gebhart/patrepeval huggingface dataset:
Proofs, Programs and Executable Specifications in Higher Order Logic (2003)

This thesis presents several extensions to the generic theorem prover Isabelle, a logical framework based on higher order logic. The central contribution of this thesis is the extension of Isabelle with a calculus of primitive proof terms, in which proofs are represented using lambda-terms in the spirit of the Curry-Howard isomorphism. Primitive proof terms allow for an independent verification of proofs constructed in Isabelle by a small and reliable proof checker, and are an important prerequisite for the application of proof transformation and analysis techniques, as well as the exchange of proofs with other systems. In particular, the proof term calculus is used to study the relationship between proofs and programs. For this purpose, we first develop a generic mechanism for the extraction of provably correct programs from constructive proofs, then instantiate it for the particular object logic Isabelle/HOL, and finally apply it to several case studies, ranging from simple textbook examples to complex applications from the field of combinatorics or the theory of lambda-calculus. Moreover, we introduce an alternative approach for obtaining programs from specifications by directly interpreting inductive definitions as logic programs.
Minimal Escherichia coli Cell for the Most Efficient Production of Ethanol from Hexoses and Pentoses (2008)

To obtain an efficient ethanologenic Escherichia coli strain, we reduced the functional space of the central metabolic network, with eight gene knockout mutations, from over 15,000 pathway possibilities to 6 pathway options that support cell function. The remaining pathways, identified by elementary mode analysis, consist of four pathways with non-growth-associated conversion of pentoses and hexoses into ethanol at theoretical yields and two pathways with tight coupling of anaerobic cell growth with ethanol formation at high yields. Elimination of three additional genes resulted in a strain that selectively grows only on pentoses, even in the presence of glucose, with a high ethanol yield. We showed that the ethanol yields of strains with minimized metabolic functionality closely matched the theoretical predictions. Remarkably, catabolite repression was completely absent during anaerobic growth, resulting in the simultaneous utilization of pentoses and hexoses for ethanol production.
Using RFID to Improve Hospital Supply Chain Management for High Value and Consignment Items (2011)

This paper presents a radio-frequency identification (RFID)-enabled traceability system for the management of consignment and high value products requiring item level traceability in a hospital environment. The solution can be considered (i) as an alternative to RFID-enabled cabinets used in the replenishment of consignment and high value supplies in certain operating rooms, cardiac catheterization laboratories and interventional radiology departments, or (ii) as a complementary solution facilitating the tracking of medical devices removed from RFID-enabled cabinets. In short, the end-to-end traceability of medical products in the healthcare supply chain can be significantly enhanced.
Effects of mouse interferon on human tumour xenografts in the nude mouse host (1986)

Murine interferon (IFN) inhibited the growth of 3/3 human tumour xenografts growing in nude mice. This inhibition was independent of the sensitivity of the xenograft to human IFN. In contrast to human IFN, the murine IFN did not directly affect the human tumour cells in vitro as measured by levels of the IFN-induced enzyme 2-5A synthetase or elevation of HLA expression. In preliminary investigations into the role of the host in the murine IFN-mediated tumour inhibition, we found equal activities of this IFN in nude and in beige (NK-deficient) nude mice. Moreover, murine IFN did not elevate levels of NK-cell activity in either of these mouse strains. We conclude that murine IFN mediates this tumour inhibition via an effect on the tumour-bearing host that may or may not involve immune mechanisms.
Expression of fibroblast growth factor receptors (FGFR1, FGFR2, FGFR3) in the developing head and face (1997)

Fibroblast growth factors may play an important role in the differential growth of the skull, brain, and facial prominences. In order to understand the role of FGFs in vivo, we have analyzed the competency of head mesenchyme to respond to FGFs via expression of the high affinity receptors FGFR1, 2, and 3. Receptor transcripts, especially those of FGFR2 and FGFR3, were localized to specific regions of the head. We raise the possibilities of particular receptor-ligand combinations and the possible functions of these interactions in the morphogenesis of the head, face, and brain. Finally, we discuss the relationship between FGF receptor expression in the chicken and the phenotypes of FGF receptor mutations in humans.
INDUCTION OF LONG-TERM SURVIVAL OF HAMSTER HEART XENOGRAFTS IN RATS (1991)

The aim of this study was to determine the mechanisms responsible for concordant xenograft rejection using the hamster-to-rat heart graft model. Even though it was known that rat CD4 positive T cells proliferated to hamster stimulators in mixed lymphocyte reactions, the depletion of CD4 positive T cells in rat recipients did not lead to an extension of xenograft survival. Suppression of T cell immunity using other monoclonal antibodies or cyclosporine also failed to improve survival. Only by depleting complement with cobra-venom factor could hamster xenograft survival be prolonged, and long-term survival was achieved by combining CsA with COF. High-antibody titers to hamster cells were found after transplantation of hamster hearts, and evidence is presented that rejection of these "concordant" xenografts is mediated primarily by antibody-complement mechanisms. The antihamster antibodies were produced in the absence of T cell help, which suggests that antibody-mediated graft destruction cannot be inhibited by suppression or depletion of T cells. Pharmacologic depletion of complement for the clinical application of concordant xenografts is a promising avenue of future research.
Microfabricated Differential Mobility Spectrometry with Pyrolysis Gas Chromatography for Chemical Characterization of Bacteria (2004)

A microfabricated drift tube for differential mobility spectrometry (DMS) was used with pyrolysis-gas chromatography (py-GC) to chemically characterize bacteria through three-dimensional plots of ion intensity, compensation voltage from differential mobility spectra, and chromatographic retention time. The DMS analyzer provided chemical information for positive and negative ions simultaneously from chemical reactions between pyrolysis products in the GC effluent and reactant ions of H+(H2O)n and O2-(H2O)n in air at ambient pressure. Authentic standards for chemicals formed in the pyrolysis of bacteria showed favorable matches with plots from py-GC/DMS analysis and were supported by py-GC/MS results. These and other yet-unidentified constituents provided a means to distinguish Escherichia coli from Micrococcus luteus. A Gram-positive spore former (Bacillus megaterium) was distinguished by an abundant peak for crotonic acid evident in positive and negative ions and not observed with M. luteus. In contrast, plots from py-GC/DMS of lipid A and lipoteichoic acid showed poor matches to plots for a Gram-negative (E. coli) bacterium and a Gram-positive (M. luteus) bacterium and the differences were attributed to differences in genus sources of the biopolymers. A significant percentage of the chemical information available in py-GC/DMS is unidentified, and the analytical utility must be established. Precision in the chemical measurement was determined as +/- 0.2 V, 10% relative standard deviation (RSD), and +/- 0.05 min for compensation voltage, peak intensity, and retention time, respectively. The minimum number of total bacteria (cell forming units) detected was 6000 though detection limits and resolution could be varied by the magnitude of the separation voltage in the differential mobility spectrometer.
Immunohistochemical localization of cathepsin B in neoplastic human prostate (1995)

Cathepsin B (CB) has been shown to degrade extracellular matrix (ECM) proteins, and has been reported to be involved in invasion and metastasis of several types of solid organ tumors in human and animals, but CB has not been studied in human prostate cancer (CAP). Our objective was to determine the CB protein immunostaining pattern in CAP and to correlate the immunostaining with the degree of malignancy as reflected in the Gleason grading system. We used two types of CB antibodies (namely, monospecific, polyclonal antibodies to human liver CB prepared in rabbits, and polyclonal antibody produced in sheep) to establish CB localization patterns in neoplastic prostate. Our analysis showed a heterogeneous CB immunostaining pattern in the neoplastic human prostate. CB immunostaining occurred in many, but not all, of the neoplastic columnar/cuboidal cells of acini and isolated cells, i.e., in small ragged glands and clusters (groups) of invasive cells in the prostatic stroma. We have shown that, in general, there was a positive correlation of the intensity of CB immunostaining with the Gleason histologic score (or Gleason grade sum) tumors, i.e., from the lowest scores through score 8, but many of the tumors with scores 9 and 10 showed little CB immunostaining. Our study indicated that the increased CB immunostaining in the Gleason grade sum 5-8 tumors may be associated with increased degradation of ECM, but not in 9 and 10 despite the fact that the latter tumors are more malignant clinically. In well-differentiated tumors, fewer CB immunostaining cells were present than the moderately-differentiated tumors. In other words, most of the stromal invasion of the prostatic ECM occurred in tumors of Gleason grade sums 5-8. We suggest that CB immunostaining might be a useful method to assess stromal invasion of prostatic carcinoma, especially in the higher grade tumors.
Effect of pinitol treatment on insulin action in subjects with insulin resistance. (2000)

Four weeks of pinitol treatment did not alter baseline glucose production, insulin-mediated glucose disposal, or rates of appearance of free fatty acids and glycerol in plasma. We conclude that plasma levels of both pinitol and D-chiro-inositol are very responsive to pinitol ingestion, but insulin sensitivity does not increase after pinitol treatment in individuals with obesity and mild type 2 diabetes.
Role of a phenazine antibiotic from Pseudomonas fluorescens in biological control of Gaeumannomyces graminis var. tritici (1988)

Pseudomonas fluorescens 2-79 (NRRL B-15132) and its rifampin-resistant derivative 2-79RN10 are suppressive to take-all, a major root disease of wheat caused by Gaeumannomyces graminis var. tritici. Strain 2-79 produces the antibiotic phenazine-1-carboxylate, which is active in vitro against G. graminis var. tritici and other fungal root pathogens. Mutants defective in phenazine synthesis (Phz-) were generated by Tn5 insertion and then compared with the parental strain to determine the importance of the antibiotic in take-all suppression on wheat roots. Six independent, prototrophic Phz- mutants were noninhibitory to G. graminis var. tritici in vitro and provided significantly less control of take-all than strain 2-79 on wheat seedlings. Antibiotic synthesis, fungal inhibition in vitro, and suppression of take-all on wheat were coordinately restored in two mutants complemented with cloned DNA from a 2-79 genomic library. These mutants contained Tn5 insertions in adjacent EcoRI fragments in the 2-79 genome, and the restriction maps of the region flanking the insertions and the complementary DNA were colinear. These results indicate that sequences required for phenazine production were present in the cloned DNA and support the importance of the phenazine antibiotic in disease suppression in the rhizosphere.
PASIC. A sensor/processor array for computer vision (2002)

The PASIC prototype chip contains 256*256 photosensors, a linear array of 256 A/D converters, two 256 8-bit shift registers, 256 bit-serial processors, and a 256*256 bit dynamic RAM. It appears to be a viable architecture for low-level vision processing. The processors operate in SIMD model at 20 MHz. To avoid high speed transfer of analog data, an A/D converter in the form of a linear array of comparators is used. The architecture of the processing part conforms to the row parallel output from the A/D-converters. A simple but efficient processor excellently suited to the special VLSI constraints of the sensor was designed. The pitch in the present version of PASIC is 30 mu m and it was possible to fit the A/D-converter circuitry, the shift register, the ALU, and the memory into this narrow slot. A key factor is the unified structure achieved by extending the memory data bus to all other units within the same column. The versatility of the chip is shown using three algorithms: edge detection, shading correction, and histogram-based thresholding. Each is executed in approximately 10 ms.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Alpha2beta1 integrin is the major collagen‐binding integrin expressed on human Th17 cells (2010)

Growing evidence indicates that collagen-binding integrins are important costimulatory molecules of effector T cells. In this study, we demonstrate that the major collagen-binding integrin expressed by human Th17 cells is alpha2beta1 (α2β1) or VLA-2, also known as the receptor for collagen I on T cells. Our results show that human naïve CD4(+) T cells cultured under Th17 polarization conditions preferentially upregulate α2β1 integrin rather than α1β1 integrin, which is the receptor for collagen IV on T cells. Double staining analysis for integrin receptors and intracellular IL-17 showed that α2 integrin but not α1 integrin is associated with Th17 cells. Cell adhesion experiments demonstrated that Th17 cells attach to collagen I and collagen II using α2β1 integrin but did not attach to collagen IV. Functional studies revealed that collagens I and II but not collagen IV costimulate the production of IL-17A, IL-17F and IFN-γ by human Th17 cells activated with anti-CD3. These results identify α2β1 integrin as the major collagen receptor expressed on human Th17 cells and suggest that it can be an important costimulatory molecule of Th17 cell responses.
Drug repositioning for orphan diseases (2011)

The need and opportunity to discover therapeutics for rare or orphan diseases are enormous. Due to limited prevalence and/or commercial potential, of the approximately 6000 orphan diseases (defined by the FDA Orphan Drug Act as <200 000 US prevalence), only a small fraction (5%) is of interest to the biopharmaceutical industry. The fact that drug development is complicated, time-consuming and expensive with extremely low success rates only adds to the low rate of therapeutics available for orphan diseases. An alternative and efficient strategy to boost the discovery of orphan disease therapeutics is to find connections between an existing drug product and orphan disease. Drug Repositioning or Drug Repurposing--finding a new indication for a drug--is one way to maximize the potential of a drug. The advantages of this approach are manifold, but rational drug repositioning for orphan diseases is not trivial and poses several formidable challenges--pharmacologically and computationally. Most of the repositioned drugs currently in the market are the result of serendipity. One reason the connection between drug candidates and their potential new applications are not identified in an earlier or more systematic fashion is that the underlying mechanism 'connecting' them is either very intricate and unknown or indirect or dispersed and buried in an ever-increasing sea of information, much of which is emerging only recently and therefore is not well organized. In this study, we will review some of these issues and the current methodologies adopted or proposed to overcome them and translate chemical and biological discoveries into safe and effective orphan disease therapeutics.
Optical Networks Come of Age (2014)

Big data and insatiable consumer demand for broadband are driving a new generation of intelligent, programmable, energy-efficient networks—powered by optical switching—to support Internet services reaching terabit-per-second speeds.
Toward rational protein crystallization: A Web server for the design of crystallizable protein variants (2007)

Growing well-diffracting crystals constitutes a serious bottleneck in structural biology. A recently proposed crystallization methodology for "stubborn crystallizers" is to engineer surface sequence variants designed to form intermolecular contacts that could support a crystal lattice. This approach relies on the concept of surface entropy reduction (SER), i.e., the replacement of clusters of flexible, solvent-exposed residues with residues with lower conformational entropy. This strategy minimizes the loss of conformational entropy upon crystallization and renders crystallization thermodynamically favorable. The method has been successfully used to crystallize more than 15 novel proteins, all stubborn crystallizers. But the choice of suitable sites for mutagenesis is not trivial. Herein, we announce a Web server, the surface entropy reduction prediction server (SERp server), designed to identify mutations that may facilitate crystallization. Suggested mutations are predicted based on an algorithm incorporating a conformational entropy profile, a secondary structure prediction, and sequence conservation. Minor considerations include the nature of flanking residues and gaps between mutation candidates. While designed to be used with default values, the server has many user-controlled parameters allowing for considerable flexibility. Within, we discuss (1) the methodology of the server, (2) how to interpret the results, and (3) factors that must be considered when selecting mutations. We also attempt to benchmark the server by comparing the server's predictions with successful SER structures. In most cases, the structure yielding mutations were easily identified by the SERp server. The server can be accessed at http://www.doe-mbi.ucla.edu/Services/SER.
Propionyl coenzyme A carboxylase is required for development of Myxococcus xanthus (1997)

A dcm-1 mutant, obtained by transposon mutagenesis of Myxococcus xanthus, could aggregate and form mounds but was unable to sporulate under nutrient starvation. A sequence analysis of the site of insertion of the transposon showed that the insertion lies within the 3' end of a 1,572-bp open reading frame (ORF) designated the M. xanthus pccB ORF. The wild-type form of the M. xanthus pccB gene, obtained from a lambdaEMBL library of M. xanthus, shows extensive similarity to a beta subunit of propionyl coenzyme A (CoA) carboxylase, an alpha subunit of methylmalonyl-CoA decarboxylase, and a 12S subunit of transcarboxylase. In enzyme assays, extracts of the dcm-1 mutant were deficient in propionyl-CoA carboxylase activity. This enzyme catalyzes the ATP-dependent carboxylation of propionyl-CoA to yield methylmalonyl-CoA. The methylmalonyl-CoA rescued the dcm-1 mutant fruiting body and spore development. During development, the dcm-1 mutant cells also had reduced levels of long-chain fatty acids (C16 to C18) compared to wild-type cells.
Seroprevalence of antibodies against Leishmania spp among dogs in the United States (2003)

Results suggested that the seroprevalence of antibodies against Leishmania spp in dogs in the United States was low. However, results further suggested that leishmaniasis may not be limited to Foxhounds in the United States.
Enhanced performance of resonant sub-terahertz detection in a plasmonic cavity (2012)

A multi-gate high electron mobility transistor coupled to a log-periodic antenna was engineered to detect sub-terahertz radiation through resonant excitation of plasmon modes in the channel. The device was integrated with a silicon hyper-hemispherical lens in order to enhance radiation collection and eliminate parasitic substrate modes. The continuous detector response spectrum from 185 GHz to 380 GHz indicates the presence of distinct collective plasmonic cavity modes resulting from the quantization of the plasmon wavevector. In a bolometric detection mode, a noise equivalent power of less than 50 pW/Hz1/2 and a responsivity exceeding 100 kV/W have been measured at 11.5 K.
The Design and Analysis of Virtual Network Configuration for a Wireless Mobile ATM Network (1999)

This research concentrates on the design and analysis of an algorithm referred to as Virtual Network Configuration (VNC) which uses predicted future states of a system for faster network configuration and management. VNC is applied to the configuration of a wireless mobile ATM network. VNC is built on techniques from parallel discrete event simulation merged with constraints from real-time systems and applied to mobile ATM configuration and handoff. Configuration in a mobile network is a dynamic and continuous process. Factors such as load, distance, capacity and topology are all constantly changing in a mobile environment. The VNC algorithm anticipates configuration changes and speeds the reconfiguration process by pre-computing and caching results. VNC propagates local prediction results throughout the VNC enhanced system. The Global Positioning System is an enabling technology for the use of VNC in mobile networks because it provides location information and accurate time for each node. This research has resulted in well defined structures for the encapsulation of physical processes within Logical Processes and a generic library for enhancing a system with VNC. Enhancing an existing system with VNC is straight forward assuming the existing physical processes do not have side effects. The benefit of prediction is gained at the cost of additional traffic and processing. This research includes an analysis of VNC and suggestions for optimization of the VNC algorithm and its parameters.
Characterization of a secreted glycoprotein of the immunoglobulin superfamily inducible by mitogen and oncogene (1992)

The T1 gene is transiently activated by the Ha-ras (EJ) or v-mos oncoproteins and by mitogens in NIH3T3 fibroblasts. Its primary gene product of 337 amino acids (38 kDa) undergoes extensive post-translational modification. For biochemical analysis, the T1 gene product was over-expressed in a vaccinia virus system. Cells infected with a recombinant T1-vaccinia virus produce and secrete multiple proteins of 60-70 kDa which react with polyclonal antisera raised against two T1-specific peptides. Two lines of evidence suggest that the apparent size heterogeneity of the T1 protein is due to a variable carbohydrate content of 40-50% of the total molecular mass. First, in the presence of an inhibitor of N-glycosylation (tunicamycin), a single 38-kDa protein is detected by the antisera in the cells infected with T1-vaccinia virus. Second, glycosidase digestions show that T1 protein maturation involves glycosylation and sialylation. These post-translational modification steps appear to be similar in different types of cells.
The cardioprotective effect of interleukin-11 against ischemia-reperfusion injury in a heart donor model (2018)

The administration of IL-11 showed a significant recovery of cardiac contractile function after 6 hours of cold ischemia. Our data suggest that it may have significant therapeutic potential for maintaining the functional viability of the heart exposed to prolonged hypothermic global ischemia.