gebhart/patrepeval huggingface dataset:
Regulation of Alternative Splicing in Vivo by Overexpression of Antagonistic Splicing Factors (1994)

The opposing effects of SF2/ASF and heterogeneous nuclear ribonucleoprotein (hnRNP) A1 influence alternative splicing in vitro. SF2/ASF or hnRNP A1 complementary DNAs were transiently overexpressed in HeLa cells, and the effect on alternative splicing of several cotransfected reporter genes was measured. Increased expression of SF2/ASF activated proximal 5' splice sites, promoted inclusion of a neuron-specific exon, and prevented abnormal exon skipping. Increased expression of hnRNP A1 activated distal 5' splice sites. Therefore, variations in the intracellular levels of antagonistic splicing factors influence different modes of alternative splicing in vivo and may be a natural mechanism for tissue-specific or developmental regulation of gene expression.
Targeting of Functional Antibody-Decay-accelerating Factor Fusion Proteins to a Cell Surface (2001)

Recombinant soluble complement inhibitors hold promise for the treatment of inflammatory disease and disease states associated with transplantation. Targeting complement inhibitors to the site of complement activation and disease may enhance their efficacy and safety. Data presented show that targeting of decay-accelerating factor (DAF, an inhibitor of complement activation) to a cell surface by means of antibody fragments is feasible and that cell-targeted DAF provides significantly enhanced protection from complement deposition and lysis compared with soluble untargeted DAF. An extracellular region of DAF was joined to an antibody combining site with specificity for the hapten dansyl, at the end of either C(H)1 or C(H)3 Ig regions. The recombinant IgG-DAF chimeric proteins retained antigen specificity and bound to dansylated Chinese hamster ovary cells. Both soluble C(H)1-DAF and C(H)3-DAF were effective at inhibiting complement-mediated lysis of untargeted Chinese hamster ovary cells at molar concentrations within the range reported by others for soluble DAF. However, when targeted to a dansyl-labeled cell membrane, C(H)1-DAF was significantly more potent at inhibiting complement deposition and complement-mediated lysis. Cell-bound C(H)1-DAF also provided cells with protection from complement lysis after removal of unbound C(H)1-DAF. Of further importance, the insertion of a nonfunctional protein domain of DAF (the N-terminal short consensus repeat) between C(H)1 and the functional DAF domain increased activity of the fusion protein. In contrast to C(H)1-DAF, C(H)3-DAF was not significantly better at protecting targeted versus untargeted cells from complement, indicating that a small targeting vehicle is preferable to a large one. We have previously shown that for effective functioning of soluble complement inhibitor CD59, binding of CD59 to the cell surface close to the site of complement activation is required. Significantly, such a constraint did not apply for effective DAF function.
An FPGA Implementation of Information Theoretic Visual-Saliency System and Its Optimization (2011)

Biological vision systems use saliency-based visual attention mechanisms to limit higher-level vision processing on the most visually-salient subsets of an input image. Among several computational models that capture the visual-saliency in biological system, an information theoretic AIM(Attention based on Information Maximization) algorithm has been demonstrated to predict human gaze patterns better than other existing models. We present an FPGA based implementation of this computationally intensive AIM algorithm to support embedded vision applications. Our implementation provides performance of processing about 4M pixels/sec for 25 basis functions with a convolution kernel size of 21 by 21 for each of the R, G, and B color-channels, when implemented on a Virtex-6 LX240T. We also provide an optimization aimed at controlling the trade-off between power consumption and latency, and performance comparisons with a GPU implementation.
The Human Genome Contains Hundreds of Genes Coding for Finger Proteins of the Krüppel Type (1989)

Our aim was to identify new human proteins with potential DNA binding activity, related to the Krüppel protein which regulates Drosophila segmentation. We screened a human placenta cDNA library and a human genomic DNA library with a synthetic oligonucleotide probe corresponding to the H/C link region that connects finger loops in the multifingered Krüppel protein. We found more than 100 different mRNAs encoding Krüppel multifingered proteins in the human placenta. In the whole human genome, the number of genes encoding such proteins reaches about 300. Sequence analysis of 14 cloned cDNAs indicated that they code for at least nine undescribed human finger proteins. The sequences of the 106 finger repeats present in these nine proteins are highly homologous. Most of the variability lies in a limited number of positions located in their postulated alpha-helical structure, and therefore could be implicated in their DNA-binding specificity.
A 0.5-to-3 GHz software-defined radio receiver using sample domain signal processing (2013)

A 0.5-to-3 GHz software-defined radio receiver leveraging Sampled Domain Signal Processing (SPSD) is demonstrated in a 65nm LP CMOS technology. The SDSP approach achieves band-pass filtering, harmonic rejection, and frequency translation simultaneously. Input impedance matching is achieved in an active translational loop that tracks the desired RF frequency. The chip includes a wideband frequency synthesizer, multi-phase nonoverlapping clock generation circuitry, bandgap and power supply regulators. It achieves out-of-band IIP3 > 11.7 dBm, IIP2 > 58 dBm, NF = 5.5 ~ 8.8 dB, and uncalibrated 3 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rd</sup> and 5 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sup> order harmonic rejections exceeding 47 dB and 52 dB, respectively.
A Randomized Controlled Trial of Cold-Adapted and Inactivated Vaccines for the Prevention of Influenza A Disease (1994)

A double-blind, randomized controlled trial over 5 years compared the safety, immunogenicity, and efficacy of cold-adapted and inactivated influenza A vaccines in 5210 normal subjects. Both vaccines were well tolerated. Inactivated vaccine significantly increased hemagglutination inhibition antibody titers. Significant titer rises were also noted after cold-adapted vaccine but of lesser magnitude than with inactivated vaccine. The efficacyof inactivated vaccine in preventing culture-positive influenza was 76% (95% confidence interval [CI], 58%–87%) for HINI disease and 74% (95% CI, 52%–86%) for H3N2; for cold-adapted vaccine, 85% (95% CI, 70%–92%) and 58% (95% CI, 29%–75%), respectively. The efficacy of inactivated vaccine in preventing a four-fold rise in antibody titer over the influenza season was 69% (95% CI, 61%–76%) for H1N1 and 73% (95% CI, 65%–79%) for H3N2; for cold-adapted vaccine, 54% (95% CI, 44%–62%) and 32% (95% CI, 17%–44%), respectively. Cold-adapted and inactivated influenza vaccines are safe and effective for preventing influenza A disease.
COX‐2 expression in DCIS: correlation with VEGF, HER‐2/neu, prognostic molecular markers and clinicopathological features (2005)

Our results suggest that COX-2 is highly expressed in DCIS and takes part in the molecular pathway implicated in progression of breast cancer and may provide a rationale for targeting COX-2 in preinvasive breast cancer therapy.
Cystic fibrosis transmembrane conductance regulator modulators in cystic fibrosis: current perspectives (2016)

Mutations of the <i>CFTR</i> gene cause cystic fibrosis (CF), the most common recessive monogenic disease worldwide. These mutations alter the synthesis, processing, function, or half-life of CFTR, the main chloride channel expressed in the apical membrane of epithelial cells in the airway, intestine, pancreas, and reproductive tract. Lung disease is the most critical manifestation of CF. It is characterized by airway obstruction, infection, and inflammation that lead to fatal tissue destruction. In spite of great advances in early and multidisciplinary medical care, and in our understanding of the pathophysiology, CF is still considerably reducing the life expectancy of patients. This review highlights the current development in pharmacological modulators of CFTR, which aim at rescuing the expression and/or function of mutated CFTR. While only Kalydeco® and Orkambi® are currently available to patients, many other families of CFTR modulators are undergoing preclinical and clinical investigations. Drug repositioning and personalized medicine are particularly detailed in this review as they represent the most promising strategies for restoring CFTR function in CF.
Histone Deacetylase Inhibitors in Psoriasis Therapy (2004)

Psoriasis is recognised as a multifactorial disease with inflammatory, proliferative, angiogenic and genetic components contributing to the pathology. The disease, which may vary in intensity, remains clinically unmet although there have been several recent advances that have had a substantial impact on suffering. Histone deacetylase inhibitors represent a new class of therapeutic agent, initially developed for oncology, which prevent cell proliferation and induce differentiation. Here we discuss the possible application of HDAC inhibitors to psoriasis, focussing particularly on their anti-proliferative and anti-inflammatory activity. Our view, based upon the emerging clinical properties of HDAC inhibitors, reflects the growing recognition that HDAC inhibitors will be important therapeutic agents in diseases other than cancer.
Isolation of cellulolytic enzymes from Trichoderma reesei QM 9414. (1985)

Two cellobiohydrolases and two endoglucanases were purified from a culture filtrate of the fungus Trichoderma reesei QM 9414 by simple and straightforward purification techniques. Molecular weights, isoelectric points, amino acid compositions, and carbohydrate contents are reported.
[IEX-1: an unique protein in regulating apoptosis]. (2011)

Immediate early response gene X-1 (IEX-1) gene was discovered by Charles in 1993, which plays an important role in regulating apoptosis. Previous studies demonstrated that IEX-1 gene was expressed in a variety of human tissues and played an important role in regulating apoptosis and cell growth through a positive or negative way. It can inhibit cell growth and apoptosis. However, it can also promote cell apoptosis. There is evidence that IEX-1 is involved in viral infections and cardiovascular diseases and it is highly expressed in many tumor tissues. The regulatory mechanisms for IEX-1 under normal and pathophysiological conditions are complicated and remain largely unknown. In this paper, we reviewed the recent progress of IEX-1 in different disease models.
Low-threshold current density 1.3-μm InAs quantum-dot lasers with the dots-in-a-well (DWELL) structure (2000)

The wavelength of InAs quantum dots in an In/sub 0.15/Ga/sub 0.85/As quantum-well (DWELL) lasers grown on a GaAs substrate has been extended to 1.3-μm. The quantum dot lasing wavelength is sensitive to growth conditions and sample thermal history resulting in blue shifts as much as 73 nm. The room temperature threshold current density is 42.6 A cm/sup -2/ for 7.8-mm cavity length cleaved facet lasers under pulsed operation.
Targeting HSP90 for cancer therapy (2009)

Heat-shock proteins (HSPs) are molecular chaperones that regulate protein folding to ensure correct conformation and translocation and to avoid protein aggregation. Heat-shock proteins are increased in many solid tumours and haematological malignancies. Many oncogenic proteins responsible for the transformation of cells to cancerous forms are client proteins of HSP90. Targeting HSP90 with chemical inhibitors would degrade these oncogenic proteins, and thus serve as useful anticancer agents. This review provides an overview of the HSP chaperone machinery and the structure and function of HSP90. We also highlight the key oncogenic proteins that are regulated by HSP90 and describe how inhibition of HSP90 could alter the activity of multiple signalling proteins, receptors and transcriptional factors implicated in carcinogenesis.
Effects of site-directed mutagenesis at residues cysteine-31 and cysteine-184 on lecithin-cholesterol acyltransferase activity. (1991)

Native lecithin-cholesterol acyltransferase (LCAT; phosphatidylcholine-sterol acyltransferase; phosphatidylcholine:sterol O-acyltransferase, EC 2.3.1.43) protein, and LCAT in which either or both of the enzyme free cysteines had been replaced with glycine residues by site-directed mutagenesis, has been expressed in cultured Chinese hamster ovary cells stably transfected with the human LCAT gene. The mass of LCAT secreted, determined by immunoassay, did not differ in the native and mutant species. LCAT specific activity was also unchanged in the mutant species. In particular, the cysteine-free double mutant, in which Cys-31 and Cys-184 had both been replaced, was fully active in the synthesis of cholesteryl esters. This result is not consistent with a catalytic role for LCAT free cysteine residues. The classical inhibitor of LCAT activity, 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB), which strongly (89%) inhibited the native enzyme, had partial (45%) inhibitory activity with mutant enzyme species containing a single -SH residue, while the double mutant was not significantly inhibited by DTNB. These data are interpreted to suggest that Cys-31 and Cys-184 are vicinal both to each other and to the "interfacial binding site" at residues 177-182, and that DTNB exerts its effect by steric inhibition.
Using annotated video as an information retrieval interface (2000)

The ability to deliver appropriate information to learners at the most appropriate time is an essential component of good instruction. In the best learning environments, this information is received in the context of the performance of the skills that are being acquired. This paper explores a technological approach to situated information retrieval by linking materials to segments of a video recording a skill performance. An interface is described where users navigate through a video performance and are presented with information relevant to the current video location. An approach to algorithmically generating interfaces of this type is then presented. The system takes as input annotations that describe a video recording of a performance, translates these annotations into subject terms used to catalog information resources, and then retrieves materials from online database servers using the Z39.50 information retrieval protocol. As an example application, the system was used to generate online teacher professional development materials by linking annotated video of classroom teaching with resources cataloged in the ERIC database.
Validation of Malondialdehyde and 4-Hydroxy-2-trans-Nonenal Measurement in Plasma by NICI-GC-MS (1998)

Measurement of the concentrations of aldehydes in biological samples has become the object of much effort due to their relevance in relation to the toxic effects of lipid peroxidation, through which a number of aldehydes are derived. We have reconsidered a previously proposed method based on gas chromatographic mass spectrometric analysis of derivatives obtained by the treatment of aldehydes with O-pentafluorobenzyl hydroxylamine followed by a trimethylsilylating agent. In view of the possible use of the method for the simultaneous evaluation of the plasma levels of malondialdehyde and 4-hydroxy-2-trans-nonenal, we have studied the linearity of the analysis using various internal standards. Commercially available, inexpensive 2,4-dihydroxybenzaldehyde gave optimal results, the correlation coefficient of the calibration curve for plasma being r > 0.995 in the 0.1-5 microM range for both the tested aldehydes. The between-day imprecision (%CV) and accuracy (%bias) of the procedure determined using plasma samples spiked with the two aldehydes and with an internal standard reached maximum values of 3 and 8%, and 5 and 12% for HNE and MDA, respectively. The results obtained on analysis of plasma samples before and after oxidation with copper ions indicate the flexibility of the method for evaluation of the levels of MDA and HNE in plasma samples both under basal conditions and after an oxidative burst.
Sequence-Function Relationships Within the Expanding Family of Prolactin, Growth Hormone, Placental Lactogen, and Related Proteins in Mammals* (1996)

I. Introduction PRL PL, and GH are homologous proteins that are thought to have arisen from a common ancestral gene by two successive tandem duplications (Refs. 1–5; for review, see Ref. 6). PRL and GH are mainly secreted by the anterior pituitary of all vertebrates. The divergence of the PRL and GH lineage from the common ancestral gene has been located some 400 million years ago, which is in good agreement with the presence of distinct PRL and GH in fish (2, 3, 6, 7). PL is uniquely observed in mammals and is secreted in the placenta by syncytiotrophoblastic cells (for reviews, see Refs. 8–10). Initially, PLs were proposed to have evolved from the common PRL/GH precursor gene (1). Further cloning and analysis of PRL, GH, and PL genes from different species (chromosome carrier, gene size, splicing sites, sequence identity; see Refs. 6, 7, 11, and 12) have led to a reconsideration of this hypothesis, and it is now assumed that primate PLs evolved from the GH lineage while nonprimate PLs arose from the PRL...
Small-molecule factor B inhibitor for the treatment of complement-mediated diseases (2019)

Dysregulation of the alternative complement pathway (AP) predisposes individuals to a number of diseases including paroxysmal nocturnal hemoglobinuria, atypical hemolytic uremic syndrome, and C3 glomerulopathy. Moreover, glomerular Ig deposits can lead to complement-driven nephropathies. Here we describe the discovery of a highly potent, reversible, and selective small-molecule inhibitor of factor B, a serine protease that drives the central amplification loop of the AP. Oral administration of the inhibitor prevents KRN-induced arthritis in mice and is effective upon prophylactic and therapeutic dosing in an experimental model of membranous nephropathy in rats. In addition, inhibition of factor B prevents complement activation in sera from C3 glomerulopathy patients and the hemolysis of human PNH erythrocytes. These data demonstrate the potential therapeutic value of using a factor B inhibitor for systemic treatment of complement-mediated diseases and provide a basis for its clinical development.
Rectal tacrolimus in the treatment of resistant ulcerative proctitis (2008)

This prospective pilot study demonstrated that topical rectal tacrolimus ointment can be effective in ulcerative proctitis. The preparation was well tolerated with no significant adverse effects. Further controlled studies are required.
Identification and structural characterization of the 75-kDa rabbit zona pellucida protein (1993)

A cDNA (rc75) encoding a 75-kDa rabbit zona pellucida (ZP) glycoprotein (R75) has been cloned and sequenced. The predicted amino acid sequence consists of 676 amino acids including seven potential N-glycosylation sites. The cDNA hybridizes to a 2.4-kilobase mRNA in ovary that is not detectable in other rabbit tissues. The R75 mRNA was also found to be expressed during the early stages of rabbit ovarian development (2-6 weeks of age) when the ovary contains primordial, primary, and early secondary follicles. The deduced amino acid sequence of rc75 has 77% similarity to the mouse ZP2 protein but no similarity to mouse ZP3. R75 also contains regions with 35-55% similarity to a previously cloned rabbit 55-kDa ZP protein. Monte Carlo simulation comparison confirmed that R75 has a significant probability of homology with mouse ZP2 and the rabbit 55-kDa ZP protein. Antibodies were developed against a fragment of R75 (rc75a cDNA) expressed in the pEX expression vector. These antibodies were used to confirm that the expressed protein contained epitopes found in the native rabbit ZP glycoprotein. These data suggest that some, but not all, ZP proteins may be conserved among different species and that within a species ZP proteins may share similar regions.
The complete nucleotide sequence of theilvGMEDAOperon ofEscherichia ColiK-12 (1987)

In this report we present the complete nucleotide sequence of the ilvGMEDA operon of Escherichia coli. This operon contains five genes encoding four of the five enzymes required for the biosynthesis of isoleucine and valine. We identify and describe the coding regions for these five structural genes and the structural and functional features of the flanking and internal regulatory regions of this operon. This new information contributes to a more complete understanding of the overall control of the biosynthesis of isoleucine and valine.
Experimental Intra-Abdominal Abscesses in Rats: Development of an Experimental Model (1974)

An animal model has been developed to study the evolution of intra-abdominal abscesses. Gelatin capsules containing pooled colonic contents and barium sulfate were prepared in an anaerobic chamber and implanted into the pelvic region of Wistar rats. The natural course of the ensuing disease was studied in various groups according to the source of the inoculum and sex of the recipient. Colonic contents derived from rats fed a grain diet produced a highly lethal disease with an 80% mortality rate for males and 100% for females. Most deaths occurred within 3 days of implantation, and autopsies showed generalized peritonitis. The addition of blood to the inoculum caused a rapidly fatal peritonitis in all animals. With an inoculum derived from meat-fed rats implanted in male recipients, there was a biphasic disease. Initially, there was peritonitis associated with 43% mortality. All animals that survived this acute period developed discrete intra-abdominal abscesses by the seventh postoperative day. The latter stage was characterized by an indolent course and progressive enlargement of abscesses.
HIV‐1 Causes an Imbalance in the Production of Interleukin‐18 and Its Natural Antagonist in HIV‐Infected Individuals: Implications for Enhanced Viral Replication (2010)

Production of IL-18 and its antagonist becomes imbalanced in HIV-1-infected persons. The infection and the cytokine milieu play a role in this decreased production. The increased biological activities of IL-18 may enhance viral replication in human CD4(+) T cells.
Iterated extended Kalman filter based visual-inertial odometry using direct photometric feedback (2017)

This paper presents a visual-inertial odometry framework that tightly fuses inertial measurements with visual data from one or more cameras, by means of an iterated extended Kalman filter. By employing image patches as landmark descriptors, a photometric error is derived, which is directly integrated as an innovation term in the filter update step. Consequently, the data association is an inherent part of the estimation process and no additional feature extraction or matching processes are required. Furthermore, it enables the tracking of noncorner-shaped features, such as lines, and thereby increases the set of possible landmarks. The filter state is formulated in a fully robocentric fashion, which reduces errors related to nonlinearities. This also includes partitioning of a landmark’s location estimate into a bearing vector and distance and thereby allows an undelayed initialization of landmarks. Overall, this results in a compact approach, which exhibits a high level of robustness with respect to low scene texture and motion blur. Furthermore, there is no time-consuming initialization procedure and pose estimates are available starting at the second image frame. We test the filter on different real datasets and compare it with other state-of-the-art visual-inertial frameworks. Experimental results show that robust localization with high accuracy can be achieved with this filter-based framework.