bluuebunny/crossref_metadata_2025_split huggingface dataset:
Retrospective Study of Recurrence and Associated Factors of Type 2 Diabetes Treated at Adama General Hospital, Oromia, Ethiopia: A Comparison of Cox-PH and Shared Lognormal Frailty Models
Authors: Legesse Alemayehu 
Published: June 2022

Background. Recovery from type 2 diabetes is frequently recurrent, as a single patient may recover from more than one over time. The goal of this study was to know the recurrent event (time to recovery) and associated factors of type 2 diabetes in Adama General Hospital, Ethiopia, by comparing shared lognormal frailty and Cox-PH models. Methods. A retrospective analysis of 302 type 2 diabetic patients (01, 2011–01, and 2016) was considered. Descriptive statistics were used to summarize the study variables. The standard Cox-proportional hazards model and a shared lognormal frailty model have been compared. The latter model with a 95% significance level was fitted, variables with

P
value
<
0.
05

were considered significant, and the adjusted hazard ratio has been used to measure the strength of the risk. Results. About 56.6% of the patients recovered. The average recovery time was 33.53 (standard deviation, 20.404 ) weeks. Gender (adjusted HR = 1.168, 95% CI = (0.93, 1.46),

P
<
0.05

), family history (adjusted HR = 0.765, 95% CI = (0.59, 0.99),

P
<
0.05

), cholesterol level (adjusted HR = 0.738, 95% CI = (0.57, 0.96),

P
<
0.05

), alcohol use (adjusted HR = 0.698, 95% CI = (0.53, 0.92),

P
<
0.05

), and smoking cigarette (adjusted HR = 0.674, 95% CI = (0.51, 0.89),

P
<
0.05

) were statistically significant. The estimated frailty term’s variance was 0.426 (

P
value
=
0.
028

). Also, the author presents a comparison study for the same data by using a model selection criterion and suggests a better model (shared lognormal frailty model). Conclusion. Finally, the median recovery time was 30 weeks. Female patients had a better chance of recovery than male patients. A shared lognormal frailty model outperformed the Cox-PH model in fitting the data and controlling event interdependence. There was risk heterogeneity among patients. Positive family history, high cholesterol level, alcohol use, and smoking have an inverse relationship with the overall likelihood of the patients’ recovery time. Therefore, future improvement measures against type 2 DM recovery should take all events (for example, the first, second, and third recovery in this study) and these identified factors into account.
Interrogation of T Cell–enriched Tumors Reveals Prognostic and Immunotherapeutic Implications of Polyamine Metabolism
Authors: Harbison R. Alex , Pandey Rajeev , Considine Michael , Leone Robert D. , Murray-Stewart Tracy , Erbe Rossin , Mandal Raj , Burns Mark , Casero Robert A. , Seiwert Tanguy , Fakhry Carole , Pardoll Drew , Fertig Elana , Powell Jonathan D. 
Published: June 2022

Metabolic features of the tumor microenvironment (TME) antagonize antitumor immunity. We hypothesized that T cell–infiltrated (Thi) tumors with a known antigen should exhibit superior clinical outcomes, though some fare worse given unfavorable metabolic features leveraging T cell–infiltrated (Thi), human papillomavirus–related (HPV+) head and neck squamous cell carcinomas (HNSC) to test this hypothesis. Expression of 2,520 metabolic genes was analyzed among Thi HPV+ HNSCs stratified by high-risk molecular subtype. RNA sequencing (RNA-seq) data from The Cancer Genome Atlas (TCGA; 10 cancer types), single-cell RNA-seq data, and an immunotherapy-treated melanoma cohort were used to test the association between metabolic gene expression and clinical outcomes and contribution of tumor versus stromal cells to metabolic gene expression. Polyamine (PA) metabolism genes were overexpressed in high-risk, Thi HPV+ HNSCs. Genes involved in PA biosynthesis and transport were associated with T-cell infiltration, recurrent or persistent cancer, overall survival status, primary site, molecular subtype, and MYC genomic alterations. PA biogenesis gene sets were associated with tumor-intrinsic features while myeloid cells in HPV+ HNSCs were enriched in PA catabolism, regulatory, transport, putrescine, and spermidine gene set expression. PA gene set expression also correlated with IFNγ or cytotoxic T-cell single-sample gene set enrichment analysis (ssGSEA) scores across TCGA tumor types. PA transport ssGSEA scores were associated with poor survival whereas putrescine ssGSEA scores portended better survival for several tumor types. Thi melanomas enriched in PA synthesis or combined gene set expression exhibited worse anti-PD-1 responses. These data address hurdles to antitumor immunity warranting further investigation of divergent PA metabolism in the TME.Significance:Despite the presence of tumor-infiltrating lymphocytes and antigen, antitumor immunity is often insufficient in tumor control. We leverage HPV-related head and neck cancers to identify metabolic challenges to antitumor immune responses. PA metabolism is associated with tumor-intrinsic features while the myeloid compartment exhibits enriched PA regulatory gene expression.
Adult and neonate TSH blood spot reference intervals
Authors: Morris Thomas G , Layley Jonathan , Geevarghese Robin , Steele Lucille , Ssali Joshua , Mirzazadeh Mehdi 
Published: June 2022

Background: Neonatal congenital hypothyroidism screening is performed by measuring thyroid-stimulating hormone (TSH) in a dried blood spot (DBS) sample, whereas acquired hypothyroidism uses serum TSH. There is no established DBS TSH reference interval, but knowing this is useful, as some patients cannot tolerate venepuncture, so DBS collection is seen as an acceptable alternative. The aim of this study was to establish DBS TSH reference intervals in adults and neonates (day 5–8), and determine the relationship between serum and DBS TSH.Methods: Euthyroid adults, not on thyroid medication and with a normal haematocrit, were selected. If they had a paired lithium heparin sample, DBS were prepared by spotting 50 µL of whole blood onto filter paper. Dried blood spot TSH was measured using the PerkinElmer Neonatal hTSH kit on the GSP instrument and serum using the Abbott Architect assay. The relationship between DBS and serum TSH was analysed using Passing–Bablok regression and the adult DBS TSH reference interval calculated using transformed data. The neonatal reference interval was calculated from screening results using the non-parametric method.Results: Overall, 109 adult samples were included in the study (61 female). The Passing–Bablok regression was: DBS TSH = 0.68 × serum TSH + 0.07, and reference interval was 0.49–3.07 mU/L. The neonatal DBS reference interval was 0.40–4.10 mU/L from 8351 results.Conclusion: This study derived adult and neonate TSH DBS reference intervals using the GSP analyser and established the relationship between serum and DBS TSH. Knowing this information will allow for improved interpretation of DBS TSH results.
Nurse Practitioners Navigating the Consequences of Directives, Policies, and Recommendations Related to the COVID-19 Pandemic in Long-Term Care Homes
Authors: McGilton Katherine S. , Krassikova Alexandra , Wills Aria , Durante Vanessa , Yeung Lydia , Vellani Shirin , Sidani Souraya , Escrig-Pinol Astrid 
Published: June 2022

Objectives New models for the workforce are required in long-term care (LTC) homes, as was made evident during the Coronavirus Disease 2019 (COVID-19) pandemic. Nurse Practitioner (NP)-led models of care represent an effective solution. This study explored NPs’ roles in supporting LTC homes as changes in directives, policies, and recommendations related to COVID-19 were introduced. Design Qualitative exploratory study. Context Thirteen NPs working in LTC homes in Ontario, Canada. Methods Semi-structured interviews were conducted in March/April 2021. A five-step inductive thematic analysis was applied. Findings Analysis generated four themes: leading the COVID-19 vaccine rollout; promoting staff wellbeing related to COVID-19 fatigue; addressing complexities of new admissions; and negotiating evolving collaborative relationships. Conclusions Nurse practitioners were instrumental in supporting LTC homes through COVID-19 regulatory changes producing unintended consequences. The NPs’ leadership in transforming care is equally essential in LTC homes as in other established healthcare settings, such as primary and acute care.
Self-care practices and correlates among patients with type 2 diabetes in Eastern Ethiopia: A hospital-based cross-sectional study
Authors: Letta Shiferaw , Aga Fekadu , Assebe Yadeta Tesfaye , Geda Biftu , Dessie Yadeta 
Published: June 2022

Objective: This study investigated the level and correlates of self-care practices among patients with type 2 diabetes on follow-up in two public hospitals in Harar, Eastern Ethiopia. Methods: We conducted a hospital-based cross-sectional study on adult patients with type 2 diabetes, surveying diabetes self-care practices using a 15-item Summary of Diabetes Self-Care Activities. Responses ranged from 0 to 7 days, and a composite score was computed representing the mean days of diabetes self-care practices. A generalized Poisson regression model with robust variance was used. The association between the diabetes self-care practices and correlates was examined using the incidence rate ratio with a 95% confidence level. The statistical significance was set at a p value of ⩽0.05. Results: This study included 879 patients with type 2 diabetes. The overall mean (standard deviation) diabetes self-care practices were 3.7 ± 1.1 days out of the recommended 7 days, indicating low self-care practices. After controlling for other variables, tertiary educational level (incidence rate ratio = 1.06; 95% confidence interval: 1.01, 1.12), adequate diabetes knowledge (incidence rate ratio = 1.04; 95% confidence interval: 1.00, 1.08), moderate (incidence rate ratio = 1.07; 95% confidence interval: 1.02, 1.11) and high perceived self-efficacy (incidence rate ratio = 1.14; 95% confidence interval: 1.09, 1.13) (incidence rate ratio = 1.07; 95% confidence interval: 1.02, 1.11), high to marginal food security (incidence rate ratio = 1.13; 95% confidence interval: 1.03, 1.24), and receiving dietary advice (incidence rate ratio = 1.11; 95% confidence interval: 0.06, 1.15) were positively correlated with diabetes self-care practices. A history of hospitalization, on the other hand, was found to be inversely correlated with diabetes self-care practices (incidence rate ratio = 0.94; 95% confidence interval: 0.88, 0.99). Conclusion: The study indicated that adherence of patients with type 2 diabetes to the recommended self-care practices was considerably low. Therefore, tailored diabetes self-management education to enhance self-efficacy and diabetes self-care practices must be in place. This can be achieved through the system or individual-based integrated intervention efforts.
Attitudes toward safe abortion care and its associated factors among health care providers working in public health facilities in eastern Ethiopia
Authors: Balcha Tegenu , Semahegn Agumasie , Tamiru Dawit , Yadeta Elias , Abdisa Lemesa , Tesfaye Gezahegn 
Published: June 2022

Objectives: The main aim of this study was to assess health care providers’ attitudes toward safe abortion services and its associated factors in public health facilities of Harar city, Eastern Ethiopia. Methods: Facility-based cross-sectional study was conducted among 411 health care providers who were working at public health facilities in Harari regional state, in eastern Ethiopia. A simple random sampling technique was used to select study participants. Data were collected using self-administered questionnaires, and collected data were entered into EpiData version 4.6 and then exported to SPSS version 26 for cleaning and analysis. Descriptive statistics, bivariable, and multivariable logistic regression analysis were carried out to compute the prevalence of the outcome variables and to identify factors associated with the outcome variable, respectively. Adjusted odds ratio at 95% confidence interval and p-value < 0.05 was used to declare a significant association. Results: More than half (58.4%, 95% confidence interval: 53.8–63.2) of the health care providers had a favorable attitude toward safe abortion care. Being male (adjusted odds ratio = 2.90; 95% confidence interval: 1.80–4.65), ever trained on safe abortion (adjusted odds ratio = 2.55; 95% confidence interval: 1.39–4.66), familiarity with the current abortion law of Ethiopia (adjusted odds ratio = 2.38; 95% confidence interval: 1.40–4.05), preference of unrestricted abortion law (adjusted odds ratio = 1.86; 95% confidence interval: 1.15–3.02), and being medical doctors or health officers (adjusted odds ratio = 1.90; 95% confidence interval: 1.06–3.41) were the factors significantly associated with health care providers’ favorable attitude toward safe abortion care. Conclusion: Approximately three in five of the health care providers working at public health facilities had a favorable attitude toward safe abortion care in eastern Ethiopia. We suggest giving pre-service or in-service training on safe abortion care and supporting health care providers to be familiar with the country’s abortion laws are crucial to improve health care providers’ attitudes toward safe abortion service in Ethiopia.
Aberrant expansion of spontaneous splenic germinal centers induced by hallmark genetic lesions of aggressive lymphoma
Authors: Pindzola Grace M. , Razzaghi Raud , Tavory Rachel N. , Nguyen Hang T. , Morris Vivian M. , Li Moyi , Agarwal Shreya , Huang Bonnie , Okada Takaharu , Reinhardt Hans C. , Knittel Gero , Kashkar Hamid , Young Ryan M. , Pittaluga Stefania , Muppidi Jagan R. 
Published: June 2022

Abstract
Unique molecular vulnerabilities have been identified in the aggressive MCD/C5 genetic subclass of diffuse large B-cell lymphoma (DLBCL). However, the premalignant cell-of-origin exhibiting MCD-like dependencies remains elusive. In this study, we examined animals carrying up to 4 hallmark genetic lesions found in MCD consisting of gain-of-function mutations in Myd88 and Cd79b, loss of Prdm1, and overexpression of BCL2. We discovered that expression of combinations of these alleles in vivo promoted a cell-intrinsic accumulation of B cells in spontaneous splenic germinal centers (GCs). As with MCD, these premalignant B cells were enriched for B-cell receptors (BCRs) with evidence of self-reactivity, displayed a de novo dependence on Tlr9, and were more sensitive to inhibition of Bruton’s tyrosine kinase. Mutant spontaneous splenic GC B cells (GCB) showed increased proliferation and IRF4 expression. Mice carrying all 4 genetic lesions showed a &gt;50-fold expansion of spontaneous splenic GCs exhibiting aberrant histologic features with a dark zone immunophenotype and went on to develop DLBCL in the spleen with age. Thus, by combining multiple hallmark genetic alterations associated with MCD, our study identifies aberrant spontaneous splenic GCBs as a likely cell-of-origin for this aggressive genetic subtype of lymphoma.
Repeated inflammatory dural stimulation-induced cephalic allodynia causes alteration of gut microbial composition in rats
Authors: Miao Shuai , Tang Wenjing , Li Heng , Li Bozhi , Yang Chunxiao , Xie Wei , Wang Tao , Bai Wenhao , Gong Zihua , Dong Zhao , Yu Shengyuan 
Published: June 2022

Abstract
Background
Gut microbial dysbiosis and gut-brain axis dysfunction have been implicated in the pathophysiology of migraine. However, it is unclear whether migraine-related cephalic allodynia could induce the alteration of gut microbial composition.

Methods
A classic migraine rat model was established by repeated dural infusions of inflammatory soup (IS). Periorbital mechanical threshold and nociception-related behaviors were used to evaluate IS-induced cephalic allodynia and the preventive effect of topiramate. The alterations in gut microbial composition and potential metabolic pathways were investigated based on the results of 16 S rRNA gene sequencing. Microbiota-related short-chain fatty acids and tryptophan metabolites were detected and quantified by mass spectrometry analysis.

Results
Repeated dural IS infusions induced cephalic allodynia (decreased mechanical threshold), migraine-like behaviors (increased immobility time and reduced moving distance), and microbial composition alteration, which were ameliorated by the treatment of topiramate. Decreased Lactobacillus was the most prominent biomarker genus in the IS-induced alteration of microbial composition. Additionally, IS infusions also enhanced metabolic pathways of the gut microbiota in butanoate, propanoate, and tryptophan, while the increased tryptophan-related metabolites indole-3-acetamide and tryptophol in feces could be the indicators.

Conclusions
Inflammatory dural stimulation-induced cephalic allodynia causes the alterations of gut microbiota profile and microbial metabolic pathways.
Transcriptomic analysis of tuberous root in two sweet potato varieties reveals the important genes and regulatory pathways in tuberous root development
Authors: Cai Zhaoqin , Cai Zhipeng , Huang Jingli , Wang Aiqin , Ntambiyukuri Aaron , Chen Bimei , Zheng Ganghui , Li Huifeng , Huang Yongmei , Zhan Jie , Xiao Dong , He Longfei 
Published: June 2022

AbstractBackgroundTuberous root formation and development is a complex process in sweet potato, which is regulated by multiple genes and environmental factors. However, the regulatory mechanism of tuberous root development is unclear.ResultsIn this study, the transcriptome of fibrous roots (R0) and tuberous roots in three developmental stages (Rl, R2, R3) were analyzed in two sweet potato varieties, GJS-8 and XGH. A total of 22,914 and 24,446 differentially expressed genes (DEGs) were identified in GJS-8 and XGH respectively, 15,920 differential genes were shared by GJS-8 and XGH. KEGG pathway enrichment analysis showed that the DEGs shared by GJS-8 and XGH were mainly involved in “plant hormone signal transduction” “starch and sucrose metabolism” and “MAPK signal transduction”. Trihelix transcription factor (Tai6.25300) was found to be closely related to tuberous root enlargement by the comprehensive analysis of these DEGs and weighted gene co-expression network analysis (WGCNA).ConclusionA hypothetical model of genetic regulatory network for tuberous root development of sweet potato is proposed, which emphasizes that some specific signal transduction pathways like “plant hormone signal transduction” “Ca2+signal” “MAPK signal transduction” and metabolic processes including “starch and sucrose metabolism” and “cell cycle and cell wall metabolism” are related to tuberous root development in sweet potato. These results provide new insights into the molecular mechanism of tuberous root development in sweet potato.
Genomic characterization of Streptococcus parasuis, a close relative of Streptococcus suis and also a potential opportunistic zoonotic pathogen
Authors: Guo Genglin , Wang Zhuohao , Li Quan , Yu Yanfei , Li Yubao , Tan Zhongming , Zhang Wei 
Published: June 2022

AbstractStreptococcus parasuis (S. parasuis) is a close relative of Streptococcus suis (S. suis), composed of former members of S. suis serotypes 20, 22 and 26. S. parasuis could infect pigs and cows, and recently, human infection cases have been reported, making S. parasuis a potential opportunistic zoonotic pathogen. In this study, we analysed the genomic characteristics of S. parasuis, using pan-genome analysis, and compare some phenotypic determinants such as capsular polysaccharide, integrative conjugative elements, CRISPR-Cas system and pili, and predicted the potential virulence genes by associated analysis of the clinical condition of isolated source animals and genotypes. Furthermore, to discuss the relationship with S. suis, we compared these characteristics of S. parasuis with those of S. suis. We found that the characteristics of S. parasuis are similar to those of S. suis, both of them have “open” pan-genome, their antimicrobial resistance gene profiles are similar and a srtF pilus cluster of S. suis was identified in S. parasuis genome. But S. parasuis still have its unique characteristics, two novel pilus clusters are and three different type CRISPR-Cas system were found. Therefore, this study provides novel insights into the interspecific and intraspecific genetic characteristics of S. parasuis, which can be useful for further study of this opportunistic pathogen, such as serotyping, diagnostics, vaccine development, and study of the pathogenesis mechanism.
VisProDom: an interactive Shiny/R application for displaying protein domains with transcriptional features
Authors: Wang Hongwei , Zhang Xiaotian , Ding Shuangcheng , Huang Yujie , Wang Shengyong , Chen Huili , Chen Yuhang , Li Yuting 
Published: June 2022

Abstract
Background
Both the protein domains and transcript structures influence protein functional variation. The genomic location of both protein domains and transcript structural features can be described using the genomic coordinates of their encoded sequences. However, the coordinates of protein domains and transcriptional features often differ greatly, and it is difficult to view them in combination at the genome-wide level. In this paper, we describe the development of a new tool that allows users to visualize domains and transcript features together, using either built-in or uploaded genome datasets, and export publication-ready figures.

Results
We developed a user-friendly, independent R package and Shiny web application named “VisProDom”. VisProDom consists of a genome-wide database containing entire annotated transcripts merged with annotated protein domains from the Pfam database. The built-in dataset includes 82 files, which merge genome general feature format (GFF) annotations with rpsblast tabular outputs from protein sequence searches in the Pfam database. Multiple genomes can be simultaneously screened for protein domains or transcript names. VisProDom includes step-by-step introductions and clickable elements for ease of use.

Conclusion
VisProDom can display hundreds of transcripts alongside protein domains and export figures in a publication-ready format. This makes it a valuable tool for molecular evolution and comparative genomics.