gebhart/patrepeval huggingface dataset:
Cross-Genotype Immunity to Hepatitis C Virus (2004)

Recent studies in humans and chimpanzees suggest that immunity can be induced to diminish the incidence of chronic hepatitis C virus (HCV) infection. However, the immunity that promotes viral recovery is poorly understood, and whether the breadth of this adaptive immunity is sufficient to overcome the substantial intergenotype antigenic diversity represents a final obstacle to demonstrating the feasibility of vaccine development. Here we demonstrate that recovery from a genotype 1 HCV infection protects chimpanzees against infection with representatives of other genotypes that exhibit up to 30% divergence at the amino acid level, including challenges with genotype 4, a mixture of genotypes 2 and 3, and a complex inoculum containing genotypes 1, 2, 3, and 4. In each instance, the level and duration of viremia were markedly reduced in comparison to the primary infection in the same animal. The data indicate that epitopes conserved between genotypes must play an essential role in immunity. The inocula used in the rechallenge studies induced typical primary infection profiles in naïve chimpanzees. Rechallenge infections were associated with rapid increases in the intrahepatic transcripts of interferon-stimulated genes, even in animals exhibiting apparent sterilizing immunity. Protective immunity was often associated with an early increase in gamma interferon transcripts in the liver and increases in intrahepatic transcripts of Mig, a T-cell chemokine that is a gamma interferon response gene. These studies are the first to show that cross-genotype immunity can be induced to HCV, demonstrating the feasibility of developing a vaccine protective against all HCV strains.
Static locality analysis for cache management (1997)

Most memory references in numerical codes correspond to array references whose indices are affine functions of surrounding loop indices. These array references follow a regular predictable memory pattern that can be analyzed at compile time. This analysis can provide valuable information like the locality exhibited by the program, which can be used to implement a more intelligent caching strategy. In this paper we propose a static locality analysis oriented to the management of data caches. We show that previous proposals on locality analysis are not appropriate when the programs have a high conflict miss ratio. This paper extends those proposals by introducing a compile time interference analysis that significantly improve the performance of them. We first show how this analysis can be used to characterize the dynamic locality properties of numerical codes. This evaluation show for instance that a large percentage of references exhibit only temporal locality and another significant percentage does not exhibit any type of locality. This motivates the use of a dual data cache, which has a module specialized to exploit temporal locality, and a selective cache respectively. Then, the performance provided by these two cache organizations is evaluated. In both organizations, the static locality analysis is responsible for tagging each memory instruction accordingly to the particular type(s) of locality that it exhibits.
An Efficient Camera Calibration Technique Offering Robustness and Accuracy Over a Wide Range of Lens Distortion (2011)

In the field of machine vision, camera calibration refers to the experimental determination of a set of parameters that describe the image formation process for a given analytical model of the machine vision system. Researchers working with low-cost digital cameras and off-the-shelf lenses generally favor camera calibration techniques that do not rely on specialized optical equipment, modifications to the hardware, or an a priori knowledge of the vision system. Most of the commonly used calibration techniques are based on the observation of a single 3-D target or multiple planar (2-D) targets with a large number of control points. This paper presents a novel calibration technique that offers improved accuracy, robustness, and efficiency over a wide range of lens distortion. This technique operates by minimizing the error between the reconstructed image points and their experimentally determined counterparts in "distortion free" space. This facilitates the incorporation of the exact lens distortion model. In addition, expressing spatial orientation in terms of unit quaternions greatly enhances the proposed calibration solution by formulating a minimally redundant system of equations that is free of singularities. Extensive performance benchmarking consisting of both computer simulation and experiments confirmed higher accuracy in calibration regardless of the amount of lens distortion present in the optics of the camera. This paper also experimentally confirmed that a comprehensive lens distortion model including higher order radial and tangential distortion terms improves calibration accuracy.
CYBERMAP (1991)

dynamic linking and automatic link generation into the automatic generation of an overview map we get a unique tool for navigation in hyperspace. We introduce the concept of HYPERDRAWERS to get a means for the partitioning of nodes in ordered sequences. CYBERMAP either complements existing navigational aids for hyperdocuments or provides a self sufficient navigation tool for browsing in a document. In addition CYBERMAP offers the capability of horizontal growth and easy hypertextualization of non-hypertextual documents without restricting the use of already installed browsing mechanisms besides CYBERMAP.
[Association study between NPY and YWHAH gene polymorphisms and schizophrenia]. (2005)

A case-control study was carried out on a sample of 583 cases vs. 372 controls in the Chinese Han population, investigating several published polymorphisms in the YWHAH and NPY genes, which reported to be associated with schizophrenia. The polymorphism -134 (GCCTGCA)2-4, in the YWHAH was not analyzed for the failure of amplification, and the polymorphism T1128C in the NPY is not existent in the samples. The analysis was then emphasized on the variants -485C > T(NPY) and G753A(YWHAH). However, no significant differences of allele frequencies (with P values of 0.696 and 0.743, OR values of 1.041 and 0.962 respectively) or genotype frequencies (with P value of 0.45 and 0.75, chi2 = 1.51 and 0.58 respectively) among the matched groups were found. No sex-dependent effect was found either. Also,the analysis of the relative risk between the genotypes of the two genes indicates that the two genes could not cooperate with each other to add the risk of disease (P > 0.05). The results suggest that the polymorphisms - 485C > T (NPY) and G753A (YWHAH) are unlikely to be linked with genetic susceptibility to schizophrenia in the Chinese Han population.
β‐Hairpin folding and stability: molecular dynamics simulations of designed peptides in aqueous solution (2004)

The structural properties of a 10-residue and a 15-residue peptide in aqueous solution were investigated by molecular dynamics simulation. The two designed peptides, SYINSDGTWT and SESYINSDGTWTVTE, had been studied previously by NMR at 278 K and the resulting model structures were classified as 3:5 beta-hairpins with a type I + G1 beta-bulge turn. In simulations at 278 K, starting from the NMR model structure, the 3:5 beta-hairpin conformers proved to be stable over the time period evaluated (30 ns). Starting from an extended conformation, simulations of the decapeptide at 278 K, 323 K and 353 K were also performed to study folding. Over the relatively short time scales explored (30 ns at 278 K and 323 K, 56 ns at 353 K), folding to the 3:5 beta-hairpin could only be observed at 353 K. At this temperature, the collapse to beta-hairpin-like conformations is very fast. The conformational space accessible to the peptide is entirely dominated by loop structures with different degrees of beta-hairpin character. The transitions between different types of ordered loops and beta-hairpins occur through two unstructured loop conformations stabilized by a single side-chain interaction between Tyr2 and Trp9, which facilitates the changes of the hydrogen-bond register. In agreement with previous experimental results, beta-hairpin formation is initially driven by the bending propensity of the turn segment. Nevertheless, the fine organization of the turn region appears to be a late event in the folding process.
Complete Khoisan and Bantu genomes from southern Africa (2010)

The genetic structure of the indigenous hunter-gatherer peoples of southern Africa, the oldest known lineage of modern human, is important for understanding human diversity. Studies based on mitochondrial and small sets of nuclear markers have shown that these hunter-gatherers, known as Khoisan, San, or Bushmen, are genetically divergent from other humans. However, until now, fully sequenced human genomes have been limited to recently diverged populations. Here we present the complete genome sequences of an indigenous hunter-gatherer from the Kalahari Desert and a Bantu from southern Africa, as well as protein-coding regions from an additional three hunter-gatherers from disparate regions of the Kalahari. We characterize the extent of whole-genome and exome diversity among the five men, reporting 1.3 million novel DNA differences genome-wide, including 13,146 novel amino acid variants. In terms of nucleotide substitutions, the Bushmen seem to be, on average, more different from each other than, for example, a European and an Asian. Observed genomic differences between the hunter-gatherers and others may help to pinpoint genetic adaptations to an agricultural lifestyle. Adding the described variants to current databases will facilitate inclusion of southern Africans in medical research efforts, particularly when family and medical histories can be correlated with genome-wide data.
Desorption Electrospray Ionization Mass Spectrometry Analysis of Lipids after Two-Dimensional High-Performance Thin-Layer Chromatography Partial Separation (2010)

Molecular imaging of separate but still incompletely resolved spots on high-performance thin-layer chromatography (HPTLC) plates is used for the direct analysis of porcine brain lipids by desorption electrospray ionization mass spectrometry (DESI-MS). Eight class-specific spots were imaged in the negative ion mode and shown to contain more than fifty lipids. A low lateral resolution of 400 x 400 microm allowed simple, rapid, and incomplete separation to be combined with DESI imaging for the identification of many components of these extremely complex mixtures. In this work, tandem mass spectrometry (MS/MS) was also employed to confirm the identity of particular lipids directly on HPTLC plates.
Activation of glycogen synthase kinase 3 beta (GSK‐3β) by platelet activating factor mediates migration and cell death in cerebellar granule neurons (2001)

Children with vertically acquired HIV-1 can present with a rapidly progressive encephalopathy and neuronal apoptosis in the first 12-18 months of life. Furthermore, abnormal prenatal platelet activating factor (PAF) signalling may result in lissencephaly, a disorder of neuronal migration. PAF, produced from human immunodeficiency virus type 1 (HIV-1) -infected brain-resident macrophages, induces neuronal apoptosis in cultured cerebellar granule neurons (CGNs) in part by activating glycogen synthase kinase 3 beta (GSK-3beta). However, PAF can also inhibit migration of CGNs that are dispersed and allowed to reaggregate. Therefore, we investigated the biological effects following activation of GSK-3beta by PAF, and whether these effects were dependent on the culture conditions of the CGNs. We show here that activation of neuronal GSK-3beta by PAF is receptor-specific, with similar kinetics of activation in both monolayer cultures of CGNs that have ceased to migrate and reaggregate cultures of CGNs that are actively migrating. However, PAF receptor activation in reaggregated CGNs inhibits neuronal migration and induces approximately half the level of neuronal apoptosis compared with PAF-treated CGN cultures that have ceased to migrate. PAF-mediated inhibition of neuronal migration in reaggregated CGNs or induction of apoptosis in CGNs that have ceased to migrate can be reversed by either PAF receptor antagonists, or the GSK-3beta inhibitors lithium or valproic acid, in a dose-dependent manner. Abnormal PAF signalling that results in GSK-3beta overactivation may represent a common mechanism for pathological defects in neuronal migration in the prenatal period and neuronal apoptosis in the postnatal period.
Electrochemical Properties of Organic Liquid Electrolytes Based on Quaternary Onium Salts for Electrical Double‐Layer Capacitors (1994)

The electrolytic conductivities and limiting reduction and oxidation potentials for various organic liquid electrolytes based on quaternary onium salts have been measured to find better electrolytes for electrical double‐layer capacitors. An electrolyte composed of tetraethylammonium cation, tetrafluoroborate anion, and propylene carbonate solvent showed well‐balanced performance of high electrolytic conductivity, a wide stable potential window and resistance to hydrolysis. Among quaternary onium salts, triethylmethylammonium, ethylmethylpyrrolidinium, and tetramethylenepyrrolidinium tetrafluoroborate salts exhibited higher electrolytic conductivity than the conventional tetraethylammonium salt due to their much greater solubility.
Ordering Genes in a Flagella Pathway by Analysis of Expression Kinetics from Living Bacteria (2001)

The recent advances in large-scale monitoring of gene expression raise the challenge of mapping systems on the basis of kinetic expression data in living cells. To address this, we measured promoter activity in the flagellar system of Escherichia coli at high accuracy and temporal resolution by means of reporter plasmids. The genes in the pathway were ordered by analysis algorithms without dependence on mutant strains. The observed temporal program of transcription was much more detailed than was previously thought and was associated with multiple steps of flagella assembly.
Sequence-specific double-strand cleavage of DNA by bis(EDTA-distamycin.iron(II)) and EDTA-bis(distamycin).iron(II) (1983)

We report the synthesis of two sequence-specific double-strand&#13;\nDNA cleaving molecules, bis(EDTA-distamycin·Fe^(II) (BED·Fe^(II))&#13;\nand EDTA-bis(distamycin)·Fe^(II) (EBD·Fe^(II)) (Chart 1). These molecules contain two N-methylpyrrole tripeptide units coupled at the amino termini via a flexible tether with EDTA attached to one or both carboxy termini. In the presence of O_2 and dithiothreitol (DTT), nanomolar concentrations of BED·Fe^(II) and EBD·Fe^(II) cleave DNA (25 °C, pH 7.9). BED·Fe^(II) and EBD·Fe^(II) cleave pBR 322 plasmid DNA (4362 base pairs) on opposite strands to afford discrete DNA fragments. High-resolution gel electrophoresis of an end-labeled restriction fragment containing a major binding site reveals cleavage contiguous to an eight base pair sequence 5'-TTTTTATA-3'.
Studies on linkage and association of atopy with the chromosomal region 12q13–24 (2000)

We conclude from our data that genes in the chromosomal region 12q13-24 and in particular SCF are unlikely to exert a major effect on the induction of the atopic phenotype in our Caucasian population. However, we did not focus on the asthmatic and thereby inflammatory aspect of atopy which might explain these results in contradiction to previous studies.
A comparison of the effects on follicular development between clomiphene citrate, its two separate isomers and spontaneous cycles (1989)

An investigation of the effects on follicular development of clomiphene citrate and its two isomers En clomiphene and Zu clomiphene given separately was carried out on 19 normally cycling women being treated with donor insemination. All women received clomiphene citrate in the first cycle and, following a washout control cycle, were treated with either En clomiphene or Zu clomiphene alone. The number of follicles present, follicular phase oestrogen secretion and luteal phase pregnanediol excretion were not significantly different when Zu clomiphene cycles were compared with control cycles, but were significantly increased in En clomiphene and clomiphene citrate cycles. It is concluded that the En isomer, which has largely antioestrogenic properties, is the isomer active in inducing follicular development. The oestrogenic properties of Zu isomer did not appear to protect it from the possibly detrimental effects on sperm-cervical mucus interaction observed in both isomers and in the combined preparation.
The ftsH gene of Bacillus subtilis is transiently induced after osmotic and temperature upshift (1995)

The ftsH gene of Bacillus subtilis has been identified as a salt-sensitive insertion mutation in strain UG1. Here, we show that UG1 has an insertion near the 3' end of ftsH. The salt sensitivity of this mutant was caused by reduction of ftsH mRNA levels by the synthesis of an artificial antisense RNA originating at a promoter located within the insertion and reading backwards into the ftsH gene. The salt-sensitive phenotype could be overcome by deleting the promoter from which the antisense RNA was transcribed. A physiological analysis of the isogenic wild-type strain in minimal medium revealed unimpaired growth at up to 1 M NaCl, and growth above 1.2 M NaCl was observed only after addition of the osmoprotectant proline or glycine betaine. In contrast, growth of strain UG1 was reduced at a salt concentration above 0.2 M, which could be rescued by the two compatible solutes already mentioned and also by trehalose. Primer extension revealed one potential transcription start site downstream of a putative vegetative promoter, which was activated after osmotic or temperature upshift. Northern (RNA blot) experiments led to the detection of a 2.1-kb transcript, suggesting that ftsH is monocistronic. A transcriptional fusion between ftsH and the gus reporter gene exhibited a twofold increase in beta-glucuronidase activity after osmotic upshift. To further confirm the need for an enhanced level of FtsH protein after osmotic upshift, the promoter was replaced by the sucrose-inducible promoter PsacB. Whereas this mutant strain could grow in the absence of inducer in LB medium, it stopped growth immediately after addition of 1.1 M NaCl. We conclude that an increased amount of FtsH protein is essential for B. subtilis to cope with an increase in osmolarity or temperature.
Identification, cloning, and sequencing of the immunoglobulin A1 protease gene of Streptococcus pneumoniae (1996)

The pneumococcus expresses a protease that hydrolyzes human immunoglobulin A1 (IgA1). A gene for IgA1 protease was identified from a plasmid library of pneumococcal DNA because of the effect of its overexpression on the colony morphology of Streptococcus pneumoniae. The deduced 1,964-amino-acid sequence is highly homologous to that of the IgA1 protease from Streptococcus sanguis. The similarity to the S. sanguis enzyme and the presence of a putative zinc-binding site suggest that the pneumococcal enzyme is a metalloprotease. The two streptococcal sequences differ in a hydrophilic region with 10 tandem repeats of a 20-mer in S. sanguis, which is replaced by a similar but less repetitive sequence in S. pneumoniae. Antiserum reactive with the pneumococcal IgA1 protease was used to demonstrate that the majority of the protein is cell associated. The expression and function of this gene were confirmed by insertional mutagenesis. Interruption of the chromosomal gene resulted in loss of expression of an approximately 200-kDa protein and complete elimination of detectable IgA1 protease activity.
Osmium Tetroxide-Promoted Catalytic Oxidative Cleavage of Olefins:  An Organometallic Ozonolysis (2002)

A mild, organometallic alternative to ozonolysis utilizing oxone and OsO(4) is presented. This is a direct oxidation of olefins via the carbon-carbon cleavage of an osmate ester by the action of oxone. Twenty-four different olefins were converted to their corresponding ketones or carboxylic acids in high yields (>80%). Free alcohols, acetate- and benzyl-protected alcohols, and 1,2-diols were stable under these conditions. This method should be applicable for traditional organic synthesis.
A Mutation in the mip Gene Results in an Attenuation of Legionella pneumophila Virulence (1990)

Infection by Legionella pneumophila is believed to depend upon its ability to multiply within host alveolar macrophages. To investigate this, a site-specific mutation was introduced into a gene (mip) that encodes a 24,000-Da surface protein; an 80-fold loss of infectivity for both U937 cells and explanted human alveolar macrophages was observed. Further phenotypic analysis of the mutant strain has failed to show alterations in bacterial factors (e.g., proteinase, lipopolysaccharide) that have suspected roles in virulence. To substantiate that this mutation also results in reduced virulence in animals, the lethality and clinical illnesses produced by the parent and mutant L. pneumophila strains were compared in guinea pigs after intratracheal inoculation. The mutant strain produced fewer illnesses, slower-progressing disease, and fewer lethal infections than either the parent strain or a derivative of the mutant strain with the wild-type mip gene reintroduced. When sublethal inocula of the three strains were used, the mutant bacteria were recovered in slightly lower numbers from lung homogenates and in significantly lower numbers from the spleen, at 48 h, than were the other two test strains. Thus mip seems to be necessary for full virulence of L. pneumophila and may represent the first genetically defined virulence factor in this species.
Adipose Tissue-Derived Mesenchymal Stem Cells Acquire Bone Cell-Like Responsiveness to Fluid Shear Stress on Osteogenic Stimulation (2005)

To engineer bone tissue, mechanosensitive cells are needed that are able to perform bone cell-specific functions, such as (re)modeling of bone tissue. In vivo, local bone mass and architecture are affected by mechanical loading, which is thought to provoke a cellular response via loading-induced flow of interstitial fluid. Adipose tissue is an easily accessible source of mesenchymal stem cells for bone tissue engineering, and is available in abundant amounts compared with bone marrow. We studied whether adipose tissue-derived mesenchymal stem cells (AT-MSCs) are responsive to mechanical loading by pulsating fluid flow (PFF) on osteogenic stimulation in vitro. We found that ATMSCs show a bone cell-like response to fluid shear stress as a result of PFF after the stimulation of osteogenic differentiation by 1,25-dihydroxyvitamin D3. PFF increased nitric oxide production, as well as upregulated cyclooxygenase-2, but not cyclooxygenase-1, gene expression in osteogenically stimulated AT-MSCs. These data suggest that AT-MSCs acquire bone cell-like responsiveness to pulsating fluid shear stress on 1,25-dihydroxyvitamin D3-induced osteogenic differentiation. ATMSCs might be able to perform bone cell-specific functions during bone (re)modeling in vivo and, therefore, provide a promising new tool for bone tissue engineering.