bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lung Adenocarcinoma Metastatic to the Cervix: Report of a Rare Case and Review of the Literature
Authors: Hosseini Hossein , Steinberg Jordan M. , Ratzon Fanni , Unger Pamela , Yurovitsky Alyssa 
Published: September 2021

Abstract
Metastatic involvement of the cervix by nongynecologic malignancies is an extremely rare occurrence. We report a case of metastatic lung adenocarcinoma to the cervix. The patient is a 70-year-old woman who was admitted because of acute kidney injury. Imaging studies revealed left-sided hydronephrosis and a 3.2-cm heterogeneous pelvic mass involving the left pelvic wall. The patient underwent hysteroscopy with dilatation and curettage. Specimens labeled with endometrial and endocervical curettings were notable for tumor cells infiltrating the fibromuscular tissue. Immunohistochemical studies showed that the tumor cells were positive for CK7, napsin A, and TTF1, whereas they were negative for PAX8, p16, p40, p53, GATA3, and ER. This immunophenotype was consistent with a metastatic adenocarcinoma of the lung primary.
Localized Mesothelioma of the Pleura: Report of 2 Cases, From Benign to Malignant
Authors: Canbeldek Leyla , Legesse Teklu , Burke Allen 
Published: September 2021

Abstract
Localized mesotheliomas of the pleura are rare, and form a spectrum of low-grade noninvasive indolent lesions that are presumably benign, to more aggressive invasive cancers that, although fully malignant, have a relatively better prognosis than the diffuse type of mesothelioma. Localized mesotheliomas can be either epithelioid, sarcomatoid, or biphasic. The defining characteristics are circumscription and origin from the visceral pleura. The vast majority are single lesions, although multifocal ones, as the second case in this report, have rarely been described. We present a “benign” localized epithelioid mesothelioma and a malignant localized sarcomatoid mesothelioma with multiple satellite nodules.
Fraternal Coopers Develop Sinonasal Intestinal-Type Adenocarcinoma
Authors: Mallinger Wesley D. , Read Paul W. , Stelow Edward B. 
Published: September 2021

Abstract
We describe 2 brothers with a history of working in the family business of whiskey barrel making who both developed sinonasal intestinal-type adenocarcinomas (ITACs) around their seventh decade of life. This highlights the strong association of ITAC with occupational wood dust exposure, and the typical development of disease occurring around the sixth to seventh decade of life. Intestinal-type adenocarcinomas show morphologic and phenotypic similarities to their primary intestinal counterparts, particularly expression of CDX2 and CK20. Despite the morphologic and phenotypic similarities, the molecular alterations that are common to many adenocarcinomas of the intestinal tract are not present in ITAC. This description highlights the wide morphologic spectrum of ITAC and the often protracted course of this disease process.
Human Papillomavirus–Related Multiphenotypic Sinonasal Carcinoma
Authors: Crawford Michael P. , Stelow Edward B. 
Published: September 2021

Abstract
Human papillomavirus–related mulitphenotypic sinonasal carcinoma is a recently described high-grade malignancy demonstrating significant morphologic overlap with adenoid cystic carcinoma and other salivary-type malignancies. We present a prototypical case of human papillomavirus–related mulitphenotypic sinonasal carcinoma in a 51-year-old woman and discuss the diagnosis, as well as the differential diagnosis.
Ultrasonographic Features of Hypertrophic Interureteral Cristae in Transabdominal and Transrectal Ultrasonography
Authors: Wang Xiaofeng , Nie Fang , Li Yan , Li Jing 
Published: September 2021

Purpose
The aim of this study was to determine the value of transrectal ultrasound in the definitive diagnosis of hypertrophic interureteral cristae and to provide a definitive diagnostic basis for clinical treatment.

Materials and Methods
When the patient's bladder fills moderately, the ultrasound physician uses the transabdominal ultrasound probe to examine the patient's bladder and prostate carefully, focusing on bilateral ureterovesical portals, a cord-like hyperechoic structure visible between the bilateral ureterovesical portals. For further detailed observation, transrectal probe was used to measure the size of Hypertrophic Interureteral Cristae and describe the shape and internal echo. After the examination, the residual urine volume of bladder was measured after one-time urination.

Results
Hypertrophic interureteral cristae was a trilinear structure with a “high-low-high” echo. All the 33 patients had bladder wall thickening. In 9 cases of overfilling of bladder, there were slightly dilated ureterovesical portals at both ends of hypertrophic interureteral cristae. Thirty cases of benign prostatic hyperplasia, 11 patients who had undergone prostate hyperplasia surgery, 26 cases with different degrees trabecular and reticular hyperplasia of bladder wall, there were 9 cases with bladder diverticulum and 23 cases with mild hydronephrosis.

Conclusions
Transrectal ultrasound can confirm the diagnosis of Hypertrophic Interureteral Cristae.
The Rare, the Odd, and the Atypical
Authors: Houser Margaret , Khati Nadia J. 
Published: September 2021

Abstract
Understanding a variety of scrotal diseases is essential to developing an accurate differential diagnosis and is critical in providing optimal patient care. Ultrasound is the imaging modality of choice when evaluating for scrotal pathology, with the major purpose of locating such pathology to either the testis, or epididymis, or other intrascrotal structures, as well as characterizing lesions as solid or cystic. It is generally assumed that most solid intratesticular masses are more likely malignant, whereas most extratesticular ones are benign, although some exceptions to that rule exist. This pictorial essay will focus on rare and less commonly encountered benign and malignant testicular and paratesticular pathologies, which may pose a diagnostic dilemma for interpreting radiologists and treating physicians. Knowledge of their imaging characteristics will help narrow the differential diagnosis and assist in proper patient management and care.
Sonographic Evaluation of Pelvic Venous Disorders
Authors: Brahmbhatt Akshaar , Macher Jared , Shetty Anisha N. , Chughtai Komal , Baah Nana Ohene , Dogra Vikram S. 
Published: September 2021

Abstract
Pelvic venous disorders are a group of interrelated conditions characterized by venous incompetence. These conditions often manifest with nonspecific symptoms that overlap with many gynecological, gastrointestinal, and urologic diseases. Clinical diagnosis can be difficult, and imaging can play a vital role in differentiating etiology. Sonographic evaluation is often the first step in evaluating these symptoms. Special attention to possible underlying pelvic venous disorders can reveal characteristic findings, support diagnosis, and guide treatment. Here we review pelvic congestion syndrome, nutcracker syndrome, May-Thurner syndrome, and other venous disorders, with a specific focus on sonographic findings and considerations.
Brain–Computer Interfaces in Acute and Subacute Disorders of Consciousness
Authors: Xu Ren , Spataro Rossella , Allison Brendan Z. , Guger Christoph 
Published: September 2021

Summary:
Disorders of consciousness include coma, unresponsive wakefulness syndrome (also known as vegetative state), and minimally conscious state. Neurobehavioral scales such as coma recovery scale—revised are the gold standard for disorder of consciousness assessment. Brain–computer interfaces have been emerging as an alternative tool for these patients. The application of brain–computer interfaces in disorders of consciousness can be divided into four fields: assessment, communication, prediction, and rehabilitation. The operational theoretical model of consciousness that brain–computer interfaces explore was reviewed in this article, with a focus on studies with acute and subacute patients. We then proposed a clinically friendly guideline, which could contribute to the implementation of brain–computer interfaces in neurorehabilitation settings. Finally, we discussed limitations and future directions, including major challenges and possible solutions.
Machine learning methods applied to genotyping data capture interactions between single nucleotide variants in late onset Alzheimer’s disease
Authors: Segura Magdalena Arnal , Orth Dietmar Fernandez , Giambartolomei Claudia , Bini Giorgio , Samaras Eleftherios , Kassis Maya , Aisopos Fotis , De Argila Jordi Rambla , Paliouras Georgios , Garrard Peter , Tartaglia Gian Gaetano 
Published: September 2021

INTRODUCTIONGenome-wide association studies (GWAS) in late onset Alzheimer’s disease (LOAD) provide lists of individual genetic determinants. However, GWAS are not good at capturing the synergistic effects among multiple genetic variants and lack good specificity.METHODSWe applied tree-based machine learning algorithms (MLs) to discriminate LOAD (> 700 individuals) and age-matched unaffected subjects using single nucleotide variants (SNVs) from AD studies, obtaining specific genomic profiles with the prioritized SNVs.RESULTSThe MLs prioritized a set of SNVs located in close proximity genes PVRL2, TOMM40, APOE and APOC1. The captured genomic profiles in this region showed a clear interaction between rs405509 and rs1160985. Additionally, rs405509 located in APOE promoter interacts with rs429358 among others, seemingly neutralizing their predisposing effect. Interactions are characterized by their association with specific comorbidities and the presence of eQTL and sQTLs.DISCUSSIONOur approach efficiently discriminates LOAD from controls, capturing genomic profiles defined by interactions among SNVs in a hot-spot region.
Tracking COVID-19 Cases and Deaths in the United States: Distribution of Events by Day of Pandemic
Authors: Moore Andrew , Lyu Mingdong , Hall Randolph 
Published: September 2021

AbstractIn this paper, we analyze the progression of COVID-19 in the United States over a nearly one-year period beginning March 1, 2020, with a novel metric representing the partial-average day-of-event, where events are new cases and new deaths. The metric is calculated as a function of date and location to illustrate patterns of disease, showing growing or waning cases and deaths. The metrics enable the direct comparison of the time distribution of cases and deaths, revealing data coherence and how patterns varied over a one-year period. We also compare different methods of estimating actual infections and deaths to better understand on the timing and dynamics of the pandemic by state. We used three example states to graphically compare metrics as functions of date and also compared statistics derived from all 50 states. Over the period studied, average case day and average death day vary by two to five months among the 50 states, depending on data source, with the earliest averages in New York and surrounding states, as well as Louisiana. The average day of death has preceded the average day of case in Centers for Disease Control (CDC) data for most states and most dates since June of 2020. In contrast, “COVID-19 Projections” more closely align deaths and cases, which are similarly distributed.
DunedinPACE: A DNA methylation biomarker of the Pace of Aging
Authors: Belsky DW , Caspi A , Corcoran DL , Sugden K , Poulton R , Arseneault L , Baccarelli A , Chamarti K , Gao X , Hannon E , Harrington HL , Houts R , Kothari M , Kwon D , Mill J , Schwartz J , Vokonas P , Wang C , Williams B , Moffitt TE 
Published: September 2021

ABSTRACTMeasures to quantify changes in the pace of biological aging in response to intervention are needed to evaluate geroprotective interventions for humans. We used data from the Dunedin Study 1972-3 birth cohort tracking within-individual decline in 19 indicators of organ-system integrity across four time points spanning two decades to model Pace of Aging. We distilled this two-decade Pace of Aging into a single-time-point DNA-methylation blood-test using elastic-net regression and a DNA-methylation dataset restricted to exclude probes with low test-retest reliability. We evaluated the resulting measure, named DunedinPACE, in five additional datasets. DunedinPACE showed high test-retest reliability, was associated with morbidity, disability, and mortality, and indicated faster aging in young adults with childhood adversity. DunedinPACE effect-sizes were similar to GrimAge Clock effect-sizes. In analysis of morbidity, disability, and mortality, DunedinPACE and added incremental prediction beyond GrimAge. DunedinPACE is a novel blood biomarker of the pace of aging for gerontology and geroscience.
Griffin: Framework for clinical cancer subtyping from nucleosome profiling of cell-free DNA
Authors: Doebley Anna-Lisa , Ko Minjeong , Liao Hanna , Cruikshank A. Eden , Kikawa Caroline , Santos Katheryn , Hiatt Joseph , Patton Robert D. , De Sarkar Navonil , Hoge Anna C.H. , Chen Katharine , Weber Zachary T. , Adil Mohamed , Reichel Jonathan , Polak Paz , Adalsteinsson Viktor A. , Nelson Peter S. , Parsons Heather A. , Stover Daniel G. , MacPherson David , Ha Gavin 
Published: September 2021

AbstractCell-free DNA (cfDNA) has the potential to inform tumor subtype classification and help guide clinical precision oncology. Here we developed Griffin, a new method for profiling nucleosome protection and accessibility from cfDNA to study the phenotype of tumors using as low as 0.1x coverage whole genome sequencing (WGS) data. Griffin employs a novel GC correction procedure tailored to variable cfDNA fragment sizes, which improves the prediction of chromatin accessibility. Griffin achieved excellent performance for detecting tumor cfDNA in early-stage cancer patients (AUC=0.96). Next, we applied Griffin for the first demonstration of estrogen receptor (ER) subtyping in metastatic breast cancer from cfDNA. We analyzed 254 samples from 139 patients and predicted ER subtype with high performance (AUC=0.89), leading to insights about tumor heterogeneity. In summary, Griffin is a framework for accurate clinical subtyping and can be generalizable to other cancer types for precision oncology applications.
Public-private partnership to rapidly strengthen and scale COVID-19 response in Western Kenya
Authors: van Duijn Shannen , Barsosio Hellen C. , Omollo Mevis , Milimo Emmanuel , Akoth Isdorah , Aroka Robert , de Sanctis Teresa , K’Oloo Alloys , June Micah J. , Houben Nathalie , Wilming Charlotte , Otieno Kephas , Kariuki Simon , Onsongo Simon , Odhiambo Albert , Ganda Gregory , de Wit Tobias F. Rinke 
Published: September 2021

AbstractINTRODUCTIONIn Africa almost half of healthcare services are delivered through private sector providers. These are often underused in national public health responses. In line with our previous HIV experience and to support and accelerate the public sector’s COVID-19 response, we initiated a public-private project (PPP) in Kisumu County, Kenya. In this manuscript we demonstrate this PPP’s performance, using COVID-19 testing as an aggregator and with semi-real time digital monitoring tools for rapid scaling of COVID-19 response.METHODSCOVID-19 diagnostic testing formed the basis for a PPP between KEMRI, Department of Health Kisumu County, PharmAccess Foundation, and local faith-based and private healthcare facilities: COVID-Dx. COVID-Dx was implemented from June 01, 2020, to March 31, 2021 in Kisumu County, Kenya. Trained laboratory technologists in participating healthcare facilities collected nasopharyngeal and oropharyngeal samples from patients meeting the Kenyan MoH COVID-19 case definition. Samples were rapidly transported by motorbike and tested using RT-PCR at the central reference laboratory in KEMRI. Healthcare workers in participating facilities collected patient clinical data using a digitized MoH COVID-19 Case Identification Form. We shared aggregated results from these data via (semi-) live dashboards with all relevant stakeholders through their mobile phones. Statistical analyses were performed using Stata 16 to inform project processes.RESULTSNine private facilities participated in the project. A detailed patient trajectory was developed from case identification to result reporting, all steps supported by a semi-real time digital dashboard. A total of 4,324 PCR tests for SARS-CoV-2 (16%) were added to the public response, identifying 425 positives. Geo-mapped and time-tagged information on incident cases was depicted on Google maps dashboards and fed back to policymakers for informed rapid decision making. Preferential COVID-19 testing was performed on health workers at risk, with 1,009 tested (43% of all County health workforce).CONCLUSIONWe demonstrate feasibility of rapidly increasing the public health sector response to a COVID-19 epidemic outbreak in an African setting. Our PPP intervention in Kisumu, Kenya was based on a joint testing strategy and demonstrated that semi-real time digitalization of patient trajectories in the healthcare system can gain significant efficiencies, linking public and private healthcare efforts, increasing transparency, support better quality health services and informing policy makers to target interventions. This PPP has since scaled to 33 facilities in Kisumu and subsequently to 84 sites in 14 western Kenyan Counties.
Impairments in goal-directed action and reversal learning in a proportion of individuals with psychosis: evidence for differential phenotypes in early and persistent psychosis
Authors: Suetani Shuichi , Baker Andrea , Garner Kelly , Cosgrove Peter , Mackay-Sim Matilda , Siskind Dan , Murray Graham K , Scott James G , Kesby James P 
Published: September 2021

ABSTRACTCognitive impairments in psychosis are one of the strongest predictors of functional decline. Cortico-striatal dysfunction may contribute to both psychosis and cognitive impairment in psychotic illnesses. The decision-making processes underlying goal-directed action and serial reversal learning can be measured and are sensitive to changes reflecting cortico-striatal dysfunction. As such, changes in decision-making performance may assist with predicting functional decline in people with psychosis. We assessed decision-making processes in healthy controls (N=34), and those with early psychosis (N=15) and persistent psychosis (N=45). We subclassified subjects based on intact/impaired goal-directed action. Compared with healthy controls (<20%), a large proportion (58%) of those with persistent psychosis displayed impaired goal-directed action, predicting poor serial reversal learning performance. Computational approaches indicated that those with persistent psychosis were less deterministic in their decision-making. Those with impaired goal-directed action had a decreased capacity to rapidly update their prior beliefs in the face of changing contingencies. In contrast, the early psychosis group included a lower proportion of individuals with impaired goal-directed action (20%) and displayed a different cognitive phenotype from those with persistent psychosis. These findings suggest prominent decision-making deficits, indicative of cortico-striatal dysfunction, are present in a large proportion of people with persistent psychosis while those with early psychosis have relatively intact decision-making processes compared to healthy controls. It is unclear if there is a progressive decline in decision-making processes in some individuals with psychosis or if the presence of decision-making processes in early psychosis is predictive of a persistent trajectory of illness.
Parameter inference on brain network models with unknown node dynamics and spatial heterogeneity
Authors: Sip Viktor , Petkoski Spase , Hashemi Meysam , Dickscheid Timo , Amunts Katrin , Jirsa Viktor 
Published: September 2021

AbstractModel-based data analysis of whole-brain dynamics links the observed data to model parameters in a network of neural masses. In recent years a special focus was placed on the role of regional variance of model parameters for the emergent activity. Such analyses however depend on the properties of the employed neural mass model, which is often obtained through a series of major simplifications or analogies. Here we propose a data-driven approach where the neural mass model needs not to be specified. Building on the recent progresses in identification of dynamical systems with neural networks, we propose a method to infer from the functional data both the neural mass model representing the regional dynamics as well as the region- and subject-specific parameters, while respecting the known network structure. We demonstrate on two synthetic data sets that our method is able to recover the original model parameters, and that the trained generative model produces dynamics resembling the training data both on the regional level and on the whole-brain level. We further apply the method to resting-state fMRI data from Human Connectome Project. We find that to achieve best fit, the model needs two dimensional state space and three regional parameters, one of which is strongly correlated with the map of genetic expression in human brain. The present approach opens a novel way to the analysis of resting-state fMRI with possible applications in understanding the changes of whole-brain dynamics during aging or in neurodegenerative diseases.
Gut microbiome and its cofactors are linked to lipoprotein distribution profiles
Authors: Castro-Mejía Josué L. , Khakimov Bekzod , Lind Mads V. , Garne Eva , Paulová Petronela , Tavakkoli Elnaz , Hansen Lars H. , Smilde Age K. , Holm Lars , Engelsen Søren B. , Nielsen Dennis S. 
Published: September 2021

AbstractIncreasing evidence indicates that the gut microbiome (GM) plays an important role in the etiology of dyslipidemia. To date, however, no in-depth characterization of the associations between GM and its metabolic attributes with deep profiling of lipoproteins distributions (LPD) among healthy individuals has been conducted. To determine associations and contributions of GM composition and its cofactors with distribution profiles of lipoprotein subfractions, we studied blood plasma LPD, fecal short-chain fatty acids (SCFA) and GM of 262 healthy Danish subjects aged 19-89 years.Stratification of LPD segregated subjects into three clusters of profiles that reflected differences in the lipoprotein subclasses, corresponded well with limits of recommended levels of main lipoprotein fractions and were largely explained by host characteristics such as age and body mass index. Higher levels of HDL, particularly driven by large subfractions (HDL2a and HDL2b), were associated with a higher relative abundance of Ruminococcaceae and Christensenellaceae. Increasing levels of total cholesterol and LDL, which were primarily associated with large 1 and 2 subclasses, were positively associated with Lachnospiraceae and Coriobacteriaceae, and negatively with Bacteroidaceae and Bifidobacteriaceae. Metagenome sequencing showed a higher abundance of genes involved in the biosynthesis of multiple B-vitamins and SCFA metabolism among subjects with healthier LPD profiles. Metagenomic assembled genomes (MAGs) affiliated mainly to Eggerthellaceae and Clostridiales were identified as the contributors of these genes and whose relative abundance correlated positively with larger subfractions of HDL.The results of this study demonstrate that remarkable differences in composition and metabolic traits of the GM are associated with variations in LPD among healthy subjects. Findings from this study provide evidence for GM considerations in future research aiming to shade light on mechanisms of the GM – dyslipidemia axis.