150,049 results match your criteria clusters

Patterns of Recording Epileptic Spasms in an Electronic Seizure Diary Compared With Video-EEG and Historical Cohorts.

Pediatr Neurol 2021 Apr 23;122:27-34. Epub 2021 Apr 23.

MD Program, Weill Cornell Medicine, New York, New York; Department of Pediatrics, Weill Cornell Medicine, New York, New York; Department of Population Health Sciences, Weill Cornell Medicine, New York, New York. Electronic address:

Background: Use of electronic seizure diaries (e-diaries) by caregivers of children with epileptic spasms is not well understood. We describe the demographic and seizure-related information of children with epileptic spasms captured in a widely used e-diary and explore the potential biases in how caregivers report these data.

Methods: We analyzed children with epileptic spasms in an e-diary, Seizure Tracker, from 2007 to 2018. Read More

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Neurological presentations and cognitive outcome in Sturge-Weber syndrome.

Eur J Paediatr Neurol 2021 Jul 9;34:21-32. Epub 2021 Jul 9.

Great Ormond Street Hospital for Children Neurodisability Department, Great Ormond Street, UCL Great Ormond Street Institute of Child Health Clinical Neurosciences, London, United Kingdom.

Introduction: This study of children with Sturge-Weber syndrome (SWS) profiled neurological presentations; compared patients with (+) and without (-) port-wine stain (PWS); and determined risk factors for intellectual and language impairments.

Methods: A retrospective case note review was conducted at a national centre.

Results: This cohort (n = 140, male 72, median follow up 114 months) showed sex parity. Read More

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DNA methylation array identifies golli-MBP as a biomarker for the disease severity in childhood atopic dermatitis.

J Invest Dermatol 2021 Jul 19. Epub 2021 Jul 19.

Department of Pediatrics and Kawasaki Disease Center, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan 83301; Division of Pulmonary & Critical Care Medicine, Department of Internal Medicine, Department of Respiratory Therapy, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan. 83301. Electronic address:

In this study, we investigated the changes in the global methylation status and its functional relevance in childhood atopic dermatitis (AD). Differences in epigenome-scale methylation events in peripheral blood associated with childhood AD were screened using DNA methylation arrays of 24 AD patients compared to 24 control subjects (C). Of the 16,840 differentially methylated CpG regions between AD and C, > 97% CpG loci revealed hypomethylation in childhood AD patients. Read More

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Potentially toxic elements in soil and road dust around Sonbhadra industrial region, Uttar Pradesh, India: Source apportionment and health risk assessment.

Environ Res 2021 Jul 19:111685. Epub 2021 Jul 19.

Department of Hydrogeology and Environmental Geology, Institute of Geosciences, Martin Luther University, Halle (Saale), 06120, Germany.

Potentially toxic elements (PTEs) are directly linked with various kinds of adverse health issues. Available reports related to symptoms of mercury contamination in the local population of the study region motivated us to carry out this work in detail. To estimate potentially toxic elements (As, Cd, Cr, Cu, Fe, Hg, Mn, Ni, Pb, Zn) contamination status, a total of 48 samples of soil & road dust from industrial clusters were collected and analyzed for source identification and human health risk assessment in the Sonbhadra region of Uttar Pradesh, India. Read More

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Cyclic, Hydrophobic Hexapeptide Fusahexin Is the Product of a Nonribosomal Peptide Synthetase in .

J Nat Prod 2021 Jul 22. Epub 2021 Jul 22.

Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers Vej 7H, DK-9220 Aalborg, Denmark.

The plant pathogenic fungus is known to produce a wide array of secondary metabolites during plant infection. This includes several nonribosomal peptides. Recently, the fusaoctaxin (/9) and gramilin () gene clusters were shown to be induced by host interactions. Read More

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Irritability-related neural responses to frustrative nonreward in adolescents with trauma histories: A preliminary investigation.

Dev Psychobiol 2021 Jul 22. Epub 2021 Jul 22.

Department of Psychology, San Diego State University, San Diego, California, USA.

Irritability, conceptualized as a lowered frustration response threshold to blocked goal attainment (i.e., frustrative nonreward), is a common, detrimental symptom in adolescence. Read More

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Biochemical Approaches to Probe the Role of the Auxiliary Iron-Sulfur Cluster of Lipoyl Synthase from Mycobacterium Tuberculosis.

Methods Mol Biol 2021 ;2353:307-332

Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.

Lipoic acid is an essential sulfur-containing cofactor used by several multienzyme complexes involved in energy metabolism and the breakdown of certain amino acids. It is composed of n-octanoic acid with sulfur atoms appended at C6 and C8. Lipoic acid is biosynthesized de novo in its cofactor form, in which it is covalently bound in an amide linkage to a target lysyl residue on a lipoyl carrier protein (LCP). Read More

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January 2021

Characterization of Fe-S Clusters in Proteins by Mӧssbauer Spectroscopy.

Methods Mol Biol 2021 ;2353:281-305

Department of Biochemistry, Brandeis University, Waltham, MA, USA.

Fe Mӧssbauer spectroscopy is unparalleled in the study of Fe-S cluster-containing proteins because of its unique ability to detect all forms of iron. Enrichment of biological samples with the Fe isotope and manipulation of experimental parameters such as temperature and magnetic field allow for elucidation of the number of Fe-S clusters present in a given protein, their nuclearity, oxidation state, geometry, and ligation environment, as well as any transient states relevant to enzyme chemistry. This chapter is arranged in five sections to help navigate an experimentalist to utilize Fe Mӧssbauer spectroscopy for delineating the role and structure of biological Fe-S clusters. Read More

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January 2021

Characterization of Paramagnetic Iron-Sulfur Clusters Using Electron Paramagnetic Resonance Spectroscopy.

Troy A Stich

Methods Mol Biol 2021 ;2353:259-280

Department of Chemistry, Wake Forest University, Winston-Salem, NC, USA.

Continuous-wave (CW) electron paramagnetic resonance (EPR) spectroscopy is a powerful ally in characterizing the multitude of redox-active iron-sulfur cluster-containing ([Fe-S]) species present in biological samples. The technique detects only those clusters that are paramagnetic-having a nonzero total electron spin (S > 0)-thus, it can discriminate between clusters in different oxidation states. The low-temperature CW-EPR spectrum of an [Fe-S] yields the three magnetic g-values that serve as a fingerprint of its electronic structure. Read More

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January 2021

Native Mass Spectrometry of Iron-Sulfur Proteins.

Methods Mol Biol 2021 ;2353:231-258

Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, UK.

Iron-sulfur clusters constitute a large and widely distributed group of protein cofactors that play key roles in a wide range of metabolic processes. The inherent reactivity of iron-sulfur clusters toward small molecules, for example, O, NO, or free Fe, makes them ideal for sensing changes in the cellular environment. Nondenaturing, or native, MS is unique in its ability to preserve the noncovalent interactions of many (if not all) species, including stable intermediates, while providing accurate mass measurements in both thermodynamic and kinetic experimental regimes. Read More

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January 2021

Circular Dichroism to Probe the Synthesis, Transfer, and Stability of Fe-S Clusters.

Methods Mol Biol 2021 ;2353:209-229

Section of Chemistry and Biomolecular Sciences, DeFENS, University of Milan, Milan, Italy.

All Fe-S proteins are characterized by distinctive circular dichroism (CD) features in the visible region of the spectrum due to chiral interaction between the cluster itself and the protein backbone. Therefore, the presence of a CD signal in the visible region relates to the presence of the cluster, whereas the disappearance of the signal refers to cluster breakdown or redox changes. The position of the CD features in the spectrum and the intensity of individual components of the CD signal show great variations among different Fe-S proteins. Read More

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January 2021

A Fast and Ratiometric Method for Quantification of Cysteine-Bound Persulfides Based on Alkylation and Gel-Shift Assays.

Methods Mol Biol 2021 ;2353:191-205

Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.

Cysteine-bound persulfides (Cys-SSH) in proteins are sulfur carrier intermediates in the synthesis of essential cofactors such as iron-sulfur clusters, molybdenum cofactor, vitamin (thiamine), and thionucleosides (thiolated tRNA). Protein-bound persulfides are also used for signaling purposes as a carrier of the "HS" signal. Several methods have been developed to detect and quantify cysteine-bound persulfides in protein and monitor their exchange. Read More

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January 2021

Methods to Investigate the Kinetic Profile of Cysteine Desulfurases.

Methods Mol Biol 2021 ;2353:173-189

Department of Chemistry, Wake Forest University, Winston-Salem, NC, USA.

Biological iron-sulfur (Fe-S) clusters are essential protein prosthetic groups that promote a range of biochemical reactions. In vivo, these clusters are synthesized by specialized protein machineries involved in sulfur mobilization, cluster assembly, and cluster transfer to their target proteins. Cysteine desulfurases initiate the first step of sulfur activation and mobilization in cluster biosynthetic pathways. Read More

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January 2021

Methods to Unravel the Roles of ATPases in Fe-S Cluster Biosynthesis.

Methods Mol Biol 2021 ;2353:155-171

Department of Chemistry, Boston University, Boston, MA, USA.

Complex biosynthetic pathways are required for the assembly and insertion of iron-sulfur (Fe-S) cluster cofactors. Each of the four cluster biogenesis systems that have been discovered requires at least one ATPase. Generally, the function of nucleotide hydrolysis in Fe-S cluster biogenesis is understudied. Read More

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January 2021

tRNA Modifications as a Readout of S and Fe-S Metabolism.

Methods Mol Biol 2021 ;2353:137-154

Department of Chemistry, Wake Forest University, Winston Salem, NC, USA.

Iron-Sulfur (Fe-S) clusters function as core prosthetic groups known to modulate the activity of metalloenzymes, act as trafficking vehicles for biological iron and sulfur, and participate in several intersecting metabolic pathways. The formation of these clusters is initiated by a class of enzymes called cysteine desulfurases, whose primary function is to shuttle sulfur from the amino acid L-cysteine to a variety of sulfur transfer proteins involved in Fe-S cluster synthesis as well as in the synthesis of other thiocofactors. Thus, sulfur and Fe-S cluster metabolism are connected through shared enzyme intermediates, and defects in their associated pathways cause a myriad of pleiotropic phenotypes, which are difficult to dissect. Read More

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January 2021

Enzymatic and Chemical In Vitro Reconstitution of Iron-Sulfur Cluster Proteins.

Methods Mol Biol 2021 ;2353:79-95

Department of Pharmaceutical Technology, University of Turin, Turin, Italy.

Iron-sulfur (Fe-S) clusters are key cofactors for proteins involved in essential cellular processes such as DNA replication and repair, ribosome biogenesis, tRNA thio-modification, and co-enzyme synthesis. Fe-S clusters can assemble spontaneously from inorganic compounds, but their biogenesis requires dedicated machineries to circumvent the toxic nature of iron and sulfur. To address how these machines work, different laboratories have applied various biochemical and biophysical approaches, both in vivo and in vitro. Read More

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January 2021

Methods for Heterologous Overproduction of Fe-S Proteins.

Methods Mol Biol 2021 ;2353:69-78

Department of Biological Sciences, Marquette University, Milwaukee, WI, USA.

Proteins carrying iron-sulfur ([Fe-S]) clusters are critical to the basic metabolism of all organisms. Structural and biochemical investigations of many such [Fe-S] cluster proteins depend on recombinant overproduction using heterologous bacterial hosts such as Escherichia coli . Here, we describe a detailed procedure for the overproduction and purification of two oxygen-sensitive component proteins of the dark-operative protochlorophyllide oxidoreductase (DPOR) complex. Read More

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January 2021

Genetic Approaches to Uncover Gene Products Involved in Iron-Sulfur Protein Maturation: High-Throughput Genomic Screening Using Transposon Sequencing.

Methods Mol Biol 2021 ;2353:51-68

Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, NJ, USA.

Iron-sulfur (Fe-S) clusters are one of the most ubiquitous and versatile prosthetic groups exploited by nature. Fe-S clusters aid in conducting redox reactions, carbon activation, and environmental sensing. This chapter presents an overview of the genetic approaches that have been useful for identifying and characterizing bacterial factors involved in Fe-S protein assembly. Read More

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January 2021

Study of Fe-S Cluster Proteins in Methanococcus maripaludis , a Model Archaeal Organism.

Methods Mol Biol 2021 ;2353:37-50

Corporate Strategic Research, ExxonMobil Research & Engineering Company, Annandale, NJ, USA.

Iron-sulfur (Fe-S) clusters are among the oldest and most versatile cofactors present in all domains of life. Many bacterial and eukaryotic Fe-S proteins have been well-characterized, whereas the archaeal ones are less studied. Fe-S proteins are particularly abundant and play essential roles in methanogenic archaea. Read More

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January 2021

Molecular Biology and Genetic Tools to Investigate Functional Redundancy Among Fe-S Cluster Carriers in E. coli.

Methods Mol Biol 2021 ;2353:3-36

Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS UMR 7283, Aix-Marseille University, Marseille, France.

Iron-sulfur (Fe-S) clusters are among the oldest protein cofactors, and Fe-S cluster-based chemistry has shaped the cellular metabolism of all living organisms. Over the last 30 years, thanks to molecular biology and genetic approaches, numerous actors for Fe-S cluster assembly and delivery to apotargets have been uncovered. In prokaryotes, Escherichia coli is the best-studied for its convenience of growth and its genetic amenability. Read More

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January 2021

Using Clustering to Examine Inter-individual Variability in Topography of Auditory Event-Related Potentials in Autism and Typical Development.

Brain Topogr 2021 Jul 22. Epub 2021 Jul 22.

Department of Psychology, UC Davis, Davis, USA.

Although prior studies have compared sensory event-related potential (ERP) responses between groups of autistic and typically-developing participants, it is unclear how heterogeneity contributes to the results of these studies. The present study used examined individual differences in these responses. 130 autistic children and 81 typically-developing children, aged between 2 and 5 years, listened to tones at four identity levels while 61-channel electroencephalography was recorded. Read More

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Single cell analysis of M. tuberculosis phenotype and macrophage lineages in the infected lung.

J Exp Med 2021 Sep 22;218(9). Epub 2021 Jul 22.

Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY.

In this study, we detail a novel approach that combines bacterial fitness fluorescent reporter strains with scRNA-seq to simultaneously acquire the host transcriptome, surface marker expression, and bacterial phenotype for each infected cell. This approach facilitates the dissection of the functional heterogeneity of M. tuberculosis-infected alveolar (AMs) and interstitial macrophages (IMs) in vivo. Read More

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September 2021

Quantitative particle agglutination assay for point-of-care testing using mobile holographic imaging and deep learning.

Lab Chip 2021 Jul 22. Epub 2021 Jul 22.

Electrical & Computer Engineering Department, University of California, Los Angeles, California 90095, USA. and California NanoSystems Institute (CNSI), University of California, Los Angeles, California 90095, USA and Bioengineering Department, University of California, Los Angeles, California 90095, USA.

Particle agglutination assays are widely adopted immunological tests that are based on antigen-antibody interactions. Antibody-coated microscopic particles are mixed with a test sample that potentially contains the target antigen, as a result of which the particles form clusters, with a size that is a function of the antigen concentration and the reaction time. Here, we present a quantitative particle agglutination assay that combines mobile lens-free microscopy and deep learning for rapidly measuring the concentration of a target analyte; as its proof-of-concept, we demonstrate high-sensitivity C-reactive protein (hs-CRP) testing using human serum samples. Read More

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Ti-Decorated B/N-doped graphene as a high-capacity hydrogen storage material: a DFT study.

Dalton Trans 2021 Jul 22. Epub 2021 Jul 22.

Center for Organic Electronic and Alternative Energy, Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand.

The adsorption properties of the hydrogen atom on our newly designed materials were investigated using density functional theory (DFT) calculations, focusing on the role of dopants in modulating the binding properties of the metal. We proposed decorating Ti4 on pristine, B- and N-doped graphene surfaces for preparing a large-capacity hydrogen-storage device. Computational results indicate that the doping of B on graphene enhances the interaction between the metal cluster and the supporting substrate with a very strong binding energy of -6. Read More

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Pioneer neutrophils release chromatin within in vivo swarms.

Elife 2021 Jul 21;10. Epub 2021 Jul 21.

The Bateson Centre and Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield Medical School, Sheffield, United Kingdom.

Neutrophils are rapidly recruited to inflammatory sites where their coordinated migration forms clusters, a process termed neutrophil swarming. The factors that modulate early stages of neutrophil swarming are not fully understood, requiring the development of new in vivo models. Using transgenic zebrafish larvae to study endogenous neutrophil migration in a tissue damage model, we demonstrate that neutrophil swarming is a conserved process in zebrafish immunity, sharing essential features with mammalian systems. Read More

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Ambiguities in solvation free energies from cluster-continuum quasichemical theory: lithium cation in protic and aprotic solvents.

Phys Chem Chem Phys 2021 Jul 22. Epub 2021 Jul 22.

N.N. Semenov Federal Research Center for Chemical Physics RAS, Kosygina Street 4, 119991 Moscow, Russia. and Joint Institute for High Temperatures, Russian Academy of Sciences, 13-2 Izhorskaya Street, Moscow 125412, Russia.

Gibbs free energies for Li+ solvation in water, methanol, acetonitrile, DMSO, dimethylacetamide, dimethoxyethane, dimethylformamide, gamma-butyrolactone, pyridine, and sulfolane have been calculated using the cluster-continuum quasichemical theory. With n independent solvent molecules S initial state forming the "monomer" thermodynamic cycle, Li+ solvation free energies are found to be on average 14 kcal mol-1 more positive compared to those from the "cluster" thermodynamic cycle where the initial state is the cluster Sn. We ascribe the inconsistency between the "monomer" and "cluster" cycles mainly to the incorrectly predicted solvation free energies of solvent clusters Sn from the SMD and CPCM continuum solvation models, which is in line with the earlier study of Bryantsev et al. Read More

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Development and validation of an immune gene set-based prognostic signature in cutaneous melanoma.

Future Oncol 2021 Jul 22. Epub 2021 Jul 22.

Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China.

We aimed to fully understand the landscape of the skin cutaneous melanoma (SKCM) microenvironment and develop an immune prognostic signature that can predict the prognosis for SKCM patients. RNA sequencing data and clinical information were downloaded from the Cancer Genome Atlas and Gene Expression Omnibus databases. The immune-prognostic signature was constructed by LASSO Cox regression analysis. Read More

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Genetic variation and relationships between Azerbaijani and Turkish olive genetic resources.

Mol Biol Rep 2021 Jul 21. Epub 2021 Jul 21.

Department of Crop and Animal Production, Organic Agriculture Programme, Karacabey Vocational School, Bursa Uludağ University, Bursa, Turkey.

Olive (Olea europaea L.) is one of the most economically important crop from east to the west around the world. The aim of this research was to investigate the genetic relationship among 41 olive genotypes, including 11 well-known Turkish cultivars and 30 Azerbaijani olive genotypes using simple sequence repeat (SSR) markers. Read More

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Codependency and mutual exclusivity for gene community detection from sparse single-cell transcriptome data.

Nucleic Acids Res 2021 Jul 22. Epub 2021 Jul 22.

Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

Single-cell RNA-seq (scRNA-seq) can be used to characterize cellular heterogeneity in thousands of cells. The reconstruction of a gene network based on coexpression patterns is a fundamental task in scRNA-seq analyses, and the mutual exclusivity of gene expression can be critical for understanding such heterogeneity. Here, we propose an approach for detecting communities from a genetic network constructed on the basis of coexpression properties. Read More

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Total Fat Content and Fatty Acid Profile of Fine-Aroma Cocoa From Northeastern Peru.

Front Nutr 2021 5;8:677000. Epub 2021 Jul 5.

Facultad de Ingeniería y Ciencias Agrarias, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas, Chachapoyas, Peru.

Cocoa beans are the raw material for the chocolate industry. In this study, the total fat contents and fatty acid profiles of fine-aroma cocoa beans of 30 cocoa ecotypes from northeastern Peru were evaluated. Results showed that SJJ-1 and ACJ-11 ecotypes from San Martin and Amazonas regions, respectively, presented highest percentages of total fat with an average of 30. Read More

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