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Improving protein tertiary structure prediction by deep learning and distance prediction in CASP14.

Proteins 2021 Jul 21. Epub 2021 Jul 21.

Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA.

Substantial progresses in protein structure prediction have been made by utilizing deep-learning and residue-residue distance prediction since CASP13. Inspired by the advances, we improve our CASP14 MULTICOM protein structure prediction system by incorporating three new components: (1) a new deep learning-based protein inter-residue distance predictor to improve template-free (ab initio) tertiary structure prediction, (2) an enhanced template-based tertiary structure prediction method, and (3) distance-based model quality assessment methods empowered by deep learning. In the 2020 CASP14 experiment, MULTICOM predictor was ranked 7th out of 146 predictors in tertiary structure prediction and ranked 3rd out of 136 predictors in inter-domain structure prediction. Read More

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Early detection of COVID-19 outbreaks using human mobility data.

PLoS One 2021 20;16(7):e0253865. Epub 2021 Jul 20.

Department of Management Science and Engineering, Stanford University, Stanford, California, United States of America.

Background: Contact mixing plays a key role in the spread of COVID-19. Thus, mobility restrictions of varying degrees up to and including nationwide lockdowns have been implemented in over 200 countries. To appropriately target the timing, location, and severity of measures intended to encourage social distancing at a country level, it is essential to predict when and where outbreaks will occur, and how widespread they will be. Read More

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A symptom-based approach in predicting ECT outcome in depressed patients employing MADRS single items.

Eur Arch Psychiatry Clin Neurosci 2021 Jul 16. Epub 2021 Jul 16.

Department of Psychiatry, Centre for Affective Neuroscience (CAN), Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Charité-Universitätsmedizin Berlin, Campus Benjamin, Franklin, Hindenburgdamm 30, 12203, Berlin, Germany.

Establishing symptom-based predictors of electroconvulsive therapy (ECT) outcome seems promising, however, findings concerning the predictive value of distinct depressive symptoms or subtypes are limited; previous factor-analytic approaches based on the Montgomery-Åsberg Depression Rating Scale (MADRS) remained inconclusive, as proposed factors varied across samples. In this naturalistic study, we refrained from these previous factor-analytic approaches and examined the predictive value of MADRS single items and their change during the course of ECT concerning ECT outcome. We used logistic and linear regression models to analyze MADRS data routinely assessed at three time points in 96 depressed psychiatric inpatients over the course of ECT. Read More

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[Assessment of nutritive status and its correction in oncological patients after operations in the hepatopancreatoduodenal zone].

Vopr Pitan 2021;90(3):77-83. Epub 2021 May 17.

Nonprofit Joint Stock Company "Medical University of Karaganda", 100000, Karaganda, Republic of Kazakhstan.

Surgical interventions in the hepatopancreatoduodenal zone in cancer patients are associated with high risk of nutritional deficiency in the postoperative period. This feature is due to both the volume of the operation itself (pancreatoduodenectomy), and the predominance of catabolic processes in the early postoperative period. In this regard, the monitoring of the main indicators of carbohydrate, protein and fat metabolism in the early postoperative period becomes fundamental for choosing the correct tactics of nutritional support for this patients. Read More

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Outcomes of 3-D corrective osteotomies for paediatric malunited both-bone forearm fractures.

J Hand Surg Eur Vol 2021 Jul 14:17531934211029511. Epub 2021 Jul 14.

Department of Orthopaedics and Sports Medicine, Erasmus University Medical Centre, Rotterdam, The Netherlands.

Closed treatment of paediatric diaphyseal forearm fractures carries the risk of re-displacement, which can lead to symptomatic malunions. This is because growth will not correct angulation deformity as it does in metaphyseal fractures. The purpose of this prospective cohort study was to evaluate the outcomes after 3-D-planned corrective osteotomy with patient-specific surgical guides for paediatric malunited forearm fractures causing impaired pro-supination. Read More

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Evaluation of mortality predictors in hospitalized COVID-19 patients: Retrospective cohort study.

Tuberk Toraks 2021 Jun;69(2):196-206

Clinic of Chest Diseases, University of Health Sciences, Atatürk Chest Diseases and Chest Surgery Training and Research Hospital, Ankara, Turkey.

Introduction: Evaluation of parameters that will predict prognosis in COVID19 disease ensures correct determination of treatment strategy. In this study, it was aimed to determine the clinical, radiological and laboratory parameters affecting mortality and to evaluate the risk factors.

Materials And Methods: Patients hospitalized with the diagnosis of COVID-19 in September 2020 were included in the study. Read More

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Prolonged grief disorder in DSM-5-TR: Early predictors and longitudinal measurement invariance.

Aust N Z J Psychiatry 2021 Jul 7:48674211025728. Epub 2021 Jul 7.

Department of Clinical Psychology, Faculty of Social Sciences, Utrecht University, Utrecht, The Netherlands.

Objective: The , 5th Edition, Text Revision includes prolonged grief disorder as a novel disorder. Prolonged grief disorder can be diagnosed when acute grief stays distressing and disabling, beyond 12 months following bereavement. Evidence indicates that elevated prolonged grief disorder symptoms in the first year of bereavement predict pervasive grief later in time; targeting early elevated grief may potentially prevent symptoms getting chronic. Read More

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Performance of Web tools for predicting changes in protein stability caused by mutations.

BMC Bioinformatics 2021 Jul 5;22(Suppl 7):345. Epub 2021 Jul 5.

CNR-ISA, National Research Council, Institute of Food Science, Avellino, Italy.

Background: Despite decades on developing dedicated Web tools, it is still difficult to predict correctly the changes of the thermodynamic stability of proteins caused by mutations. Here, we assessed the reliability of five recently developed Web tools, in order to evaluate the progresses in the field.

Results: The results show that, although there are improvements in the field, the assessed predictors are still far from ideal. Read More

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Alternative to body surface area as a solution to correct systematic bias in pediatric echocardiography Z scores.

Can J Cardiol 2021 Jun 30. Epub 2021 Jun 30.

Centre de recherche du Centre Hospitalier Universitaire de Sherbrooke and Université de Sherbrooke, Sherbrooke, QC, Canada. Electronic address:

Background: Z scores are the method of choice to report dimensions in pediatric echocardiography. Z scores based on body surface area (BSA) have been shown to cause systematic biases in overweight and obese children. Using aortic valve (AoV) diameters as a paradigm, the aims of this study were to assess the magnitude of Z score underestimation in children with increased body mass index Z score (BMI-Z) and to determine if a predicting model with height and weight as independent predictors would minimize this bias. Read More

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Prediction of early vascular cement leakage following percutaneous vertebroplasty in spine metastases: the Peking University First Hospital Score (PUFHS).

BMC Cancer 2021 Jul 2;21(1):764. Epub 2021 Jul 2.

Department of Orthopedic Surgery, Hainan Hospital of Chinese PLA General Hospital, Haitang District, Jianglin Rd, Sanya, 572013, China.

Background: Cement leakage into venous blood posed significant challenge to surgeons. The aim of the study was to create a Peking University First Hospital Score (PUFHS) which could evaluate the probability of vascular cement leakage among spine metastases patients following percutaneous vertebroplasty.

Methods: The study retrospectively enrolled 272 spine metastases patients treated with percutaneous vertebroplasty. Read More

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Knowledge, attitude and practice of health care professionals on laboratory diagnosis of COVID-19.

J Family Med Prim Care 2021 May 31;10(5):1922-1930. Epub 2021 May 31.

Department of Hospital Administration, All India Institute of Medical Sciences, New Delhi, India.

Background: Coronavirus disease-2019 (COVID-19) is currently a global public health concern. Thorough knowledge of diagnostics of COVID-19 amongst health care professionals (HCPs) is critical for timely and accurate diagnosis. The aim of the study was to assess the knowledge, attitude, and practice among HCPs related to the laboratory diagnosis of COVID-19. Read More

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Occult lymph node metastasis in patients with laryngeal cancer and relevant predicting factors: a single-center experience.

Tumori 2021 Jun 30:3008916211026977. Epub 2021 Jun 30.

Department of Otolaryngology, Head and Neck Surgery, University of Health Sciences, Dışkapı Yıldırım Beyazıt Training and Research Hospital, Ankara, Turkey.

Objective: To reveal the incidence and predictive parameters of occult cervical lymph node metastasis (LNM) in patients with cN0 laryngeal squamous cell cancer (LSCC) who underwent surgery as definitive treatment.

Methods: Patients with cN0 laryngeal cancer who had undergone elective neck dissection together with partial or total laryngectomy between January 2006 and November 2020 were retrospectively analyzed. Clinical and histopathologic predictors of occult metastasis were also analyzed. Read More

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Correlation of correct needle placement in caudal epidural space and anatomical structures of sacral canal in paediatric patients: An observational study.

Indian J Anaesth 2021 May 10;65(Suppl 2):S74-S79. Epub 2021 May 10.

Department of Anaesthesiology, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh, India.

Background And Aims: Caudal epidural block (CEB) is commonly performed using surface landmark-based technique in the paediatric patients, with a good success rate. Failure to perform CEB is usually attributable to anatomic variations. The aim of this study was to perform measurements of the anatomical landmarks that are generally used to perform CEB and find a relation between these measurements and successful needle placement. Read More

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MULTICOM2 open-source protein structure prediction system powered by deep learning and distance prediction.

Sci Rep 2021 Jun 23;11(1):13155. Epub 2021 Jun 23.

Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, 65211, USA.

Protein structure prediction is an important problem in bioinformatics and has been studied for decades. However, there are still few open-source comprehensive protein structure prediction packages publicly available in the field. In this paper, we present our latest open-source protein tertiary structure prediction system-MULTICOM2, an integration of template-based modeling (TBM) and template-free modeling (FM) methods. Read More

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COVID-19 Knowledge, Perception, Preventive Measures, Stigma, and Mental Health Among Healthcare Workers in Three Sub-Saharan African Countries: A Phone Survey.

Am J Trop Med Hyg 2021 Jun 23. Epub 2021 Jun 23.

3Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts.

The coronavirus disease 2019 (COVID-19) pandemic is an unprecedented public health crisis globally. Understanding healthcare providers' (HCPs') knowledge and perceptions of COVID-19 is crucial to identifying effective strategies to improve their ability to respond to the pandemic in sub-Saharan Africa. A phone-based survey of 900 HCPs in Burkina Faso, Ethiopia, and Nigeria (300 per country) was conducted to assess knowledge, perceptions, COVID-19 prevention measures, stigma, and mental health of HCPs. Read More

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Factors Associated with Clinician Adherence to USPSTF Diabetes Screening Recommendations.

J Prim Care Community Health 2021 Jan-Dec;12:21501327211016579

Department of Family Medicine, Lehigh Valley Health Network, Allentown, PA, USA.

Introduction/objectives: Diabetes and prediabetes impact nearly half of the US adult population and are associated with significant health risks but may be underdiagnosed. Effective screening may improve diagnosis and give patients opportunity to manage their disease. The purpose of this study was to determine screening rates, identify characteristics predictive of screening, and evaluate correct diagnosis of diabetes and prediabetes. Read More

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Work-family conflict during the Covid-19 pandemic: teleworking of administrative and technical staff in healthcare. An Italian study.

Med Lav 2021 Jun 15;112(3):229-240. Epub 2021 Jun 15.

Azienda Sanitaria Locale TO3.

Background: Remote working (more appropriately, mandatory work from home) during the Covid-19 healthcare emergency has increased significantly. Amidst many critical issues, work-family conflict (WFC) remains a central topic, due to the hardships in separating different life domains, the pervasiveness of technology, and decreased opportunities for recovery, all considering new, emerging job demands. Although many studies have involved healthcare workers, less attention has been paid to technical-administrative staff (TA); moreover, previous studies about the impact of remote working on WFC have provided mixed results. Read More

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Knowledge about mother to child transmission of HIV/AIDS, its prevention and associated factors among reproductive-age women in sub-Saharan Africa: Evidence from 33 countries recent Demographic and Health Surveys.

PLoS One 2021 11;16(6):e0253164. Epub 2021 Jun 11.

Department of Human Anatomy, College of Medicine and Health Science, School of Medicine, University of Gondar, Gondar, Ethiopia.

Background: In sub-Saharan Africa (SSA) 90 percent of babies acquired HIV/AIDS from infected mothers. Maternal knowledge about mother to child transmission (MTCT) of HIV/AIDS and its prevention is a cornerstone for elimination of MTCT of HIV/AIDS. Despite this, there is limited evidence about knowledge about MTCT of HIV/AIDS and its prevention and associated factors in SSA. Read More

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Evolutionary history expands the range of signaling interactions in hybrid multikinase networks.

Sci Rep 2021 Jun 3;11(1):11763. Epub 2021 Jun 3.

Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France.

Two-component systems (TCSs) are ubiquitous signaling pathways, typically comprising a sensory histidine kinase (HK) and a response regulator, which communicate via intermolecular kinase-to-receiver domain phosphotransfer. Hybrid HKs constitute non-canonical TCS signaling pathways, with transmitter and receiver domains within a single protein communicating via intramolecular phosphotransfer. Here, we report how evolutionary relationships between hybrid HKs can be used as predictors of potential intermolecular and intramolecular interactions ('phylogenetic promiscuity'). Read More

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Transmission Based Precaution Practices among Nurses in Edo State, Nigeria during COVID-19 Pandemic.

Afr J Reprod Health 2020 Jun;24(s1):98-107

Department of Nursing Science, School of Basic Medical Sciences, College of Medical Sciences, University of Benin, Benin City, Nigeria.

The novel covid-19 pandemic is a highly infectious disease without known specific treatment and vaccine. Transmission based precautions are important in the fight against the virus. This study investigated the level of transmission-based precautions practiced, the predictors of correct practices, and the challenges experienced by nurses in public health facilities in Edo State during the outbreak of the Covid-19 pandemic. Read More

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Vaccine Production Process: How Much Does the General Population Know about This Topic? A Web-Based Survey.

Vaccines (Basel) 2021 May 29;9(6). Epub 2021 May 29.

Department of Health Sciences, University of Florence, 50134 Florence, Italy.

Background: Vaccine hesitancy has been recognized as a major global health threat by the World Health Organization. Many studies have investigated vaccine safety as a determinant for vaccine hesitancy; however, not much attention has been paid to vaccine production and quality control during the vaccine production process or whether knowledge about this topic may influence vaccine confidence. The aim of this study was to characterize the common knowledge about the vaccine production process. Read More

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Machine Learning for Predicting Heart Failure Progression in Hypertrophic Cardiomyopathy.

Front Cardiovasc Med 2021 13;8:647857. Epub 2021 May 13.

Cardiovascular Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, United States.

Development of advanced heart failure (HF) symptoms is the most common adverse pathway in hypertrophic cardiomyopathy (HCM) patients. Currently, there is a limited ability to identify HCM patients at risk of HF. In this study, we present a machine learning (ML)-based model to identify individual HCM patients who are at high risk of developing advanced HF symptoms. Read More

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QUARTERplus: Accurate disorder predictions integrated with interpretable residue-level quality assessment scores.

Comput Struct Biotechnol J 2021 27;19:2597-2606. Epub 2021 Apr 27.

Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA.

A recent advance in the disorder prediction field is the development of the quality assessment (QA) scores. QA scores complement the propensities produced by the disorder predictors by identifying regions where these predictions are more likely to be correct. We develop, empirically test and release a new QA tool, QUARTERplus, that addresses several key drawbacks of the current QA method, QUARTER. Read More

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Neurocognitive and Psychopathological Predictors of Weight Loss After Bariatric Surgery: A 4-Year Follow-Up Study.

Front Endocrinol (Lausanne) 2021 5;12:662252. Epub 2021 May 5.

Obesity Unit, Department of Surgery, University of Rome "Tor Vergata", Rome, Italy.

Twenty to thirty percent of patients experience weight regain at mid and long-term follow-up. Impaired cognitive functions are prevalent in people suffering from obesity and in those with binge eating disorder, thereby, affecting the weight-loss outcomes. The aim of our study was to investigate neurocognitive and psychopathological predictors of surgical efficacy in terms of percentage of excess weight loss (%EWL) at follow-up intervals of one year and 4-year. Read More

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Speech production factors and verbal working memory in children and adults with developmental language disorder.

Appl Psycholinguist 2021 May 18;42(3):673-702. Epub 2021 Feb 18.

Department of Communication Sciences and Disorders, The Pennsylvania State University.

Verbal working memory (VWM) deficits are common in individuals with developmental language disorder (DLD) but are not well understood. This study evaluated how both memory and language production factors influence VWM performance in children and adults with DLD, focusing on the influence of serial position, phonological activation (PA), and lexical frequency. Participants were 30 children with DLD and 26 with typical language (TL), and 21 adults with DLD and 23 with TL. Read More

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Evaluation of common genetic variants in vitamin E-related pathway genes and colorectal cancer susceptibility.

Arch Toxicol 2021 Jul 19;95(7):2523-2532. Epub 2021 May 19.

Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.

Vitamin E is effective for preventing the risk of cancer. However, few studies have elucidated the mechanism of vitamin E in cancer occurrence. Herein, we aimed to identify the genetic variants in vitamin E-related pathway genes associated with colorectal cancer risk. Read More

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Association of Intima-Media Texture with Prevalence of Clinical Cardiovascular Disease.

IEEE Trans Ultrason Ferroelectr Freq Control 2021 May 17;PP. Epub 2021 May 17.

Background: Recent studies have suggested that textural characteristics of the intima-media complex (IMC), may be more useful than intima-media thickness (IMT) in evaluating cardiovascular risk.

Aims: The primary aim of our study was to investigate the association between texture features of the common carotid IMC and prevalent clinical cardiovascular disease (CVD). A secondary aim was to determine whether IMT and IMC texture features vary between the left and the right carotid arteries. Read More

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Anthropogenic litter density and composition data acquired flying commercial drones on sandy beaches along the Saudi Arabian Red Sea.

Data Brief 2021 Jun 20;36:107056. Epub 2021 Apr 20.

Red Sea Research Center and Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.

Anthropogenic litter density and composition data were obtained by conducting aerial surveys on 44 beaches along the Saudi Arabian Coast of the Red Sea [1]. The aerial surveys were completed with commercial drones of the DJI Phantom suite flown at a 10 m altitude. The stills have a resolution of less than 0. Read More

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Variable selection methods for identifying predictor interactions in data with repeatedly measured binary outcomes.

J Clin Transl Sci 2020 Nov 16;5(1):e59. Epub 2020 Nov 16.

Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC, USA.

Introduction: Identifying predictors of patient outcomes evaluated over time may require modeling interactions among variables while addressing within-subject correlation. Generalized linear mixed models (GLMMs) and generalized estimating equations (GEEs) address within-subject correlation, but identifying interactions can be difficult if not hypothesized . We evaluate the performance of several variable selection approaches for clustered binary outcomes to provide guidance for choosing between the methods. Read More

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November 2020

Impact of corrected sinus node recovery time in predicting recurrence in patients with paroxysmal atrial fibrillation.

J Int Med Res 2021 May;49(5):3000605211010103

Department of Cardiology, Tongji Hospital Affiliated to 12476Tongji University, Shanghai, China.

Objective: Atrial fibrillation (AF) and sinus node dysfunction (SND) have common underlying pathophysiological mechanisms. As an index of SND, corrected sinus node recovery time (CSNRT) may also reflect atrial function. The aim of the present study was to determine whether CSNRT predicts AF recurrence in patients undergoing AF ablation. Read More

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