gebhart/patrepeval huggingface dataset:
A chromosomal location of the mupA gene in Staphylococcus aureus expressing high-level mupirocin resistance (2003)

The absence of mupA on any of the plasmids and its detection only in the chromosomal DNA of the parents and in their derivatives cured of the 26 kb plasmid strongly supports a chromosomal location for mupA in these isolates.
Impact of genotype on survival of children with T-cell acute lymphoblastic leukemia treated according to the French protocol FRALLE-93: the effect of TLX3/HOX11L2 gene expression on outcome (2008)

TLX3 gene expression is an independent risk factor predicting poor survival in childhood T-cell acute lymphoblastic leukemia. When co-expressed with TLX3, NUP214-ABL1 transcripts may increase the risk of poor survival.
Edible vaccines. (1997)

Vaccines were the result of trial and error research until molecular biology and genetic engineering made possible the creation of of many new and improved vaccines. New vaccines need to be inexpensive, easily administered, and capable of being stored and transported without refrigeration; without these characteristics, developing countries find it difficult to adopt vaccination as the central strategy for preventing their most devastating diseases. The authors describe a promising approach to inexpensive and effective vaccines: producing them in plants we commonly consume.
The Unified Medical Language System (1993)

In 1986, the National Library of Medicine began a long-term research and development project to build the Unified Medical Language System (UMLS). The purpose of the UMLS is to improve the ability of computer programs to "understand" the biomedical meaning in user inquiries and to use this understanding to retrieve and integrate relevant machine-readable information for users. Underlying the UMLS effort is the assumption that timely access to accurate and up-to-date information will improve decision making and ultimately the quality of patient care and research. The development of the UMLS is a distributed national experiment with a strong element of international collaboration. The general strategy is to develop UMLS components through a series of successive approximations of the capabilities ultimately desired. Three experimental Knowledge Sources, the Metathesaurus, the Semantic Network, and the Information Sources Map have been developed and are distributed annually to interested researchers, many of whom have tested and evaluated them in a range of applications. The UMLS project and current developments in high-speed, high-capacity international networks are converging in ways that have great potential for enhancing access to biomedical information.
Regulation of fatty acid composition and lipid storage by thyroid hormone in mouse liver (2014)

Taken together, our study here suggested that hypothyroidism in mice might not lead to the development of NAFLD although the liver became enlarged. However, disturbed TH levels led to altered hepatic fatty acid composition and glycogen accumulation.
Improvement of Peroxygenase Activity by Relocation of a Catalytic Histidine within the Active Site of Horseradish Peroxidase (1998)

To examine the role of Arg38 in the peroxidative and peroxygenative activity of horseradish peroxidase (HRP), we have expressed the R38A, R38H, and R38H/H42V mutants. The R38A HRP mutant gives a normal compound I species with H2O2 that is reduced by ferrocyanide to the ferric state without the detectable formation of a compound II species. In the case of the R38H and R38H/H42V mutants, compound I itself is only detected by stopped flow methods. The rates of compound I formation at 4 degrees C are 8.0 x 10(4), 1.3 x 10(6), and 1.6 x 10(3) M-1 s-1 for the R38A, R38H, and R38H/H42V mutants, respectively. The R38A, R38H, and R38H/H42V mutants oxidize guaiacol 10-, 2-, and 55-fold, respectively, more slowly than the wild-type enzyme and oxidize ABTS 6-, 3-, and 32-fold more slowly than the wild-type enzyme. The apparent kcat/K(m) values for thioanisole sulfoxidation and styrene epoxidation indicate that the reaction efficiencies of the R38H and wild-type enzymes are comparable. However, the R38A and R38H/H42V mutants are 190- and 1400-fold more efficient as sulfoxidation catalysts, and 25- and 26-fold more efficient as styrene epoxidation catalysts, respectively, than the wild-type enzyme. Thus, even though Arg38 plays a role in the formation and stabilization of compounds I and II, its replacement by other residues can be used to improve peroxygenative catalysis.
Robust variance-components approach for assessing genetic linkage in pedigrees. (1994)

To assess evidence for genetic linkage from pedigrees, I developed a limited variance-components approach. In this method, variability among trait observations from individuals within pedigrees is expressed in terms of fixed effects from covariates and effects due to an unobservable trait-affecting major locus, random polygenic effects, and residual nongenetic variance. The effect attributable to a locus linked to a marker is a function of the additive and dominance components of variance of the locus, the recombination fraction, and the proportion of genes identical by descent at the marker locus for each pair of sibs. For unlinked loci, the polygenic variance component depends only on the relationship between the relative pair. Parameters can be estimated by either maximum-likelihood methods or quasi-likelihood methods. The forms of quasi-likelihood estimators are provided. Hypothesis tests derived from the maximum-likelihood approach are constructed by appeal to asymptotic theory. A simulation study showed that the size of likelihood-ratio tests was appropriate but that the monogenic component of variance was generally underestimated by the likelihood approach.
The human antibody repertoire specific for rabies virus glycoprotein as selected from immune libraries (2005)

Antibody phage display technology was used to identify human monoclonal antibodies that neutralize rabies virus (RV). A phage repertoire was constructed using antibody genes harvested from the blood of vaccinated donors. Selections using this repertoire and three different antigen formats of the RV glycoprotein (gp) resulted in the identification of 147 unique antibody fragments specific for the RV gp. Analysis of the DNA sequences of these antibodies demonstrated a large variation in the heavy- and light-chain germ-line gene usage, suggesting that a broad antibody repertoire was selected. The single-chain variable fragment (scFv) antibodies were tested in vitro for RV neutralization, resulting in 39 specificities that neutralize the virus. Of the scFv clones, 21 were converted into full-length human IgG(1) format. Analysis of viral escape variants and binding competition experiments indicated that the majority of the neutralizing antibodies are directed against antigenic site III of the RV gp. The obtained specificities expand the set of human anti-RV antibodies eligible for inclusion in an antibody cocktail aimed for use in rabies post-exposure prophylaxis.
The Natural History of Hepatitis C Virus (HCV) Infection (2006)

Hepatitis C virus (HCV) is a leading cause of chronic liver disease, cirrhosis, and hepatocellular carcinoma, as well as the most common indication for liver transplantation in many countries. Although the incidence of hepatitis C infection has dramatically decreased during the past decade, the worldwide reservoir of chronically infected persons is estimated at 170 million, or 3% of the global population. There is much controversy surrounding the natural history of hepatitis C infection. The rate of chronic HCV infection is affected by a person's age, gender, race, and viral immune response. Approximately 75%-85% of HCV-infected persons will progress to chronic HCV infection, and are at risk for the development of extrahepatic manifestations, compensated and decompensated cirrhosis, and hepatocellular carcinoma (HCC). The rate of progression to cirrhosis is highly variable, and is influenced by several factors, including the amount of alcohol consumption, age of initial HCV infection, degree of inflammation and fibrosis on liver biopsy, HIV and HBV coinfection, and comordid conditions. An estimated 10%-15% of HCV-infected persons will advance to cirrhosis within the first 20 years. Persons with cirrhosis are at increased risk of developing HCC. An understanding of the natural history of hepatitis C is essential to effectively manage, treat, and counsel individuals with HCV infection.
DNA nanotubes self-assembled from triple-crossover tiles as templates for conductive nanowires (2004)

DNA-based nanotechnology is currently being developed as a general assembly method for nanopatterned materials that may find use in electronics, sensors, medicine, and many other fields. Here we present results on the construction and characterization of DNA nanotubes, a self-assembling superstructure composed of DNA tiles. Triple-crossover tiles modified with thiol-containing double-stranded DNA stems projected out of the tile plane were used as the basic building blocks. Triple-crossover nanotubes display a constant diameter of approximately 25 nm and have been observed with lengths up to 20 microm. We present high-resolution images of the constructs, experimental evidence of their tube-like nature as well as data on metallization of the nanotubes to form nanowires, and electrical conductivity measurements through the nanowires. DNA nanotubes represent a potential breakthrough in the self-assembly of nanometer-scale circuits for electronics layout because they can be targeted to connect at specific locations on larger-scale structures and can subsequently be metallized to form nanometer-scale wires. The dimensions of these nanotubes are also perfectly suited for applications involving interconnection of molecular-scale devices with macroscale components fabricated by conventional photolithographic methods.
Generation and Characterization of B7-H4/B7S1/B7x-Deficient Mice (2006)

Members of the B7 family of cosignaling molecules regulate T-cell proliferation and effector functions by engaging cognate receptors on T cells. In vitro and in vivo blockade experiments indicated that B7-H4 (also known as B7S1 or B7x) inhibits proliferation, cytokine production, and cytotoxicity of T cells. B7-H4 binds to an unknown receptor(s) that is expressed on activated T cells. However, whether B7-H4 plays nonredundant immune regulatory roles in vivo has not been tested. We generated B7-H4-deficient mice to investigate the roles of B7-H4 during various immune reactions. Consistent with its inhibitory function in vitro, B7-H4-deficient mice mounted mildly augmented T-helper 1 (Th1) responses and displayed slightly lowered parasite burdens upon Leishmania major infection compared to the wild-type mice. However, the lack of B7-H4 did not affect hypersensitive inflammatory responses in the airway or skin that are induced by either Th1 or Th2 cells. Likewise, B7-H4-deficient mice developed normal cytotoxic T-lymphocyte reactions against viral infection. Thus, B7-H4 plays a negative regulatory role in vivo but the impact of B7-H4 deficiency is minimal. These results suggest that B7-H4 is one of multiple negative cosignaling molecules that collectively provide a fine-tuning mechanism for T-cell-mediated immune responses.
Abstract 1476: A therapeutic antibody that inhibits CD73 activity by dual mechanisms (2016)

Abstract CD73 has a central role in dictating the adenosine concentration within the tumor as it is the final step in converting extracellular ATP to adenosine. Thus, substantial reduction of CD73 enzymatic activity has the potential to reduce immunosuppression of effector immune cells within the tumor. We present data describing an anti-human CD73 antibody that suppresses CD73 by two mechanisms: 1. direct inhibition of enzymatic activity upon binding to CD73 and 2. rapid, near-complete internalization of the enzyme. Durable reduction of cell-surface CD73 was observed in multiple tumor cell lines both in vitro and in vivo. The unique properties of this antibody are a result of the use of a human IgG2-IgG1 hybrid antibody with effector function eliminated by specific mutations of the Fc. The IgG2 sequence of this antibody drives superior internalization of CD73 and enhanced CD73 inhibition. Syngeneic tumor models demonstrate that CD73 contributes to resistance to anti-tumor therapy. Combination therapy with PD-1 blockade and a surrogate anti-mouse-CD73 antibody resulted in a better anti-tumor efficacy than either treatment alone. Finally, we demonstrate a novel technique for assessing CD73 enzymatic activity in situ that has potential for clinical application. These data support antibody-based anti-CD73 therapy in cancer and highlight a novel mechanism for inhibition of CD73 enzymatic activity. Citation Format: Bryan C. Barnhart, Emanuela Sega, Aaron Yamniuk, Sandra Hatcher, Ming Lei, Haben Ghermazien, Anne Lewin, Xi-Tao Wang, Haichun Huang, Pingping Zhang, Alan Korman. A therapeutic antibody that inhibits CD73 activity by dual mechanisms. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1476.
Transform-limited pulse generation in the gigahertz region from a gain-switched distributed-feedback laser diode using spectral windowing (1990)

For the first time, to our knowledge, transform-limited and high-power picosecond pulses in the gigahertz region are successfully generated from a distributed-feedback laser diode using spectral manipulation with a narrow-band Fabry-Perot resonator and erbium fiber amplifiers. The pulses, which before the optical filtering have a width of 27 psec and a spectral width of 1.24 nm, are transformed to transform-limited pulses with a width of 17 psec and a spectral width of 0.21 nm. The peak power of the pulse at a 6-GHz repetition rate is amplified to greater than 90 mW with an erbium fiber amplifier.
Effects of calmodulin antagonists on hormone release and cyclic AMP levels in GH3pituitary cells (1987)

In GH3 cells the calmodulin antagonists trifluoperazine and N-(6-aminohexyl)-5-chloro-1-napthalene sulphonamide hydrochloride (W-7) showed a dose-dependent, biphasic effect on the release of growth hormone (GH) and prolactin (PRL). Hormone release was inhibited with 15-30 microM trifluoperazine and with 30-80 microM W-7, while stimulation was observed with 50-100 microM trifluoperazine and with 150 microM W-7. Trifluoperazine (greater than or equal to 30 microM) and W-7 (greater than or equal to 80 microM) increased the concentration of cellular cyclic AMP. Sulphoxides of trifluoperazine and chlorpromazine (less than or equal to 150 microM were without effect on hormone release and cellular cyclic AMP. Hydrolysis of cyclic AMP by GH3 cytosol was reduced after incubation of intact GH3 cells with trifluoperazine (15-60 microM). When trifluoperazine was incubated with cytosol, both the high and low affinity forms of cyclic AMP phosphodiesterase were inhibited competitively with calculated Ki of 4.5 and 56 microM, respectively. Stimulation of cyclic AMP phosphodiesterase caused by endogenous calmodulin was blocked by trifluoperazine. Particulate bound adenylyl cyclase activity was inhibited by trifluoperazine, and this effect was counteracted by endogenous calmodulin.
Interactive Order-Independent Transparency (2001)

this document is to enable OpenGL developers to implement this technique with NVIDIA OpenGL extensions and GeForce3 hardware. Since shadow mapping is integral to the technique a very basic introduction is provided, but the interested reader is encouraged to explore the referenced material for more detail
Continuously variable gigahertz phase-shifter IC covering more than one frequency decade (1992)

A monolithic integrated silicon bipolar circuit which allows phase shifting of arbitrarily shaped clock signals by 0 to -2 pi within a frequency range from about 60 MHz to 1.8 GHz is described. The phase can be adjusted by a single potentiometer or by an externally applied voltage. The wide frequency and phase-shifting ranges were achieved by a mainly digital circuit principle. The temperature coefficient of the phase can be adjusted within a specific range. The circuit was realized by use of a very conservative 2- mu m standard technology.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
In Vivo Antagonism with Zidovudine plus Stavudine Combination Therapy (2000)

Human immunodeficiency virus (HIV)-infected subjects receiving zidovudine were randomized either to add stavudine (d4T) or didanosine (ddI) to their current regimen or to switch to ddI or d4T monotherapy. After 16 weeks of therapy, the mean reduction in HIV RNA from baseline was 0.14 log(10) copies/mL in patients receiving d4T or zidovudine plus d4T. In subjects receiving ddI or ddI plus zidovudine, reductions were 0.39 and 0.56 log(10), respectively. CD4 cell counts remained stable or showed modest increases in all arms except the zidovudine plus d4T arm. Patients receiving zidovudine plus d4T showed progressive declines in CD4 cell counts with a median of 22 cells/mm(3) below baseline by 16 weeks. Examination of intracellular levels of d4T-triphosphate in 6 subjects was consistent with previous in vitro studies demonstrating pharmacologic antagonism between zidovudine and d4T. Analysis of these data suggests that zidovudine and d4T should not be prescribed in combination and that ddI provides greater antiviral activity than d4T in zidovudine-treated patients.
Virtual Reality: Scientific and Technological Challenges (1994)

From the Publisher:
Despite widespread popular and professional interest in virtual reality, research and development efforts in synthetic environments (SE) - the field encompassing virtual environments, augmented reality, and teleoperation - have remained fragmented. Virtual Reality is the first serious, integrated treatment of the topic, presenting current knowledge from several disciplines along with thought-provoking vignettes about a future in which SE is commonplace. This volume discusses all aspects of creating a system that will allow human operators to see, hear, smell, taste, move about, give commands, respond to conditions, and manipulate objects effectively in a virtual environment. The committee of computer scientists, engineers, and psychologists on the leading edge of SE development explores the potential applications of SE in the areas of manufacturing, medicine, education, training, scientific visualization, and teleoperation in hazardous environments. The committee also charts directions for development of improved SE technology, needed studies of human behavior and evaluation of SE systems, and government policy and infrastructure.
Analysis of Transcriptionally Active Gene Clusters of Major Outer Membrane Protein Multigene Family inEhrlichia canisandE. chaffeensis (2001)

Ehrlichia canis and E. chaffeensis are tick-borne obligatory intramonocytic ehrlichiae that cause febrile systemic illness in humans and dogs, respectively. The current study analyzed the pleomorphic multigene family encoding approximately 30-kDa major outer membrane proteins (OMPs) of E. canis and E. chaffeensis. Upstream from secA and downstream of hypothetical transcriptional regulator, 22 paralogs of the omp gene family were found to be tandemly arranged except for one or two genes with opposite orientations in a 28- and a 27-kb locus in the E. canis and E. chaffeensis genomes, respectively. Each locus consisted of three highly repetitive regions with four nonrepetitive intervening regions. E. canis, in addition, had a 6.9-kb locus which contained a repeat of three tandem paralogs in the 28-kb locus. These total 47 paralogous and orthologous genes encoded OMPs of approximately 30 to 35 kDa consisting of several hypervariable regions alternating with conserved regions. In the 5'-end half of the 27-kb locus or the 28-kb locus of each Ehrlichia species, 14 paralogs were linked by short intergenic spaces ranging from -8 bp (overlapped) to 27 bp, and 8 remaining paralogs in the 3'-end half were connected by longer intergenic spaces ranging from 213 to 632 bp. All 22 paralogs, five unknown genes, and secA in the omp cluster in E. canis were transcriptionally active in the monocyte culture, and the paralogs with short intergenic spaces were cotranscribed with their adjacent genes, including the respective intergenic spaces at both the 5' and the 3' sides. Although omp genes are diverse, our results suggest that the gene organization of the clusters and the gene locus are conserved between two species of Ehrlichia to maintain a unique transcriptional mechanism for adaptation to environmental changes common to them.
Model-Agnostic Meta-Learning for Fast Adaptation of Deep Networks (2017)

We propose an algorithm for meta-learning that is model-agnostic, in the sense that it is compatible with any model trained with gradient descent and applicable to a variety of different learning problems, including classification, regression, and reinforcement learning. The goal of meta-learning is to train a model on a variety of learning tasks, such that it can solve new learning tasks using only a small number of training samples. In our approach, the parameters of the model are explicitly trained such that a small number of gradient steps with a small amount of training data from a new task will produce good generalization performance on that task. In effect, our method trains the model to be easy to fine-tune. We demonstrate that this approach leads to state-of-the-art performance on two few-shot image classification benchmarks, produces good results on few-shot regression, and accelerates fine-tuning for policy gradient reinforcement learning with neural network policies.
THE CONSTITUTION OF A SYNTHETIC XYLAN: II. CONTROLLED PERIODATE DEGRADATION (1962)

The controlled periodate degradation of the synthetic xylan resulted in the formation of ethylene glycol, glycerol, xylose, and at least eight non-reducing oligosaccharides. The composition, approximate D.P., periodate oxidation, and possible structure of these oligosaccharides are reported and discussed.
Biology and treatment of chronic myeloid leukemia (1997)

The BCR-ABL gene rearrangement, the initial event in the development of chronic myeloid leukemia, primarily produces clonal expansion in CML by blocking apoptosis, a genetically programmed process of autonomous cell death. The mechanism by which BCR-ABL blocks apoptosis remains unclear, although recent data are beginning to shed light on the signaling pathway. As with other antiapoptotic signals, BCR-ABL induces cellular resistance to a wide spectrum of cytotoxic antitumor agents. However, apoptosis induced by both cytotoxic T lymphocytes and natural killer or lymphokine-activated killer cells is not blocked by BCR-ABL. A substantial number of patients with chronic myeloid leukemia can now be cured, and the prognosis has improved even for those patients who are not cured. Interferon-alpha has emerged as the treatment of choice for patients who do not undergo an allogeneic bone marrow transplantation. The availability of allogeneic bone marrow transplantation has been increased by the ability to find unrelated donors, although graft-versus-host disease remains a major problem. Adoptive immunotherapy with donor lymphocyte transfusions will induce durable remissions and possibly cures in many patients who relapse after allogeneic BMT. Moreover, a number of investigational approaches, especially autologous BMT, appear promising.