bluuebunny/crossref_metadata_2025_split huggingface dataset:
Excreted 99mTc-Pertechnetate in a Renal Pelvis as a Potential False Positive in a Meckel’s Scan
Authors: Lanzo Shannon M. , Pantel Austin R. , Zhuang Hongming 
Published: July 2022

Abstract
A 14-year-old girl presented with right lower quadrant pain. A 99mTc-pertechnetate scan with SPECT/CT was performed to exclude a Meckel's diverticulum. The images demonstrated focal tracer uptake in the right midabdomen, which appeared early and decreased over time. However, SPECT/CT revealed that this uptake corresponded to the right renal pelvis, which was located more inferior than expected. This case emphasizes the importance of recognizing anatomic variants that may cause focal tracer uptake, as well as leveraging an understanding of tracer kinetics to inform a diagnosis.
Relating Metopic Craniosynostosis Severity to Intracranial Pressure
Authors: Blum Jessica D. , Beiriger Justin , Kalmar Christopher , Avery Robert A. , Lang Shih-Shan , Villavisanis Dillan F. , Cheung Liana , Cho Daniel Y. , Tao Wenzheng , Whitaker Ross , Bartlett Scott P. , Taylor Jesse A. , Goldstein Jesse A. , Swanson Jordan W. 
Published: July 2022

Purpose:
A subset of patients with metopic craniosynostosis are noted to have elevated intracranial pressure (ICP). However, it is not known if the propensity for elevated ICP is influenced by the severity of metopic cranial dysmorphology.

Methods:
Children with nonsyndromic single-suture metopic synostosis were prospectively enrolled and underwent optical coherence tomography to measure optic nerve head morphology. Preoperative head computed tomography scans were assessed for endocranial bifrontal angle as well as scaled metopic synostosis severity score (MSS) and cranial morphology deviation score determined by CranioRate, an automated severity classifier.

Results:
Forty-seven subjects were enrolled between 2014 and 2019, at an average age of 8.5 months at preoperative computed tomography and 11.8 months at index procedure. Fourteen patients (29.7%) had elevated optical coherence tomography parameters suggestive of elevated ICP at the time of surgery. Ten patients (21.3%) had been diagnosed with developmental delay, eight of whom demonstrated elevated ICP. There were no significant associations between measures of metopic severity and ICP. Metopic synostosis severity score and endocranial bifrontal angle were inversely correlated, as expected (r=−0.545, P<0.001). A negative correlation was noted between MSS and formally diagnosed developmental delay (r=−0.387, P=0.008). Likewise, negative correlations between age at procedure and both MSS and cranial morphology deviation was observed (r=−0.573, P<0.001 and r=−0.312, P=0.025, respectively).

Conclusions:
Increased metopic severity was not associated with elevated ICP at the time of surgery. Patients who underwent later surgical correction showed milder phenotypic dysmorphology with an increased incidence of developmental delay.
Retrospective Analysis of Retroperitoneal-Abdominal-Pelvic Ganglioneuromas
Authors: Noh Sangkyu , Nessim Carolyn , Keung Emily Z. , Roland Christina L. , Strauss Dirk , Sivarajah Gausihi , Fiore Marco , Biasoni Davide , Cioffi Stefano Piero Bernardo , Mehtsun Winta , Cananzi Ferdinando Carlo Maria , Sicoli Federico , Quagliuolo Vittorio , Chen Jun , Luo Chenghua , Gladdy Rebecca A. , Swallow Carol , Johnston Wendy , Ford Samuel J. , Evenden Caroline , Tirotta Fabio , Almond Max , Nguyen Laura , Rutkowski Piotr , Krotewicz Maria , Pennacchioli Elisabetta , Cardona Kenneth , Gamboa Adriana , Hompes Daphne , Renard Marleen , Kollár Attila , Ryser Christoph O. , Vassos Nikolaos , Raut Chandrajit P. , Fairweather Mark , Krakorova Dagmar Adamkova , Quildrian Sergio , Perhavec Andraz , Nizri Eran , Farma Jeffrey M. , Greco Stephanie H. , Vincenzi Bruno , Lopez José Antonio González , Solerdecoll Mireia Solans , Iwata Shintaro , Fukushima Suguru , Kim Teresa , Tolomeo Francesco , Snow Hayden , Howlett-Jansen Ynez , Tzanis Dimitri , Nikulin Maxim , Gronchi Alessandro , Sicklick Jason K. ,   on behalf of the Transatlantic Australasian Retroperitoneal Sarcoma Working Group
Published: July 2022

Objective:
The Transatlantic Australasian Retroperitoneal Sarcoma Working Group conducted a retrospective study on the disease course and clinical management of ganglioneuromas.

Background:
Ganglioneuromas are rare tumors derived from neural crest cells. Data on these tumors remain limited to case reports and single-institution case series.

Methods:
Patients of all ages with pathologically confirmed primary retroperitoneal, intra-abdominal, and pelvic ganglioneuromas between January 1, 2000, and January 1, 2020, were included. We examined demographic, clinicopathologic, and radiologic characteristics, as well as clinical management.

Results:
Overall, 328 patients from 29 institutions were included. The median age at diagnosis was 37 years with 59.1% of patients being female. Symptomatic presentation comprised 40.9% of cases, and tumors were often located in the extra-adrenal retroperitoneum (67.1%). At baseline, the median maximum tumor diameter was 7.2 cm. One hundred sixteen (35.4%) patients underwent active surveillance, whereas 212 (64.6%) patients underwent resection with 74.5% of operative cases achieving an R0/R1 resection. Serial tumor evaluations showed that malignant transformation to neuroblastoma was rare (0.9%, N=3). Tumors undergoing surveillance had a median follow-up of 1.9 years, with 92.2% of ganglioneuromas stable in size. With a median follow-up of 3.0 years for resected tumors, 84.4% of patients were disease free after resections, whereas recurrences were observed in 4 (1.9%) patients.

Conclusions:
Most ganglioneuromas have indolent disease courses and rarely transform to neuroblastoma. Thus, active surveillance may be appropriate for benign and asymptomatic tumors particularly when the risks of surgery outweigh the benefits. For symptomatic or growing tumors, resection may be curative.
Outcome of Pancreatic Surgery During the First 6 Years of a Mandatory Audit Within the Dutch Pancreatic Cancer Group
Authors: Suurmeijer J. Annelie , Henry Anne Claire , Bonsing Bert A. , Bosscha Koop , van Dam Ronald M. , van Eijck Casper H. , Gerhards Michael F. , van der Harst Erwin , de Hingh Ignace H. , Intven Martijn P. , Kazemier Geert , Wilmink Johanna W. , Lips Daan J. , Wit Fennie , de Meijer Vincent E. , Molenaar I. Quintus , Patijn Gijs A. , van der Schelling George P. , Stommel Martijn W.J. , Busch Olivier R. , Groot Koerkamp Bas , van Santvoort Hjalmar C. , Besselink Marc G. ,   for the Dutch Pancreatic Cancer Group
Published: July 2022

Objective:To describe outcome after pancreatic surgery in the first 6 years of a mandatory nationwide audit.Background:Within the Dutch Pancreatic Cancer Group, efforts have been made to improve outcome after pancreatic surgery. These include collaborative projects, clinical auditing, and implementation of an algorithm for early recognition and management of postoperative complications. However, nationwide changes in outcome over time have not yet been described.Methods:This nationwide cohort study included consecutive patients after pancreatoduodenectomy (PD) and distal pancreatectomy from the mandatory Dutch Pancreatic Cancer Audit (January 2014–December 2019). Patient, tumor, and treatment characteristics were compared between 3 time periods (2014–2015, 2016–2017, and 2018–2019). Short-term surgical outcome was investigated using multilevel multivariable logistic regression analyses. Primary endpoints were failure to rescue (FTR) and in-hospital mortality.Results:Overall, 5345 patients were included, of whom 4227 after PD and 1118 after distal pancreatectomy. After PD, FTR improved from 13% to 7.4% [odds ratio (OR) 0.64, 95% confidence interval (CI) 0.50–0.80,P<0.001] and in-hospital mortality decreased from 4.1% to 2.4% (OR 0.68, 95% CI 0.54–0.86,P=0.001), despite operating on more patients with age >75 years (18%–22%,P=0.006), American Society of Anesthesiologists score ≥3 (19%–31%,P<0.001) and Charlson comorbidity score ≥2 (24%–34%,P<0.001). The rates of textbook outcome (57%–55%,P=0.283) and major complications remained stable (31%–33%,P=0.207), whereas complication-related intensive care admission decreased (13%–9%,P=0.002). After distal pancreatectomy, improvements in FTR from 8.8% to 5.9% (OR 0.65, 95% CI 0.30–1.37,P=0.253) and in-hospital mortality from 1.6% to 1.3% (OR 0.88, 95% CI 0.45–1.72,P=0.711) were not statistically significant.Conclusions:During the first 6 years of a nationwide audit, in-hospital mortality and FTR after PD improved despite operating on more high-risk patients. Several collaborative efforts may have contributed to these improvements.
Integrating large scale genetic and clinical information to predict cases of heart failure
Authors: Wu Kuan-Han H. , Wolford Brooke N. , Yu Xianshi , Douville Nicholas J. , Mathis Michael R. , Graham Sarah E. ,   Global Biobank Meta-analysis Initiative (GBMI), Surakka Ida , Hornsby Whitney E. , Bian Jiang , Zhao Lili , Willer Cristen J. , Shi Xu 
Published: July 2022

ABSTRACTBackgroundHeart failure (HF) is a major cause of death globally. Prediction of HF risk and early initiation of treatment could mitigate disease progression.ObjectivesThe study aimed to improve the prediction accuracy of HF by integrating genome-wide association studies (GWAS)- and electronic health records (EHR)-derived risk scores.MethodsWe previously performed the largest HF GWAS to date within the Global Biobank Meta-analysis Initiative to create a polygenic risk score (PRS). To extract clinical information from high-dimensional EHR data, we treated diagnosis codes as ‘words’ and leveraged natural language processing techniques to create a clinical risk score (ClinRS). Our method first learned code co-occurrence patterns and extracted 350 latent phenotypes (low-dimensional features) representing EHR codes, then used coefficients from regression of HF on the latent phenotypes in a training set as weights to calculate patient ClinRS in a validation set. Model performances were compared between baseline (age and sex) model and models with risk scores added: 1) PRS, 2) ClinRS, and 3) PRS+ClinRS. We further compared the proposed models with Atherosclerosis Risk in Communities (ARIC) heart failure risk score.ResultsResults showed that PRS and ClinRS were each able to predict HF outcomes significantly better than the baseline model, up to eight years prior to HF diagnosis. By including both PRS and ClinRS in the model, we achieved superior performance in predicting HF up to ten years prior to HF diagnosis, two years earlier than using a single risk predictor alone. Additionally, we found that ClinRS performed significantly better than ARIC model at one year prior to disease diagnosis.ConclusionsWe demonstrate the additive power of integrating GWAS- and EHR-derived risk scores to predict HF cases prior to diagnosis.
Impact of Selection Bias on Polygenic Risk Score Estimates in Healthcare Settings
Authors: Lee Younga Heather , Thaweethai Tanayott , Sheu Yi-han , Feng Yen-Chen Anne , Karlson Elizabeth W. , Ge Tian , Kraft Peter , Smoller Jordan W. 
Published: July 2022

ABSTRACTBackgroundHospital-based biobanks have become an increasingly prominent resource for evaluating the clinical impact of disease-related polygenic risk scores (PRS). However, biobank cohorts typically rely on selection of volunteers who may differ systematically from non-participants.MethodsPRS weights for schizophrenia, bipolar disorder, and depression were derived using summary statistics from the largest available genomic studies. These PRS were then calculated in a sample of 24,153 European ancestry participants in the Mass General Brigham (MGB) Biobank. To correct for selection bias, we fitted a model with inverse probability (IP) weights estimated using 1,839 sociodemographic and clinical features extracted from electronic health records (EHRs) of eligible MGB patients. Finally, we tested the utility of a modular specification of the IP weight model for selection.ResultsCase prevalence of bipolar disorder among participants in the top decile of bipolar disorder PRS was 10.0% (95% CI: 8.8%-11.2%) in the unweighted analysis but only 6.2% (5.0%-7.5%) when selection bias was accounted for using IP weights. Similarly, case prevalence of depression among those in the top decile of depression PRS was reduced from 33.5% (31.7%-35.4%) in the unweighted analysis to 28.9% (25.8%-31.9%) after IP weighting. Modular correction for selection bias in intermediate selection steps did not substantially impact PRS effect estimates.ConclusionsNon-random selection of participants into volunteer biobanks may induce clinically relevant selection bias that could impact implementation of PRS and risk communication in clinical practice. As efforts to integrate PRS in medical practice expand, recognition and mitigation of these biases should be considered.
Association between pregnancy and severe COVID-19 symptoms in Qatar: a cross-sectional study
Authors: Al-Qassem Alla’ K. , Humaidi Ammar B. , Al-Kuwari Amna K. , Hasan Elham M. , Yakti Nosaiba H. , Al-Hathal Rakan M. , Bansal Devendra , Abd Farag Elmoubashar Abu Baker , Al-Romaihi Hamad E. , Al-Thani Mohammed H. J. , Musa Omran A. H. , Doi Suhail , Chivese Tawanda 
Published: July 2022

AbstractBackgroundThere is inconclusive evidence whether pregnancy exacerbates COVID-19 symptoms or not, and scarce data from the Middle East and North Africa region. The aim of this study was to investigate the association between pregnancy and COVID-19 symptoms in Qatar.MethodsThis cross-sectional study was carried out using data of all women with confirmed COVID-19, comparing pregnant and non-pregnant women of child-bearing age (18-49 years). Data of all COVID-19 cases were collected by the Ministry of Public Health (MoPH) in Qatar, between March and September 2020. Symptoms were compared by pregnancy status and classified into moderate and severe. Multivariable logistic and poisson regression was carried out to investigate the association between pregnancy and severity of COVID-19 symptoms.ResultsDuring the study period, 105744 individuals were diagnosed with COVID-19, 16908 were women of childbearing age. From that sample, 799 women who were pregnant (mean age 29.9 years (SD 5.2)) and 16109 women who were not pregnant (mean age 33.1 years (SD 7.8)). After multivariable logistic regression, pregnancy was associated with a 1.4-fold higher odds of reporting any symptoms of COVID-19 (OR 1.41, 95% CI 1.18-1.68), and 1.3-fold higher odds of reporting shortness of breath (OR 1.29, 95% CI 1.02-1.63). After multivariable poisson regression, pregnancy was also associated with a higher number of symptoms (IRR 1.03, 95%CI 0.98-1.08).ConclusionOur findings suggest that, in this setting, pregnant women are more likely to have symptomatic COVID-19, and shortness of breath, compared to non-pregnant women of childbearing age.
Ocular Biometry Profile of Adult Cataract Surgery Candidates at University of Gondar, Tertiary Eye Care and Training Center, North West Ethiopia
Authors: Feleke Bemnet , Mulugeta Wossen , Wondale Teshager , Tsegaw Asamere 
Published: July 2022

AbstractBackgroundPrecise measurement of the radius of curvature [K (mm)] and axial length (AL) of the eye are vital for a good outcome of a cataract extraction surgery. Average values of these dimensions of the optical components depend on race, age and gender. Although there are a number of studies that describe these mean parameters in the Caucasian, Hispanic and Asian populations, there has been little attention given to the African population.ObjectivesThe aim of this study was to estimate the biometric parameters of patients who had cataract surgery at University of Gondar (UoG), Tertiary eye care and training centre.Materials and methodsHospital based cross sectional study was done on patients who visited UoG Tertiary Eye Care and Training Center for cataract extraction surgery. Righton retinomax K plus 3 autorefractor,(Hutama Medical, Indonesia) and Pac Scan 300A contact A scan ultrasound, (Sonomed Escalon, NY, USA) were used to measure K (mm) and AL and calculate intraocular lens (IOL) power, respectively. Data were collected using a structured questionnaire, then entered to SPSS version 25 statistical software and analyzed.ResultA total of 838 eyes (433 right eyes and 405 left eyes) of 486 of patients were included in this study. The mean age was 62.5 ±12.88 years. The mean K1 and K2 were 7.75±0.38 mm and 7.48±0.33 mm, respectively. The mean average of K1 and K2 (AVK) was 7.61±0.33 mm. The mean AL measured was 23.06±1.05 mm and the mean Intraocular Lens (IOL) power calculated was 21.12±2.95 D. Significant difference in mean AVK and mean AL of the eye exists between male and female patients, p value =0.000.ConclusionThis study provides the mean values of radius of curvature of cornea, axial length of the eye and IOL power of patients who were about to undergo cataract extraction surgery at the study center. Male patients had steeper corneas and longer axial lengths than females. But age had a variable effect on both AVK and AL.
Flowering cues in a Costa Rican cloud forest: analyzing the effect of climate
Authors: Travers Steven E. , Dochtermann Ned A. 
Published: July 2022

ABSTRACTThe influence of a changing climate on the phenology of organisms in a region is dependent on how regional climate cues or modifies the timing of local life history events and how those cues are changing over time. There is extensive evidence of phenolological shifts in flowering time over the past 50 years in response to increasing temperatures in temperate regions, but far less is known about tropical regions where seasonality is less temperature driven. We examined historical datasets of flowering patterns in two guilds of ornithophilous plants in the montane cloud forests of Monteverde, Costa Rica in order to identify environmental cues for flowering in nine species of plant that are important resources for hummingbirds. Bimonthly censuses of flower production were used to quantify flower production during two sampling periods:1981-1983, 1986-1991., the species studied here appear to cue flowering patterns to either accumulated drought units or a combination of accumulated drought units and chill units prior to flowering. These results have implications for how tropical cloud forest plants will respond to climate change to the extent that drought and chill patterns are changing with time.
COLLAPSE: A representation learning framework for identification and characterization of protein structural sites
Authors: Derry Alexander , Altman Russ B. 
Published: July 2022

AbstractThe identification and characterization of the structural sites which contribute to protein function are crucial for understanding biological mechanisms, evaluating disease risk, and developing targeted therapies. However, the quantity of known protein structures is rapidly outpacing our ability to functionally annotate them. Existing methods for function prediction either do not operate on local sites, suffer from high false positive or false negative rates, or require large site-specific training datasets, necessitating the development of new computational methods for annotating functional sites at scale. We present COLLAPSE (Compressed Latents Learned from Aligned Protein Structural Environments), a framework for learning deep representations of protein sites. COLLAPSE operates directly on the 3D positions of atoms surrounding a site and uses evolutionary relationships between homologous proteins as a self-supervision signal, enabling learned embeddings to implicitly capture structure-function relationships within each site. Our representations generalize across disparate tasks in a transfer learning context, achieving state-of-the-art performance on standardized benchmarks (protein-protein interactions and mutation stability) and on the prediction of functional sites from the Prositedatabase. We use COLLAPSE to search for similar sites across large protein datasets and to annotate proteins based on a database of known functional sites. These methods demonstrate that COLLAPSE is computationally efficient, tunable, and interpretable, providing a general-purpose platform for computational protein analysis.
Biological condensates form percolated networks with molecular motion properties distinctly different from dilute solutions
Authors: Shen Zeyu , Jia Bowen , Xu Yang , Wessén Jonas , Pal Tanmoy , Chan Hue Sun , Du Shengwang , Zhang Mingjie 
Published: July 2022

AbstractFormation of membraneless organelles or biological condensates via phase separation hugely expands cellular organelle repertoire. Biological condensates are dense and viscoelastic soft matters instead of canonical dilute solutions. Unlike discoveries of numerous different biological condensates to date, mechanistic understanding of biological condensates remains scarce. In this study, we developed an adaptive single molecule imaging method that allows simultaneous tracking of individual molecules and their motion trajectories in both condensed and dilute phases of various biological condensates. The method enables quantitative measurements of phase boundary, motion behavior and speed of molecules in both condensed and dilute phases as well as the scale and speed of molecular exchanges between the two phases. Surprisingly, molecules in the condensed phase do not undergo uniform Brownian motion, but instead constantly switch between a confined state and a random motion state. The confinement is consistent with formation of large molecular networks (i.e., percolation) specifically in the condensed phase. Thus, molecules in biological condensates behave distinctly different from those in dilute solutions. This finding is of fundamental importance for understanding molecular mechanisms and cellular functions of biological condensates in general.
Genomewide identification of subtelomeric silencing factors in budding yeast
Authors: Juárez-Reyes Alejandro , Avelar-Rivas J. Abraham , Hernandez-Valdes Jhonatan A. , Hua Bo , Campos Sergio E. , González James , González Alicia , Springer Michael , Mancera Eugenio , DeLuna Alexander 
Published: July 2022

ABSTRACTSubtelomeric gene silencing is the negative transcriptional regulation of genes located close to telomeres. This phenomenon occurs in a variety of eukaryotes with salient physiological implications, such as cell adherence, virulence, immune-system escape, and aging. The process has been widely studied in the budding yeast Saccharomyces cerevisiae, where genes involved in this process have been identified mostly on a gene-by-gene basis. Here, we introduce a quantitative approach to study subtelomeric gene silencing, that couples the classical URA3 reporter with GFP monitoring, amenable to high-throughput flow cytometry analysis. This reporter was integrated into several subtelomeric loci in the genome, where it showed a gradual range of silencing effects. By crossing strains with this dual reporter at the COS12 and YFR057W subtelomeric query loci with gene-deletion mutants, we carried out a genome-wide, comprehensive screen for subtelomeric-silencing factors. The approach was replicable and allowed detection of expression changes caused by previously described silencing factors. We also identified new molecular players affecting this process, most of which are related to functions underlying chromatin conformation. This was the case of LGE1, a novel silencing factor herein reported, associated with histone ubiquitination. Our strategy can be readily combined with other reporters and gene perturbation collections, making it a versatile tool to study gene silencing at a genome-wide scale.