gebhart/patrepeval huggingface dataset:
Cloning and characterization of GPD2, a second gene encoding sn‐glycerol 3‐phosphate dehydrogenase (NAD+) in Saccharomyces cerevisiae, and its comparison with GPD1 (1995)

We have cloned and characterized a homologue of the previously isolated GPD1 gene, encoding sn-glycerol 3-phosphate dehydrogenase (NAD+) in Saccharomyces cerevisiae. This second gene, called GPD2, encodes a protein of 384 amino acids that shares 69% sequence identity with GPD1. Like GPD1 it has an amino-terminal extension of unknown function. GPD2 is located on chromosome VII and cross-hybridizes with GPD1 at chromosome IV as well as with an unknown homologue at chromosome XV. Disruption of the GPD2 gene did not reveal any observable phenotypic effects, whereas overexpression resulted in a slight, but significant, increase of GPD enzyme activity in wild-type cells. Analysis of gene transcription by a CAT-reporter gene fused to the GPD promoters revealed decreased transcriptional activity of the GPD2 promoter in cells grown on nonfermentable as opposed to fermentable carbon sources, and no induction in cells exposed to high osmolarity or heat shock. Similar analysis of GPD1 demonstrated an 8-17-fold higher basal level of transcription compared to GPD2. Furthermore, such analysis revealed that the GPD1 promoter was induced by increased osmolarity essentially independent of the type of stress solute used, the level of GPD1 transcription being increased about sevenfold in cells growing at 1.4 M NaCl.
Starburst (2008)

Acquiring small targets on a tablet or touch screen can be challenging. To address the problem, researchers have proposed techniques that enlarge the effective size of targets by extending targets into adjacent screen space. When applied to targets organized in clusters, however, these techniques show little effect because there is no space to grow into. Unfortunately, target clusters are common in many popular applications. We present Starburst, a space partitioning algorithm that works for target clusters. Starburst identifies areas of available screen space, grows a line from each target into the available space, and then expands that line into a clickable surface. We present the basic algorithm and extensions. We then present 2 user studies in which Starburst led to a reduction in error rate by factors of 9 and 3 compared to traditional target expansion.
Influence of Hydration Status on Thermoregulation and Cycling Hill Climbing (2007)

Exercise-induced dehydration in a warm environment is detrimental to laboratory cycling hill-climbing performance despite reducing the power output required for a given speed.
HIV Viral Load Monitoring in Resource‐Limited Regions: Optional or Necessary? (2006)

Although it is a standard practice in high-income countries, determination of the human immunodeficiency virus (HIV) load is not recommended in developing countries because of the costs and technical constraints. As more and more countries establish capacity to provide second-line therapy, and as costs and technological constraints associated with viral load testing decrease, the question of whether determination of the viral load is necessary deserves attention. Viral load testing could increase in importance as a guide for clinical decisions on when to switch to second-line treatment and on how to optimize the duration of the first-line treatment regimen. In addition, the viral load is a particularly useful tool for monitoring adherence to treatment, performing sentinel surveillance, and diagnosing HIV infection in children aged <18 months. Rather than considering viral load data to be an unaffordable luxury, efforts should be made to ensure that viral load testing becomes affordable, simple, and easy to use in resource-limited settings.
A Sustained Rat Model for Studying the Long-Lasting Catabolic State of Sepsis (1999)

Most animal models of sepsis induced high mortality or early recovery and do not mimic the long-lasting catabolic state observed in patients. The purpose of this study is to develop a model of sepsis which reproduces these disorders, especially the long-lasting muscle wasting. This report summarizes our observations in a series of seven experiments using this model with rats to study the route of live Escherichia coli administration, dose of bacteria, reproducibility of the model, bacterial count in tissues, comparison of injection of live or dead bacteria, metabolic perturbations linked to infection, and potential role of tumor necrosis factor alpha (TNF-alpha) in muscle wasting. After intravenous infection, animals were anorexic and the catabolic state was long-lasting: body weight loss for 2 to 3 days followed by a chronic wasting state for several days. Liver, spleen, lung protein content, and plasma concentration of alpha2-macroglobulin were increased 2 and 6 days after infection. At 6 days, muscle protein content was substantially (-40%) reduced. The plasma TNF-alpha level measured 1.5 h after infection correlated with body weight loss observed 9 days later. The inhibition of TNF-alpha secretion by administration of pentoxifylline 1 h before infection reduced muscle wasting and activation of proteolysis at day 2 and abolished them at day 6. This septic model mimics in rats the prolonged protein metabolism alterations and muscle atrophy characteristics of infected patients and thus is useful for studying the impact of nutritional support on outcome.
Molecular Pathways in Virus-Induced Cytokine Production (2001)

Virus infections induce a proinflammatory response including expression of cytokines and chemokines. The subsequent leukocyte recruitment and antiviral effector functions contribute to the first line of defense against viruses. The molecular virus-cell interactions initiating these events have been studied intensively, and it appears that viral surface glycoproteins, double-stranded RNA, and intracellular viral proteins all have the capacity to activate signal transduction pathways leading to the expression of cytokines and chemokines. The signaling pathways activated by viral infections include the major proinflammatory pathways, with the transcription factor NF-kappaB having received special attention. These transcription factors in turn promote the expression of specific inducible host proteins and participate in the expression of some viral genes. Here we review the current knowledge of virus-induced signal transduction by seven human pathogenic viruses and the most widely used experimental models for viral infections. The molecular mechanisms of virus-induced expression of cytokines and chemokines is also analyzed.
Targeted sonodynamic therapy of cancer using a photosensitizer conjugated with antibody against carcinoembryonic antigen. (2002)

The goal of this study was to develop a strategy for the selective destruction of cancer cells by ultrasonic irradiation in the presence of an antibody-conjugated photosensitizer. To this end, a photoimmunoconjugate (PIC) was prepared between ATX-70, a photosensitizer of a gallium-porphyrin analogue, and F11-39, a high affinity monoclonal antibody (MAb) against carcinoembryonic antigen (CEA), which is often overexpressed in various carcinoma cells. This conjugate, designated F39/ATX-70, retained immunoreactivity against purified CEA and CEA-expressing cells as determined by enzyme-linked immunosorbent assay, flow cytometry and immunofluorescence microscopic analysis. The cytotoxicity of F39/ATX-70 against CEA-expressing human gastric carcinoma cells in vitro was found to be greater than that of ATX-70 when applied in combination with ultrasound irradiation. When in vivo anti-tumor effects in a mouse xenograft model were assessed, intravenous administration of F39/ATX-70 followed by ultrasonic irradiation produced a marked growth inhibition of tumor compared with irradiation alone or irradiation after administration of ATX-70. These results suggest that the PIC between anti-CEA MAb and ATX-70 may have applications in sonodynamic therapy where destruction of CEA-expressing tumor is required.
CRISPR Interference Directs Strand Specific Spacer Acquisition (2012)

The E. coli Type I-E CRISPR/Cas system provides resistance against bacteriophage infection, but also enables removal of residing plasmids. We established that there is a positive feedback loop between active spacers in a cluster--in our case the first acquired spacer--and spacers acquired thereafter, possibly through the use of specific DNA degradation products of the CRISPR interference machinery by the CRISPR adaptation machinery. This loop enables a rapid expansion of the spacer repertoire against an actively present DNA element that is already targeted, amplifying the CRISPR interference effect.
Aberrant Extracellular and Dendritic Cell (DC) Surface Expression of Heat Shock Protein (hsp)70 in the Rheumatoid Joint: Possible Mechanisms of hsp/DC-Mediated Cross-Priming (2003)

We describe, in rheumatoid arthritis (RA), abnormalities in the expression and distribution of heat shock protein (hsp) and dendritic cells (DCs) that are conducive to cross-priming and DC cross-talk. As detected by ELISA, inducible (i)hsp70 was dramatically increased in RA synovial fluid (RASF) vs normal human and RA sera and osteoarthritis and gout synovial fluid. Immunoblot analysis of fresh RASF cells revealed marked increases in ihsp70 and activation of its transcription factor heat shock factor-1, compared with fresh normal peripheral blood cells. Flow cytometry and microscopy demonstrated high levels of ihsp70 on the surface of RASF myeloid DCs (but not normal myeloid DCs) that occurred concurrently with hspRs (CD91/CD14). ihsp70 present in RASF exhibited chaperoning potential, as indicated by the capture of ihsp70 present in RASF on the surface of normal DCs. Binding was partially competitively inhibited by excess alpha(2)-macroglobulin, indicating that hspRs in addition to CD91 participate in the capture process. These data indicate that ihsp70 may chaperone autologous Ags into immature RASF DCs via hspRs, and that cross-talk between DCs coexpressing hsp/hspRs reflects a disease process in RA. The induction of surface ihsp70 on normal cells after sublethal heat stress and the release of ihsp70 from normal DCs after inflammatory stress also suggest that the pattern of ihsp70 expression in RASF occurs in response to sustained stress.
Quantitative analysis of small molecules by desorption electrospray ionization mass spectrometry from polytetrafluoroethylene surfaces (2008)

Desorption electrospray ionization mass spectrometry (DESI-MS) is an emerging technique for ambient analysis. However, its application to routine quantitation has not been explored extensively and this is undertaken here. We present studies that utilize a particularly suitable surface, porous polytetrafluoroethylene (porous PTFE), which shows less cross contamination between samples and improved sensitivity and signal stability compared to other surfaces. Quantitative experiments for 1 microL spotted solutions of the beta-blocker propranolol, using isotopically labeled propranolol as internal standard, showed a good linear correlation (r2 > 0.996) over the range 0.01-100 microM. The inter-day precision, based on the relative standard deviation, for replicates analyzed on three different days was 13% for 0.01 microM and better than 7% for the remainder of the calibration points. The inter-day accuracy, expressed as relative error, was better than +/-7% for all calibration points along the curve. These day-to-day measurements suggest that DESI-MS can be successfully employed for routine quantitative analysis. The use of the analog atenolol as an internal standard and further considerations that should improve quantitation by DESI-MS are also presented.
Aiming to induce broadly reactive neutralizing antibody responses with HIV-1 vaccine candidates (2006)

Neutralizing antibody induction is a key feature of many effective vaccines and is the only immune response that has proven to be capable of completely blocking AIDS virus infection in animal models. Unfortunately, the extensive genetic variability and complex immune-evasion strategies of HIV-1 have thwarted all attempts to date at eliciting an effective neutralizing antibody response with candidate HIV-1 vaccine immunogens. Recent advances in our understanding of how these evasion strategies operate, coupled with growing progress in unravelling the structure and immunobiology of the viral envelope glycoproteins, are contributing to novel immunogen designs to overcome the many barriers to inducing protective antibodies against HIV-1.
Involvement of the "I" domain of LFA-1 in selective binding to ligands ICAM-1 and ICAM-3. (1994)

To analyze the binding requirements of LFA-1 for its two most homologous ligands, ICAM-1 and ICAM-3, we compared the effects of various LFA-1 activation regimes and a panel of anti-LFA-1 mAbs in T cell binding assays to ICAM-1 or ICAM-3 coated on plastic. These studies demonstrated that T cell binding to ICAM-3 was inducible both from the exterior of the cell by Mn2+ and from the interior by an agonist of the "inside-out" signaling pathway. T cells bound both ICAM ligands with comparable avidity. A screen of 29 anti-LFA-1 mAbs led to the identification of two mAbs specific for the alpha subunit of LFA-1 which selectively blocked adhesion of T cells to ICAM-3 but not ICAM-1. These two mAbs, YTH81.5 and 122.2A5, exhibited identical blocking properties in a more defined adhesion assay using LFA-1 transfected COS cells binding to immobilized ligand. Blocking was not due to a steric interference between anti-LFA-1 mAbs and N-linked carbohydrate residues present on ICAM-3 but not ICAM-1. The epitopes of mAbs YTH81.5 and 122.2A5 were shown to map to the I domain of the LFA-1 alpha subunit. A third I domain mAb, MEM-83, has been previously reported to uniquely activate LFA-1 to bind ICAM-1 (Landis, R. C., R. I. Bennett, and N. Hogg. 1993. J. Cell Biol. 120:1519-1527). We now show that mAb MEM-83 is not able to stimulate binding of T cells to ICAM-3 over a wide concentration range. Failure to induce ICAM-3 binding by mAb MEM-83 was not due to a blockade of the ICAM-3 binding site on LFA-1. This study has demonstrated that two sets of functionally distinct mAbs recognizing epitopes in the I domain of LFA-1 are able to exert differential effects on the binding of LFA-1 to its ligands ICAM-1, and ICAM-3. These results suggest for the first time that LFA-1 is capable of binding these two highly homologous ligands in a selective manner and that the I domain plays a role in this process.
Structure and Properties of Poly(vinyl alcohol) Hydrogels Obtained by Freeze/Thaw Techniques (2005)

Abstract The relationships between the structure and the viscoelastic properties of freeze/thaw PVA hydrogels obtained by repeatedly freezing and thawing dilute solutions of PVA in D 2 O(11% w/w PVA) in as‐prepared and rehydrated states are investigated. Our results indicate that the PVA chains and solvent molecules are organized at different hierarchical length scales, which include the presence of micro‐ and macro‐pores, into a network scaffolding. The porous network is ensured by the presence of crystallites, which act as knots interconnected by portions of PVA chains swollen by the solvent. X‐ray diffraction and SANS techniques are used to obtain structural information at short (angstroms) and medium (nanometers) ranges of length scales, concerning the crystallinity, the size of small crystalline aggregates and the average distance between crystallites in PVA hydrogels. Indirect information concerning the structural organization on the large length scales (microns) are provided by viscoelastic measurements. The dynamic shear elastic moduli at low frequency and low strain amplitude, G′, are determined and related to the degree of crystallinity. These data indicate that a minimum crystallinity of 1% is required for these PVA samples to exhibit gel behaviour and have allowed obtaining the order of magnitude of the average mesh size in these gels. Finally, it is shown that the negative effect of aging, inducing worse physical and mechanical properties in these systems, may be prevented using a drying/re‐hydration protocol able to keep the physical properties of the as‐prepared PVA hydrogels.
Detection of human papillomavirus in cervical scrapes by the polymerase chain reaction in relation to cytology: possible implications for cervical cancer screening. (1992)

An HPV screening strategy based on general primer-mediated and type-specific PCR is described. A relationship was found between an increasing HPV prevalence rate and a higher degree of cervical dysplasia (up to 100% in cervical carcinoma). Based on these prevalence studies in the Netherlands and preliminary data showing that progression of cervical lesions is always associated with persistent infection of oncogenic/high-risk HPV types, a cervical cancer screening scheme incorporating PCR-based HPV detection is proposed for use in industrialized countries.
Pathogenic mechanism of a human mitochondrial tRNA Phe mutation associated with myoclonic epilepsy with ragged red fibers syndrome (2007)

Human mitochondrial tRNA (hmt-tRNA) mutations are associated with a variety of diseases including mitochondrial myopathies, diabetes, encephalopathies, and deafness. Because the current understanding of the precise molecular mechanisms of these mutations is limited, there is no efficient method to treat their associated mitochondrial diseases. Here, we use a variety of known mutations in hmt-tRNA(Phe) to investigate the mechanisms that lead to malfunctions. We tested the impact of hmt-tRNA(Phe) mutations on aminoacylation, structure, and translation elongation-factor binding. The majority of the mutants were pleiotropic, exhibiting defects in aminoacylation, global structure, and elongation-factor binding. One notable exception was the G34A anticodon mutation of hmt-tRNA(Phe) (mitochondrial DNA mutation G611A), which is associated with MERRF (myoclonic epilepsy with ragged red fibers). In vitro, the G34A mutation decreases aminoacylation activity by 100-fold, but does not affect global folding or recognition by elongation factor. Furthermore, G34A hmt-tRNA(Phe) does not undergo adenosine-to-inosine (A-to-I) editing, ruling out miscoding as a possible mechanism for mitochondrial malfunction. To improve the aminoacylation state of the mutant tRNA, we modified the tRNA binding domain of the nucleus-encoded human mitochondrial phenylalanyl-tRNA synthetase, which aminoacylates hmt-tRNA(Phe) with cognate phenylalanine. This variant enzyme displayed significantly improved aminoacylation efficiency for the G34A mutant, suggesting a general strategy to treat certain classes of mitochondrial diseases by modification of the corresponding nuclear gene.
Color Signals in the Primate Superior Colliculus (2010)

Color is important for segmenting objects from backgrounds, which can in turn facilitate visual search in complex scenes. However, neural substrates that control overt visual orienting towards interesting objects (i.e., saccadic eye movements) are not believed to encode visual features such as color (Bichot, Schall, & Thompson, 1996; McPeek & Keller, 2002), despite direct projections from color-related areas to saccadic substrates such as the Superior Colliculus (SC)(Lock, Baizer, & Bender, 2003). Using a delayed saccade task, we measured the activity of visually responsive SC neurons (N=68) in two monkeys to stimuli derived from the DKL color space (Derrington, Krauskopf, & Lennie, 1984). We show the first evidence that neurons in the intermediate SC layers can respond to pure chromatic stimuli with the same magnitude as the best luminance stimulus (100% contrast). This activity is not adequately explained by residual luminance signals because 1) neurons with an equal or better color response showed significantly longer visual onset latencies (25–30ms), and 2) the luminance control-stimulus was more than 20cd/m2 different from the color stimuli. Furthermore, the color response was not seen for phasic-visual neurons obtained from the superficial SC layers. This implies that the color-related activity in the SC involves different pathways than luminance, and projects primarily to the intermediate SC layers. The delayed color response is also reflected by the longer saccadic reaction times previously reported for chromatic DKL stimuli (White, Kerzel, & Gegenfurtner, 2006). We conclude that this activity represents a true colour response only one stage from the brainstem premotor circuitry that drives the eyes. BichotN. P.SchallJ. D.ThompsonK. G. (1996). Visual feature selectivity in frontal eye fields induced by experience in mature macaques. Nature, 381(6584), 697–699. DerringtonA. M.KrauskopfJ.LennieP. (1984). Chromatic mechanisms in lateral geniculate nucleus of macaque. J Physiol, 357, 241–265. LockT. M.BaizerJ. S.BenderD. B. (2003). Distribution of corticotectal cells in macaque. Exp Brain Res, 151(4), 455–470. McPeekR. M.KellerE. L. (2002). Saccade target selection in the superior colliculus during a visual search task. J Neurophysiol, 88(4), 2019–2034. WhiteB. J.KerzelD.GegenfurtnerK. R. (2006). Visually guided movements to color targets. Exp Brain Res, 175(1), 110–126.
Stimulation of human T cells by an influenza A vector expressing a CTL epitope from the HER-2/neu protooncogene results in higher numbers of antigen-specific TCRhi cells than stimulation with peptide. Divergent roles of IL-2 and IL-15. (2005)

Development of cancer vaccines requires approaches to induce expansion and functional differentiation of tumor antigen-specific effector and memory cells. The later are particularly relevant for prevention of disease relapse. Efficient induction of memory cells is hindered by the lack of information about the relationship between TCR stimulation and the cytokines required for Ag-specific memory CD8+ cells and proliferation and survival. Since viruses are known to induce memory T cells, an attenuated influenza A/PR8/34 virus with a truncated nonstructural (NS1) gene was generated containing the HER-2 CTL E75 epitope in its neuraminidase protein (KIF-NS virus). Stimulation of PBMC from healthy donors and of tumor-associated lymphocytes (TAL) from ovarian cancer patients with dendritic cells (DC) infected with KIF-NS (KIF-NS-DC), induced higher numbers of immediate memory effector CD8+ CD44hi CD122hi cells, expressing TCR specific for E75 (E75-TCR) than stimulation with peptide E75. Survival of CD44hi CD122hi cells was dependent on the levels of TCR; cells expressing lower levels of E75-TCR (MFI: 10(2)-10(3)) survived better in IL-2 while cells expressing high levels of TCR (MFI: 10(3)-10(4)) survived better in IL-15. This is the first report demonstrating induction of human Ag-specific memory CD8+ cells against a human tumor-antigen using a live attenuated recombinant influenza virus vector. Such vectors may provide a novel approach for preventive immunity in human cancer vaccine development.
Direct Ink Writing of 3D Functional Materials (2006)

Abstract The ability to pattern materials in three dimensions is critical for several technological applications, including composites, microfluidics, photonics, and tissue engineering. Direct‐write assembly allows one to design and rapidly fabricate materials in complex 3D shapes without the need for expensive tooling, dies, or lithographic masks. Here, recent advances in direct ink writing are reviewed with an emphasis on the push towards finer feature sizes. Opportunities and challenges associated with direct ink writing are also highlighted.