bluuebunny/crossref_metadata_2025_split huggingface dataset:
Living standard and access to tetanus toxoid immunization among women in Bangladesh
Authors: Islam Ummay Nayeema , Sen Kanchan Kumar , Bari Wasimul 
Published: May 2022

Abstract
Background
Although Bangladesh has an impressive track record in the reduction of maternal and child mortality, tetanus, a dreadful disease, impedes the way to achieve Sustainable Development Goal (SDG) in this respect. Sufficient doses of tetanus toxoid containing vaccine during pregnancy ensure immunity against tetanus to mothers as well as newborns. Since inequalities persist across vaccination programs globally, in this paper, an attempt has been made to examine whether tetanus toxoid immunization (TTI) status among the women of reproductive age in Bangladesh for their most recent live birth born preceding 2 years of the survey changes with their living standard index (LSI).

Methods
Five domains of deprivation such as energy use, improved sanitation, drinking water, housing and assets ownership were used to compute the LSI using a approach proposed by Alkire and Foster. The adjusted association between LSI and TTI was established by using logistic regression model. For the purpose of statistical analysis, a nationally representative cross-sectional data extracted from Bangladesh Multiple Indicator Cluster Survey (BMICS), 2019 have been used.

Result
The bivariate analysis revealed that 79.5% (95% CI 78.0–81.0) of women with low and 83.1% (95% CI 81.3–84.9) with moderate living standards had sufficient vaccination coverage for their most recent pregnancies while this percentage was higher for the women who belonged to high living standard (85.2, 95% CI = 84.2–86.2). A strong evidence for greater odds of sufficient immunization with TT among the women maintaining a high standard of living (AOR = 1.24, 95% CI = 1.08–1.42, p < 0.01) was found from regression analysis.

Conclusion
The results depict existing living standard disparity with respect to TT vaccination coverage among women in Bangladesh. Present research suggests that immunization campaigns need to be conducted especially for the disadvantaged people to improve their health care and immunization service utilization among women within the age bracket of 15 to 49. This study proposed a scientific way to enhance TT vaccination among Bangladeshi women, which could help Bangladesh attain a widespread tetanus protection and thus, meet the SDGs for maternal and child mortality reduction.
Osteoporosis in nontuberculous mycobacterial pulmonary disease: a cross-sectional study
Authors: Tanaka Hiromu , Asakura Takanori , Suzuki Shoji , Okamori Satoshi , Kusumoto Tatsuya , Ogawa Takunori , Uno Shunsuke , Morita Atsuho , Lee Ho , Namkoong Ho , Kamata Hirofumi , Sato Yasunori , Uwamino Yoshifumi , Nishimura Tomoyasu , Ishii Makoto , Fukunaga Koichi , Hasegawa Naoki 
Published: May 2022

Abstract
Background
Since nontuberculous mycobacterial pulmonary disease (NTM-PD) is common in middle-aged/elderly slender women at risk of osteoporosis, we hypothesized that NTM-PD could be associated with osteoporosis. The study aimed to evaluate the prevalence of osteoporosis in patients with NTM-PD compared with that in the general population and determine the factors associated with osteoporosis in the subjects, including the serum estradiol (E2) and 25-hydroxyvitamin D (25OHD) levels.

Methods
We have recruited 228 consecutive adult patients with NTM-PD from a prospective cohort study at the Keio University Hospital, who had no history of osteoporosis or osteoporosis-associated bone fracture but underwent dual-energy X-ray absorptiometry-based bone mineral density (BMD) evaluation from August 2017–September 2019. The E2 and 25OHD levels were measured in 165 patients with available stored serum samples. We performed multivariable logistic regression analyses for osteopenia and osteoporosis.

Results
Osteoporosis (T-score ≤  − 2.5) and osteopenia (T-score − 1 to − 2.5) were diagnosed in 35.1% and 36.8% of patients with NTM-PD, respectively. Compared with the general population, the proportion of osteoporosis was significantly higher in 50–59-, 60–69-, and 70–79-year-old women with NTM-PD. Multivariable analysis revealed that older age (adjusted odds ratio [aOR] for 1-year increase = 1.12; 95% confidence interval [CI] = 1.07–1.18), female sex (aOR = 36.3; 95% CI = 7.57–174), lower BMI (aOR for 1 kg/m2 decrease = 1.37; 95% CI = 1.14–1.65), and chronic Pseudomonas aeruginosa (PA) infection (aOR = 6.70; 95% CI = 1.07–41.8) were independently associated with osteoporosis. Additionally, multivariable analysis in 165 patients whose serum E2 and 25OHD levels were measured showed that both low E2 levels (< 10 pg/mL) and lower 25OHD levels were independently associated with osteoporosis.

Conclusions
Middle-aged/elderly women with NTM-PD have a higher prevalence of osteoporosis than the general population. BMD screening should be considered in NTM-PD, especially in older females with severe diseases such as chronic PA infection and lower BMI, and low serum E2 and 25OHD levels.
Papillary muscle avulsion following balloon mitral valvotomy evaluated with three-dimensional echocardiography
Authors: Bai Wenjuan , Deng Ling , Tang Hong 
Published: May 2022

Abstract
Background
Percutaneous balloon mitral valvotomy is a common therapeutic approach for rheumatic mitral stenosis. Avulsion of the papillary muscle is a rare but serious complication of balloon mitral valvotomy. The papillary muscles are derived from the trabecular layer of the developing ventricular walls. When subjected to a force, avulsion of papillary muscle from the trabecular layer may occur.

Case presentation
In this case report, we describe a patient with rheumatic mitral stenosis, who experienced avulsion of the mitral papillary muscle from the left ventricular wall after undergoing balloon mitral valvotomy. Papillary muscle alvusion resulted in severe mitral regurgitation, which was finally treated by mitral valve replacement.

Conclusion
We successfully diagnosed avulsion of the papillary muscle following balloon mitral valvotomy. Three-dimensional transthoracic echocardiography provides more information on mitral apparatus structure than two-dimensional transthoracic echocardiography.
Piloting ‘Virtual Ward’: a novel platform for delivering medical student education by residents
Authors: Kappel Coralea , Hijazi Waseem , Singhal Nishma 
Published: May 2022

Abstract
Background
Clinical experiences lie at the heart of undergraduate medical education (UGME). COVID-19 related disruptions in Medical Education impacted medical students substantially. As educators, efforts directed at developing new mediums to educate our medical students in the face of these new limitations were vital. The Virtual Ward (VW) pilot was an inaugural resident-driven, virtual educational opportunity aimed at supplement the learning of core internal medicine skills for undergraduate medical students.

Methods
Interested medical students were paired in groups of 5–6 with an internal medicine resident tutor. The McMaster University UGME core internal medicine topic list was provided to resident tutors to teach in an open, morning-report format in which students directed content selection. Following completion of the VW series, we distributed an online anonymous survey using a 5-point Likert scale to gauge the efficacy of the intervention and compare it to existing learning modalities offered by the UGME.

Results
In total, 166 medical students and 27 internal medicine resident tutors participated in the VW pilot. 46 (28%) medical students responded to the survey and 96% of survey respondents rated the sessions as being helpful to their learning. The majority rated VW superior to existing learning modalities and 94% thought VW should continue after COVID-related restrictions abate.

Conclusions
VW is a novel educational platform that was very well received by learners. We propose VW may have a continued supplemental role post-pandemic to help with translation of knowledge to clinical skills and provide an additional avenue of mentorship for students.
Identification of individuals benefiting from the kakaritsuke-yakuzaishi (family pharmacist) system in Japan: a retrospective cohort study using an employment-based health insurance claims database
Authors: Iketani Ryo , Konomura Keiko 
Published: May 2022

Abstract
Background
The kakaritsuke-yakuzaishi system (henceforth, the family pharmacist system) which provides more health services than those by general pharmaceutical practice, was implemented in Japan in April 2016. To distribute medical resources and medical care expenditures appropriately, identifying the possible major beneficiaries of this system is essential. By analyzing administrative claims data through this retrospective cohort study, we identified modifiers of the potential benefits of the system. Further, we integrated the identified modifiers into a scoring system that indicates the possible benefitting subpopulations.

Methods
We obtained data about individuals under 75 years old routinely using community pharmacies in Japan from the JMDC database. We classified the individuals as users or non-users. We used claims related to “choufukutouyaku-sougosayoutou-boushi-kasan (additional therapeutic duplication and drug interaction [TDDI] prevention fees)” filed between April 2018 and March 2020, which indicate that individuals’ prescriptions were modified to adjust leftover drugs or to avoid TDDI as indicators of potential benefit. We estimated adjusted absolute risk differences and 95% confidence intervals for product terms using multiple generalized linear regression models. We included the factors whose 95% confidence interval lower limits did not reach 0 in the multiple logistic regression models for developing a scoring system.

Results
The eligible cohort included 162,340 individuals (1,214 users and 161,126 non-users). The leftover drugs adjustment significantly increased for individuals prescribed antidepressants. However, as only one modifier was identified, we did not develop a scoring system for the leftover drugs adjustment. For TDDI prevention, the following factors were included in the scoring system: being female, being prescribed ≥ 6 drug types, using ≥ 2 medical institutions, and being prescribed proton pump inhibitors, antibiotics, probiotics, or traditional Japanese herbal medicines. The developed scoring system for TDDI prevention scored “female” and “traditional Japanese herbal medicines prescription” factors higher than other factors.

Conclusions
Individuals who are female or prescribed traditional Japanese herbal medicines, or antidepressants may benefit significantly from the family pharmacist system.
APOBEC3 mutational signatures are associated with extensive and diverse genomic instability across multiple tumour types
Authors: Jakobsdottir G. Maria , Brewer Daniel S , Cooper Colin , Green Catherine , Wedge David C 
Published: May 2022

Abstract
Background
The APOBEC3 (apolipoprotein B mRNA editing enzyme catalytic polypeptide 3) family of cytidine deaminases is responsible for two mutational signatures (SBS2 and SBS13) found in cancer genomes. APOBEC3 enzymes are activated in response to viral infection, and have been associated with increased mutation burden and TP53 mutation. In addition to this, it has been suggested that APOBEC3 activity may be responsible for mutations that do not fall into the classical APOBEC3 signatures (SBS2 and SBS13), through generation of double strand breaks.Previous work has mainly focused on the effects of APOBEC3 within individual tumour types using exome sequencing data. Here, we use whole genome sequencing data from 2451 primary tumours from 39 different tumour types in the Pan-Cancer Analysis of Whole Genomes (PCAWG) data set to investigate the relationship between APOBEC3 and genomic instability (GI).

Results and conclusions
We found that the number of classical APOBEC3 signature mutations correlates with increased mutation burden across different tumour types. In addition, the number of APOBEC3 mutations is a significant predictor for six different measures of GI. Two GI measures (INDELs attributed to INDEL signatures ID6 and ID8) strongly suggest the occurrence and error prone repair of double strand breaks, and the relationship between APOBEC3 mutations and GI remains when SNVs attributed to kataegis are excluded.We provide evidence that supports a model of cancer genome evolution in which APOBEC3 acts as a causative factor in the development of diverse and widespread genomic instability through the generation of double strand breaks. This has important implications for treatment approaches for cancers that carry APOBEC3 mutations, and challenges the view that APOBECs only act opportunistically at sites of single stranded DNA.
Multiple metastases of androgen indifferent prostate cancer in the urinary tract: two case reports and a literature review
Authors: Masuda Tsukasa , Kosaka Takeo , Nakamura Kohei , Hongo Hiroshi , Yuge Kazuyuki , Nishihara Hiroshi , Oya Mototsugu 
Published: May 2022

Abstract
Background
Prostate cancer (PC) is mainly known to metastasize to bone, lung and liver, but isolated metastases of prostate cancer, including ductal carcinoma, in the urinary tract are very rare. We describe two patients with nodular masses in the urinary tract (the anterior urethra or the urinary bladder) that were found on cystoscopy during treatment of castration-resistant prostate cancer.

Case presentation
In both cases, the pathological diagnosis from transurethral tumor resection showed that they were androgen indifferent prostate cancer (AIPC), including aggressive variant prostate cancer (AVPC) in Case 1 and treatment-induced neuroendocrine differentiation prostate cancer (NEPC) in Case 2. In Case 1, Loss of genetic heterozygosity (LOH) of BRCA2 and gene amplification of KRAS was identified from the urethra polyps. In Case 2, homozygous deletion was observed in PTEN, and LOH without mutation was observed in RB1.

Conclusion
These are the first reports of two cases of urinary tract metastasis of AIPC.
Exome-wide analysis of copy number variation shows association of the human leukocyte antigen region with asthma in UK Biobank
Authors: Fawcett Katherine A. , Demidov German , Shrine Nick , Paynton Megan L. , Ossowski Stephan , Sayers Ian , Wain Louise V. , Hollox Edward J. 
Published: May 2022

Abstract
Background
The role of copy number variants (CNVs) in susceptibility to asthma is not well understood. This is, in part, due to the difficulty of accurately measuring CNVs in large enough sample sizes to detect associations. The recent availability of whole-exome sequencing (WES) in large biobank studies provides an unprecedented opportunity to study the role of CNVs in asthma.

Methods
We called common CNVs in 49,953 individuals in the first release of UK Biobank WES using ClinCNV software. CNVs were tested for association with asthma in a stage 1 analysis comprising 7098 asthma cases and 36,578 controls from the first release of sequencing data. Nominally-associated CNVs were then meta-analysed in stage 2 with an additional 17,280 asthma cases and 115,562 controls from the second release of UK Biobank exome sequencing, followed by validation and fine-mapping.

Results
Five of 189 CNVs were associated with asthma in stage 2, including a deletion overlapping the HLA-DQA1 and HLA-DQB1 genes, a duplication of CHROMR/PRKRA, deletions within MUC22 and TAP2, and a duplication in FBRSL1. The HLA-DQA1, HLA-DQB1, MUC22 and TAP2 genes all reside within the human leukocyte antigen (HLA) region on chromosome 6. In silico analyses demonstrated that the deletion overlapping HLA-DQA1 and HLA-DQB1 is likely to be an artefact arising from under-mapping of reads from non-reference HLA haplotypes, and that the CHROMR/PRKRA and FBRSL1 duplications represent presence/absence of pseudogenes within the HLA region. Bayesian fine-mapping of the HLA region suggested that there are two independent asthma association signals. The variants with the largest posterior inclusion probability in the two credible sets were an amino acid change in HLA-DQB1 (glutamine to histidine at residue 253) and a multi-allelic amino acid change in HLA-DRB1 (presence/absence of serine, glycine or leucine at residue 11).

Conclusions
At least two independent loci characterised by amino acid changes in the HLA-DQA1, HLA-DQB1 and HLA-DRB1 genes are likely to account for association of SNPs and CNVs in this region with asthma. The high divergence of haplotypes in the HLA can give rise to spurious CNVs, providing an important, cautionary tale for future large-scale analyses of sequencing data.
The autonomic balance of heart rhythm complexity after renal artery denervation: insight from entropy of entropy and average entropy analysis
Authors: Lin Po-Lin , Lin Ping-Yen , Huang Han-Ping , Vaezi Hamideh , Liu Lawrence Yu-Min , Lee Ying-Hsiang , Huang Chun-Che , Yang Ten-Fang , Hsu Long , Hsu Chang Francis 
Published: May 2022

AbstractBackgroundThe current method to evaluate the autonomic balance after renal denervation (RDN) relies on heart rate variability (HRV). However, parameters of HRV were not always predictive of response to RDN. Therefore, the complexity and disorder of heart rhythm, measured by entropy of entropy (EoE) and average entropy (AE), have been used to analyze autonomic dysfunction. This study evaluated the dynamic changes in autonomic status after RDN via EoE and AE analysis.MethodsFive patients were prospectively enrolled in the Global SYMPLICITY Registry from 2020 to 2021. 24-h Holter and ambulatory blood pressure monitoring (ABPM) was performed at baseline and 3 months after RDN procedures. The autonomic status was analyzed using the entropy-based AE and EoE analysis and the conventional HRV-based low frequency (LF), high frequency (HF), and LF/HF.ResultsAfter RDN, the ABPM of all patients showed a significant reduction in blood pressure (BP) and heart rate. Only AE and HF values of all patients had consistent changes after RDN (p < 0.05). The spearman rank-order correlation coefficient of AE vs. HF was 0.86, but AE had a lower coefficient of variation than HF.ConclusionsMonitoring the AE and EoE analysis could be an alternative to interpreting autonomic status. In addition, a relative change of autonomic tone, especially an increasing parasympathetic activity, could restore autonomic balance after RDN.
P-selectin glycoprotein ligand-1 (PSGL-1/CD162) is incorporated into clinical HIV-1 isolates and can mediate virus capture and subsequent transfer to permissive cells
Authors: Burnie Jonathan , Persaud Arvin Tejnarine , Thaya Laxshaginee , Liu Qingbo , Miao Huiyi , Grabinsky Stephen , Norouzi Vanessa , Lusso Paolo , Tang Vera A. , Guzzo Christina 
Published: May 2022

Abstract
Background
P-selectin glycoprotein ligand-1 (PSGL-1/CD162) has been studied extensively for its role in mediating leukocyte rolling through interactions with its cognate receptor, P-selectin. Recently, PSGL-1 was identified as a novel HIV-1 host restriction factor, particularly when expressed at high levels in the HIV envelope. Importantly, while the potent antiviral activity of PSGL-1 has been clearly demonstrated in various complementary model systems, the breadth of PSGL-1 incorporation across genetically diverse viral isolates and clinical isolates has yet to be described. Additionally, the biological activity of virion-incorporated PSGL-1 has also yet to be shown.

Results
Herein we assessed the levels of PSGL-1 on viruses produced through transfection with various amounts of PSGL-1 plasmid DNA (0–250 ng), compared to levels of PSGL-1 on viruses produced through infection of T cell lines and primary PBMC. We found that very low levels of PSGL-1 plasmid DNA (< 2.5 ng/well) were necessary to generate virus models that could closely mirror the phenotype of viruses produced via infection of T cells and PBMC. Unique to this study, we show that PSGL-1 is incorporated in a broad range of HIV-1 and SIV isolates and that virions with incorporated PSGL-1 are detectable in plasma from viremic HIV-1-infected individuals, corroborating the relevance of PSGL-1 in natural infection. Additionally, we show that PSGL-1 on viruses can bind its cognate selectin receptors, P-, E-, and L-selectins. Finally, we show viruses with endogenous levels of PSGL-1 can be captured by P-selectin and transferred to HIV-permissive bystander cells, highlighting a novel role for PSGL-1 in HIV-1 infection. Notably, viruses which contained high levels of PSGL-1 were noninfectious in our hands, in line with previous findings reporting the potent antiviral activity of PSGL-1.

Conclusions
Our results indicate that levels of PSGL-1 incorporation into virions can vary widely among model systems tested, and that careful tailoring of plasmid levels is required to recapitulate physiological systems when using pseudovirus models. Taken together, our data suggest that PSGL-1 may play diverse roles in the physiology of HIV-1 infection, particularly due to the functionally active state of PSGL-1 on virion surfaces and the breadth of PSGL-1 incorporation among a wide range of viral isolates.
Neutralizing antibody and T cell responses against SARS-CoV-2 variants of concern following ChAdOx-1 or BNT162b2 boosting in the elderly previously immunized with CoronaVac vaccine
Authors: Liwsrisakun Chalerm , Pata Supansa , Laopajon Witida , Takheaw Nuchjira , Chaiwong Warawut , Inchai Juthamas , Pothirat Chaicharn , Bumroongkit Chaiwat , Deesomchok Athavudh , Theerakittikul Theerakorn , Limsukon Atikun , Tajarernmuang Pattraporn , Niyatiwatchanchai Nutchanok , Trongtrakul Konlawij , Chuensirikulchai Kantinan , Kasinrerk Watchara 
Published: May 2022

AbstractBackgroundThe existence of SARS-CoV-2 variants of concern (VOCs) in association with evidence of breakthrough infections despite vaccination resulted in the need for vaccine boosting. In elderly individuals, information on the immunogenicity of booster vaccinations is limited. In countries where the CoronaVac inactivated vaccine is the primary vaccine, the appropriate boosting regimen is not clear. Immunologic studies of the effects of booster vaccination against VOCs, particularly Delta and Omicron, following CoronaVac in elderly individuals are helpful for policy makers. In this study, we determined the immune responses against VOCs following ChAdOx-1 or BNT162b2 boosting in elderly individuals previously immunized with CoronaVac.ResultsBefore boosting, the median % inhibition of neutralizing antibodies (NAbs) against the wild-type (WT), Alpha, Beta, Delta and Omicron variants in the ChAdOx-1 and BNT162b2 groups was 52.8% vs. 53.4, 36.6% vs. 39.9, 5.2% vs. 13.7, 34.3% vs. 44.9, and 20.8% vs. 18.8%, respectively. After boosting with ChAdOx-1 or BNT162b2, the % inhibition of NAbs were increased to 97.3% vs. 97.4, 94.3% vs. 97.3%, 79.9 vs. 93.7, 95.5% vs. 97.5, and 26.9% vs. 31.9% for WT, Alpha, Beta, Delta and Omicron variants, respectively. Boosting with BNT162b2 induced significantly higher NAb levels than boosting with ChAdOx-1 against the Alpha, Beta and Delta variants but not the WT and Omicron variants. NAb levels against Omicron variant were not significantly different before and after boosting with ChAdOx-1 or BNT162b2. To evaluate T-cell responses, S peptides of the WT, Alpha, Beta and Delta variants were used to stimulate T cells. Upon stimulation, the expression of IL-17A in CD8 T cells was higher in the BNT162b2 group than in the ChAdOx-1 boosting group. However, IFN-γ production in CD4 and CD8 T cells did not significantly differ under all vaccination regimens. The expression of FasL in CD4 T cells, but not CD8 T cells, was higher in the BNT162b2-boosted group.ConclusionBoosting with either ChAdOx-1 or BNT162b2 in CoronaVac-primed healthy elderly individuals induced high NAb production against all examined VOCs except Omicron. BNT162b2 stimulated higher NAb and some T-cell responses than ChAdOx-1. Vaccine boosting is, therefore, recommended for elderly individuals previously immunized with CoronaVac.