bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary origins of the lampriform pelagic radiation
Authors: Brownstein Chase Doran , Near Thomas J 
Published: October 2023

Abstract
Ray-finned fishes, which compose nearly half of living vertebrate diversity, provide an excellent system for studying the evolution of novel body forms. Lampriformes is a species-poor lineage of acanthomorph ray-finned fishes that has evolved two very different and highly specialized body plans suited to life in pelagic oceanic habitats: the deep, round-bodied bathysomes and the ribbon-like taeniosomes. Here, we present a new phylogenetic hypothesis and divergence time estimates for lampriform fishes based on an updated morphological dataset and DNA sequences from nuclear genes for all but one of the living lampriform families and 55% of recognized extant genera. Our analyses resolve two major clades in Lampriformes: the Bathysomi and the Taeniosomi. A time calibrated phylogeny shows that the origin of living lampriforms coincides with the aftermath of the Cretaceous–Palaeogene extinction and that anatomically modern pelagic morphotypes evolved 10 Myr after the start of the Palaeogene.
The gut microbiome in the fight against obesity: The potential of dietary factors
Authors: Ahmad Jamil , Khan Imran , Zengin Gokhan , Mahomoodally Mohamad Fawzi 
Published: October 2023

AbstractObesity as a global public health burden has experienced a drastic growing trend recently. The management of obesity is challenging because of its complex etiology, and various factors are involved in its development, such as genetic and environmental factors. Different approaches are available to treat and/or manage obesity, including diet, physical activity, lifestyle changes, medications, and surgery. However, some of these approaches have inherent limitations and are closely associated with adverse effects. Therefore, probing into a novel/safe approach to treat and/or manage obesity is of fundamental importance. One such approach gaining renewed interest is the potential role of gut microbiota in obesity and its effectiveness in treating this condition. However, there is a dearth of comprehensive compilation of data on the potential role of the gut microbiome in obesity, particularly regarding dietary factors as a therapeutic approach. Therefore, this review aims to provide an updated overview of the role of gut microbiota in obesity, further highlighting the importance of dietary factors, particularly diet, prebiotics, and probiotics, as potential complementary and/or alternative therapeutic options. Moreover, the association of gut microbiota with obese or lean individuals has also been discussed.
Utilization of Healthcare Resources by Vascular Anomaly Patients: An Assessment of Healthcare Burden by Lesion Complexity
Authors: Truong Albert Y. , Iaconetti Emma , Clapp Averill , Brackett Shannon , Fallon Erica M. , Garzon Maria C. , Tulin-Silver Sheryl , Wu June K. 
Published: October 2023

Background:
Vascular anomalies (VAs) are heterogeneous lesions. Symptoms vary widely by lesion type and complexity. VA patients often require life-long interdisciplinary care; however, there is a paucity of data on the healthcare utilization of VA patients, and their burden on the healthcare system remains largely unquantified. We hypothesize that healthcare utilization by complex lymphatic malformation (LM) and venous malformation (VM) patients will be significantly higher compared with simple LM and VM patients.

Methods:
A retrospective, longitudinal study was performed of LM/VM patients seen through multidisciplinary VA clinics between January 1, 2019 and December 31, 2020. Data were collected from each patient’s first presentation through December 31, 2021 and included number of office visits, imaging studies, specialists involved, procedures, hospitalization data, and approximate costs, normalized to per year utilization. Patients were divided into “simple” and “complex” LMs/VMs. Involvement of the airway, more than one anatomic area, and/or complex lymphatic anomalies were defined as “complex.”

Results:
In total, 28 simple and 29 complex LM patients and 51 simple and 18 complex VM patients were identified. Complex LM and VM patients had significantly higher numbers of imaging studies, specialists involved, procedures and hospitalizations, and costs incurred. Complex LM patients also had significantly higher per year office visits.

Conclusions:
VA care is chronic and costly, especially for complex LM/VM patients. LM/VM complexity was a predictor for increased inpatient and outpatient healthcare utilization and higher costs. Better awareness of the healthcare utilization trends of LM/VM patients will allow for improved counseling for these patients regarding prognosis and expectations.
Efficacy and safety of Xiang-Sha-Liu-Jun-Zi (XSLJZ) for treatment of Semaglutide-induced gastrointestinal side effects: Study protocol for a multicentre, randomized, open-label trial
Authors: Liu Meixi , Qiu Xianliang , Fu Shunlian , Tian Yuting , Li Wen , Li Qing , Chen Qiu 
Published: October 2023

Background:
Semaglutide is a newly approved glucagon-like peptide 1 receptor agonist(GLP-1 RA), significantly reducing HbA1c and body weight. However, it is associated with an increased incidence of gastrointestinal adverse events. Xiang-Sha-Liu-jun-Zi (XSLJZ), is a classic traditional Chinese medicine (TCM) formula with the effects of modulating gastrointestinal disturbance.
This study aims to evaluate the clinical efficacy and safety of the XSLJZ for treatment of Semaglutide-induced gastrointestinal side effects.

Methods:
This is a multicentre, randomized, open-label trial. The trial included a run-in period within 2 weeks, a 4-week treatment period, and another 4 weeks after the end of the experimental phase. Patients who have Gastrointestinal Adverse Reactions during the run-in period will be randomly divided (1:1) into 2 groups. The primary outcome measures were changes in scores on the Gastrointestinal System Rating Scale(GSRS), the duration of individual gastrointestinal adverse events. The secondary outcomes were TCM syndrome score, changes in glycaemic excursions, homeostatic model assessment 2-B (HOMA2-B)and homeostatic model assessment 2-insulin resistance(HOMA2-IR), glucagon, C-peptide, plasma lipids, Anthropometric parameters: body weight, body mass index, waist-hip circumference, waist-hip ratio.

Discussion:
The results of this trial will provide initial evidence for the use of XSLJZ as an alternative and complementary intervention to manage Semaglutide-induced gastrointestinal side effects.
Exploring the rationale for prescribing ankle–foot orthoses and supramalleolar orthoses in children with cerebral palsy: A narrative synthesis of rationale statements
Authors: Dailey Asumi H. , Landers Jessica , Anderson Sarah , Dillon Michael P. 
Published: October 2023

Background:
To help improve outcomes for children with cerebral palsy (CP), ankle–foot orthoses (AFOs) and supramalleolar orthoses (SMOs) are prescribed. However, it is not clear why one intervention is prescribed over the other.

Objectives:
To explore the rationale for prescribing AFOs and SMOs in children with CP and its link to the choice of outcome measure used.

Study design:
Narrative review.

Methods:
Six databases were searched (eg, Medline) and data extracted from articles that met the inclusion criteria. Data describing the participant demographics, type of orthosis, and outcome measures used were summarized to provide context for the different rationale for orthotic prescription that were thematically analyzed.

Discussion:
Forty-seven articles were included. Participants were aged 9 ± 2 years, 59% were male, 79% had diplegia, and 38% were classified as Gross Motor Function Classification System level I. All studies included a rationale for prescribing AFOs that, in most cases, reflected the outcome measures used. These rationale statements were synthesized into 5 specific themes (e.g., reduced energy expenditure and metabolic costs). By comparison, 5 of these studies described the rationale for providing SMOs, and of those that did, most of the rationale statements were nonspecific.

Conclusions:
A large and contemporary body of literature describes the rationale for prescribing AFOs for children with CP. There are opportunities for future research that clearly articulates the rationale for prescribing SMOs for children living with CP and to focus the rational for orthotic intervention on the real-world challenges that are most important to children living with CP, such as the ability to participate among peers.
Initial Staging and Response Evaluation With 18F-FDG PET/CT in a Rare Case of Nested Variant Urothelial Urethral Cancer
Authors: Barashki Somaye , Aghaee Atena , Sahebkari Azade , Norouzbeigi Nasim , Sadeghi Ramin 
Published: October 2023

Abstract
Primary urothelial urethral cancer is a relatively infrequent but serious form of cancer in the urinary tract, and nested variant is extremely rare. Until now, no studies have been published regarding 18F-FDG PET/CT in patients with primary urothelial urethral cancer. In this study, we discussed the role of 18F-FDG PET/CT in the initial staging, treatment response evaluation, and recurrence assessment of a 53-year-old woman with nested variant urothelial urethral cancer, which could lead to timely diagnosis and evaluation of the extent of involvement, thus achieving the best treatment plan for this group of patients.
Radioligand Therapy With 177Lu-PSMA-I&T in Patients With Metastatic Prostate Cancer
Authors: Demirkol Mehmet Onur , Esen Barış , Seymen Hülya , Şen Melis , Uçar Burcu , Kurtuldu Sevgilay , Mandel Nil Molinas , Bavbek Sevil , Falay Okan , Tilki Derya , Esen Tarık 
Published: October 2023

Introduction
This study aimed to investigate the oncological outcomes and toxicity profile of 177Lu-PSMA-I&T radioligand therapy (RLT) in patients with metastatic castration-resistant prostate cancer (mCRPC), as well as our initial experience in metastatic hormone-sensitive prostate cancer (mHSPC).

Patients and Methods
A total of 38 consecutive patients with metastatic prostate cancer (33 mCRPC and 5 mHSPC) received 177Lu-PSMA-I&T RLT, with a median of 2 cycles per patient (range, 1–7). Response to RLT was evaluated based on prostate-specific antigen (PSA) changes and imaging response. Clinical progression-free survival and overall survival were used to report oncological outcomes. Toxicity was assessed using the Common Toxicity Criteria for Adverse Events criteria.

Results
In mCRPC, 22 (69%), 18 (56%), and 11 (34%) patients achieved any PSA decline, PSA response of ≥30%, and PSA response of ≥50%, respectively. The clinical progression-free survival and overall survival after the first cycle of RLT were 6.3 and 21.4 months, respectively. In mHSPC, 177Lu-PSMA-I&T RLT resulted in excellent PSA response (93.0%–99.9%) in all cases. Clinical progression and cancer-related mortality occurred in only 1 case. Toxicity profile was favorable in both mHSPC and mCRPC.

Conclusions

177Lu-PSMA-I&T RLT demonstrated favorable PSA response (≥30%) in over half of the patients with mCRPC and excellent PSA response in all patients with mHSPC. Toxicity profile was favorable in both mHSPC and mCRPC settings. Further studies are needed to evaluate the role of 177Lu-PSMA-I&T RLT in the management of metastatic prostate cancer.
Poly-N-acetylglucosamine mediatesCutibacterium acnesbiofilm formation and biocide resistance
Authors: Kaplan Jeffrey B. 
Published: October 2023

ABSTRACTBiofilm formation likely plays an important role in the pathogenesis of implant-related infections caused byCutibacterium acnes. Biofilms protect bacteria from antimicrobials and host defenses which makes biofilm-related infections difficult to treat. Here we demonstrate that the exopolysaccharide poly-N-acetylglucosamine (PNAG) contributes toC. acnesbiofilm formationin vitro. By treatingC. acnescells and biofilms with the PNAG-degrading enzyme dispersin B, we found that PNAG mediates the attachment ofC. acnescells to polystyrene rods and the formationC. acnesbiofilms in glass and polypropylene tubes. We further show that PNAG protectsC. acnesbiofilm cells from killing by tetracycline and benzoyl peroxide. PNAG may play an important role in biofilm formation, antibiotic tolerance, and virulence in this opportunistic pathogen.
Did “long COVID” increase road deaths in the U.S.?
Authors: Robertson Leon S. 
Published: October 2023

AbstractObjectiveTo examine data on COVID-19 disease associated with a 10 percent increase in U.S. road deaths from 2020 to 2021 that raises the question of the potential effect of pandemic stress and neurological damage from COVID-19 disease.MethodsPoisson regression was used to estimate the association of recent COVID-19 cases, accumulated cases, maximum temperatures, truck registrations, and gasoline prices with road deaths monthly among U.S. states in 2021. Using the regression coefficients, changes in each risk factor from 2020 to 2021 were used to calculate expected deaths in 2021 if each factor had remained the same as in 2020.ResultsCorrected for the other risk factors, road deaths were associated with accumulated COVID-19 cases but not cases in the previous month. More than 20,700 road deaths were associated with the changes in accumulated COVID-19 cases but were substantially offset by about 19,100 less-than-expected deaths associated with increased gasoline prices.ConclusionsWhile more research is needed, the data are sufficient to warn people with “long COVID” to minimize road use.What is already known about this topicPrevious short-term fluctuations in road deaths are related to changes in temperature, fuel prices, and truck registrations.What this study addsCorrected for other risk factors, the monthly changes in road deaths from 2020 to 2021 in U.S. states were associated with cumulative COVID-19 cases.How this study might affect research, practice, or policyStudies are needed to distinguish the potential relative effects of neurological damage as well as the stress of coping with the pandemic on driving, walking, and bicyclist behavior. Warning people with “long covid” about road risk is warranted.
New insights into iodide metabolism based on preclinical models: impact on radiotherapy efficacy and protection against radioactive iodine exposure
Authors: Guglielmi Julien , D’Andréa Grégoire , Graslin Fanny , Chatti Kaouthar , Schiazza Aurélie , Lindenthal Sabine , Darcourt Jacques , Cambien Béatrice , Pourcher Thierry 
Published: October 2023

AbstractBackgroundThe main basic aspects of the regulation of thyroid metabolism by iodine are known, but given the complexity of the mechanisms involved, further analyzes in living animals are still required. Here, we provided new insights into iodine physiology but also into the optimization of radiotherapy with iodine, as well as effective countermeasures in the case of an exposure to radioactive iodine.MethodsWe performed Single Photon Emission Computed Tomography (SPECT) coupled to an X-ray scanner to record radiotracers in living mice and rats. Our imaging system was similar to that routinely used in nuclear medicine but was specifically designed for studies with small animals. Different modalities of administration of radioactive iodine or its radioactive analogues combined with a low or high iodine diet have been studied in pregnant, lactating and control animals. To optimize countermeasures against acute or chronic iodine exposure, the protective effects of potassium iodide (KI) administration protocols were analyzed. Perchlorate was administered to study the iodine metabolism in the kidney and stomach.ResultsOur results showed how the various organs capable of iodine uptake adapt to an iodine-deficient diet. Indeed, the uptake capacity of the thyroid gland, but also that of the salivary glands was significantly increased on a low iodine diet. In contrast, the iodine uptake capacity of the thyroid and lactating mammary glands was reduced on an iodide-rich diet. Our results also showed the physiological role of the kidneys in controlling excess circulating iodide. In addition, they revealed an active iodine cycle in the stomach. We also investigated the protective effects of daily KI administration during radioactive iodine exposure and found that the overall protection was better in rats (85%) than in mice (65%). We also included pregnant females and newborns, and we revealed the existence of specific mechanisms for the inhibition of the fetal thyroid by circulating iodine. Indeed, an iodine-rich diet or repeated daily administration of KI led to a strong inhibition of the iodide uptake capacity of the fetal thyroid.ConclusionsOur study contributes to a better understanding of iodine metabolism and its regulation in the thyroid and in non-thyroidal organs in adult, fetal and newborn animals. Extrapolated to humans, our results not only provide better understanding of iodide withdrawal as a clinical preparatory measure for patients with differentiated thyroid cancer, but also help to optimize countermeasures in the case of an exposure to radioactive iodine.
Retinal waves in adaptive rewiring networks orchestrate convergence and divergence in the visual system
Authors: Luna Raul , Li Jia , Bauer Roman , van Leeuwen Cees 
Published: October 2023

AbstractSpontaneous retinal wave activity shaping the visual system is a complex neurodevelopmental phenomenon. Retinal ganglion cells are the hubs through which activity diverges throughout the visual system. We consider how these divergent hubs emerge, using an adaptively rewiring neural network model. Adaptive rewiring models show in a principled way how brains could achieve their complex topologies. Modular small-world structures with rich club effects and circuits of convergent-divergent units emerge as networks evolve, driven by their own spontaneous activity. Arbitrary nodes of an initially random model network were designated as retinal ganglion cells. They were intermittently exposed to the retinal waveform, as the network evolved through adaptive rewiring. A significant proportion of these nodes developed into divergent hubs within the characteristic complex network architecture. The proportion depends parametrically on the wave incidence rate. Higher rates increase the likelihood of hub formation, while increasing the potential of ganglion cell death. In addition, direct neigbours of designated ganglion cells differentiate like amacrine cells. The divergence observed in ganglion cells resulted in enhanced convergence downstream, suggesting that retinal waves control the formation of convergence in LGN. We conclude that retinal waves stochastically control the distribution of converging and diverging activity in evolving complex networks.
Healthy adults favor stable left/right hand choices over performance at an unconstrained reach-to-grasp task
Authors: Kim Taewon , Zhou Ruiwen , Gassass Samah , Liu Lei , Philip Benjamin A. 
Published: October 2023

AbstractReach-to-grasp actions are fundamental to the daily activities of human life, but few methods exist to assess individuals’ reaching and grasping actions in unconstrained environments. The Block Building Task (BBT) provides an opportunity to directly observe and quantify these actions, including left/right hand choices. Here we sought to investigate the motor and non-motor causes of left/right hand choices, and optimize the design of the BBT, by manipulating motor and non-motor difficulty in the BBT’s unconstrained reach-to-grasp task We hypothesized that greater motor and non-motor (e.g. cognitive/perceptual) difficulty would drive increased usage of the dominant hand. To test this hypothesis, we modulated block size (large vs. small) to influence motor difficulty, and model complexity (10 vs. 5 blocks per model) to influence non-motor difficulty, in healthy adults (n=57). We hypothesized that healthy adults with high non-dominant hand performance in a precision drawing task should be more likely to use their non-dominant hand in the BBT. Our data revealed that increased motor and non-motor difficulty led to lower task performance (slower speed), but participants only increased use of their dominant hand only under the most difficult combination of conditions: in other words, participants allowed their performance to degrade before changing hand choices, even though participants were instructed only to optimize performance. These results demonstrate that hand choices during reach-to grasp actions are more stable than motor performance in healthy right-handed adults, but tasks with multifaceted difficulties can drive individuals to rely more on their dominant hand.Statements and DeclarationsDr. Philip and Washington University in St. Louis have a licensing agreement with PlatformSTL to commercialize the iPad app used in this study.
Regulatory Landscape Enrichment Analysis (RLEA) using gaiaAssociation
Authors: Sosa Eric A. , Rosean Samuel , O’Shea Dónal , Raj Srilakshmi M. , Seoighe Cathal , Greally John M. 
Published: October 2023

ABSTRACTMotivationTo understand whether sets of genomic loci are enriched at the regulatory loci of one or more cell types, we developed the gaiaAssociation package to perform Regulatory Landscape Enrichment Analysis (RLEA). RLEA is a novel analytical process that tests for enrichment of sets of loci in cell type-specific open chromatin regions (OCRs) in the genome.ResultsWe demonstrate that the application of RLEA to genome-wide association study (GWAS) data reveals cell types likely to be mediating the phenotype studied, and clusters OCRs based on their shared regulatory profiles. GaiaAssociation is Python code that is freely available for use in functional genomics studies.Availability and ImplementationGaia Association is available on PyPi (https://pypi.org/project/gaiaAssociation/0.6.0/#description) for pip download and use on the command line or as an inline Python package. Gaia Association can also be installed from GitHub athttps://github.com/GreallyLab/gaiaAssociation.Contactjohn.greally@einsteinmed.edu
SAGERank: Inductive Learning of Protein-Protein Interaction from Antibody-Antigen Recognition using Graph Sample and Aggregate Networks Framework
Authors: Sun Chuance , Bai Ganggang , Xu Honglin , Wang Yanjing , Ma Buyong 
Published: October 2023

AbstractNumerous experiments and computationally solved antibody-antigen interfaces offer the possibility of training deep-learning models to help predict their biological correlations. Predicting antibody-antigen docking and structure-based design represent significant long-term and therapeutically important challenges in computational biology. We present SAGERank, a general, configurable deep learning framework for antibody design using Graph Sample and Aggregate Networks, which mainly includes ranking docking decoys, detecting binding, and identifying biological interfaces. The model proved its reliability in three different tasks. For both problems ranking docking decoys and identifying biological interfaces, SAGERank is competitive with or outperforms, state-of-the-art methods. Besides, the SAGERank model still showed a high degree of confidence in determining whether the antibody-antigen could bind. All of these demonstrate the versatility of SAGERank for structural biology research. Most importantly, our study demonstrated the real potential of inductive deep learning to overcome small dataset problem in molecular science. The SAGERank models trained for antibody-antigen docking can be used to examine generally protein-protein interaction docking and differentiate crystal packing from biological interface.