gebhart/patrepeval huggingface dataset:
Role of intracerebroventricular vasopressin in the development of stress-induced gastric lesions in rats. (1999)

We investigated whether arginine vasopressin (AVP) has a central influence on the development of gastric mucosal lesions evoked by restraint-cold stress in rats. AVP and vasopressin V1 receptor antagonist were injected intracerebroventricularly (i.c.v.) and the rats were exposed to restraint-cold stress for five hours. After decapitation the stomachs were examined for gastric mucosal lesions which were evaluated according to an ulcer score. Three different doses of AVP and V1 receptor antagonist were administered in order to investigate the effects of exogenous and endogenous AVP on stress-induced gastric mucosal lesions. The intensity of gastric mucosal lesions was reduced when exogenous AVP was injected intracerebroventricularly. On the other hand, vasopressin V1 receptor antagonist, which was administered by the same route, augmented gastric mucosal lesions. Our findings indicate that AVP, injected centrally, plays a role in preventing the formation of gastric mucosal lesions induced by stress via a central V1 receptor.
Alphavirus replicon vaccines (2012)

The alphavirus replicon technology has been utilized for many years to develop vaccines for both veterinary and human applications. Many developments have been made to the replicon platform recently, resulting in improved safety and efficacy of replicon particle (RP) vaccines. This review provides a broad overview of the replicon technology and safety features of the system and discusses the current literature on RP and replicon-based vaccines.
Enhancing silhouette-based human motion capture with 3D motion fields (2004)

High-quality nonintrusive human motion capture is necessary for acquisition of model-based free-viewpoint video of human actors. Silhouette-based approaches have demonstrated that they are able to accurately recover a large range of human motion from multiview video. However, they fail to make use of all available information, specifically that of texture information. This paper presents an algorithm that uses motion fields constructed from optical flow in multiview video sequences. The use of motion fields augments the silhouette-based method by incorporating texture-information into the tracking process. The algorithm is a key-component in a larger free-viewpoint video system of human actors. Our results demonstrate that our method accurately estimates pose parameters and allows for realistic texture generation in 3D video sequences.
Human-Specific Integrations of the HERV-K Endogenous Retrovirus Family (1998)

Several distinct families of endogenous retrovirus-like sequences (HERVs) exist in the genomes of humans and other primates. One of these families, the HERV-K group, contains members that encode functional proteins and that have been implicated in the etiology of insulin-dependent diabetes mellitus (IDDM). Because of potential functional and disease relevance, it is important to determine if there are HERV-K-associated genetic differences between individuals. In this study, we have investigated the divergence and evolutionary age of HERV-K long terminal repeats (LTRs). Thirty-seven LTRs, taken primarily from random human clones in GenBank, were aligned and grouped into nine clusters with decreasing sequence divergence. Cluster 1 sequences are 8.6% divergent, on average, whereas cluster 9 LTRs, represented by the LTRs of the fully sequenced HERV-K10 clone, show an average of only 1.1% divergence from each other. The evolutionary age of 18 LTRs from different clusters was then investigated by genomic PCR to determine presence or absence of the retroviral element in different primate species. LTRs from clusters of higher divergence were detected in monkeys and apes, whereas LTRs in clusters with lower divergence were acquired later in evolution. Notably, LTRs of cluster 9 were found only in humans at all nine loci examined. Genomic Southern analysis with an oligonucleotide probe specific for cluster 9 LTRs suggests that HERV-K elements with this type of LTR expanded independently in the genomes of humans and the great apes. This is the first report of endogenous retroviral integrations that are specific to humans and indicates that some HERVs have amplified much later than previously thought. These elements may still be actively transposing and may therefore represent a source of genetic variation linked to disease development.
Stage specific embryonic carbohydrate surface antigens of primordial germ cells in mouse embryos: FAL (S.S.E.A.-1) and globoside (S.S.E.A.-3). (1986)

Immunodetections of carbohydrate surface antigens were carried out for SSEA-1 and SSEA-3. Using alkaline phosphatase for the detection of primordial germ cells these surface antigens were detected at the cell membrane and the cytoplasm of the germ cells at E 10.
An unusual specificity in the activation of neutrophil serine proteinase zymogens (1990)

The majority of proteinases exist as zymogens whose activation usually results from a single proteolytic event. Two notable exceptions to this generalization are the serine proteinases neutrophil elastase (HNE) and cathepsin G (cat G), proteolytic enzymes of human neutrophils that are apparently fully active in their storage granules. On the basis of amino acid sequences inferred from the gene and cDNAs encoding these enzymes, it is likely that both are synthesized as precursors containing unusual C-terminal and N-terminal peptide extensions absent from the mature proteins. We have used biosynthetic radiolabeling and radiosequencing techniques to identify the kinetics of activation of both proteinases in the promonocyte-like cell line U937. We find that both N- and C-terminal extensions are removed about 90 min after the onset of synthesis, resulting in the activation of the proteinases. HNE and cat G are, therefore, transiently present as zymogens, presumably to protect the biosynthetic machinery of the cell from adventitious proteolysis. Activation results from cleavage following a glutamic acid residue to give an activation specificity opposite to those of almost all other serine proteinase zymogens, but shared, possibly, by the "granzyme" group of related serine proteinases present in the killer granules of cytotoxic T-lymphocytes and rat mast cell proteinase II.
Alterations in glyceride composition during interesterifi‐cation of mixtures of sunflower oil with lard and tallow (1977)

Abstract and Summary An analytical approach is presented for the study of one‐phase interesterification of mixtures of sun‐flowerseed oil with fully hydrogenated lard, natural lard, and tallow, based on triglyceride group analysis by argentation thin layer chromatography. The curves for the changes of each of ten triglyceride groups, differing in unsaturation, are reported. These are used to establish the conversion of the initial composition to the random limits in the mixtures cited. The altera‐tions in the differential dilatation curves are ex‐plained in part by the changes in the triglyceride com‐position.
Impact of blastomere biopsy and cryopreservation techniques on human embryo viability (1999)

The purpose of the present study was to evaluate the effect of cryopreservation on 55 embryos which had one blastomere biopsied for preimplantation genetic diagnosis of aneuploidy before freezing. The thawing outcome was compared to that obtained in 94 embryos which derived from our conventional freezing programme in patients with comparable characteristics who were treated in the same period. Their embryos were morphologically similar but the incidence of aneuploidy was 100% in the biopsy group and unknown in the controls. The percentage of embryos which survived intact after thawing was significantly lower in the biopsied group compared to the controls (9 versus 25% respectively; P < 0.025), whereas the rate of lysis was superior among biopsied embryos (34 versus 13% in the controls; P < 0.001). Similarly, the survival index was higher in the frozen-intact embryos than in the embryos which were frozen after biopsy (61 versus 38%; P < 0.001). No empty zonae resulted in the control group, while six were found after thawing biopsied embryos. In the second part of the study, blastomere biopsy was implemented on 102 thawed embryos generated by 16 patients. The chromosomal analyses revealed that 49 were normal, leading to the transfer of 2.5 +/- 0.8 embryos per patient. Only three clinical pregnancies were obtained, and are presently ongoing. In conclusion, the present findings discourage the use of conventional cryopreservation protocols in strategies involving preimplantation genetic diagnosis in human reproductive medicine. Adequate protocols are required for freezing and thawing embryos which have been subjected to biopsy procedures.
Detecting and Localizing Wireless Spoofing Attacks (2007)

Wireless networks are vulnerable to spoofing attacks, which allows for many other forms of attacks on the networks. Although the identity of a node can be verified through cryptographic authentication, authentication is not always possible because it requires key management and additional infrastructural overhead. In this paper we propose a method for both detecting spoofing attacks, as well as locating the positions of adversaries performing the attacks. We first propose an attack detector for wireless spoofing that utilizes K-means cluster analysis. Next, we describe how we integrated our attack detector into a realtime indoor localization system, which is also capable of localizing the positions of the attackers. We then show that the positions of the attackers can be localized using either area-based or point-based localization algorithms with the same relative errors as in the normal case. We have evaluated our methods through experimentation using both an 802.11 (WiFi) network as well as an 802.15.4 (ZigBee) network. Our results show that it is possible to detect wireless spoofing with both a high detection rate and a low false positive rate, thereby providing strong evidence of the effectiveness of the K-means spoofing detector as well as the attack localizer.
Identification and mapping of two polypeptides encoded within the herpes simplex virus type 1 thymidine kinase gene sequences (1981)

mRNA's homologous to the herpes simplex virus type 1 DNA restriction endonuclease fragment BamHI p, which contains the thymidine kinase gene, have been identified and mapped by hybrid-arrested translation and mRNA selection. Such mRNA's, when translated in vitro, directed the synthesis of polypeptides of apparent molecular weights 43,000 (VI43) and 39,000 (VI39). mRNA for enzymatically active thymidine kinase was enriched by more than 20-fold after selection. Mapping was carried out with restriction endonuclease fragments of BamHI p, and locations of the 5' and 3' termini of VI43 mRNA were deduced. Analysis of nucleotide sequences around the 5' terminus revealed several consensus sequences commonly found at the start of eucaryotic mRNA's and which are presumably involved in initiation of transcription by RNA polymerase II. Translation of mRNA's for VI43, VI39, and the thymidine kinase enzyme was arrested only by a 1,170-base-pair region of BamHI p. Since this region is insufficient for adjacent genes, coding sequences for VI43 and VI39 must overlap; the possible relationship of these two polypeptides is discussed. A virus-induced product equivalent to VI39 was detected in infected cells.
The coefficient rate and equivalent bandwidth in source coding (2002)

By directly using the asymptotic equipartition property (AEP), we give a more physically meaningful explanation of the coefficient rate defined by Campbell (1960). The equivalent bandwidth explanation shows that the coefficient rate call be used as a measure of the number of significant coefficients in transform coding problems, and the AEP approach also implies the distribution of the significant coefficients, hence the code rate for the significance map, i.e., the side information, can be estimated. Similar ideas can also be used in embedded coding, where the coefficient rate approach is used to estimate the code rate for the side information in embedded coders.
Self-Aligned Nanolithography in a Nanogap (2009)

A self-aligned nanolithography approach is reported to form a nanoscale via hole in a nanogap. Field emission between two opposite electrodes of a nanogap is used to expose the polymer resist within the nanogap region. A via hole pattern forms in the nanogap area after the exposure process. The via hole pattern is obtained by ablating the polymer resists within the nanogap between two nanoelectrodes upon applying a certain bias voltage. The diameter of the via holes can be controlled to have comparable dimension to the nanogap width. Single or array of via holes have been demonstrated with variable diameters from 20 nm to over 100 nm. The self-aligned via nanoholes can be used to deposit functional nanostructures that are precisely aligned with the nanogap electrodes to form electrode-nanoisland-electrode tunneling junction devices. Electrical characterization of such devices shows typical tunneling characteristics at room temperature. These studies demonstrate a general pathway to making electrical contacts to individual nanostructures for functional nanodevice engineering.
Biofilm Formation as Microbial Development (2000)

Biofilms can be defined as communities of microorganisms attached to a surface. It is clear that microorganisms undergo profound changes during their transition from planktonic (free-swimming) organisms to cells that are part of a complex, surface-attached community. These changes are reflected in the new phenotypic characteristics developed by biofilm bacteria and occur in response to a variety of environmental signals. Recent genetic and molecular approaches used to study bacterial and fungal biofilms have identified genes and regulatory circuits important for initial cell-surface interactions, biofilm maturation, and the return of biofilm microorganisms to a planktonic mode of growth. Studies to date suggest that the planktonic-biofilm transition is a complex and highly regulated process. The results reviewed in this article indicate that the formation of biofilms serves as a new model system for the study of microbial development.
Assessment of Hyperphagia in Prader‐Willi Syndrome (2007)

The Hyperphagia Questionnaire is a robust tool for relating breakthroughs in the neurobiology of hyperphagia to in vivo food-seeking behavior and for examining the psychological and developmental correlates of hyperphagia in PWS. The Hyperphagia Questionnaire also offers a nuanced, real-life outcome measure for future clinical trials aimed at curbing the life-threatening drive for food in PWS.
<title>Wide-dynamic-range APS star tracker</title> (1996)

Design considerations and description of a CMOS Active Pixel image sensor (APS) star tracker are reported. APS technology has been thought of being most appropriate for guidance and navigation. However, making APS useful for future star tracker missions means a few challenges have to be overcome. A wider dynamic range is required, while fill factor ought to be high and simple geometry of the pixel active area is desired. These requirements are analyzed and tradeoff considerations are explained for a practical future celestial tracker. A 64 X 64 element CMOS APS array with individual pixel reset is described.
Chiron: Translating nanopore raw signal directly into nucleotide sequence using deep learning (2017)

ABSTRACT Sequencing by translocating DNA fragments through an array of nanopores is a rapidly maturing technology which offers faster and cheaper sequencing than other approaches. However, accurately deciphering the DNA sequence from the noisy and complex electrical signal is challenging. Here, we report Chiron, the first deep learning model to achieve end-to-end basecalling: directly translating the raw signal to DNA sequence without the error-prone segmentation step. Trained with only a small set of 4000 reads, we show that our model provides state-of-the-art basecalling accuracy even on previously unseen species. Chiron achieves basecalling speeds of over 2000 bases per second using desktop computer graphics processing units.
Molecular and immunological analysis of a fibronectin‐binding protein antigen secreted by Mycobacterium leprae (1992)

By screening a Mycobacterium leprae lambda gt11 genomic DNA library with leprosy-patient sera we have previously identified 50 recombinant clones that expressed novel M. leprae antigens (Sathish et al., 1990). In this study, we show by DNA sequencing and immunoblot analysis that three of these clones express a M. leprae homologue of the fibronectin-binding antigen 85 complex of mycobacteria. The complete gene was characterized and it encodes a 327-amino-acid polypeptide, consisting of a consensus signal sequence of 38 amino acids followed by a mature protein of 289 amino acids. This is the first sequence of a member of the M. leprae antigen 85 complex, and Southern blotting analysis indicated the presence of multiple genes of the 85 complex in the genome of M. leprae. The amino acid sequence displays 75-85% sequence identity with components of the antigen 85 complex from M. tuberculosis, M. bovis BCG and M. kansasii. Furthermore, antibodies to the antigen 85 complex of M. tuberculosis and M. bovis BCG reacted with two fusion proteins containing the amino acid regions 55-266 and 266-327 of the M. leprae protein. The M. leprae 30/31 kDa protein induces strong humoral and cellular responses, as judged by Western blot analysis with patient sera and proliferation of T cells derived from healthy individuals and leprosy patients. Amino acid regions 55-266 and 265-327 both were shown to bind to fibronectin, indicating the presence of at least two fibronectin-binding sites on the M. leprae protein. These data indicate that this 30/31 kDa protein is not only important in the immune response against M. leprae, but may also have a biological role in the interaction of this bacillus with the human host.
Major Histocompatibility Complex Class I–Recognizing Receptors Are Disease Risk Genes in Rheumatoid Arthritis (2001)

Rheumatoid arthritis (RA) is a heterogeneous syndrome of which a subset of patients develops vascular inflammation. The genetic determinants that confer risk for rheumatoid vasculitis are not known, but patients with vascular complications are known to have an expansion of CD4(+)CD28(null) T cells, a cell population potentially involved in endothelial damage. CD4(+)CD28(null) T cell clones isolated from RA patients with vasculitis were found to express killer cell immunoglobulin-like receptors (KIRs) with the stimulatory KIR2DS2 often present in the absence of opposing inhibitory receptors with related specificities. To test the hypothesis that the KIR2DS2 gene is involved in the development of vasculitis, association studies were performed. The KIR2DS2 gene was significantly enriched among patients with rheumatoid vasculitis compared with normal individuals (odds ratio 5.56, P = 0.001) and patients with RA but no vasculitis (odds ratio 7.96, P = 0.001). Also, the distribution of human histocompatibility leukocyte antigen (HLA)-C, the putative ligand for KIRs, was significantly different in patients with rheumatoid vasculitis in comparison with the control populations. These data suggest that HLA class I-recognizing receptors and HLA class I genes are genetic risk determinants that modulate the pattern of RA expression. Specifically, KIR2DS2 in conjunction with the appropriate HLA-C ligand may have a role in vascular damage by regulating CD4(+)CD28(null) T cells.
Cloning, sequencing, and expression of a fibronectin/fibrinogen-binding protein from group A streptococci (1994)

Lipoteichoic acid and several streptococcal proteins have been reported to bind fibronectin (Fn) or fibrinogen (Fgn), which may serve as host receptors. We searched for such proteins by screening a library of genes from M type 5 group A streptococci cloned into Escherichia coli. Lysates of clones were probed with biotinylated Fn and biotinylated Fgn. One clone expressed a 54-kDa protein that reacted with Fn and Fgn. The protein, termed FBP54, was purified and used to immunize rabbits. Anti-FBP54 serum reacted with purified, recombinant FBP54 and with a protein of similar electrophoretic mobility in extracts of M type 5, 6, and 24 streptococci. Anti-FBP54 serum also reacted with 5 of 15 strains of intact, live streptococci, suggesting that FBP54 may be a surface antigen. Southern blot analysis confirmed that the gene is found in group A streptococci but not in Staphylococcus aureus or E. coli. The cloned gene was sequenced and contained an open reading frame encoding a protein with a calculated molecular weight of 54,186. Partial amino acid sequencing of purified FBP54 confirmed that this open reading frame encoded the protein. As determined by utilizing fusion proteins containing truncated forms of FBP54, the primary Fn/Fgn-binding domain appears to be contained in residues 1 to 89. These data suggest that FBP54 may be a surface protein of streptococci that reacts with both Fn and Fgn and therefore may participate in the adhesion of group A streptococci to host cells.
Synthesis of Peptides and Peptidomimetics (2003)

It is now over 100 years since the first report of peptide synthesis by Emil Fischer in 1899. Houben-Weyl Synthesis of Peptides and Peptidomimetics, published in the English language, will reflect the current changes of this important discipline, which is at the center of modern chemistry and biology. The four-volume set, edited by the internationally renowned peptide chemists Professors Murray Goodman, Arthur Felix, Luis Moroder, and Claudio Toniolo will comprise a critical selection of synthetic methods in a consistent style. Synthesis of Peptides includes protecting groups, peptide bond formation, the synthesis of peptides and proteins detailing general and specific methods, and analytical techniques used to determine the structure and composition of peptides. Synthesis of Peptidomimetics features side and/or main chain modified peptides, peptides with secondary structure mimetics and inducers, de novo peptide structures, macropeptide structures and reactive peptides. Synthesis of Peptides and Peptidomimetics will be indispensable for every synthetic chemist.