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Optimization of Metabolic Oligosaccharide Engineering with AcGalNAlk and AcGlcNAlk by an Engineered Pyrophosphorylase.

ACS Chem Biol 2021 Apr 9. Epub 2021 Apr 9.

Department of Chemistry, Imperial College London, 80 Wood Lane, W12 0BZ London, United Kingdom.

Metabolic oligosaccharide engineering (MOE) has fundamentally contributed to our understanding of protein glycosylation. Efficient MOE reagents are activated into nucleotide-sugars by cellular biosynthetic machineries, introduced into glycoproteins and traceable by bioorthogonal chemistry. Despite their widespread use, the metabolic fate of many MOE reagents is only beginning to be mapped. Read More

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Combining natural language processing and metabarcoding to reveal pathogen-environment associations.

PLoS Negl Trop Dis 2021 Apr 7;15(4):e0008755. Epub 2021 Apr 7.

Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America.

Cryptococcus neoformans is responsible for life-threatening infections that primarily affect immunocompromised individuals and has an estimated worldwide burden of 220,000 new cases each year-with 180,000 resulting deaths-mostly in sub-Saharan Africa. Surprisingly, little is known about the ecological niches occupied by C. neoformans in nature. Read More

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Human-lineage-specific genomic elements are associated with neurodegenerative disease and APOE transcript usage.

Nat Commun 2021 04 6;12(1):2076. Epub 2021 Apr 6.

Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London (UCL), London, UK.

Knowledge of genomic features specific to the human lineage may provide insights into brain-related diseases. We leverage high-depth whole genome sequencing data to generate a combined annotation identifying regions simultaneously depleted for genetic variation (constrained regions) and poorly conserved across primates. We propose that these constrained, non-conserved regions (CNCRs) have been subject to human-specific purifying selection and are enriched for brain-specific elements. Read More

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Nematicidal Activity of Benzyloxyalkanols against Pine Wood Nematode.

Biomolecules 2021 Mar 5;11(3). Epub 2021 Mar 5.

Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.

Pine wilt disease (PWD) is caused by the pine wood nematode (PWN; ) and causes severe environmental damage to global pine forest ecosystems. The current strategies used to control PWN are mainly chemical treatments. However, the continuous use of these reagents could result in the development of pesticide-resistant nematodes. Read More

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Improving RNA Branching Predictions: Advances and Limitations.

Genes (Basel) 2021 Mar 25;12(4). Epub 2021 Mar 25.

School of Mathematics, Georgia Institute of Technology, Atlanta, GA 30308, USA.

Minimum free energy prediction of RNA secondary structures is based on the Nearest Neighbor Thermodynamics Model. While such predictions are typically good, the accuracy can vary widely even for short sequences, and the branching thermodynamics are an important factor in this variance. Recently, the simplest model for multiloop energetics-a linear function of the number of branches and unpaired nucleotides-was found to be the best. Read More

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Hunting for Familial Parkinson's Disease Mutations in the Post Genome Era.

Genes (Basel) 2021 Mar 17;12(3). Epub 2021 Mar 17.

Griffith Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, QLD 4111, Australia.

Parkinson's disease (PD) is typically sporadic; however, multi-incident families provide a powerful platform to discover novel genetic forms of disease. Their identification supports deciphering molecular processes leading to disease and may inform of new therapeutic targets. The p. Read More

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A comprehensive metagenomics framework to characterize organisms relevant for planetary protection.

Microbiome 2021 04 1;9(1):82. Epub 2021 Apr 1.

Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.

Background: Clean rooms of the Space Assembly Facility (SAF) at the Jet Propulsion Laboratory (JPL) at NASA are the final step of spacecraft cleaning and assembly before launching into space. Clean rooms have stringent methods of air-filtration and cleaning to minimize microbial contamination for exoplanetary research and minimize the risk of human pathogens, but they are not sterile. Clean rooms make a selective environment for microorganisms that tolerate such cleaning methods. Read More

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Visuo-motor attention during object interaction in children with developmental coordination disorder.

Cortex 2021 Mar 4;138:318-328. Epub 2021 Mar 4.

Department of Sport and Health Sciences, College of Life and Environmental Sciences, University of Exeter, UK; Translational Research Exchange @ Exeter, University of Exeter, UK. Electronic address:

Developmental coordination disorder (DCD) describes a condition of poor motor performance in the absence of intellectual impairment. Despite being one of the most prevalent developmental disorders, little is known about how fundamental visuomotor processes might function in this group. One prevalent idea is children with DCD interact with their environment in a less predictive fashion than typically developing children. Read More

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The effects of GC-biased gene conversion on patterns of genetic diversity among and across butterfly genomes.

Genome Biol Evol 2021 Mar 24. Epub 2021 Mar 24.

Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.

Recombination reshuffles the alleles of a population through crossover and gene conversion. These mechanisms have considerable consequences on the evolution and maintenance of genetic diversity. Crossover, for example, can increase genetic diversity by breaking the linkage between selected and nearby neutral variants. Read More

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Strong, Hydrostable, and Degradable Straws Based on Cellulose-Lignin Reinforced Composites.

Small 2021 Mar 24:e2008011. Epub 2021 Mar 24.

Department of Mechanical Engineering, University of Maryland, College Park, MD, 20742, USA.

The huge consumption of single-use plastic straws has brought a long-lasting environmental problem. Paper straws, the current replacement for plastic straws, suffer from drawbacks, such as a high cost of the water-proof wax layer and poor water stability due to the easy delamination of the wax layer. It is therefore crucial to find a high-performing alternative to mitigate the environmental problems brought by plastic straws. Read More

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Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions.

Nat Commun 2021 03 12;12(1):1660. Epub 2021 Mar 12.

Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.

In less than nine months, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) killed over a million people, including >25,000 in New York City (NYC) alone. The COVID-19 pandemic caused by SARS-CoV-2 highlights clinical needs to detect infection, track strain evolution, and identify biomarkers of disease course. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs and a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, viral, and microbial profiling. Read More

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Photosynthesis tunes quantum-mechanical mixing of electronic and vibrational states to steer exciton energy transfer.

Proc Natl Acad Sci U S A 2021 Mar;118(11)

Department of Chemistry, The University of Chicago, Chicago, IL 60637;

Photosynthetic species evolved to protect their light-harvesting apparatus from photoxidative damage driven by intracellular redox conditions or environmental conditions. The Fenna-Matthews-Olson (FMO) pigment-protein complex from green sulfur bacteria exhibits redox-dependent quenching behavior partially due to two internal cysteine residues. Here, we show evidence that a photosynthetic complex exploits the quantum mechanics of vibronic mixing to activate an oxidative photoprotective mechanism. Read More

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X Chromosome Contribution to the Genetic Architecture of Primary Biliary Cholangitis.

Gastroenterology 2021 Mar 4. Epub 2021 Mar 4.

Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases, San Gerardo Hospital, Monza, Italy. Electronic address:

Background & Aims: Genome-wide association studies in primary biliary cholangitis (PBC) have failed to find X chromosome (chrX) variants associated with the disease. Here, we specifically explore the chrX contribution to PBC, a sexually dimorphic complex autoimmune disease.

Methods: We performed a chrX-wide association study, including genotype data from 5 genome-wide association studies (from Italy, United Kingdom, Canada, China, and Japan; 5244 case patients and 11,875 control individuals). Read More

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Exploring the differences between men's and women's perceptions of gender-based violence in rural Tajikistan: a qualitative study.

BMC Womens Health 2021 Mar 4;21(1):91. Epub 2021 Mar 4.

Social and Behavioral Science, College of Public Health and Health Professions, University of Florida, 1225 Center Drive, P.O. Box 100182, Gainesville, FL, 32610-0182, USA.

Background: Most women living in rural provinces of Tajikistan, specifically Khatlon, experience little to no opportunities for education and economic growth, making them vulnerable to gender-based violence (GBV). Unfortunately due to social norms that are bolstered by a patriarchal society, GBV has become tolerated and even normalized in rural areas. This study looks to investigate the differences in perceptions of violence as it relates to empowerment among men and women in rural Tajikistan. Read More

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Perceived helpfulness of bipolar disorder treatment: Findings from the World Health Organization World Mental Health Surveys.

Bipolar Disord 2021 Feb 26. Epub 2021 Feb 26.

Department of Health Care Policy, Harvard Medical School, Boston, MA, USA.

Objectives: To examine patterns and predictors of perceived treatment helpfulness for mania/hypomania and associated depression in the WHO World Mental Health Surveys.

Methods: Face-to-face interviews with community samples across 15 countries found n = 2,178 who received lifetime mania/hypomania treatment and n = 624 with lifetime mania/hypomania who received lifetime major depression treatment. These respondents were asked whether treatment was ever helpful and, if so, the number of professionals seen before receiving helpful treatment. Read More

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February 2021

Complex hydroperiod induced carryover responses for survival, growth, and endurance of a pond-breeding amphibian.

Oecologia 2021 Feb 26. Epub 2021 Feb 26.

Department of Biological Sciences, Ohio University, 107 Irvine Hall, Athens, OH, 45701, USA.

Assessing carryover effects from the aquatic to the terrestrial stage of pond-breeding amphibians is critical as temperature and hydrologic regimes of temporary ponds continue to be altered as a result of climate change and other stressors. We evaluated carryover effects of hydroperiod length (50-62 days) on amphibian survival, developmental rates, and locomotor performance using a model organism, the wood frog (Rana sylvatica), through aquatic and terrestrial mesocosm experiments with individual tests of locomotor performance. We found that shorter hydroperiods (50 days) had low larval survival (0. Read More

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February 2021

Conservative treatment for uncomplicated appendicitis in children: the CONTRACT feasibility study, including feasibility RCT.

Health Technol Assess 2021 Feb;25(10):1-192

Department of Health Services Research, Institute of Population Health Sciences, University of Liverpool, Liverpool, UK.

Background: Although non-operative treatment is known to be effective for the treatment of uncomplicated acute appendicitis in children, randomised trial data comparing important outcomes of non-operative treatment with those of appendicectomy are lacking.

Objectives: The objectives were to ascertain the feasibility of conducting a multicentre randomised controlled trial comparing the clinical effectiveness and cost-effectiveness of a non-operative treatment pathway with appendicectomy for the treatment of uncomplicated acute appendicitis in children.

Design: This was a mixed-methods study, which included a feasibility randomised controlled trial, embedded and parallel qualitative and survey studies, a parallel health economic feasibility study and the development of a core outcome set. Read More

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February 2021

Interdisciplinary influences in headache literature: A network citation analysis of PubMed Central articles.

Headache 2021 Jan 8;61(1):143-148. Epub 2020 Dec 8.

Department of Neurology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA.

Background: Non-headache literature inevitably influences headache research, but the way this interdisciplinary interaction occurs has seldom been evaluated.

Objective: Utilizing network analysis techniques within the PubMed Central (PMC) database, we illustrate a novel method by which to identify and characterize the important non-headache literature with significant impact within the headache world.

Methods: Using the National Center for Biotechnology Information E-utilities application programing interface and custom backend software, all PMC articles containing the words "headache(s)" and/or "migraine(s)" in the title were identified. Read More

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January 2021

A commercial antibody to the human condensin II subunit NCAPH2 cross-reacts with a SWI/SNF complex component.

Wellcome Open Res 2021 13;6. Epub 2021 Jan 13.

MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK.

Condensin complexes compact and disentangle chromosomes in preparation for cell division. Commercially available antibodies raised against condensin subunits have been widely used to characterise their cellular interactome. Here we have assessed the specificity of a polyclonal antibody (Bethyl A302-276A) that is commonly used as a probe for NCAPH2, the kleisin subunit of condensin II, in mammalian cells. Read More

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January 2021

Federated semi-supervised learning for COVID region segmentation in chest CT using multi-national data from China, Italy, Japan.

Med Image Anal 2021 May 6;70:101992. Epub 2021 Feb 6.

Nvidia Corporation, 4500 East West Highway, Bethesda, Maryland 20814, USA. Electronic address:

The recent outbreak of Coronavirus Disease 2019 (COVID-19) has led to urgent needs for reliable diagnosis and management of SARS-CoV-2 infection. The current guideline is using RT-PCR for testing. As a complimentary tool with diagnostic imaging, chest Computed Tomography (CT) has been shown to be able to reveal visual patterns characteristic for COVID-19, which has definite value at several stages during the disease course. Read More

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Evidence for reduced immune gene diversity and activity during the evolution of termites.

Proc Biol Sci 2021 Feb 17;288(1945):20203168. Epub 2021 Feb 17.

Institute of Biology, Freie Universität Berlin, Schwendenerstr. 1, 14195 Berlin, Germany.

The evolution of biological complexity is associated with the emergence of bespoke immune systems that maintain and protect organism integrity. Unlike the well-studied immune systems of cells and individuals, little is known about the origins of immunity during the transition to eusociality, a major evolutionary transition comparable to the evolution of multicellular organisms from single-celled ancestors. We aimed to tackle this by characterizing the immune gene repertoire of 18 cockroach and termite species, spanning the spectrum of solitary, subsocial and eusocial lifestyles. Read More

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February 2021

Twin-Screw Extrusion Process to Produce Renewable Fiberboards.

J Vis Exp 2021 01 27(167). Epub 2021 Jan 27.

Laboratoire de Chimie Agro-industrielle (LCA), Université de Toulouse, INRAE, INPT.

A versatile twin-screw extrusion process to provide an efficient thermo-mechano-chemical pre-treatment on lignocellulosic biomass before using it as source of mechanical reinforcement in fully bio-based fiberboards was developed. Various lignocellulosic crop by-products have already been successfully pre-treated through this process, e.g. Read More

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January 2021

Durable Goods Drive Two-Thirds of Global Households' Final Energy Footprints.

Environ Sci Technol 2021 Mar 12;55(5):3175-3187. Epub 2021 Feb 12.

Industrial Ecology Programme (IndEcol), NTNU, NO-7491 Trondheim, Norway.

Sustainability endorses high quality, long-lasting goods. Durable goods, however, often require substantial amounts of energy during their production and use-phase and indirectly through complementary products and services. We quantify the global household's final energy footprints (EFs) of durable goods and the complementary goods needed to operate, service and maintain durables. Read More

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Mode Coarsening or Fracture: Energy Transfer Mechanisms in Dynamic Buckling of Rods.

Phys Rev Lett 2021 Jan;126(4):045501

MIT-CNRS Joint Lab "Multiscale Materials Science for Energy and the Environment," Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

We present results of a hybrid experimental, theoretical, and simulation-based investigation of the postbuckling behavior of thin elastic rods axially impacted by a projectile. We find a new postbuckling mechanism: mode coarsening. Much akin to inverse energy cascade phenomena in other nonlinear dynamic systems, energy is transferred during mode coarsening from higher to lower wave numbers-unless the rod breaks, abruptly dissipating in the course of fracture the rod's strain energy. Read More

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January 2021

Integrating Computational and Experimental Workflows for Accelerated Organic Materials Discovery.

Adv Mater 2021 Mar 9;33(11):e2004831. Epub 2021 Feb 9.

Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London, W12 0BZ, UK.

Organic materials find application in a range of areas, including optoelectronics, sensing, encapsulation, molecular separations, and photocatalysis. The discovery of materials is frustratingly slow however, particularly when contrasted to the vast chemical space of possibilities based on the near limitless options for organic molecular precursors. The difficulty in predicting the material assembly, and consequent properties, of any molecule is another significant roadblock to targeted materials design. Read More

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Words Matter: What Do Patients Find Judgmental or Offensive in Outpatient Notes?

J Gen Intern Med 2021 Feb 2. Epub 2021 Feb 2.

Department of Medicine, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, USA.

Background: Sharing outpatient notes with patients may bring clinically important benefits, but notes may sometimes cause patients to feel judged or offended, and thereby reduce trust.

Objective: As part of a larger survey examining the effects of open notes, we sought to understand how many patients feel judged or offended due to something they read in outpatient notes, and why.

Design: We analyzed responses from a large Internet survey of adult patients who used secure patient portals and had at least 1 visit note available in a 12-month period at 2 large academic medical systems in Boston and Seattle, and in a rural integrated health system in Pennsylvania. Read More

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February 2021

Fungal Community and Biodeterioration Analysis of Hull Wood and Its Storage Environment of the Nanhai No. 1 Shipwreck.

Front Microbiol 2020 15;11:609475. Epub 2021 Jan 15.

Ministry of Education Key Laboratory of Molecular Microbiology and Technology, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China.

The Nanhai No. 1 shipwreck is a Chinese merchant ship in the Southern Song Dynasty, and now it is stored in a huge enclosed glass warehouse in Maritime Silk Road Museum in Guangdong Province. At present, the hull of the Nanhai No. Read More

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January 2021

Trends in particle matter and its elemental composition in Santiago de Chile, 2011 - 2018.

J Air Waste Manag Assoc 2021 Mar 1:1-16. Epub 2021 Mar 1.

Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard, USA.

Daily fine (PM) and coarse (PM) particle matter (PM) samples collected at Parque O'Higgins station in downtown Santiago de Chile have been studied to find the trends in concentration from 1998 to 2018. Elemental concentration was obtained using X-ray fluorescence (XRF). Regression models from previous studies indicate that the PM and PM fractions have had a continuous decrease since 1988 mostly due to several policy control measures carried out over several decades. Read More

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Historic and Modern Approaches for the Discovery of Abandoned Wells for Methane Emissions Mitigation in Oil Creek State Park, Pennsylvania.

Environ Manage 2021 May 22;67(5):852-867. Epub 2021 Jan 22.

Department of Energy, National Energy Technology Laboratory, Pittsburgh, PA, USA.

Hundreds of oil wells were drilled along Oil Creek in Pennsylvania in the mid-1800s, birthing the modern oil industry. No longer in operation, many wells are now classified as abandoned, and, due to their age, their locations are either unknown or inaccurately recorded. These historic-well sites present environmental, safety, and economic concerns in the form of possible methane leaks and physical hazards. Read More

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Deubiquitinating enzyme amino acid profiling reveals a class of ubiquitin esterases.

Proc Natl Acad Sci U S A 2021 Jan;118(4)

Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, DD1 5EH, Scotland, United Kingdom

The reversibility of ubiquitination by the action of deubiquitinating enzymes (DUBs) serves as an important regulatory layer within the ubiquitin system. Approximately 100 DUBs are encoded by the human genome, and many have been implicated with pathologies, including neurodegeneration and cancer. Non-lysine ubiquitination is chemically distinct, and its physiological importance is emerging. Read More

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January 2021