gebhart/patrepeval huggingface dataset:
Deconstructing Myotonic Dystrophy (2000)

Triplet repeat diseases are disorders in which there is expansion of a repeat sequence of three nucleotides in the affected gene. Although the pathology usually results from production of a defective protein, myotonic dystrophy (DM) has proved to be a puzzle because the expanded repeats appear in a non-coding region of the affected DMPK gene. In a Perspective, Tapscott explains how findings from a new mouse model of DM (Mankodi et al.) could solve this paradox.
Phase II study of temozolomide, thalidomide, and celecoxib for newly diagnosed glioblastoma in adults (2008)

We conducted a phase II study of the combination of temozolomide and angiogenesis inhibitors for treating adult patients with newly diagnosed glioblastoma. Patients who had stable disease following standard radiation therapy received temozolomide for 5 days in 28-day cycles, in combination with daily thalidomide and celecoxib. Patients were treated until tumor progression or development of unacceptable toxicity. Four-month progression-free survival (PFS) from study enrollment was the primary end point, and overall survival (OS) was the secondary end point. In addition, we sought to correlate response with O(6)-methylguanine-DNA methyltransferase promoter methylation status and serum levels of angiogenic peptides. Fifty patients with glioblastoma were enrolled (18 women, 32 men). Median age was 54 years (range, 29-78) and median KPS score was 90 (range, 70-100). From study enrollment, median PFS was 5.9 months (95% confidence interval [CI]: 4.2-8.0) and 4-month PFS was 63% (95% CI: 46%-75%). Median OS was 12.6 months (95% CI: 8.5-16.4) and 1-year OS was 47%. Of the 47 patients evaluable for best response, none had a complete response, five (11%) had partial response, four (9%) had minor response, 22 (47%) had stable disease, and 16 (34%) had progressive disease. Analysis of serial serum samples obtained from 47 patients for four angiogenic peptides failed to show a significant correlation with response or survival for three of the peptides; higher vascular endothelial growth factor levels showed a trend toward correlation with decreased OS (p=0.07) and PFS (p=0.09). The addition of celecoxib and thalidomide to adjuvant temozolomide was well tolerated but did not meet the primary end point of improvement of 4-month PFS from study enrollment.
Coexpression of a multidrug-resistance gene (MDR1) and herpes simplex virus thymidine kinase gene as part of a bicistronic messenger RNA in a retrovirus vector allows selective killing of MDR1-transduced cells (1995)

A new retroviral vector, pSXLC/pHa, was constructed to coexpress drug-selectable markers with a second gene of interest as a part of a bicistronic mRNA in a retroviral vector using an internal ribosome entry site (IRES) from encephalomyocarditis virus. This system was used to develop a new retroviral vector pHa-MDR-IRES-TK which expresses a single mRNA from which translation of the MDR1 gene is cap dependent and translation of the herpes simplex virus thymidine kinase gene is IRES dependent. The pHa-MDR-IRES-TK transfectants showed high levels of P-glycoprotein expression and multidrug resistance. More than 95% of the vincristine-resistant cells transfected or transduced with pHa-MDR-IRES-TK showed hypersensitivity to ganciclovir, which selects against cells expressing herpes simplex virus thymidine kinase. An amphotropic retrovirus titer of 7.8 x 10(4)/ml was obtained with this vector. This safety-modified vector should be useful for introducing the MDR1 gene into bone marrow cells to protect normal cells from the toxic effects of cancer chemotherapy because this vector allows the elimination of cancer cells that have been unintentionally transduced with the MDR1 vector.
A composite high-frame-rate system for clinical cardiovascular imaging (2008)

High frame-rate ultrasound RF data acquisition has been proved to be critical for novel cardiovascular imaging techniques, such as high-precision myocardial elastography, pulse wave imaging (PWI), and electromechanical wave imaging (EWI). To overcome the frame-rate limitations on standard clinical ultrasound systems, we developed an automated method for multi-sector ultrasound imaging through retrospective electrocardiogram (ECG) gating on a clinically used open architecture system. The method achieved both high spatial (64 beam density) and high temporal resolution (frame rate of 481 Hz) at an imaging depth up to 11 cm and a 100% field of view in a single breath-hold duration. Full-view imaging of the left ventricle and the abdominal aorta of healthy human subjects was performed using the proposed technique in vivo. ECG and ultrasound RF signals were simultaneously acquired on a personal computer (PC). Composite, full-view frames both in RF- and B-mode were reconstructed through retrospective combination of seven small (20%) juxtaposed sectors using an ECG-gating technique. The axial displacement of the left ventricle, in both long-axis and short-axis views, and that of the abdominal aorta, in a long-axis view, were estimated using a RF-based speckle tracking technique. The electromechanical wave and the pulse wave propagation were imaged in a ciné-loop using the proposed imaging technique. Abnormal patterns of such wave propagation can serve as indicators of early cardiovascular disease. This clinical system could thus expand the range of applications in cardiovascular elasticity imaging for quantitative, noninvasive diagnosis of myocardial ischemia or infarction, arrhythmia, abdominal aortic aneurysms, and early-stage atherosclerosis.
Pharmacokinetics of sodium humate in chickens. (1994)

Free or liposome-encapsulated sodium humate was administered to chickens intracardially, orally or subcutaneously and the following principal pharmacokinetic parameters were determined using the MW Pharm software for two-compartment models: elimination half-life (t1/2 el), steady state distribution volume (Vdss), blood clearance (Cl), maximal drug concentration (Cmax), time required for appearance of Cmax (tmax), area under the curve (AUC) and bioavailability (F). Blood clearance of liposome-encapsulated sodium humate was higher than that of free sodium humate regardless of the way of administration. On the other hand, the elimination half-life was longer after the extravascular than after the intracardial administration. Cmax values indicate that the penetration of sodium humate from the injection site into blood circulation is very slow. Biological availability of sodium humate also depended on the way of administration and dosage form. Aside from the intracardial administration, the highest bioavailability was found after subcutaneous administration of free sodium humate.
Duplication of the mmoX gene in Methylosinus sporium: cloning, sequencing and mutational analysis (2006)

The soluble methane monooxygenase (sMMO) is a key enzyme for methane oxidation, and is found in only some methanotrophs, including Methylosinus sporium 5. sMMO expression is regulated at the level of transcription from a sigma(54) promoter by a copper-switch, and is only expressed when the copper-to-biomass ratio during growth is low. Extensive phylogenetic and genetic analyses of sMMOs and other soluble di-iron monooxygenases reveal that these enzymes have only been acquired relatively recently through horizontal gene transfer. In this study, further evidence of horizontal gene transfer was obtained, through cloning and sequencing of the genes encoding the sMMO enzyme complex plus the regulatory genes mmoG and mmoR, and identification of a duplicate copy of the mmoX gene in Ms. sporium. mmoX encodes the alpha subunit of the hydroxylase of the sMMO enzyme, which constitutes the active site (Prior & Dalton, 1985). The mmoX genes were characterized at the molecular and biochemical levels. Although both copies were transcribed, only mmoX copy 1 was essential for sMMO activity. Construction of an sMMO(-) mutant by marker-exchange mutagenesis gave some possible insights into the role of the water-soluble pigment in siderophore-mediated iron acquisition. Finally, the amenability of Ms. sporium to genetic manipulation was demonstrated by complementing the sMMO(-) mutant by heterologous expression of sMMO genes from Methylosinus trichosporium OB3b and Methylococcus capsulatus (Bath), and it was shown that Ms. sporium could be used as an alternative model organism for molecular analysis of MMO regulation.
Close and focal contact adhesions of fibroblasts to a fibronectin-containing matrix. (1985)

The fibroblast cell line Balb/c 3T3 makes both close and tight-focal adhesive contacts with the plasma fibronectin (pFn)-coated tissue culture substratum. Detachment of these cells mediated by ethylene glycol bis(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid leaves tight-focal contacts and a subset of close contacts as substratum-attached material (SAM). The enrichment of heparan sulfate (HS) proteoglycan (HS-PG) in SAM under specific attachment conditions, as well as the recent demonstration of HS binding to pFn or cellular Fn, has evolved a series of experiments with the selective HS-binding protein platelet factor-4 to analyze the requirement of the HS-binding activity of pFn in the formation of these two types of adhesive contacts. In addition, the cell-binding domain (CBD) of pFn, which recognizes an unidentified cell surface receptor, has been isolated free of HS-binding domains after proteolytic cleavage of pFn. These functional studies indicate that the binding of pFn on the substratum to cell surface HS-PG is necessary and sufficient to generate close contacts with transmembrane signaling of this proteoglycan to reorganize lengthy microfilament bundles in the cytoplasm. Cells spread incompletely on CBD alone, form only close contacts, and reorganize highly concentrated actin filaments only in their spiky projections. Furthermore, the formation of tight-focal contacts with associated stress fibers appears to require both reactions of pFn, binding to cell surface HS-PG and to its unidentified receptor. The importance of HS-PG in these functional studies has led to its better biochemical characterization in SAM. Initially formed close contacts of these cells contain principally a large HS-PG that aggregates into high-molecular-weight complexes by some unknown mechanism. With time, there are two different mechanisms of catabolism of HS-PG, one of which includes the liberation of single-chain HS. The importance of these changes in the HS-PG in SAM are now being analyzed with regard to the formation and disappearance of close and tight-focal adhesions.
Data‐adaptive algorithms for calling alleles in repeat polymorphisms (1997)

Data-adaptive algorithms are presented for separating overlapping signatures of heterozygotic allele pairs in electrophoresis data. Application is demonstrated for human microsatellite CA-repeat polymorphisms in LiCor 4000 and ABI 373 data. The algorithms allow overlapping alleles to be called correctly in almost every case where a trained observer could do so, and provide a fast automated objective alternative to human reading of the gels. The algorithm also supplies an indication of confidence level which can be used to flag marginal cases for verification by eye, or as input to later stages of statistical analysis.
In Vitro Polymerization of Heparan Sulfate Backbone by the EXT Proteins (2003)

Multiple exosotoses is a dominantly inherited bone disorder caused by defects in EXT1 and EXT2, genes encoding glycosyltransferases involved in heparan sulfate chain elongation. Heparan sulfate polymerization occurs by the alternating addition of glucuronic acid and N-acetylglucosamine units to the nonreducing end of the polysaccharide. EXT1 and EXT2 are suggested to be dual glucuronyl/N-acetylglucosaminyltransferases, and a heterooligomeric complex of EXT1 and EXT2 (EXT1/2) is considered to be the biological functional polymerization unit. Here, we have investigated the in vitro polymerization capacities of recombinant soluble EXT1, EXT2, and EXT1/2 complex on exogenous oligosaccharide acceptors derived from Escherichia coli K5 capsular polysaccharide. Incubations of recombinant EXT1 or EXT1/2 complex with 3H-labeled oligosaccharide acceptors and the appropriate nucleotide sugars resulted in conversion of the acceptors to higher molecular weight compounds but with different efficacies for EXT1 and EXT1/2. In contrast, incubations with recombinant EXT2 resulted in the addition of a single glucuronic acid but no further polymerization. These results indicate that EXT1 alone and the EXT1/2 heterocomplex can act as heparan sulfate polymerases in vitro without the addition of additional auxiliary proteins.
Effect of Germanium content on mobility enhancement for strained silicon FET (2017)

This paper reports on mobility enhancement in the strained silicon (Si) based field effect transistor (FET) structure corresponds to variation of germanium (Ge) content. The investigations were performed via Silvaco TCAD virtual fabrication and characterizations platforms, ATHENA and ATLAS tools, respectively. In this study, it involved physical modelling of both conventional and strained Si FETs for comparison. The doping dose of the polysilicon was manipulated from 1.0 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">13</sup> to 4.2 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">14</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> which results in variation of the channel length from 90 nm to 22 nm. The threshold voltage of both structure had been compared where for the case of the conventional FET, the threshold voltage decreased as the channel length decreased. Accordingly, as the channel length of strained Si FET decreased, the threshold voltage increased with the Ge content in the channel that varied from 10% to 90%. The sub-threshold voltage was observed to increase as the strained Si FET entered the short channel regime, however it continued to slightly decrease as it went deeper into the sub-nanometer technology node. The strained Si FET had up to ~4.2 times carrier mobility enhancement compared to that of conventional FET as the mole fraction of Ge increased in the Si <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1-x</sub> Ge <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> layer of the strain channel. The presence of Ge in the strain layer at the channel has been proved to further enhance the mobility thus improving the drive current. Large drive current aids to the faster switching speed of the transistor, making the circuits to run at higher clock rates.
Protein Kinase C δ Is Essential for Etoposide-induced Apoptosis in Salivary Gland Acinar Cells (1999)

We have previously shown that parotid C5 salivary acinar cells undergo apoptosis in response to etoposide treatment as indicated by alterations in cell morphology, caspase-3 activation, DNA fragmentation, sustained activation of c-Jun N-terminal kinase, and inactivation of extracellular regulated kinases 1 and 2. Here we report that apoptosis results in the caspase-dependent cleavage of protein kinase C-delta (PKCdelta) to a 40-kDa fragment, the appearance of which correlates with a 9-fold increase in PKCdelta activity. To understand the function of activated PKCdelta in apoptosis, we have used the PKCdelta-specific inhibitor, rottlerin. Pretreatment of parotid C5 cells with rottlerin prior to the addition of etoposide blocks the appearance of the apoptotic morphology, the sustained activation of c-Jun N-terminal kinase, and inactivation of extracellular regulated kinases 1 and 2. Inhibition of PKCdelta also partially inhibits caspase-3 activation and DNA fragmentation. Immunoblot analysis shows that the PKCdelta cleavage product does not accumulate in parotid C5 cells treated with rottlerin and etoposide together, suggesting that the catalytic activity of PKCdelta may be required for cleavage. PKCalpha and PKCbeta1 activities also increase during etoposide-induced apoptosis. Inhibition of these two isoforms with Gö6976 slightly suppresses the apoptotic morphology, caspase-3 activation, and DNA fragmentation, but has no effect on the sustained activation of c-Jun N-terminal kinase or inactivation of extracellular regulated kinase 1 and 2. These data demonstrate that activation of PKCdelta is an integral and essential part of the apoptotic program in parotid C5 cells and that specific activated isoforms of PKC may have distinct functions in cell death.
Checking Concise Specifications for Multithreaded Software. (2004)

Ensuring the reliability of multithreaded software systems is difficult due to the potential for subtle interactions between threads. We present a new modular verification technique to check concise specifications of large multithreaded programs. Our analysis scales to systems with large numbers of procedures and threads. We achieve thread-modular analysis by annotating each shared variable by an access predicate that summarizes the condition under which a thread may access that variable. We achieve procedure-modular analysis by annotating each procedure with a specification related to its implementation by an abstraction relation combining the notions of simulation and reduction. We have implemented our analysis in Calvin-R, a static checker for multithreaded Java programs.
Delta-sigma modulation in fractional-N frequency synthesis (1993)

A description is given of a delta-sigma ( Delta - Sigma ) modulation and fractional-N frequency division technique for performing indirect digital frequency synthesis using a phase-locked loop (PLL). The use of Delta - Sigma modulation concepts results in beneficial shaping of the phase noise (jitter) introduced by fractional-N division. The technique has the potential to provide low phase noise, fast settling time, and reduced impact of spurious frequencies when compared with existing fractional-N PLL techniques.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The distributed ASCI Supercomputer project (2000)

The Distributed ASCI Supercomputer (DAS) is a homogeneous wide-area distributed system consisting of four cluster computers at different locations. DAS has been used for research on communication software, parallel languages and programming systems, schedulers, parallel applications, and distributed applications. The paper gives a preview of the most interesting research results obtained so far in the DAS project.
Johne's Disease: A Threat to the Dairy Industry (1984)

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Flow-insensitive type qualifiers (2006)

We describe flow-insensitive type qualifiers, a lightweight, practical mechanism for specifying and checking properties not captured by traditional type systems. We present a framework for adding new, user-specified type qualifiers to programming languages with static type systems, such as C and Java. In our system, programmers add a few type qualifier annotations to their program, and automatic type qualifier inference determines the remaining qualifiers and checks the annotations for consistency. We describe a tool CQual for adding type qualifiers to the C programming language. Our tool CQual includes a visualization component for displaying browsable inference results to the programmer. Finally, we present several experiments using our tool, including inferring const qualifiers, finding security vulnerabilities in several popular C programs, and checking initialization data usage in the Linux kernel. Our results suggest that inference and visualization make type qualifiers lightweight, that type qualifier inference scales to large programs, and that type qualifiers are applicable to a wide variety of problems.
Comparable Studies of the Incidence of Stroke and its Pathological Types (1997)

The similarities in stroke incidence and pathological types are perhaps not surprising given that all the populations were westernized and mainly white. The higher rates in Novosibirsk, disappearing in the elderly, and the lower rates in Dijon have several potential explanations. These include methodological artifact and different patterns of population risk factors. Further work is needed to explore these possibilities and to extend our knowledge of stroke incidence to other parts of the world, especially developing countries.
Crystal Structure of the Ribosome at 5.5 Å Resolution (2001)

We describe the crystal structure of the complete Thermus thermophilus 70S ribosome containing bound messenger RNA and transfer RNAs (tRNAs) at 5.5 angstrom resolution. All of the 16S, 23S, and 5S ribosomal RNA (rRNA) chains, the A-, P-, and E-site tRNAs, and most of the ribosomal proteins can be fitted to the electron density map. The core of the interface between the 30S small subunit and the 50S large subunit, where the tRNA substrates are bound, is dominated by RNA, with proteins located mainly at the periphery, consistent with ribosomal function being based on rRNA. In each of the three tRNA binding sites, the ribosome contacts all of the major elements of tRNA, providing an explanation for the conservation of tRNA structure. The tRNAs are closely juxtaposed with the intersubunit bridges, in a way that suggests coupling of the 20 to 50 angstrom movements associated with tRNA translocation with intersubunit movement.
A 3D-stacked logic-in-memory accelerator for application-specific data intensive computing (2013)

This paper introduces a 3D-stacked logic-in-memory (LiM) system that integrates the 3D die-stacked DRAM architecture with the application-specific LiM IC to accelerate important data-intensive computing. The proposed system comprises a fine-grained rank-level 3D die-stacked DRAM device and extra LiM layers implementing logic-enhanced SRAM blocks that are dedicated to a particular application. Through silicon vias (TSVs) are used for vertical interconnections providing the required bandwidth to support the high performance LiM computing. We performed a comprehensive 3D DRAM design space exploration and exploit the efficient architectures to accelerate the computing that can balance the performance and power. Our experiments demonstrate orders of magnitude of performance and power efficiency improvements compared with the traditional multithreaded software implementation on modern CPU.