bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficacy of greater occipital nerve block for pain relief in patients with postdural puncture headache
Authors: Chang Ying-Jen , Hung Kuo-Chuan , Chen I-Wen , Kuo Chi-Lin , Teng I-Chia , Lin Ming-Chung , Yew Ming , Liao Shu-Wei , Wu Chung-Yi , Yu Chia-Hung , Lan Kuo-Mao , Sun Cheuk-Kwan 
Published: December 2021

Abstract

Background:
This study aimed at assessing the therapeutic effectiveness of greater occipital nerve block (GONB) against postdural puncture headache (PDPH).

Methods:
Studies investigating analgesic effects of GONB against PDPH in adults were retrieved from the MEDLINE, EMBASE, Google scholar, and Cochrane central databases from their inception dates to May, 2021. Pain score at postprocedural 24 hours was the primary endpoint, while secondary endpoints were pain score at postprocedural 1 hour and 12 hours as well as the risk of intervention failure.

Results:
Of the 7 studies (randomized controlled trials [RCTs], n = 4; non-RCTs, n = 3) that recruited 275 patients, 2 investigated female patients undergoing cesarean section and the other 5 were conducted in both obstetric and nonobstetric settings. Pooled results showed a lower mean pain score at 24 hours (i.e., primary outcome) (mean difference [MD] = –2.66, 95%: CI: –3.98 to –1.33, P < .001; I
2 = 97%, 6 studies), 1 hour (MD = –4.23, 95% confidence interval [CI]: –5.08 to –3.37, P < .00001; I
2 = 86%, 5 studies), and 6 hours (MD = –2.78, 95% CI: –4.99 to –0.57, P = .01; I
2 = 98%, 4 studies) in patients with GONB compared to those without. Trial sequential analysis supported the robustness of evidence at postprocedural 24 hours. The use of GONB also decreased the risk of intervention failure (relative ratio [RR] = 0.4, 95% CI: 0.19 to 0.82, P = .01; I
2 = 96%, 6 studies, 277 patients).

Conclusion:
Our results suggested a therapeutic effect of greater occipital nerve block against postdural puncture headache up to postprocedural 24 hours. Further large-scale studies are warranted to evaluate its therapeutic benefit beyond the acute stage.
Comparative Study of Acute Anogenital Injury Between Consensual and Nonconsensual Postmenarche Adolescents
Authors: Suttipasit Papanu , Sinlapamongkolkul Phakatip , Wongwittayapanich Surachet 
Published: December 2021

Abstract
In Thailand, sexual activity involving those under the legal age of consent may be legally and medically problematic, even if it is consensual. Thus, differentiating anogenital injury characteristics that occur during consensual versus nonconsensual acts with adolescent female subjects could aid legal advocates and improve health care and social support for these patients. Our study included postmenarche female patients having acute anogenital injuries after consensual and nonconsensual penetration. We found that nonconsenting patients had more cases of anogenital injury than consenting (69.8% vs 55.5%), with at least 1 abrasion, contusion, laceration, labia major or minor injury, and external or internal site injury. Both consensual and nonconsensual cases had the same common sites for injury type, reflecting the same injury mechanism; prior sexual intercourse was a significant protective factor against some anogenital injury prevalence, types, and sites for both groups. Adolescents forced into nonconsensual acts had more nonanogenital injuries. Looking at factors such as age, prior sexual activity history, and use of condom and/or contraceptive pills, it is very clear that early sexual education, particularly around consent, is critically needed in Thailand for the best interests of adolescents and children so that they and/or their guardians can access the health and legal resources required.
Characterizing Financial Sustainability of Sexually Transmitted Disease Clinics Through Insurance Billing Practices
Authors: Pearson William S. , Chan Philip A. , Cramer Ryan , Gift Thomas L. 
Published: December 2021

Context:
Sexually transmitted infections (STIs) continue to increase in the United States. Publicly funded sexually transmitted disease (STD) clinics provide important safety net services for communities at greater risk for STIs. However, creating financially sustainable models of STI care remains a challenge.

Objective:
Characterization of clinic insurance billing practices and patient willingness to use insurance.

Design:
Cross-sectional survey assessment of clinic administrators and patients.

Setting:
Twenty-six STD clinics and 4138 patients attending these clinics in high STD morbidity metropolitan statistical areas in the United States.

Participants:
Clinic administrators and patients of these clinics.

Intervention:
Survey assessment.

Main Outcome Measure:
Insurance billing practices of STD clinics and patient insurance status and willingness to use their insurance.

Results:
Fifteen percent of clinics (4/26) indicated that they billed only Medicaid, 58% (15/26) billed both Medicaid and private insurance, 27% (7/26) did not bill for any health insurance, and none (0%) billed only private health insurance companies. Of 4138 patients surveyed, just more than one-half of patients (52.6%) were covered by some form of health insurance. More than one-half (57.2%) of all patients covered by health insurance indicated that they would be willing to use their health insurance for that visit. After adjusting for patient demographics and clinic characteristics, the patients covered by government insurance were 3 times as likely (odds ratio: 3.16; 95% confidence interval, 2.44-4.10) than patients covered by private insurance to be willing to use their insurance for their visit.

Conclusion:
Opportunities exist for sustainable STI services through the enhancement of billing practices in STD clinics. The STD clinics provide care to large numbers of individuals who are both insured and who are willing to use their insurance for their care. As Medicaid expansion continues across the country, efforts focused on improving reimbursement rates for Medicaid may improve financial sustainability of STD clinics.
Omeprazole Increases Survival Through the Inhibition of Inflammatory Mediaters in Two Rat Sepsis Models
Authors: Kotsuka Masaya , Hashimoto Yuki , Nakatake Richi , Okuyama Tetsuya , Hatta Masahiko , Yoshida Terufumi , Okumura Tadayoshi , Nishizawa Mikio , Kaibori Masaki , Sekimoto Mitsugu 
Published: December 2021

ABSTRACT

Background:
Omeprazole (OMZ) is a proton pump inhibitor that is used to reduce gastric acid secretion, but little is known about its possible liver protective effects. This study investigated whether OMZ has beneficial effects in rat septic models of LPS-induced liver injury after D-galactosamine (GalN) treatment and 70% hepatectomy (PH), and to determine the mechanisms of OMZ in an in vitro model of liver injury.

Methods:
In the in vivo models, the effects of OMZ were examined 1 h before treatments in both models on survival, nuclear factor (NF)-κB activation, histopathological analysis, and proinflammatory mediator expression in the liver and serum. In the in vitro model, primary cultured rat hepatocytes were treated with IL-1β in the presence or absence of OMZ. The influence of OMZ on nitric oxide (NO) product and inducible NO synthase (iNOS) induction and on the associated signaling pathway was analyzed.

Results:
OMZ increased survival and decreased tumor necrosis factor-alpha, iNOS, cytokine-induced neutrophil chemoattractant 1, IL-6, and IL-1β mRNA expression, and increased IL-10 mRNA expression in the livers of both GaIN/LPS- and PH/LPS-treated rats. Necrosis and apoptosis were inhibited by OMZ in GaIN/LPS rats, but OMZ had no effects on necrosis in PH/LPS rats. OMZ inhibited iNOS induction partially through suppression of NF-κB signaling in hepatocytes.

Conclusions:
OMZ inhibited the induction of several inflammatory mediators, resulting in the prevention of LPS-induced liver injury after GalN liver failure and PH, although OMZ showed different doses and mechanisms in the two models.
The experience of remote recruitment for Essential Coaching for Every Mother during the coronavirus disease 2019 pandemic
Authors: Dol Justine , Murphy Gail Tomblin , McMillan Douglas , Aston Megan , Campbell-Yeo Marsha 
Published: December 2021

ABSTRACT

Introduction and aims:
Due to physical distancing recommendations because of the COVID-19 pandemic, recruitment approaches for perinatal research needed to shift from in-person to remote. The purpose of this study is to describe the recruitment and retention of women for an mHealth intervention study for Essential Coaching for Every Mother.

Methods:
Three methods were used for recruitment: social media, posters in hospital, and media outreach. First time mothers were eligible for enrollment antenatally (37+ weeks) and postnatally (<3 weeks). Eligibility screening occurred remotely via text message. Outcomes were days to recruit 75 participants, eligibility vs. ineligibility rates, dropout and exclusion reasons, survey completion rates, perinatal timing of enrollment, and recruitment sources.

Results:
Recruitment ran from 15 July to 19 September 2020 (67 days) with 200 potential participants screened and 88 enrolled. It took 50 days to enroll 75 participants. Women recruited antenatally were more likely to receive all intervention messages (68 vs. 19%) and miss fewer messages (6.4 vs. 13.8) than women enrolled postnatally. Participants heard about the study through family/friends (31%), news (20%), Facebook groups/ads (30%), posters (12%), or other (7%).

Conclusion:
Antenatal recruitment resulted in participants enrolling earlier and receiving more messages. Remote recruitment was a feasible way to recruit, with word of mouth and media outreach being most successful, followed by Facebook.
vRhyme enables binning of viral genomes from metagenomes
Authors: Kieft Kristopher , Adams Alyssa , Salamzade Rauf , Kalan Lindsay , Anantharaman Karthik 
Published: December 2021

AbstractGenome binning has been essential for characterization of bacteria, archaea, and even eukaryotes from metagenomes. Yet, no approach exists for viruses. We developed vRhyme, a fast and precise software for construction of viral metagenome-assembled genomes (vMAGs). vRhyme utilizes single- or multi-sample coverage effect size comparisons between scaffolds and employs supervised machine learning to identity nucleotide feature similarities, which are compiled into iterations of weighted networks and refined bins. Using simulated viromes, we displayed superior performance of vRhyme compared to available binning tools in constructing more complete and uncontaminated vMAGs. When applied to 10,601 viral scaffolds from human skin, vRhyme advanced our understanding of resident viruses, highlighted by identification of a Herelleviridae vMAG comprised of 22 scaffolds, and another vMAG encoding a nitrate reductase metabolic gene, representing near-complete genomes post-binning. vRhyme will enable a convention of binning uncultivated viral genomes and has the potential to transform metagenome-based viral ecology.
Prior exposure to microcystin alters host gut resistome and is associated with dysregulated immune homeostasis in translatable mouse models
Authors: Saha Punnag , Bose Dipro , Stebliankin Vitalii , Cickovski Trevor , Seth Ratanesh K. , Porter Dwayne E. , Brooks Bryan W. , Mathee Kalai , Narasimhan Giri , Colwell Rita , Scott Geoff I. , Chatterjee Saurabh 
Published: December 2021

AbstractThe increased propensity of harmful algal blooms (HABs) and exposure from HABs-cyanotoxin causes human toxicity. It has been associated with the progression of several diseases that encompass the liver, kidneys, and immune system. Recently, a strong association of cyano-HAB toxicity with the altered host gut microbiome has been shown. We tested the hypothesis that prior exposure to cyanotoxin microcystin may alter the microbiome and induce microbiome-host-resistome crosstalk. Using both wild-type and humanized mice, we show that the mice exposed to microcystin had an altered microbiome signature that harbored antimicrobial resistance genes. Host resistome phenotypes such as mefA, msrD, mel, ant6, and tet40 increased in diversity and relative abundance following microcystin exposure. Interestingly, the increased abundance of these genes was traced to resistance to common antibiotics such as tetracycline, macrolides, glycopeptide, and aminoglycosides, crucial for modern-day treatment for several diseases. Increased abundance of these genes was positively associated with increased expression of PD1, a T-cell homeostasis marker, and pleiotropic inflammatory cytokine IL-6 with a concomitant negative association with immunosurveillance markers IL7 and TLR2. Microcystin exposure also caused decreased TLR2, TLR4, and REG3G expressions, increased immunosenescence, and higher systemic levels of IL-6 in both wild-type and humanized mice. In conclusion, the results show a first-ever characterization of the host resistome of microcystin exposure and its connection to host immune status and antibiotic resistance. The results may be crucial for understanding the ability of exposed subjects to fight future bacterial infections and the progression of the debilitating disease in hospital settings.
Non-toxigenic Vibrio cholerae challenge strains for evaluating vaccine efficacy and inferring mechanisms of protection
Authors: Fakoya Bolutife , Hullahalli Karthik , Rubin Daniel H. F. , Leitner Deborah R. , Chilengi Roma , Sack David A. , Waldor Matthew K. 
Published: December 2021

AbstractHuman challenge studies are instrumental for testing cholera vaccines, but these studies use outdated strains and require inpatient facilities. Here, we created next-generation isogenic Ogawa and Inaba V. cholerae challenge strains (ZChol strains) derived from a contemporary Zambian clinical isolate representative of current dominant pandemic V. cholerae. To minimize the risk of severe diarrhea these strains were rendered non-toxigenic, since antibody responses which limit V. cholerae colonization are the primary mechanism of immune protection. These strains did not cause diarrhea in infant mice and proved to accurately gauge reduction in intestinal colonization mediated by effective vaccination. They are also valuable as targets for measuring vibriocidal antibody responses. Using barcoded ZChol strains, we discovered that vaccination tightens the infection bottleneck without restricting pathogen expansion in vivo. ZChol strains have the potential to enhance the safety, relevance, and scope of future cholera vaccine challenge studies and be valuable reagents for studies of immunity to cholera.
Characterization of sequence determinants of enhancer function using natural genetic variation
Authors: Yang Marty G. , Ling Emi , Cowley Christopher J. , Greenberg Michael E. , Vierbuchen Thomas 
Published: December 2021

ABSTRACTSequence variation in enhancers, a class of cis-regulatory elements that control cell type-specific gene transcription, contributes significantly to phenotypic variation within human populations. Enhancers are short DNA sequences (∼200 bp) composed of multiple binding sites (4-10 bp) for transcription factors (TFs). The transcriptional regulatory activity of an enhancer is encoded by the type, number, and distribution of TF binding sites that it contains. However, the sequence determinants of TF binding to enhancers and the relationship between TF binding and enhancer activity are complex, and thus it remains difficult to predict the effect of any given sequence variant on enhancer function. Here, we generate allele-specific maps of TF binding and enhancer activity in fibroblasts from a panel of F1 hybrid mice that have a high frequency of sequence variants. We identified thousands of enhancers that exhibit differences in TF binding and/or activity between alleles and use these data to define features of sequence variants that are most likely to impact enhancer function. Our data demonstrate a critical role for AP-1 TFs at many fibroblast enhancers, reveal a hierarchical relationship between AP-1 and TEAD TF binding at enhancers, and delineate the nature of sequence variants that contribute to AP-1 TF binding. These data represent one of the most comprehensive assessments to date of the impact of sequence variation on enhancer function in chromatin, with implications for identifying functional cis-regulatory variation in human populations.
2FAST2Q: A general-purpose sequence search and counting program for FASTQ files
Authors: Bravo Afonso M. , Typas Athanasios , Veening Jan-Willem 
Published: December 2021

AbstractThe increasingly widespread use of next generation sequencing protocols has brought the need for the development of user-friendly raw data processing tools. Here, we present 2FAST2Q, a versatile and intuitive standalone program capable of extracting and counting feature occurrences in FASTQ files. 2FAST2Q can be used in any experimental setup that requires feature extraction from raw reads, being able to quickly handle mismatch alignments, nucleotide wise Phred score filtering, custom read trimming, and sequence searching within a single program. Using published CRISPRi datasets in whichEscherichia coliandMycobacterium tuberculosisgene essentiality, as well as host-cell sensitivity towards SARS-CoV2 infectivity were tested, we demonstrate that 2FAST2Q efficiently recapitulates the output in read counts per provided feature as with traditional pipelines. Moreover, we show how different FASTQ read filtering parameters impact downstream analysis, and suggest a default usage protocol. 2FAST2Q has a familiar user interface and uses a custom sequence mismatch search algorithm, taking advantage of Python’s numba module JIT runtime speeds. It is thus easier to use and faster than currently available tools, efficiently processing large CRISPRi-Seq or random-barcode sequencing datasets on any up-to-date laptop. 2FAST2Q is available as an executable file for all current operating systems without installation and as a Python3 module on the PyPI repository (available athttps://veeninglab.com/2fast2q). We expect that 2FAST2Q will not only be useful for people working in microbiology but also for other fields in which amplicon sequencing data is generated.
Microcin MccI47 selectively inhibits enteric bacteria and reduces carbapenem-resistant Klebsiella pneumoniae colonization in vivo when administered via an engineered live biotherapeutic
Authors: Mortzfeld Benedikt M. , Palmer Jacob D. , Bhattarai Shakti K. , Dupre Haley L. , Mercado-Lubo Regino , Silby Mark W. , Bang Corinna , McCormick Beth A. , Bucci Vanni 
Published: December 2021

AbstractBackgroundThe gastrointestinal (GI) tract is the reservoir for multidrug-resistant (MDR) pathogens, specifically carbapenem-resistant (CR) Klebsiella pneumoniae and other Enterobacteriaceae, which often lead to the spread of antimicrobial resistance genes, severe extraintestinal infections, and lethal outcomes. Selective GI decolonization has been proposed as a new strategy for preventing transmission to other body sites and minimizing spreading to susceptible individuals.ResultsHere, we purify the to-date uncharacterized class IIb microcin I47 (MccI47) and demonstrate potent inhibition of numerous Enterobacteriaceae, including multidrug-resistant clinical isolates, in vitro at concentrations resembling those of commonly prescribed antibiotics. We then genetically modify the probiotic bacterium Escherichia coli Nissle 1917 (EcN) to produce MccI47 from a stable multicopy plasmid by using MccI47 toxin production in a counterselection mechanism to engineer one of the native EcN plasmids, which renders provisions for inducible expression and plasmid selection unnecessary. We then test the clinical relevance of the MccI47-producing engineered EcN in a murine CR K. pneumoniae colonization model and demonstrate significant MccI47-dependent reduction of CR K. pneumoniae abundance after seven days of daily oral live biotherapeutic administration without disruption of the resident microbiota.ConclusionsThis study provides the first demonstration of MccI47 as a potent antimicrobial against certain Enterobacteriaceae, and its ability to significantly reduce the abundance of CR K. pneumoniae in a preclinical animal model, when delivered from an engineered live biotherapeutic product. This study serves as the foundational step towards the use of engineered live biotherapeutic products aimed at the selective removal of MDR pathogens from the GI tract
Comprehensive transcriptional profiling and mouse phenotyping reveals dispensable role for adipose tissue selective long noncoding RNA Gm15551
Authors: Engelhard Christoph Andreas , Huang Chien , Khani Sajjad , Kasparek Petr , Prochazka Jan , Rozman Jan , Reguera David Pajuelo , Sedlacek Radislav , Kornfeld Jan-Wilhelm 
Published: December 2021

1AbstractCold and nutrient activated brown adipose tissue (BAT) is capable of increasing systemic energy expenditure via uncoupled respiration and secretion of endocrine factors thereby protecting mice against diet-induced obesity and improving insulin response and glucose tolerance in men. Long non-coding RNAs (lncRNAs) have recently been identified as fine tuning regulators of cellular function. While certain lncRNAs have been functionally characterised in adipose tissue, their overall contribution in the activation of BAT remains elusive. We identified lncRNAs correlating to inter-scapular brown adipose tissue (iBAT) function in high fat diet (HFD) and cold stressed mice. We focused on Gm15551 which has an adipose tissue specific expression profile, is highly upregulated during adipogenesis and downregulated by β-adrenergic activation in mature adipocytes. Albeit we performed comprehensive transcriptional and adipocyte physiology profiling in vitro and in vivo, we could not detect an effect of gain or loss of function of Gm15551.
The acquisition of clinically relevant amoxicillin resistance in Streptococcus pneumoniae requires ordered horizontal gene transfer of four loci
Authors: Gibson Paddy S. , Bexkens Evan , Zuber Sylvia , Cowley Lauren A. , Veening Jan-Willem 
Published: December 2021

AbstractUnderstanding how antimicrobial resistance spreads is critical for optimal application of new treatments. In the naturally competent human pathogen Streptococcus pneumoniae, resistance to β-lactam antibiotics is mediated by recombination events in genes encoding the target proteins, resulting in reduced drug binding affinity. However, for the front-line antibiotic amoxicillin, the exact mechanism of resistance still needs to be elucidated. Through successive rounds of transformation with genomic DNA from a clinically resistant isolate, we followed amoxicillin resistance development. Using whole genome sequencing, we showed that multiple recombination events occurred at different loci during one round of transformation. We found examples of non-contiguous recombination, and demonstrated that this could occur either through multiple D-loop formation from one donor DNA molecule, or by the integration of multiple DNA fragments. We also show that the final minimum inhibitory concentration (MIC) differs depending on recipient genome, explained by differences in the extent of recombination at key loci. Finally, through back transformations of mutant alleles and fluorescently labelled penicillin (bocillin-FL) binding assays, we confirm that pbp1a, pbp2b, pbp2x, and murM are the main resistance determinants for amoxicillin resistance, and that the order of allele uptake is important for successful resistance evolution. We conclude that recombination events are complex, and that this complexity contributes to the highly diverse genotypes of amoxicillin-resistant pneumococcal isolates.