bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rat PRDM9 shapes recombination landscapes, duration of meiosis, gametogenesis, and age of fertility
Authors: Mihola Ondrej , Landa Vladimir , Pratto Florencia , Brick Kevin , Kobets Tatyana , Kusari Fitore , Gasic Srdjan , Smagulova Fatima , Grey Corinne , Flachs Petr , Gergelits Vaclav , Tresnak Karel , Silhavy Jan , Mlejnek Petr , Camerini-Otero R. Daniel , Pravenec Michal , Petukhova Galina V. , Trachtulec Zdenek 
Published: April 2021

AbstractBackgroundVertebrate meiotic recombination events are concentrated in regions (hotspots) that display open chromatin marks, such as trimethylation of lysines 4 and 36 of histone 3 (H3K4me3 and H3K36me3). Mouse and human PRDM9 proteins catalyze H3K4me3 and H3K36me3 and determine hotspot positions, whereas other vertebrates lacking PRDM9 recombine in regions with chromatin already opened for another function, such as gene promoters. While these other vertebrate species lacking PRDM9 remain fertile, inactivation of the mousePrdm9gene, which shifts the hotspots to the functional regions (including promoters), typically causes gross fertility reduction; and the reasons for these species differences are not clear.ResultsWe introducedPrdm9deletions into theRattus norvegicusgenome and generated the first rat genome-wide maps of recombination-initiating double-strand break hotspots. Rat strains carrying the same wild-typePrdm9allele shared 88% hotspots but strains with differentPrdm9alleles only 3%. AfterPrdm9deletion, rat hotspots relocated to functional regions, about 40% to positions corresponding toPrdm9-independent mouse hotspots, including promoters. Despite the hotspot relocation and decreased fertility,Prdm9-deficient rats of the SHR/OlaIpcv strain produced healthy offspring. The percentage of normal pachytene spermatocytes in SHR-Prdm9mutants was almost double than in the PWD male mouse oligospermic sterile mutants. We previously found a correlation between the crossover rate and sperm presence in mousePrdm9mutants. The crossover rate of SHR is more similar to sperm-carrying mutant mice, but it did not fully explain the fertility of the SHR mutants. Besides mild meiotic arrests at rat tubular stages IV (mid-pachytene) and XIV (metaphase), we also detected postmeiotic apoptosis of round spermatids. We found delayed meiosis and age-dependent fertility in both sexes of the SHR mutants.ConclusionsWe hypothesize that the relative increased fertility of rat versus mousePrdm9mutants could be ascribed to extended duration of meiotic prophase I. While rat PRDM9 shapes meiotic recombination landscapes, it is unnecessary for recombination. We suggest that PRDM9 has additional roles in spermatogenesis and speciation—spermatid development and reproductive age—that may help to explain male-specific hybrid sterility.
Community views on short birth interval in Northern Uganda: a participatory grounded theory
Authors: Belaid Loubna , Atim Pamela , Ochola Emmanuel , Omara Bruno , Atim Eunice , Ogwang Martin , Bayo Pontius , Oola Janet , Okello Isaac Wonyima , Sarmiento Ivan , Rojas-Rozo Laura , Zinszer Kate , Zarowsky Christina , Andersson Neil 
Published: April 2021

Abstract
Background
Short birth interval is associated with adverse perinatal, maternal, and infant outcomes, although evidence on actionable factors underlying short birth interval remains limited. We explored women and community views on short birth intervals to inform potential solutions to promote a culturally safe child spacing in Northern Uganda.

Methods
Gendered fuzzy cognitive mapping sessions (n = 21), focus group discussions (n = 12), and an administered survey questionnaire (n = 255) generated evidence on short birth intervals. Deliberative dialogues with women, their communities, and service providers suggested locally relevant actions promote culturally safe child spacing.

Results
Women, men, and youth have clear understandings of the benefits of adequate child spacing. This knowledge is difficult to translate into practice as women are disempowered to exercise child spacing. Women who use contraceptives without their husbands’ consent risk losing financial and social assets and are likely to be subject to intra-partner violence. Women were not comfortable with available contraceptive methods and reported experiencing well-recognized side effects. They reported anxiety about the impact of contraception on the health of their future children. This fear was fed by rumors in their communities about the effects of contraceptives on congenital diseases. The women and their communities suggested a home-based sensitization program focused on improving marital relationships (spousal communication, mutual understanding, male support, intra-partner violence) and knowledge and side-effects management of contraceptives.

Conclusions
The economic context, gender power dynamics, inequality, gender bias in land tenure and ownership regulations, and the limited contraceptive supply reduce women’s capacity to practice child spacing.
Determinants of gender disparities in scaling up the first 90 towards the UNAIDS 90–90–90 targets in South Africa: findings from the 2017 household-based national cross-sectional survey
Authors: Jooste S. , Mabaso M. , Taylor M. , North A. , Shean Y. L. , Simbayi L. C. 
Published: April 2021

Abstract
Background
The first 90 of UNAIDS 90–90–90 targets to have 90% of the people living with HIV know their status is an important entry point to the HIV treatment cascade and care continuum, but evidence shows that there is a large gap between males and females in this regard. It is therefore important to understand barriers and facilitators of achieving the first 90 target. This study examined determinants of the first 90 target among females and males in order to inform strategies aimed at improving the HIV cascade in South Africa.

Methods
The data used in the analysis were obtained from a 2017 household-based cross-sectional nationally representative survey conducted using a multi-stage stratified cluster random sampling design. A series of hierarchical multiple logistic regression models were fitted to identify the determinants of the first 90 target by gender.

Results
Overall, 84.8% of HIV-positive individuals aged 15 years and older were aware of their HIV status. Females were significantly more aware of their HIV status compared to males (88.7% vs 78.2%, p < 0.001). Both females aged 25 to 49 years [aOR = 3.20 (95% CI 1.35–7.57), p = 0.008], and 50 years and older [aOR = 3.19 (95% CI 1.04–9.76), p = 0.042] and males aged 25 to 49 years [aOR = 3.00 (95% CI 1.13–7.97), p = 0.028], and 50 years and older [aOR = 7.25 (95% CI 2.07–25.36), p = 0.002] were significantly more likely to know their HIV status compared to those aged 15 to 19 years. Males with tertiary education level were significantly more likely to be aware of their HIV positive status [aOR = 75.24 (95% CI 9.07–624.26), p < 0.001] compared to those with no education or with primary level education. Females with secondary [aOR = 3.28 (95% CI 1.20–8.99), p = 0.021] and matric [aOR = 4.35 (95% CI 1.54–12.37), p = 0.006] educational levels were significantly more likely to be aware of their HIV positive status, compared to those with no education or with primary level education.

Conclusion
Significant progress has been made with regards to reaching the UNAIDS first 90 target. In this context achieving the first 90 target is feasible but there is a need for additional interventions to reach the males especially youth including those with no education or low levels of education.
Chiropractic case reports: a review and bibliometric analysis
Authors: Trager Robert J. , Dusek Jeffery A. 
Published: April 2021

AbstractObjectiveTo determine publication trends, gaps, and predictors of citation of chiropractic case reports (CRs).MethodsA bibliometric review was conducted by searching PubMed, Index to Chiropractic Literature (ICL), and Google Scholar to identify PubMed-indexed CRs, which were screened according to selection criteria. Case reports were categorized by International Classification of Disease (ICD-10) code, patient age, topic describing case management or adverse effects of care, focus being spinal or non-spinal, journal type, integrative authorship, title metrics, and citation metrics. Binary logistic regression was used to identify independent predictors of citations per year and total citations greater than the median values.ResultsThe search identified 1176 chiropractic CRs meeting selection criteria. There was an increasing trend of CRs having a case management topic, non-spinal focus, non-chiropractic journal, neuromusculoskeletal-focus, diagnosis of vascular pathology, and a decreasing trend of adverse effect vascular pathology CRs. Independent predictors of greater total citations (or citation rate) included ICD-10 categories of perinatal conditions, infections, “case” in title, case management topic, and physical therapy, integrative, and dental journal type. Predictors of fewer citations included diseases of the blood, neoplasms, other findings not elsewhere classified, a title > 11 words, and multidisciplinary authorship. ICD-10 categories describing non-musculoskeletal diseases and special populations such as pediatrics, pregnancy, and perinatal conditions had few CRs.ConclusionChiropractic CRs are diversifying from spine-related topics. Chiropractors are encouraged to publish objective, structured CRs within defined research gaps. Published CRs can inform the design of future research studies with a higher level of clinical relevance and evidence.
Complete vertebrate mitogenomes reveal widespread repeats and gene duplications
Authors:   The Vertebrate Genomes Project Consortium, Formenti Giulio , Rhie Arang , Balacco Jennifer , Haase Bettina , Mountcastle Jacquelyn , Fedrigo Olivier , Brown Samara , Capodiferro Marco Rosario , Al-Ajli Farooq O. , Ambrosini Roberto , Houde Peter , Koren Sergey , Oliver Karen , Smith Michelle , Skelton Jason , Betteridge Emma , Dolucan Jale , Corton Craig , Bista Iliana , Torrance James , Tracey Alan , Wood Jonathan , Uliano-Silva Marcela , Howe Kerstin , McCarthy Shane , Winkler Sylke , Kwak Woori , Korlach Jonas , Fungtammasan Arkarachai , Fordham Daniel , Costa Vania , Mayes Simon , Chiara Matteo , Horner David S. , Myers Eugene , Durbin Richard , Achilli Alessandro , Braun Edward L. , Phillippy Adam M. , Jarvis Erich D. 
Published: April 2021

Abstract
Background
Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly.

Results
As part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (> 10 kbp, PacBio or Nanopore) and short (100–300 bp, Illumina) reads. Our pipeline leads to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We observe that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. Our assemblies also identify novel gene region duplications. The presence of repeats and duplications in over half of the species herein assembled indicates that their occurrence is a principle of mitochondrial structure rather than an exception, shedding new light on mitochondrial genome evolution and organization.

Conclusions
Our results indicate that even in the “simple” case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone.
Deletion of a non-canonical regulatory sequence causes loss of Scn1a expression and epileptic phenotypes in mice
Authors: Haigh Jessica L. , Adhikari Anna , Copping Nycole A. , Stradleigh Tyler , Wade A. Ayanna , Catta-Preta Rinaldo , Su-Feher Linda , Zdilar Iva , Morse Sarah , Fenton Timothy A. , Nguyen Anh , Quintero Diana , Agezew Samrawit , Sramek Michael , Kreun Ellie J. , Carter Jasmine , Gompers Andrea , Lambert Jason T. , Canales Cesar P. , Pennacchio Len A. , Visel Axel , Dickel Diane E. , Silverman Jill L. , Nord Alex S. 
Published: April 2021

AbstractBackgroundGenes with multiple co-active promoters appear common in brain, yet little is known about functional requirements for these potentially redundant genomic regulatory elements.SCN1A,which encodes the NaV1.1 sodium channel alpha subunit, is one such gene with two co-active promoters. Mutations inSCN1Aare associated with epilepsy, including Dravet syndrome (DS). The majority of DS patients harbor coding mutations causingSCN1Ahaploinsufficiency; however, putative causal non-coding promoter mutations have been identified.MethodsTo determine the functional role of one of these potentially redundantScn1apromoters, we focused on the non-codingScn1a1b regulatory region, previously described as a non-canonical alternative transcriptional start site. We generated a transgenic mouse line with deletion of the extended evolutionarily conserved 1b non-coding interval and characterized changes in gene and protein expression, and assessed seizure activity and alterations in behavior.ResultsMice harboring a deletion of the 1b non-coding interval exhibited surprisingly severe reductions ofScn1aand NaV1.1 expression throughout the brain. This was accompanied by electroencephalographic and thermal-evoked seizures, and behavioral deficits.ConclusionsThis work contributes to functional dissection of the regulatory wiring of a major epilepsy risk gene,SCN1A. We identified the 1b region as a critical disease-relevant regulatory element and provide evidence that non-canonical and seemingly redundant promoters can have essential function.
Engineered endolysin-based “artilysins” for controlling the gram-negative pathogen Helicobacter pylori
Authors: Xu Dengyuan , Zhao Shanshan , Dou Jun , Xu Xiaofeng , Zhi Yanyan , Wen Liangzhu 
Published: April 2021

AbstractHelicobacter pylori infection can cause a variety of gastrointestinal diseases. In severe cases, there is a risk of gastric cancer. Antibiotics are often used for clinical treatment of H. pylori infections. However, because of antibiotic overuse in recent years and the emergence of multidrug-resistant bacteria, there is an urgent need to develop new treatment methods and drugs to achieve complete eradication of H. pylori. Endolysins and holins encoded by bacterial viruses (i.e., phages) represent a promising avenue of investigation. These lyase-based antibacterial drugs act on the bacterial cell wall to destroy the bacteria. Currently, a type of endolysin that has been studied more frequently acts on the amide bond between peptidoglycans, and holin is a transmembrane protein that can punch holes in the cell membrane. However, as a Gram-negative bacterium, H. pylori possesses a layer of impermeable lipopolysaccharides on the cell wall, which prevents endolysin interaction with the cell wall. Therefore, we designed a genetic linkage between an endolysin enzyme and a holin enzyme with a section of polypeptides (e.g., polycations and hydrophobic peptides) that enable penetration of the outer membrane. These complexes were designated “artilysins” and were efficiently expressed in Escherichia coli. In vitro bacteriostasis experiments showed that the purified artilysins had strong bacteriostatic effects on H. pylori. In addition, the surface of H. pylori was perforated and destroyed, as confirmed by electron microscopy, which was proved that artilysins had bacteriolytic effect on H. pylori.
Proactive psychological programs designed to mitigate posttraumatic stress injuries among at-risk workers: a systematic review and meta-analysis
Authors: Di Nota Paula M. , Bahji Anees , Groll Dianne , Carleton R. Nicholas , Anderson Gregory S. 
Published: April 2021

Abstract
Background
Public safety personnel and frontline healthcare professionals are at increased risk of exposure to potentially psychologically traumatic events (PPTE) and developing posttraumatic stress injuries (PTSI, e.g., depression, anxiety) by the nature of their work. PTSI are also linked to increased absenteeism, suicidality, and performance decrements, which compromise occupational and public health and safety in trauma-exposed workers. Evidence is lacking regarding the effectiveness of “prevention” programs designed to mitigate PTSI proactively. The purpose of this review is to measure the effectiveness of proactive PTSI mitigation programs among occupational groups exposed to PPTE on measures of PTSI symptoms, absenteeism, and psychological wellness.

Methods
Five electronic databases were searched per PRISMA guidelines for English or French peer-reviewed studies from 2008 to 2019 evaluating PTSI and psychological wellness in adults exposed to occupational PPTE. The risk of bias was assessed using the Newcastle-Ottawa Scale.

Results
We identified 42 studies evaluating 3182 public safety and frontline healthcare professionals, PPTE-exposed educational staff, and miners. Significant overlap was found across program themes that included mindfulness, psychoeducation, resilience promotion, and stress management strategies. Post-program effect sizes were small (SMD < 0.5) to moderate (SMD < 0.8) for reductions in PTSI symptoms and for promoting measures of well-being as indicated by a meta-analysis on 36 studies. There was no evidence for significant reductions in substance use, absenteeism, or biomarkers of distress except for heart rate. Subgroup analyses indicated that multimodal programs effectively improved general psychological health, while resilience programs improved measures of depression, burnout, coping, and resilience. Effect sizes for resilience, depression, and general psychological health improvements were greatest immediately or 1-month post-training, while improvements in PTSD symptoms and coping were larger at longer follow-up. Studies were of moderate quality and risk of bias.

Conclusions
The current results showcase modest evidence for time-limited reductions in PTSI following participation in holistic programs that promote resilience, stress, and emotion regulation among at-risk workers. Implications for organizational implementation of proactive PTSI mitigation programs and areas of future research are discussed.

Systematic review registration
PROSPERO (CRD42019133534)
Patient-reported outcome measures (PROMs) use in post-stroke patient care and clinical practice: a realist synthesis protocol
Authors: Smith A. , Hewitt J. , Quinn T. J. , Robling M. 
Published: April 2021

Abstract
Background
There is growing interest in the use of routine patient-reported outcome measures (PROMs) to influence the care of individual patients with stroke. However, there are significant gaps in our understanding as to how PROMs influence post-stroke patient care and clinical practice. This is due to factors including the number of purported uses for PROMs and that PROMs are complex interventions, which attempt to stimulate varied actions or behaviours. Therefore, the objective of this realist synthesis is to offer theory-based explanations as to how PROMs influence post-stroke clinical practice and patient care.

Methods
This is a protocol for a realist synthesis, which involves three distinct phases: theory building (phase 1), theory testing and refinement (phase 2) and synthesis (phase 3). Phase 1 will develop initial rough programme theories (IRPTs), through literature searches (from January 2000 onwards) of MEDLINE, EMBASE, PsycINFO, CINAHL, Cochrane Library and the grey literature. Only secondary sources will be included that contribute to the development of IRPTs. Only two IRPTs, prioritised by the stakeholder group, will be taken forward to be tested and refined during phase 2. Further novel searches will be employed in phase 2, utilising the same criteria as phase 1; however, phase 2 searches will not utilise grey literature searches, and only primary research studies that contribute to the refinement of programme theories under investigation will be included. Two independent reviewers will screen and select all returned results. The reviewers will code and annotate relevant sources, resulting in ‘fragments’ to be extracted and graded based on the richness of their contribution to explanation and causal insight. Further, these fragments will be organised into ‘Context-Mechanism-Outcome’ configurations. Phase 3 of the review will involve the synthesis of context-mechanism-outcome configurations to form middle-range theory-based explanations and developed logic models for stakeholders to understand how PROMs in post-stroke clinical practice and patient care work for whom, how and under what circumstances.

Discussion
The resulting realist synthesis will provide guidance on the implementation of PROMs within routine post-stroke clinical practice and patient care and act as a touchstone for further testing and refinement of PROMs programmes.

Systematic review registration
PROSPERO CRD42020138649.
Tandem fecal microbiota transplantation cycles in an allogeneic hematopoietic stem cell transplant recipient targeting carbapenem-resistant Enterobacteriaceae colonization: a case report and literature review
Authors: Su Fengqin , Luo Yi , Yu Jian , Shi Jimin , Zhao Yanmin , Yan Mengni , Huang He , Tan Yamin 
Published: April 2021

AbstractBackgroundDue to limited antibiotic options, carbapenem-resistant Enterobacteriaceae (CRE) infections are associated with high non-relapse mortality after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Also, intestinal CRE colonization is a risk factor for subsequent CRE infection. Several clinical studies have reported successful fecal microbiota transplantation (FMT) for the gut decontamination of a variety of multidrug-resistant bacteria (MDRB), even in immunosuppressed patients. Similarly, other studies have also indicated that multiple FMTs may increase or lead to successful therapeutic outcomes.Case presentationWe report CRE colonization in an allo-HSCT patient with recurrent CRE infections, and its successful eradication using tandem FMT cycles at 488 days after allo-HSCT. We also performed a comprehensive microbiota analysis. No acute or delayed adverse events (AEs) were observed. The patient remained clinically stable with CRE-negative stool culture at 26-month follow-up. Our analyses also showed some gut microbiota reconstruction. We also reviewed the current literature on decolonization strategies for CRE.ConclusionsCRE colonization led to a high no-relapse mortality after allo-HSCT; however, well-established decolonization strategies are currently lacking. The successful decolonization of this patient suggests that multiple FMT cycles may be potential options for CRE decolonization.