bluuebunny/crossref_metadata_2025_split huggingface dataset:
HIV-1 integrase resistance associated mutations and the use of dolutegravir in Sub-Saharan Africa: A systematic review and meta-analysis
Authors: Ngoufack Jagni Semengue Ezechiel , Santoro Maria Mercedes , Ndze Valantine Ngum , Ka’e Aude Christelle , Yagai Bouba , Nka Alex Durand , Dambaya Beatrice , Takou Desiré , Teto Georges , Fabeni Lavinia , Colizzi Vittorio , Perno Carlo-Federico , Ceccherini-Silberstein Francesca , Fokam Joseph 
Published: October 2022

As sub-Saharan Africa (SSA) countries are transitioning to dolutegravir (DTG)-based ART, baseline data are required for optimal monitoring of therapeutic response. In this frame, we sought to generate up-to-date evidence on the use of integrase-strand transfer inhibitors (INSTI) and associated drug resistance mutations (DRMs) within SSA. In this systematic review and meta-analysis, we included randomized and non-randomized trials, cohort-studies, cross-sectional studies, and case-reports published on INSTI or integrase DRMs in SSA. We included studies of patients exposed to DTG, raltegravir (RAL) or elvitegravir (EVG). Primary outcomes were “the rate of virological control (VC:<50copies/ml)” and “the presence of DRMs” on INSTI-based regimens among patients in SSA. We synthesised extracted data using subgroup analysis, and random effect models were used where appropriate. Additional analyses were conducted to assess study heterogeneity. We identified 1,916 articles/citations through database searches, of which 26 were included in the analysis pertaining to 5,444 patients (mean age: 37±13 years), with 67.62% (3681/5444) female. Specifically, 46.15% (12/26) studies focused on DTG, 26.92% (7/26) on RAL, 23.08% (6/26) on both DTG and RAL, and 3.85% (1/26) on EVG. We found an increasing use of DTG overtime (0% before 2018 to 100% in 2021). Median treatment duration under INSTI-based regimens was 12 [9–36] months. Overall, the rate of VC was 88.51% [95%CI: 73.83–97.80] with DTG vs. 82.49% [95%CI: 55.76–99.45] and 96.55% [95%CI: 85.7–100.00] with RAL and EVG, respectively. In univariate analysis, VC with DTG-containing vs. other INSTI-regimens was significantly higher (OR = 1.44 [95%CI: 1.15–1.79], p = 0.0014). Among reported DRMs at failure, the only DTG resistance-mutations were G118R and R263K. In SSA, DTG presents a superiority effect in VC compared to other INSTIs. Nonetheless, the early detection of INSTI-DRMs calls for sentinel surveillance for a successful transition and a sustained efficacy of DTG in SSA.
PROSPERO Registration Number: CRD42019122424.
The burden of physical disability among patients with newly detected leprosy in Yunnan, China, 1990–2020: A population-based, cross-sectional survey
Authors: Chen Xiaohua , Shui Tie-Jun 
Published: October 2022

Background
Physical disability is the main complication of leprosy. Although understanding the leprosy rate, prevalence, spatiotemporal distribution, and physical nerve characteristic trends is crucial for the implementation of leprosy control programs and identification of remaining challenges, these data are still unclear. We assessed physical disability trends among newly detected leprosy cases over the past 31 years in 129 counties and territories in Yunnan, China.

Methodology/Principal findings
We analyzed the data of newly detected leprosy cases from the Leprosy Management Information System in Yunnan, China, from 1990–2020. All available data related to physical disability were analyzed, including demographic characteristics (sex, age, ethnicity, education level); clinical characteristics (diagnosis duration, detection mode, contact history, leprosy reaction, skin lesions, nerve lesions, disability classification); World Health Organization (WHO) leprosy physical disability indicators; and nerve and eyes, hands and feet (EHF) involvement. A total of 10758 newly diagnosed leprosy cases were identified, and 7328 (65.60%), 1179 (10.55%) and 2251 (20.15%) were associated with grade 0, 1, and 2 disability (G0D, G1D, and G2D), respectively. Male sex, older age, Han ethnicity, urban employment, a longer diagnosis duration, a contact history, greater nerve involvement, and tuberculoid-related forms of leprosy were associated with increased prevalence rates of physical disability. The rates of physical disability in newly detected leprosy cases per 1 million population decreased from 5.41, 2.83, and 8.24 in 1990 to 0.29, 0.25, and 0.54 per 1 million population in 2020, with decreases of 94.64%, 91.17%, and 93.44% in G2D, G1D and total physical disability (G1D + G2D) rates, respectively. In the same period, the proportions of G2D, G1D and total physical disability decreased from 28.02%, 14.65%, and 42.67% in 1990 to 10.08%, 11.76%, and 21.85% in 2020, with decreases of 64.03%, 19.73%, and 48.79%, respectively. Nerve thickening was more common than nerve tenderness, and claw hand, plantar insensitivity, and lagophthalmos were the most frequently reported EHF-related disabilities.

Conclusions
Despite general progress in reducing the prevalence of leprosy-related physical disability, the proportion of physical disability among leprosy disease remains high, especially in specific counties. This implies that leprosy cases are being detected at a later stage and that transmission in the community still exists. Further efforts focusing on early detection are crucial for leprosy control and the elimination of the disease burden.
Impact of vaccine pause due to Thrombosis with thrombocytopenia syndrome (TTS) following vaccination with the Ad26.COV2.S vaccine manufactured by Janssen/Johnson & Johnson on vaccine hesitancy and acceptance among the unvaccinated population
Authors: Salmon Daniel A. , Schuh Holly B. , Sargent Rikki H. , Konja Alexis , Harvey Steven A. , Laurie Shaelyn , Mai Brandy S. , Weakland Leo F. , Lavery James V. , Orenstein Walter A. , Breiman Robert F. 
Published: October 2022

Background
In response to reports of thrombosis with thrombocytopenia syndrome (TTS) post-vaccination, the Johnson & Johnson (J&J) vaccine was paused and then restarted in April 2021. Our objective was to assess whether this pause adversely impacted vaccine confidence.

Methods
Two large internet-based surveys were conducted in the US among adults to measure knowledge, attitudes and perceptions of the J&J vaccine pause and rates of vaccine hesitancy among unvaccinated persons before, during and after the pause.

Results
Among 66% of respondents aware of the pause, 44% identified blood clots as the reason for the pause without prompting. The impact of the pause on vaccine behavior among unvaccinated persons and perception of the vaccine safety system was mixed and modified by trust in the public health authorities. Those who were less willing to get vaccinated because of the pause were less inclined for all vaccines, not only the J&J product. Moreover, a notable proportion (22.1%) of the small number of persons (n = 30) vaccinated with the J&J vaccine after the pause reported not receiving information about the risk of TTS. The proportion of unvaccinated persons who were hesitant was increasing before and during the pause and then leveled off after the pause.

Conclusions
The J&J vaccine pause is unlikely to be a major barrier to vaccine uptake. Public attitudes about vaccines may be more resilient than appreciated, especially when safety issues are investigated with transparent communication. This paper has important implications for messaging and program administration with future vaccine-specific adverse events. Efforts may be warranted to ensure all persons being offered the J&J vaccine are made aware of the risk of TTS.
Circulating tumor necrosis factor receptors are associated with mortality and disease severity in COVID-19 patients
Authors: Gohda Tomohito , Murakoshi Maki , Suzuki Yusuke , Hiki Makoto , Naito Toshio , Takahashi Kazuhisa , Tabe Yoko 
Published: October 2022

Background
Although hyperinflammatory response influences the severity of coronavirus disease 2019 (COVID-19), little has been reported about the utility of tumor necrosis factor (TNF)-related biomarkers in reflecting the prognosis. We examined whether TNF receptors (TNFRs: TNFR1, TNFR2) and progranulin (PGRN) levels, in addition to interleukin 6 (IL-6) and C-reactive protein (CRP), are associated with mortality or disease severity in COVID-19 patients.

Methods
This retrospective study was conducted at Juntendo University Hospital. Eighty hospitalized patients with various severities of COVID-19 were enrolled. Furthermore, serum levels of TNF-related biomarkers were measured using enzyme-linked immunosorbent assay.

Results
Twenty-five patients died during hospitalization, and 55 were discharged. The median (25th and 75th percentiles) age of the study patients was 70 (61–76) years, 44 (55.0%) patients were males, and 26 (32.5%) patients had chronic kidney disease (CKD). When comparing with patients who received and did not receive treatment at the intensive care unit (ICU), the former had a higher tendency of being male and have diabetes, hypertension, and CKD; had higher levels of white blood cells, D-dimer, and lactate dehydrogenase; and had lower body mass index, estimated glomerular filtration rate, and lymphocyte counts. Significant differences were observed in TNFR, PGRN, IL-6, and CRP levels between each severity (mild–severe) group. Furthermore, the serum levels of TNFR, IL-6, and CRP, but not PGRN, in ICU patients were significantly higher than in the patients who were not admitted to the ICU. Multivariate logistic regression analysis demonstrated that high levels of TNFR2 were only associated with mortality in patients with COVID-19 even after adjustment for relevant clinical parameters.

Conclusions
High TNFR2 level might be helpful for predicting mortality or disease severity in patients with COVID-19.
Incidence of Pediatric Celiac Disease Varies by Region
Authors: Stahl Marisa , Li Qian , Lynch Kristian , Koletzko Sibylle , Mehta Pooja , Gragert Loren , Norris Jill M. , Andrén Aronsson Carin , Lindfors Katri , Kurppa Kalle , Ilonen Jorma , Krischer Jeffrey , Alkolkar Beena , Ziegler Anette-G , Toppari Jorma , Rewers Marian J. , Agardh Daniel , Hagopian William , Liu Edwin ,   the TEDDY Study Group
Published: October 2022

INTRODUCTION:
The Environmental Determinants of Diabetes in the Young study follows an HLA risk selected birth cohort for celiac disease (CD) development using a uniform protocol. Children under investigation come from 6 different regions within Europe and the United States. Our aim was to identify regional differences in CD autoimmunity and CD cumulative incidence for children born between 2004 and 2010.

METHODS:
Children (n = 6,628) with DQ2.5 and/or DQ8.1 were enrolled prospectively from birth in Georgia, Washington, Colorado, Finland, Germany, and Sweden. Children underwent periodic study screening for tissue transglutaminase antibodies and then CD evaluation per clinical care. Population-specific estimates were calculated by weighting the study-specific cumulative incidence with the population-specific haplogenotype frequencies obtained from large stem cell registries from each site.

RESULTS:
Individual haplogenotype risks for CD autoimmunity and CD varied by region and affected the cumulative incidence within that region. The CD incidence by age 10 years was highest in Swedish children at 3%. Within the United States, the incidence by age 10 years in Colorado was 2.4%. In the model adjusted for HLA, sex, and family history, Colorado children had a 2.5-fold higher risk of CD compared to Washington. Likewise, Swedish children had a 1.4-fold and 1.8-fold higher risk of CD compared with those in Finland and Germany, respectively.

DISCUSSION:
There is high regional variability in cumulative incidence of CD, which suggests differential environmental, genetic, and epigenetic influences even within the United States. The overall high incidence warrants a low threshold for screening and further research on region-specific CD triggers.
Capsule Endoscopy in the Diagnosis, Disease Mapping, and Monitoring of Treatment Response in Gastrointestinal Whipple's Disease
Authors: Davenport Emily , Mitsopoulos Grigorios , Stafford Nina , Sangwaiya Arvind , Shariq Sohail 
Published: October 2022

ABSTRACT
Whipple's disease is a rare systemic infection causing malabsorption. Affected patients often undergo extensive investigation until final diagnosis with periodic acid-Schiff-positive histology. We present the case of a 73-year-old man diagnosed with Whipple's disease after a prolonged history, with a focus on capsule endoscopy (CE) in both mapping the extent of the pathology and follow-up. We demonstrate pre-treatment and post-treatment CE images, allowing visualization of resolved small bowel pathology, and demonstrate histological resolution. The early use of CE in the investigation of Whipple's disease may expedite diagnosis in patients with more distal bowel pathology and help assess disease severity.
Use of a Second-Generation Irrigation Device May Shorten Time to Successful Inpatient Colonoscopy: A Case Series
Authors: Canakis Andrew , Guo Ling , Parsons David , Shah Hely , Jacobson Brian C. 
Published: October 2022

ABSTRACT
Inpatient bowel preparations are often inadequate, lengthening hospital stay and increasing costs. In this case series, we assessed whether a new irrigation device could shorten times to successful colonoscopy and hospital discharge. The device includes a disposable sleeve fitted over the colonoscope, delivering 4 streams of a pulsed air–water mixture to liquify stool, and contains 2 large-bore suction channels to evacuate fecal material. We present 6 inpatient colonoscopies where the device was used, demonstrating its utility in facilitating timely procedures and efficient patient care. Further study is required to determine whether the consistent use of the device can shorten time to successful inpatient colonoscopy.
The effects of task complexity on L2 English rapport-building language use and its relationship with paired speaking test task performance
Authors: Chen Tzu-Hua 
Published: October 2022

Abstract
Although task complexity effects on L2 oral production have been widely studied in teaching contexts, their application to task-based language assessment and pragmatic language use remains underexplored. Since pragmatic competence is part of effective communication and interactional abilities and is context-dependent, an investigation of the relationships among task complexity, pragmatic language use, and paired speaking test performance is needed. This study examined the effect of the resource-directing and resource-dispersing dimensions (the number of elements, causal reasoning demand, and planning time) of Robinson’s task complexity construct on fifty-two intermediate-level English as a Second Language (ESL) learners’ rapport-building language use during two decision-making tasks as the achievement test in an EAP program, and the relationships between rapport language use and three dimensions of paired speaking test performance: collaboration, task completion, and style. The results showed that frequency and variety of rapport-building language use did not significantly differ between the two tasks. However, the study found that only in the simple task did different types of rapport-building language have statistically significant positive or negative relationships with different dimensions of paired speaking test scores. Specifically, greeting language use had a strong or close to strong positive relationship with collaboration and style scores, whereas agreeing language had a strong negative relationship with collaboration scores. Additionally, thanking language had a strong negative association with task completion scores. The findings further suggest that task complexity effects learners’ production of rapport-building language in terms of alignment with their peer interlocutors and formality of style, and also impacts raters’ perceptions of paired speaking task performance. The findings highlight the importance of task effects, paired oral assessment rubrics development, and rapport-building language instruction.
Turnaround time prediction for clinical chemistry samples using machine learning
Authors: Tsai Eline R. , Demirtas Derya , Hoogendijk Nick , Tintu Andrei N. , Boucherie Richard J. 
Published: October 2022

Abstract

Objectives
Turnaround time (TAT) is an essential performance indicator of a medical diagnostic laboratory. Accurate TAT prediction is crucial for taking timely action in case of prolonged TAT and is important for efficient organization of healthcare. The objective was to develop a model to accurately predict TAT, focusing on the automated pre-analytical and analytical phase.

Methods
A total of 90,543 clinical chemistry samples from Erasmus MC were included and 39 features were analyzed, including priority level and workload in the different stages upon sample arrival. PyCaret was used to evaluate and compare multiple regression models, including the Extra Trees (ET) Regressor, Ridge Regression and K Neighbors Regressor, to determine the best model for TAT prediction. The relative residual and SHAP (SHapley Additive exPlanations) values were plotted for model evaluation.

Results
The regression-tree-based method ET Regressor performed best with an R2 of 0.63, a mean absolute error of 2.42 min and a mean absolute percentage error of 7.35%, where the average TAT was 30.09 min. Of the test set samples, 77% had a relative residual error of at most 10%. SHAP value analysis indicated that TAT was mainly influenced by the workload in pre-analysis upon sample arrival and the number of modules visited.

Conclusions
Accurate TAT predictions were attained with the ET Regressor and features with the biggest impact on TAT were identified, enabling the laboratory to take timely action in case of prolonged TAT and helping healthcare providers to improve planning of scarce resources to increase healthcare efficiency.
Estimates of lengths of shortest nonzero vectors in some lattices, II
Authors: Rybakov Alexander S. 
Published: October 2022

AbstractIn 1988, Friese et al. put forward lower estimates for the lengths of shortest nonzero vectors for “almost all” lattices of some families in the dimension 3. In 2004, the author of the present paper obtained a similar result for the dimension 4. Here by means of results obtained in part of the paper we show that these estimates also hold in the dimension 5.
Wooden Wax-Covered Writing Boards asVorlageforkudurruInscriptions in the Middle Babylonian Period
Authors: Zimmermann Lynn-Salammbô 
Published: October 2022

AbstractThe inscriptions on Middle Babyloniankudurrumonuments contain references to a certain type ofVorlage, wooden wax-covered writing boards. Thekudurrumonuments were erected in temples as (legal) proof of a royal land grant. In this article I explore three ways in which wooden wax-covered writing boards may have functioned as aVorlageforkudurruinscriptions. Wooden wax-covered writing boards may have served as aVorlagefor literary passages, as a draft for thekudurruinscription or as a writing material for land survey documents (possibly the Middle Babylonianammatudocuments). Firstly, parallels between the colophons ofkudurruinscriptions and first millennium literary and scholarly texts imply a shared scholarly practice in a temple context, in which wooden wax-covered writing boards were used as aVorlage. Secondly, the use of wooden wax-covered writing boards to draft monumental inscriptions is well attested in the 1st millennium BC. Thirdly, I propose that writing boards may have been used to record the land survey necessary for the royal land grant, since land surveys and ground plans were traditionally recorded on writing boards in Mesopotamia. Wooden wax-covered writing boards and wooden writing materials became more widespread in the Middle Babylonian period. The Middle Babylonian land survey document was calledammatudocument. Further, in this article I demonstrate that the equation of the Middle Babylonianammatudocument with the Old Babylonianṭuppi ummātim, a term for title deeds written on clay tablets, is problematic.
What exactly does an editor do?
Authors: Piller Ingrid 
Published: October 2022

Abstract
This final editorial by outgoing Multilingua editor Ingrid Piller provides a glimpse behind the scenes of academic publishing. The work of a journal editor falls into five broad areas: desk-rejecting; managing peer review; evaluating and assessing research; taking affirmative action; and solving problems and setting directions. This article provides a brief overview of what is involved in each area, and includes recommendations for improvement, both for the field and individual researchers.
Serum vitamin D receptor and fibroblast growth factor-23 levels in postmenopausal primary knee osteoarthritis patients
Authors: Yağmur Tekeli Feyza , Özgür Tekeli Seçkin , Köse Özkan 
Published: October 2022

Abstract

Objectives
The role of vitamin D in primary osteoarthritis (OA) has not been clarified yet. vitamin D receptor (VDR) and fibroblast growth factor-23 (FGF-23) are proteins that play an important role in the metabolism of vitamin D. In this preliminary study, we aimed to examine serum 25-(OH) vitamin D3, VDR, and FGF-23 levels in primary knee OA patients.

Methods
This study includes 60 post-menopausal women who were enrolled into two groups with primary knee OA (n=30, age range between 59.6 ± 5.7 years) and control (n=30, age range between 61.7 ± 6.3 years). Serum levels of 25-(OH) vitamin D3 were measured by chemiluminescence and serum VDR, and FGF-23 were measured by enzyme-linked immunosorbent assay methods.

Results
In knee OA group, serum levels of 25-(OH) vitamin D3 were significantly lower (p=0.033), and serum VDR and FGF-23 levels were significantly higher than those of the control group respectively (p=0.000 and p=0.006). Also, FGF-23 levels showed correlations with 25-(OH) vitamin D3, VDR, and calcium levels (p<0.05).

Conclusions
This is the first study showing a relationship between serum VDR and FGF-23 in knee OA patients. Extensive clinical studies are required to assess the applicability of these parameters in clinical practice.
Oxidative stress‐induced phosphorylation of JIP4 regulates lysosomal positioning in coordination with TRPML1 and ALG2
Authors: Sasazawa Yukiko , Souma Sanae , Furuya Norihiko , Miura Yoshiki , Kazuno Saiko , Kakuta Soichiro , Suzuki Ayami , Hashimoto Ryota , Hirawake‐Mogi Hiroko , Date Yuki , Imoto Masaya , Ueno Takashi , Kataura Tetsushi , Korolchuk Viktor I , Tsunemi Taiji , Hattori Nobutaka , Saiki Shinji 
Published: October 2022

AbstractRetrograde transport of lysosomes is recognised as a critical autophagy regulator. Here, we found that acrolein, an aldehyde that is significantly elevated in Parkinson's disease patient serum, enhances autophagy by promoting lysosomal clustering around the microtubule organising centre via a newly identified JIP4‐TRPML1‐ALG2 pathway. Phosphorylation of JIP4 at T217 by CaMK2G in response to Ca2+ fluxes tightly regulated this system. Increased vulnerability of JIP4 KO cells to acrolein indicated that lysosomal clustering and subsequent autophagy activation served as defence mechanisms against cytotoxicity of acrolein itself. Furthermore, the JIP4‐TRPML1‐ALG2 pathway was also activated by H2O2, indicating that this system acts as a broad mechanism of the oxidative stress response. Conversely, starvation‐induced lysosomal retrograde transport involved both the TMEM55B‐JIP4 and TRPML1‐ALG2 pathways in the absence of the JIP4 phosphorylation. Therefore, the phosphorylation status of JIP4 acts as a switch that controls the signalling pathways of lysosoma l distribution depending on the type of autophagy‐inducing signal.