gebhart/patrepeval huggingface dataset:
Recombinant HIV2 protease processes HIV1 Pr53gag and analogous junction peptides in vitro. (1990)

A synthetic DNA fragment encoding a protease precursor of the human immunodeficiency virus type 2 (HIV2) was cloned and expressed in bacteria and yeast. A recombinant plasmid encoding a hybrid polypeptide consisting of human superoxide dismutase and an HIV2 protease precursor of 113 amino acids was constructed for regulated intracellular expression in bacteria. Induction of this plasmid produced an autoprocessed form of the retroviral enzyme possessing the correct molecular weight. Overexpression and secretion of the protease from yeast was achieved with an expression vector encoding the yeast pheromone alpha-factor signal/leader sequence fused to a protease precursor of 115 amino acids. Amino-terminal sequence analysis confirmed that the viral enzyme exported from yeast was correctly processed from its precursor by cleavage of the predicted Ala-Pro peptide bond located at the NH2 terminus of the protease in the pol open reading frame. No additional amino acid residues were required at the COOH terminus of the protease for this autoproteolytic event. The HIV2 protease expressed in bacteria and yeast was active in an in vitro assay when tested on the HIV1 polyprotein precursor, myristylated Pr53gag. Two synthetic peptides representing junction sequences in the HIV1 gag-pol precursor were used to assay purified HIV2 protease. The enzyme exhibited a kcat/KM of 23.2 min-1 mM-1 on the HIV1 matrix-capsid junction peptide and a kcat/KM of 71.4 min-1 mM-1 on the protease-reverse transcriptase junction peptide. These rates show that the HIV2 enzyme is efficient at hydrolyzing the HIV1 peptide junctions, revealing the analogous nature of the substrate specificities of the two enzymes.
Systematic sequencing of the 283 kb 210 -232 region of the Bacillus subtilis genome containing the skin element and many sporulation genes (1996)

As part of the Bacillus subtilis genome sequencing project, we have determined a 283 kb contiguous sequence from 210 degrees to 232 degrees of the B. subtilis genome. This region contains the 48 kb skin element which is excised during sporulation by a site-specific recombinase. In this region, 310 complete ORFs and one tRNA gene were identified: 66 ORFs have been sequenced and characterized previously by other workers, e.g. acc, ans, bfm, blt, bmr, comE, comG, dnaK, rpoD and sin operons; cwiA, gpr and lysA genes; many sporulation genes and operons, spo0A, spoIIA, spoIIM, spoiiP, spoIIIA, spoIIIC, spoIVB, spoIVCA, spoIVCB and spoVA, etc. The products of 84 ORFs were found to display significant similarity to proteins with known function in data banks, e.g., proteins involved in nucleotide metabolism, lipid biosynthesis, amino acid transport (ABC transporter), phosphate-specific transport, the glycine cleavage system, the two-component regulatory system, cell wall autolysis, ferric uptake and sporulation. However, the functions of more than half of the ORFs (52%, 160 ORFs) are still unknown. In the skin element containing 60 ORFs, 32 ORFs (53%) encode proteins which have significant homology to gene products of the B. subtilis temperate phage phi 105 and/or the defective phage PBSX.
Importance of Glucose-6-phosphate Dehydrogenase Activity for Cell Growth (1998)

The intracellular redox potential, which is determined by the level of oxidants and reductants, has been shown to play an important role in the regulation of cell growth. The principal intracellular reductant is NADPH, which is mainly produced by the pentose phosphate pathway through the actions of glucose-6-phosphate dehydrogenase (G6PD), the rate-limiting enzyme of the pentose phosphate pathway, and by 6-phosphogluconate dehydrogenase. Previous research has suggested that an increase in G6PD activity is important for cell growth. In this article, we suggest that G6PD activity plays a critical role in cell growth by providing NADPH for redox regulation. The results show the following: 1) inhibition of G6PD activity abrogated growth factor stimulation of [3H]thymidine incorporation in all cell lines tested; 2) overexpression of G6PD stimulated cell growth, as measured by an increase in [3H]thymidine incorporations as compared with cells transfected with vector alone; 3) inhibition of G6PD caused cells to be more susceptible to the growth inhibitory effects of H2O2; 4) inhibition of G6PD led to a 30-40% decrease in the NADPH/NADP ratio; and 5) inhibition of G6PD inhibited cell anchorage and significantly decreased the growth-related stimulation of tyrosine phosphorylation.
Implicit visibility and antiradiance for interactive global illumination (2007)

We reformulate the rendering equation to alleviate the need for explicit visibility computation, thus enabling interactive global illumination on graphics hardware. This is achieved by treating visibility implicitly and propagating an additional quantity, called antiradiance, to compensate for light transmitted extraneously. Our new algorithm shifts visibility computation to simple local iterations by maintaining additional directional antiradiance information with samples in the scene. It is easy to parallelize on a GPU. By correctly treating discretization and filtering, we can compute indirect illumination in scenes with dynamic objects much faster than traditional methods. Our results show interactive update of indirect illumination with moving characters and lights.
Frataxin activates mitochondrial energy conversion and oxidative phosphorylation (2000)

Friedreich's ataxia (FA) is an autosomal recessive disease caused by decreased expression of the mitochondrial protein frataxin. The biological function of frataxin is unclear. The homologue of frataxin in yeast, YFH1, is required for cellular respiration and was suggested to regulate mitochondrial iron homeostasis. Patients suffering from FA exhibit decreased ATP production in skeletal muscle. We now demonstrate that overexpression of frataxin in mammalian cells causes a Ca(2+)-induced up-regulation of tricarboxylic acid cycle flux and respiration, which, in turn, leads to an increased mitochondrial membrane potential (delta psi(m)) and results in an elevated cellular ATP content. Thus, frataxin appears to be a key activator of mitochondrial energy conversion and oxidative phosphorylation.
Telemetry Options for Small Water Systems (1999)

At present, information on cost-effectiveness and risks involved in integrating telemetry into small water systems is scarce.The overall goal of the telemetry research at Virginia Tech is to develop procedures for evaluating costeffectiveness and risk assessment for small water systems.The goal of this report, as a component of the overall project, is to provide guidelines for telemetry selection and the costs involved.This report builds on a previous study conducted by the U.S. EPA (Remote Sensing/Control for Small Water Systems: Literature Review/Assessment, 1998).The EPA report is complete in describing the four basic types of telemetry links but lacks details or supporting data from which its conclusions were drawn.This report expands on the EPA report and includes details of each type of system, its basic operation, and the associated cost.The end product of this report is a matrix of physical links and their parameters as associated with Supervisory Control and Data Acquisition (SCADA) to aid the small water systems in selecting the appropriate telemetry for their needs.
Semiconductor Nanocrystals: Structure, Properties, and Band Gap Engineering (2009)

Semiconductor nanocrystals are tiny light-emitting particles on the nanometer scale. Researchers have studied these particles intensely and have developed them for broad applications in solar energy conversion, optoelectronic devices, molecular and cellular imaging, and ultrasensitive detection. A major feature of semiconductor nanocrystals is the quantum confinement effect, which leads to spatial enclosure of the electronic charge carriers within the nanocrystal. Because of this effect, researchers can use the size and shape of these "artificial atoms" to widely and precisely tune the energy of discrete electronic energy states and optical transitions. As a result, researchers can tune the light emission from these particles throughout the ultraviolet, visible, near-infrared, and mid-infrared spectral ranges. These particles also span the transition between small molecules and bulk crystals, instilling novel optical properties such as carrier multiplication, single-particle blinking, and spectral diffusion. In addition, semiconductor nanocrystals provide a versatile building block for developing complex nanostructures such as superlattices and multimodal agents for molecular imaging and targeted therapy. In this Account, we discuss recent advances in the understanding of the atomic structure and optical properties of semiconductor nanocrystals. We also discuss new strategies for band gap and electronic wave function engineering to control the location of charge carriers. New methodologies such as alloying, doping, strain-tuning, and band-edge warping will likely play key roles in the further development of these particles for optoelectronic and biomedical applications.
Le Bio Wall : Un Tissue Informatique pour le Prototypage de Systèmes Bio-Inspirés (2002)

Dans cet article, nous décrivons le BioWall, un tissu informatique reconfigurable géant développé dans le but d’y implémenter des machines mettant en oeuvre les principes de notre projet Embryonique. Bien que ses dimensions et ses caractéristiques en font d’abord un objet de démonstration publique, le BioWall constitue également un outil de recherche précieux, du fait que sa faculté de reprogrammation et sa structure cellulaire s’adaptent parfaitement à l’implémentation de toutes sortes de systèmes bioinspirés. Pour illustrer ces capacités, nous décrivons un ensemble d’applications qui reflètent différentes sources d’inspiration biologique allant des systèmes biologiques ontogénétiques aux dispositifs évolutifs phylogénétiques, en passant par les réseaux neuromimétiques épigénétiques. Toutes ces applications ont été implémentées et testées matériellement dans le BioWall.
A study and optimization of eigenmode calculations using the imaginary-distance beam-propagation method (1994)

Recently, it has been shown that if the paraxial wave equation is modified such that fields travel imaginary distances, the field resulting from an imaginary-distance propagation is the fundamental mode of an optical waveguide. For the finite-difference beam-propagation method, we derive the factor by which each eigenmode is amplified during one propagation step. This amplification factor places limits on the inputs-step size, input field, effective index guess, and implicitness parameter-and gives clues on how to optimize the inputs. In particular, we identify and study two optimal sets of inputs, which can reduce computational time significantly. We can obtain the fundamental mode and its propagation constant within a few propagation steps.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
NKG2D CARs as Cell Therapy for Cancer (2014)

The NKG2D cell receptor and its ligands have attracted considerable interest as a potential strategy to attack tumor cells. NKG2D ligands are expressed on most types of tumors, and they demonstrate relative selectivity of ligand expression on tumor cells compared to healthy cells. Several different variants of NKG2D-based chimeric antigen receptors (CARs) have been developed, and extensive in vivo mechanistic studies performed demonstrated that cytotoxicity and cytokines are important for the efficacy NKG2D CAR adoptive T-cell therapy. NKG2D CARs target tumor cells, and they also target immunosuppressive cells within the tumor microenvironment. Under certain conditions, NKG2D ligand expression can be found on nontumor tissue, so potential off-tumor toxicity remains. In this article, we review the use of NKG2D as a basis for CAR targeting of tumors.
TutorialVQA: Question Answering Dataset for Tutorial Videos (2019)

Despite the number of currently available datasets on video question answering, there still remains a need for a dataset involving multi-step and non-factoid answers. Moreover, relying on video transcripts remains an under-explored topic. To adequately address this, We propose a new question answering task on instructional videos, because of their verbose and narrative nature. While previous studies on video question answering have focused on generating a short text as an answer, given a question and video clip, our task aims to identify a span of a video segment as an answer which contains instructional details with various granularities. This work focuses on screencast tutorial videos pertaining to an image editing program. We introduce a dataset, TutorialVQA, consisting of about 6,000manually collected triples of (video, question, answer span). We also provide experimental results with several baselines algorithms using the video transcripts. The results indicate that the task is challenging and call for the investigation of new algorithms.
Antigen-Specific T-Cell Activation Independently of the MHC: Chimeric Antigen Receptor-Redirected T Cells (2013)

Adoptive T-cell therapy has recently shown promise in initiating a lasting anti-tumor response with spectacular therapeutic success in some cases. Specific T-cell therapy, however, is limited since a number of cancer cells are not recognized by T cells due to various mechanisms including the limited availability of tumor-specific T cells and deficiencies in antigen processing or major histocompatibility complex (MHC) expression of cancer cells. To make adoptive cell therapy applicable for the broad variety of cancer entities, patient's T cells are engineered ex vivo with pre-defined specificity by a recombinant chimeric antigen receptor (CAR) which consists in the extracellular part of an antibody-derived domain for binding with a "tumor-associated antigen" and in the intracellular part of a T-cell receptor (TCR)-derived signaling moiety for T-cell activation. The specificity of CAR-mediated T-cell recognition is defined by the antibody domain, is independent of MHC presentation and can be extended to any target for which an antibody is available. We discuss the advantages and limitations of MHC-independent T-cell targeting by an engineered CAR in comparison to TCR modified T cells and the impact of the CAR activation threshold on redirected T-cell activation. Finally we review most significant progress recently made in early stage clinical trials to treat cancer.
Anemia increases the risk of renal cortical and medullary hypoxia during cardiopulmonary bypass (2013)

The clear difference in the degree of hypoxia in the renal cortex and medulla may be useful in understanding the progress of medullary hypoxia during CPB with anemia and the potential development of AKI. Further studies should aim at identifying early markers of medullary hypoxia and potential agents that may decrease the work and O2 consumption in the renal medulla to reduce the risk of hypoxic damage during CPB and anemia.
Anti-Cryptosporidium parvum antibodies inhibit infectivity in vitro and in vivo (1993)

Cryptosporidium parvum causes acute diarrhea in immunocompetent individuals and a severe life-threatening disease in immunocompromised individuals, including AIDs patients. No efficacious therapy for cryptosporidiosis has yet been reported. However, treatment of some patients with cryptosporidiosis with hyperimmune bovine colostrum has ameliorated or eliminated clinical symptoms. Consequently, it is important to identify and characterize C. parvum antigens which are the targets of protective antibodies to facilitate the development of more efficacious therapy. We report that hyperimmune bovine colostral immunoglobulin inhibits C. parvum infectivity in a reproducible in vitro assay, and we correlate this inhibition with the protective capacity of the bovine colostrum in vivo. We have also identified the major C. parvum sporozoite antigens recognized on Western blots (immunoblots) by this colostral immunoglobulin preparation. Antibodies that recognize some surface molecules of other Apicomplexan parasites are protective in vivo. Consequently, we radioiodinated membrane proteins of sporozoites and immunoprecipitated 19 molecules which are the target of immunoglobulin that is protective in vivo and in vitro.
Active-Constraint Robotics for Surgery (2006)

The concepts and benefits of hands-on robotic surgery and active-constraint robotics are introduced. The argument is made for systems to be cost effective and simple in order that they can be justified for a large range of surgical procedures. The case is made for robotic systems to have a clear justification, with benefits compared to those from cheaper navigation systems. The need to have robust systems, that require little surgical training and no technical presence in the operating room, is also discussed. An active constraint medical robot, the Acrobot System, is described together with its use in a prospective randomized controlled trial of unicondylar knee arthroplasty (UKA), comparing the performance of the Acrobot System with conventional surgery. Twenty-eight patients awaiting UKA were randomly allocated to have the operation performed conventionally or with the assistance of the Acrobot. The results of the trial are presented together with a discussion of the need for measures of accuracy to be introduced so that the efficacy of the robotic surgery can be immediately identified, rather than having to wait for a number of years before long-term clinical improvements can be demonstrated.
Dynamic disorder in methylammoniumtrihalogenoplumbates (II) observed by millimeter-wave spectroscopy (1987)

The temperature-dependent structure of crystalline methylammoniumtrihalogenoplumbates (II)—CH3NH+3PbX−3 (X=Cl, Br, I)—as determined by x-ray diffraction, is compared with measurements of the temperature-dependent complex permittivity at frequencies of 50–150 GHz. The dielectric measurements reveal a picosecond relaxation process which corresponds to a dynamic disorder of the methylammonium group in the high-temperature phases of the trihalogenoplumbates.
Focal Loss for Dense Object Detection (2017)

The highest accuracy object detectors to date are based on a two-stage approach popularized by R-CNN, where a classifier is applied to a sparse set of candidate object locations. In contrast, one-stage detectors that are applied over a regular, dense sampling of possible object locations have the potential to be faster and simpler, but have trailed the accuracy of two-stage detectors thus far. In this paper, we investigate why this is the case. We discover that the extreme foreground-background class imbalance encountered during training of dense detectors is the central cause. We propose to address this class imbalance by reshaping the standard cross entropy loss such that it down-weights the loss assigned to well-classified examples. Our novel Focal Loss focuses training on a sparse set of hard examples and prevents the vast number of easy negatives from overwhelming the detector during training. To evaluate the effectiveness of our loss, we design and train a simple dense detector we call RetinaNet. Our results show that when trained with the focal loss, RetinaNet is able to match the speed of previous one-stage detectors while surpassing the accuracy of all existing state-of-the-art two-stage detectors. Code is at: https://github.com/facebookresearch/Detectron.
Phagocyte Impotence Caused by an Invasive Bacterial Adenylate Cyclase (1982)

For unknown reasons, humans infected with the bacterium Bordetella pertussis are exceptionally vulnerable to secondary infections. Bordetella species elaborate a soluble, heat-stable, and highly active adenylate cyclase. This enzyme is internalized by phagocytic cells and catalyzes the unregulated formation of adenosine 3',5'-monophosphate (cyclic AMP), thereby disrupting normal cellular function. This unusual phenomenon may explain Bordetella-induced aphylaxis and may prove to be useful for investigating a variety of cyclic AMP-governed processes.
REACTIVE OXYGEN SPECIES: Metabolism, Oxidative Stress, and Signal Transduction (2004)

Several reactive oxygen species (ROS) are continuously produced in plants as byproducts of aerobic metabolism. Depending on the nature of the ROS species, some are highly toxic and rapidly detoxified by various cellular enzymatic and nonenzymatic mechanisms. Whereas plants are surfeited with mechanisms to combat increased ROS levels during abiotic stress conditions, in other circumstances plants appear to purposefully generate ROS as signaling molecules to control various processes including pathogen defense, programmed cell death, and stomatal behavior. This review describes the mechanisms of ROS generation and removal in plants during development and under biotic and abiotic stress conditions. New insights into the complexity and roles that ROS play in plants have come from genetic analyses of ROS detoxifying and signaling mutants. Considering recent ROS-induced genome-wide expression analyses, the possible functions and mechanisms for ROS sensing and signaling in plants are compared with those in animals and yeast.
Clinical Outcome Prediction by MicroRNAs in Human Cancer: A Systematic Review (2012)

MiR classifiers show promising prognostic associations with major cancer outcomes and specific miRs are consistently identified across diverse studies and platforms. These types of classifiers require careful external validation in large groups of cancer patients that have adequate protection from bias. -
Enhancing effect of platelet‐derived microvesicles on the invasive potential of breast cancer cells (2006)

It was shown than PMVs enhance the in vitro invasive potential of invasive breast cancer cell lines and therefore could mediate the progression of breast cancer. These findings warrant further evaluation of the implications of PLT transfusions in cancer patients.
Recombinant NY-ESO-1 protein with ISCOMATRIX adjuvant induces broad integrated antibody and CD4+ and CD8+ T cell responses in humans (2004)

NY-ESO-1 is a "cancer-testis" antigen expressed in many cancers. ISCOMATRIX is a saponin-based adjuvant that induces antibody and T cell responses. We performed a placebo-controlled clinical trial evaluating the safety and immunogenicity of recombinant NY-ESO-1 protein with ISCOMATRIX adjuvant. Forty-six evaluable patients with resected NY-ESO-1-positive tumors received three doses of vaccine intramuscularly at monthly intervals. The vaccine was well tolerated. We observed high-titer antibody responses, strong delayed-type hypersensitivity reactions, and circulating CD8(+) and CD4(+) T cells specific for a broad range of NY-ESO-1 epitopes, including known and previously unknown epitopes. In an unplanned analysis, vaccinated patients appeared to have superior clinical outcomes to those treated with placebo or protein alone. The vaccine is safe and highly potent immunologically.