bluuebunny/crossref_metadata_2025_split huggingface dataset:
Office, central and ambulatory blood pressure for predicting incident atrial fibrillation in older adults
Authors: Matsumoto Kenji , Jin Zhezhen , Homma Shunichi , Elkind Mitchell S.V. , Schwartz Joseph E. , Rundek Tatjana , Mannina Carlo , Ito Kazato , Sacco Ralph L. , Di Tullio Marco R. 
Published: October 2020

Objectives:
Recently, more sophisticated blood pressure (BP) measurements, such as central and ambulatory BP (ABP), have proven to be stronger predictors of future cardiovascular disease than conventional office BP. Their predictive value for atrial fibrillation development is not established. We investigated the prognostic impact for incident atrial fibrillation of office, central and ambulatory BP measurements in a predominantly older population-based cohort.

Methods:
Of 1004 participants in the Cardiovascular Abnormalities and Brain Lesions (CABL) study, 769 in sinus rhythm with no history of atrial fibrillation or stroke (mean age 70.5 years) underwent ABP and arterial wave reflection analysis for central BP determination. Fine and Gray's proportional subdistribution hazards models were used to assess the association of BP parameters with incident atrial fibrillation.

Results:
During 9.5 years, atrial fibrillation occurred in 83 participants. No office BP variable showed a significant association with incident atrial fibrillation. Central SBP and central pulse pressure were marginally associated with incident atrial fibrillation in multivariate analysis. Among ABP variables, 24-h SBP [adjusted hazard ratio per 10 mmHg, 1.24; 95% confidence interval (CI) 1.07--1.44; P = 0.004], daytime SBP (adjusted hazard ratio per 10 mmHg, 1.21; 95% CI 1.04--1.40; P = 0.011) and night-time SBP (adjusted hazard ratio per 10 mmHg, 1.22; 95% CI 1.07--1.39; P = 0.002) were significantly associated with incident atrial fibillation.

Conclusion:
In a predominantly older, stroke-free community-based cohort, ABP was a better independent predictor of incident atrial fibrillation than central BP, whereas office BP was inadequate for this purpose.
How Does Cataract Surgery Rate Affect Angle-closure Prevalence
Authors: Jin Guangming , Wang Lanhua , Scheetz Jane , Zhang Jian , He Mingguang 
Published: October 2020

Précis:
A data simulation study suggests that prevalence of occludable angle will decrease when the cataract surgical rate increases in particularly when the surgery focuses on 70+ years old.

Purpose:
The purpose of this study was to estimate the effects of cataract surgical rates (CSR) on the prevalence of primary angle-closure glaucoma in the Chinese population.

Methods:
Participants aged 50 years and older from the Liwan Eye Study were included as the study sample. Occludable angle (OA) as a surrogate of primary angle-closure glaucoma was evaluated using static gonioscopy and anterior chamber depth was measured before dilation using A-mode ultrasound. Random sampling was used to generate 50 cohorts with a sample size of 200 for each predefined CSR at 2000, 4000, 6000, 8000, 10,000, 12,000, according to the multinomial distribution. The mean anterior chamber depth and OA rates of each cohort were calculated. Logistic function models of nonlinear least-squares estimation were used to predict the prevalence of OA.

Results:
Data of the right eye from 1280 participants were included. The prevalence of cataract surgery and OA was 2.27% and 11.3%, respectively. The projected prevalence of OA in the cohorts with CSR of 2000, 4000, 6000, 8000, 10,000 and 12,000 was 11.4% [95% confidence interval (CI), 10.8%-12.0%], 11.2% (95% CI, 10.6%-11.9%), 10.9% (95% CI, 10.3%-11.6%), 11.4% (95% CI, 10.8%-12.1%), 10.8% (95% CI, 10.2-11.4%), and 10.1% (95% CI, 9.46-10.7%), respectively. The OA rates decreased remarkably as CSR increased for those aged 70 years and older.

Conclusions:
Our study indicated that with CSR increased, the OA prevalence could decrease remarkably especially in the older population. It is advisable to perform cataract surgery at an appropriate time for patients in their late 60s to 70s with significant cataracts.
Critical effect of Pol escape mutations associated with detrimental allele HLA-C∗15:05 on clinical outcome in HIV-1 subtype A/E infection
Authors: Murakoshi Hayato , Chikata Takayuki , Akahoshi Tomohiro , Zou Chengcheng , Borghan Mohamed Ali , Van Tran Giang , Nguyen Trung Vu , Van Nguyen Kinh , Kuse Nozomi , Takiguchi Masafumi 
Published: October 2020

Objective:
The mechanism explaining the role of detrimental HLA alleles in HIV-1 infections has been investigated in very few studies. HLA-A∗29:01-B∗07:05-C∗15:05 is a detrimental haplotype in HIV-1 subtype A/E-infected Vietnamese individuals. The accumulation of mutations at Pol 653/657 is associated with a poor clinical outcome in these individuals. However, the detrimental HLA allele and the mechanism responsible for its detrimental effect remains unknown. Therefore, in this current study we identified the detrimental HLA allele and investigated the mechanism responsible for the detrimental effect.

Design and methods:
A T-cell epitope including Pol 653/657 and its HLA restriction were identified by using overlapping HIV-1 peptides and cell lines expressing a single HLA. The effect of the mutations on the T-cell recognition of HIV-1-infected cells was investigated by using target cells infected with the mutant viruses. The effect of these mutations on the clinical outcome was analyzed in 74 HLA-C∗15:05+ Vietnamese infected with the subtype A/E virus.

Results:
We identified HLA-C∗15:05-restricted SL9 epitope including Pol 653/657. PolS653A/T/L mutations within this epitope critically impaired the T-cell recognition of HIV-1-infected cells, indicating that these mutations had escaped from the T cells. T-cell responders infected with these mutants showed significantly lower CD4+ T-cell counts than those with the wild-type virus or Pol S653K/Q mutants, which are not associated with HLA-C∗15:05.

Conclusion:
The accumulation of Pol S653A/T/L escape mutants critically affected the control of HIV-1 by SL9-specific T cells and led to a poor clinical outcome in the subtype A/E-infected individuals having the detrimental HLA-C∗15:05 allele.
Effect of Truvada lawsuit advertising on preexposure prophylaxis attitudes and decisions among sexual and gender minority youth and young adults at risk for HIV
Authors: Serrano Pedro A. , Daubert Elizabeth , Munoz Alejandro , Hosek Sybil G. , French Audrey L. 
Published: October 2020

Objective:
In 2019, US advocates reported misleading language regarding the safety of TDF/FTC (Truvada) used by lawsuit advertisements against Gilead Sciences. We sought to ascertain the reach and effects of the advertisements on preexposure prophylaxis (PrEP) opinions and decisions in a cohort of youth and young adults at-risk for HIV.

Design:
An online survey was administered to participants enrolled in Keeping it LITE, a prospective US cohort study of ethnically diverse, sexually active, cisgender and transgender persons ages 13–37.

Methods:
Quantitative data were analyzed using descriptive and inferential analysis in SAS, and qualitative data via thematic analysis.

Results:
Survey response rate was 51.3% (n = 1485). Mean age at baseline was 24. Previous PrEP use was reported by 43% of respondents and 32.7% reported PrEP use in the past 6 months. Almost half (48.7%) were aware of the lawsuit. Most of these participants (81.3%) reported the advertisements did not impact their PrEP use, but 13.2% decided to not to begin a Truvada-based PrEP regimen and 5.5% decided to stop taking Truvada due to the advertisements claims. Predictors of changing PrEP behavior were lower education and no previous PrEP use. The qualitative analysis revealed the advertisements increased skepticism about safety and benefit of Truvada PrEP and led to greater distrust of the pharmaceutical industry.

Conclusion:
The advertisements reached a large, diverse US audience. Disturbingly, 18.7% of PrEP candidates who were aware of the lawsuit attributed not initiating or cessation of a Truvada-based PrEP regimen to exposure to the Truvada lawsuit advertisements.
Quality and Safety in Health Care, Part LXXX
Authors: Harolds Jay A. , Miller Laura B. 
Published: October 2020

Abstract
The National Database for Nursing Quality Indicators is an important source of information used to benchmark nursing by unit category in multiple areas related to not only structure and process but also outcome. It also provides some information regarding best practices and the cost to achieve certain results. The Practice Environment Scale of the Nursing Work Index is a frequently used way to measure the professional practice environment of nurses and the relationship of the latter to quality, safety, and other outcomes.
An Incidental Uptake of 18F-Choline at PET/CT in Gastric Neuroendocrine Tumor
Authors: Evangelista Laura , Cassarino Gianluca , Capobianco Decio , Povolato Michele , Battista Serena , Rensi Marco 
Published: October 2020

Abstract
We present a case of neuroendocrine tumor localized in the gastric mucosa, incidentally detected by 18F-choline PET/CT in a 69-year-old man with prostate cancer. 18F-choline PET/CT scan showed an increased activity in the stomach, later diagnosed as a well-differentiated neuroendocrine tumor, at biopsy. A careful attention of reading 18F-choline PET/CT images should be made, in order to avoid the missing of potential concomitant neoplasia in patients with prostate cancer.
Pituitary Metastases Discovered by 18F-FDG PET/CT During Other Cancers Monitoring
Authors: Piciu Andra , Mester Alexandru , Piciu Doina 
Published: October 2020

Abstract

18F-FDG PET/CT might discover incidental pituitary lesions. We present the case of a 46-year-old woman with breast cancer metastasis in her pituitary. We analyzed 10,347 FDG PET/CT examinations from a tertiary center, finding 4 cases (0.038%) of pituitary metastatic disease from other cancers. We analyzed the differences between SUVmax in cases of physiological high uptake, primary tumor, and hypophysis metastases from other cancers in our database compared with the literature.
Maximum Uptake and Hypermetabolic Volume of 18F-FDOPA PET Estimate Molecular Status and Overall Survival in Low-Grade Gliomas
Authors: Tatekawa Hiroyuki , Yao Jingwen , Oughourlian Talia C. , Hagiwara Akifumi , Wang Chencai , Raymond Catalina , Lai Albert , Cloughesy Timothy F. , Nghiemphu Phioanh L. , Liau Linda M. , Salamon Noriko , Ellingson Benjamin M. 
Published: October 2020

PurposeWe evaluated18F-FDOPA PET and MRI characteristics in association with the molecular status and overall survival (OS) in a large number of low-grade gliomas (LGGs).MethodsEighty-six patients who underwent18F-FDOPA PET and MRI and were diagnosed with new or recurrent LGGs were retrospectively evaluated with respect to their isocitrate dehydrogenase (IDH) and 1p19q status (10 IDH wild type, 57 mutant, 19 unknown; 1p19q status in IDH mutant: 20 noncodeleted, 37 codeleted). After segmentation of the hyperintense area on fluid-attenuated inversion recovery image (FLAIRROI), the following were calculated: normalized SUVmax (nSUVmax) of18F-FDOPA relative to the striatum,18F-FDOPA hypermetabolic volume (tumor-to-striatum ratios >1), FLAIRROIvolume, relative cerebral blood volume, and apparent diffusion coefficient within FLAIRROI. Receiver operating characteristic curve and Cox regression analyses were performed.ResultsPET and MRI metrics combined with age predicted the IDH mutation and 1p19q codeletion statuses with sensitivities of 73% and 76% and specificities of 100% and 94%, respectively. Significant correlations were found between OS and the IDH mutation status (hazard ratio [HR] = 4.939), nSUVmax (HR = 2.827),18F-FDOPA hypermetabolic volume (HR = 1.048), and FLAIRROIvolume (HR = 1.006). The nSUVmax (HR = 151.6) for newly diagnosed LGGs and the18F-FDOPA hypermetabolic volume (HR = 1.038) for recurrent LGGs demonstrated significant association with OS.ConclusionsCombining18F-FDOPA PET and MRI with age proved useful for predicting the molecular status in patients with LGGs, whereas the nSUVmax and18F-FDOPA hypermetabolic volume may be useful for prognostication.
Cognitive Event-Related Potentials–The P300 Wave Is a Prognostic Factor of Long-Term Disability Progression in Patients With Multiple Sclerosis
Authors: Szilasiová Jarmila , Rosenberger Jaroslav , Mikula Pavol , Vitková Marianna , Fedičová Miriam , Gdovinová Zuzana 
Published: October 2020

Purpose:
Multiple sclerosis (MS) is a chronic disorder with a variable course. The aim of our study was to find out whether cognitive event-related potentials are prognostic for patient disability at the 15-year follow-up.

Methods:
In the observed cohort of patients with MS, we examined the event-related potentials at baseline (2003). Functional status (Expanded Disability Status Scale score) was then assessed 15 years later, and the prognostic model was developed using binary logistic regression analysis. The independent variables included demographic (age, sex, and education), clinical (disability in 2003), radiologic (MRI lesion load), and event-related potentials parameters. The prognostic accuracy of the proposed model was evaluated by calculating the area under the receiver-operating characteristics curve.

Results:
The study sample consisted of 85 patients with MS. The mean age was 35.5 (SD, 11.2) years, and the median disability score was 3.0 (1–7) in 2003 and 5.0 (1.5–9.5) in 2018. The significant prognostic factors of poor Expanded Disability Status Scale are higher baseline Expanded Disability Status Scale, longer MS duration, and prolonged P300 latency. The sensitivity and specificity of the cutoff at 5.0 for the disability score were 94% and 89%, respectively, with the area under the receiver-operating characteristics curve 0.94 (95% confidence interval, 0.889–0.984; P < 0.001).

Conclusions:
The results show that out of event-related potentials, the P300 wave latency is a prognostic of long-term disability progression in patients with MS.
What to do when everything happens at once: Analytic approaches to estimate the health effects of co-occurring social policies
Authors: Matthay Ellicott C. , Gottlieb Laura M. , Rehkopf David , Tan May Lynn , Vlahov David , Maria Glymour M. 
Published: October 2020

AbstractSocial policies have great potential to improve population health and reduce health disparities. Thus, increasing empirical research seeks to quantify the health effects of social policies by exploiting variation in the timing of policy changes across places. Multiple social policies are often adopted simultaneously or in close succession in the same locations, creating co-occurrence which must be handled analytically for valid inferences. Although this is a substantial methodological challenge for studies aiming to isolate social policy effects, limited prior work has systematically considered analytic solutions within a causal framework or assessed whether these solutions are being adopted. We designated seven analytic solutions to policy co-occurrence, including efforts to disentangle individual policy effects and efforts to estimate the combined effects of co-occurring policies. We leveraged an existing systematic review of social policies and health to evaluate how often policy co-occurrence is identified as a threat to validity and how often each analytic solution is applied in practice. Of the 55 studies, only 17 (31%) reported checking for any co-occurring policies, although 36 (67%) used at least one approach that helps address policy co-occurrence. The most common approaches were: adjusting for measures of co-occurring policies; defining the outcome on subpopulations likely to be affected by the policy of interest (but not other co-occurring policies); and selecting a less-correlated measure of policy exposure. As health research increasingly focuses on policy changes, we must systematically assess policy co-occurrence and apply analytic solutions to strengthen future studies on the health effects of social policies.
Fast and interpretable scRNA-seq data analysis
Authors: Çobanoğlu Murat Can 
Published: October 2020

AbstractOne of the key challenges in single-cell data analysis is the annotation of cells with their cell types. This task is divided into two different sub-tasks: identifying known cell types and identifying novel cell types. In the former case, we can benefit from being able to transfer annotations from bulk RNA-seq because there are many more types profiled with that more established technology. In the latter case, we would benefit from interpretable models that can describe the reasons for grouping a number of cells together. We propose that both of these problems can be solved by generative Bayesian Dirichlet-multinomial models. In the supervised learning context, we propose a generative Bayesian Dirichlet-multinomial classifier. We show that such a classifier can effectively transfer cell labels from bulk to single-cell RNA-sequencing data. We also show that alternative well-established machine learning models have difficulty with this transition, even if they are effective within the same regime (i.e. single cell to single cell). In the unsupervised learning context, we propose a Bayesian Dirichlet-multinomial mixture model. We show that the proposed model learns meaningful clusters where the automatically learned relationships between cell types and genes overlap with ground truth associations. Furthermore, there are no density or connectivity based clustering assumptions in this model, which differs with almost every approach in this field. Consequently the clustering results from the generative method can effectively represent nuanced differences among cells.Contactmurat.cobanoglu@utsouthwestern.edu
Haisu: Hierarchical Supervised Nonlinear Dimensionality Reduction
Authors: VanHorn Kevin C. , Çobanoğlu Murat Can 
Published: October 2020

AbstractWe propose a novel strategy for incorporating hierarchical supervised label information into nonlinear dimensionality reduction techniques. Specifically, we extend t-SNE, UMAP, and PHATE to include known or predicted class labels and demonstrate the efficacy of our approach on multiple single-cell RNA sequencing datasets. Our approach, “Haisu,” is applicable across domains and methods of nonlinear dimensionality reduction. In general, the mathematical effect of Haisu can be summarized as a variable perturbation of the high dimensional space in which the original data is observed. We thereby preserve the core characteristics of the visualization method and only change the manifold to respect known or assumed class labels when provided. Our strategy is designed to aid in the discovery and understanding of underlying patterns in a dataset that is heavily influenced by parent-child relationships. We show that using our approach can also help in semi-supervised settings where labels are known for only some datapoints (for instance when only a fraction of the cells is labeled). In summary, Haisu extends existing popular visualization methods to enable a user to incorporate known, relevant relationships via a user-defined hierarchical distancing factor.Availabilitygithub.com/Cobanoglu-Lab/Haisu
Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks
Authors: Li Yang , Zhang Chengxin , Bell Eric W. , Zheng Wei , Zhou Xiaogen , Yu Dong-Jun , Zhang Yang 
Published: October 2020

AbstractThe topology of protein folds can be specified by the inter-residue contact-maps and accurate contact-map prediction can helpab initiostructure folding. We developed TripletRes to deduce protein contact-maps from discretized distance profiles by end-to-end training of deep residual neural-networks. Compared to previous approaches, the major advantage of TripletRes is in its ability to learn and directly fuse a triplet of coevolutionary matrices extracted from the whole-genome and metagenome databases and therefore minimize the information loss during the course of contact model training. TripletRes was tested on a large set of 245 non-homologous proteins from CASP and CAMEO experiments, and outperformed other state-of-the-art methods by at least 58.4% for the CASP 11&12 and 44.4% for the CAMEO targets in the top-Llong-range contact precision. On the 31 FM targets from the latest CASP13 challenge, TripletRes achieved the highest precision (71.6%) for the top-L/5 long-range contact predictions. These results demonstrate a novel efficient approach to extend the power of deep convolutional networks for high-accuracy medium- and long-range protein contact-map predictions starting from primary sequences, which are critical for constructing 3D structure of proteins that lack homologous templates in the PDB library.AvailabilityThe training and testing data, standalone package, and the online server for TripletRes are available athttps://zhanglab.ccmb.med.umich.edu/TripletRes/.Author SummaryAb initioprotein folding has been a major unsolved problem in computational biology for more than half a century. Recent community-wide Critical Assessment of Structure Prediction (CASP) experiments have witnessed exciting progress onab initiostructure prediction, which was mainly powered by the boosting of contact-map prediction as the latter can be used as constraints to guideab initiofolding simulations. In this work, we proposed a new open-source deep-learning architecture, TripletRes, built on the residual convolutional neural networks for high-accuracy contact prediction. The large-scale benchmark and blind test results demonstrate significant advancement of the proposed methods over other approaches in predicting medium- and long-range contact-maps that are critical for guiding protein folding simulations. Detailed data analyses showed that the major advantage of TripletRes lies in the unique protocol to fuse multiple evolutionary feature matrices which are directly extracted from whole-genome and metagenome databases and therefore minimize the information loss during the contact model training.
Lexical parafoveal previewing predicts reading speed
Authors: Pan Yali , Frisson Steven , Jensen Ole 
Published: October 2020

AbstractWhile reading is an essential human skill, many of the neuronal mechanisms supporting reading are not well understood. In spite of the reduced visual acuity, parafoveal information plays a critical role in natural reading1; however, it is strongly debated whether words are previewed parafoveally at the lexical level2–9. This is a key dispute for competing models on reading and of great significance since lexical retrieval is important for guiding eye movements. We found evidence for parafoveal previewing at the lexical level by combining a novelrapid invisible frequency tagging(RIFT)10, 11approach with magnetoencephalography (MEG) and eye-tracking. In a silent reading task, target words of either low or high lexical frequency were tagged (flickered) subliminally at 60 Hz. The tagging response measured when fixating on the pre-target word reflected parafoveal previewing of the target word. We observed a stronger tagging response as early as 100 ms following fixations on pre-target words that were followed by target words of low compared with high lexical frequency. Moreover, the difference in tagging response with respect to target lexicality predicted individual reading speed. Our findings demonstrate that reading unfolds in the fovea and parafovea simultaneously to support fluent reading.