bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of RNA virus-encoded proteinases
Authors: Ryan M D , Flint M , Donnelly M L L , Byrne E , Cowton V 
Published: November 2023

Abstract
An extremely common strategy of positive-strand RNA viruses is to encode some, if not all, of their proteins in the form of polyproteins. Picoma-, flavi-, and potyviruses, for example, encode all their proteins in a single, long, open reading frame (ORF). Other viruses may have monopartite genomes encoding more than one polyprotein (e.g. togaviruses). Multipartite genomes are very common in plant viruses and each of the different RNA strands may also encode a polyprotein (e.g. bymo-, como-, nepoviruses).
Medical genetics resources in the genomic era
Authors: Pruitt Kim D 
Published: November 2023

Abstract
While the past few decades have yielded impressive gains in our understanding of biology and inherited diseases, the availability of the human genome sequence, polymorphism, and expression data will have a critical impact on the field of medical genetics. The human genome sequence data opens powerful new approaches to integrate and access information. The power, and promise, of medical genetics lies in the ability to intercalate disparate data from multiple sources. At the intersection of genetics, genomics, and medicine, medical genetics holds great promise for understanding the fundamental nature of many diseases, which in tum will lead to better diagnoses, treatments, and even cures.
Virome in immunodeficiency: what we know currently
Authors: Wang Hu , Xu Siqi , Li Shuang , Su Bin , Sherrill-Mix Scott , Liang Guanxiang 
Published: November 2023

Abstract
Over the past few years, the human virome and its complex interactions with microbial communities and the immune system have gained recognition as a crucial factor in human health. Individuals with compromised immune function encounter distinctive challenges due to their heightened vulnerability to a diverse range of infectious diseases. This review aims to comprehensively explore and analyze the growing evidence regarding the role of the virome in immunocompromised disease status. By surveying the latest literature, we present a detailed overview of virome alterations observed in various immunodeficiency conditions. We then delve into the influence and mechanisms of these virome changes on the pathogenesis of specific diseases in immunocompromised individuals. Furthermore, this review explores the clinical relevance of virome studies in the context of immunodeficiency, highlighting the potential diagnostic and therapeutic gains from a better understanding of virome contributions to disease manifestations.
Epidemiology of obesity among people with HIV
Authors: Talathi Ria , Anekwe Chika V. , Toribio Mabel 
Published: November 2023

Purpose of review
People with HIV (PWH) on antiretroviral therapy (ART) globally are disproportionately affected by obesity, with prevalence rates highest among women with HIV. The purpose of this review is to discuss rates of obesity, factors associated with obesity, and adverse consequences of obesity among PWH.

Recent findings
Among PWH on ART, rates of obesity have increased over the last several decades and tend to be higher than the general population. Weight gain with the initiation of new ART regimens such as integrase strand transfer inhibitor (INSTI)-based regimens are thought to contribute to higher rates of obesity among PWH on ART. Other factors, such as sex and ethnicity, also are associated with obesity among PWH on ART. Higher obesity rates among PWH may contribute to heightened cardiometabolic disease risk and lower health-related quality of life.

Summary
Prospective studies which identify factors associated with increased obesity prevalence and weight gain among PWH are necessary for the development and implementation of obesity prevention and treatment strategies among PWH on ART and, in turn, reduce the prevalence of obesity in this population.
Neuroimaging Correlates of Internet Gaming Disorder: Can We Achieve the Promise of Translating Understanding of Brain Functioning Into Clinical Advances?
Authors: Mestre-Bach Gemma , Potenza Marc N. 
Published: November 2023

ABSTRACT

Objectives:
Here, we aimed to consider the neural factors associated with internet gaming disorder (IGD), as well as the associations between these factors and existing treatments for the disorder.

Methods:
A narrative review was conducted.

Results:
Pharmacological as well as psychological treatments for IGD may be associated with specific changes in multiple brain areas and circuits. In particular, frontostriatal and subcortical regions and pathways appear relevant to IGD and its treatment.

Conclusions:
Neuroimaging holds promise for identifying specific mechanisms underlying IGD interventions. However, to date, firm conclusions are difficult to draw and more research examining neural mechanisms of empirically supported treatments for IGD is needed.

Objectifs:
Nous avons cherché à examiner les facteurs neuronaux associés au trouble du jeu sur internet (TJI), ainsi que les associations entre ces facteurs et les traitements existants pour ce trouble.

Méthodes:
Une étude narrative a été réalisée.

Résultats:
Les traitements pharmacologiques et psychologiques du TJI peuvent être associés à des changements spécifiques dans de multiples zones et circuits cérébraux. En particulier, les régions et voies fronto-striatales et sous-corticales semblent pertinentes pour le TJI et son traitement.

Conclusions:
La neuro-imagerie est prometteuse pour l’identification des mécanismes spécifiques qui sous-tendent les interventions du TJI. Cependant, à ce jour, il est difficile de tirer des conclusions définitives et il est nécessaire de poursuivre les recherches sur les mécanismes neuronaux des traitements empiriques du TJI.
Further decompensation in cirrhosis: Results of a large multicenter cohort study supporting Baveno VII statements
Authors: D’Amico Gennaro , Zipprich Alexander , Villanueva Càndid , Sordà Juan Antonio , Morillas Rosa Maria , Garcovich Matteo , García Retortillo Montserrat , Martinez Javier , Calès Paul , D’Amico Mario , Dollinger Matthias , García-Guix Marta , Gonzalez Ballerga Esteban , Tsochatzis Emmanuel , Cirera Isabel , Albillos Agustìn , Roquin Guillaume , Pasta Linda , Colomo Alan , Daruich Jorge , Canete Nuria , Boursier Jérôme , Dallio Marcello , Gasbarrini Antonio , Iacobellis Angelo , Gobbo Giulia , Merli Manuela , Federico Alessandro , Svegliati Baroni Gianluca , Pozzoni Pietro , Addario Luigi , Chessa Luchino , Ridola Lorenzo , Garcia-Tsao Guadalupe 
Published: November 2023

Background and Aims:
The prognostic weight of further decompensation in cirrhosis is still unclear. We investigated the incidence of further decompensation and its effect on mortality in patients with cirrhosis.

Approach and Results:
Multicenter cohort study. The cumulative incidence of further decompensation (development of a second event or complication of a decompensating event) was assessed using competing risks analysis in 2028 patients. A 4-state model was built: first decompensation, further decompensation, liver transplant, and death. A cause-specific Cox model was used to assess the adjusted effect of further decompensation on mortality. Sensitivity analyses were performed for patients included before or after 1999. In a mean follow-up of 43 months, 1192 patients developed further decompensation and 649 died. Corresponding 5-year cumulative incidences were 52% and 35%, respectively. The cumulative incidences of death and liver transplant after further decompensation were 55% and 9.7%, respectively. The most common further decompensating event was ascites/complications of ascites. Five-year probabilities of state occupation were 24% alive with first decompensation, 21% alive with further decompensation, 7% alive with a liver transplant, 16% dead after first decompensation without further decompensation, 31% dead after further decompensation, and <1% dead after liver transplant. The HR for death after further decompensation, adjusted for known prognostic indicators, was 1.46 (95% CI: 1.23–1.71) (p<0.001). The significant impact of further decompensation on survival was confirmed in patients included before or after 1999.

Conclusions:
In cirrhosis, further decompensation occurs in ~60% of patients, significantly increases mortality, and should be considered a more advanced stage of decompensated cirrhosis.
Light adjustable intraocular lenses in cataract surgery: considerations
Authors: Jun Jong Hwa , Lieu Alexander , Afshari Natalie A. 
Published: November 2023

Purpose of review
Light adjustable intraocular lens (LAL) is a promising concept in cataract surgery. This review explores considerations for the use of LALs.

Recent findings
Through updates, the safety of LALs and light delivery devices have been enhanced, enabling more efficient treatment with lower ultraviolet (UV) energy. Preoperative topography and aberration are essential for understanding indications for LALs. Furthermore, when determining intraocular lens power, it is crucial to factor in potential postoperative myopia or hyperopic adjustments. This is achieved by establishing a proper postimplantation refractive target and considering potential wavefront changes. Postoperative adjustments for defocus and astigmatism have demonstrated excellent outcomes. Monovision strategy by adjustable blended vision of LALs revealed distance vision of 20/20 along with near vision of J2 in 96% of patients. However, the results of clinical studies on postrefractive cataract surgery showed contrasting outcomes at distance, indicating the need for further research results regarding its effectiveness. A new postoperative workflow needs to be designed to enable a systematic follow-up process.

Summary
LALs are safe and demonstrate promising refractive outcomes. To achieve appropriate results, understanding the changes in optical characteristics associated with adjustment and constructing a new postoperative workflow are necessary.
An optimized post-surgery follow-up strategy for patients with esophageal cancer: a cohort study
Authors: Mai Zihang , Xie Jiaxin , Leng Changsen , Xie Xiuying , Wen Jing , Yang Hong , Liu Qianwen , Fu Jianhua 
Published: November 2023

Background:
After radical surgery, patients with esophageal cancer should undergo long-term surveillance of disease relapse. However, the optimal follow-up strategy remains to be explored.

Method:
A total of 4688 patients were recruited. Recursive partition analysis was applied to develop recurrence risk stratification for patients. The follow-up strategies of each stratification were developed based on monthly recurrence probability and validated by bootstrap validation and an external dataset. Markov decision-analytic model was constructed to evaluate the cost-effectiveness of the follow-up strategies.

Results:
Patients were stratified into four groups according to four pathological features. We applied random survival forest to calculate the monthly recurrence probability of each group. Based on the temporal distribution of recurrences, we further established surveillance strategies for four groups. The strategies were validated as optimal protocols by bootstrap resampling and another dataset. Markov decision-analytic analysis indicated that our recommended strategies outperformed the mainstream protocols from guidelines and were most cost-effective. Using less than 12 visits across the first 5 years on average, our follow-up strategies were more efficient than the NCCN recommended strategies (14 visits average). Our results also supported the computerized tomography from the neck to the upper abdomen as routine examination and PETCT of distant metastasis for some groups with high risks.

Conclusion:
Our study provided data-driven evidence of personalized and economic follow-up strategies for EC patients and shed light on follow-up optimization for other cancer types.
Efficacy of electroacupuncture in improving postoperative ileus in patients receiving colorectal surgery: A systematic review and meta-analysis
Authors: Chen Hsiao-Tien , Hung Kuo-Chuan , Huang Yen-Ta , Wu Jheng-Yan , Hsing Chung-Hsi , Lin Chien-Ming , Chen I-Wen , Sun Cheuk-Kwan 
Published: November 2023

Background:
This meta-analysis aimed to evaluate the efficacy and safety of electroacupuncture (EA) in improving postoperative ileus (POI) after colorectal surgery.

Methods:
Electronic databases (e.g., Medline) were screened to identify randomized controlled trials (RCTs) that focused on the association between EA and POI. Time to first flatus served as the primary outcome, while the secondary outcomes included time required for the recovery of other gastrointestinal functions (e.g., bowel sound recovery), time to tolerability of liquid/solid food, postoperative pain scores, risk of overall complications, and hospital length of stay (LOS).

Results:
Our meta-analysis focusing on 16 studies with a total of 1562 patients demonstrated positive associations of EA with shorter times to the first flatus (mean difference [MD):-10.1 hours, P<0.00001, n=1562), first defecation (MD:-11.77 hours, P<0.00001, n=1231), bowel sound recovery (MD:-10.76 hours, P<0.00001, n=670), tolerability of liquid (MD: -16.44 hours, P=0.0002, n=243), and solid food (MD: -17.21 hours, P=0.005, n=582) than those who received standard care. The use of EA was also correlated with a lower risk of overall complications [risk ratio (RR):0.71, P=0.04, n=1011], shorter hospital LOS (MD: -1.22 days, P=0.0001, n=988), and a lower pain score on postoperative days two (standardized MD: -0.87, P=0.009, n=665) and three (standardized MD: -0.45, P<0.00001, n=795), without a difference in time to first ambulation.

Conclusion:
Our findings showed an association between EA and enhanced gastrointestinal functional recovery and reduced pain severity following colorectal surgery, highlighting the potential benefits of incorporating EA into perioperative care to enhance recovery outcomes in this setting.
Diagnostic consistency between computed tomography and adrenal vein sampling of primary aldosteronism: Leading to successful curative outcome after adrenalectomy: A retrospective study
Authors: Kim Byung-Chang , Yoon Hyun-Ki , Park Kye Jin , Kim Gun Ha , Pak Shin Jeong , Kwon Douk , Cho Jae Won , Kim Won Woong , Lee Yu-mi , Koh Jung-Min , Lee Seung Hun , Chung Ki-Wook , Sung Tae-Yon 
Published: November 2023

Background:
Adrenal Computed tomography (CT) is a useful tool for locating adrenal lesion in primary aldosteronism(PA) patients. However, adrenal vein sampling(AVS) is considered as a gold standard for subtype diagnosis of PA. The aim of this study was to investigate the consistency of CT and AVS for the diagnosis of PA subtypes and evaluate the concordance of surgical outcomes.

Materials and methods:
This retrospective study included 264 PA patients having both CT and AVS. Diagnostic consistency between CT and AVS was accessed, and clinical and biochemical outcomes were evaluated at 6 months after adrenalectomy.

Results:
Of all, 207 (78%) had CT unilateral lesion, 32 (12%) CT bilateral lesion, and 25 (9%) CT bilateral normal findings. Among CT unilateral lesion group, 138 (67%) had ipsilateral AVS lateralization. For CT bilateral lesion and bilateral normal, AVS unilateral lateralization was found in 17 (55%) and 2 (8%), respectively. The consistency between CT lesion and AVS lateralization including CT unilateral with AVS ipsilateral, and CT bilateral lesion with AVS bilateral patients was 63.8%(152/238). Of 77 patients with available data out of 138 patients who underwent adrenalectomy with consistency between CT and AVS, clinical success rate was 96%, for 17 inconsistency patients out of 22 patients who underwent adrenalectomy, clinical success rate was 94% after adrenalectomy following the lateralization result of AVS.

Conclusion:
CT is a useful tool to diagnose the adrenal lesion in PA patients. However, AVS is more sufficient to detect the unilateral PA subtype which could provide curable treatment to surgical candidates of PA such that AVS can identify patients with contralateral PA in CT unilateral lesion and unilateral PA in CT bilateral lesion. The surgical outcome was successful when adrenalectomy was performed according to the AVS lateralization result.
Artificial intelligence in interventional pulmonology
Authors: Ishiwata Tsukasa , Yasufuku Kazuhiro 
Published: November 2023

Purpose of review
In recent years, there has been remarkable progress in the field of artificial intelligence technology. Artificial intelligence applications have been extensively researched and actively implemented across various domains within healthcare. This study reviews the current state of artificial intelligence research in interventional pulmonology and engages in a discussion to comprehend its capabilities and implications.

Recent findings
Deep learning, a subset of artificial intelligence, has found extensive applications in recent years, enabling highly accurate identification and labeling of bronchial segments solely from intraluminal bronchial images. Furthermore, research has explored the use of artificial intelligence for the analysis of endobronchial ultrasound images, achieving a high degree of accuracy in distinguishing between benign and malignant targets within ultrasound images. These advancements have become possible due to the increased computational power of modern systems and the utilization of vast datasets, facilitating detections and predictions with greater precision and speed.

Summary
Artificial intelligence integration into interventional pulmonology has the potential to enhance diagnostic accuracy and patient safety, ultimately leading to improved patient outcomes. However, the clinical impacts of artificial intelligence enhanced procedures remain unassessed. Additional research is necessary to evaluate both the advantages and disadvantages of artificial intelligence in the field of interventional pulmonology.
Organ storage in renal transplantation
Authors: Guo Yanbo , Luke Patrick , Sener Alp 
Published: November 2023

Purpose of review
Kidney transplantation is vital for those with end-stage renal disease, enhancing quality of life and longevity. It is the preferred treatment but is hindered by a global disparity between donor kidney availability and demand. Therefore, optimizing organ storage techniques is crucial to mitigate the effects of ischemia reperfusion injury in available organs. Recent interest has centered on innovative methods like oxygenated normothermic perfusion and abdominal regional perfusion.

Recent findings
Multiple recent metanalyses, including a Cochrane review, confirm the benefits of hypothermic machine perfusion (HMP) for deceased donor kidneys, demonstrating its utility and cost effectiveness. The benefits of oxygenated normothermic perfusion have been seen in retrospective data sets but not in prospective trials. Abdominal regional perfusion (aNRP) is gaining interest, especially for liver transplantation, but kidney specific data are scant.

Summary
High-quality evidence backs the use of HMP for deceased donor kidneys. Despite interest in other techniques, clinical evidence for their benefits in kidney transplantation is lacking. The gap between innovation and verified success emphasizes the need for continued research and collaboration between medical professionals, researchers, and ethical committees. This review aims to further illuminate the complexities and advancements in the field, bridging the knowledge gap and aiding in the continual pursuit of excellence in transplantation.
Characterizing residential mobility among people with HIV in Tennessee and its impact on HIV care outcomes
Authors: Ahonkhai Aima A. , Bian Aihua , Robbins Natalie N. , Maurer Laurie A. , Clouse Kate , Pierce Leslie J. , Perkins Jessica M. , Wernke Steven A. , Shepherd Bryan E. , Brantley Meredith 
Published: November 2023

Objective:
Our objective was to assess the prevalence and patterns of mobility among people with HIV (PWH) in Tennessee and its impact on HIV care outcomes.

Design:
Retrospective cohort study.

Methods:
We combined residential address and HIV surveillance data from PWH in Tennessee from 2016 to 2018. Using Poisson regression, we estimated associations between in-state mobility (change in address or total miles moved) in 1 year and outcomes in the subsequent year; retention: having two CD4+/HIV RNA values (labs) in a calendar year at least 3 months apart, loss to follow-up (LTFU): having labs at baseline but not the subsequent year, and viral suppression: HIV RNA less than 200 copies/ml. We applied a kernel density estimator to origin-destination address lines to visualize mobility patterns across demographic subgroups.

Results:
Among 17 428 PWH [median age 45 years (interquartile range; IQR 34–53)], 6564 (38%) had at least one move. Median miles moved was 8.9 (IQR 2.6–143.4)). We observed in-state movement between major cities (Chattanooga, Knoxville, Memphis and Nashville) and out-of-state movement to and from Georgia and Florida. Having at least one in-state move was associated with a decreased likelihood of retention [adjusted relative risk (aRR) = 0.91; 95% confidence interval (CI) 0.88–0.95], and an increased risk of LTFU (aRR = 1.17; 95% CI 1.04–1.31, two to three moves vs. none). Greater distance moved in-state was associated with decreased retention and increased LTFU (aRR = 0.53; 95% CI 0.49–0.58, aRR = 2.52; 95% CI 2.25–2.83, respectively for 1000 vs. 0 miles). There was no association between mobility and viral suppression.

Conclusion:
Mobility is common among PWH in Tennessee and is associated with initial poor engagement in HIV care.
Exploring Reliable and Identifiable Quantitative Anatomical, Timing, and Displacement Measures in the VFS of Speech
Authors: Street Melanie , Morrison Maeve , Miles Anna 
Published: November 2023

Aim:
Videofluroscopy studies of speech are a recognized assessment of velopharyngeal insufficiency (VPI). Yet, this method is subjective and has low inter-rater reliability. Quantitative measures of timing, distance, and area in videofluoroscopic studies of swallowing have been shown to be valid and reliable, but quantitative measures are not routinely used in videofluroscopy studies for VPI. This study explored the use of quantitative measures in patients with VPI in terms of feasibility and reliability.

Methods:
Forty patients of mixed etiology diagnosed with VPI through perceptual speech assessment underwent videofluroscopy. Anatomical landmarks and timing, distance, and area measurements were taken of the velopharyngeal port at rest and during speech tasks using specialized Swallowtail software. 50% of measures were double-blind rated to test inter-rater reliability. Raters reported on the time they took to complete each assessment and the challenges they had. Associations between measures were explored.

Results:
Ten timing, line, and area measures were developed based on 3 landmarks. Measures had moderate-substantial inter-rater reliability (intraclass coefficient: 0.69–0.91) except for time to lift (secs), which only achieved fair agreement (intraclass coefficient: 0.56). Measures demonstrated internal consistency (R>0.60). Raters took, on average, 15 mins per patient and reported some challenges with image resolution, especially in timing measures where structures were blurred by movement.

Conclusion:
Quantitative measures are reliable and have the potential to add novel information regarding VPI to support multidisciplinary decision-making. Further research with larger patient cohorts is needed to clarify how quantitative measures can support tailored decisions about surgical and therapeutic interventions in order to maximize outcomes for individuals.