gebhart/patrepeval huggingface dataset:
Differential expression of the three yeast glyceraldehyde-3-phosphate dehydrogenase genes. (1985)

Utilizing yeast strains containing insertion mutations in each of the three glyceraldehyde-3-phosphate dehydrogenase structural genes, the level of expression of each gene was determined in logarithmically growing cells. The contribution of the TDH1, TDH2, and TDH3 gene products to the total glyceraldehyde-3-phosphate dehydrogenase activity in wild type cells is 10-15, 25-30, and 50-60%, respectively. The relative proportions of expression of each gene is the same in cells grown in the presence of glucose or ethanol as carbon source although the total glyceraldehyde-3-phosphate dehydrogenase activity in cells grown in the presence of glucose is 2-fold higher than in cells grown on ethanol. The polypeptides encoded by each of the structural genes were identified by two-dimensional polyacrylamide gel electrophoresis. The TDH3 structural gene encodes two resolvable forms of glyceraldehyde-3-phosphate dehydrogenase which differ by their net charge. The apparent specific activity of glyceraldehyde-3-phosphate dehydrogenase encoded by the TDH3 structural gene is severalfold lower than the enzymes encoded by TDH1 or TDH2. The polypeptides encoded by the TDH2 or TDH3 structural genes form catalytically active homotetramers. The apparent Vmax for the homotetramer encoded by TDH3 is 2-3-fold lower than the homotetramer encoded by TDH2. Evidence is presented that isozymes of glyceraldehyde-3-phosphate dehydrogenase exist in yeast cells, however, the number of different isozymes formed was not established. These data confirm that the three yeast glyceraldehyde-3-phosphate dehydrogenase genes encode catalytically active enzyme and that the genes are expressed at different levels during logarithmic cell growth.
Overexpression of Bcl-xLin β-cells prevents cell death but impairs mitochondrial signal for insulin secretion (2000)

To study effects of Bcl-x(L) in the pancreatic beta-cell, two transgenic lines were produced using different forms of the rat insulin promoter. Bcl-x(L) expression in beta-cells was increased 2- to 3-fold in founder (Fd) 1 and over 10-fold in Fd 2 compared with littermate controls. After exposure to thapsigargin (10 microM for 48 h), losses of cell viability in islets of Fd 1 and Fd 2 Bcl-x(L) transgenic mice were significantly lower than in islets of wild-type mice. Unexpectedly, severe glucose intolerance was observed in Fd 2 but not Fd 1 Bcl-x(L) mice. Pancreatic insulin content and islet morphology were not different from control in either transgenic line. However, Fd 2 Bcl-x(L) islets had impaired insulin secretory and intracellular free Ca(2+) ([Ca(2+)](i)) responses to glucose and KCl. Furthermore, insulin and [Ca(2+)](i) responses to pyruvate methyl ester (PME) were similarly reduced as glucose in Fd 2 Bcl-x(L) islets. Consistent with a mitochondrial defect, glucose oxidation, but not glycolysis, was significantly lower in Fd 2 Bcl-x(L) islets than in wild-type islets. Glucose-, PME-, and alpha-ketoisocaproate-induced hyperpolarization of mitochondrial membrane potential, NAD(P)H, and ATP production were also significantly reduced in Fd 2 Bcl-x(L) islets. Thus, although Bcl-x(L) promotes beta-cell survival, high levels of expression of Bcl-x(L) result in reduced glucose-induced insulin secretion and hyperglycemia due to a defect in mitochondrial nutrient metabolism and signaling for insulin secretion.
Developmentally regulated protein-tyrosine kinase genes in Dictyostelium discoideum. (1990)

Dictyostelium discoideum, an organism that undergoes development and that is amenable to biochemical and molecular genetic approaches, is an attractive model organism with which to study the role of tyrosine phosphorylation in cell-cell communication. We report the presence of protein-tyrosine kinase genes in D. discoideum. Screening of a Dictyostelium cDNA expression library with an anti-phosphotyrosine antibody identifies fusion proteins that exhibit protein-tyrosine kinase activity. Two distinct cDNAs were identified and isolated. Though highly homologous to protein kinases in general, these kinases do not exhibit many of the hallmarks of protein-tyrosine kinases of higher eucaryotes. In addition, these genes are developmentally regulated, which suggests a role for tyrosine phosphorylation in controlling Dictyostelium development.
Regulation of the c-met Proto-oncogene Promoter by p53 (1999)

In the present study, we have investigated the possible involvement of p53 in the transcriptional regulation of the c-met gene. Cotransfection of various c-met promoter reporter vectors with p53 expression plasmids demonstrated that only wild-type p53 but not tumor-derived mutant forms of p53 resulted in a significant enhancement of c-met promoter activity. Functional assays revealed that the p53 responsive element in the c-met promoter region is located at position -278 to -216 and confers p53 responsiveness not only in the context of the c-met promoter but also in the context of a heterologous promoter. Electrophoretic mobility shift assays using purified recombinant p53 protein showed that the p53 binding element identified within the c-met promoter specifically binds to p53 protein. Induction of p53 by UV irradiation in RKO cells that express wild-type p53 increased the level of the endogenous c-met gene product and p21(WAF1/CIP1), a known target of p53 regulation. On the other hand, in RKO cells in which the function of p53 is impaired either by stable transfection of a dominant negative form of p53 or by HPV-E6 viral protein, no induction of the endogenous c-met gene or p21(WAF1/CIP1) was noted by UV irradiation. These results suggest that the c-met gene is also a target of p53 gene regulation.
Rationality and the Normative/Descriptive Distinction (2004)

This chapter contains section titled: Introduction Instrumental Rationality Evolution and Rationality Prescriptive Rules Concluding Comments
Rapid Genetic Grouping of Factor H-Binding Protein (Genome-Derived Neisserial Antigen 1870), a Promising Group B Meningococcal Vaccine Candidate (2006)

The most important antigen component of a promising multicomponent group B meningococcal recombinant protein vaccine is based on genome-derived neisserial antigen 1870, which recently was renamed factor H-binding protein (FHBP) to reflect one of its critical functions as a complement regulatory protein. Neisseria meningitidis strains can be subdivided into three FHBP variant groups based on divergence of FHBP amino acid sequences. Within each variant group, amino acid sequences are >90% conserved. To develop an FHBP-based group B vaccine, it is important to know the distribution of FHBP variant 1, 2, and 3 strains in different geographic regions, since antibodies against FHBP are bactericidal against strains within the homologous group but show minimal activity against strains from other groups. We have devised a high-throughput, quantitative PCR-based method that allows rapid and precise assignment of FHBP genes into each of the three major variant lineages. Among 48 group B isolates from patients hospitalized in California in 2003 to 2004, 83%, 13%, and 4%, respectively, had variant 1, 2, and 3 genes. Thus, a vaccine based on the variant 1 protein has the potential to prevent the majority of cases of group B disease. The quantitative PCR-based method will be useful for determining and monitoring the prevalence of meningococcal isolates with genes encoding different FHBP variant proteins. The technique also is suitable for monitoring variation of genes encoding other protein antigens targeted for vaccination.
Fast Sorting Algorithms using AVX-512 on Intel Knights Landing (2017)

This paper describes fast sorting techniques using the recent AVX-512 instruction set. Our implementations benefit from the latest possibilities offered by AVX-512 to vectorize a two-parts hybrid algorithm: we sort the small arrays using a branch-free Bitonic variant, and we provide a vectorized partitioning kernel which is the main component of the well-known Quicksort. Our algorithm sorts in-place and is straightforward to implement thanks to the new instructions. Meanwhile, we also show how an algorithm can be adapted and implemented with AVX-512. We report a performance study on the Intel KNL where our approach is faster than the GNU C++ sort algorithm for any size in both integer and double floating-point arithmetics by a factor of 4 in average.
Study on the Utilization of Aphid Resistant Character in Wild Soybean. I. Aphid Resistant Performance of F2 Generation from Crosses Between Cultivated and Wild Soybeans (2017)

Three crosses between 3 cultivat ed (G. max) and 2 aphid resistant wild soybean (G. soja) lines were made to study the inheritance of resistance and segregation patterns in F 2 generation with artificial inoculation technique s. The aphid resistance of F2 plants showed continuous mono-peek distributions which are inclined towards the susceptible parents. Most F2 plants were susceptible or highly susceptible. Only about 7.2 to 10.2% of the F2 plants were resistant to soybean aphid. The segregations in 2 out of 3 crosses studied fitted the hyp othesis that there are 2 independent gene pairs controlling the aphid resistant character of the wild soybean lines (P &gt; 0.50). The segregation of the other cross also tended to fit the 2 major gene model. These results indicated that the aphid resistance of the wild parents might be controlled by 2 independent recessive genes and some other minor genes. Supposing that the aphid resistant character was quantitatively inherited, the overall inheritability estimated from the variances of parents and F 2 populations was between 85.5% and 97.0%. Despite of the high inheritability of aphid resistance, it is recommended that the selection of resistance should be postponed to later generations such as F3 or F4 , because the scarcity of resistant genes may be recessively inherited, and the number of backcrosses made in each cycle of selection should be limited to avoid the resistant genes being lost.
Efficient Fully Homomorphic Encryption from (Standard) LWE (2011)

We present a fully homomorphic encryption scheme that is based solely on the (standard) learning with errors (LWE) assumption. Applying known results on LWE, the security of our scheme is based on the worst-case hardness of "short vector problems" on arbitrary lattices. Our construction improves on previous works in two aspects: 1) We show that "somewhat homomorphic" encryption can be based on LWE, using a new re-linearization technique. In contrast, all previous schemes relied on complexity assumptions related to ideals in various rings. 2) We deviate from the "squashing paradigm" used in all previous works. We introduce a new dimension-modulus reduction technique, which shortens the ciphertexts and reduces the decryption complexity of our scheme, without introducing additional assumptions. Our scheme has very short ciphertexts and we therefore use it to construct an asymptotically efficient LWE-based single-server private information retrieval (PIR) protocol. The communication complexity of our protocol (in the public-key model) is k · polylog(k) + log |DB| bits per single-bit query (here, A; is a security parameter).
Synthesis and Structure−Activity Relationships of a New Set of 2-Arylpyrazolo[3,4-c]quinoline Derivatives as Adenosine Receptor Antagonists (2000)

In a recent paper (Colotta et al. J. Med. Chem. 2000, 43, 1158-1164) we reported the synthesis and adenosine receptor binding activity of two sets of 2-aryl-1,2,4-triazolo[4,3-a]quinoxalines (A and B) some of which were potent and selective A(1) or A(3) antagonists. In this paper the synthesis of a set of 2-arylpyrazolo[3,4-c]quinolin-4-ones 1-10, 4-amines 11-18, and 4-amino-substituted derivatives 19-35 are reported. The binding activity at bovine A(1) and A(2A) and human cloned A(3) adenosine receptors showed that (i) the substituent on the appended 2-phenyl ring could be used to modulate A(1) and A(3) affinity, (ii) the 4-amino group was necessary for A(1) and A(2A) binding activity, and (iii) a nuclear or extranuclear C=O proton acceptor at position 4 yielded potent and selective A(3) antagonists. These results are in agreement with those of the previously reported series A and B suggesting a similar adenosine receptor binding mode. In particular, the A(3) nanomolar affinity of 1-8, 31-33, and 35 confirms the hypothesis of the presence in the N-6 region of the adenosine A(3) subtype of a proton donor able to bind to a C=O proton acceptor at position 4.
Frequency tunable near-infrared metamaterials based on VO_2 phase transition (2009)

Engineering metamaterials with tunable resonances from mid-infrared to near-infrared wavelengths could have far-reaching consequences for chip based optical devices, active filters, modulators, and sensors. Utilizing the metal-insulator phase transition in vanadium oxide (VO(2)), we demonstrate frequency-tunable metamaterials in the near-IR range, from 1.5 - 5 microns. Arrays of Ag split ring resonators (SRRs) are patterned with e-beam lithography onto planar VO(2) and etched via reactive ion etching to yield Ag/VO(2) hybrid SRRs. FTIR reflection data and FDTD simulation results show the resonant peak position red shifts upon heating above the phase transition temperature. We also show that, by including coupling elements in the design of these hybrid Ag/VO(2) bi-layer structures, we can achieve resonant peak position tuning of up to 110 nm.
PhotochemCAD‡: A Computer‐Aided Design and Research Tool in Photochemistry (1998)

Abstract A database of absorption and fluorescence spectra, including molar absorption coefficients and fluorescence quantum yields, has been compiled for 125 photochemically relevant compounds. An accompanying program enables calculation of oscillator strengths, natural radiative lifetimes, transition dipole moments, Forster energy‐transfer rates, multicomponent analysis, simulations of fluorescence spectra upon energy transfer among linear arrays of pigments, calculations of blackbody radiator curves at different temperatures and Lorentzian and Gaussian peak distributions. The program runs under Windows 95 and is equipped with extensive literature references and help features.
Oncogenic transformation and hypoxia synergistically act to modulate vascular endothelial growth factor expression. (1996)

Hypoxia can select for cells that have lost their apoptotic potential, thereby making them resistant to adverse conditions. However, long-term survival of transformed cells which have diminished apoptotic sensitivity when exposed to low oxygen conditions would require the activation of their angiogenic program to compensate for an insufficient oxygen supply. In this report, we show that the activity (of oncogenic Ha-ras, either constitutively or transiently, enhances the induction of the angiogenic mitogen, vascular endothelial growth factor (VEGF), by hypoxia. Analysis of the 5' flanking region of the VEGF promoter indicates that a HIF-1-like sequence is to promote a 15-fold increase in reporter gene activity in Ha-ras-transformed cells when exposed to hypoxia, whereas mutations in the same site totally inhibited VEGF induction. Under low oxygen conditions, VEGF induction is inhibited in cells expressing a mutant inhibitory allele of Ha-ras (RasN17), indicating a direct role for Ras in modulating VEGF activity. We propose that the angiogenic switch in Ras-transformed cells may be physiologically promoted by the tumor microenvironment through VEGF induction.
Cytologic Evaluation of Breast Fluid in the Detection of Breast Disease 2 (1977)

The availability and cell content of aspirated breast fluid from 1,706 women were evaluated to determine the usefulness of breast fluid cytology as an indicator of breast disease. A newly developed aspirator was used to obtain cells adequate for diagnosis from approximately 50% of the women tested. Fluids were most readily available from women between the ages of 30 and 50 years. Although abnormal cytologies were observed in all age groups, the relative proportion of abnormal specimens as well as the degree of abnormality increased as a function of age. More women over 40 years of age with a high risk of breast cancer had cells classified in the more abnormal categories than did women in the normal risk group. To localize otherwise occult lesions, contrast ductography was performed on all women with very abnormal ductal cells. Women with atypical hyperplastic cytologies most commonly had benign and premalignant breast disease at subsequent biopsy. Of 27 women with fluids classified as suspected carcinomas 18 (66%) had small carcinomas. These observations strongly suggested that the presence of atypical cells in aspirated breast fluids has important clinical application for early detection of breast cancer. One limitation of cytology was that the technique rarely detected carcinomas greater than 1 cm.
Serum antibodies to enterotoxins produced by Staphylococcus aureus with special reference to enterotoxin F and toxic shock syndrome (1983)

The presence of antibodies to staphylococcal enterotoxins (enterotoxins A through F) in sera of healthy subjects (n = 567) and in sera of patients with toxic shock syndrome (n = 20) was determined. Furthermore, production of enterotoxins by Staphylococcus aureus isolated from humans was investigated. In 46, 86, 78, 41, 20, and 91% of the sera of healthy subjects, antibodies were found against enterotoxins A, B, C, D, E, and F, respectively. The high percentage of sera with antibodies against enterotoxin F correlated with the relatively high frequency of enterotoxin F-producing S. aureus isolated from humans (one-third of the isolates produced enterotoxin F). In patients with toxic shock syndrome, antibodies against enterotoxin F were not present or were present only at very low levels. An increase of antibodies after onset of the disease was observed in two of eight patients investigated. From the results, it can be concluded that only those humans who show low levels of antibodies are susceptible to toxic shock syndrome.
Worldwide Experience in Newborn Screening for Classical Congenital Adrenal Hyperplasia due to 21-Hydroxylase Deficiency (1988)

The need for a reliable screening test for classical congenital adrenal hyperplasia prompted development of newborn screening programs. Worldwide incidence of classical congenital adrenal hyperplasia in this report was taken from newborn screening programs in France, Italy, Japan, New Zealand, Scotland, and the United States. Two populations in which the occurrence of congenital adrenal hyperplasia among live births has been reported with greater than usual frequency are the Yupik Eskimos of southwestern Alaska (1:282) and the people of La Reunion, France (1:2,141). Aside from these populations, 1,093,310 newborns were screened between 1980 and 1988, of whom 77 had congenital adrenal hyperplasia. Thus, worldwide incidence of this disorder was estimated at 1:14,199 live births for homozygous patients, 1:60 for heterozygous subjects, with a gene frequency of 0.0083. Incidence of congenital adrenal hyperplasia among whites was estimated to be 1:11,909 (41:488,279) for homozygous patients, 1:55 for heterozygous subjects with a gene frequency of 0.0091. Incidence for the salt-wasting form of congenital adrenal hyperplasia was 1:18,850 (58:1,093,310) compared with 1:57,543 (19:1,093,310) for congenital adrenal hyperplasia in the simple virilizing form. Thus, salt-wasting congenital adrenal hyperplasia was three times more common than simple virilizing congenital adrenal hyperplasia. Estimated incidence of congenital adrenal hyperplasia in white populations in Italy and France (1:10,866) was higher than in Scotland (1:17,098), New Zealand (1:14,500). The incidence in an Asian population (Japan) (1:15,800) did not differ significantly from that of the white population. In four of five populations, overall incidence was higher than previously reported, as was the frequency of the salt-wasting form (75% v 50% to 66%), suggesting improved case detection by newborn screening.(ABSTRACT TRUNCATED AT 250 WORDS)
Studies on Simulated Vitreous Hemorrhages (1958)

Simulated vitreous hemorrhages were produced in rabbits by injection of homologous blood tagged with radioactive chromium. The course of the hemorrhage was followed by measuring the rate of change of radioactivity of the eye and by visual and histologic methods. <h3>Methods and Materials</h3> Rabbit blood was collected in oxalated tubes. The erythrocytes were separated by centrifugation and thoroughly washed with isotonic saline. Radioactive sodium chromate (Na<sub>2</sub>Cr<sup>51</sup>O<sub>4</sub>) was used to label the hemoglobin of the cells by the procedure of Gray and Sterling<sup>1</sup>as modified by Reilly et al.2 The tagged erythrocytes were then either suspended in the original plasma to reconstitute whole blood or were laked in a volume of distilled water equal to the initial plasma volume. Hemorrhage was simulated by injection, through a 30-gauge needle, of 0.10 ml. of this blood into the vitreous. Since γ-rays and soft x-rays from the radioactive chromium in
The development of a clinician‐administered PTSD scale (1995)

Abstract Several interviews are available for assessing PTSD. These interviews vary in merit when compared on stringent psychometric and utility standards. Of all the interviews, the Clinician‐Administered PTSD Scale (CAPS‐1) appears to satisfy these standards most uniformly. The CAPS‐1 is a structured interview for assessing core and associated symptoms of PTSD. It assesses the frequency and intensity of each symptom using standard prompt questions and explicit, behaviorally‐anchored rating scales. The CAPS‐1 yields both continuous and dichotomous scores for current and lifetime PTSD symptoms. Intended for use by experienced clinicians, it also can be administered by appropriately trained paraprofessionals. Data from a large scale psychometric study of the CAPS‐1 have provided impressive evidence of its reliability and validity as a PTSD interview.
Analysis of themucRgene regulating biosynthesis of exopolysaccharides: implications for biofilm formation inSinorhizobium melilotiRm1021 (2009)

Bacterial surface polysaccharides are crucial for establishment of successful rhizobia-legume symbiosis, and in most bacteria, are also critical for biofilm formation and surface colonization. In Sinorhizobium meliloti, the regulatory protein MucR controls exopolysaccharide production. To clarify the relationship between exopolysaccharide synthesis and biofilm formation, we studied mucR expression under growth conditions that influence attachment to polyvinylchloride, developed a microtiter plate assay to quantify biofilm formation in S. meliloti strain Rm1021 and mutants defective in succinoglycan (EPS I) and/or galactoglucan (EPS II) production, and analyzed expression of EPS I and EPS II genes by quantitative reverse transcriptase-PCR. Consistent with previous studies of planktonic bacteria, we found that disruption of the mucR gene in Rm1021 biofilms increased EPS II, but reduced EPS I gene expression. mucR expression was not affected by environmental conditions that influence biofilm formation on polyvinylchloride, and biofilm formation by Rm1021 was independent of exopolysaccharide synthesis. Other factors on the Rm1021 cell surface, and growth conditions, presumably regulate attachment and/or growth as a biofilm on polyvinylchloride.