gebhart/patrepeval huggingface dataset:
Quantitative separation of murine leukemia virus proteins by reversed-phase high-pressure liquid chromatography reveals newly described gag and env cleavage products (1984)

The structural proteins of murine type C retroviruses are proteolytic cleavage products of two different precursor polyproteins coded by the viral gag and env genes. To further investigate the nature and number of proteolytic cleavages involved in virus maturation, we quantitatively isolated the structural proteins of the Rauscher and Moloney strains of type C murine leukemia virus (R-MuLV and M-MuLV, respectively) by reversed-phase high-pressure liquid chromatography. Proteins and polypeptides isolated from R-MuLV included p10, p12, p15, p30, p15(E), gp69, and gp71 and three previously undescribed virus components designated here as p10', p2(E), and p2(E). Homologous proteins and polypeptides were isolated from M-MuLV. Complete or partial amino acid sequences of all the proteins listed above were either determined in this study or were available in previous reports from this laboratory. These data were compared with those from the translation of the M-MuLV proviral DNA sequence (Shinnick et al., Nature [London] 293:543-548, 1981) to determine the exact nature of proteolytic cleavages for all the structural proteins described above and to determine the origin of p10' and p2(E)s. The results showed that, during proteolytic processing of gp80env from M-MuLV (M-gp 80env), a single Arg residue was excised between gp70 and p15(E) and a single peptide bond was cleaved between p15(E) and p2(E). The structure of M-gPr80env is gp70-(Arg)-p15(E)-p2(E). The data suggest that proteolytic cleavage sites in R-gp85env are identical to corresponding cleavage sites in M-gp80env. The p2(E)s are shown to be different genetic variants of p2(E) present in the uncloned-virus preparations. The data for R- and M-p10's shows that they are cleavage products of the gag precursor with the structure p10-Thr-Leu-Asp-Asp-OH. The complete structure of Pr65gag is p15-p12-p30-p10'. Stoichiometries of the gag and env cleavage products in mature R- and M-MuLV were determined. In each virus, gag cleavage products (p15, p12, p30, and p10 plus p10') were found in equimolar amounts and p15(E)s were equimolar with p2(E)s. The stoichiometry of gag to env cleavage products was 4:1. These data are consistent with the proposal that proteolytic processing of precursor polyproteins occurs after virus assembly and that the C-terminal portion of Pr15(E) [i.e., p15(E)-p2(E)] is located on the inner side of the lipid bilayer of the virus.
Propargyl-Linked Antifolates are Dual Inhibitors of <i>Candida albicans</i> and <i>Candida glabrata</i> (2014)

Species of Candida, primarily C. albicans and with increasing prevalence, C. glabrata, are responsible for the majority of fungal bloodstream infections that cause morbidity, especially among immune compromised patients. While the development of new antifungal agents that target the essential enzyme, dihydrofolate reductase (DHFR), in both Candida species would be ideal, previous attempts have resulted in antifolates that exhibit inconsistencies between enzyme inhibition and antifungal properties. In this article, we describe the evaluation of pairs of propargyl-linked antifolates that possess similar physicochemical properties but different shapes. All of these compounds are effective at inhibiting the fungal enzymes and the growth of C. glabrata; however, the inhibition of the growth of C. albicans is shape-dependent with extended para-linked compounds proving more effective than compact, meta-linked compounds. Using crystal structures of DHFR from C. albicans and C. glabrata bound to lead compounds, 13 new para-linked compounds designed to inhibit both species were synthesized. Eight of these compounds potently inhibit the growth of both fungal species with three compounds displaying dual MIC values less than 1 μg/mL. Analysis of the active compounds shows that shape and distribution of polar functionality is critical in achieving dual antifungal activity.
Pneumonia: the forgotten killer of children. (2006)

This report examines the epidemiological evidence on the burden and distribution of pneumonia and assesses current levels of treatment and prevention. The results are sobering: Only about 1 in 5 caregivers knows the danger signs of pneumonia; only about half of children sick with pneumonia receive appropriate medical care; and according to the limited data available less than 20 per cent of children with pneumonia received antibiotics the recommended treatment. Effective interventions to reduce pneumonia deaths are available but reach too few children. Scaling up treatment coverage is possible and at relatively low cost. Estimates suggest that if antibiotic treatment were universally delivered to children with pneumonia around 600000 lives could be saved each year at a cost of $600 million. Furthermore the number of lives saved could more than double to 1.3 million if both prevention and treatment interventions to reduce pneumonia deaths were universally delivered. (excerpt)
Expression of the R2R3-MYB Transcription Factor TaMYB14 from<i>Trifolium arvense</i>Activates Proanthocyanidin Biosynthesis in the Legumes<i>Trifolium repens</i>and<i>Medicago sativa</i>      (2012)

Proanthocyanidins (PAs) are oligomeric flavonoids and one group of end products of the phenylpropanoid pathway. PAs have been reported to be beneficial for human and animal health and are particularly important in pastoral agricultural systems for improved animal production and reduced greenhouse gas emissions. However, the main forage legumes grown in these systems, such as Trifolium repens and Medicago sativa, do not contain any substantial amounts of PAs in leaves. We have identified from the foliar PA-accumulating legume Trifolium arvense an R2R3-MYB transcription factor, TaMYB14, and provide evidence that this transcription factor is involved in the regulation of PA biosynthesis in legumes. TaMYB14 expression is necessary and sufficient to up-regulate late steps of the phenylpropanoid pathway and to induce PA biosynthesis. RNA interference silencing of TaMYB14 resulted in almost complete cessation of PA biosynthesis in T. arvense, whereas Nicotiana tabacum, M. sativa, and T. repens plants constitutively expressing TaMYB14 synthesized and accumulated PAs in leaves up to 1.8% dry matter. Targeted liquid chromatography-multistage tandem mass spectrometry analysis identified foliar PAs up to degree of polymerization 6 in leaf extracts. Hence, genetically modified M. sativa and T. repens plants expressing TaMYB14 provide a viable option for improving animal health and mitigating the negative environmental impacts of pastoral animal production systems.
Source code comprehension analysis in software maintenance (2017)

Source code comprehension is considered as an essential part of the software maintenance process. It is considered as one of the most critical and time-consuming task during software maintenance process. The difficulties of source code comprehension is analyzed. A static Bottom-up code comprehension model is used. The code is partitioned into functional-based blocks and their data and control dependencies that preserve the functionality of the program are analyzed. The data-flow and control-flow graphs reflects the dependencies and assist in refactoring process. The proposed strategy helps in improving the readability of the program code, increase maintainer productivity, and reducing the time and effort of code comprehension. It helps maintainers to locate the required lines of code that constitute the functional area that the maintainers are searching for in their maintenance work.
Location and the functionality of erythropoietin receptor(s) in A2780 cells (2012)

Erythropoietin (Epo) is a critical regulator of erythroid cell proliferation, differentiation and apoptosis. In the form of a recombinant protein, it is widely used to treat various forms of anemia, including that associated with cancer and with the myelosuppressive effects of chemotherapy. Studies of ovarian cancer cell lines have demonstrated the presence of the Epo receptor (EpoR), but there are disagreements regarding its localization and functionality in these cells. Using fluorescence microscopy, we were not able to identify the EpoR on the surface of A2780 cells, in contrast to the positive control K562 cells. Flow cytometry did reveal a weak surface EpoR signal in A2780 cells. Interestingly, most of the EpoR in A2780 cells was found in the cytoplasm, more abundantly as an intracellular membrane-associated protein than a soluble one. Silencing EpoR expression by lentiviral-mediated shRNA resulted in reduced A2780 proliferation as well as reduction in Epo-induced phosphorylation of Erk1/2. Our findings provide important insights into the biology of the EpoR in ovarian cancer cells.
CC chemokines induce the generation of killer cells from CD56<sup>+</sup> cells (1996)

We describe here that members of the CC chemokines exhibit biological activities other than chemotaxis. Macrophage inflammatory protein (MIP)-1 alpha, MIP-1 beta, monocyte chemoattractant protein-1 and RANTES, but not interleukin (IL)-8, induce the generation of cytolytic cells, designated here as CHAK (CC chemokine-activated killer) cells to distinguish them from IL-2-activated (LAK) cells. Like IL-2, CC chemokines can induce the proliferation and activation of killer cells. While incubating CC chemokines with CD4+ or CD8+ cells did not generate CHAK activity, all CC chemokines were capable of inducing CHAK activity upon incubating with CD56+ cells, suggesting that the primary effectors are NK cells. However, the presence of other cell types, such as CD4+ or CD8+, are necessary to induce the proliferation of CD56+ cells. Confirming the involvement of T cell-derived factors in inducing the proliferation of these cells, anti-IL-2 and anti-interferon-gamma, but not anti-IL-1 beta, anti-tumor necrosis factor-alpha, anti-IL-8, or anti-granulocyte/monocyte-colony-stimulating factor inhibited RANTES-induced proliferation of nylon wool column-nonadherent cells. Our results may have important clinical applications for the utilization of CHAK cells in the treatment of cancer and immunodeficient patients.
Triple wire technique for a bifurcation lesion and a subtotal occlusive lesion. (2003)

In a critical distal right coronary artery bifurcation lesion, the proximal course of the posterior descending artery was also subtotally occluded. The posterior descending artery gave rise to a small sidebranch just before the occlusion. In the subsequent revascularization procedure, the bifurcation lesion was double-wired. One wire was placed in the postero-lateral branch, and another wire was intended for placement in the posterior descending artery, but it repeatedly selected the sidebranch despite multiple shapings of the wire tip. While the second wire was deliberately kept in the sidebranch, a third wire was used and crossed the occlusive lesion without much difficulty. The second wire was then withdrawn and the revascularization procedure proceeded in the usual manner. The positioning of the second wire in the sidebranch significantly shortened the procedure.
Alignments of DNA and protein sequences containing frameshift errors (1996)

Molecular sequences, like all experimental data, are subject to error. Many current DNA sequencing protocols have very significant error rates and often generate artefactual insertions and deletions of bases (indels) which corrupt the translation of sequences and compromise the detection of protein homologies. The impact of these errors on the utility of molecular sequence data is dependent on the analytic technique used to interpret the data. In the presence of frameshift errors, standard algorithms using six-frame translation can miss important homologies because only subfragments of the correct translation are available in any given frame. We present a new algorithm which can detect and correct frameshift errors in DNA sequences during comparison of translated sequences with protein sequences in the databases. This algorithm can recognize homologous proteins sharing 30% identity even in the presence of a 7% frameshift error rate. Our algorithm uses dynamic programming, producing a guaranteed optimal alignment in the presence of frameshifts, and has a sensitivity equivalent to Smith-Waterman. The computational efficiency of the algorithm is O(nm) where n and m are the sizes of two sequences being compared. The algorithm does not rely on prior knowledge or heuristic rules and performs significantly better than any previously reported method.
Coagulation of Iron Oxide Particles in the Presence of Organic Materials (1990)

Experiments using hematite particles (70 nm in diameter) in the presence of organics (phthalic acid, fatty acids, polyaspartic acid, fulvic and humic acid) reveal important features of particle coagulation dynamics. A light scattering technique was used to determine quantitatively the initial coagulation rates of hematite particles. Electrokinetic measurements were taken to obtain the sign and magnitude of electrical potential at the oxide/aqueous solution interface. Adsorption experiments were carried out to evaluate affinities of aqueous molecules for the metal oxide surface. Intrinsic equilibrium constants for surface complexes are derived from a Surface Complex Formation/Diffuse Layer Model (SCF/DLM) accounting for interfacial electrostatic charge and potential. Small organic molecules, such as phthalate, show specific chemical reaction with the hematite surface and influence colloidal hematite coagulation kinetics by altering interfacial charge and potential. For fatty acids, hydrophobic interaction, in addition to covalent and electrostatic interaction, offers a plausible explanation for observed systematic changes in hematite stability and electrokinetic data. In the presence of polyelectrolytes, such as polyaspartic acid, fulvic and humic acids, a combination of specific chemical, electrostatic, and hydrophobic energies of carboxyl segments favors adsorption, and these materials have a relatively great impact on particle coagulation and stability.
Antiplaque effects and mode of action of a combination of zinc citrate and a nonionic antimicrobial agent (1988)

The effect upon plaque growth of adding a nonionic antimicrobial agent, triclosan, to a dentifrice containing zinc citrate was established in short-term in vivo studies. Plaque regrowth was inhibited by brushing with dentifrices which contained either zinc citrate or triclosan. When both were combined in the same dentifrice, the inhibition of overnight plaque regrowth was significantly greater. In two 4-day non-brushing studies, the dentifrices containing both zinc citrate and triclosan were applied either undiluted by the use of a cap splint or as 23% suspensions in water. Both methods resulted in significant reductions in plaque accumulation, with the greater activity being observed for the undiluted application of the dentifrice. Analysis of results of the overnight plaque studies for individual teeth revealed that the two agents had a complementary inhibitory action on plaque regrowth, zinc citrate being more effective on existing plaque whereas triclosan inhibited plaque formation on clean surfaces. The dentifrice containing both agents was effective against both existing plaque and new plaque formation. It is concluded that the addition of triclosan to a dentifrice containing zinc citrate improves its antiplaque potential.
Genetic identification of exported proteins in <i>Streptococcus pneumoniae</i> (1993)

A strategy was developed to mutate and genetically identify exported proteins in Streptococcus pneumoniae. Vectors were created and used to screen pneumococcal DNA in Escherichia coli and S. pneumoniae for translational gene fusions to alkaline phosphatase (PhoA). Twenty five PhoA+ pneumococcal mutants were isolated and the loci from eight of these mutants showed similarity to known exported or membrane-associated proteins. Homologues were found to: (i) protein-dependent peptide permeases, (ii) penicillin-binding proteins, (iii) Clp proteases, (iv) two-component sensor regulators, (v) the phosphoenolpyruvate: carbohydrate phosphotransferases permeases, (vi) membrane-associated dehydrogenases, (vii) P-type (E1E2-type) cation transport ATPases, (viii) ABC transporters responsible for the translocation of the RTX class of bacterial toxins. Unexpectedly one PhoA+ mutant contained a fusion to a member of the DEAD protein family of ATP-dependent RNA helicases suggesting export of these proteins.
Sequence of RNA2 of the Helicoverpa armigera stunt virus (Tetraviridae) and bacterial expression of its genes (1995)

The complete nucleotide sequence of RNA2 of Helicoverpa armigera stunt virus (HaSV), a member of the Tetraviridae, was determined by characterization of cloned cDNA and PCR products and direct sequencing of genomic RNA. The capped, positive sense, single-stranded RNA is 2478 nucleotides in length and has two overlapping open reading frames (ORFs) likely to be cistrons which are situated between terminal non-coding regions of 282 and 168 bases, 5' and 3', respectively. Extensive secondary structure of the RNA strand is indicated, including a tRNA-like structure at the 3' terminus which is the first such structure discerned in an animal virus. The first ORF encodes a 17 kDa PEST protein (p17) of unknown function while the second ORF encodes the 71 kDa coat protein precursor (p71) that is cleaved at an Asn-Phe site into the 64 kDa and 7 kDa coat proteins. The precursor coat protein is 66% identical to that of another tetravirus, the Nudaurelia omega virus, with most of the difference residing in a 165 amino acid region located in the middle of the sequence. Despite the extensive similarity, no serological relationship was observed between the two viruses, suggesting that the dissimilar region is exposed on the capsid exterior. Expression in bacteria of the two RNA2 gene products shows they are likely to be expressed by a leaky scan-through mechanism. Bacterial expression of p71 did not produce virus-like particles while expression of p17 produced large arrays of mostly hollow, hexagonal tube-like structures.
Expressed and cryptic flagellin genes in the H44 and H55 type strains of Escherichia coli (2007)

Bacterial H antigens are specified by flagellin molecules, which constitute the flagellar filament. Escherichia coli 781-55 and E2987-73 are the type strains for H44 and H55 antigens, respectively. Unlike E. coli K-12, they possess two flagellin genes, fliC and fllA, on their chromosomes. However, they are monophasic, expressing exclusively the fllA genes, which specify the type antigens. In this study, the flagellin genes were cloned from these strains and their structure and expression were analyzed. It was found that the fliC genes encode apparently intact flagellin subunits but possess inefficient sigma28-dependent promoters, which may result in these genes being silent. The chromosomal locations of the fllA genes are approximately, but not exactly, identical with that of the phase-2 flagellin gene, fljB, of diphasic Salmonella strains. However, unlike the Salmonella fljB gene, the invertible H segment and the fljA gene responsible for the control of flagellar phase variation are both absent from the fllA loci. The fllA genes are highly homologous to the E. coli fliC gene but distantly related to the Salmonella fljB gene. These results suggest a hypothesis that the fllA genes may have emerged by an intra-species lateral transfer of the fliC gene. This hypothesis is further supported by the observation that the fllA genes are flanked by several IS elements and located within cryptic prophage elements.
Synthesis of 2-Alkyl-2-cyclopenten-1-ones. A Versatile Kinetic Alkylation-Ozonolysis Procedure for the Preparation of γ-Ketoaldehydes (1989)

A range of 2-alkyl-2-cyclopenten-1-ones including the prostaglandin precursor 2-(6-methoxycarbonylhexyl)-2-cyclopenten-1-one and the jasmonoid precursor 2-[(Z)-2-pentenyl]-2-cyclopenten-1-one, have been prepared by a short synthetic route which begins with 6-methyl-5-hepten-2-one and generates the key 1,4-ketoaldehyde intermediates by a kinetic alkylation-ozonolysis procedure.
Laboratory studies of the spectral properties of sea spikes (2002)

An experimental system used to study the spectral content of sea spike echoes generated in a wave tank is described. Some illustrative data are presented. The objective is to determine the spectral evolution of radar returns from a disturbed water surface and to relate any spectral changes to changes in the geometry of the surface feature responsible for the backscatter, thereby determining the dynamic transfer function for surface scattering events. In order to obtain high resolution radar data and water surface geometry data simultaneously, a two-channel, ultrawideband radar based on a microwave time-domain reflectometer (TDR) is used in concert with a scanning laser slope gauge (SLSG). Data from these experiments are presented to illustrate the dynamic nature of the sea spike transfer function.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
‘Codington’, a High-Yielding, High-Quality, Large-Seeded Soybean (2013)

Soybean [Glycine max (L.) Merr.] ‘Codington’ (Reg. No. CV-511, PI 667736) was developed at South Dakota State University (SDSU), Brookings, SD. It was released by the South Dakota Agricultural Experiment Station in April 2013 for high yield, a large seed with high protein and oil content suitable for soy food production. Codington (experimental line SD04CV-611) is a late maturity group (MG) 0 cultivar (relative maturity 1.0). It originated from the F5 progeny of a single F4 plant derived from the cross of ‘Surge’ × A96-591033 by a modified single-seed descent method. Following yield trials within the SDSU soybean breeding program, it was evaluated for yield and quality through the USDA Northern Regional Uniform Soybean Tests (UT) in 2007 to 2010 and South Dakota Crop Performance Tests (CPT) in 2010 to 2012. Over all 36 environments, the yield of Codington averaged 3611.3 kg ha−1, 1.2% higher than the check cultivar Surge. In the UT tests (24 year-locations), Codington also exhibited an average yield 2.9% higher than the check cultivar Sheyenne. The average protein and oil content of Codington for the UT tests (22 year-locations) was 365.3 and 174.4 g kg−1 at 13% moisture, compared with Surge (364.0 and 174.4 g kg−1) and Sheyenne (342.0 and 178.2 g kg−1). Its 100-seed weight was 21 g. Codington is a conventional, high-yield, high-quality (relatively higher protein and oil concentration as well as good visual seed quality), MG 0 cultivar with large seeds, and thus it is particularly suitable for soy food production in South Dakota and similar regions.
Current Challenges and Future Directions (2010)

This chapter contains sections titled: Kinase Inhibitor Drug Resistance Combination Therapy With Kinase Inhibitors Systems Biology and Translational Medicine Conclusions References
Abstract 16531: Absence of Remodeling Benefit of Lv-crt Over Bv-crt in Patients With Heart Failure and Wide Qrs: Insight From the Evaluation of Resynchronization Therapy for Heart Failure (EARTH) Trial (2011)

Purpose: Cardiac Resynchronization Therapy (CRT) is recommended for patients with advanced heart failure (HF) and wide QRS, but 30% of these patients fail to respond to CRT. The EARTH trial showed ...
Shape-Memory Wires Switch Rotary Actuator (1992)

Thermomechanical rotary actuator based shape-memory property of alloy composed of equal parts of titanium and nickel. If alloy stretched while below transition temperature, it reverts to original length when heated above transition temperature. Two capstans same shaft wrapped with shape-memory wires. As one wire heated, it contracts and stretches opposite wire. Wires heated in alternation so they switch shaft between two extreme angular positions; on and off positions of rotary valve.