bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prognostic variations between “primary” and “progressive” muscle-invasive bladder cancer following radical cystectomy: A novel propensity score-based multicenter cohort study
Authors: Lai Shicong , Liu Jianyong , Lai Chinhui , Seery Samuel , Hu Haopu , Wang Mingrui , Hu Hao , Xu Tao 
Published: September 2023

Objective:
To assess prognostic differences between primary and progressive muscle-invasive bladder cancer (MIBC) following radical cystectomy.

Material and methods:
The Surveillance, Epidemiology, and End Results (SEER) database was used to abstract MIBC data following radical cystectomy from 2000-2019. Patients were classified as either ‘Primary’ MIBC (defined as the presentation of muscle-invasive disease at initial diagnosis) or ‘Progressive’ MIBC (defined as a non-muscle invasive disease that later progressed to MIBC). Baseline characteristics for the two groups were balanced using a propensity score overlap weight (PSOW) technique. Survival differences between the two groups were analyzed using Kaplan-Meier’s plots and log-rank tests. Cox’s proportional hazard regression was used to assess risk factors associated with overall survival (OS) and cancer-specific survival (CSS).

Results:
6,632 MIBC patients were identified in the SEER database. Among them, 83.3% (n=5,658) were considered primary MIBC patients, and 16.7% (n=974) were categorized as progressive MIBC patients. Distribution of baseline covariates, including age, sex, race, T stage, N stage, tumor grade, marital status, and chemotherapy, were well-balanced after PSOWs were applied. After stable PSOW adjustments, Kaplan-Meier survival analysis showed that the CSS for progressive MIBC (hazard ratio [HR]=1.25, 95% confidence interval [CI]: 1.12-1.38, P<0.001) was poorer than the primary MIBC group. However, the difference in OS (HR=1.08, 95%CI: 0.99-1.18) was not significant (P=0.073). Multivariate analysis also suggested that patients with progressive MIBC have significantly poorer CSS (HR=1.24, 95%CI: 1.19-1.38, P<0.001) but not OS (HR=1.08, 95%CI: 0.99-1.18, P=0.089).

Conclusion:
CSS for progressive MIBC patients appears worse than for those with primary MIBC. This highlights the need to direct more resources for this patient population and particularly for high-risk cases of non-NMIBC, where timely radical surgery will improve patients prognoses.
The value of total caudate lobe resection for hilar cholangiocarcinoma
Authors: Wang Da , Xiong Fei , Wu Guanhua , Wang Qi , Chen Junsheng , Liu Wenzheng , Wang Bing , Chen Yongjun 
Published: September 2023

Hilar cholangiocarcinoma is widely considered to have poor prognosis. In particular, combined caudate lobe resection (CLR) as a strategy for radical resection in hilar cholangiocarcinoma is important for improving the R0 resection rate. However, the criteria for R0 resection, necessity of CLR, optimal extent of hepatic resection, and surgical approach are still controversial. This review aimed to summarize the findings and discuss the controversies surrounding caudate lobe resection. Numerous clinical studies have shown that combined CLR treatment for hilar cholangiocarcinoma improves the R0 resection rate and postoperative survival time. Whether surgery for Bismuth type I or II is combined with CLR depends on the pathological type. Considering the anatomical factors, total rather than partial caudate lobe resection is recommended to achieve a higher R0 resection rate. In the resection of hilar cholangiocarcinoma, a proximal ductal margin ≥ 10 mm should be achieved to obtain a survival benefit. Although there is no obvious boundary between the right side (especially the paracaval portion) and right posterior lobe of the liver, Peng’s resection line can serve as a reference marker for right-sided resection. Laparoscopic resection of the caudate lobe may be safer, more convenient, accurate, and minimally invasive than open surgery, but it needs to be completed by experienced laparoscopic doctors.
Summarizing Implementation Support for School-Based COVID-19 Testing Programs in Southwest American Indian Communities
Authors: Archuleta Shannon , Ingalls Allison , Allison-Burbank Joshuaa D. , Begay Renae , Harvey Benjamin , Grass Ryan , Haroz Emily E. 
Published: September 2023

Context:
American Indian communities have been disproportionately affected by the COVID-19 pandemic, with school closures exacerbating health and education disparities.

Program:
Project SafeSchools' COVID-19 school-based testing program utilized federal and state funding to provide weekly pooled testing with follow-up rapid antigen testing to students and staff from the White Mountain Apache Tribe and Navajo Nation.

Implementation:
The project provided partner schools with training and continual logistical and technical support to aid in school-based testing and adherence to state and local reporting requirements.

Evaluation:
Using the EPIS (Exploration, Preparation, Implementation, and Sustainment) framework, we identified facilitators and barriers to successful program function. While community support and buy-in were essential for successfully implementing school-based testing in these communities, communication, school staff turnover, and funding are among the most significant challenges.

Discussion:
Community partnerships in American Indian communities involving schools and local health authorities can successfully implement testing protocols by remaining flexible and working together to maintain strong lines of communication.
Resection Outcomes of Posttraumatic Elbow Heterotopic Ossification: Multicenter Case Series at a Minimum 5-Year Follow-Up
Authors: Li Juehong , Liu Hang , Hu Yuehao , Liu Weixuan , Wang Wei , Tu Bing , Cui Haomin , Ruan Hongjiang , Sun Ziyang , Fan Cunyi 
Published: September 2023

Background:
Heterotopic ossification (HO), a common complication after elbow trauma, causes severe limb disability. Resection is usually performed for posttraumatic elbow HO (PTEHO) to regain mobility, and although heavily reported, there has been no long-term (minimum, 5-year) follow-up.

Methods:
A total of 173 patients who underwent PTEHO resection were followed up for a minimum of 5 years in 4 hospitals between January of 2015 and August of 2016. Demographics, disease characteristics, and preoperative and minimum 5-year assessments were collected. After controlling for potential variables when dividing long-term range of motion (ROM) into less than 120 degrees and greater than or equal to 120 degrees, risk factors for ROM recovery to modern functional arc were identified through multivariable regression analysis.

Results:
Clinically important improvements in ROM from 39 degrees to 124 degrees were obtained at final follow-up, and 74.6% achieved modern functional arc (≥120 degrees). Mayo Elbow Performance Index had clinically important increases from 69 to 93 points at final follow-up, and 96.5% reported excellent to good. Pain (numeric rating scale, from 1.9 to 0.6 points) and ulnar nerve symptoms were improved. The total complication rate was 15.6%, including new-onset ulnar nerve symptoms (5.8%), HO recurrence with clinical symptoms (6.9%), elbow instability (1.7%), and joint infection (1.2%). Previously reported high body mass index (P = 0.002) and long disease duration (P = 0.033) were equally identified as risk factors for not achieving modern functional arc; meanwhile, tobacco use (P = 0.024) and ankylosed HO (P < 0.001) were found to be new risk factors.

Conclusions:
Resection yields satisfactory outcomes for PTEHO at long-term follow-up of a minimum of 5 years. High body mass index, tobacco use, long disease duration, and ankylosed HO would negatively affect ROM recovery to a modern functional arc (≥120 degrees).

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Risk, III.
Impact of Sling at Time of Prolapse Surgery on Overactive Bladder
Authors: Kowalski Joseph T. , Maetzold Erin , Kenne Kimberly A. , Bradley Catherine S. 
Published: September 2023

Importance
Prolapse surgery and sling surgery both lead to improvement in overactive bladder. However, less is known regarding how slings performed concurrently with less is know about how overactive bladder symptoms change in patients having prolapse surgery with a sling compared to prolapse surgery without a sling.

Objective
The primary aim was to compare change in postoperative overactive bladder symptoms in patients with preoperative overactive bladder who underwent sling placement versus no sling with prolapse surgery.

Study Design
This was a secondary analysis of a cohort study evaluating overactive bladder in patients undergoing prolapse surgery. Sling procedures were performed concomitantly for treatment or prevention of stress incontinence. Baseline and 3-month follow-up urinary symptoms were assessed with the Overactive Bladder Questionnaire Short Form (OAB-q SF) and Urinary Distress Inventory-6 (UDI-6).

Results
Of patients with overactive bladder, 26 (40.0%) underwent midurethral sling (MUS) placement and 39 (60.0%) no sling. Preoperative OAB-q SF bother (score [SD], 46.8 [20.2] vs 40.2 [22.1]; P = 0.23) was similar between groups, but UDI-6 scores (59.2 [28.8] vs 43.8 [29.1]; P = 0.04) were higher in the sling group. At 3 months, the change (improvement) in OABq-SF bother (−16.9 [24.1] vs −22.4 [23.0]; P = 0.36), OABq-SF health-related quality of life (22.8 [28.6] vs 22.9 [23.9]; P = 0.99), and UDI-6 (−38.8 [32.9] vs −34.0 [27.8]; P = 0.53) were similar in the MUS and no MUS groups.

Conclusion
Patients with prolapse and overactive bladder undergoing prolapse surgery with a sling had similar improvements in OAB-q SF bother scores compared with those who did not have a sling.
Genome-enabled analysis of population dynamics and virulence associated loci in the oat crown rust fungusPuccinia coronataf. sp.avenae
Authors: Hewitt Tim C. , Henningsen Eva C. , Pereira Danilo , McElroy Kerensa , Nazareno Eric S. , Dugyala Sheshanka , Nguyen-Phuc Hoa , Li Feng , Miller Marisa E. , Visser Botma , Pretorius Zacharias A. , Boshoff Willem H.P. , Sperschneider Jana , Stukenbrock Eva H. , Kianian Shahryar F. , Dodds Peter N. , Figueroa Melania 
Published: September 2023

ABSTRACTPuccinia coronataf. sp.avenae(Pca) is an important fungal pathogen causing crown rust that impacts oat production worldwide. Genetic resistance for crop protection againstPcais often overcome by the rapid virulence evolution of the pathogen. This study investigated the factors shaping adaptive evolution ofPcausing pathogen populations from distinct geographic regions within the USA and South Africa (SA). Phenotypic and genome-wide sequencing data of these diversePcacollections, including 217 isolates, uncovered phylogenetic relationships and established distinct genetic composition between populations from northern and southern regions from the USA and SA. The population dynamics ofPcainvolve a bidirectional movement of inoculum between northern and southern regions of the USA and contributions from clonality and sexuality. The population from SA is solely clonal. A genome-wide association study (GWAS) employing a haplotype-resolvedPcareference genome was used to define eleven virulence-associated loci corresponding to twenty-five oat differential lines. These regions were screened to determine candidateAvreffector genes. Overall, the GWAS results allowed us to identify the underlying genetic traits controlling pathogen recognition in an oat differential set used in the USA to assign pathogen races (pathotypes). Key GWAS findings support complex genetic interactions in several oat lines suggesting allelism among resistance genes or redundancy of genes included in the differential set, multiple resistance genes recognising genetically linkedAvreffector genes, or potentially epistatic relationships. A careful evaluation of the composition of the oat differential set accompanied by the development or implementation of molecular markers is recommended.
A resource-based mechanistic framework for castration-resistant prostate cancer (CRPC)
Authors: Vibishan B. , Harshavardhan B.V. , Dey Sutirth 
Published: September 2023

AbstractCancer therapy often leads to the selective elimination of drug-sensitive cells from the tumour. This can favour the growth of cells resistant to the therapeutic agent, ultimately causing a tumour relapse. Castration-resistant prostate cancer (CRPC) is a well-characterised instance of this phenomenon. In CRPC, after systemic androgen deprivation therapy (ADT), a subset of drug-resistant cancer cells autonomously produce testosterone, thus enabling tumour regrowth. A previous theoretical study has shown that such a tumour relapse can be delayed by inhibiting the growth of drug-resistant cells using biotic competition from drug-sensitive cells. In this context, the centrality of resource dynamics to intra-tumour competition in the CRPC system indicates clear scope for the construction of theoretical models that can explicitly incorporate the underlying mechanisms of tumour ecology. In the current study, we use a modified logistic framework to model cell-cell interactions in terms of the production and consumption of resources. Our results show that steady state composition of CRPC can be understood as a composite function of the availability and utilisation efficiency of two resources-oxygen and testosterone. In particular, we show that the effect of changing resource availability or use efficiency is conditioned by their general abundance regimes. Testosterone typically functions in trace amounts and thus affects steady state behaviour of the CRPC system differently from oxygen, which is usually available at higher levels. Our data thus indicate that explicit consideration of resource dynamics can produce novel and useful mechanistic understanding of CRPC. Furthermore, such a modelling approach also incorporates variables into the system’s description that can be directly measured in a clinical context. This is therefore a promising avenue of research in cancer ecology that could lead to therapeutic approaches that are more clearly rooted in the biology of CRPC.HighlightsCancer growth and progression can be driven by intra-tumour interactions.Prostate cancer cells compete among each other for resources like testosterone and oxygen.We model these interactions using a modified logistic model with resource dynamics.Equilibrium behaviour can be understood through resource supply and use efficiency.Explicitly ecological models could enable better strategies for cancer control.
Structural phylogenetics unravels the evolutionary diversification of communication systems in gram-positive bacteria and their viruses
Authors: Moi David , Bernard Charles , Steinegger Martin , Nevers Yannis , Langleib Mauricio , Dessimoz Christophe 
Published: September 2023

AbstractRecent advances in AI-based protein structure modeling have yielded remarkable progress in predicting protein structures. Since structures are constrained by their biological function, their geometry tends to evolve more slowly than the underlying amino acids sequences. This feature of structures could in principle be used to reconstruct phylogenetic trees over longer evolutionary timescales than sequence-based approaches, but until now a reliable structure-based tree building method has been elusive. Here, we demonstrate that structure-informed phylogenies can outperform sequence-only ones not only for distantly related proteins but also, remarkably, for more closely related ones. This is achieved by inferring trees from protein structures using a local structural alphabet, an approach robust to conformational changes that confound traditional structural distance measures. As an illustration, we used structures to decipher the evolutionary diversification of a particularly challenging family: the fast-evolving RRNPPA quorum sensing receptors enabling gram-positive bacteria, plasmids and bacteriophages to communicate and coordinate key behaviors such as sporulation, virulence, antibiotic resistance, conjugation or phage lysis/lysogeny decision. The advent of high-accuracy structural phylogenetics enables myriad of applications across biology, such as uncovering deeper evolutionary relationships, elucidating unknown protein functions, or refining the design of bioengineered molecules.
Disentangling non-random structure from random placement when estimating β-diversity through space or time
Authors: McGlinn Daniel J. , Blowes Shane A. , Dornelas Maria , Engel Thore , Martins Inês S. , Shimadzu Hideyasu , Gotelli Nicholas J. , Magurran Anne , McGill Brian , Chase Jonathan M. 
Published: September 2023

AbstractThere is considerable interest in understanding patterns of β-diversity that measure the amount of change in species composition through space or time. Most hypotheses for β-diversity evoke nonrandom processes that generate spatial and temporal within species aggregation; however, β-diversity can also be driven by random sampling processes. Here, we describe a framework based on rarefaction curves that quantifies the non-random contribution of species compositional differences across samples to β-diversity. We isolate the effect of within-species spatial or temporal aggregation on beta-diversity using a coverage standardized metric of β-diversity (βC). We demonstrate the utility of our framework using simulations and an empirical case study examining variation in avian species composition through space and time in engineered versus natural riparian areas. The primary strengths of our approach are that it provides an intuitive visual null model for expected patterns of biodiversity under random sampling that allows integrating analyses across α-, γ-, and β-scales. Importantly, the method can accommodate comparisons between communities with different species pool sizes, and can be used to examine species turnover both within and between meta-communities.Open Research statement:all code and data used in this manuscript are available at the following link:https://github.com/MoBiodiv/beta_concept
Intravenous iron and iron deficiency anemia in gastrointestinal cancer patients: a systematic review
Authors: Nandakumar Shankavi , Singh Navreet , Remtulla Tharani Alliya , Brezden-Masley Christine 
Published: September 2023

AbstractBackgroundIron deficiency anemia (IDA) is a prevalent hematological complication associated with gastrointestinal (GI) cancers due to an increased loss of iron and decreased iron absorption. We estimated the efficacy of parenteral iron on hemoglobin levels, blood transfusion needs and overall quality of life in patients with GI malignancies.MethodsIn this systematic review, we used PubMed, Cochrane, EMBASE, CINHAL and Scopus to conduct an electronic search from January 1, 2010 to March 24, 2022 with no language or study design restrictions. Studies were included if they discussed IDA, GI neoplasms, use of iron supplementation (with or without erythropoietin-stimulating agents [ESAs]), defined anemia and had a patient population of adults. Studies were excluded if were published before 2010. We assessed the efficacy of parenteral iron in comparison to other iron supplementation methods when treating IDA in GI cancer patients. The Cochrane Risk of Bias Tool 2 (RoB 2) and the Risk Of Bias In Non-randomized Studies of Interventions (ROBINS-I) assessment tools were used to assess the quality of the included studies. Moreover, the Cochrane Effective Practice and Organization data collection form was used to collect pertinent study information.ResultsOur search yielded 3,156 studies across all databases. With the exclusion of duplicates, ineligible study designs, as well as studies that did not pass abstract and full-text screening, 17 studies were included in our final analysis (4 randomized control trials; 13 non-randomized studies). Of the 13 studies evaluating hemoglobin (Hgb) response, seven studies found an increase in Hgb levels when patients were treated with IV iron. The 8 studies evaluating red blood cell (RBC) transfusion rates found no significant differences in RBC transfusion needs when treated with IV iron. Studies analyzing health related outcomes typically found an increase quality of life and decreased post-operative complications.DiscussionThis review reveals the improved outcomes of IDA in GI cancer patients treated with IV iron instead of other iron supplementation methods. Timely diagnosis and appropriate IDA management can greatly improve quality of life in this patient population, especially if myelosuppressive chemotherapy is required.Our systematic review presents some limitations due to heterogenous interventions in the randomized control trials, the varying time points of data collection in each study, and the use of small sample sizes.
Genetic and phenotypic heterogeneity in early neurodevelopmental traits in the Norwegian Mother, Father and Child Cohort Study
Authors: Hegemann Laura , Corfield Elizabeth C. , Askelund Adrian Dahl , Allegrini Andrea G. , Askeland Ragna Bugge , Ronald Angelica , Ask Helga , Pourcain Beate St , Andreassen Ole A. , Hannigan Laurie J. , Havdahl Alexandra 
Published: September 2023

AbstractDifferent neurodevelopmental conditions such as autism and ADHD frequently co-occur. Overlapping traits and shared genetic liability are potential explanations. We examine this using data from the population-based Norwegian Mother, Father, and Child Cohort study (MoBa), leveraging item-level data to explore the phenotypic factor structure and genetic architecture underlying neurodevelopmental traits at age 3 years (N = 41 708 – 58 630). We identified 11 latent factors at the phenotypic level using maternal reports on 76 items assessing children’s motor skills, language, social functioning, communication, attention, activity regulation, and flexibility of behaviors and interests. These factors showed associations with diagnoses of neurodevelopmental conditions and most shared genetic liabilities with autism, ADHD, and/or schizophrenia. Item-level GWAS revealed trait-specific genetic correlations with autism (itemrgrange = -0.27 – 0.78), ADHD (itemrgrange = -0.40 – 1), and/or schizophrenia (itemrgrange = -0.24 – 0.34). Based on patterns of item-level genetic covariance and genomic factor analyses, we find little evidence of common genetic liability across all neurodevelopmental traits. These results more so support genetic factors across more specific areas of neurodevelopment, some of which, such as prosocial behavior overlap with factors found in the phenotypic analyses. Other areas such as motor development seemed to have more heterogenous etiology, with indicators in this domain showing a less consistent pattern of genetic correlations with each other. Overall, these exploratory findings emphasize the etiological complexity of neurodevelopmental traits at this early age. In particular, diverse associations with neurodevelopmental conditions and genetic heterogeneity could inform follow-up work to identify shared and differentiating factors in the early manifestations of neurodevelopmental traits, which in turn could have implications for clinical screening tools and programs.