bluuebunny/crossref_metadata_2025_split huggingface dataset:
Capturing the incidence of patient agitation amongst conscious sedation ERCPs and the impact on therapeutic outcomes
Authors: Keating Eoin , Bennett Gayle , Martir Harvey , Kelleher Barry , Stewart Stephen , Ramlaul Navneet , McKenny Michael , Leyden Jan 
Published: November 2024

Background:
Completing advanced endoscopic procedures such as endoscopic retrograde cholangiopancreatography (ERCP) under conscious sedation is challenging. International recommendations favor enhanced sedation (e.g. propofol) for ERCP. Conscious sedation can result in sedation-related failure (SRF) and agitation for some patients, limiting therapeutic efficacy.

Aim:
The aim of this study is to establish the risk of SRF and the impact on therapeutic success under conscious sedation practice in a single tertiary referral center.

Methods:
A retrospective review of a prospectively maintained ERCP database, analyzing sedation, procedural success, and complications.

Results:
Over 19 months, 807 conscious sedation ERCPs were recorded. Median midazolam dose was 5 mg (range 1–14 mg) and median fentanyl dose was 75 µg (0–200 µg). Sedation reversal was required in 0.1% of cases (1/807). Overall ductal cannulation rate was 92%. Severe agitation was recorded in 11% (86/807) of conscious sedation ERCP reports with SRF present in 3% (22/807). Patient agitation resulted in significantly lower cannulation (81% vs 92%, P = 0.002) and successful clearance rates (49% vs 85%, P = 0.002) versus non-agitated cases. Complication and pancreatitis rates were unaffected. Highest rates of SRF and agitation were identified in female patients, patients aged <50 years old, and post-operative biliary leak indications.

Conclusion:
Over 10% of conscious sedation ERCPs are compromised by sedation issues, resulting in procedure abandonment or significantly diminished therapeutic success. General anesthetic ERCP is beneficial in facilitating biliary access, removing the risk of agitation and providing stability to aid cannulation. Female patients, patients aged <50 years, and post-operative biliary leak ERCPs appear as the priority cases for enhanced sedation support.
Risk factors of complications after thermal ablation for hepatocellular carcinoma: the role of assessment of liver background
Authors: Xie Yuhua , Liu Jing , Shi Yifan , Xie Xiaoyan , Yu Jie , Xu Ming , Xie Xiaohua , Huang Guangliang , Zhuang Bowen , Bi Mingsen , Qu Dongjie , Fan Fangying , Ying Minghua , Sun Qingqing , Lin Manxia , Liang Ping 
Published: November 2024

Objective
To use an elastography technology and other clinical and radiological data for assessment of liver background and analyze risk factors of complications after thermal ablation in patients with hepatocellular carcinoma.

Methods
Demographics, laboratory analyses, and radiological characteristics were collected from all patients. Main elastography-related indicators included F index (fibrosis index), A index (inflammation index), ATT (attenuation coefficient), E (kPa), AREA (area of blue parts), and CORR (correlation). All complications after thermal ablation were collected. Univariate analysis was performed to detect significant variables, which subsequently entered a stepwise logistic regression analysis (conditional forward selection) to identify independent variables.

Results
A total of 218 patients from October 2020 to June 2023 with 291 thermal ablation sessions were enrolled. 115 patients (52.8%) developed complications. Fifteen patients (6.9%) developed major complications. Minor complications included postoperative pain (20.6%), fever (19.3%), effusion (22.5%), and hyperammonemia (1.8%). AREA (P = 0.034), tumor size (P = 0.005), and abnormal aspartate aminotransferase (AST) (P = 0.018) were independent predictors for complications. F index (P = 0.021), tumor size (P < 0.001), and abnormal AST (P = 0.047) were independent predictors for effusion. The results of univariate analysis of infection showed that tumor size, CORR, ATT, diabetes, Child–Turcotte–Pugh grade, abnormal AST, total protein, and albumin were significant (all P < 0.05).

Conclusion
Several radiological and combinational elastography indicators related to liver fibrosis, steatosis, or inflammation were significantly correlated with the occurrence of complications. Clinical assessment of the liver background should not be neglected in the management of postablation complications.
Diagnostic and therapeutic challenges in implementing hypertension management after kidney transplantation
Authors: Tantisattamo Ekamol , Ferrey Antoney J. , Reddy Uttam G. , Redfield Robert R. , Ichii Hirohito , Al Ammary Fawaz , Lau Wei Ling 
Published: November 2024

Purpose of review
Evidence for blood pressure (BP) measurement and hypertension management in kidney transplant recipients (KTR) remains lacking.

Recent findings
Accurate BP measurement technique is a critical component of hypertension management, and 24-h ambulatory BP monitoring remains the gold standard for diagnosis of hypertension in KTR. BP target at different periods posttransplant is uncertain, but likely higher than that in nontransplant patients given factors related to long-standing uremic milieu and kidney transplantation such as vascular calcification altering transplant renal hemodynamic and allograft perfusion and immunosuppression. Dividing BP target into immediate, early, and late posttransplant periods can guide differential diagnoses of hypertension and BP control with a target SBP less than 160 mmHg in general and BP 115–135/65–85 mmHg for adult KTR receiving pediatric kidneys during the immediate posttransplant period, 130/80 mmHg during early and late posttransplant periods. Calcium channel blockers were shown to have favorable graft outcomes. Novel antihypertensive medications for resistant and refractory hypertension and device-based therapies are limited due to KTR's ineligibility for participating in clinical trials.

Summary
In KTR, BP measurement and monitoring practice should follow the standard clinical practice guideline for nontransplant patients by considering posttransplant factors and immunosuppressive state. Novel treatment options required further studies.
A pilot study of the impact of repeated blink refrainment on ocular surface temperature and the interblink period
Authors: Li Wing , Graham Andrew D. , Lin Meng C. 
Published: November 2024

SIGNIFICANCE
This study examines a potential stress test of repeated blink refrainment and its effects on the interblink period and the rate of evaporative ocular surface cooling. Such a test could aid in the study of computer vision syndrome, in which screen users unconsciously delay blinking, leading to onset of symptoms.

PURPOSE
This study aimed to examine the relationship between the length of the maximum achievable interblink time and the rate of ocular surface cooling under stress test conditions of repeated refrainment from blinking for as long as possible.

METHODS
Subjects acclimated to the examination room for 10 minutes before measurement and then were asked to hold the eyes open and refrain from blinking for as long as possible (the maximum blink interval), while ocular surface temperature was recorded using an infrared thermographic video camera. Subjects completed 20 trials with four successive blinks separating each trial.

RESULTS
Fifteen subjects (8 female and 7 male subjects) completed the study. The grand mean ocular surface cooling rate was −0.027°C/s (range, −0.338 to +0.014°C/s). A faster ocular surface cooling rate was significantly related to an exponentially shorter maximum blink interval (p<0.001). An increasing number of trials was related to a clinically insignificant increase in the length of the maximum blink interval overall, and a post hoc analysis revealed subject subgroups for whom the stress test was effective or ineffective.

CONCLUSIONS
The ocular surface evaporatively cools exponentially during periods of blink refrainment. With a subgroup of subjects with initially stable tear films and normal lipid layer thickness, cumulative tear film stress from repeated, longer-term blink refrainment could contribute to tear evaporation and symptoms of computer vision syndrome.
Noninferiority Randomized Clinical Trial: KIM Sling With Reusable Trocars Versus TVT Exact Sling
Authors: Margulies Samantha L. , Osment Anna E. , Bernard Adele , Schroeder Michelle N. , Askew Amy L. , Agu Ijeoma S. , Kunycky Christina A. , Geller Elizabeth J. , Willis-Gray Marcella , Chu Christine M. , Wu Jennifer M. 
Published: November 2024

Importance
The Neomedic Knotless Incontinence Mesh (KIM) sling with sterilizable trocars decreases medical waste versus midurethral slings with disposable trocars. Limited comparative data exist.

Objective
The aim of the study was to assess to the success of the retropubic KIM sling compared to the Gynecare TVT Exact sling.

Study Design
This was a single-center, randomized noninferiority trial comparing outcomes of 2 retropubic slings—KIM sling and TVT Exact sling—in women with stress urinary incontinence from August 2021 to May 2023. Primary outcome was subjective success at 6 weeks defined by a composite outcome of the response to the question #17 on the The Pelvic Floor Distress Inventory-20 questionnaire and no retreatment of stress urinary incontinence. Secondary outcomes included rates of urinary retention, mesh erosion, and reoperation for mesh complications. Sample size estimate based on noninferiority margin of 14%, equal success of 90%, alpha 0.05, and 80% power with a 20% dropout was 72 per group.

Results
Among 147 patients, 74 (50.3%) were randomized to KIM sling versus 73 (49.7%) to TVT exact. The rates of 6-week success were 68.5% for the KIM sling and 83.3% for the TVT exact with a risk difference 14.8% (95% confidence interval, 1.1–28.5). The KIM sling is not noninferior to the TVT Exact sling. There were no differences in secondary outcomes.

Conclusions
The KIM sling is not noninferior to the TVT Exact sling for success at 6 weeks based on a composite outcome score. This clinical trial is ongoing to assess outcomes at 6 months and 1 year. (Clinicaltrials.gov NCT04985799)
Family screening for hypertrophic cardiomyopathy: initial cardiologic assessment, and long-term follow-up of genotype-positive phenotype-negative individuals
Authors: Schoonvelde Stephan A.C. , Alexandridis Georgios M. , Price Laura B. , Schinkel Arend F.L. , Hirsch Alexander , Zwetsloot Peter-Paul , Kammeraad Janneke A.E. , van Slegtenhorst Marjon A. , Verhagen Judith M.A. , de Boer Rudolf A. , Michels Michelle 
Published: November 2024

AbstractAims(i) Investigate the prevalence of hypertrophic cardiomyopathy (HCM) in individuals with pathogenic/likely pathogenic (P/LP) gene variants detected through family cascade testing in relatives, and (ii) evaluate phenotypic progression in genotype-positive phenotype-negative (G+/P-) individuals during follow-up.ResultsFrom 2000-2023, 273 individuals underwent cardiologic evaluation following P/LP variant detection through family screening. Upon initial evaluation, HCM was diagnosed in 128 (47%) individuals. Comparing with 145 G+/P- individuals, HCM patients were older (48 vs 38 years,p<0.001) and more likely male (57% vs 34%,p<0.001). During follow-up (median 11 years), 14 (11%) of the HCM patients died (two from sudden cardiac death), four (3%) underwent myectomy, 15 (12%) developed atrial fibrillation and 17 (13%) required implantable cardioverter-defibrillator implantation (15 primary prevention, 88%). HCM-related adverse outcomes correlated with younger diagnosis age.During follow-up (median 8 years), out of the 118 G+/P- subjects, seven (6%) individuals (71% female, diagnosed age 39-77, after median follow-up 6 years) developed HCM (mean maximal wall thickness increasing from 10.2 mm to 13.3 mm). In this G+/P- cohort, significant echocardiographic changes from baseline to last visit were negligible. Over half (56%) had <1 mm change of maximal wall thickness. No adverse cardiac outcomes occurred.ConclusionThe initial evaluation was high-yield, with HCM being diagnosed in 47% of G+ individuals, more frequently in older males. Over a median 8-year follow-up, 6% of G+/P- individuals developed mild HCM, with no adverse cardiac outcomes. These data support initial screening in all first degree relatives, but (very) low-frequency cardiologic evaluations for G+/P- individuals thereafter.
The Fly Disco: Hardware and software for optogenetics and fine-grained fly behavior analysis
Authors: Robie Alice A. , Taylor Adam L. , Schretter Catherine E. , Kabra Mayank , Branson Kristin 
Published: November 2024

AbstractIn the fruit fly,Drosophila melanogaster, connectome data and genetic tools provide a unique opportunity to study complex behaviors including navigation, mating, aggression, and grooming in an organism with a tractable nervous system of 140,000 neurons. Here we present the Fly Disco, a flexible system for high quality video collection, optogenetic manipulation, and fine-grained behavioral analysis of freely walking and socializing fruit fly groups. The data collection hardware and software automates the collection of videos synced to programmable optogenetic stimuli. Key pipeline features include behavioral analysis based on trajectories of 21 keypoints and optogenetic-specific summary statistics and data visualization. We created themultiflydataset for pose estimation that includes 9701 examples enriched in complex behaviors. All hardware designs, software, and themultiflydataset are freely available.
The Condensin II Complex Regulates the Expression of Essential Gene Expression Programs During Erythropoiesis
Authors: Abid Deanna , Murphy Kristin , Murphy Zachary , Rahman Nabil , Getman Michael , Steiner Laurie 
Published: November 2024

AbstractErythropoiesis is characterized by dramatic changes in gene expression in the context of a cell that is rapidly proliferating while simultaneously condensing its nucleus in anticipation of enucleation. The mechanisms that maintain high level expression of erythroid genes and promote nuclear condensation remain poorly understood. Condensin II is a ring-like complex that promotes mitotic chromatin condensation and has roles in regulating interphase chromatin architecture and gene expression. We interrogated the role of Condensin II in erythropoiesis using an erythroid-specific deletion of the Condensin II subunit, Ncaph2. Ncaph2 loss resulted in severe embryonic anemia with lethality at embryonic day 13.5. Ncaph2 mutant erythroid cells had dysregulated maturation and disrupted cell cycle progression, but surprisingly Ncaph2 was dispensable for nuclear condensation. Genomic studies revealed that Ncaph2 occupied the promoter of key erythroid and cell cycle genes that were downregulated following Ncaph2 loss. Together, our results demonstrate an essential role for Ncaph2 in the gene expression programs that regulate cell cycle progression and erythroid differentiation, and identify a key role for the Condensin II complex in the regulation of a lineage-specific differentiation program.Summary StatementThe Condensin II complex regulates cell cycle progression and erythroid differentiation, but is dispensable for nuclear condensation during terminal erythroid maturation.
NovumRNA: accurate prediction of non-canonical tumor antigens from RNA sequencing data
Authors: Ausserhofer Markus , Rieder Dietmar , Facciolla Manuel , Lamberti Giorgia , Lisandrelli Rebecca , Pellegatta Serena , Trajanoski Zlatko , Finotello Francesca 
Published: November 2024

SummaryNon-canonical tumor-specific antigens (ncTSAs) can expand the pool of targets for cancer immunotherapy, but require robust and comprehensive computational pipelines for their prediction. Here, we present NovumRNA, a fully-automated Nextflow pipeline for predicting different classes of ncTSAs from patients’ RNA sequencing data. We extensively validated NovumRNA using publicly-available and newly-generated datasets, demonstrating the robustness of its analytical modules and predictions. NovumRNA analysis of colorectal cancer organoid data revealed comparable ncTSA potential for microsatellite stable and unstable tumors and candidate therapeutic targets for patients with low tumor mutational burden. Finally, our investigation of glioblastoma cell lines demonstrated increased ncTSAs burden upon indisulam treatment, and detection by NovumRNA of therapy-induced ncTSAs, which we could validate experimentally. These findings underscore the potential of NovumRNA for identifying synergistic drugs and novel therapeutic targets for immunotherapy, which could ultimately extend its benefit to a broader patient population.
Protein-RNA condensation kinetics via filamentous nanoclusters
Authors: Peralta-Martinez Ramon , Visentin Araceli , Salgueiro Mariano , Borkosky Silvina , Ajalla Aleixo Mariana Araujo , Portugal Rodrigo Villares , Sanchez Ignacio Enrique , Prat-Gay Gonzalo 
Published: November 2024

AbstractProtein-RNA phase separation is at the center of membraneless biomolecular condensates governing cell physiology and pathology. Using an archetypical viral protein-RNA condensation model, we determined the sequence of events that starts with sub-second formation of a protomer with two RNAs per protein dimer. Association of additional RNA molecules to weaker secondary binding sites in this protomer kickstarts crystallization-like assembly of a molecular condensate. Primary nucleation is faster than the sum of secondary nucleation and growth, which is a multistep process. Protein-RNA nuclei grow over hundreds of seconds into filaments and subsequently into nanoclusters with circa 600 nm diameter. Cryoelectron microscopy reveals an internal structure formed by incoming layers of protein-RNA filaments made of ribonucleoprotein oligomers, reminiscent of genome packing of a nucleocapsid. These nanoclusters progress to liquid condensate droplets that undergo further partial coalescence to yield typical hydrogel-like protein-RNA coacervates that may represent the scaffold of large viral factory condensates in infected cells. Our integrated experimental kinetic investigation exposes rate limiting steps and structures along a key biological multistep pathway present across life kingdoms.
Passing the quadrat: inferring biodiversity change over time and across investigators
Authors: Elahi Robin , Micheli Fiorenza , Watanabe James 
Published: November 2024

AbstractLong-term ecological monitoring inevitably requires a ‘passing of the quadrat’ from one investigator to another. Here we present the challenge and opportunity of inferring biodiversity change over time and across investigators using a rocky intertidal case study. The intertidal transect was surveyed initially by Willis Hewatt in 1931-1933, then resurveyed in detail by Rafe Sagarin, Sarah Gilman, and their mentors in 1993. In total, the transect has been resurveyed 17 times over the past three decades, with annual surveys nested within five distinct investigator eras. We addressed two goals with our dataset. First, we asked whether temporal change in several biodiversity metrics (species richness, Hill-Shannon and Hill-Simpson diversity, spatial beta diversity) was sensitive to investigator era. Second, we identified recent ecological ‘winners’ and ‘losers’, relative to the historical baseline, and asked whether such designations can change over time (1993-2023). We show that investigators contributed to variable trends in species richness over time, and we hypothesize that sampling effort contributed to this effect. In contrast, we highlight declines in the biodiversity of common species (Hill-Shannon) and dominant species (Hill-Simpson) over time, in the absence of investigator effects. These declines were associated with the rise of a few numerically dominant species and a trend of increasing spatial similarity. Relative to the historical baseline, ecological winners included certain barnacles, anemones, and turban snails, while losers included mussels, urchins, limpets and a host of more cryptic taxa. However, we show that such designations can be complicated by non-linear population trajectories and discuss mechanisms related to climate change versus potential artifacts related to investigator effort. We finish with recommendations and emphasize the value of marine stations in providing a venue for sustained periodic ecological monitoring at small spatial scales, long duration, and fine taxonomic resolution.
Estimating the effective reproduction number from wastewater (Rt): A methods comparison
Authors: Hill Dustin T. , Zhu Yifan , Dunham Christopher , Moran Joe , Zhou Yiquan , Collins Mary B. , Kmush Brittany L. , Larsen David A. 
Published: November 2024

AbstractBackgroundThe effective reproduction number (Rt) is a dynamic indicator of current disease spread risk. Wastewater measurements of viral concentrations are known to correlate with clinical measures of diseases and have been incorporated into methods for estimating the Rt.MethodsWe review wastewater-based methods to estimate the Rtfor SARS-CoV-2 based on similarity to the reference case-based Rt, ease of use, and computational requirements. Using wastewater data collected between August 1, 2022 and February 20, 2024 from 200 wastewater treatment plants across New York State, we fit eight wastewater Rtmodels identified from the literature. Each model is compared to the Rtestimated from case data for New York at the sewershed (wastewater treatment plant catchment area), county, and state levels.ResultsWe find a high degree of similarity across all eight methods despite differences in model parameters and approach. Further, two methods based on the common measures of percent change and linear fit reproduced the Rtfrom case data very well and a GLM accurately predicted case data. Model output varied between spatial scales with some models more closely estimating sewershed Rtvalues than county Rtvalues. Similarity to clinical models was also highly correlated with the proportion of the population served by sewer in the surveilled communities (r = 0.77).ConclusionsWhile not all methods that estimate Rtfrom wastewater produce the same results, they all provide a way to incorporate wastewater concentration data into epidemic modeling. Our results show that straightforward measures like the percent change can produce similar results of more complex models. Based on the results, researchers and public health officials can select the method that is best for their situation.Key messagesWastewater data has been used to estimate the Rtin different ways but the relative strengths and weaknesses of each method were unknown.Rtestimation results from wastewater data are influenced by sewershed population size and geographic aggregation making selection of the best method dependent on the study location and available data.Estimating the Rtfrom wastewater is desirable because wastewater data are anonymous, comprehensive, and efficient for measuring disease burden.