NAP-1) as having inhibitory activity against histone H1 acetylation by acetyltransferase p300. We found that native NAP-1 interacts with H1 in a Drosophila crude extract. We also found that it inhibits the deacetylation of histone H1 by histone deacetylase 1. The core histones in nucleosomes were acetylated in a GAL4–VP16 transcriptional activator-dependent manner in vitro. This acetylation was strongly repressed by hypoacetylated H1 but to a lesser extent by hyperacetylated H1. Consistent with these findings, a micrococcal nuclease assay indicated that hypoacetylated H1, which represses activator-dependent acetylation, was incorporated into chromatin, whereas hyperacetylated H1 was not. To determine the contribution of NAP-1 to transcriptional regulation in vivo, we compared NAP-1 knockdown (KD) with coactivator CREB-binding protein (CBP) KD using RNA sequencing in Drosophila Schneider 2 cells. Most genes were downregulated rather than upregulated by NAP-1 KD, and those downregulated genes were also downregulated by CBP KD. Our results suggest that NAP-1 plays a role in transcriptional regulation by fine-tuning the acetylation of histone H1.
A Vacancy Chain Model of Local Managers’ Career Advancement
Authors: Yi Hongtao , Chen Catherine 
Published: September 2021

AbstractLocal public managers are mobile in their career trajectories. While the extant public administration literature has predominantly examined this topic from a leadership turnover perspective, few studies have approached the career trajectories of local managers from a holistic, system-level angle. This article draws upon the vacancy chain literature and frames local managers’ interconnected career trajectories within a nationwide professional job market, which we term “leadership turnover chains.” We examine factors influencing the formation of such leadership turnover chains among cities. With a dataset containing information from the resumes of 517 US local managers across 28 years, we employ panel dyadic logistic regressions to analyze the leadership turnover chains among cities. Our findings suggest that managers are more likely to move among dyads of cities that are geographically close and with similar levels of economic prosperity, population size, racial diversity, and political climate. A promotion intercity turnover tends to take place from a populous city to a less populous city, while a demotion intercity turnover exhibits an opposite pattern. This study contributes to the theory of leadership turnover of local managers, highlighting a macro vacancy chain perspective on their career trajectories.
SBSA: an online service for somatic binding sequence annotation
Authors: Jiang Limin , Guo Fei , Tang Jijun , Yu Hui , Ness Scott , Duan Mingrui , Mao Peng , Zhao Ying-Yong , Guo Yan 
Published: September 2021

AbstractEfficient annotation of alterations in binding sequences of molecular regulators can help identify novel candidates for mechanisms study and offer original therapeutic hypotheses. In this work, we developed Somatic Binding Sequence Annotator (SBSA) as a full-capacity online tool to annotate altered binding motifs/sequences, addressing diverse types of genomic variants and molecular regulators. The genomic variants can be somatic mutation, single nucleotide polymorphism, RNA editing, etc. The binding motifs/sequences involve transcription factors (TFs), RNA-binding proteins, miRNA seeds, miRNA-mRNA 3′-UTR binding target, or can be any custom motifs/sequences. Compared to similar tools, SBSA is the first to support miRNA seeds and miRNA-mRNA 3′-UTR binding target, and it unprecedentedly implements a personalized genome approach that accommodates joint adjacent variants. SBSA is empowered to support an indefinite species, including preloaded reference genomes for SARS-Cov-2 and 25 other common organisms. We demonstrated SBSA by annotating multi-omics data from over 30,890 human subjects. Of the millions of somatic binding sequences identified, many are with known severe biological repercussions, such as the somatic mutation in TERT promoter region which causes a gained binding sequence for E26 transformation-specific factor (ETS1). We further validated the function of this TERT mutation using experimental data in cancer cells. Availability:http://innovebioinfo.com/Annotation/SBSA/SBSA.php.
SARS-CoV-2 Epidemiology on a Public University Campus in Washington State
Authors: Weil Ana A , Sohlberg Sarah L , O’Hanlon Jessica A , Casto Amanda M , Emanuels Anne W , Lo Natalie K , Greismer Emily P , Magedson Ariana M , Wilcox Naomi C , Kim Ashley E , Back Lewis , Frazar Christian D , Pelle Ben , Sibley Thomas R , Ilcisin Misja , Lee Jover , Ryke Erica L , Craft J Chris , Schwabe-Fry Kristen M , Fay Kairsten A , Cho Shari , Han Peter D , Heidl Sarah J , Pfau Brian A , Truong Melissa , Zhong Weizhi , Srivatsan Sanjay R , Harb Katia F , Gottlieb Geoffrey S , Hughes James P , Nickerson Deborah A , Lockwood Christina M , Starita Lea M , Bedford Trevor , Shendure Jay A , Chu Helen Y 
Published: September 2021

Abstract

Background
We aimed to evaluate a testing program to facilitate control of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission at a large university and measure spread in the university community using viral genome sequencing.

Methods
Our prospective longitudinal study used remote contactless enrollment, daily mobile symptom and exposure tracking, and self-swab sample collection. Individuals were tested if the participant was exposed to a known SARS-CoV-2-infected person, developed new symptoms, or reported high-risk behavior (such as attending an indoor gathering without masking or social distancing), if a member of a group experiencing an outbreak, or at enrollment. Study participants included students, staff, and faculty at an urban public university during the Autumn quarter of 2020.

Results
We enrolled 16 476 individuals, performed 29 783 SARS-CoV-2 tests, and detected 236 infections. Seventy-five percent of positive cases reported at least 1 of the following: symptoms (60.8%), exposure (34.7%), or high-risk behaviors (21.5%). Greek community affiliation was the strongest risk factor for testing positive, and molecular epidemiology results suggest that specific large gatherings were responsible for several outbreaks.

Conclusions
A testing program focused on individuals with symptoms and unvaccinated persons who participate in large campus gatherings may be effective as part of a comprehensive university-wide mitigation strategy to control the spread of SARS-CoV-2.
Coronavirus Disease 2019 Vaccine Impact on Rates of Severe Acute Respiratory Syndrome Coronavirus 2 Cases and Postvaccination Strain Sequences Among Health Care Workers at an Urban Academic Medical Center: A Prospective Cohort Study
Authors: Bouton Tara C , Lodi Sara , Turcinovic Jacquelyn , Schaeffer Beau , Weber Sarah E , Quinn Emily , Korn Cathy , Steiner Jacqueline , Schechter-Perkins Elissa M , Duffy Elizabeth , Ragan Elizabeth J , Taylor Bradford P , Miller Nancy , Davidoff Ravin , Hanage William P , Connor John , Pierre Cassandra , Jacobson Karen R 
Published: September 2021

Abstract

Background
Coronavirus disease 2019 (COVID-19) vaccine trials and post-implementation data suggest that vaccination decreases infections. We examine vaccination’s impact on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) case rates and viral diversity among health care workers (HCWs) during a high community prevalence period.

Methods
In this prospective cohort study, HCW received 2 doses of BNT162b2 or mRNA-1273. We included confirmed cases among HCWs from 9 December 2020 to 23 February 2021. Weekly SARS-CoV-2 rates per 100,000 person-days and by time from first injection (1–14 and ≥15 days) were compared with surrounding community rates. Viral genomes were sequenced.

Results
SARS-CoV-2 cases occurred in 1.4% (96/7109) of HCWs given at least a first dose and 0.3% (17/5913) of HCWs given both vaccine doses. Adjusted rate ratios (95% confidence intervals) were 0.73 (.53–1.00) 1–14 days and 0.18 (.10–.32) ≥15 days from first dose. HCW ≥15 days from initial dose compared to 1-14 days were more often older (46 vs 38 years, P = .007), Latinx (10% vs 8%, P = .03), and asymptomatic (48% vs 11%, P = .0002). SARS-CoV-2 rates among HCWs fell below the surrounding community, an 18% vs 11% weekly decrease, respectively (P = .14). Comparison of 50 genomes from post–first dose cases did not indicate selection pressure toward known spike antibody escape mutations.

Conclusions
Our results indicate an early positive impact of vaccines on SARS-CoV-2 case rates. Post-vaccination isolates did not show unusual genetic diversity or selection for mutations of concern.
Efficient and high-throughput pseudorecombinant-chimeric Cucumber mosaic virus-based VIGS in maize
Authors: Li Huangai , Zhang Danfeng , Xie Ke , Wang Yan , Liao Qiansheng , Hong Yiguo , Liu Yule 
Published: September 2021

Abstract
Virus-induced gene silencing (VIGS) is a versatile and attractive approach for functional gene characterization in plants. Although several VIGS vectors for maize (Zea mays) have been previously developed, their utilities are limited due to low viral infection efficiency, insert instability, short maintenance of silencing, inadequate inoculation method, or abnormal requirement of growth temperature. Here, we established a Cucumber mosaic virus (CMV)-based VIGS system for efficient maize gene silencing that overcomes many limitations of VIGS currently available for maize. Using two distinct strains, CMV-ZMBJ and CMV-Fny, we generated a pseudorecombinant-chimeric (Pr) CMV. Pr CMV showed high infection efficacy but mild viral symptoms in maize. We then constructed Pr CMV-based vectors for VIGS, dubbed Pr CMV VIGS. Pr CMV VIGS is simply performed by mechanical inoculation of young maize leaves with saps of Pr CMV-infected Nicotiana benthamiana under normal growth conditions. Indeed, suppression of isopentenyl/dimethylallyl diphosphate synthase (ZmIspH) expression by Pr CMV VIGS resulted in non-inoculated leaf bleaching as early as 5 d post-inoculation (dpi) and exhibited constant and efficient systemic silencing over the whole maize growth period up to 105 dpi. Furthermore, utilizing a ligation-independent cloning (LIC) strategy, we developed a modified Pr CMV-LIC VIGS vector, allowing easy gene cloning for high-throughput silencing in maize. Thus, our Pr CMV VIGS system provides a much-improved toolbox to facilitate efficient and long-duration gene silencing for large-scale functional genomics in maize, and our pseudorecombination-chimera combination strategy provides an approach to construct efficient VIGS systems in plants.
Genome Sequence of the Agrobacterium salinitolerans DG3-1 Isolated from Cotton Roots
Authors: Hao Haiting , Wang Zhe , Gou Changqing , Sha Shuaishuai , Yan Chengcai , Niu Dongdong , Wang Lan , Feng Hongzu 
Published: September 2021

Agrobacterium salinitolerans DG3-1 is an endophytic bacterium isolated from cotton root tissue. Our previous work has shown that it can inhibit the growth of Fusarium and Verticillium wilt pathogens as well as increase the chlorophyll content of cotton leaves. Here, we reported the complete genome sequence of strain DG3-1, which was analyzed by sequence reads generated from Nanopore PromethION and Illumina NovaSeq PE150 platforms. This genome sequence could be used to clarify the possible mechanism of DG3-1 at the gene level. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
The Impact of Elsinoë ampelina Infection on Key Metabolic Properties in Vitis vinifera ‘Red Globe’ Berries via Multiomics Approaches
Authors: Li Zhi , Gao Linlin , Chang Pingping , Chen Ziqiu , Zhang Xiuming , Yin Wuchen , Fan Yanchun , Wang Xiping 
Published: September 2021

Grape anthracnose caused by Elsinoë ampelina (Shear) is one of the most serious fungal diseases that lead to the quality reduction and yield losses of grape (Vitis vinifera ‘Red Globe’) berries. In the present study, metabolome and transcriptome analyses were conducted using grape berries in the field after infection with E. ampelina at 7, 10, and 13 days to identify the metabolic properties of berries. In total, 132 metabolites with significant differences and 6,877 differentially expressed genes were detected and shared by three comparisons. The analyses demonstrated that phenylpropanoid, flavonoid, stilbenoid, and nucleotide metabolisms were enriched in E. ampelina-infected grape berries but not amino acid metabolism. Phenolamide, terpene, and polyphenole contents also accumulated during E. ampelina infection. The results provided evidence of the enhancement of secondary metabolites such as resveratrol, α-viniferin, ε-viniferin, and lignins involved in plant defense. The results showed the plant defense-associated metabolic reprogramming caused by E. ampelina infection in grape berry and provided a global metabolic mechanism under E. ampelina stimulation. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Distal Humerus Fractures in the Elderly: When to Fix and When to Replace?
Authors: Mayer Ryan , Choo Andrew , Zuelzer David 
Published: September 2021

Summary:
Distal humerus fractures in the elderly population can be difficult to manage because of substantial articular comminution, poor bone quality, and soft tissue compromise. Important patient considerations for treatment include physiologic age, mental status, activity level, and independence with activities of daily living. Elderly patients may be reliant on their upper extremity as a weight-bearing limb when using a walker or rising to stand which creates additional demand. The goal of surgical treatment is to recreate a stable, painless elbow with a functional range of motion to preserve independence for daily activities and mobilization. The main surgical treatment options are open reduction and internal fixation and arthroplasty. Here, we discuss indications and operative goals in each clinical scenario.