gebhart/patrepeval huggingface dataset:
Data Mining on DNA Sequences of Hepatitis B Virus (2009)

Extraction of meaningful information from large experimental data sets is a key element in bioinformatics research. One of the challenges is to identify genomic markers in Hepatitis B Virus (HBV) that are associated with HCC (liver cancer) development by comparing the complete genomic sequences of HBV among patients with HCC and those without HCC. In this study, a data mining framework, which includes molecular evolution analysis, clustering, feature selection, classifier learning, and classification, is introduced. Our research group has collected HBV DNA sequences, either genotype B or C, from over 200 patients specifically for this project. In the molecular evolution analysis and clustering, three subgroups have been identified in genotype C and a clustering method has been developed to separate the subgroups. In the feature selection process, potential markers are selected based on Information Gain for further classifier learning. Then, meaningful rules are learned by our algorithm called the Rule Learning, which is based on Evolutionary Algorithm. Also, a new classification method by Nonlinear Integral has been developed. Good performance of this method comes from the use of the fuzzy measure and the relevant nonlinear integral. The nonadditivity of the fuzzy measure reflects the importance of the feature attributes as well as their interactions. These two classifiers give explicit information on the importance of the individual mutated sites and their interactions toward the classification (potential causes of liver cancer in our case). A thorough comparison study of these two methods with existing methods is detailed. For genotype B, genotype C subgroups C1, C2, and C3, important mutation markers (sites) have been found, respectively. These two classification methods have been applied to classify never-seen-before examples for validation. The results show that the classification methods have more than 70 percent accuracy and 80 percent sensitivity for most data sets, which are considered high as an initial scanning method for liver cancer diagnosis.
Analysis of polarity effects in the electrical breakdown of liquids (2006)

Electrical breakdown simulations are carried out for liquids in response to a sub-microsecond (∼100–200 ns) voltage pulse. This model builds on our previous analysis and focuses particularly on the polarity effect seen experimentally in point–plane geometries. The flux-corrected transport approach is used for the numerical implementation. Our model adequately explains experimental observations of pre-breakdown current fluctuations, streamer propagation and branching as well as disparities in hold-off voltage and breakdown initiation times between the anode and cathode polarities. It is demonstrated that polarity effects basically arise from the large mobility difference between electrons and ions. The higher electron mobility leads to greater charge smearing and diffusion that impacts the local electric field distributions. Non-linear couplings between the number density, electric field and charge generation rates then collectively affect the formation of ionized channels and their temporal dynamics.
NMR in Metabolomics and Natural Products Research: Two Sides of the Same Coin (2011)

Small molecules are central to biology, mediating critical phenomena such as metabolism, signal transduction, mating attraction, and chemical defense. The traditional categories that define small molecules, such as metabolite, secondary metabolite, pheromone, hormone, and so forth, often overlap, and a single compound can appear under more than one functional heading. Therefore, we favor a unifying term, biogenic small molecules (BSMs), to describe any small molecule from a biological source. In a similar vein, two major fields of chemical research,natural products chemistry and metabolomics, have as their goal the identification of BSMs, either as a purified active compound (natural products chemistry) or as a biomarker of a particular biological state (metabolomics). Natural products chemistry has a long tradition of sophisticated techniques that allow identification of complex BSMs, but it often fails when dealing with complex mixtures. Metabolomics thrives with mixtures and uses the power of statistical analysis to isolate the proverbial "needle from a haystack", but it is often limited in the identification of active BSMs. We argue that the two fields of natural products chemistry and metabolomics have largely overlapping objectives: the identification of structures and functions of BSMs, which in nature almost inevitably occur as complex mixtures. Nuclear magnetic resonance (NMR) spectroscopy is a central analytical technique common to most areas of BSM research. In this Account, we highlight several different NMR approaches to mixture analysis that illustrate the commonalities between traditional natural products chemistry and metabolomics. The primary focus here is two-dimensional (2D) NMR; because of space limitations, we do not discuss several other important techniques, including hyphenated methods that combine NMR with mass spectrometry and chromatography. We first describe the simplest approach of analyzing 2D NMR spectra of unfractionated mixtures to identify BSMs that are unstable to chemical isolation. We then show how the statistical method of covariance can be used to enhance the resolution of 2D NMR spectra and facilitate the semi-automated identification of individual components in a complex mixture. Comparative studies can be used with two or more samples, such as active vs inactive, diseased vs healthy, treated vs untreated, wild type vs mutant, and so on. We present two overall approaches to comparative studies: a simple but powerful method for comparing two 2D NMR spectra and a full statistical approach using multiple samples. The major bottleneck in all of these techniques is the rapid and reliable identification of unknown BSMs; the solution will require all the traditional approaches of both natural products chemistry and metabolomics as well as improved analytical methods, databases, and statistical tools.
Tumoral Environment Triggers Transcript Anomalies in Established Tumors: Induction of Altered Gene Expression and of Aberrant, Truncated and B2 Repeat-Containing Gene Transcripts (1999)

In addition to eugenetic changes, cancerous cells exhibit extensive modifications in the expression levels of a variety of genes. The phenotypic switch observed after inoculation of T lymphoma cells into syngenic mice illustrates the active participation of tumoral environment in the induction of an aberrant gene expression pattern. To further substantiate this contribution, we performed polymerase chain reaction (PCR)-based subtraction suppression hybridization (SSH) to identify genes that are differentially expressed in tumor-derived EL4/13.3 cells compared to the same cells isolated from cultures. Besides a number of unknown genes, the subtracted library contained several known genes that have been reported to be expressed at increased levels in tumors and/or to contribute to carcinogenesis. Apart from clones representing translated transcripts, the subtracted library also contained a high number of clones representing B2 repeat elements, viz. short interspersed repetitive elements that are transcribed by RNA polymerase III. Northern blotting confirmed the induction of B2 transcripts in tumor tissue and also revealed induction of chimeric, B2 repeat-containing mRNA. The appearance of chimeric transcripts was accompanied by aberrant, shorter-than-full-length transcripts, specifically from upregulated genes. Accordingly, in addition to altered gene expression, tumoral environmental triggers constitute a potent mechanism to create an epigenetic diversity in cancers by inducing extensive transcript anomalies.
Monoclonal Antibody–Mediated Toxicity inCryptococcus neoformansInfection: Mechanism and Relationship to Antibody Isotype (1999)

Antibody reagents represent an alternative for the therapy of human cryptococcosis, and monoclonal antibody 18B7 (IgG1) is a candidate for phase I trial in humans with cryptococcosis. However, antibody administration to mice with established Cryptococcus neoformans infection has been reported to produce acute lethal toxicity (ALT). The present study confirmed this phenomenon and investigated the mechanism of ALT. ALT was associated with hemoconcentration, hypotension, and circulatory collapse; however, toxicity could be prevented by platelet-activating factor inhibitor, rat antibody to Fc receptor, or IgM before IgG1. Significant isotype-specific differences were found in ALT, which can be interpreted as consistent with the hypothesis that there are distinct Fc receptors for murine IgG1 and IgG3. The IgM and IgG3 isotype preference in antibody responses to polysaccharide antigens in mice may translate to a lack of toxicity of antigen-antibody complexes during the course of infections with encapsulated pathogens.
Premixed direct injection disk (2023)

A fuel/air mixing disk for use in a fuel/air mixing combustor assembly is provided. The disk includes a first face, a second face, and at least one fuel plenum disposed therebetween. A plurality of fuel/air mixing tubes extend through the pre-mixing disk, each mixing tube including an outer tube wall extending axially along a tube axis and in fluid communication with the at least one fuel plenum. At least a portion of the plurality of fuel/air mixing tubes further includes at least one fuel injection hole have a fuel injection hole diameter extending through said outer tube wall, the fuel injection hole having an injection angle relative to the tube axis. The invention provides good fuel air mixing with low combustion generated NOx and low flow pressure loss translating to a high gas turbine efficiency, that is durable, and resistant to flame holding and flash back.
A MINDO/3 investigation of cyclic chloronium ion-chloroalkyl carbocation equilibriums. Comparisons with stable ion solution chemistry (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA MINDO/3 investigation of cyclic chloronium ion-chloroalkyl carbocation equilibriums. Comparisons with stable ion solution chemistrySamuel D. Beatty, S. D. Worley, and Samuel P. McManusCite this: J. Am. Chem. Soc. 1978, 100, 13, 4254–4260Publication Date (Print):June 1, 1978Publication History Published online1 May 2002Published inissue 1 June 1978https://pubs.acs.org/doi/10.1021/ja00481a041https://doi.org/10.1021/ja00481a041research-articleACS PublicationsRequest reuse permissionsArticle Views68Altmetric-Citations6LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Mapping the Cytochrome c Folding Landscape (2002)

The solution to the riddle of how a protein folds is encoded in the conformational energy landscape for the constituent polypeptide. Employing fluorescence energy transfer kinetics, we have mapped the S. cerevisiae iso-1 cytochrome c landscape by monitoring the distance between a C-terminal fluorophore and the heme during folding. Within 1 ms after denaturant dilution to native conditions, unfolded protein molecules have evolved into two distinct and rapidly equilibrating populations: a collection of collapsed structures with an average fluorophore-heme distance (r) of 27 A and a roughly equal population of extended polypeptides with r > 50 A. Molecules with the native fold appear on a timescale regulated by heme ligation events (~300 ms, pH 7). The experimentally derived landscape for folding has a narrow central funnel with a flat upper rim on which collapsed and extended polypeptides interchange rapidly in a search for the native structure. Nonnative states of proteins are involved in a variety of cellular processes, including translocation of proteins across membranes and formation of amyloid fibrils. Probes that report on the structural heterogeneity of a polypeptide ensemble could resolve ambiguities in the classification of these states. We have shown that added anions shift the equilibrium between the compact and extended polypeptide structures that are present during refolding of Saccaromyces cerevisiae iso-1 cytochrome c. Specifically, at high salt concentrations (>= 700 mM), all the polypeptides are compact with a mean C-terminal fluorophore-heme separation quite close to that in the native protein (25 A). Addition of chemical detaturants, on the other hand, tends to shift the equilibrium towards unfolded structures. Folding of modified Fe(II) cyt c was probed by fluorescence in presence of imidazole with NADH as photochemical sensitizer. At very high imidazole concentrations (400 mM), protein was still found to fold but the rate that coincides with Met80 ligation was slowed down significantly. Reductive flash-quench/scavenge experiments, in which ascorbic acid was used to scavenge MeODMAA+, were shown to keep ferrocyt c reduced for up to 500 ms. Electron injection into unfolded modified yeast Fe(III)cyt c was fast in comparison to injection using NADH as photochemical sensitizer. The overall electron transfer process was reversible. This photoreduction system could be used to trigger folding of Fe(II) cyt c to monitor the changes in dansyl fluorescence intensity on ms time scales.
Orientation Dependence of Nonlinearity and Hysteresis in PZN-4.5%PT Single Crystals II: Bipolar Electromechanical Response (2006)

Relaxor ferroelectric single crystals exhibit orientation dependent hysteresis. In this study, combined bipolar electric field and compressive stress are applied to relaxor single crystals of [Pb(Zn 1/3 Nb 2/3 )O 3 ]0.955-[PbTiO 3 ]0.045 (PZN-4.5%PT) in a series of crystal orientations between h001i and h111i. The resulting bipolar electromechanical response is presented. The observed hysteresis and nonlinear phenomena related to polarization reorientation and phase transitions are discussed.
Long-Term Stabilization and Operation of a Soliton Micro-Comb for 9-Days (2019)

We report the long-term stabilization of a soliton micro-comb over 9 days of continuous operation. Using an integrated heater, the original pump-cavity detuning is maintained with a simple active feedback method.
Desensitization by Progressive Up-Titration Prevents First-Dose Effects on the Heart: Guinea Pig Study with Ponesimod, a Selective S1P1 Receptor Modulator (2013)

Ponesimod, a selective S1P1 receptor modulator, reduces the blood lymphocyte count in all tested species by preventing egress of T and B cells from thymus and peripheral lymphoid organs. In addition, ponesimod transiently affects heart rate and atrioventricular (AV) conduction in humans, effects not observed in mice, rats, and dogs with selective S1P1 receptor modulators, suggesting that the regulation of heart rate and rhythm is species dependent. In the present study, we used conscious guinea pigs implanted with a telemetry device to investigate the effects of single and multiple oral doses of ponesimod on ECG variables, heart rate, and blood pressure. Oral administration of ponesimod did not affect the sinus rate (P rate) but dose-dependently induced AV block type I to III. A single oral dose of 0.1 mg/kg had no effect on ECG variables, while a dose of 3 mg/kg induced AV block type III in all treated guinea pigs. Repeated oral dosing of 1 or 3 mg/kg ponesimod resulted in rapid desensitization, so that the second dose had no or a clearly reduced effect on ECG variables as compared with the first dose. Resensitization of the S1P1 receptor in the heart was concentration dependent. After desensitization had been induced by the first dose of ponesimod, the cardiac system remained desensitized as long as the plasma concentration was ≥75 ng/ml. By using a progressive up-titration regimen, the first-dose effect of ponesimod on heart rate and AV conduction was significantly reduced due to desensitization of the S1P1 receptor. In summary, conscious guinea pigs implanted with a telemetry device represent a useful model to study first-dose effects of S1P1 receptor modulators on heart rate and rhythm. This knowledge was translated to a dosing regimen of ponesimod to be tested in humans to avoid or significantly reduce the first-dose effects.
Energy-Spectral Efficiency Trade-off for a Massive SU-MIMO System with Transceiver Power Consumption (2014)

We consider a single user (SU) massive MIMO system with multiple antennas at the transmitter (base station) and a single antenna at the user terminal (UT). Taking transceiver power consumption into consideration, for a given spectral efficiency (SE) we maximize the energy efficiency (EE) as a function of the number of base station (BS) antennas $M$, resulting in a closed-form expression for the optimal SE-EE trade-off. It is observed that in contrast to the classical SE-EE trade-off (which considers only the radiated power), with transceiver power consumption taken into account, the EE increases with increasing SE when SE is sufficiently small. Further, for a fixed SE we analyze the impact of varying cell size (i.e., equivalently average channel gain $G_c$) on the optimal EE. We show the interesting result that for sufficiently small $G_c$, the optimal EE decreases as $\mathcal{O}(\sqrt{G_c})$ with decreasing $G_c$. Our analysis also reveals that for sufficiently small SE (or large $G_c$), the EE is insensitive to the power amplifier efficiency.
In vivo inhibitory effect of Aloe vera gel on the ability of mouse parental splenic lymphocytes to induce cutaneous angiogenesis in recipient F1 mice (2014)

This observation opens the promise of safe and ethically acceptable possibility of use of Aloe vera gel in human donors in prevention of GVHD in recipients of bone marrow grafts.
Quaternionic Attitude Estimation for Robotic and Human Motion Tracking Using Sequential Monte Carlo Methods With von Mises-Fisher and Nonuniform Densities Simulations (2013)

In recent years, wireless positioning and tracking devices based on semiconductor micro electro-mechanical system (MEMS) sensors have successfully integrated into the consumer electronics market. Information from the sensors is processed by an attitude estimation program. Many of these algorithms were developed primarily for aeronautical applications. The parameters affecting the accuracy and stability of the system vary with the intended application. The performance of these algorithms occasionally destabilize during human motion tracking activities, which does not satisfy the reliability and high accuracy demand in biomedical application. A previous study accessed the feasibility of using semiconductor based inertial measurement units (IMUs) for human motion tracking. IMU hardware has been redesigned and an attitude estimation algorithm using sequential Monte Carlo (SMC) methods, or particle filter, for quaternions was developed. The method presented in this paper uses von Mises-Fisher and a nonuniform simulation to provide density estimation of the rotation group SO(3). Synthetic signal simulation, robotics applications, and human applications have been investigated.
Fabrication of Sandwich Structure with Functionally Graded Porous Aluminum Core (2019)

A porous aluminum (Al) has light weight and high energy absorption characteristics. However, the tensile strength and bending strength of porous Al is lower than those of dense Al materials. It is promised that a sandwich structure consisting of a porous Al core and dense metallic face sheets is effective to use as structural elements. In this study, sandwich structures of a functionally graded (FG) porous Al core of ADC12 and A6061 with two face sheets of A1050 were fabricated using friction stir welding (FSW) route. The fabricated sandwich structures of FG porous Al core were observed by X-ray computed tomography (CT). Through the observations of the pore structures and the thickness of ADC12 layer or A6061 layer in FG porous Al core, foaming conditions for sandwich structure of FG porous Al core were examined. It was found that sandwich structure with each layer of ADC12 and A6061 of good pore structures and almost same thickness was successfully fabricated by controlling holding time and thickness of ADC12 and A6061 precursors.
Facilitating systems-level analyses of all-cause and Covid-mediated sepsis through SeptiSearch, a manually-curated compendium of dysregulated gene sets (2023)

Background Sepsis is a dysfunctional host response to infection. The syndrome leads to millions of deaths annually (19.7% of all deaths in 2017) and is the cause of most deaths from severe Covid infections. High throughput sequencing or ‘omics’ experiments in molecular and clinical sepsis research have been widely utilized to identify new diagnostics and therapies. Transcriptomics, quantifying gene expression, has dominated these studies, due to the efficiency of measuring gene expression in tissues and the technical accuracy of technologies like RNA-Seq. Objective Most of these studies seek to uncover novel mechanistic insights into sepsis pathogenesis and diagnostic gene signatures by identifying genes differentially expressed between two or more relevant conditions. However, little effort has been made, to date, to aggregate this knowledge from such studies. In this study we sought to build a compendium of previously described gene sets that combines knowledge gained from sepsis-associated studies. This would enable the identification of genes most associated with sepsis pathogenesis, and the description of the molecular pathways commonly associated with sepsis. Methods PubMed was searched for studies using transcriptomics to characterize acute infection/sepsis and severe sepsis (i.e., sepsis combined with organ failure). Several studies were identified that used transcriptomics to identify differentially expressed (DE) genes, predictive/prognostic signatures, and underlying molecular responses and pathways. The molecules included in each gene set were collected, in addition to the relevant study metadata (e.g., patient groups used for comparison, sample collection time point, tissue type, etc.). Results After performing extensive literature curation of 74 sepsis-related publications involving transcriptomics, 103 unique gene sets (comprising 20,899 unique genes) from thousands of patients were collated together with associated metadata. Frequently described genes included in gene sets as well as the molecular mechanisms they were involved in were identified. These mechanisms included neutrophil degranulation, generation of second messenger molecules, IL-4 and -13 signaling, and IL-10 signaling among many others. The database, which we named SeptiSearch, is made available in a web application created using the Shiny framework in R, (available at https://septisearch.ca ). Conclusions SeptiSearch provides members of the sepsis community the bioinformatic tools needed to leverage and explore the gene sets contained in the database. This will allow the gene sets to be further scrutinized and analyzed for their enrichment in user-submitted gene expression data and used for validation of in-house gene sets/signatures.