Uber-Claws : unsupervised pattern classification for multi-unit extracellular neuronal burst extraction

To further an understanding of how a neuronal population generates patterns of rhythmic activity, the temporal dynamics of the group of neurons must be formalized. Essential to this pursuit, is the ability to reliably detect and separate the classes of single-unit neuronal activity from multi-unit extracellular signals recorded in a single channel. This study proposes a unified approach to automatically detect and classify single-unit bursts, and to observe the precise onset and offset of burst activity. Existing approaches to the problem fundamentally depend on the statistics of spike waveform variability, both extrinsic and intrinsic to the neuron. In contrast, the proposed approach depends on statistics that characterize the burst variability. An unsupervised learning procedure is implemented using hierarchical clustering to derive a complete and natural description of the variability in terms of clusters of bursts that possess strong internal similarities. Redundant solution vectors are used to parameterize each cluster, and a fuzzy classification approach assigns each burst to a class. Accuracy of the technique is demonstrated on in vivo and in vitro recordings of the triphasic pyloric rhythm in stomatogastric ganglion of crab Cancer borealis. The results, evaluated against a widely used manual classification approach, show that the technique performs detection and classification with comparable accuracy and quantifiable certainty, and is robust to background activity and noise

Low-temperature Molecular Beam Epitaxy of GaAs: A Theoretical Investigation of Antisite Incorporation and Reflection High-energy Diffraction Oscillations

Surface dynamics dominate the incorporation of charged, As+Ga, and neutral, As0Ga, antisite arsenic, and the temporal variation of reflection high-energy electron diffraction(RHEED) intensity in the low-temperature molecular beam epitaxy of (100) gallium arsenide(GaAs). A rate equation model is proposed which includes the presence and dynamics of a physisorbed arsenic (PA) layer riding the growth surface. The PA layer dictates the incorporation and concentration of As+Ga and As0Ga. Additionally, it influences the RHEED oscillations (ROs) behavior and the RO’s dependence on its coverage through its contribution to the reflected intensity. The model results for the dependence of As+Ga and As0Ga concentrations on beam equivalent pressure (BEP) and growth temperature are in good agreement with experimental data. The experimental observations can be explained based on the saturation of the PA coverage at one monolayer and the competing rate processes such as the AsGa incorporation into and evaporation from the crystalline surface. Using the same kinetic model for the temporal behavior of the surface, the contribution of the PA layer to the RHEED intensity is computed based on kinematical theory of electron diffraction. The experimental observation of the ROs during growth at high and low temperatures with no ROs in the intermediate temperature range of 300–450 °C is in good agreement with our model results. At low temperatures, the surface is covered by the PA layer whose step density depends on that of the subsurface crystalline GaAs. Thus, a temporal variation of the step density of subsurface crystalline GaAs results in ROs, but with a different step height, that of the PA layer, of 2.48 Å. At high temperatures, the crystalline GaAs is exposed to the RHEED beam due to the evaporation of the PA layer and the ROs appear due to periodic step-density oscillations with a step height of 1.41 Å, which is the Ga–As crystalline interplanar distance. At intermediate temperatures, the surface is partially covered by the PA layer resulting in RHEED reflection contributions from both surfaces covered by the PA layer and crystal. Due to the very different interplanar distances between the crystalline GaAs and the PA layers, complete destructive interference of the RHEED intensity results at a 0.5 surface coverage of the PA layer. The RO dependence on the As BEP is also presented and discussed

Seamless scalability, consistency and quality of transient protein production in CHO Cells by using MaxCyte flow electroporation technology

Recombinant protein production often suffers from process inconsistencies as cell cultures are scaled up. High levels of process consistency and scalability are important not only for GMP stage manufacturing, but they are also critical for early stage R&D studies since good predictivity of any scale production can shorten timelines and minimize costs. There are many parameters that influence consistency of production during scale up. These include agitation rates, dissolved oxygen levels and pH. Consistency of production following transient gene expression (TGE) is further impacted by process variabilities that are inherent to many transient transfection methodologies. The aim of this study is to show how MaxCyte’s flow electroporation technology (STX technology) can transiently produce therapeutic materials from milligram to gram scales quickly to support early to mid-stage drug development. We collected data on cell growth, viability and productivity post electroporation, demonstrating that this technology is highly consistent and scalable (from 0.5 x 106 to 2 x 1011 cells of transfected cells) Antibody titers from 1 g/L up to 2.7 g/L were achieved by transient gene expression in CHO-S cells. Furthermore, we showed that TGE materials have the comparable protein quality as proteins produced by a stable cell line. The high TGE productivity, product quality and scalability in CHO cells by using MaxCyte transfection technology can accelerate the drug development process and reduce the risk of drug evaluation and selection

Characterizing response behavior in multisensory perception with conflicting cues

We explore a recently proposed mixture model approach to understanding interactions between conflicting sensory cues. Alternative model formulations, differing in their sensory noise models and inference methods, are compared based on their fit to experimental data. Heavy-tailed sensory likelihoods yield a better description of the subjects' response behavior than standard Gaussian noise models. We study the underlying cause for this result, and then present several testable predictions of these models

Emerging Role of Long Non-Coding RNAs in Diabetic Vascular Complications

Chronic metabolic disorders such as obesity and diabetes are associated with accelerated rates of macrovascular and microvascular complications, which are leading causes of morbidity and mortality worldwide. Further understanding of the underlying molecular mechanisms can aid in the development of novel drug targets and therapies to manage these disorders more effectively. Long non-coding RNAs (lncRNAs) that do not have protein-coding potential are expressed in a tissue- and species-specific manner and regulate diverse biological processes. LncRNAs regulate gene expression in cis or in trans through various mechanisms, including interaction with chromatin-modifying proteins and other regulatory proteins and via posttranscriptional mechanisms, including acting as microRNA sponges or as host genes of microRNAs. Emerging evidence suggests that major pathological factors associated with diabetes such as high glucose, free fatty acids, proinflammatory cytokines, and growth factors can dysregulate lncRNAs in inflammatory, cardiac, vascular, and renal cells leading to altered expression of key inflammatory genes and fibrotic genes associated with diabetic vascular complications. Here we review recent reports on lncRNA characterization, functions, and mechanisms of action in diabetic vascular complications and translational approaches to target them. These advances can provide new insights into the lncRNA-dependent actions and mechanisms underlying diabetic vascular complications and uncover novel lncRNA-based biomarkers and therapies to reduce disease burden and mortality

Lymphocytes From Patients With Type 1 Diabetes Display a Distinct Profile of Chromatin Histone H3 Lysine 9 Dimethylation : An Epigenetic Study in Diabetes

OBJECTIVE—The complexity of interactions between genes and the environment is a major challenge for type 1 diabetes studies. Nuclear chromatin is the interface between genetics and environment and the principal carrier of epigenetic information. Because histone tail modifications in chromatin are linked to gene transcription, we hypothesized that histone methylation patterns in cells from type 1 diabetic patients can provide novel epigenetic insights into type 1 diabetes and its complications

Chromatin variation associated with liver metabolism is mediated by transposable elements

Additional file 1: Supplementary methods. Figure S1. Phenotypic diversity in different inbred strains. Figure S2. Chromatin variability across inbred strains of mice. Figure S3. Association between chromatin variation and SNPs. Figure S4. Accessible chromatin sites and TE sequences. Figure S5. DNA transposons and chromatin accessibility variation. Figure S6. Differential accessibility at young L1Md subfamilies across different strains. Figure S7. Chromatin accessibility at younger L1Md subfamilies in recombinant inbred strains. Figure S8. Chromatin variability and age of LINE subfamilies. Figure S9. Differential chromatin accessibility profile at younger and older LINEs in A/J mice liver. Figure S10. Accessibility and transcription of LINE subfamilies. Figure S11. CRISPR-Cas9 deletion of additional TEs. Figure S12. Guide RNA and genotyping primers used for CRISPR-Cas9 genome editing. Figure S13. Genotyping for TE deletions. Figure S14. Example of an eQTL that associated with variable chromatin accessibility at a LTR. Table S1. Summary of FAIRE-seq data sets in all the strains in this study. Table S3. Enriched biological process from GREAT analysis of accessible chromatin sites. Table S4. Sequences used in this study

Environmental Exposures during Puberty: Window of Breast Cancer Risk and Epigenetic Damage.

During puberty, a woman's breasts are vulnerable to environmental damage ("window of vulnerability"). Early exposure to environmental carcinogens, endocrine disruptors, and unhealthy foods (refined sugar, processed fats, food additives) are hypothesized to promote molecular damage that increases breast cancer risk. However, prospective human studies are difficult to perform and effective interventions to prevent these early exposures are lacking. It is difficult to prevent environmental exposures during puberty. Specifically, young women are repeatedly exposed to media messaging that promotes unhealthy foods. Young women living in disadvantaged neighborhoods experience additional challenges including a lack of access to healthy food and exposure to contaminated air, water, and soil. The purpose of this review is to gather information on potential exposures during puberty. In future directions, this information will be used to help elementary/middle-school girls to identify and quantitate environmental exposures and develop cost-effective strategies to reduce exposures

Lymphoblastoid Cell Lines as a Tool to Study Inter-Individual Differences in the Response to Glucose

Background: White blood cells have been shown in animal studies to play a central role in the pathogenesis of diabetic retinopathy. Lymphoblastoid cells are immortalized EBV-transformed primary B-cell leukocytes that have been extensively used as a model for conditions in which white blood cells play a primary role. The purpose of this study was to investigate whether lymphoblastoid cell lines, by retaining many of the key features of primary leukocytes, can be induced with glucose to demonstrate relevant biological responses to those found in diabetic retinopathy. Methods: Lymphoblastoid cell lines were obtained from twenty-three human subjects. Differences between high and standard glucose conditions were assessed for expression, endothelial adhesion, and reactive oxygen species. Results: Collectively, stimulation of the lymphoblastoid cell lines with high glucose demonstrated corresponding changes on molecular, cellular and functional levels. Lymphoblastoid cell lines up-regulated expression of a panel of genes associated with the leukocyte-mediated inflammation found in diabetic retinopathy that include: a cytokine (IL-1B fold change = 2.11, p-value = 0.02), an enzyme (PKCB fold change = 2.30, p-value = 0.01), transcription factors (NFKB-p50 fold change = 2.05, p-value = 0.01), (NFKB-p65 fold change = 2.82, p-value = 0.003), and an adhesion molecule (CD18 fold change = 2.59, 0.02). Protein expression of CD18 was also increased (p-value = 2.14x10-5). The lymphoblastoid cell lines demonstrated increased adhesiveness to endothelial cells (p = 1.28x10-5). Reactive oxygen species were increased (p = 2.56x10-6). Significant inter-individual variation among the lymphoblastoid cell lines in these responses was evident (F = 18.70, p Conclusions: Exposure of lymphoblastoid cell lines derived from different human subjects to high glucose demonstrated differential and heterogeneous gene expression, adhesion, and cellular effects that recapitulated features found in the diabetic state. Lymphoblastoid cells may represent a useful tool to guide an individualized understanding of the development and potential treatment of diabetic complications like retinopathy.</p

Peptide-based direct electrochemical detection of receptor binding domains of SARS-CoV-2 spike protein in pristine samples

RNA isolation and amplification-free user-friendly detection of SARS-CoV-2 is the need of hour especially at resource limited settings. Herein, we devised the peptides of human angiotensin converting enzyme-2 (hACE-2) as bioreceptor at electrode interface for selective targeting of receptor binding domains (RBD) of SARS-CoV-2 spike protein (SP). Disposable carbon-screen printed electrode modified with methylene blue (MB) electroadsorbed graphene oxide (GO) has been constructed as cost-efficient and scalable platform for hACE-2 peptide-based SARS-CoV-2 detection. In silico molecular docking of customized 25 mer peptides with RBD of SARS-CoV-2 SP were validated by AutoDock CrankPep. N-terminal region of ACE-2 showed higher binding affinity of − 20.6 kcal/mol with 15 H-bond, 9 of which were < 3 Å. Electrochemical biosensing of different concentrations of SPs were determined by cyclic voltammetry (CV) and chronoamperometry (CA), enabling a limit of detection (LOD) of 0.58 pg/mL and 0.71 pg/mL, respectively. MB-GO devised hACE-2 peptide platform exert an enhanced current sensitivity of 0.0105 mA/pg mL(−1) cm(−2) (R(2) = 0.9792) (CV) and 0.45 nA/pg mL(−1) (R(2) = 0.9570) (CA) against SP in the range of 1 pg/mL to 1 µg/mL. For clinical feasibility, nasopharyngeal and oropharyngeal swab specimens in viral transport medium were directly tested with the prepared peptide biosensor and validated with RT-PCR, promising for point-of-need analysis