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The COVIDome Explorer researcher portal.

Cell Rep 2021 Jul 28:109527. Epub 2021 Jul 28.

Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA. Electronic address:

COVID-19 pathology involves dysregulation of diverse molecular, cellular, and physiological processes. To expedite integrated and collaborative COVID-19 research, we completed multi-omics analysis of hospitalized COVID-19 patients, including matched analysis of the whole-blood transcriptome, plasma proteomics with two complementary platforms, cytokine profiling, plasma and red blood cell metabolomics, deep immune cell phenotyping by mass cytometry, and clinical data annotation. We refer to this multidimensional dataset as the COVIDome. Read More

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(Cham & Schltdl) DC.: phytochemical composition, cyto- and genotoxicity analyses.

Nat Prod Res 2021 Aug 4:1-7. Epub 2021 Aug 4.

Pharmaceutical Sciences Graduate Program, Federal University of Santa Maria, Santa Maria, RS, Brazil.

is a Brazilian native species used in folk medicine. Scientific information regarding the toxicology and phytochemistry of this plant remains unclear. We aimed to produce a extract, identify its chemical matrix, and evaluate its safety profile. Read More

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Women's empowerment in agriculture and productivity change: The case of Bangladesh rice farms.

PLoS One 2021 4;16(8):e0255589. Epub 2021 Aug 4.

Division of Applied Social Sciences, University of Missouri, Columbia, MO, United States of America.

Using productivity change as a measure of farm economic performance, we analyze the relationship between women's empowerment in agriculture and farm productivity change and its components, which include efficiency change, technological change, and scale efficiency change. A non-parametric Malmquist approach is used to measure farm specific productivity change and its decomposition. We use a bootstrap regression to analyze factors that cause differences in productivity change and its components, testing, in particular, the role women's empowerment plays. Read More

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Differential Antibody Response to mRNA COVID-19 Vaccines in Healthy Subjects.

Microbiol Spectr 2021 Aug 4:e0034121. Epub 2021 Aug 4.

Department of Pathology, University of Pittsburghgrid.471408.egrid.21925.3d Medical Center, Pittsburgh, Pennsylvania, USA.

Knowledge about development and duration of virus-specific antibodies after COVID-19 vaccination is important for understanding how to limit the pandemic via vaccination in different populations and societies. However, the clinical utility of postvaccination testing of antibody response and selection of targeted SARS-CoV-2 antigen(s) has not been established. The results of such testing from clinical teams independent from vaccine manufacturers are also limited. Read More

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Simulating drug concentrations in PDMS microfluidic organ chips.

Lab Chip 2021 Aug 4. Epub 2021 Aug 4.

Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA. and Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA and Vascular Biology Program and Department of Surgery, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA.

Microfluidic organ-on-a-chip (Organ Chip) cell culture devices are often fabricated using polydimethylsiloxane (PDMS) because it is biocompatible, transparent, elastomeric, and oxygen permeable; however, hydrophobic small molecules can absorb to PDMS, which makes it challenging to predict drug responses. Here, we describe a combined simulation and experimental approach to predict the spatial and temporal concentration profile of a drug under continuous dosing in a PDMS Organ Chip containing two parallel channels separated by a porous membrane that is lined with cultured cells, without prior knowledge of its log P value. First, a three-dimensional finite element model of drug loss into the chip was developed that incorporates absorption, adsorption, convection, and diffusion, which simulates changes in drug levels over time and space as a function of potential PDMS diffusion coefficients and log P values. Read More

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A machine learning approach for prioritizing groundwater testing for per-and polyfluoroalkyl substances (PFAS).

J Environ Manage 2021 Jul 24;295:113359. Epub 2021 Jul 24.

Coral Genomics, San Francisco, CA, 94107, USA. Electronic address:

Regulatory agencies are beginning to recognize and regulate per-and polyfluoroalkyl substances (PFAS) as concerning environmental contaminants. In groundwater management, testing and mitigation strategies are desirable, but can be time and cost-intensive processes. As a result, only a fraction of all groundwater wells has been tested for PFAS levels, resulting in potentially extended drinking water exposure to PFAS in the meantime. Read More

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Advances in multiplex electrical and optical detection of biomarkers using microfluidic devices.

Anal Bioanal Chem 2021 Aug 4. Epub 2021 Aug 4.

Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA.

Microfluidic devices can provide a versatile, cost-effective platform for disease diagnostics and risk assessment by quantifying biomarkers. In particular, simultaneous testing of several biomarkers can be powerful. Here, we critically review work from the previous 4 years up to February 2021 on developing microfluidic devices for multiplexed detection of biomarkers from samples. Read More

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Extracellular vesicles from immortalized cardiosphere-derived cells attenuate arrhythmogenic cardiomyopathy in desmoglein-2 mutant mice.

Eur Heart J 2021 Jul 29. Epub 2021 Jul 29.

Smidt Heart Institute, Cedars-Sinai Medical Center, 127 S. San Vicente Boulevard, Los Angeles, CA 90048, USA.

Aims: Arrhythmogenic cardiomyopathy (ACM) is characterized by progressive loss of cardiomyocytes, and fibrofatty tissue replacement. Extracellular vesicles (EVs) secreted by cardiosphere-derived cells, immortalized, and engineered to express high levels of β-catenin, exert anti-inflammatory, and anti-fibrotic effects. The aim of the current study was to assess efficacy of EVs in an ACM murine model. Read More

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Toxicological testing of syringaresinol and enterolignans.

Curr Res Toxicol 2020 Jun 16;1:104-110. Epub 2020 Sep 16.

Department of Chemistry, Division of Food Chemistry and Toxicology, University of Kaiserslautern, Erwin-Schroedinger-Str. 52, D-67663 Kaiserslautern, Germany.

Lignans are secondary plant constituents with dibenzylbutane skeletons found in cereals, oilseeds, and nuts. Two members of this class, syringaresinol (Syr) and secoisolariciresinol (Seco), occur at relatively high levels in cereals and processed food products as well as in coniferous trees studies have shown that Seco and its metabolites enterodiol (END) and enterolactone (ENL), which are formed by intestinal microbes, exhibit strong antioxidant activity because of their phenolic character. The biological activity and discussion of dietary supplementation with these substances led to questions about the potential adverse health effects of these compounds, which are explored here. Read More

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Characterization and acute oral toxicity of concentrated minerals of Pamekasan Madura seawater.

J Adv Pharm Technol Res 2021 Jul-Sep;12(3):305-309. Epub 2021 Jul 16.

Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Jatinangor, Indonesia.

Indonesia is a maritime country with abundant seawater mineral content. One of the regions with the highest salt production is Pamekasan Madura. Minerals are known to have many roles and benefits for our bodies, such as regulating fluid balance and metabolism. Read More

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Classroom aerosol dispersion: desk spacing and divider impacts.

Int J Environ Sci Technol (Tehran) 2021 Jul 30:1-14. Epub 2021 Jul 30.

Department of Civil and Mechanical Engineering, United States Military Academy, West Point, NY 10996 USA.

A study of aerosol dispersion was conducted in a university classroom using a CO tracer gas emitted from three source locations in a steady release, one source location per test. The tracer gas emitted from the single source location represented the potentially infectious aerosol droplets emitted from a single student and was thus a way to examine the influence of one sick student on the rest of the class. Two parameters were adjusted during the testing-the spacing of the desks, which included a spread and compressed configuration, and the inclusion of three-sided clear dividers attached to the student desk surfaces. Read More

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Ruggedness Testing-Part I: Ignoring Interactions.

J Res Natl Bur Stand (1977) 1986 Jan-Feb;91(1):3-8

National Bureau of Standards, Gaithersburg, MD 20899.

A straightforward explanation of the statistical technique of ruggedness testing is presented. Efficient Plackett-Burman designs are used in ruggedness tests. These designs involve the simultaneous change of levels of a number of variables. Read More

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Thioesterase induction by 2,3,7,8-tetrachlorodibenzo-p-dioxin results in a futile cycle that inhibits hepatic β-oxidation.

Sci Rep 2021 Aug 3;11(1):15689. Epub 2021 Aug 3.

Department of Biochemistry and Molecular Biology, Michigan State University, Biochemistry Building, 603 Wilson Road, East Lansing, MI, 48824, USA.

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD), a persistent environmental contaminant, induces steatosis by increasing hepatic uptake of dietary and mobilized peripheral fats, inhibiting lipoprotein export, and repressing β-oxidation. In this study, the mechanism of β-oxidation inhibition was investigated by testing the hypothesis that TCDD dose-dependently repressed straight-chain fatty acid oxidation gene expression in mice following oral gavage every 4 days for 28 days. Untargeted metabolomic analysis revealed a dose-dependent decrease in hepatic acyl-CoA levels, while octenoyl-CoA and dicarboxylic acid levels increased. Read More

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Anxiety, stress, and binge eating tendencies in adolescence: a prospective approach.

J Eat Disord 2021 Aug 3;9(1):94. Epub 2021 Aug 3.

Department of Experimental Psychology, University of Oxford, Anna Watts Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, UK.

Background: Recent years have witnessed an increasing prevalence of binge eating tendencies in adolescence-warranting a clearer understanding of their underlying predisposing and precipitating factors. The current study investigated whether the interaction between high levels of anxiety and stress predicted increased levels of binge eating tendencies in a prospective cohort of adolescents (N = 324).

Methods: Measurements were taken over three waves (M ages: 13. Read More

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Sensitivity to targeted therapy differs between HER2-amplified breast cancer cells harboring kinase and helical domain mutations in PIK3CA.

Breast Cancer Res 2021 Aug 3;23(1):81. Epub 2021 Aug 3.

Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA.

Background: HER2-amplified breast cancer is a clinically defined subtype of breast cancer for which there are multiple viable targeted therapies. Resistance to these targeted therapies is a common problem, but the mechanisms by which resistance occurs remain incompletely defined. One mechanism that has been proposed is through mutation of genes in the PI3-kinase pathway. Read More

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Biochemical and molecular features of Chinese patients with glutaric acidemia type 1 detected through newborn screening.

Orphanet J Rare Dis 2021 Aug 3;16(1):339. Epub 2021 Aug 3.

Department of Neonatology, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, 362000, Fujian Province, China.

Background: Glutaric acidemia type 1 (GA1) is a treatable disorder affecting cerebral organic acid metabolism caused by a defective glutaryl-CoA dehydrogenase (GCDH) gene. GA1 diagnosis reports following newborn screening (NBS) are scarce in the Chinese population. This study aimed to assess the acylcarnitine profiles and genetic characteristics of patients with GA1 identified through NBS. Read More

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Investigation of the levels of circulating miR-29a, miR-122, sestrin 2 and inflammatory markers in obese children with/without type 2 diabetes: a case control study.

BMC Endocr Disord 2021 Aug 3;21(1):152. Epub 2021 Aug 3.

Department of Pediatrics, Unaizah College of Medicine and Medical Sciences, Qassim University, Unaizah, Saudi Arabia.

Aim: The present work investigated serum levels of miR-29a, miR-122 and sestrin2 in obese children with/without type-2-diabetes mellitus (T2DM), and their correlations with inflammatory, metabolic and anthropometric parameters.

Methods: The study included 298 children, divided into: G1 (control, n = 136), G2 (obese without diabetes, n = 90) and G3 (obese with T2DM, n = 72). Metabolic and anthropometric parameters, miR-29a, miR-122 relative expressions, and sestrin2, high sensitivity C-reactive protein (hsCRP), interleukin-6 (IL-6), and tumor necrosis factor-α (TNF-α) levels were measured by their specific methods. Read More

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Monitoring sound levels in the intensive care unit: A mixed-methods system development project to optimize design features for a new electronic interface in the healthcare environment.

Int J Med Inform 2021 Jul 22;153:104538. Epub 2021 Jul 22.

Nuffield Department of Clinical Neurosciences, Unhiniversity of Oxford, UK.

Background: Intensive care units (ICU) are busy round the clock and it is difficult to maintain low sound levels that support patient rest. To help ICU staff manage activities we developed a visual display that monitors and reports sound levels in real-time. This facilitates immediate feedback, encouraging proactive behavior change to limit disturbances. Read More

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Agile fusion method for the determination of Pu isotopes in diverse sediments.

Megan Cook

Appl Radiat Isot 2021 Jul 29;176:109878. Epub 2021 Jul 29.

School of Earth, Atmosphere & Environment, Monash University, Wellington Road, 3800, Clayton, Australia. Electronic address:

Atmospheric nuclear testing has occurred worldwide resulting in trace amounts of plutonium (Pu) isotopes in soils and sediments across the globe. Soils and sediments can vary greatly in both physical and chemical properties within close geographic regions presenting a major challenge for sample preparation in the analysis of fallout radionuclides. It is vital to have a rapid, agile method for the complete digestion of samples containing refractory Pu particles to address this challenge. Read More

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Immune Treatments for Alcohol Use Disorder: A Translational Framework.

Brain Behav Immun 2021 Jul 31. Epub 2021 Jul 31.

Department of Psychology, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA, USA. Electronic address:

While the immune system is essential for survival, an excessive or prolonged inflammatory response, such as that resulting from sustained heavy alcohol use, can damage the host and contribute to psychiatric disorders. A growing body of literature indicates that the immune system plays a critical role in the development and maintenance of alcohol use disorder (AUD). As such, there is enthusiasm for treatments that can restore healthy levels of inflammation as a mechanism to reduce drinking and promote recovery. Read More

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Changes and prognostic value of cardiopulmonary exercise testing parameters in elderly patients undergoing cardiac rehabilitation: The EU-CaRE observational study.

PLoS One 2021 3;16(8):e0255477. Epub 2021 Aug 3.

Department of Cardiology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.

Objective: We aimed 1) to test the applicability of the previously suggested prognostic value of CPET to elderly cardiac rehabilitation patients and 2) to explore the underlying mechanism of the greater improvement in exercise capacity (peak oxygen consumption, VO2) after CR in surgical compared to non-surgical cardiac patients.

Methods: Elderly patients (≥65 years) commencing CR after coronary artery bypass grafting, surgical valve replacement (surgery-group), percutaneous coronary intervention, percutaneous valve replacement or without revascularisation (non-surgery group) were included in the prospective multi-center EU-CaRE study. CPETs were performed at start of CR, end of CR and 1-year-follow-up. Read More

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A Deep Neural Network for Estimating Low-Density Lipoprotein Cholesterol From Electronic Health Records: Real-Time Routine Clinical Application.

JMIR Med Inform 2021 Aug 3;9(8):e29331. Epub 2021 Aug 3.

Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea.

Background: Previously, we constructed a deep neural network (DNN) model to estimate low-density lipoprotein cholesterol (LDL-C).

Objective: To routinely provide estimated LDL-C levels, we applied the aforementioned DNN model to an electronic health record (EHR) system in real time (deep LDL-EHR).

Methods: The Korea National Health and Nutrition Examination Survey and the Wonju Severance Christian Hospital (WSCH) datasets were used as training and testing datasets, respectively. Read More

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Green Tea Suppresses Amyloid β Levels and Alleviates Cognitive Impairment by Inhibiting APP Cleavage and Preventing Neurotoxicity in 5XFAD Mice.

Mol Nutr Food Res 2021 Aug 3:e2100626. Epub 2021 Aug 3.

State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science & Technology, Anhui Agricultural University.

Scope: The consumption of green tea is considered to be associated with a lower incidence of neurodegenerative diseases. In the present study, we investigated the role of amyloid precursor protein cleavage, glial cell activation, neuroinflammation and synaptic alterations in the protective effects of green tea against the amyloid β (Aβ) accumulation and cognitive impairment.

Methods And Results: 5XFAD mice were treated with green tea extract (GTE) for 8 or 16 weeks. Read More

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Monogenic and polygenic causes of low and extremely low LDL-C levels in patients referred to specialty lipid clinics: Genetics of low LDL-C.

J Clin Lipidol 2021 Jul 17. Epub 2021 Jul 17.

Division of Nutrition and Metabolic Diseases, Department of Internal Medicine, UT Southwestern Medical Center, 5323 Harry Hines Blvd, MC 8537, Dallas, TX 75390, United States. Electronic address:

Background: In clinical setting, current standard-of-care does not include genetic testing for patients with low (<50 mg/dL) and extremely low (<20 mg/dL) levels of serum low-density lipoprotein-cholesterol (LDL-C).

Objective: We aimed identify the underlying molecular cause - both monogenic and polygenic - of low and extremely low LDL-C levels in a cohort of patients presenting to specialty lipid clinics.

Methods: Whole exome sequencing was done in patients with low or extremely low LDL-C not due to any secondary causes. Read More

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Impact of the 2016 Canadian Lipid Guidelines on Daily Practice at a Community Hospital.

Can J Diabetes 2021 Jun 9. Epub 2021 Jun 9.

Centre Hospitalier Universitaire de Québec-Université Laval, Québec, Québec City, Canada.

Objectives: The aim of this study was to determine the impact of the 2016 Canadian cardiovascular society guidelines for the management of dyslipidemia. More specifically, we assessed the use of 1) alternate lipid targets when triglyceride (TG) levels are high; and 2) nonfasting lipid testing.

Methods: Lipid profiles and pharmacy data were obtained from patients with a history of myocardial infarction and from patients ≥40 years of age with a diagnosis of diabetes. Read More

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The impact of atypical sensory processing on adaptive functioning within and beyond autism: The role of familial factors.

Autism 2021 Aug 2:13623613211019852. Epub 2021 Aug 2.

Karolinska Institutet, Sweden.

Lay Abstract: Individuals diagnosed with autism tend to process sensory information differently than individuals without autism, resulting for instance in increased sensitivity to sounds or smells. This leads to challenges in everyday life and may restrict the individual's daily functioning. How direct this link is, however, is currently unclear. Read More

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Pelvic floor, abdominal and uterine tenderness in relation to pressure pain sensitivity among women with endometriosis and chronic pelvic pain.

Eur J Obstet Gynecol Reprod Biol 2021 Jul 22;264:247-253. Epub 2021 Jul 22.

Departments of Anesthesiology, Critical Care, & Pain Medicine and Psychiatry, Boston Children's Hospital, Department of Psychiatry, Harvard Medical School, Boston, MA, USA; Biobehavioral Pediatric Pain Lab, Boston Children's Hospital, Boston, MA, USA. Electronic address:

Objective: Pelvic floor pain, abdominal wall pain, and central nervous system pain amplification can be contributing factors in chronic pelvic pain (CPP), however; limited research has investigated the association of pelvic floor, abdominal, and uterine tenderness with central nervous system pain amplification. We assessed whether pressure pain thresholds on the non-dominant thumbnail, a marker of central nervous system pain amplification, were associated with pelvic floor, abdominal, and uterine tenderness among women with endometriosis or CPP.

Study Design: We conducted a cross-sectional study among 88 females with endometriosis and/or CPP. Read More

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Expressive and Receptive Language in Russian Primary-School-Aged Children with Autism Spectrum Disorder.

Res Dev Disabil 2021 Jul 30;117:104042. Epub 2021 Jul 30.

Center for Language and Brain, HSE University, Moscow, Russia; Institute of Linguistics, Russian Academy of Sciences, Moscow, Russia.

Background: Abnormal language development in both expressive and receptive domains occurs in most children with Autism Spectrum Disorder (ASD), although the language deficit is not a core symptom of ASD. However, previous studies disagree on the difference in the degree of impairment between expressive and receptive language in ASD. Existing research has concentrated on vocabulary and 'global expressive and receptive language', often using parental reports for language assessment. Read More

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Quantification of age-related decline in transcriptional homeostasis.

J Mol Biol 2021 Jul 30:167179. Epub 2021 Jul 30.

Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi-110020, India; Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi-110020, India; Centre for Artificial Intelligence, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi-110020, India; Institute of Health and Biomedical Innovation, Queensland University of Technology, Australia. Electronic address:

Age-dependent dysregulation of transcription regulatory machinery triggers modulations in the gene expression levels leading to the decline in cellular fitness. Tracking of these transcripts along the temporal axis in multiple species revealed a spectrum of evolutionarily conserved pathways, such as electron transport chain, translation regulation, DNA repair, etc. Recent shreds of evidence suggest that aging deteriorates the transcription machinery itself, indicating the hidden complexity of the aging transcriptomes. Read More

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Optimal Noninvasive Medicare Access Promotion: Patients with Central Sleep Apnea A Technical Expert Panel Report from the American College of Chest Physicians, the American Association for Respiratory Care, the American Academy of Sleep Medicine, and the American Thoracic Society.

Chest 2021 Jul 28. Epub 2021 Jul 28.

Department of Medicine, Veterans Affairs Medical Center, Martinsburg, WV.

This document summarizes suggestions of the central sleep apnea (CSA) technical expert panel (TEP) working group. This paper shares our vision for bringing the right device to the right patient at the right time. For patients with CSA, current coverage criteria do not align with guideline treatment recommendations. Read More

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