gebhart/patrepeval huggingface dataset:
Entodoxin tolerance in humans in vivo (2009)

Service de Réanimation Médicale CHU Poitiers, Université de Poitiers, France; (Robert) Laboratoire de Bactériologie CHU Poitiers, Université de Poitiers, France (Janvier, Grollier)
The degradation of platelet-activating factor in the plasma of a patient with familial high density lipoprotein deficiency (Tangier disease) (1985)

Platelet Activating Factor (PAF) (1-O-alkyl-2-acetyl sn-glycerol 3- phosphocholine) has been characterized by its ability to aggregate platelets at low concentrations and its profound hypotensive effects. There is evidence that the rate of catabolism of this compound in the plasma regulates its concentration. In humans, we and others have shown that a PAF acetylhydrolase is associated with low density lipoprotein (LDL). The LDL particle in the plasma of patients with Tangier disease is quite different from normal as its lipid core appears to be enriched with triacylglycerol. Thus, we have studied the potential of this abnormal lipoprotein to degrade PAF. The assay for PAF acetylhydrolase was based on the release of 3H from PAF that was labelled in the acetate moiety of the sn-2 position. Tangier disease plasma had approximately 3.3-fold higher PAF acetylhydrolase activity (208 +/- 9 nmol/min/mL) than controls (63 +/- 18 nmol/min/mL). This increase was brought about by an increase in the Vmax (400 +/- 40, Tangier disease; 54 +/- 5, controls) and Km for PAF (120 +/- 20 mumol/L, Tangier disease; 28 +/- 4 mumol/L, controls). The activity appears to be a specific acetylhydrolase rather than a phospholipase A2 as preincubation of the substrate with 0 to 100 mumol/L phosphatidylcholine did not affect the amount of [3H] acetate released. The role of PAF, and its degradation by LDL-bound PAF acetylhydrolase in the phenotypic expression of this patient with Tangier disease, is not known. However, this is the first patient so far described who has an increased ability to degrade PAF in the plasma.
SAGA: sequence alignment by genetic algorithm (1996)

We describe a new approach to multiple sequence alignment using genetic algorithms and an associated software package called SAGA. The method involves evolving a population of alignments in a quasi evolutionary manner and gradually improving the fitness of the population as measured by an objective function which measures multiple alignment quality. SAGA uses an automatic scheduling scheme to control the usage of 22 different operators for combining alignments or mutating them between generations. When used to optimise the well known sums of pairs objective function, SAGA performs better than some of the widely used alternative packages. This is seen with respect to the ability to achieve an optimal solution and with regard to the accuracy of alignment by comparison with reference alignments based on sequences of known tertiary structure. The general attraction of the approach is the ability to optimise any objective function that one can invent.
Adenovirus-Mediated Delivery of Catalase to Retinal Pigment Epithelial Cells Protects Neighboring Photoreceptors from Photo-Oxidative Stress (2004)

Oxidative stress is involved in the pathogenesis of many diseases. Overexpression of antioxidant enzymes by gene therapy may protect tissues from oxidative damage. Because the reactive oxygen species hydrogen peroxide can diffuse across cell membranes, we hypothesized that overexpression of the antioxidant catalase within certain cells might protect neighboring cells. To test this hypothesis, we transduced retinal pigment epithelial (RPE) cells in vitro and in vivo with adenovirus carrying the catalase gene (Ad.CMV.catalase). After transduction of only a subset of RPE cells in vitro, all cells in the culture were protected from exogenous hydrogen peroxide. Similarly, in vivo, eyes injected with Ad. CMV. catalase had high catalase levels in the RPE, which protected the adjacent photoreceptors from light damage and reduced photoreceptor oxidative stress as measured by the markers 4-hydroxynonenal and nitrotyrosine. Both in vitro and in vivo, gene therapy with Ad. CMV. catalase protected neighboring cells from oxidative stress-induced terminal deoxynucleotidyltransferase-mediated dUTP nick end labeling (TUNEL) positivity. The data provide a paradigm for antioxidant gene therapy with catalase, designed to protect not only transduced cells, but also neighboring cells.
Inhibition of the CD28-CD80 co-stimulation signal by a CD28-binding affibody ligand developed by combinatorial protein engineering (2003)

CD28 is one of the key molecules for co-stimulatory signalling in T cells. Here, novel ligands (affibodies) showing selective binding to human CD28 (hCD28) have been selected by phage display technology from a protein library constructed through combinatorial mutagenesis of a 58-residue three-helix bundle domain derived from staphylococcal protein A. Analysis of selected affibodies showed a marked sequence homology and biosensor analyses showed that all investigated affibodies bound to hCD28 with micromolar affinities (KD). No cross-reactivity towards the related protein human CTLA-4 could be observed. This lack of cross-reactivity to hCTLA-4 suggests that the recognition site on hCD28 for the affibodies resides outside the conserved MYPPPYY motif. The apparent binding affinity for hCD28 could be improved through fusion to an Fc fragment fusion partner, resulting in a divalent presentation of the affibody ligand. For the majority of selected anti-CD28 affibodies, in co-culture experiments involving Jurkat T-cells and CHO cell lines transfected to express human CD80 (hCD80) or LFA-3 (hLFA-3) on the cell surface, respectively, pre-incubation of Jurkat cells with affibodies resulted in inhibition of IL-2 production when they were co-cultured with CHO (hCD80+) cells, but not with CHO (hLFA-3+) cells. For one affibody variant denoted Z(CD28:5) a clear concentration-dependent inhibition was seen, indicating that this affibody binds hCD28 and specifically interferes in the interaction between hCD28 and hCD80.
A compact self-shielding prober for accurate measurement of on-wafer electron devices (1989)

A compact self-shielding prober is proposed for measuring low-current-voltage characteristics of on-wafer electron devices. In the prober, a wafer and a wafer stage are set in a very small shielded region mostly enclosed by a plane top-board, a wafer-stage shield, and a sidewall shielding ring. A current of less than a picoampere can easily be measured without any shielding box. A prober designed to observe all devices on 4-in wafers can be as small as 27 cm*27 cm*12 cm. High-speed input/output waveforms of on-wafer large scale integrated circuits (LSIs) observed with this prober are as clear as those of packaged LSIs observed directly.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Capillary Electrophoresis-SELEX Selection of Aptamers with Affinity for HIV-1 Reverse Transcriptase (2005)

Capillary electrophoresis-SELEX (CE-SELEX) was used to select ssDNA aptamers with affinity for HIV reverse transcriptase (HIVRT). A library of ssDNA was incubated with HIVRT. Sequences bound to HIVRT were isolated using CE, PCR amplified, and purified, yielding an enriched ssDNA pool suitable for further rounds of selection. Aptamers with dissociation constants as low as 180 pM were isolated after four rounds of selection. This is the first report of aptamers isolated by CE-SELEX with higher affinity than those obtained for the same target using conventional selection techniques. No sequence motifs were identified in the 27 clones sequenced, suggesting that there are many sequences that can bind HIVRT with low picomolar dissociation constants.
A Two-hybrid Dual Bait System to Discriminate Specificity of Protein Interactions (1999)

Biological regulatory systems require the specific organization of proteins into multicomponent complexes. Two hybrid systems have been used to identify novel components of signaling networks based on interactions with defined partner proteins. An important issue in the use of two-hybrid systems has been the degree to which interacting proteins distinguish their biological partner from evolutionarily conserved related proteins and the degree to which observed interactions are specific. We adapted the basic two-hybrid strategy to create a novel dual bait system designed to allow single-step screening of libraries for proteins that interact with protein 1 of interest, fused to DNA binding domain A (LexA), but do not interact with protein 2, fused to DNA binding domain B (lambda cI). Using the selective interactions of Ras and Krev-1(Rap1A) with Raf, RalGDS, and Krit1 as a model, we systematically compared LexA- and cI-fused baits and reporters. The LexA and cI baitr reporter systems are well matched for level of bait expression and sensitivity range for interaction detection and allow effective isolation of specifically interacting protein pairs against a nonspecific background. These reagents should prove useful to refine the selectivity of library screens, to reduce the isolation of false positives in such screens, and to perform directed analyses of sequence elements governing the interaction of a single protein with multiple partners.
Potential role of the Slit/Robo signal pathway in angiogenesis (2006)

Intensive investigations on angiogenesis and vasculogenesis have increased our understanding of molecular mechanisms of blood vessel formation during pathologic and developmental conditions. However, endothelial cells (ECs), the main component of vasculature, are heterogeneous, as revealed by our phenotypic and molecular biological studies in the laboratory, and it is still hard to adequately understand the molecular mechanisms of angiogenesis and vasculogenesis. Indeed, there are several major ligand/receptor signal pathways: VEGF/VEGFR, Jagged-1/Notch, Wnt ligand/frizzled receptor, and ephrin/Eph; each of which having distinct and independent roles during vascular formation. In this review, we focus on the angiogenic effect of the Slit and Robo signal pathway that was formally known as neuronal axon guidance. Among the existing vascular signals, this pathway is the most recently found ligand/receptor vascular signal, and may play important physiological roles as other major receptor/ligand signals do. Here, we briefly address: (1) the background of Slit and Robo families; (2) expression patterns of Slit and Robo; (3) functional roles of the Slit/Robo pathway in vascular formation; and (4) confronting tasks of this novel vascular pathway in the near future. Together, a summary of these data suggest the essential role of the Slit/Robo pathway in angiogenesis, and may explain why multiple vascular signals exist in heterogenic endothelial cells.
A dendrimer-based platform for simultaneous dual fluorescence imaging of hydrogen peroxide and pH gradients produced in living cells (2011)

We present a modular dendrimer-based platform for simultaneous dual fluorescence imaging of hydrogen peroxide (H2O2) and pH gradients produced in living cells. Acetyl-capped G5 PAMAM dendrimers functionalized with boronate-caged Peroxyfluor-1 (PF1) fluorophores for H2O2 detection and semi-naphthorhodafluor (SNARF2) dyes for pH sensing provide a single probe system that is capable of sensing multiple analytes at a time by multicolor fluorescence imaging. Spectroscopic measurements of the doubly-labeled dendrimer conjugates establish their ability to simultaneously monitor changes in both H2O2 and pH using different excitation/emission profiles. Moreover, this dual-probe platform allows for selective discrimination between H2O2 and pH changes in live RAW 264.7 macrophage cells when stimulated by an immune insult. Further imaging experiments show that pharmacological inhibition of NADPH oxidase (Nox) proteins triggers a decrease in both oxidative burst and in pH regulation within phagocytic compartments and leads to disruptions of endocytic activity, suggesting that Nox-derived H2O2 signaling is critical to the maintenance of multiple components of the immune response. This work establishes a general molecular platform for simultaneous, real-time imaging of multiple analytes associated with redox biology in living systems and should be applicable to a wide range of chemosensor constructs.
Influence of Seaweed Concentrate On the Reproduction of Pratylenchuszeae (Nematoda) On Maize (1988)

Seaweed concentrate prepared from Ecklonia maxima (Osbeck) significantly suppressed the reproduction of Pratylenchus zeae on excised maize roots by 47-63 %, compared with the untreated control, during an in vitro experiment. In a greenhouse experiment, reproduction of P. zeae on maize was not affected by any of the seaweed concentrations. Plant growth of the maize plants was not stimulated by the seaweed concentrate in the in vitro or in the greenhouse experiment. In the greenhouse experiment, plants were weakened by the toxic effects of the highest seaweed concentrate and became more intolerant to nematode attack.
Detection of enteroviruses and hepatitis a virus in water by consensus primer multiplex RT-PCR (2002)

The consensus primers multiplex RT-PCR has more advantages over monoplex RT-PCR for enteric viruses detection, namely, the rapid turnaround time and cost effectiveness.
Persistence of ResistantStaphylococcus epidermidisafter Single Course of Clarithromycin (2005)

We examined how a common therapy that includes clarithromycin affects normally colonizing Staphylococcus epidermidis. Samples from the nostrils of 5 patients receiving therapy were collected before, immediately after, 1 year after, and 4 years after treatment. From each patient and sample, S. epidermidis strains were isolated and analyzed for clarithromycin susceptibility and presence of the erm(C) gene. We show that macrolide-resistant strains of S. epidermidis were selected during therapy and that the same resistant strain may persist for 4 years, in the absence of further antimicrobial treatment.
Sustained Protection in Mice Immunized with Fractional Doses of Salmonella Enteritidis Core and O Polysaccharide-Flagellin Glycoconjugates (2013)

Non-typhoidal Salmonella (NTS) serovars S. Enteritidis and S. Typhimurium are a major cause of invasive bacterial disease (e.g., bacteremia, meningitis) in infants and young children in sub-Saharan Africa and also occasionally cause invasive disease in highly susceptible hosts (young infants, the elderly, and immunocompromised subjects) in industrialized countries. No licensed vaccines exist against human NTS infections. NTS core and O polysaccharide (COPS) and FliC (Phase 1 flagellin subunits) each constitute protective antigens in murine models. S. Enteritidis COPS conjugated to FliC represents a promising vaccine approach that elicits binding and opsonophagocytic antibodies and protects mice against lethal challenge with virulent S. Enteritidis. We examined the protective efficacy of fractional dosages of S. Enteritidis COPS:FliC conjugate vaccines in mice, and also established that protection can be passively transferred to naïve mice by administering sera from mice immunized with conjugate. Mice were immunized with three doses of either 10 µg, 2.5 µg (full dose), 0.25 µg, or 0.025 µg S. Enteritidis COPS:FliC conjugate at 28 day intervals. Antibody titers to COPS and FliC measured by ELISA fell consonant with progressively smaller vaccine dosage levels; anti-FliC IgG responses remained robust at fractional dosages for which anti-COPS serum IgG titers were decreased. Nevertheless, >90% protection against intraperitoneal challenge was observed in mice immunized with fractional dosages of conjugate that elicited diminished titers to both FliC and COPS. Passive transfer of immune sera from mice immunized with the highest dose of COPS:FliC to naïve mice was also protective, demonstrating the role of antibodies in mediating protection. These results provide important insights regarding the potency of Salmonella glycoconjugate vaccines that use flagellin as a carrier protein.
Synthesis of 1,3,4-oxadiazoles as promising anticoagulant agents (2016)

A series of 1,3,4-oxadiazoles were designed and subjected to molecular docking simulation onto the enzymes vitamin K epoxide reductase (PDB: <bold>3KP9</bold>) and factor Xa (PDB: <bold>1NFY</bold>) to visualize their binding affinity towards the said target proteins.
NONLINEAR ANALYSIS OF SPEECH FROM A SYNTHESIS PERSPECTIVE (1996)

With the emergence of nonlinear dynamical systems analysis over recent years it has become clear that conventional time domain and frequency domain approaches to speech synthesis may be far from optimal. Using state space reconstructions of the time domain speech signal it is, at least in theory, possible to investigate a number of invariant geometrical measures for the underlying system which give a more thorough understanding of the dynamics of the system and therefore the form that any model should take. This thesis introduces a number of nonlinear dynamical analysis tools which are then applied to a database of vowels to extract the underlying invariant geometrical properties. The results of this analysis are then applied, using ideas taken from nonlinear dynamics, to the problem of speech synthesis and a novel synthesis technique is described and demonstrated. The tools used for the analysis are time delay embedding, singular value decomposition, correlation dimension, local singular value analysis, Lyapunov spectra and short term prediction properties. Although there have been many papers written about these tools, and algorithms proposed, there are currently no generally accepted techniques, especially for the calculation of Lyapunov spectra in the presence of noise and data length limitations. This thesis introduces all of the above tools and looks in detail at Lyapunov exponents and two major novel modifications are proposed that are demonstrated to be more robust than conventional techniques. The novel robust techniques are applied to a large database of vowel sounds showing that the vowels tested show evidence of nonlinear, low-dimensional, non-chaotic behaviour. It is particularly the evidence of non-chaotic behaviour that is of importance from a synthesis point of view and is used in the final section of the thesis which introduces a novel synthesis technique. The synthesis technique, which is based on ideas taken from nonlinear dynamics theory is detailed and demonstrated showing that it is capable of high quality natural sounding speech.
Bovine Lymphocyte Antigen Class II Alleles as Risk Factors for High Somatic Cell Counts in Milk of Lactating Dairy Cows (1997)

Lactating Holstein cows (n = 1100) from 93 dairy herds in Iowa, Wisconsin, Minnesota, and Illinois were genotyped at the bovine lymphocyte antigen DRB3.2 locus by a genotyping system that used polymerase chain reaction and restriction fragment length polymorphisms. Milk samples were obtained after routine processing at a Dairy Herd Improvement Association facility and returned to the National Animal Disease Center for DNA extraction. Somatic cells were used to classify cows that had acutely elevated SCC (one test of SCC > 500,000; group 1), or chronically elevated SCC (three consecutive tests of SCC > 300,000 or two consecutive tests of > 500,000; group 2), or that were eligible as controls. For each cow in groups 1 and 2, controls were selected that were matched for breed, lactation, herd, and days in lactation (+/-60 d). A conditional model for stepwise logistic regression was used to determine the relative odds for the 10 alleles with a frequency > 3%. No significant associations were observed when the 292 cows in group 2 were compared with their 292 controls. Allele *16 was associated with an increased risk of disease for cows classified with an acute SCC (258 cases and 258 controls). This study has identified DRB3.2*16 as a potential risk factor for acute intramammary infection and established the use of Dairy Herd Improvement Association milk samples as a source of DNA that is useful for genetic epidemiologic studies.
Ego-net community mining applied to friend suggestion (2015)

In this paper, we present a study of the community structure of ego-networks---the graphs representing the connections among the neighbors of a node---for several online social networks. Toward this goal, we design a new technique to efficiently build and cluster all the ego-nets of a graph in parallel (note that even just building the ego-nets efficiently is challenging on large networks). Our experimental findings are quite compelling: at a microscopic level it is easy to detect high quality communities. Leveraging on this fact we, then, develop new features for friend suggestion based on co-occurrences of two nodes in different ego-nets' communities. Our new features can be computed efficiently on very large scale graphs by just analyzing the neighborhood of each node. Furthermore, we prove formally on a stylized model, and by experimental analysis that this new similarity measure outperforms the classic local features employed for friend suggestions.
Comprehensive student support efforts lead to impressive outcomes (2017)

NEW ORLEANS — “In the last 40 years, if you are among the 25 percent of wealthiest Americans, you more than doubled your chance of getting a college degree,” said Timothy Renick, vice provost and vice president for enrollment management at Georgia State University. But there has been little change in the percentage of people in the bottom quartile who earn credentials, Renick said, speaking at a session at the American Association of Community Colleges annual convention.
Adaptive post-processing of OCR text via knowledge acquisition (1991)

According to Wikipedia, Optical Character Recognition (OCR) “is the mechanical or electronic translation of images of handwritten or typewritten text (usually captured by a scanner) into machine-editable text. ” Even though a lot of academic research has been carried out on this topic, there are still needs for improving the accuracy and completeness of the scanned text. More specifically, scanned documents are prone to inaccuracy and error. This is especially true with large amounts of aged books in libraries across the country. Our group plans on creating a solution which will help to reduce some of these errors in scanned documents. 2. Related work
Channel estimation using pilot tones in OFDM systems (1999)

Channel estimation techniques using pilot tones in OFDM systems are investigated. Two time-domain channel estimation methods are proposed. Based on theoretical analysis and computer simulation, for a channel with multipath distortion and AWGN, the proposed time-domain channel estimation schemes perform better than the conventional frequency-domain channel estimation techniques.
New Pyrolysis Route to GaN Quantum Dots (2006)

A new chemical reaction is reported that produces GaN. Under the appropriate conditions, this reaction yields colloidal GaN quantum dots exhibiting strong exciton quantum confinement. High-yield production of 2−3 nm diameter particles is reported. Band edge absorption and emission is observed near 4.1 eVmore than 600 meV above the bulk band gap energy of GaN.
Bidirectional effects of opioids in motivational processes and the involvement of D1 dopamine receptors. (1988)

Exogenous and endogenous opioids significantly affect motivational processes; depending on the particular opioid receptor type with which they interact opposite effects are induced: activation of mu and delta opioid receptors is rewarding whereas activation of kappa opioid receptors induces aversive effects. Antagonism of mu-opioid receptors also induces aversion, suggesting the existence of a tonically active opioidergic reward pathway. There is evidence that beta-endorphin pathways arising from the hypothalamus play an important role in this respect. Opioid-induced reward as well as aversion seem to be mediated by the mesolimbic dopamine system, reward by increased, aversion by decreased transmission at D1 dopamine receptors.