gebhart/patrepeval huggingface dataset:
An equivalent Markov model for burst errors in digital channels (1995)

A hidden Markov model for burst errors is specified by a probability transition matrix P, an initial probability vector p, and the state dependent probability of error matrix B. Several procedures are available for estimating P, p and B from a given error (observation) sequence. However, even with some restrictions on the structure of the underlying Markov models, the estimation procedures are computationally intensive particularly when the observation sequence contains long strings of identical symbols. We show that, under some mild assumptions, a Markov model with an arbitrary transition matrix P is equivalent to a Markov model with a unique "block diagonal" transition matrix /spl Lambda/. We also present a computationally very efficient algorithm for estimating /spl Lambda/ from a set of observation using a modified Baum-Welch (1972) algorithm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Cluster Randomized Trial of Tailored Breastfeeding Support for Women with Gestational Diabetes (2020)

Background: Women with gestational diabetes mellitus (GDM) and their infants are at increased risk of developing metabolic disease; however, longer breastfeeding is associated with a reduction in these risks. We tested an intervention to increase breastfeeding duration among women with GDM.
Lipid biomarker-based verification of TB infection in mother’s and daughter’s mummified human remains (Vác Mummy Collection, 18th century, CE, Hungary) (2021)

The perpetual burden of tuberculosis (TB) keeps drawing the focus of research on this disease. Among other risk factors (e.g., poor living conditions, malnutrition, smoking, HIV infection, etc.), being in close contact with a TB infected person requires special attention. For a better understanding of the disease, paleopathological investigations concerning TB have been carried out with various techniques for a long a time; nevertheless, analysis of incidence among family members is hardly possible in past populations. An exceptional group of naturally mummified individuals, the collection of the Vác mummies (Hungary, 18th century CE), is known about the large TB incidence rate, which has been revealed by aDNA analysis. Besides the high rate of TB infection, another interesting aspect of the collection is that in some cases, the family connections could be reconstructed. In this paper, we present the mycocerosic acid profiles gained by HPLC-HESI-MS measurements of two Vác mummies, who were mother and daughter according to the personal records. Earlier metagenomic analysis already revealed mixed M. tuberculosis infection with the same bacterial strains in both individuals; moreover, the same bacterial strains were recorded in both cases.
Burst analysis of chemically stimulated spinal cord neuronal networks cultured on microelectrode arrays (2005)

Planar microelectrode arrays allow the recording of the electrophysiological activity of cultured neurons for long time periods and from different sites of the network. In the developing Central Nervous System, several neural networks are spontaneously active and show a typical high frequency activity pattern called burst. Such behavior seems to play an important role in subsequent maturation. Here we analyze how the bursting electrophysiological activity of cultured spinal cord neurons (14-18 DIV) from the chick embryo is affected by cyclothiazide (CTZ) which acts on AMPA receptors. Changes in the patterns of electrophysiological activity are described in detail.
High-Sensitivity Assay for Pesticide Using a Peroxidase as Chemiluminescent Label (1999)

The application of a newly isolated transgenic tobacco peroxidase (TOP) as a chemiluminescent label for immunoassay purposes is described for the first time. The enzyme has been oxidized with m-periodate and subsequently coupled to the model compound 2,4-dichlorophenoxyacetic acid (2,4-D) using a carbodiimide method. As compared to the native horseradish peroxidase used in control experiments, the TOP enzyme showed significantly higher efficiency of coupling to the antigen and no loss of the specific activity was observed. The obtained 2,4-D-TOP conjugate demonstrated unique properties in chemiluminescent detection. The latter allowed the minimization of the conjugate concentration due to the superior chemiluminescent activity of the enzyme. A highly sensitive capillary chemiluminescent immunoassay using the 2,4-D-TOP conjugate as labeled competitor is reported. Direct competitive ELISA has been performed using a specific monoclonal antibody immobilized onto the sol-gel treated glass capillary surface. A modified photomultiplier tube with a special holder for a capillary was used for the resulting chemiluminescent signal detection. The typical standard calibration curve for the 2,4-D pesticide detection is linear between 30 pg and 500 ng/mL.
Isolator-Free Integration of C-Band InAs-InP Quantum Dash Buried Heterostructure Lasers with Silicon Waveguides (2020)

An InAs-on-InP quantum dash buried heterostructure laser and silicon chip optimized for mutual integration by direct facet-to-facet coupling have achieved -1.2 dB coupling efficiency, with coupled laser RIN of -150 dB/Hz and 152 kHz linewidth.
Biologically Complex Planar Cell Plasma Membranes Supported on Polyelectrolyte Cushions Enhance Transmembrane Protein Mobility and Retain Native Orientation (2017)

Reconstituted supported lipid bilayers (SLB) are widely used as in vitro cell-surface models because they are compatible with a variety of surface-based analytical techniques. However, one of the challenges of using SLBs as a model of the cell surface is the limited complexity in membrane composition, including the incorporation of transmembrane proteins and lipid diversity that may impact the activity of those proteins. Additionally, it is challenging to preserve the transmembrane protein native orientation, function, and mobility in SLBs. Here, we leverage the interaction between cell plasma membrane vesicles and polyelectrolyte brushes to create planar bilayers from cell plasma membrane vesicles that have budded from the cell surface. This approach promotes the direct incorporation of membrane proteins and other species into the planar bilayer without using detergent or reconstitution and preserves membrane constituents. Furthermore, the structure of the polyelectrolyte brush serves as a cushion between the planar bilayer and rigid supporting surface, limiting the interaction of the cytosolic domains of membrane proteins with this surface. Single particle tracking was used to analyze the motion of GPI-linked yellow fluorescent proteins (GPI-YFP) and neon-green fused transmembrane P2X2 receptors (P2X2-neon) and shows that this platform retains over 75% mobility of multipass transmembrane proteins in its native membrane environment. An enzyme accessibility assay confirmed that the protein orientation is preserved and results in the extracellular domain facing toward the bulk phase and the cytosolic side facing the support. Because the platform presented here retains the complexity of the cell plasma membrane and preserves protein orientation and mobility, it is a better representative mimic of native cell surfaces, which may find many applications in biological assays aimed at understanding cell membrane phenomena.
Abomasal Infusion of Glucose and Fat—Effect on Digestion, Production, and Ovarian and Uterine Functions of Cows (1997)

Four ruminally cannulated lactating dairy cows, arranged in a 4 x 4 Latin square design, were infused abomasally with 1) water (control), 2) 1 kg/d of glucose, 3) 0.45 kg/d of tallow, and 4) 0.45 kg/d of yellow grease. Cows were synchronized for estrus within each 35-d period by injection of a GnRH agonist followed 7 d later by an injection of PGF2 alpha. Dry matter intake was not affected by infusates. Apparent digestibility of total fatty acids was greater for cows receiving the fat infusions relative to those receiving the glucose infusion and tended to increase for cows receiving the yellow grease infusion compared with those receiving the tallow infusion. Energy infusions decreased apparent acid detergent fiber digestibility compared with effects of the control infusion. Fat infusions tended to increase milk fat percentage and decrease the energy status of cows relative to the glucose infusion. The feed efficiency was greater for cows receiving fat infusions than for those receiving the glucose infusion and was greater for cows receiving the yellow grease infusion than for those receiving the tallow infusion. Plasma progesterone concentration peaked higher during the estrous cycle for cows infused with fat than for those infused with glucose. Mean growth rate and maximum size of the first wave dominant follicle were greater with tallow than with yellow grease. During the period of infusion of yellow grease and afterward, release of 13,14-dihydro-15-keto-PGF2 alpha in response to an injection of oxytocin on d 15 of the estrous cycle was attenuated.
Aryl hydrocarbon receptor (AhR) and its endogenous agonist – indoxyl sulfate in chronic kidney disease (2017)

The indoxyl sulfate (IS, indoxyl sulphate) is the end product of dietary tryptophan degradation by indole pathway and significantly higher serum and tissue concentrations of this compound is observed in patients with impaired renal function. Despite the high albumin binding affinity, the remaining free fraction of IS has a number of biological effects related to the generation of oxidative stress andactivation of signaling pathways related to NF-кB, p53 protein, STAT3, TGF-β and Smad2/3. IS induces the inflammatory process, exerts nephrotoxic activity and is also a factor impairing the cardiovascular system.Its high concentrations are associated with the occurrence of cardiovascular incidents, whose frequency is significantly higher in patients with chronic kidney disease. Evaluation of the mechanisms that underlie the high reactivity of indoxyl sulfate and its biological effects showed that this compound is an agonist of the aryl hydrocarbon receptor (AhR). This receptor plays an important role in maintaining homeostasis Moreover, AhR exerts high transcriptional activity, so ligands of obciążethis receptor may exert different biological effects. The following paper describes the role of indoxyl sulfate as AhR ligand in the context of the excessive accumulation, which appears as one of the symptoms associated with chronic kidney disease.
Chinese Automatic Question Answering System of Specific-domain Based on Vector Space Model (2005)

In order to meet the demand to acquire necessary information efficiently from large electronic text, the Question and Answering (QA) technology to show a clear reply automatically to a question asked in the user's natural language has widely attracted attention in recent years. Although the research of QA system in China is later than that in western countries and Japan, it has attracted more and more attention recently. In this paper, we propose a Question-Answering construction, which synthesizes the answer retrieval to the questions asked most frequently based on common knowledge, and the document retrieval concerning sightseeing information. In order to improve reply accuracy, one must consider the synthetic model based on statistic VSM and the shallow semantic analysis, and the domain is limited to sightseeing information. A Chinese QA system about sightseeing based on the proposed method has been built. The result is obtained by evaluation experiments, where high accuracy can be achieved when the results of retrieval were regarded as correct, if the correct answer appeared among those of the top three resemblance degree. The experiments proved the efficiency of our method and it is feasible to develop Question-Answering technology based on this method.
Characterization of the Novel Focal Adhesion Kinase RAFTK in Hematopoietic Cells (1997)

Protein tyrosine kinases (PTKs) mediate signals that respond to many pivotal cellular functions. Tyrosine phosphorylation, controlled by the coordinated actions of protein tyrosine phosphatases (PTPs) and PTKs, is a critical control mechanism for various physiological processes, including cell growth, differentiation, metabolism, cell cycle regulation and cytoskeleton function. The focal adhesion kinase (FAK) is a widely expressed non-receptor tyrosine kinase that is implicated in integrin-mediated signaling and plays a role in signal transduction pathways mediating cell adhesion, motility and anchorage-independent growth. Recently, we and others have identified a novel protein tyrosine kinase termed RAFTK, (also known as Pyk2 or Cak-beta), which is related to FAK. This review describes the role of RAFTK in various signaling cascades mainly in reference to hematopoietic cell lineages.
Die Relevanz des Biologischen (2017)

Learning and memory are major areas of research in modern neurobiology. Progress in this field has led to promises of a new scientific foundation for pedagogics. Many experts in psychology and education, however, have not embraced this input from the natural sciences, and the dialogue has been much less fruitful than anticipated. In this article, we discuss two possible reasons for this failure which may provide new perspectives on a more productive interaction between disciplines. First,we state that causal biological explanations of complex mental phenomena are rare and far from complete. The complexity of living organisms, the simplicity of model systems, and the multi-level nature of causal interactions set limits on the explanatory power of neurobiological explanations. Second, both neurobiology and pedagogics tend to reduce their respective phenomena to information processing or mental operations, respectively. Both approaches neglect the embodiment of processes, and therefore miss the chance to integrate all relevant biological boundary conditions of learning. Taking these limitations into account, we suggest a series of potential contributions from neurobiology to pedagogics and - most importantly - from pedagogics to neurobiology. Neurobiology and pedagogics have much to offer for each other, provided that they reflect on their limitations and specific differences.
Kinetic analysis of Ly‐6 gene induction in a T lymphoma by interferons and interleukin 1, and demonstration of Ly‐6 inducibility in diverse cell types (1989)

The Ly-6 locus contains multiple genes encoding cell surface proteins, two of which, when cross-linked by antibodies, effect antigen-independent activation of T lymphocytes. In this study, cDNA for Ly-6-encoded antigens have been used as probes to examine RNA from various tissues and transformed cell lines for constitutive levels of Ly-6 RNA expression. Analyses of RNA prepared from several different tissues revealed a high level of expression of Ly-6 RNA in kidney, spleen, heart and thymus, with a more moderate level of expression in liver, brain and lung tissue cells. A survey of various cell lines demonstrated the presence of Ly-6 RNA in many, but not all T lymphocytic cell lines, in L cells, the Meth A fibrosarcoma, in the TCMK kidney cell line, and in the Neuro-2a neuroblastoma. We also evaluated the expression of Ly-6 RNA in cells after treatments with interferons (IFN) and interleukin 1 (IL1). Treatment of lymphoid cells with IFN (alpha/beta and gamma), known to increase cell surface Ly-6 antigen expression in normal T cells, was correlated with increases in Ly-6 RNA levels. Increases in levels of RNA correlated with increases in levels of the Ly-6A/E or Ly-6C antigens. Several T lymphoid cell lines exhibiting Ly-6 RNA inducibility by IFN were similarly inducible with IL1. Kinetic experiments using one such line, (YAC-1), showed that the induction of Ly-6 RNA mediated by IFN-alpha/beta occurred rapidly (within 4 h), while the induction by IL1 required relatively more time (approximately 8 h). Although the actions of IFN-alpha/beta were not blocked by cycloheximide, the presence of this protein synthesis inhibitor significantly attenuated the effects of IL1 and IFN-gamma on Ly-6 RNA transcription. Induction by IFN-gamma as well as IL1 could be blocked completely by co-culture with anti-IFN-gamma, implicating IFN-gamma as a mediator of the induction by IL1.
Spatio-temporal ToF data enhancement by fusion (2012)

We propose an extension of our previous work on spatial domain Time-of-Flight (ToF) data enhancement to the temporal domain. Our goal is to generate enhanced depth maps at the same frame rate of the 2-D camera that, coupled with a ToF camera, constitutes a hybrid ToF multi-camera rig. To that end, we first estimate the motion between consecutive 2-D frames, and then use it to predict their corresponding depth maps. The enhanced depth maps result from the fusion between the recorded 2-D frames and the predicted depth maps by using our previous contribution on ToF data enhancement. The experimental results show that the proposed approach overcomes the ToF camera drawbacks; namely, low resolution in space and time and high level of noise within depth measurements, providing enhanced depth maps at video frame rate.
Knowledge Driven Synthesis Using Resource-Capability Semantics for Control Software Design (2023)

This paper presents a knowledge-driven approach for automated synthesis of controllers in three different use-cases. The approach addresses the engineering challenge posed by Industrie 4.0, which requires fast, reliable, and flexible integration of multiple heterogeneous hardware and software components. Manual design approaches are not scalable for large systems due to their complexity. The proposed approach captures resource-capability knowledge and uses a reasoning-based synthesis mechanism to compose a controller design for a plant goal. The approach uses domain-specific languages (DSLs) to describe the components, their interfaces, and capabilities. The generated control designs are executable codes that implement the control strategy. The proposed approach reduces the average engineering time by 70% and generates on an average 60% of the executable code in each use-case. The approach uses a knowledge repository to store resource-capability knowledge and enables rapid prototyping and iterative design. The proposed approach provides a promising solution to automate the synthesis of controllers in different use-cases with multiple heterogeneous hardware and software components satisfaction.
VCSEL-based gain-switching short optical pulse source with time-jitter suppression by self-seeding method (2011)

A gain-switching short optical pulse source using vertical-cavity surface-emitting laser (VCSEL) as a gain medium is experimentally investigated. Modulated driving current is supplied to the VCSEL and short optical pulse train is generated by gain-switching. Partial reflector connected with VCSEL is used to suppress timing fluctuation of pulse generation by feeding back a part of the lased pulses just before of the following pulse. The investigated short optical pulse source is able to generate short optical pulse with the repetition rate, the pulse width, the RMS time-jitter, and the pulse peak intensity of about 1.048GHz, 72ps, 3.5ps, and 0.7mW respectively.
Characterization of the reception environment of GNSS signals using a texture and color based adaptive segmentation technique (2010)

This paper is focused on the characterization of GNSS signals reception environment by estimating the percentage of visible sky. A new segmentation technique based on a color watershed using an adaptive combination of color and texture information is proposed. This information is represented by two morphological gradients, a classical color gradient and a texture gradient based on co-occurrence matrices. The segmented images are then used as input for a k-means classifier in order to determine the percentage of visible sky in fish-eye images. The obtained classification results are evaluated to demonstrate the effectiveness and the reliability of the proposed approach.
Progesterone is an Inducement of Heritable Pulmonary Arterial Hypertension with BMPR2 Mutation (2023)

Abstract Background Bone morphogenetic protein type II receptor (BMPR2) gene mutation accounts for 80% of patients with heritable pulmonary artery hypertension (HPAH), and female mutation carriers have significantly higher penetrance rate than males. The inducement of HPAH penetrance and the mechanism of sex differential penetrance are still elusive. Methods We infected or transfected pulmonary artery smooth muscle cells (PASMCs) with shBMPR2 lentivirus or siBMPR2 to simulate the pathologic condition of BMPR2 heterozygous mutation and treated them with progesterone. The HPAH patient-derived induced pluripotent stem cells (iPSCs) were induced into vascular smooth muscle cells (VSMCs) to further verify the cellular phenotype. Wild-type flox +/- female mice and SM22-cre BMPR2 flox +/- female mice (CKO mice) were administered with 1-month progesterone, and their phenotype of PAH was evaluated by right heart catheterization and histopathological examination. Results Progesterone promoted the proliferation of PASMCs with BMPR2-knockdownby activating ERK pathway via progesterone receptor (PGR). Activated ERK not only upregulated the phosphorylation and elevation of cMYC, but also induced the transcription of endothelin (EDN1) by promoting the nuclear entry of c-JUN and combination on the its promoter region. Similar results were confirmed by iPSCs-VSMCs experiment. CKO mice developed PAH spontaneously and had increased expression of EDN1, which was further aggravated by exogenous progesterone. Conclusions Progesterone might be an inducement of HPAH penetrance caused by BMPR2 mutation, accounting for sex differential penetrance.
Swelling, strength, and biocompatibility of acrylate-based superporous hydrogel hybrids (2014)

A hydrogel hybrid of chemically cross-linked hydroxyethyl acrylate interpenetrated with physically cross-linked carboxymethylcellulose was prepared as a superporous structure with swelling rates ranging from a few seconds to minutes depending on the swelling medium. A new method was adopted to evaluate the swelling capacity and rate in superporous hydrogel hybrid using a modified texture analyzer. Based on the extensive data acquisition, swelling data at any time point were obtainable and fit into a Voigt viscoelastic model. Moreover, the two mechanisms by which a superporous hydrogel hybrid swells in an aqueous medium were differentiated and used to estimate the onset of the diffusion-controlled swelling, which was found to be dependent on the actual composition of the swelling medium. A correlation was found between the mechanical strength of the fully swollen hydrogels and their respective swelling force in different swelling media. The concentration of alcohol in the medium was a critical factor in the swelling characteristics and strength of these hydrogels. Two HeLa and mesenchymal stem cells derived from human umbilical cord cell lines were used to evaluate biocompatibility of the prepared hydrogels.
Adaptive Signature Design: An Adaptive Clinical Trial Design for Generating and Prospectively Testing A Gene Expression Signature for Sensitive Patients (2005)

Development of a gene expression-based classifier to identify the subset of sensitive patients can be prospectively incorporated into a randomized phase III design without compromising the ability to detect an overall effect.