bluuebunny/crossref_metadata_2025_split huggingface dataset:
At-home Disease Monitoring by Patient-performed Intestinal Ultrasound in Severe Ulcerative Colitis
Authors: Krugliak Cleveland Noa , Miyatani Yusuke , Picker Emma A , Rubin David T 
Published: October 2023

Lay Summary
We describe the first reported case of a nonmedically trained patient using a handheld ultrasound device to monitor his ulcerative colitis in real time at home during induction therapy for severe colitis.
Clinical and Endoscopic Outcomes Through 78 Weeks of Tofacitinib Therapy for Ulcerative Colitis in a US Cohort
Authors: Dalal Rahul S , Sharma Puza P , Bains Kanwal , Pruce Jordan C , Allegretti Jessica R 
Published: October 2023

Abstract

Background
Tofacitinib is an oral JAK inhibitor for the treatment of ulcerative colitis (UC). We assessed outcomes through 78 weeks of tofacitinib therapy for UC in a real-world setting.

Methods
This retrospective cohort study included adults initiating tofacitinib for UC from May 1, 2018, to April 1, 2021, at a large academic center in the United States. The primary outcome was steroid-free clinical remission at 78 (+/-4) weeks (SFCR 78; simple clinical colitis activity index ≤2 with no corticosteroid use within 30 days). The secondary outcome was tofacitinib discontinuation due to nonresponse (treatment persistence). Additional outcomes were endoscopic response/remission and adverse events (AEs).

Results
Seventy-three patients initiated tofacitinib, with a median follow-up of 88 weeks. Among patients with available data, 31 of 60 (51.7%) achieved SFCR 78, 21 of 47 (44.7%) achieved endoscopic remission during follow-up, and 25 of 73 (34.2%) discontinued tofacitinib during follow-up due to nonresponse (including 11 patients who required colectomy). Nineteen AEs were reported among 15 patients during follow-up: shingles (n = 4, all without documented vaccinations), deep venous thrombosis (n = 2), elevated liver enzymes (n = 2), skin abscess (n = 2), pneumonia (n = 2), possible miscarriage (n = 2), norovirus (n = 1), COVID-19 (n = 1), lymphopenia (n = 1), Clostridioides difficile infection (n = 1), and heart block (n = 1). One patient discontinued therapy due to an AE (elevated liver enzymes), and no deaths occurred.

Conclusion
Tofacitinib treatment was effective in achieving SFCR for the majority of patients with UC through 78 weeks. Adverse events were consistent with the known safety profile of tofacitinib, and AEs requiring discontinuation were rare. Due to limitations regarding sample size, larger studies are needed to confirm these findings.
Waterpipe tobacco smoking and risk of all-cause mortality: a prospective cohort study
Authors: Le Phuoc Hong , Van Phan Can , Truong Dung Thuy Thi , Ho Nguyet Minh , Shuyna Ikeda , Le Ngoan Tran 
Published: October 2023

Abstract

Background
Despite an increasing proportion of smokers who use non-cigarette products, the harmfulness of these is inconsistent. This study aimed to evaluate the impact of waterpipe tobacco (WTP) smoking on all-cause mortality.

Methods
A prospective cohort study followed up on 35 646 participants from 2007 to 2019 in Northern Viet Nam. Data for each type of cigarette and WTP smoking were collected based on demographic lifestyle and semi-quantitative food frequency questionnaires. Smokers were categorized as current smokers and former smokers who were lifetime ever smokers but stopped smoking &gt;6 months before the interview. Data on all-cause mortality (2449 deaths) were obtained from medical records at the state health facilities. The hazard ratios (HRs) and 95% CIs for mortality were estimated using a Cox proportional-hazards model.

Results
Compared with non-smokers, ever smokers had a higher all-cause mortality risk (HR = 1.29, 95% CI = 1.16–1.43). Current WTP (HR = 1.37, 95% CI = 1.19–1.57), current cigarette (HR = 1.40, 95% CI = 1.22–1.60) and former WTP smokers (HR = 1.39, 95% CI = 1.10–1.76) showed an elevated risk of dying. The mortality risk was significantly elevated in dual smokers using WTP and cigarettes (HR = 1.55, 95% CI = 1.35–1.79) and exclusive WTP smokers (HR = 1.38, 95% CI = 1.21–1.57). Elevated risk was observed for the main targeted attractions of cancer, diabetes and heart diseases. Smoking cessation of &gt;10 years decreased the risk of all-cause mortality (HR = 0.61, 95% CI = 0.44–0.85) and cancer (HR = 0.24, 95% CI = 0.11–0.52).

Conclusions
WTP smoking increases the risk of all-cause mortality. A unique programme to control exposure to WTP should be a high priority in Viet Nam and other countries.
The Evolution of Mobile Phone Surveys in Low- and Middle-Income Countries: A Study of Coverage Structure
Authors: Elkasabi Mahmoud , Khan Azam 
Published: October 2023

Abstract
Mobile phone interviews are becoming an increasingly appealing mode of data collection in low- and middle-income countries. Therefore, we used data from 36 countries to examine mobile phone coverage of adults aged 15–49 years. We paid special attention to the (1) coverage rate (percentage of individuals who own at least one mobile phone) versus penetration rate (mobile phone subscriptions per 100 inhabitants), and (2) proxy-covered population (i.e., persons who do not own mobile phones but are potentially accessible through devices owned by other household members). Study findings suggest that (1) penetration rates notably overestimate mobile phone coverage of the population; (2) mobile phone coverage structure varies substantially; (3) mobile phone owners are more likely to be males, urban residents, literate, married, and relatively wealthy; and (4) proxy-covered adults are distinct with regard to demographic characteristics and survey outcomes in comparison to directly covered and not-covered adults. This study informs practitioners about the current coverage structure in several low- and middle-income countries and promotes proper procedures for studying coverage structure before implementing mobile phone interviews in those countries. Finally, this study introduces the term proxy-coverage and advocates for approaching the proxy-covered population to reduce noncoverage bias, especially in settings where mobile phone sharing among family members is common.
Female pond bats hunt in other areas than males and consume lighter prey when pregnant
Authors: Haarsma Anne-Jifke , Jongejans Eelke , Duijm Elza , van der Graaf Carolien , Lammers Youri , Sharma Milan , Siepel Henk , Gravendeel Barbara 
Published: October 2023

Abstract
Animals with large energy requirements are forced to optimize their hunting strategy, which may result in differentiation of the diet between sexes and across seasons. Here, we examined spatiotemporal variation in the diet of both sexes of the Pond Bat Myotis dasycneme, a species known to have spatial segregation of sexes when the young are born and lactating. Fecal pellets were collected from live animals for a period of 15 years at various locations in the Netherlands. A total of 535 pellets were successfully analyzed by microscopy and an additional 160 pellets by DNA metabarcoding. Morphological and molecular analyses showed that the diet of pregnant and lactating pond bats differed significantly from the diet of females with no reproductive investment. Further analyses of the data showed that pregnant female pond bats are highly dependent on small prey and pupae, mainly nonbiting midges and mosquitoes (Diptera: Chironomidae and Culicidae). These insects can be found in large quantities in peatlands intersected with shallow waterways, the habitat type in which female pond bats were observed more often than males. Our results suggest that during pregnancy the spatial segregation of sexes coincides with sex-specific diets, which might reflect habitat selection based on energy requirements, in addition to lowered intraspecific competition.
OrthoMaM v12: a database of curated single-copy ortholog alignments and trees to study mammalian evolutionary genomics
Authors: Allio Rémi , Delsuc Frédéric , Belkhir Khalid , Douzery Emmanuel J P , Ranwez Vincent , Scornavacca Céline 
Published: October 2023

AbstractTo date, the databases built to gather information on gene orthology do not provide end-users with descriptors of the molecular evolution information and phylogenetic pattern of these orthologues. In this context, we developed OrthoMaM, a database of ORTHOlogous MAmmalian Markers describing the evolutionary dynamics of coding sequences in mammalian genomes. OrthoMaM version 12 includes 15,868 alignments of orthologous coding sequences (CDS) from the 190 complete mammalian genomes currently available. All annotations and 1-to-1 orthology assignments are based on NCBI. Orthologous CDS can be mined for potential informative markers at the different taxonomic levels of the mammalian tree. To this end, several evolutionary descriptors of DNA sequences are provided for querying purposes (e.g. base composition and relative substitution rate). The graphical web interface allows the user to easily browse and sort the results of combined queries. The corresponding multiple sequence alignments and ML trees, inferred using state-of-the art approaches, are available for download both at the nucleotide and amino acid levels. OrthoMaM v12 can be used by researchers interested either in reconstructing the phylogenetic relationships of mammalian taxa or in understanding the evolutionary dynamics of coding sequences in their genomes. OrthoMaM is available for browsing, querying and complete or filtered download at https://orthomam.mbb.cnrs.fr/.
Immunoprecipitation of RNA–DNA hybrid interacting proteins in Trypanosoma brucei reveals conserved and novel activities, including in the control of surface antigen expression needed for immune evasion by antigenic variation
Authors: Girasol Mark J , Briggs Emma M , Marques Catarina A , Batista José M , Beraldi Dario , Burchmore Richard , Lemgruber Leandro , McCulloch Richard 
Published: October 2023

Abstract
RNA–DNA hybrids are epigenetic features of genomes that provide a diverse and growing range of activities. Understanding of these functions has been informed by characterising the proteins that interact with the hybrids, but all such analyses have so far focused on mammals, meaning it is unclear if a similar spectrum of RNA–DNA hybrid interactors is found in other eukaryotes. The African trypanosome is a single-cell eukaryotic parasite of the Discoba grouping and displays substantial divergence in several aspects of core biology from its mammalian host. Here, we show that DNA–RNA hybrid immunoprecipitation coupled with mass spectrometry recovers 602 putative interactors in T. brucei mammal- and insect-infective cells, some providing activities also found in mammals and some lineage-specific. We demonstrate that loss of three factors, two putative helicases and a RAD51 paralogue, alters T. brucei nuclear RNA–DNA hybrid and DNA damage levels. Moreover, loss of each factor affects the operation of the parasite immune survival mechanism of antigenic variation. Thus, our work reveals the broad range of activities contributed by RNA–DNA hybrids to T. brucei biology, including new functions in host immune evasion as well as activities likely fundamental to eukaryotic genome function.
A rice variation map derived from 10 548 rice accessions reveals the importance of rare variants
Authors: Wang Tianyi , He Wenchuang , Li Xiaoxia , Zhang Chao , He Huiying , Yuan Qiaoling , Zhang Bin , Zhang Hong , Leng Yue , Wei Hua , Xu Qiang , Shi Chuanlin , Liu Xiangpei , Guo Mingliang , Wang Xianmeng , Chen Wu , Zhang Zhipeng , Yang Longbo , Lv Yang , Qian Hongge , Zhang Bintao , Yu Xiaoman , Liu Congcong , Cao Xinglan , Cui Yan , Zhang Qianqian , Dai Xiaofan , Guo Longbiao , Wang Yuexing , Zhou Yongfeng , Ruan Jue , Qian Qian , Shang Lianguang 
Published: October 2023

Abstract
Detailed knowledge of the genetic variations in diverse crop populations forms the basis for genetic crop improvement and gene functional studies. In the present study, we analyzed a large rice population with a total of 10 548 accessions to construct a rice super-population variation map (RSPVM), consisting of 54 378 986 single nucleotide polymorphisms, 11 119 947 insertion/deletion mutations and 184 736 presence/absence variations. Assessment of variation detection efficiency for different population sizes revealed a sharp increase of all types of variation as the population size increased and a gradual saturation of that after the population size reached 10 000. Variant frequency analysis indicated that ∼90% of the obtained variants were rare, and would therefore likely be difficult to detect in a relatively small population. Among the rare variants, only 2.7% were predicted to be deleterious. Population structure, genetic diversity and gene functional polymorphism of this large population were evaluated based on different subsets of RSPVM, demonstrating the great potential of RSPVM for use in downstream applications. Our study provides both a rich genetic basis for understanding natural rice variations and a powerful tool for exploiting great potential of rare variants in future rice research, including population genetics and functional genomics.
Engineering of cytosine base editors with DNA damage minimization and editing scope diversification
Authors: Yuan Bo , Zhang Shuqian , Song Liting , Chen Jinlong , Cao Jixin , Qiu Jiayi , Qiu Zilong , Chen Jingqi , Zhao Xing-Ming , Cheng Tian-Lin 
Published: October 2023

Abstract
Cytosine base editors (CBEs), which enable precise C-to-T substitutions, have been restricted by potential safety risks, including DNA off-target edits, RNA off-target edits and additional genotoxicity such as DNA damages induced by double-strand breaks (DSBs). Though DNA and RNA off-target edits have been ameliorated via various strategies, evaluation and minimization of DSB-associated DNA damage risks for most CBEs remain to be resolved. Here we demonstrate that YE1, an engineered CBE variant with minimized DNA and RNA off-target edits, could induce prominent DSB-associated DNA damage risks, manifested as γH2AX accumulation in human cells. We then perform deaminase engineering for two deaminases lamprey LjCDA1 and human APOBEC3A, and generate divergent CBE variants with eliminated DSB-associated DNA damage risks, in addition to minimized DNA/RNA off-target edits. Furthermore, the editing scopes and sequence preferences of APOBEC3A-derived CBEs could be further diversified by internal fusion strategy. Taken together, this study provides updated evaluation platform for DSB-associated DNA damage risks of CBEs and further generates a series of safer toolkits with diversified editing signatures to expand their applications.
RAD51 paralogs synergize with RAD51 to protect reversed forks from cellular nucleases
Authors: Guh Chia-Lun , Lei Kai-Hang , Chen Yi-An , Jiang Yi-Zhen , Chang Hao-Yen , Liaw Hungjiun , Li Hung-Wen , Yen Hsin-Yung , Chi Peter 
Published: October 2023

Abstract
Fork reversal is a conserved mechanism to prevent stalled replication forks from collapsing. Formation and protection of reversed forks are two crucial steps in ensuring fork integrity and stability. Five RAD51 paralogs, namely, RAD51B, RAD51C, RAD51D, XRCC2 and XRCC3, which share sequence and structural similarity to the recombinase RAD51, play poorly defined mechanistic roles in these processes. Here, using purified BCDX2 (RAD51BCD-XRCC2) and CX3 (RAD51C-XRCC3) complexes and in vitro reconstituted biochemical systems, we mechanistically dissect their functions in forming and protecting reversed forks. We show that both RAD51 paralog complexes lack fork reversal activities. Whereas CX3 exhibits modest fork protection activity, BCDX2 significantly synergizes with RAD51 to protect DNA against attack by the nucleases MRE11 and EXO1. DNA protection is contingent upon the ability of RAD51 to form a functional nucleoprotein filament on DNA. Collectively, our results provide evidence for a hitherto unknown function of RAD51 paralogs in synergizing with RAD51 nucleoprotein filament to prevent degradation of stressed replication forks.
Hypoxia-induced transcriptional stress is mediated by ROS-induced R-loops
Authors: Ma Tiffany S , Worth Katja R , Maher Conor , Ng Natalie , Beghè Chiara , Gromak Natalia , Rose Anna M , Hammond Ester M 
Published: October 2023

Abstract
Hypoxia is a common feature of solid tumors and is associated with poor patient prognosis, therapy resistance and metastasis. Radiobiological hypoxia (&lt;0.1% O2) is one of the few physiologically relevant stresses that activates both the replication stress/DNA damage response and the unfolded protein response. Recently, we found that hypoxia also leads to the robust accumulation of R-loops, which led us to question here both the mechanism and consequence of hypoxia-induced R-loops. Interestingly, we found that the mechanism of R-loop accumulation in hypoxia is dependent on non-DNA damaging levels of reactive oxygen species. We show that hypoxia-induced R-loops play a critical role in the transcriptional stress response, evidenced by the repression of ribosomal RNA synthesis and the translocation of nucleolin from the nucleolus into the nucleoplasm. Upon depletion of R-loops, we observed a rescue of both rRNA transcription and nucleolin translocation in hypoxia. Mechanistically, R-loops accumulate on the rDNA in hypoxia and promote the deposition of heterochromatic H3K9me2 which leads to the inhibition of Pol I-mediated transcription of rRNA. These data highlight a novel mechanistic insight into the hypoxia-induced transcriptional stress response through the ROS–R-loop–H3K9me2 axis. Overall, this study highlights the contribution of transcriptional stress to hypoxia-mediated tumorigenesis.
Identifying Perspectives on Physical Therapist Residency Program Goals: Hallmarks of Success and Excellence
Authors: Moore James G , Hartley Gregory W , Osborne Raine , Harrington Kendra L , Rapport Mary Jane 
Published: October 2023

Abstract

Objective
The purpose of this study was to describe common perspectives important to achieving excellence and success in physical therapist residency education programs.

Methods
Individuals with direct responsibility for creating and revising physical therapist residency program goals participated in a mixed-methods study using Q-methodology. They sorted 31 goal topics based on the level of importance for achieving excellence and success in physical therapist residency education. By-participant factor analysis identified dominant perspectives, which were interpreted based on emergent themes from the topics identified as the most important. Participants’ rationale for selecting goal topics as the most important were extracted from the post-survey.

Results
Seventy-three individuals responded, representing 9 of the 11 clinical residency areas of practice. Three main perspectives emerged: resident behaviors, resident achievements, and program attributes. One shared perspective emerged across all 3 factors that emphasized the residents’ ability to become self-regulated, lifelong learners who integrate learning into practice: preparation for future learning.

Conclusions
Variability in weighting the importance of program goals associated with each perspective may include a program’s organization and mission, individual beliefs and experiences related to program leadership, and resource availability. Although respondent emphasis placed importance of some items over others, the findings do not suggest that items ranked lower were unnecessary or unimportant in achieving program excellence. The relative importance of items was weighted differently based on the perspective of program leadership and the individual completing the sorting activity.

Impact
The results of this study suggest that physical therapist residency programs should have at least 1 or 2 goals in each of the 3 distinct perspectives, as well as the 1 shared perspective identified in our findings. Some consistency in program goals based on the perspectives identified here may enable further research exploring excellence, value, and outcomes in physical therapist residency education.
Development of a Polygenic Risk Score to Predict Diverticulitis
Authors: Schaeffer H. David , Smelser Diane T. , Rao H. Shanker , Haley Jeremy S. , Long Kevin C. , Slipak Sasha H. , Carey David J. , Hoffman Rebecca L. 
Published: October 2023

BACKGROUND:
Despite its prevalence and associated morbidity, we remain limited in our ability to predict the course of a patient with diverticular disease. While several clinical and genetic risk factors have been identified, we do not know how these factors relate to one another.

OBJECTIVE:
To determine if a polygenic risk score could improve risk prediction for diverticulitis and recurrent diverticulitis compared to a model using only clinical factors.

DESIGN:
An observational study.

SETTING:
Study examines the predictive ability of a polygenic risk score for diverticulitis developed using prior genome wide association studies and validated using the MyCode biobank.

PATIENTS:
Patients of European ancestry in the Geisinger Health System who were enrolled in the MyCode Community Health biobanking program.

MAIN OUTCOME MEASURES:
The ability of a polygenic risk score to predict diverticulosis, diverticulitis, and recurrent diverticulitis.

RESULTS:
A total of 60,861 patients were included, of which 9,912 (16.3%) had diverticulosis or diverticulitis (5,015 with diverticulosis and 4,897 with diverticulitis). When divided into deciles, our polygenic risk score stratified patients by risk of both diverticulosis and diverticulitis with a 2-fold difference in disease risk between the highest and lowest deciles for diverticulitis and a 4.8-fold difference for recurrent complicated diverticulitis. When compared to clinical factors alone, our polygenic risk score was able to improve risk prediction of recurrent diverticulitis.

LIMITATIONS:
Our population is largely located in a single geographic region and were classified by disease status using international classification of diseases codes.

CONCLUSIONS:
This predictive model stratifies patients based on genetic risk for diverticular disease. The increased frequency of recurrent disease in our high-risk patients suggests that a polygenic risk score, in addition to other factors, may help to guide the discussion regarding surgical intervention.
Mixed Dentition Period Follow-up of Primary Unilateral Cleft Nose Deformity Repair
Authors: Rossell-Perry Percy , Gavino-Gutierrez Arquimedes 
Published: October 2023

Background:
Recently, there has been an increased acceptance of the primary cleft rhinoplasty providing acceptable outcomes. Nose reconstruction, and specifically cleft nose deformity, should be addressed based on this philosophy. The purpose of this study was to evaluate surgical outcomes during the mixed dentition period after primary surgery to address unilateral cleft lip nose deformity based on the proposed technique.

Methods:
This is a retrospective cohort study. Thirty-two primary complete unilateral cleft lip patients were operated on by a single surgeon using the V-Y-Z cleft rhinoplasty. This method combines a composite V-Y advancement flap with lateral Z-plasty. Data collection was accomplished by evaluation of nasal symmetry through anthropometric measurements performed under general anesthesia during primary cleft palatoplasty and alveolar bone graft. The outcomes were evaluated through anthropometric measurements of the repaired nose during the mixed dentition period of follow-up, and no type of presurgical management was performed for any of the patients.

Results:
Total nasal symmetry has been observed in 34.37% of patients at 7 years or more and 40.62% at 1-year follow-up. Nonstatistically significant differences were observed during follow-up, and major revision requirement (>3 mm of asymmetry in any of the nose measurements) was observed in 9.37% of patients.

Conclusions:
The proposed primary cleft rhinoplasty is a good approach to improve nasal appearance in patients with complete unilateral cleft lip and palate.