gebhart/patrepeval huggingface dataset:
Cardiovascular Side Effects of New Antidepressants and Antipsychotics: New Drugs, old Concerns? (2004)

The cardiovascular toxicity of older generation of tricyclic antidepressants (e.g. imipramine, desipramine, amitriptyline, clomipramine) and neuroleptics (e.g. haloperidol, droperidol, thioridazine, pimozide) is well established. These drugs inhibit cardiovascular Na(+), Ca(2+) and K(+) channels often leading to life-threatening arrhythmia. To overcome the toxicity of old generation of antidepressants and antipsychotics, selective serotonin reuptake inhibitor antidepressants (SSRIs: fluoxetine, fluvoxamine, paroxetine, sertraline, citalopram, venlafaxin) and several new antipsychotics (e.g. clozapine, olanzapine, risperidone, sertindole, aripiprazole, ziprasidone, quetiapine) were introduced during the past decade. Although these new compounds are not more effective in treating psychiatric disorders than older medications, they gained incredible popularity since they have been reported to have fewer and more benign side effect profile (including cardiovascular) than predecessors. Surprisingly, an increasing number of case reports have demonstrated that the use of SSRIs and new antipsychotics (e.g. clozapine, olanzapine, risperidone, sertindole, aripiprazole, ziprasidone, quetiapine) is associated with cases of arrhythmias, prolonged QTc interval on electrocardiogram (ECG) and orthostatic hypotension in patients lacking cardiovascular disorders, raising new concerns about the putative cardiovascular safety of these compounds. In agreement with these clinical reports these new compounds indeed show marked cardiovascular depressant effects in different mammalian and human cardiovascular preparations by inhibiting cardiac and vascular Na(+), Ca(2+) and K(+) channels. Taken together, these results suggest that the new generation of antidepressants and antipsychotics also have clinically important cardiac as well as vascular effects. Clinicians should be more vigilant about these potential adverse reactions and ECG control may be suggested during therapy, especially in patients with cardiovascular disorders. The primary goal of this review is to shed light on the recently observed clinically important cardiovascular effects of new antidepressants and antipsychotics and discuss the mechanism beyond this phenomenon.
Fetal ECG Extraction by Extended State Kalman Filtering Based on Single-Channel Recordings (2013)

In this paper, we present an extended nonlinear Bayesian filtering framework for extracting electrocardiograms (ECGs) from a single channel as encountered in the fetal ECG extraction from abdominal sensor. The recorded signals are modeled as the summation of several ECGs. Each of them is described by a nonlinear dynamic model, previously presented for the generation of a highly realistic synthetic ECG. Consequently, each ECG has a corresponding term in this model and can thus be efficiently discriminated even if the waves overlap in time. The parameter sensitivity analysis for different values of noise level, amplitude, and heart rate ratios between fetal and maternal ECGs shows its effectiveness for a large set of values of these parameters. This framework is also validated on the extractions of fetal ECG from actual abdominal recordings, as well as of actual twin magnetocardiograms.
Detection of sleep disordered breathing severity using acoustic biomarker and machine learning techniques (2018)

Acoustic biomarkers may be useful to accurately predict the severity of SDB based on the patient's breathing sounds during sleep, without conducting attended full-night PSG. This study implies that any device with a microphone, such as a smartphone, could be potentially utilized outside specialized facilities as a screening tool for detecting SDB.
Epitope mapping by solution NMR spectroscopy (2015)

Antibodies play an ever more prominent role in basic research as well as in the biotechnology and pharmaceutical sectors. Characterizing their epitopes, that is, the region that they recognize on their target molecule, is useful for purposes ranging from molecular biology research to vaccine design and intellectual property protection. Solution NMR spectroscopy is ideally suited to the atomic level characterization of intermolecular interfaces and, as a consequence, to epitope discovery. Here, we illustrate how NMR epitope mapping can be used to rapidly and accurately determine protein antigen epitopes. The basic concept is that differences in the NMR signal of an antigen free or bound by an antibody will identify epitope residues. NMR epitope mapping provides more detailed information than mutagenesis or peptide mapping and can be much more rapid than X-ray crystallography. Advantages and drawbacks of this technique are discussed together with practical considerations.
Ecotropic murine leukemia virus DNA content of normal and lymphomatous tissues of BXH-2 recombinant inbred mice (1982)

BXH-2 recombinant inbred mice spontaneously produce a B-tropic murine leukemia virus (MuLV) beginning early in life and have a high incidence of non-T-cell lymphomas. These traits are not characteristic of the progenitor strains (C57BL/6J and C3H/HeJ) or of 11 other BXH recombinant inbred strains. Since B-tropic virus expression may be causally related to the high incidence of lymphoma in this strain, we have analyzed the ecotropic MuLV DNA content of both normal and lymphomatous tissues of BXH-2 mice. Southern analysis and hybridization with an ecotropic MuLV DNA-specific probe showed that DNA of normal BXH-2 tissues contained both parental N-tropic MuLV proviruses but lacked endogenous B-tropic MuLV DNA sequences. In addition, none of 116 F1 hybrid mice derived from male BXH-2 mice spontaneously produced ecotropic MuLV early in life. These results suggest that the B-tropic virus is horizontally transmitted in BXH-2 mice. Southern analysis of DNA from tumor tissues of 12 BXH-2 mice showed that amplification of ecotropic-specific DNA sequences had occurred in lymphomatous tissues of 3 mice and suggested that these tumors were monoclonal. The number of newly acquired proviruses, which appeared to be structurally nondefective and integrated at different sites, varied from one to three copies. Since lymphomatous tissues from only 3 of 12 mice examined carried additional detectable ecotropic proviruses, these results suggest that amplification of ecotropic MuLV DNA sequences is not required for maintenance of transformation in BXH-2 lymphomas.
Formation of droplets and bubbles in a microfluidic T-junction—scaling and mechanism of break-up (2006)

This article describes the process of formation of droplets and bubbles in microfluidic T-junction geometries. At low capillary numbers break-up is not dominated by shear stresses: experimental results support the assertion that the dominant contribution to the dynamics of break-up arises from the pressure drop across the emerging droplet or bubble. This pressure drop results from the high resistance to flow of the continuous (carrier) fluid in the thin films that separate the droplet from the walls of the microchannel when the droplet fills almost the entire cross-section of the channel. A simple scaling relation, based on this assertion, predicts the size of droplets and bubbles produced in the T-junctions over a range of rates of flow of the two immiscible phases, the viscosity of the continuous phase, the interfacial tension, and the geometrical dimensions of the device.
EMBEDDED JUST DRIVE FOR AUTOMOTIVE APPLICATIONS USING CAN AND ANDROID IN SUPPORT WITH FPGA INTELLIGENCE (2015)

Abstract — Society is becoming increasingly dependent on embedded computing and sensor technology to enable complex networks of autonomous systems, such as robots, unmanned aerial vehicles (UAVs), self-driving cars, and unmanned underwater vehicles (UUVs). Infact, several recent developments highlight the realization of advanced autonomous systems that were deemed science fiction just a few decades ago. Smart Just Drive for Automotive using embedded blue tooth is designed to provide comfortable feel to the user or passenger to check the vehicle status by reading different vehicle parameters like fuel levels, engine temperature etc., and remote by using Smart mobile with Bluetooth Connectivity. This is an inexpensive device which reduces the problem associated with anti-theft control as well. This tracking system is mainly composed of PIC18F4480 Microcontroller and a Bluetooth receiver. Automotive theft has been a persisting problem around the world and greater challenge comes from professional thieves. In this paper, we present an automotive security system to disable an automobile and its key auto systems through remote control when it is stolen. It hence deters thieves from committing the theft.
WebLogo: A Sequence Logo Generator: Figure 1 (2004)

WebLogo generates sequence logos, graphical representations of the patterns within a multiple sequence alignment. Sequence logos provide a richer and more precise description of sequence similarity than consensus sequences and can rapidly reveal significant features of the alignment otherwise difficult to perceive. Each logo consists of stacks of letters, one stack for each position in the sequence. The overall height of each stack indicates the sequence conservation at that position (measured in bits), whereas the height of symbols within the stack reflects the relative frequency of the corresponding amino or nucleic acid at that position. WebLogo has been enhanced recently with additional features and options, to provide a convenient and highly configurable sequence logo generator. A command line interface and the complete, open WebLogo source code are available for local installation and customization.
Microvascular sites and characteristics of sickle cell adhesion to vascular endothelium in shear flow conditions: pathophysiological implications. (1989)

To understand the role of sickle cell adherence to the vascular endothelium in the pathophysiology of sickle cell anemia (SS) vasoocclusion, we have carried out a microcirculatory study utilizing the ex vivo mesocecum vasculature of the rat. A single bolus of washed oxy-normal (AA) erythrocytes or oxy-SS cells (unseparated or density-defined SS cell classes) was infused. Hemodynamic monitoring and intravital microscopic observations of the microvascular flow revealed higher peripheral resistance for SS erythrocytes and adherence of these cells exclusively to the venular endothelium but rare or no adherence of AA cells. The extent of adhesion was inversely correlated with venular diameters (r = -0.812; P less than 0.00001). The adhesion of SS erythrocytes is density-class dependent: reticulocytes and young discocytes (SS1) greater than discocytes (SS2) greater than irreversible sickle cells and unsicklable dense discocytes (SS4). Selective secondary trapping of SS4 (dense cells) is found in postcapillary venules where deformable SS cells are preferentially adhered. We conclude that in the oxygenated condition, vasoocclusion can be induced by two events: (i) random precapillary obstruction by a small number of SS4 cells; (ii) increased adhesion of SS1 and SS2 cells in the immediate postcapillary venules. A combination of precapillary obstruction, adhesion in postcapillary venules, and secondary trapping of dense cells may induce local hypoxia, increased polymerization of hemoglobin S, and rigidity of SS erythrocytes, thereby extending obstruction to nearby vessels.
New anticancer agents: in vitro and in vivo evaluation. (2005)

The rapid emergence of new anticancer agents is a tremendous challenge for basic, pre-clinical and clinical research to evaluate and eventually integrate these new agents into clinical routine. Standardized, well-established in vitro and in vivo methods are available for the experimental evaluation of new anticancer agents. A step-wise procedure from in vitro to in vivo experiments using non-functional, functional non-clonogenic and, if applicable, clonogenic assays allows reduction of the number of promising agents for further clinical testing.
High quality fluorinated silicon oxide films prepared by plasma enhanced chemical vapor deposition at 120 °C (1996)

Electrical characteristics of the fluorinated silicon oxide films prepared by plasma enhanced chemical vapor deposition at 120 °C using Si2H6 as silicon precursor and CF4 as fluorine precursor were studied. The addition of fluorine into Si–O network results in a decrease in the effective oxide charges as low as 1/6 of the value for the fluorine-free silicon oxide films. It also improves the film breakdown property by significantly reducing early failures, resulting in the measured average dielectric breakdown field strength of 8.91 MV/cm.
Pluripotent bovine embryonic cell lines direct embryonic development following nuclear transfer (1996)

Nuclear transfer (NT) procedures were used to determine the in vivo developmental capacity of bovine embryonic cell lines derived from both morula- and blastocyst-stage embryos. These cell lines differed in morphology from trophoblast and endoderm-like cells. Regardless of initial donor embryo stage, cells in the resulting bovine embryonic cell lines had a small cytoplasmic/nuclear volume ratio and contained cytoplasmic vesicles. Developmental rates to blastocyst stage for NT embryos were improved when smaller cells (15 microns) rather than larger cells (18 microns or 21 microns) were used in the NT procedure and the recipient oocyte was activated after the cell fusion step. NT embryos produced from these embryonic cell lines, both morula- and blastocyst-derived, initiated pregnancies following transfer into recipient females. However, all of these pregnancies were lost prior to 60 days of gestation. These NT embryos were able to direct development through organogenesis, with one NT fetus reaching 55 days before death. When viable NT embryos were recovered during early gestation (38 days), an absence of cotyledons and a hemorrhagic response in the caruncles were observed. A chimera produced by aggregating an NT embryo with two 8-cell-stage blastomeres from in vitro-produced embryos developed through the 85th day of gestation. However, this conceptus was also deficient of cotyledons. DNA markers indicated that 50% of the chimera conceptus tissues were derived from the embryonic cell line. Blastocyst- and morula-derived embryonic cell line nuclei are pluripotent in that they can direct development through organogenesis, with subsequent pregnancy loss due, at least in part, to a deficiency in placentome development.
Carbohydrate Components of Extraneuronal Gangliosides from Bovine and Human Spleen, and Bovine Kidney (1970)

The gangliosides from bovine spleen and kidney as well as human spleen, were extracted from the tissues. The carbohydrate‐portion of the gangliosides was characterized. Bovine spleen gangliosides and those isolated from bovine kidney contained the same sialo‐oligosaccharide moieties. Eleven different ganglosides from the bovine tissues and five gangliosides from human spleen were identified. They are derived from lactose, ganglio‐ N ‐triose, ganglio‐ N ‐tetraose, lacto‐ N ‐neotetraose or lacto‐ N ‐tetraose and differ in their content of sialic acid. Gangliosides from human tissue contain N ‐acetyl‐neuraminic acid only. The sialic acid of the gangliosides from bovine spleen consist of either N ‐acetyl‐neuraminic acid, N ‐glycolyl‐neuraminic acid or both.
Thiamin auxotrophy in yeast through altered cofactor dependence of the enzyme acetohydroxyacid synthase (2001)

The THI1 gene of Saccharomyces cerevisiae has been identified and found to be allelic with the previously characterized gene ILV2 that encodes acetohydroxyacid synthase (AHAS). This enzyme catalyses the first step in the parallel biosyntheses of the branched-chain amino acids isoleucine and valine, using thiamin pyrophosphate (TPP) as a cofactor. The ilv2-thi1 allele encodes a functional AHAS enzyme with an altered dependence for the cofactor TPP resulting in the thiamin auxotrophic phenotype. Nucleotide sequence analysis and site-directed mutagenesis revealed that the thi1 mutation is a single base substitution which causes the conserved amino acid substitution D176E in the AHAS protein. This study therefore implicates aspartate 176 as another amino acid residue important either for the efficient binding of TPP by AHAS or for the functional stability of the holoenzyme.
Cortical enlargement in autism is associated with a functional VNTR in the monoamine oxidase A gene (2008)

Monoamine oxidase A (MAOA) is an enzyme expressed in the brain that metabolizes dopamine, norepinephrine, epinephrine, and serotonin. Abnormalities of serotonin neurotransmission have long been implicated in the psychopathology of autism. A polymorphism exists within the promoter region of the MAOA gene that influences MAOA expression levels so that "low activity" alleles are associated with increased neurotransmitter levels in the brain. Individuals with autism often exhibit elevated serotonin levels. Additional studies indicate that the "low activity" allele may be associated with lower IQ and more severe autistic symptoms. In this study we genotyped the MAOA promoter polymorphism in a group of 29 males (age 2-3 years) with autism and a group of 39 healthy pediatric controls for whom brain MRI data was available. We found a consistent association between the "low activity" allele and larger brain volumes for regions of the cortex in children with autism but not in controls. We did not find evidence for over-transmission of the "low activity" allele in a separate sample of 114 affected sib pair families. Nor did we find any unknown SNPs in yet another sample of 96 probands. Future studies will determine if there is a more severe clinical phenotype associated with both the "low activity" genotype and the larger brain volumes in our sample.
Kinetic Analysis of Human Flap Endonuclease-1 by Flow Cytometry (1996)

Human flap endonuclease-1 (FEN-1) is a structure-specific endonuclease and exonuclease which is essential for DNA replication and repair. We have cloned a human FEN-1 gene, overexpressed it in Escherichia coli, purified the recombinant protein to near homogeneity, and characterized its cleavage of a flap DNA structure using a novel analytical approach based on flow cytometry. With this approach, we were able to measure continuously the kinetics of DNA cleavage by FEN-1 and to separate experimentally the binding and catalysis functions of the enzyme. When the reaction was initiated by the addition of FEN-1, the cleavage kinetics were dependent on enzyme concentration and appeared to saturate at high concentrations. When enzyme and substrate were preincubated in the presence of EDTA and the reaction initiated by the addition of Mg2+, rapid kinetic flow cytometry measurements showed that cleavage is fast (t1/2 approximately 6 s, k = 0.10 s-1). Using the single-turnover kinetics as a measure of the amount of enzyme-substrate complex present, we estimated the Kd for the FEN-1-flap DNA substrate to be 7.5 nM in the absence of Mg2+ and the rate constant for dissociation of the enzyme-substrate complex to be 0.07 s-1. Computer fitting of the experimental data to a kinetic model confirms these estimates for the individual steps and suggests some interesting features of enzymology using a surface-bound substrate.
The role of CD8+ T-cell response in HIV infection. (2004)

CD8+ T-cells with cytotoxic (CTL) activity play a pivotal role in controlling viral infections. Although most patients chronically infected with HIV have CTL response against the virus, for reasons that are not well understood this response is not able to successfully control viral replication. The crucial role of this type of response has been clearly demonstrated in the setting of acute infection using the simian model of AIDS, in which a strong CTL response develops, supporting its role in humans. This approach has been possible due to the development of new assays to quantify CTL activity with great sensitivity and specificity. The interaction of CTL response and HIV during this acute stage of infection is crucial, since it most probably determines the viral set-point and thus the rate of HIV disease progression. In the setting of chronic HIV infection, the use of tetrameric complexes and IFN-gamma production assays have made it possible to investigate the different functional aspects of these cells and have also facilitated the evaluation of this response in large patient populations. Defects in cytokine production and in perforin expression have been found, as well as alterations in phenotypic maturation and a low proliferation of these cells. All these findings have been cited to explain the inability of CTLs to efficiently control virus replication. Nonetheless, accumulating evidence points toward an important role for CTL response in the partial containment of HIV replication in chronic infection. An especially strong support for this observation derives from studies analyzing the selective pressure exerted by the immune response over viral evolution. Very recently, longitudinal and cross-sectional studies in large populations of patients have demonstrated that viral evolution is in part driven by HIV-specific T-cell responses.
Tendinopathy and tendon injury: The future (2008)

Tendon disorders are debilitating, and difficult to manage. Current management strategies offer symptomatic relief, but do not result in definitive disease resolution. Despite remodeling, the biochemical and mechanical properties of healed tendon tissue may never match those of intact tendons. This article presents a detailed up-to-date review of possible strategies for optimizing tendon healing and repair, such as growth factor therapy, gene therapy, and tissue engineering.
Automated Image Registration: I. General Methods and Intrasubject, Intramodality Validation (1998)

The registration algorithm described is a robust and flexible tool that can be used to address a variety of image registration problems. Registration strategies can be tailored to meet different needs by optimizing tradeoffs between speed and accuracy.
Natural covalent complexes of nucleic acids and proteins: some comments on practice and theoryon the path from well-known complexes to new ones (1998)

More than 20 years have passed since the discovery of natural covalent complexes of nucleic acids and proteins (1–5). Covalent complexes of nucleic acids and proteins are both stable and highly specific because they are nucleoproteins linked by a unique covalent bond. Two important properties are associated with these complexes: (i) a novel structure, describing a new class of natural nucleoproteins; (ii) specific functions, that have led to an understanding of previously undiscovered mechanisms of DNA and RNA replication (i.e. the protein priming mechanism) and that are ultimately needed to change the topology of DNA, for DNA integration, conjugation, DNA structure resolution and other as yet unknown functions. Due to availability and the ability to obtain homogeneous preparations, the majority of data on structure and function have been obtained with covalent nucleic acid and protein complexes of viral origin.
What Clinicians Should Know About the QT Interval (2003)

Although the use of QT-prolonging medications can predispose to torsades de pointes, there is a relative paucity of information that can help clinicians and patients make optimal informed decisions about how best to minimize the risk of this serious complication.