gebhart/patrepeval huggingface dataset:
Burst of pulses in lightning electromagnetic radiation: observations and implications for lightning test standards (1996)

Bursts of regular microsecond-scale electric field pulses produced by three multiple-stroke cloud-to-ground discharges (a total of 2782 pulses) and by three cloud discharges (a total of 1436 pulses), all recorded within 20 km or so at the NASA Kennedy Space Center, are analyzed. The regular pulse bursts are similar in both cloud-to-ground and cloud discharges. A burst is characterized by some tens of pulses, each having a total width of a few microseconds, with an average interpulse interval of 6-7 /spl mu/m. Pulse peaks in cloud-to-ground discharges are approximately two orders of magnitude smaller than return-stroke initial field peaks in the same flash. In both cloud and ground discharges, there is a tendency for the bursts to occur in the latter stages of a discharge, and positive and negative pulse polarities are about equally probable. Many bursts were found to be associated with the latter part of K changes while one pronounced M change appeared to be initiated by a regular pulse burst. The observed regular burst exhibit some similarity to the "multiple burst" (component H) of the standard lightning environment for the design and testing of aerospace vehicles. Overall, neither the present definition of the H component given in a previously published document (see Fed. Aviation Admin., US Dept. of Trans., advisory circular no. 20-136, Mar. 5, 1990) nor its newly proposed revision appears to be based on adequate experimental data.
Microbiota regulation of development of thymic microbiota-specific T cells (2022)

Abstract While exposure to microbial antigens in peripheral sites causes expansion of antigen-specific T cells, a role for antigen-specific expansion had not been identified during T cell development in the thymus. We recently found that intestinal colonization induced intestinal dendritic cells migration to the thymus, driving thymic expansion of microbiota-specific T cells early in life. In contrast, colonization in adulthood leads to expansion of peripheral but not thymic microbiota-specific T cells. Thymic microbiota-specific T cells developed early in life were undifferentiated and caused intestinal inflammation in immunocompromised hosts upon antigen reencounter. We sought to understand regulation of this developmental window and define if thymic expansion of microbiota-specific T cells could be restarted in adult mice. We found that microbiota manipulation reestablished expansion of microbiota-specific T cells in the thymus of adult mice. We are in the process of characterizing these T cells in adulthood to assess their impact on intestinal inflammation. Our data suggests that intestinal colonization controls the generation of thymic microbiota-specific T cells which has the potential to modulate inflammatory processes.
Large-scale pathway specific polygenic risk and transcriptomic community network analysis identifies novel functional pathways in Parkinson disease (2020)

Polygenic inheritance plays a central role in Parkinson disease (PD). A priority in elucidating PD etiology lies in defining the biological basis of genetic risk. Unraveling how risk leads to disruption will yield disease-modifying therapeutic targets that may be effective. Here, we utilized a high-throughput and hypothesis-free approach to determine biological processes underlying PD using the largest currently available cohorts of genetic and gene expression data from International Parkinson's Disease Genetics Consortium (IPDGC) and the Accelerating Medicines Partnership-Parkinson's disease initiative (AMP-PD), among other sources. We applied large-scale gene-set specific polygenic risk score (PRS) analyses to assess the role of common variation on PD risk focusing on publicly annotated gene sets representative of curated pathways. We nominated specific molecular sub-processes underlying protein misfolding and aggregation, post-translational protein modification, immune response, membrane and intracellular trafficking, lipid and vitamin metabolism, synaptic transmission, endosomal-lysosomal dysfunction, chromatin remodeling and apoptosis mediated by caspases among the main contributors to PD etiology. We assessed the impact of rare variation on PD risk in an independent cohort of whole-genome sequencing data and found evidence for a burden of rare damaging alleles in a range of processes, including neuronal transmission-related pathways and immune response. We explored enrichment linked to expression cell specificity patterns using single-cell gene expression data and demonstrated a significant risk pattern for dopaminergic neurons, serotonergic neurons, hypothalamic GABAergic neurons, and neural progenitors. Subsequently, we created a novel way of building de novo pathways by constructing a network expression community map using transcriptomic data derived from the blood of PD patients, which revealed functional enrichment in inflammatory signaling pathways, cell death machinery related processes, and dysregulation of mitochondrial homeostasis. Our analyses highlight several specific promising pathways and genes for functional prioritization and provide a cellular context in which such work should be done.
Tyrosinase-catalyzed melanin as a contrast agent for photoacoustic tomography (2011)

It is difficult to distinguish between tumor cells and surrounding cells without staining as is done in histology. We developed tyrosinase-catalyzed melanin as a reporter gene for photoacoustic tomography. Tyrosinase is the primary enzyme responsible for the production of melanin and alone is sufficient to produce melanin in non-melanogenic cells. Two cell lines were created: a stably transfected HeLa line and a transiently transfected 293 line. A phantom experiment was performed with the 293 transfected cells 48 hours post transfection and the results compared with oxygenated whole blood, B16 melanoma and 293 control cells. An in vivo experiment was performed using the transfected HeLa cells xenografted into a nude mouse ear, and then imaged. The results show strong contrast for tyrosinase-catalyzed melanin in both the 293 cells in the tube phantom as well as the in vivo result showing melanin in a nude mouse ear. Transfection increased expression in 293 cells 159 fold and image contrast compared to blood by as much as 50 fold. Due to the strong signal obtained at longer wavelengths and the decrease of blood signal at the same wavelengths, tyrosinase catalyzed melanin is a good candidate as a molecular imaging contrast agent for photoacoustic tomography.
Eliminate false positives in metagenomic profiling based on type IIB restriction sites (2022)

Abstract Accurate species identification and abundance estimation are critical for the interpretation of whole metagenome shotgun sequencing (WMS) data. Numerous computational methods, broadly referred to as metagenomic profilers, have been developed to identify species in microbiome samples by classification of sequencing reads and quantification of their relative abundances. Yet, existing metagenomic profilers typically suffer from false positive identifications and consequently biased relative abundance estimation (as false positives can be accounted for more than 90% of total identified species). Here, we present a new metagenomic profiler MAP2B ( M et A genomic P rofiler based on type IIB restriction site) to resolve those issues. We first illustrate the pitfalls of using relative abundance as the only feature in determining false positives. We then propose a feature set to distinguish false positives from true positives. By benchmarking the performance in metagenomic profiling using data from CAMI2 (Critical Assessment of Metagenome Interpretation: second round of challenge), we illustrate the superior performance of MAP2B (F1 score ~ 0.93) over existing metagenomic profilers (F1 score ranges from 0.18 to 0.58). We further tested the performance of MAP2B using real WMS data from an ATCC mock community, confirming its superior performance and robustness against sequencing depth. In addition, by leveraging WMS data from an IBD cohort, we demonstrate the taxonomic features obtained by MAP2B can better discriminate disease status and predict metabolomic profiles.
Organo-sulfur molecules enable iron-based battery electrodes to meet the challenges of large-scale electrical energy storage (2014)

Rechargeable iron–air and nickel–iron batteries are attractive as sustainable and inexpensive solutions for large-scale electrical energy storage because of the global abundance and eco-friendliness of iron, and the robustness of iron-based batteries to extended cycling. Despite these advantages, the commercial use of iron-based batteries has been limited by their low charging efficiency. This limitation arises from the iron electrodes evolving hydrogen extensively during charging. The total suppression of hydrogen evolution has been a significant challenge. We have found that organo-sulfur compounds with various structural motifs (linear and cyclic thiols, dithiols, thioethers and aromatic thiols) when added in milli-molar concentration to the aqueous alkaline electrolyte, reduce the hydrogen evolution rate by 90%. These organo-sulfur compounds form strongly adsorbed layers on the iron electrode and block the electrochemical process of hydrogen evolution. The charge-transfer resistance and double-layer capacitance of the iron/electrolyte interface confirm that the extent of suppression of hydrogen evolution depends on the degree of surface coverage and the molecular structure of the organo-sulfur compound. An unanticipated electrochemical effect of the adsorption of organo-sulfur molecules is “de-passivation” that allows the iron electrode to be discharged at high current values. The strongly adsorbed organo-sulfur compounds were also found to resist electro-oxidation even at the positive electrode potentials at which oxygen evolution can occur. Through testing on practical rechargeable battery electrodes we have verified the substantial improvements to the efficiency during charging and the increased capability to discharge at high rates. We expect these performance advances to enable the design of efficient, inexpensive and eco-friendly iron-based batteries for large-scale electrical energy storage.
The synthesis and relative configuration of (.+-.)-lirionol (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe synthesis and relative configuration of (.+-.)-lirionolGamini Weeratunga, Dayananda Rajapaksa, and Russell RodrigoCite this: J. Org. Chem. 1985, 50, 26, 5902–5905Publication Date (Print):December 1, 1985Publication History Published online1 May 2002Published inissue 1 December 1985https://doi.org/10.1021/jo00350a104Request reuse permissionsArticle Views346Altmetric-Citations19LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (491 KB) Get e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Patch-based over-exposure correction in image (2014)

Most of conventional over-exposure correction methods fail to reconstruct the detail information of the overexposed region (OER) in an image. This paper presents a novel method which can effectively reconstruct the texture as well as the luminance and the color of the OER without user interaction. The proposed method is performed based on a patch-based region filling method. In a patch including the over-exposed pixels, new luminance values are progressively estimated according to the luminance variation in the reference patch (RP) which is selected in the well-exposed region. For the color correction of the OER, the color values of the RP are simply copied. Once the OER is completely filled, the resultant image is refined using the Gaussian-based filters. Experimental results demonstrate that the proposed method provides more preferable results than conventional one.
HIV-1MN Recombinant Glycoprotein 160 Vaccine-Induced Cellular and Humoral Immunity Boosted by HIV-1MN Recombinant Glycoprotein 120 Vaccine (1999)

We evaluated prime-boost immunization with two recombinant envelope glycoprotein subunit vaccines (HIV-1MN recombinant gp160 vaccine in alum adjuvant [MN rgp160] and HIV-1MN recombinant gp120 vaccine in alum adjuvant [MN rgp120]) for safety and immunogenicity in healthy, HIV-1-uninfected adults. The rationale was to combine the helper T cell memory and binding antibody responses typically induced by rgp160 vaccines with the superior neutralizing antibody responses induced by rgp120 vaccines. In a double-blinded, controlled trial, volunteers were randomly assigned to receive MN rgp160 or adjuvant placebo, and a subset later received MN rgp120. The two vaccines were safe, but reactions to MN rgp160 and its adjuvant placebo exceeded those to MN rgp120. MN rgp160 induced IgG binding antibodies, including all IgG subclasses, to MN rgp160 in all vaccine recipients. HIV-1MN-neutralizing and anti-V3 MN peptide-binding antibodies were observed in a majority of volunteers after the fourth MN rgp160 immunization, but at lower levels compared with immunization with MN rgp120 in historical controls. HIV-1-binding, neutralizing, and fusion inhibition antibodies were boosted to the highest levels among MN rgp160 recipients after MN rgp120 booster injections. MN rgp120 boosting appeared to alter the distribution of MN rgp160 vaccine-induced, anti-MN rgp160 IgG subclass antibodies. MN rgp160 induced helper T cell memory, measured by lymphocyte proliferation, Thl and Th2 cytokine production, and skin testing. Strategies including both subunit vaccines may help maximize antibody and helper T cell memory responses to HIV-1 envelope glycoprotein.
Localization of calponin binding sites in the structure of 90 kDa heat shock protein (Hsp90) (1999)

The structure of rabbit liver Hsp90 was reevaluated by limited trypsinolysis, N-terminal sequencing and determination of the site that is phosphorylated by casein kinase II. Limited proteolysis results in formation of four groups of large peptides with M(r) in the range of 26-41 kDa. Peptides with M(r) 39-41 kDa were represented by large N-terminal and central peptides starting at residue 283 of the alpha-isoform of Hsp90. All sites phosphorylated by casein kinase II were located in the large 39-41 kDa peptides. Peptides with M(r) 26-27 kDa were represented by short N-terminal and central peptides starting at Glu-400 of the alpha-isoform of Hsp90. The data of affinity chromatography and light scattering indicate that smooth muscle calponin interacts with Hsp90. The calponin binding sites are located in the large (37-41 kDa) N-terminal and in a short (26-27 kDa) central peptide starting at Glu-400 of the alpha-isoform of Hsp90. Phosphorylation by casein kinase II up to 2 mol of phosphate per mol of Hsp90 does not affect interaction of Hsp90 with calponin.
Enhancing Workload-dependent Voltage Scaling for Energy-efficient Ultra-low-power Embedded Systems (2018)

Ultra-low-power (ULP) chipsets are in higher demand than ever due to the proliferation of ULP embedded systems to support growing applications like the Internet of Things (IoT), wearables and sensor networks. Since ULP systems are also cost constrained, they tend to employ general purpose processors (GPPs) rather than more energy-efficient ASICs, even though they typically run a single application for the lifetime of the system. Prior work showed that it is possible to reduce the operating voltage and thus the power of such systems without reducing the frequency, since the fixed software stack of a system typically only exercises a subset of a processor's paths, and unexercised paths need not meet timing constraints for the system to work correctly. In this context, we find additional scope for power reduction by intelligently optimizing the processor design based on the system's application-specific activity characteristics to allow an even lower safe operating voltage. We demonstrate automated techniques that maximize the application-specific voltage reduction for a system, resulting in 35% additional power savings, on average, compared to the application-specific minimum voltage before optimization and 48% total power savings compared to the original design at nominal voltage.
AIDE (Angle-Implanted Drain and Emitter): A BiCMOS technology module for mixed-signal applications (2002)

Increased mixed-signal device performance and reliability in a BiCMOS technology is achieved by using Angle-Implanted Drain and Emitter (AIDE) technology. An order of magnitude increase in lifetime is obtained in MOS/BJT transistors, while a >40% increase in transistor gain is achieved. This technology module is applicable to existing BiCMOS process with minimum increase in process complexity.
Epitaxial growth of full range of compositions of (1 1 1) PbZr1-Ti O3 on GaN (2020)

Integrating functional complex oxides with conventional (“non-oxide”) semiconductors emerges to be an important research field and has been attracting great interest. Because of their superior intrinsic material properties, such as a relatively high dielectric constant and polarization, the utilization of PbZr1-xTixO3 (PZT) materials as a dielectric layer is expected to greatly improve the performance of the GaN high electron mobility transistor. The functional PbZr1-xTixO3 exhibits quite different crystal structures and consequently physical properties depending on the composition. In this work we report the growth of full range of compositions of PZT films on MgO buffered GaN substrates. Besides revealing the temperature effect on phase formation and surface morphology, we demonstrated the strong effect of composition on the growth: pure (1 1 1) phase is formed in Ti-rich PZT (x > 0.48) while pyrochlore impurity phase is found in Zr-rich PZT (x < 0.48). By introducing an ultrathin Ti-rich PZT seed layer, we are able to achieve epitaxial growth of Zr-rich PZT. The epitaxial PZT films of different composition all exhibit good ferroelectric properties, showing great promise for future GaN device applications.
Recurrent ectopic craniopharyngioma (2001)

A 66-year-old woman developed an asymptomatic mass in the right frontal lobe 5 years after undergoing a right frontal craniotomy and removal of a craniopharyngioma. The mass progressively enlarged over the next 3 years, during which time it became multiloculated and partially cystic. Repeat craniotomy was performed 8 years after the original operation, at which time the mass was found to be an ectopic craniopharyngioma. The lesion probably resulted from seeding of tumour cells along the surgical tract at the time of the initial surgery.
The Coline Metabolite Pattern Detected by 1H HR MAS Accurately Discriminates between High and Low Human Glioma Grade (2006)

In vivo 1H MRS has been widely used to identify the different metabolites present in brain tumors. However, due to the poor resolution of the in vivo spectra, it only allows the detection and the accurate quantification of very few. The HR-MAS (High Resolution Magie Angle Spinning) Magnetic Resonance Spectroscopy has proved to be a useful tool to overcome this problem. The purpose of this work is the study of the relative contributions of the main choline containing compounds (Cho, PC and GPC) to the total choline (tCho) signal and the evaluation of the potential role of these data in the discrimination betwecn low and high grade glioma.&#13;\nHuman biopsies of grade II (low grade) and grades III and IV (high grade) astrocytomas were obtained from the neurosurgery department at "La Paz" Hospital. The HR-MAS spectra of the rumor biopsies were acquired on a 500 MHz Bruker AVANCE Spectrometer, at 4°C and 4 kHz spinning rate. Data were acquired with a classical CPMG with an effective echo time of 144 ms. Metabolite assignments were confirmed by 2D-COSY. The relative contributions of Cho, GPC and PC to the tCho were calculated by fitting lorentzian peaks to the corresponding resonances. The statistical analysis was performed using SPSS (SPSS Inc., Chicago, Illinois). &#13;\nThe HR-MAS spectra showed a very high resolution, allowing for the individuai analysis of Cho, PC and GPC. The PC/tCho and the GPC/tCho ratios were significantly different between low grade and high grade gliomas, but did not help to discriminate between grade IH and grade IV (Fig. Ib). Also, the scatter plot of all the data showed that no overlapping at all exists for these two ratios between low and high grade, which implies that no false positives would occur when using this variables as markers for diagnosis. We also calculated the tCho/Cr ratio, which is conventionally used in the in vivo spectra analysis since Cho, PC and GPC cannot be distinguished under these conditions. No statistically significant differences were found for the tCho/Cr ratio between low and high grade gliomas, indicating that the individual contributions of PC and GPC to the tCho, rather than the tCho itself, are the specific markers of tumor malignancy.
INTEROPERABLE MODEL FOR BIORESOURCE DISTRIBUTED DATABASES (2018)

Abstract. Recently, numerous frameworks and tools are being developed for enhancing access to data and services with a standardized view to communicate the advances in open information sharing. Another emerging field of data exploration is encountered in the coordination, examination and perception of bioresource data and are prompting corresponding new innovations. The bioresource information team aims to develop standards for nationwide data exchange by the establishment of a catalog service to locate and access biological data and information from across the country and information tool for decision makers. With the growth of open data sharing initiatives, the sharing of data among different and myriad sources has increased significantly, but major challenge lies in addressing the issues of interoperability during exchange and use since the data sources are heterogeneous and the data being organization specific is prepared with different (organization) specific data standards and platforms. This paper presents the model based on the study of different metadata standards and to develop a recommended standard for biodiversity information to support interoperability among heterogeneous databases under the umbrella of Indian Bioresource Information Network (IBIN) portal. The paper presents the mapping of different data standards into the IBIN standard for sharing species data in the form of distributed and interoperable web services to set the stage for interoperability.