gebhart/patrepeval huggingface dataset:
Interlanguage features of learners of English as a second language: from a multi-dimensional perspective (2017)

This study examined syntactic features in the interlanguage of learners of English as a second language (ESL) via tasks of conversation and free essay-writing. Data were collected from sixty international students of different first language backgrounds at the Monash University English Language Centre and examined with regard to language style, typological universal and language transfer. Results showed that interlanguage did vary in tandem with style in various syntactic aspects, that the typological universal (the Accessibility Hierarchy) was supported by the data, but that language transfer did not seem to play an important part in the use of topic-comment structure. The findings of the study suggest that examination from a multi-dimensional perspective provides a richer picture of English interlanguage features under investigation.
Cloning and disruption of the yeast C‐8 sterol isomerase gene (1991)

The yeast ERG2 gene codes for the C-8 sterol isomerase, an enzyme required for the isomerization of the delta 8 double bond to the delta 7 position in ergosterol biosynthesis. The ERG2 gene was cloned by complementation of a C-8 sterol isomerase mutant strain (erg2). The complementing region of DNA required to restore ergosterol synthesis to erg2 was limited to a 1.0 kb StuI-BglII fragment. In order to determine whether the ERG2 gene was essential for yeast viability, a LEU2 gene was inserted into the NdeI site (made blunt) of this 1.0 kb fragment. Transformation of a wild type diploid strain with the ERG2 substituted DNA resulted in the generation of viable haploids containing the erg2 null allele (erg2-4::Leu2). These results suggest that the C-8 sterol isomerase activity is not essential for yeast cell viability. This disruption represents the second ergosterol biosynthetic gene in the distal portion of the pathway to be disrupted without adversely affecting cell viability.
Defining Urticarial Dermatitis (2006)

Urticarial dermatitis seems to be a useful histological and clinical term for a subset of the dermal hypersensitivity reaction pattern. Although the clinical presentation is not restricted to a specific entity, eczema and drug reactions seem to be the most frequent clinical associations; and in a subset of patients, urticarial dermatitis remains as a recognizable reaction pattern. Urticarial dermatitis without eosinophilic spongiosis is not a reliable indicator for bullous pemphigoid, because the findings of immunofluorescence are often negative.
General Molecular Strategy for Development of Arenavirus Live-Attenuated Vaccines (2015)

Hemorrhagic fever arenaviruses (HFA) cause high morbidity and mortality, and pose important public health problems in the regions where they are endemic. Implementation of live-attenuated vaccines (LAV) will represent a major step in combatting HFA. Here we have used the prototypic arenavirus LCMV to document a general molecular strategy for arenavirus attenuation that can facilitate the rapid development of safe and effective, as well as stable, LAV to combat HFA.
Steviol Glycosides from Stevia: Biosynthesis Pathway Review and their Application in Foods and Medicine (2012)

Stevia rebaudiana, a perennial herb from the Asteraceae family, is known to the scientific world for its sweetness and steviol glycosides (SGs). SGs are the secondary metabolites responsible for the sweetness of Stevia. They are synthesized by SG biosynthesis pathway operating in the leaves. Most of the genes encoding the enzymes of this pathway have been cloned and characterized from Stevia. Out of various SGs, stevioside and rebaudioside A are the major metabolites. SGs including stevioside have also been synthesized by enzymes and microbial agents. These are non-mutagenic, non-toxic, antimicrobial, and do not show any remarkable side-effects upon consumption. Stevioside has many medical applications and its role against diabetes is most important. SGs have made Stevia an important part of the medicinal world as well as the food and beverage industry. This article presents an overview on Stevia and the importance of SGs.
403. Defined Vector Substrates Used To Probe rAAV DNA Integration (2005)

We have previously used specifically oriented self-complementary rAAV (scAAV) vectors to quantify the dynamics of vector DNA circle and concatemer formation in cultured cells. We have now extended these studies to the dynamics of vector DNA integration. Consistent with earlier studies, rAAV vectors integrated at a rate of approximately one per 1000 infectious units (IU). The infectous titers of single-stranded rAAV (ssAAV) and scAAV vectors were both measured using the replication center assay, which minimizes the differences between the two through the effects of the helper adenovirus on second-strand DNA synthesis. In a comparison of ssAAV to scAAV, we found that both yielded the same number of integrations per IU. This was surprising, given that the scAAV yields 5-50 fold higher transductions per IU, and implies either that ssAAV genomes that have undergone conversion to double-strand DNA are primed for integration, or that integration can be initiated using a single-strand vector genome as substrate. The ssAAV and scAAV vectors were also evaluated for the ratio of concatemeric to monomeric integrations using a split-GFP reporter that required concatemer formation to express the marker gene from the linear proviral state. Approximately 20% of integrated scAAV genomes, and 6% of integrated ssAAV genomes, were concatemeric, although concatemers comprised only 2% of the scAAV episomal forms. This suggested that either the concatemers were 10-fold more likely to integrate than monomoers, or that the monomeric forms were amplified by replication during or after the integration process. The latter hypothesis was tested by co-infecting cells with pairs of scAAV vectors, each containing half of the marker gene, such that genome amplification could not lead to gene expression. We found that the previously observed number of integrated concatemers could be accounted for by vector genomes joined end-to-end prior to integration, suggesting that amplification was not a significant factor. The implications of these studies for gene therapy are that the scAAV vector will result in fewer integrations per transducing unit than the single-strand vector, and that high multiplicities of infection that promote concatemer formation may also lead to disproportionately higher rates of integration.
Structural Insights and 3D Diffusion Pathways within the Lithium Superionic Conductor Li10GeP2S12 (2016)

Inspired by the ongoing debate about the ion dynamics in the lithium superionic conductor Li10GeP2S12 (LGPS), we present neutron powder diffraction data in combination with analyses of differential bond valence and nuclear density maps to elucidate the underlying diffusion pathways in Li10GeP2S12. LGPS exhibits quasi-isotropic three-dimensional lithium diffusion pathways, which is a combination of one-dimensional diffusion channels crossing two diffusion planes. Furthermore, ultrasonic speeds of sound measurements are used to understand the lattice dynamics and obtain the Debye temperature of LGPS. Temperature dependent X-ray diffraction is performed in order to understand the local temperature-dependent behavior of the prevalent structural backbone, as well as the thermal stability of the material. At elevated temperatures, the superionic conducting Li10GeP2S12 phase partially decomposes into Li4P2S6, explaining the deterioration of the ionic conductivity upon heating.
An Innovative Laboratory Method To Measure Pore-Pressure-Dependent Gas Permeability of Shale: Theory and Numerical Experiments (2018)

Summary This work proposes an innovative laboratory method to measure shale gas permeability as a function of pore pressure, a key parameter for characterizing and modeling gas flow in a shale gas reservoir. The development is based on a solution to 1D gas flow under certain boundary and initial conditions. The details of the theoretical background, including formulations to estimate gas permeability and conceptual design of the test setup, are provided. The advantages of our approach, surpassing the currently available ones, include that it measures gas permeability (as a function of pressure) with a single test run and without any presumption regarding the form of parametric relationship between gas permeability and pore pressure. In addition, our approach allows for estimating both shale permeability and porosity at the same time from the related measurements. Numerical experiments are conducted to verify the feasibility of the proposed methodology.
Immediate Fall of Bone Formation and Transient Increase of Bone Resorption in the Course of High-Dose, Short-Term Glucocorticoid Therapy in Young Patients with Multiple Sclerosis (2004)

Glucocorticoid (GC)-induced osteoporosis is the leading form of secondary osteoporosis. Bone loss can be rapid. However, longitudinal studies at the very beginning of treatment are scarce. Patients relapsing from multiple sclerosis are treated with high-dose, short-term iv GCs. A number of them are young, without concomitant disease affecting bone and with no substantial impairment of mobility. Such patients were selected for the present study. Thirteen patients suffering from multiple sclerosis [11 females, two males; age 32 +/- 2 yr (mean +/- se)] and receiving iv methylprednisolone 15 mg/kg daily for 10 d completed the study. We measured serum osteocalcin (OC), aminoterminal propeptide of type I collagen (PINP), bone isoform of alkaline phosphatase (bALP), carboxyterminal telopeptide of type I collagen (CTX), and urinary calcium/creatinine ratio (uCa/Cr) during the 10-d cycle and 3 months later. Dual-energy x-ray absorptiometry and calcaneal quantitative ultrasonometry were performed before and 6 months after therapy. We found an immediate, impressive fall of OC and PINP (-80 +/- 3 and -54 +/- 5% at d 2, respectively), which persisted throughout the whole treatment period (P < 0.0001 for both markers). bALP levels showed only a modest decrease at d 6 (-19 +/- 7%, P < 0.05), with subsequent return to baseline in d 7-10. After 3 months, OC, PINP, and bALP levels rose to +51 +/- 22, +37 +/- 16 (not significant), and +61 +/- 17% (P < 0.01) with respect to baseline, respectively. uCa/Cr and CTX showed a progressive, marked increase during treatment, peaking at d 7-9 (+92 +/- 44 and +149 +/- 63%, respectively), with subsequent decrement at d 10 (P < 0.01 and P < 0.05, respectively) despite continuing GC administration. After 3 months, uCa/Cr and CTX levels were also higher than baseline. No change in quantitative ultrasonometry parameters and bone mineral density was observed 6 months after therapy. In conclusion, high-dose, short-term iv GC regimens cause an immediate and persistent decrease in bone formation and a rapid and transient increase of bone resorption. Our data also support the concept that discontinuation of such regimens is followed by a high bone turnover phase.
Nucleotide sequences of mouse genomic loci including a gene or pseudogene for U6 (4.8S) nuclear RNA (1981)

We have isolated four clones which hybridize with U6 (4.8S) nuclear RNA, a mammalian small nuclear RNA(nRNA), from DNA of BALB/C mouse liver. Their restriction maps are totally different from each other, indicating that they derived from different loci in the mouse genome. The nucleotide sequences around the hybridizing region in the three clones have been determined. One clone gives a gene that is co-linear with the U6 RNA. There is a sequence TATAAAT beginning 31 nucleotides upstream of the gene, which may suggest that the U6 RNA is transcribed by RNA polymerase II. The other two clones contain a pseudogene for the U6 RNA which has 7 or 9 nucleotide changes from the RNA. The pseudogenes are surrounded by radically different sequences from those surrounding the gene, and they are closely linked to a pseudogene for another snRNA, 4.5S-I RNA, or a part of highly repetitive an interspersed sequence B1.
Rigorous testing using SnapShot (2002)

Introduces a new software testing concept called SnapShot. SnapShot is a testing mechanism which is composed of two components. The first component instruments the program to be tested with SnapShot statements, which are used to produce a special trace during the program execution. The second component implements post-processing on the trace. SnapShot implicitly defines a user-defined coverage criterion and supports its implementation. We have applied SnapShot to a variety of areas, including serial, parallel and object-oriented programs and VHDL designs.
Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM (2010)

Supplementary data are available at Bioinformatics online.
Interaction of metronidazole with DNA repair mutants of Escherichia coli (1984)

It has been proposed that one of metronidazole's partially reduced intermediates interacts either with DNA to exert a bactericidal effect or with water to form acetamide. To test this hypothesis we have examined the effect of metronidazole on several mutants of Escherichia coli that are defective in DNA repair. UV-susceptible RecA- and UvrB- point mutants have an increased susceptibility to metronidazole as manifested by both a decreased minimal inhibitory concentration and a greater bactericidal response to metronidazole in resting cultures. By these criteria, however, we find that UvrB- deletion mutants, which lack the ability to reduce nitrate and chlorate, are no more susceptible to metronidazole than is the wild type. We find, however, that these deletion mutants also lack the ability to reduce metronidazole and thus possibly to form its reactive species. When metronidazole's bactericidal effect is expressed in terms of the concurrent accumulation of acetamide derived from metronidazole, then all RecA- and UvrB- mutants are killed more efficiently than their wild types. The data are consistent, therefore, with metronidazole's lethal effect being mediated by a partially reduced intermediate on the metabolic pathway between metronidazole and acetamide. Defects in other aspects of the DNA repair system do not confer this increased susceptibility to the proposed intermediate. A Tag- mutant, for example, which is defective in 3-methyl-adenine-DNA glycosylase, does not have this increased susceptibility to the presumed precursor of acetamide. Thus, these results provide further support for the hypothesis that the bactericidal effect of metronidazole is mediated by a partially reduced intermediate in the metabolic conversion of metronidazole to acetamide and suggest that this intermediate interacts with DNA to produce a lesion similar to that caused by UV light.
The CUL7/F-box and WD Repeat Domain Containing 8 (CUL7/Fbxw8) Ubiquitin Ligase Promotes Degradation of Hematopoietic Progenitor Kinase 1 (2013)

HPK1, a member of mammalian Ste20-like serine/threonine kinases, is lost in >95% pancreatic cancer through proteasome-mediated degradation. However, the mechanism of HPK1 loss has not been defined. The aims of this study are to identify the ubiquitin ligase and to examine the mechanisms that targets HPK1 degradation. We found that the CUL7/Fbxw8 ubiquitin ligase targeted HPK1 for degradation via the 26 S proteasome. The ubiquitination of HPK1 required its kinase activity and autophosphorylation. Wild-type protein phosphatase 4 (PP4), but not the phosphatase-dead PP4 mutant, PP4-RL, inhibits the interaction of Fbxw8 with HPK1 and Fbxw8-mediated ubiquitination of HPK1. In addition, we showed that Thr-355 of HPK1 is a key PP4 dephosphorylation site, through which CUL7/Fbxw8 ubiquitin ligase and PP4 regulates HPK1 stability. Knockdown of Fbxw8 restores endogenous HPK1 protein expression and inhibits cell proliferation of pancreatic cancer cells. Our study demonstrated that targeted degradation of HPK1 by the CUL7/Fbxw8 ubiquitin ligase constitutes a negative-feedback loop to restrain the activity of HPK1 and that CUL7/Fbxw8 ubiquitin ligase promotes pancreatic cancer cell proliferation. CUL7/Fbxw8 ubiquitin ligase-mediated HPK1 degradation revealed a direct link and novel role of CUL7/Fbxw8 ubiquitin ligase in the MAPK pathway, which plays a critical role in cell proliferation and differentiation.
A simulation of the mission crew workload in a multi mission aircraft (2001)

The increased tasking and reduced manning of a multi-mission aircraft put pressures on the mission crew in terms of their workload, skills mixture and the training required. This paper describes the simulation undertake by CORDA for the UK Air Warfare Centre. Within the model, written in EXTEND/sup TM/ (from Imagine That Inc.), the mission is defined in a modular form, which allows the mission tasks to be developed and modified as the study progresses. Workloads are associated with each task which are then distributed amongst the mission crew. Within the model's supervisory roles, relief crews and rest periods are modelled. The design has provided a generic simulation approach to mission crew loading which allows the analyst to study variations and sensitivities in a controlled manner. This allows the optimum capability to be assessed and the minimum training/manning burden to be associated with the introduction of new aircraft technologies and skills.
User modeling in expert man-machine interfaces: a case study in intelligent information retrieval (1990)

The requirements of a user modeling component for an expert interface are analyzed, and the main points of a proposed approach to user modeling are stated. The authors focus on a knowledge-based system, called UM-tool, devoted to creating, maintaining, and using explicit user models within an expert interface. UM-tool supports a novel approach to user modeling, which is based both on the use of stereotypes and on a dynamic reclassification scheme. The architecture of the system is described, the organization and content of its knowledge bases are illustrated, and the modeling mechanisms utilized are presented in detail. An example of the use of UM-tool in the frame of the information-retrieval-natural-language-interface (IR-NLI II) expert interface devoted to supporting end users in accessing online information retrieval services is discussed, focusing on the specific role of the user modeling component. An evaluation of the proposed approach and a critical comparison with related work are presented. Future research directions are outlined.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Renin inhibitors containing isosteric replacements of the amide bond connecting the P3 and P2 sites (1990)

Renin inhibitors having 13 different isosteres connecting the P3 and P2 positions have been prepared. Synthetic routes and in vitro activity exhibited by these compounds are discussed. The two most potent compounds, 47 and 48, contained the hydroxyethylene isostere, psi [CHOHCH2], and had IC50 values of 61 and 22 nM, respectively.
A 400- and 600-MHz proton NMR conformational study on nucleoside cyclic 3',5' Pv-TBP systems. Conformational transmission induces diequatorial orientation of the 3',5'-dioxaphosphorinane ring in a nonchair conformation (1990)

A 400-and 600-MHz 1H NMR conformational study on nucleoside cyclic
Altered DNA conformations detected by mung bean nuclease occur in promoter and terminator regions of supercoiled pBR322 DNA (1985)

Mung bean nuclease was used to probe for recognizable DNA unwinding and unpairing in the plasmid pBR322. In negatively supercoiled DNA, but not relaxed DNA, cleavages occurred preferentially in non-coding regions of the genome. The types of nucleotide sequences cleaved and which non-coding regions were cleaved depended upon environmental conditions. At 37 degrees C, cleavages occurred in an 84 bp A+T-rich sequence in the terminator region of the ampicillin-resistance gene. Recognition is likely based on a novel DNA conformation which occurs in the longest, most dA+dT-rich region of pBR322. In the presence of 1 mM Mg2+, cleavages occurred in inverted repeated sequences in the promoter regions of the RNA primer for DNA replication and ampicillin- and tetracycline-resistance genes as well as the terminator of RNA-1. Potential loops of hairpin (cruciform) structures were cleaved. At 27 degrees C, cleavages occurred near a promoter activated by cAMP receptor protein in vitro and in the 3' non-coding region of the tetracycline-resistance gene. Thus, in supercoiled pBR322 DNA, recognizable DNA unwinding and unpairing occurs preferentially in regulatory regions for transcription and DNA replication.
Pathogenesis-Related Proteins in Plants (1999)

A great deal of research has been focused on the isolation, characterization, and regulation of expression of pathogenesis-related proteins since the discovery that several of the PR-proteins had antimicrobial or insecticidal activity and can delay the progression of diseases caused by several pathogens belonging to diverse genera. This is an excit
LocusZoom: regional visualization of genome-wide association scan results (2010)

LocusZoom can be accessed from a web interface at http://csg.sph.umich.edu/locuszoom. Users may generate a single plot using a web form, or many plots using batch mode. The software utilizes LD information from HapMap Phase II (CEU, YRI and JPT+CHB) or 1000 Genomes (CEU) and gene information from the UCSC browser, and will accept SNP identifiers in dbSNP or 1000 Genomes format. Single plots are generated in approximately 20 s. Source code and associated databases are available for download and local installation, and full documentation is available online.
Identification of Alkylidene Hydrazides as Glucagon Receptor Antagonists (2001)

High throughput screening of our small molecule combinatorial library identified a class of benzoylnaphthalenehydrazones with modest affinity for the human glucagon receptor. Optimization of this initial hit through a series of targeted libraries and traditional medicinal chemistry led to ligands with nanomolar affinities. Pharmacological evaluation demonstrated that these ligands were competitive glucagon receptor antagonists. Intravenous administration of a representative benzoylnaphthalenehydrazone into rats attenuated glucagon-stimulated glucose levels.
Interleukin-2 (IL-2) induces tyrosine kinase-dependent translocation of active raf-1 from the IL-2 receptor into the cytosol. (1992)

Stimulation of the interleukin-2 (IL-2) receptor results in phosphorylation and activation of cytosolic Raf-1 serine/threonine kinase. Herein, we report that enzymatically active Raf-1 is physically associated with the IL-2 receptor beta chain (p75) in T-cell blasts. Following stimulation with IL-2, Raf-1 dissociates from the IL-2 receptor complex and translocates to the cytosol. Genistein, a protein tyrosine kinase inhibitor, prevents the dissociation of enzymatically active Raf-1 from the ligand-stimulated IL-2 receptor complex. These data favor a model of IL-2 receptor activation in which an IL-2-activated protein tyrosine kinase phosphorylates the IL-2 receptor and/or receptor-bound Raf-1. Following tyrosine phosphorylation, enzymatically active Raf-1 dissociates from the IL-2 receptor and translocates into the cytosol.