gebhart/patrepeval huggingface dataset:
Characterization of mammalian translocase of inner mitochondrial membrane (Tim44) isolated from diabetic newborn mouse kidney (1998)

Mammalian translocase of mitochondrial inner membrane (mTim44) was isolated during representational difference analysis of cDNA from diabetic mouse kidney. Streptozotocin-induced diabetic mouse kidney cDNA was prepared and subtracted by normal mouse kidney cDNA. By using one of the isolated cDNA fragments as a screening probe, full-length cDNA of mTim44 was isolated from lambdaZAP kidney cDNA library. At the nucleotide level, mTim44 did not exhibit significant homology with any known genes; however, at the amino acid level, it had 50% similarity and 29% identity with yeast Tim44. C-terminal FLAG epitope-tagged mTim44 fusion protein was transiently expressed in COS7 cells. By using anti-FLAG epitope M2 monoclonal antibody, mTim44 was found to have its subcellular localization associated with mitochondria. By immunoelectron microscopy, mTim44 was seen in the paracrystalline structures within the mitochondria, as well as in their cristae. Mitochondrial import assay of in vitro translated mTim44 indicated that its precursor product ( approximately 50 kDa) was imported and proteolytically processed to a mature approximately 44-kDa protein, and its translocation was inner membrane potential (DeltaPsi)-dependent. Imported mTim44 was protected from protease digestion in which outer membranes were selectively permeabilized with digitonin. The mature form of mTim44 could be recovered in the supernatant of sonicated mitochondrial membrane fraction treated with 0.1 M Na2CO3, pH 11.5. The data indicate that mTim44 is a mitochondrial inner membrane protein, one of the members of the mammalian TIM complex and up-regulated in hyperglycemic states.
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data (2011)

hengli@broadinstitute.org.
Kinetic and Crystallographic Analysis of Active Site Mutants of Escherichia coli γ-Aminobutyrate Aminotransferase (2005)

The E. coli isozyme of gamma-aminobutyrate aminotransferase (GABA-AT) is a tetrameric pyridoxal phosphate-dependent enzyme that catalyzes transamination between primary amines and alpha-keto acids. The roles of the active site residues V241, E211, and I50 in the GABA-AT mechanism have been probed by site-directed mutagenesis. The beta-branched side chain of V241 facilitates formation of external aldimine intermediates with primary amine substrates, while E211 provides charge compensation of R398 selectively in the primary amine half-reaction and I50 forms a hydrophobic lid at the top of the substrate binding site. The structures of the I50Q, V241A, and E211S mutants were solved by X-ray crystallography to resolutions of 2.1, 2.5, and 2.52 A, respectively. The structure of GABA-AT is similar in overall fold and active site structure to that of dialkylglycine decarboxylase, which catalyzes both transamination and decarboxylation half-reactions in its normal catalytic cycle. Therefore, an attempt was made to convert GABA-AT into a decarboxylation-dependent aminotransferase similar to dialkylglycine decarboxylase by systematic mutation of E. coli GABA-AT active site residues. Two of the twelve mutants presented, E211S/I50G/C77K and E211S/I50H/V80D, have approximately 10-fold higher decarboxylation activities than the wild-type enzyme, and the E211S/I50H/V80D has formally changed the reaction specificity to that of a decarboxylase.
Annexin proteins PP4 and PP4-X. Comparative characterization of biological activities of placental and recombinant proteins (1990)

The human placental proteins PP4 and PP4-X, belonging to the annexin protein family, were expressed in Escherichia coli at high yield. The proteins were purified to homogeneity. The physicochemical parameters of the recombinant proteins were determined and compared with those of their natural placental counterparts. Except for a minor change in the pI, the proteins appeared to be indistinguishable by several criteria. Both recombinant PP4 and recombinant PP4-X were biologically active in a thromboplastin inhibition test and in a phospholipase A2 inhibition test.
A comparative investigation of methods for logistic regression with separated or nearly separated data (2006)

Abstract In logistic regression analysis of small or sparse data sets, results obtained by classical maximum likelihood methods cannot be generally trusted. In such analyses it may even happen that the likelihood meets the convergence criteria while at least one parameter estimate diverges to ±∞. This situation has been termed ‘separation’, and it typically occurs whenever no events are observed in one of the two groups defined by a dichotomous covariate. More generally, separation is caused by a linear combination of continuous or dichotomous covariates that perfectly separates events from non‐events. Separation implies infinite or zero maximum likelihood estimates of odds ratios, which are usually considered unrealistic. I provide some examples of separation and near‐separation in clinical data sets and discuss some options to analyse such data, including exact logistic regression analysis and a penalized likelihood approach. Both methods supply finite point estimates in case of separation. Profile penalized likelihood confidence intervals for parameters show excellent behaviour in terms of coverage probability and provide higher power than exact confidence intervals. General advantages of the penalized likelihood approach are discussed. Copyright © 2006 John Wiley &amp; Sons, Ltd.
A New Class of Easily Activated Palladium Precatalysts for Facile C−N Cross-Coupling Reactions and the Low Temperature Oxidative Addition of Aryl Chlorides (2008)

A new class of one-component Pd precatalysts bearing biarylphosphine ligands is described. These precatalysts are air- and thermally stable, are easily activated under normal reaction conditions at or below room temperature, and ensure the formation of the highly active monoligated Pd(0) complex necessary for oxidative addition. The use of these precatalysts as a convenient source of LPd(0) in C-N cross-coupling reactions is explored. The reactivity that is demonstrated in this study is unprecedented in palladium chemistry.
Direct Molecular Detection of Nucleic Acids by Fluorescence Signal Amplification (2005)

An integrated PCR-free DNA sensor, which combines a sequence-specific receptor, an optical polymeric transducer, and an intrinsic fluorescence amplification mechanism, is reported. This sensor is based on the different conformations adopted by a cationic polythiophene when electrostatically bound to ss-DNA or ds-DNA, and on the efficient and fast energy transfer between the resulting fluorescent polythiophene/ds-DNA complex and neighboring fluorophores attached to ss-DNA probes. This molecular system allows the detection of only five molecules in 3 mL of an aqueous solution, or 3 zM, in 5 min. Moreover, this work demonstrates, for the first time, the direct detection of single nucleotide polymorphisms (SNPs) from clinical samples in only a few minutes, without the need for nucleic acid amplification.
Click Chemistry for Drug Discovery (2006)

This chapter contains sections titled: Introduction Click Chemistry Reactions Click Chemistry in Drug Discovery Lead Discovery Libraries Natural Products Derivatives and the Search for New Antibiotics Synthesis of Neoglycoconjugates HIV Protease Inhibitors Synthesis of Fucosyltranferase Inhibitor Glycoarrays In Situ Click Chemistry Discovery of Highly Potent AChE by In Situ Click Chemistry Bioconjugation Through Click Chemistry Tagging of Live Organisms and Proteins Activity-based Protein Profiling Labeling of DNA Artificial Receptors Conclusion References
Purine Functional Groups in Essential Residues of the Hairpin Ribozyme Required for Catalytic Cleavage of RNA (1995)

Synthetic chemistry techniques have been used to study the functional group requirements of the essential purine residues in hairpin ribozyme cleavage. Three-stranded ribozymes were prepared that had functional group deletions or alterations at single purine sites within loops A and B of the hairpin, and the kinetics of cleavage were compared to those of the unmodified ribozyme. Adenosine analogues used were purine riboside and N7-deazaadenosine, and guanosine analogues used were inosine, N7-deazaguanosine, and O6-methylguanosine. In many cases, introduction of one of these analogues caused substantial loss of ribozyme cleavage activity. Most of the impairments of activity were found to be due to changes in kcat rather than in KM. The losses corresponded in magnitude to loss of at least one hydrogen bond, and the results were rationalized in terms of removal of potential cross-strand hydrogen bonds as well as potential hydrogen bonds between loops A and B. A new secondary structure model for loop B was proposed. Finally, the magnesium ion dependence of cleavage was studied for the modified ribozymes and compared to that of the unmodified ribozyme. It is proposed that magnesium binds in the ground state to the N7-positions of G + 1 and A43 and in the transition state to the N7-position at A9. The results provide further evidence for the folding of the two arms of the hairpin so that in the active conformation loops A and B approach closely to form a specific three-dimensional structure with a magnesium ion (or ions) placed between the loops, making contacts in the ground state and in the transition state.
hBD‐1: a novel β‐defensin from human plasma (1995)

We report the isolation and characterization of a novel peptide with significant sequence homology to beta-defensins from human blood filtrate. The human beta-defensin-1 (hBD-1) is a short basic peptide of 36 amino acid residues. It contains six cysteines forming three intramolecular disulfide bonds. The molecular mass of hBD-1 is 3928.6 Da. Cloning of the specific cDNA confirmed the amino acid sequence of the native peptide. hBD-1 shares the nine conserved amino acids characteristic for beta-defensins from respiratory epithelial cells and neutrophils of cattle and chicken leukocytes. hBD-1 is present in nanomolar concentration in human plasma.
Transforming growth factor-β and the protection from cardiovascular injury hypothesis (1995)

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Increased protein expression of DNA methyltransferase (DNMT) 1 is significantly correlated with the malignant potential and poor prognosis of human hepatocellular carcinomas (2003)

Alteration of DNA methylation is one of the most consistent epigenetic changes in human cancers. DNA methyltransferase (DNMT) 1 is a major enzyme involved in establishing genomic methylation patterns. Most of the studies concerning DNMT1 expression in human cancers have been performed only at the mRNA level. To directly examine DNMT1 protein expression levels during human hepatocarcinogenesis, 16 histologically normal liver tissues, 51 noncancerous liver tissues exhibiting chronic hepatitis or cirrhosis, which are considered to be precancerous conditions, and 53 hepatocellular carcinomas (HCCs) were subjected to immunohistochemic examination. If more than 20% of the cells exhibited nuclear DNMT1 staining, the tissue sample was considered to be DNMT1-positive. DNMT1 immunoreactivity was observed in 23 (43%) of the HCCs, but in none (0%) of the histologically normal liver or noncancerous liver tissues exhibiting chronic hepatitis or cirrhosis. The incidence of increased DNMT1 protein expression in HCCs correlated significantly with poor tumor differentiation (p = 0.0006) and portal vein involvement (p = 0.0002). Moreover, the recurrence-free (p = 0.0001) and overall (p < 0.0001) survival rates of patients with HCCs exhibiting increased DNMT1 protein expression were significantly lower than those of patients with HCCs that did not exhibit increased expression. Increased DNMT1 protein expression may play a critical role in the malignant progression of HCCs and be a biologic predictor of both HCC recurrence and a poor prognosis in HCC patients.
State Medicaid systems placed on trial: Physicians, patients attempt reforms to up payment, access (1994)

Physicians and patients who say they can9t wait for federal health care reform are taking their Medicaid systems to court, demanding better services. Increasingly, physicians in many states say they find reimbursement rates inadequate to continue accepting Medicaid-insured patients. State governments are being hit with federal demands for increased public health services, but no extra money. Low-income patients are left with few physicians willing to accept their Medicaid cards.
Cellular delivery of PEGylated PLGA nanoparticles (2011)

These preliminary findings indicated that the nanoparticle formulation prepared with 15% PEGylated PLGA showed maximum cellular uptake due to it having the smallest particle size and lowest zeta potential.
Absolute Positioning Using the Earth's Magnetic Anomaly Field (2016)

Achieving worldwide dependable alternatives to the Global Positioning System is a challenging engineering problem. Current Global Positioning System alternatives often suffer from limitations such as where and when the systems can operate. Navigation using Earth's magnetic anomaly field, which is globally available at all times, shows promise to overcome many of these limitations. We present a navigation framework that uses Earth's magnetic anomaly field as a navigation signal to aid an inertial navigation system in an aircraft. The filter utilizes ultra-accurate optically pumped cesium magnetometers to make scalar intensity measurements of Earth's magnetic field and compare them with a map using a particle filter approach. The accuracy of these measurements allows observability of not only the inertial navigation system errors but also the temporal effects of Earth's magnetic field, which corrupt the navigation signal. These temporal effects are thoroughly analyzed, and we present a simple model that allows near worldwide use of the navigation filter. We analyze the dependencies on altitude and magnetic storm activity in a realistic simulation using data from test flights and magnetic observatories. Published 2016. This article is a U.S. Government work and is in the public domain in the USA
Bifunctional transition metal-based molecular catalysts for asymmetric syntheses (2005)

The discovery and development of conceptually new chiral bifunctional transition metal-based catalysts for asymmetric reactions is described. The chiral bifunctional Ru catalyst was originally developed for asymmetric transfer hydrogenation of ketones and imines and is now successfully applicable to enantioselective C-C bond formation reaction with a wide scope and high practicability. The deprotonation of 1,3-dicarbonyl compounds with the chiral amido Ru complexes leading to the amine Ru complexes bearing C- or O-bonded enolates, followed by further reactions with electrophlies gives C-C bond formation products. The present bifunctional Ru catalyst offers a great opportunity to open up new fundamentals for stereoselective molecular transformation including enantioselective C-H and C-C as well as C-O, C-N bond formation.
A Z Approach in Validating ORA-SS Data Models (2006)

The rapid growth of the World Wide Web has resulted in more data being accessed over the Internet. In turn there is an increase in the use of semistructured data, which plays a crucial role in many web applications particularly with the introduction of XML and its related technologies. This increase in use makes the design of good semistructured data structures essential. The Object Relationship Attribute model for Semistructured data (ORA-SS) is a graphical notation for designing and representing semistructured data. In this paper, we demonstrate an approach to formally validate the ORA-SS data models in order to enhance the correctness of semistructured data design. A mathematical semantics for the ORA-SS notation is defined using the Z formal language, and further validation processes are carried out to check the correctness of the semistructured data models at both the schema and instance levels.
Business performance ? a stakeholder approach (1998)

The integration of business and stakeholder values with performance measurement and management is explored. The state of the art of business performance is investigated and subsequently related to the stakeholder theory. Strengths and weaknesses of such a philosophy are analysed and discussed. The concept of Value to the Business is focused upon by formulating a related index that is based on the organisation's major stakeholder satisfaction metrics. It is argued that the future sustainable organisation would need to be inclusive in its approach and practice, galvanizing both the economic and moral aspects in its pursuit of business excellence.
Regulation of mucosal IgA responses: lessons from primary immunodeficiencies (2011)

Adaptive co-evolution of mammals and bacteria has led to the establishment of complex commensal communities on mucosal surfaces. In spite of having available a wealth of immune-sensing and effector mechanisms capable of triggering inflammation in response to microbial intrusion, mucosal immune cells establish an intimate dialogue with microbes to generate a state of hyporesponsiveness against commensals and active readiness against pathogens. A key component of this homeostatic balance is IgA, a noninflammatory antibody isotype produced by mucosal B cells through class switching. This process involves activation of B cells by IgA-inducing signals originating from mucosal T cells, dendritic cells, and epithelial cells. Here, we review the mechanisms by which mucosal B cells undergo IgA diversification and production and discuss how the study of primary immunodeficiencies facilitates better understanding of mucosal IgA responses in humans.
The Role of Competition Policy in Canada's Industrial Policy (1993)

competition policy and industrial policy--Canada
광주,전남지역의 SOC 확충방안 -국내외적 SOC 수요 증가와 관련하여- (2002)

SOC is a material resource of national economy that contributes directly to the economic development and the national welfare promotion. In addition SOC, which offers the basic service to all product lines as an industrial capital, bears bull fruits in the increased productivity, the retrenchment of market expense, the enlargement of employment and income, and the increased export. The stock holdings of an indirect capital in a country can show a supply capacity of the government public service as an indicator of national competitiveness. There is no agreement on what way is the most desirable in invested resources needed for the expansion of social indirect capital. Especially, the SOC insufficiency of Kwangju-Cheonnam which lasted a few years, could often be under lagging behind. It is demanded that both political efforts and public participation be needed more and more.
Delivering new insight into the biology of megakaryopoiesis and thrombopoiesis (2007)

This review integrates the latest studies of megakaryocyte development into the molecular pathways that regulate megakaryopoiesis and thrombopoiesis. Decoding the pathways of megakaryopoiesis and platelet production should help revolutionize the management of thrombocytopenia and other platelet disorders.
State of the Art in Ray Tracing Animated Scenes (2007)

Ray tracing has long been a method of choice for off-line\nrendering, but traditionally was too slow for interactive\nuse. With faster hardware and algorithmic improvements this\nhas recently changed, and real-time ray tracing is finally\nwithin reach. However, real-time capability also opens up\nnew problems that do not exist in an off-line environment.\nIn particular real-time ray tracing offers the opportunity\nto interactively ray trace moving/animated scene content.\nThis presents a challenge to the data structures that have\nbeen developed for ray tracing over the past few decades.\nSpatial data structures crucial for fast ray tracing must be\nrebuilt or updated as the scene changes, and this can become\na bottleneck for the speed of ray tracing.\n\nThis bottleneck has received much recent attention by\nresearchers that has resulted in a multitude of different\nalgorithms, data structures, and strategies for handling\nanimated scenes. The effectiveness of techniques for ray\ntracing dynamic scenes vary dramatically depending on\ndetails such as scene complexity, model structure, type of\nmotion, and the coherency of the rays. Consequently, there\nis so far no approach that is best in all cases, and\ndetermining the best technique for a particular problem can\nbe a challenge. In this STAR, we aim to survey the different\napproaches to ray tracing animated scenes, discussing their\nstrengths and weaknesses, and their relationship to other\napproaches. The overall goal is to help the reader choose\nthe best approach depending on the situation, and to expose\npromising areas where there is potential for algorithmic\nimprovements.
Sirolimus Conversion Regimen Versus Continued Calcineurin Inhibitors in Liver Allograft Recipients: A Randomized Trial (2012)

A large prospective, open-label, randomized trial evaluated conversion from calcineurin inhibitor (CNI)- to sirolimus (SRL)-based immunosuppression for preservation of renal function in liver transplantation patients. Eligible patients received liver allografts 6-144 months previously and maintenance immunosuppression with CNI (cyclosporine or tacrolimus) since early posttransplantation. In total, 607 patients were randomized (2:1) to abrupt conversion (<24 h) from CNI to SRL (n = 393) or CNI continuation for up to 6 years (n = 214). Between-group changes in baseline-adjusted mean Cockcroft-Gault GFR at month 12 (primary efficacy end point) were not significant. The primary safety end point, noninferiority of cumulative rate of graft loss or death at 12 months, was not met (6.6% vs. 5.6% in the SRL and CNI groups, respectively). Rates of death at 12 months were not significantly different, and no true graft losses (e.g. liver transplantation) were observed during the 12-month period. At 52 weeks, SRL conversion was associated with higher rates of biopsy-confirmed acute rejection (p = 0.02) and discontinuations (p < 0.001), primarily for adverse events. Adverse events were consistent with known safety profiles. In conclusion, liver transplantation patients showed no demonstrable benefit 1 year after conversion from CNI- to SRL-based immunosuppression.
Incorporating track records of agents into matchmaking in middle agents (2008)

Middle agents play a very important role in multiagent systems used in open and dynamic environments. The performance of middle agents relies heavily on the matchmaking algorithms used. The actual performance of provider agents in accomplishing delegated tasks has a significant impact on the matchmaking outcomes of middle agents. With those observations in mind, this paper discusses the incorporation of the track records of agents in accomplishing delegated tasks into the matchmaking process. How to provide initial values for track records in the algorithm are detailed. A prototype is also built to verify the algorithm. Based on the improved algorithm, the matchmaking outcomes are more accurate and reasonable.
AROYLISOTHIOCYANATES IN HETEROCYCLIC SYNTHESIS: SYNTHESIS OF NEW BENZIMIDAZOLE DERIVATIVES WITH ANTICIPATED FUNGICIDAL ACTIVITY (1991)

Abstract The reactions of aroylisocyanates with 2-cyanomethylbenzimidazole (1) lead to the formation of 1:1 adducts (2a,b,c) and the corresponding α-aroyl derivatives (4a,b,c). The adducts (2a,b) could be cyclized affording pyrimido [3,4-a] benzimidazole derivatives (5a-d). They also afforded (pyrazol-4-yl) benzimidazole derivatives (7a,b) when (2a,b,c) reacts with hydrazine hydrate. Derivatives (5c,7a) could be cyclized to pyrazolo [4′,5′:5,4] pyrimidobenzimidazoles (8,9).