gebhart/patrepeval huggingface dataset:
Review (1994)

Ubiquitin modification of many protein targets within cells plays important roles in a variety of biological processes. Among these are regulation of gene expression, regulation of cell cycle and division, involvement in the cellular stress response, modification of cell surface receptors, DNA repair, import of proteins into mitochondria, uptake of precursors of neurotransmitters into synaptosomes, biogenesis of peroxisomes, assembly of ribosomes, and programmed cell death. The mechanisms that underlie these complex processes are poorly understood. The best studied modification occurs in the ubiquitin-mediated proteolytic pathway. Recent experimental evidence indicates that the ubiquitin system is involved in the degradation of mitotic cyclins, oncoproteins and tumor suppressors, in the removal of abnormal and otherwise damaged proteins, and in processing of antigens restricted to class I MHC molecules. Degradation of a protein via the ubiquitin system involves two discrete steps. Initially, multiple ubiquitin molecules are covalently linked in an ATP-dependent mode to the protein substrate. The targeted protein is then degraded by a specific, energy-dependent and high molecular mass protease complex into peptides and free amino acids, and free and reutilizable ubiquitin is released. In addition, stable mono-ubiquitin adducts are also found in the cell, for example, those involving nucleosomal histones. Despite the considerable progress that has been made in elucidating the mode of action and roles of the ubiquitin system, many problems remain unsolved. For example, little is known on the signals that target proteins for degradation. While a few proteins are targeted for degradation following recognition of their N-terminal amino acid residue, the vast majority of cellular proteins are targeted by other signals. The identity of the native cellular substrates of the system is another important, yet unresolved problem: only a few proteins have been recognized so far as substrates of the system in vivo. The scope of this review is to discuss the mechanisms involved in ubiquitin activation, selection of substrates for conjugation, and degradation of ubiquitin-conjugated proteins in the cell-free system. In addition, we shall summarize what is currently known of the physiological roles of ubiquitin-mediated proteolysis in vivo.
Absorption, Translocation, and Metabolism of Fluridone in Selected Crop Species (1978)

The uptake, translocation, and metabolism of the herbicide fluridone 1-methyl-3-phenyl-5-[3-(trifluoromethyl)phenyl]-4(1 H) -pyridinone was studied in cotton (Gossypium hirsutum L. ‘Stoneville 213’) (fluridone tolerant) and corn (Zea mays L. ‘Migro 5040’), soybean [ Glycine max (L.) Merr. ‘Calland’], and rice (Oryza sativa L. ‘Nato’) (fluridone susceptible). Uptake studies with 14 C fluridone demonstrated that all species absorbed radioactivity with rice having the highest concentration. Equivalent concentrations of radioactivity were observed in corn, cotton, and soybean. Absorbed fluridone was retained primarily in the roots and the basal region of the stem of cotton, while in the herbicide susceptible species fluridone was readily translocated into the shoots. No appreciable metabolism of fluridone was observed in the roots or shoots of cotton and soybean. Tolerance of cotton to fluridone was primarily attributed to the limited translocation of the compound.
Programmed Cell Death duringXenopusDevelopment: A Spatio-temporal Analysis (1998)

Programmed cell death (PCD) is an integral part of many developmental processes. In vertebrates little is yet known on the patterns of PCD and its role during the early phases of development, when embryonic tissue layers migrate and pattern formation takes place. We describe the spatio-temporal patterns of cell death during early Xenopus development, from fertilization to the tadpole stage (stage 35/36). Cell death was analyzed by a whole-mount in situ DNA end-labeling technique (the TUNEL protocol), as well as by serial sections of paraffin-embedded TUNEL-stained embryos. The first cell death was detected during gastrulation, and as development progressed followed highly dynamic and reproducible patterns, strongly suggesting it is an important component of development at these stages. The detection of PCD during neural induction, neural plate patterning, and later during the development of the nervous system highlights the role of PCD throughout neurogenesis. Additionally, high levels of cell death were detected in the developing tail and sensory organs. This is the first detailed description of PCD throughout early development of a vertebrate, and provides the basis for further studies on its role in the patterning and morphogenesis of the embryo.
Expression of adhesion molecule CD44 on human corneas (1997)

These results suggest that CD44, the hyaluronate receptor, may play an important role in corneal cell-cell and cell-matrix interactions. Its regulation is closely related to corneal inflammatory reactions. The induction of CD44 on corneal endothelium might play a potential role in compensatory processes when corneal endothelial cells are injured.
β-Casein Adsorption at the Silicon Oxide−Aqueous Solution Interface (2001)

Neutron reflectometry was used to investigate the time-dependent beta-casein adsorption at the silica-aqueous solution interface. The transient and steady-state structural characteristics of the adsorbed layer were determined from reflectivity curves, fitted to three-layer and two-layer models. The results show that the beta-casein adsorption to silica is very slow. The adsorption process involves the formation of an inner dense protein layer with a mean thickness of about 30 A onto which a more hydrated outer layer is self-associated. The surface excess and the total layer thickness of the asymmetric bilayer were, after 5 h adsorption time, estimated to be about 6.5 mg/m2 and 105 A, respectively. The adsorption behavior observed on silica contrasts with that previously reported for hydrophobic substrates, where beta-casein adsorption is much more rapid and the final surface excess is less than half of that observed for silica. Rinsing the silica surface with protein-free buffer resulted in a substantial desorption; much more pronounced than observed for hydrophobic substrates. This behavior suggests a weak adsorption affinity for a fraction of the adsorbed casein molecules; most likely the outer self-associated casein molecules in the adsorbed bilayer. The comparative desorption from hydrophobic surfaces was shown to be marginal. The difference between the layer structures adopted on hydrophobic and hydrophilic surfaces is also mirrored in the effects that the addition of a specific proteolytic enzyme (endoproteinase Asp-N) has on the adsorbed layer properties. The rinsing and endoproteinase cleavage processes result together in more than 80% reduction of the originally adsorbed mass at the silica surface. Only a thin but dense adsorbed layer remains after these treatments. The corresponding reduction reported for the hydrophobic adsorbent system was only about 20%. It is concluded that beta-casein adsorption on silica results in the formation of an asymmetric surface bound bilayer that stands in strong contrast to the monolayer structure formed at hydrophobic surfaces. This finding support the previous results obtained by using ellipsometry. The study also shows that neutron reflection, despite its limitations in time resolution, can be used for studying dynamic interfacial phenomena in protein systems.
Enhanced Expression of Interleukin-6 in Primary Human Renal Cell Carcinomas (1991)

We have demonstrated interleukin-6 (IL-6) production by human renal carcinoma cells. The IL-6 gene expression was detected by Northern blot analysis in 22 of 43 primary renal cell carcinoma tissues and in five of seven renal cell carcinoma cell lines. Immunohistochemical analysis confirmed the expression of IL-6 by the tumor cells. Patients with a high-level expression of IL-6 had significantly greater incidences of lymph node metastasis and a larger increase in serum C-reactive protein than those without it. We have also probed for the presence of IL-6 receptor by Northern blot analysis; we detected this receptor in 11 of the 43 primary renal cell carcinoma tissues but in none of the seven renal cell carcinoma cell lines. However, by use of the complementary DNA-polymerase chain reaction, the IL-6 receptor transcript was detected in all specimens, including the seven cell lines. No expression of the interleukin-3 (IL-3) gene was identified in any of the 43 primary renal cell tumors. These data provide evidence that IL-6 and its receptor may play a role in promoting the transformation and/or proliferation of renal cell carcinomas as well as in teh development of symptoms.
Placental peptides as markers of gestational disease (2002)

The human placenta produces a wide range of important peptides, of which an intricate balance is required throughout pregnancy. In a gestational disease, this balance may be disturbed and the identification of such changes may be used to detect a particular pathology or to ascertain its severity. This review considers the role and association of various placental peptide markers associated with the major gestational diseases including intrauterine growth retardation, pre-term labour, pre-eclampsia, chromosomal disorders, gestational diabetes and trophoblastic disease. Potential markers that may prove more reliable and specific in their diagnostic value and that may be used for identifying patients at risk are also discussed. The importance of the new fields of genomics and proteomics in the future discovery of new peptide markers is illustrated.
A study on replay attack and anti-spoofing for text-dependent speaker verification (2014)

Replay, which is to playback a pre-recorded speech sample, presents a genuine risk to automatic speaker verification technology. In this study, we evaluate the vulnerability of text-dependent speaker verification systems under the replay attack using a standard benchmarking database, and also propose an anti-spoofing technique to safeguard the speaker verification systems. The key idea of the spoofing detection technique is to decide whether the presented sample is matched to any previous stored speech samples based a similarity score. The experiments conducted on the RSR2015 database showed that the equal error rate (EER) and false acceptance rate (FAR) increased from both 2.92 % to 25.56 % and 78.36 % respectively as a result of the replay attack. It confirmed the vulnerability of speaker verification to replay attacks. On the other hand, our proposed spoofing countermeasure was able to reduce the FARs from 78.36 % and 73.14 % to 0.06 % and 0.0 % for male and female systems, respectively, in the face of replay spoofing. The experiments confirmed the effectiveness of the proposed anti-spoofing technique.
From Synapses to Circuitry: Using Memristive Memory to Explore the Electronic Brain (2011)

In a synchronous digital platform for building large cognitive models, memristive nanodevices form dense, resistive memories that can be placed close to conventional processing circuitry. Through adaptive transformations, the devices can interact with the world in real time.
Epstein-Barr virus–specific human T lymphocytes expressing antitumor chimeric T-cell receptors: potential for improved immunotherapy (2002)

Primary T cells expressing chimeric receptors specific for tumor or viral antigens have considerable therapeutic potential. Unfortunately, their clinical value is limited by their rapid loss of function and failure to expand in vivo, presumably due to the lack of costimulator molecules on tumor cells and the inherent limitations of signaling exclusively through the chimeric receptor. Epstein-Barr virus (EBV) infection of B lymphocytes is near universal in humans and stimulates high levels of EBV-specific helper and cytotoxic T cells, which persist indefinitely. Our clinical studies have shown that EBV-specific T cells generated in vitro will expand, persist, and function for more than 6 years in vivo. We now report that EBV-specific (but not primary) T cells transduced with tumor-specific chimeric receptor genes can be expanded and maintained long-term in the presence of EBV-infected B cells. They recognize EBV-infected targets through their conventional T-cell receptor and tumor targets through their chimeric receptors. They efficiently lyse both. EBV-specific T cells expressing chimeric antitumor receptors may represent a new source of effector cells that would persist and function long-term after their transfer to cancer patients.
Susceptibility of multidrug resistance tumor cells to apoptosis induction by histone deacetylase inhibitors (2003)

The main goal of our study has been to analyze the efficiency of new anticancer drugs, specifically histone deacetylase inhibitors, in tumor cells bearing a multidrug resistance phenotype. We report that the histone deacetylase inhibitors, Trichostatin A and Suberoylanilide Hydroxamic Acid (SAHA), dramatically reduce cell viability and promote apoptosis in different drug-resistant cells, affecting in a much lesser extent to their parental drug-sensitive counterparts. The differential effects induced by Trichostatin A and SAHA between drug-sensitive and drug-resistant cells are reflected on the main characteristics of the resistant phenotype. Thus, reverse transcription-PCR and Western immunoblots confirm that both histone deacetylase inhibitors promote endogenous down-regulation of P-glycoprotein, which is overexpressed in the drug-resistant cells. Transfection of drug-sensitive cells with the P-glycoprotein cDNA ruled out the a priori possible association between apoptosis and down-regulation of P-glycoprotein induced by the histone deacetylase inhibitors. The results suggest a therapeutic potential of histone deacetylase inhibitors in the treatment of cancers with acquired resistance.
Targeted disruption of G protein-coupled bile acid receptor 1 (Gpbar1/M-Bar) in mice (2006)

G protein-coupled bile acid receptor 1 (Gpbar1/M-Bar) is a novel G protein-coupled receptor for bile acid. Tissue distribution and cell-type specificity of Gpbar1 mRNA suggest a potential role for the receptor in the endocrine system; however, the precise physiological role of Gpbar1 still remains to be elucidated. To investigate the role of Gpbar1 in vivo, the Gpbar1 gene was disrupted in mice. In homozygous mice, total bile acid pool size was significantly decreased by 21-25% compared with that of the wild-type mice, suggesting that Gpbar1 contributes to bile acid homeostasis. In order to assess the impact of Gpbar1 deficiency in bile acid homeostasis more precisely, Gpbar1 homozygous mice were fed a high-fat diet for 2 months. As a result, female Gpbar1 homozygous mice showed significant fat accumulation with body weight gain compared with that of the wild-type mice. These findings were also observed in heterozygous mice to the same extent. Although the precise mechanism for fat accumulation in female Gpbar1 homozygous mice remains to be addressed, these data indicate that Gpbar1 is a potential new player in energy homeostasis. Thus, Gpbar1-deficient mice are useful in elucidating new physiological roles for Gpbar1.
Cyclical mobilization and gated importation of thymocyte progenitors in the adult mouse: evidence for a thymus‐bone marrow feedback loop (2006)

It has recently been observed, as in the fetal thymus, that the importation of hematogenous thymocyte progenitors by the adult thymus is a gated phenomenon, whereby saturating numbers of progenitors periodically enter the thymus and occupy a finite number of intrathymic niches. In addition, the mobilization of thymocyte progenitors from the bone marrow appears to be a cyclical process that coincides temporally with the periods of thymic receptivity (open gate). It is proposed that these events are coordinated by a thymus-bone marrow feedback loop in which a wave of developing triple negative (CD3- CD4- CD8-) thymocytes interacts with stromal cells in the stratified regions of the thymus cortex to sequentially induce the release of diffusible cytokines that regulate the production, mobilization, and recruitment of thymocyte progenitors. The likely components of this feedback loop are described here, as are the properties of the intrathymic vascular gates and niches for thymocyte progenitors. The cyclical production and release of thymocyte progenitors from the bone marrow is placed in the context of a general phenomenon of oscillatory feedback regulation involving all lymphohemopoietic cell lineages. Lastly, the question of whether the gated (as opposed to the continuous) entry of thymocyte progenitors is essential for normal thymocytopoiesis in adult life is discussed.
Asymmetric nucleophilic α-amino-acylation with metalated chiral amino nitriles: enantioselective synthesis of 3-substituted 5-amino-4-oxo-esters via asymmetric Michael addition (1999)

Highly stereoselective conjugate addition of an enantio-pure metalated β-amino substituted amino nitrile to α,β-unsaturated esters, with subsequent silver nitrate induced hydrolysis of the amino nitrile adducts affords 3-substituted 5-amino-4-oxo-esters with high enantiomeric purity, thus achieving the overall asymmetric Michael addition of an α-amino-acyl carbanion.
Impact of suppressive herpes therapy on genital HIV-1 RNA among women taking antiretroviral therapy: a randomized controlled trial (2006)

HSV-2 facilitates residual genital HIV-1 replication among dually infected women taking HAART despite HIV-1 suppression at the systemic level.
Killing of Caenorhabditis elegans by Pseudomonas aeruginosa used to model mammalian bacterial pathogenesis (1999)

We show that a single clinical isolate of the human opportunistic pathogen Pseudomonas aeruginosa (strain PA14), which previously was shown to be pathogenic in mice and plants, also kills Caenorhabditis elegans. The rate of PA14-mediated killing of C. elegans depends on the composition of the agar medium on which PA14 is grown. When PA14 is grown on minimal medium, killing occurs over the course of several days and is referred to as "slow" killing. When PA14 is grown on high-osmolarity medium, killing occurs over the course of several hours and is referred to as "fast" killing. Several lines of evidence, including the fact that heat-killed bacteria are still capable of fast but not slow killing of C. elegans, indicate that fast and slow killing occur by distinct mechanisms. Slow killing involves an infection-like process and correlates with the accumulation of PA14 within worm intestines. Among 10 PA14 virulence-related mutants that had been shown previously to affect pathogenicity in plants and mice, 6 were less effective in killing C. elegans under both fast- and slow-killing conditions, indicating a high degree of commonalty among the P. aeruginosa factors required for pathogenicity in disparate eukaryotic hosts. Thus, we show that a C. elegans pathogenicity model that is genetically tractable from the perspectives of both host and pathogen can be used to model mammalian bacterial pathogenesis.
The Role of Chemokines in the Microenvironmental Control of T versus B Cell Arrest in Peyer's Patch High Endothelial Venules (2000)

Chemokines have been hypothesized to contribute to the selectivity of lymphocyte trafficking not only as chemoattractants, but also by triggering integrin-dependent sticking (arrest) of circulating lymphocytes at venular sites of extravasation. We show that T cells roll on most Peyer's patch high endothelial venules (PP-HEVs), but preferentially arrest in segments displaying high levels of luminal secondary lymphoid tissue chemokine (SLC) (6Ckine, Exodus-2, thymus-derived chemotactic agent 4 [TCA-4]). This arrest is selectively inhibited by functional deletion (desensitization) of CC chemokine receptor 7 (CCR7), the receptor for SLC and for macrophage inflammatory protein (MIP)-3beta (EBV-induced molecule 1 ligand chemokine [ELC]), and does not occur in mutant DDD/1 mice that are deficient in these CCR7 ligands. In contrast, pertussis toxin-sensitive B cell sticking does not require SLC or MIP-3beta signaling, and occurs efficiently in SLC(low/-) HEV segments in wild-type mice, and in the SLC-negative HEVs of DDD/1 mice. Remarkably, sites of T and B cell firm adhesion are segregated in PPs, with HEVs supporting B cell accumulation concentrated in or near follicles, the target domain of most B cells entering PPs, whereas T cells preferentially accumulate in interfollicular HEVs. Our findings reveal a fundamental difference in signaling requirements for PP-HEV recognition by T and B cells, and describe an unexpected level of specialization of HEVs that may allow differential, segmental control of lymphocyte subset recruitment into functionally distinct lymphoid microenvironments in vivo.
Monoclonal antibodies and human sera directed to the secreted glycoprotein G of herpes simplex virus type 2 recognize type-specific antigenic determinants (2002)

Glycoprotein G-2 (gG-2) of herpes simplex virus type 2 (HSV-2) is cleaved to a secreted amino-terminal portion (sgG-2) and to a cell-associated carboxy-terminal portion which is further O-glycosylated to constitute the mature gG-2 (mgG-2). In contrast to mgG-2, which is known to elicit a type-specific antibody response in the human host, information on the immunogenic properties of sgG-2 is lacking. Here the sgG-2 protein was purified on a heparin column and used for production of monoclonal antibodies (mAbs). Four anti-sgG-2 mAbs were mapped using a Pepscan technique and identified linear epitopes which localized to the carboxy-terminal part of the protein. One additional anti-sgG-2 mAb, recognizing a non-linear epitope, was reactive to three discrete peptide stretches where the most carboxy-terminally located stretch was constituted by the amino acids (320)RRAL(323). Although sgG-2 is rapidly secreted into the cell-culture medium after infection, the anti-sgG-2 mAbs identified substantial amounts of sgG-2 in the cytoplasm of HSV-2-infected cells. All of the anti-sgG-2 mAbs were HSV-2 specific showing no cross-reactivity to HSV-1 antigen or to HSV-1-infected cells. Similarly, sera from 50 HSV-2 isolation positive patients were all reactive to sgG-2 in an enzyme immunoassay whilst no reactivity was seen in 25 sera from HSV-1 isolation positive patients or in 25 serum samples from HSV-negative patients suggesting that sgG-2 is a novel antigen potentially suitable for type-discriminating serodiagnosis.
Exploiting temporal parallelism for software-only video effects processing (1998)

Article Free Access Share on Exploiting temporal parallelism for software-only video effects processing Authors: Ketan Mayer-Patel View Profile , Lawrence A. Rowe View Profile Authors Info & Claims MULTIMEDIA '98: Proceedings of the sixth ACM international conference on MultimediaSeptember 1998Pages 161–169https://doi.org/10.1145/290747.290768Published:01 September 1998Publication History 11citation237DownloadsMetricsTotal Citations11Total Downloads237Last 12 Months8Last 6 weeks2 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF