gebhart/patrepeval huggingface dataset:
Induction of PBP74/mortalin/Grp75, a member of the hsp70 family, by low doses of ionizing radiation: a possible role in induced radioresistance (1997)

The identification of genes whose expression is altered following exposure to a low dose of ionizing radiation (IR) is an important step in understanding the phenomenon of the adaptive response. Using the differential mRNA display method we have identified a gene whose expression is up-regulated following exposure to 0.25 Gy IR. Partial DNA sequence and restriction endonuclease analysis of this gene showed that it is identical to the gene encoding for the human peptide-binding protein 74 (PBP74/mortalin/Grp75), a member of the heat shock 70 protein family. Time-course measurement of the PBP74/mortalin/Grp75 mRNA showed that its level was elevated after a lag of at least 15 min. The maximum induction appears to be at 30 min following gamma-irradiation and there is then a steady decline to control levels within 5 h in the HT29 cell line. On the other hand, the level of the PBP74/mortalin/Grp75 mRNA in the human breast adenocarcinoma cell line MCF-7 is consistently elevated after gamma-irradiation for up to 6 h post-irradiation. Furthermore, a cell line that does not demonstrate the induced radioresistance phenomenon (SW48) shows no induction of the PBP74/mortalin/Grp75 mRNA in contrast with HT29 or MCF-7. Treatment of the HT29 cells with antisense oligonucleotide directed towards the initiation codon of PBP74 sensitized cells to ionizing radiation.
The Orexin OX1 Receptor Activates a Novel Ca2+ Influx Pathway Necessary for Coupling to Phospholipase C (2000)

Ca(2+) elevations in Chinese hamster ovary cells stably expressing OX(1) receptors were measured using fluorescent Ca(2+) indicators fura-2 and fluo-3. Stimulation with orexin-A led to pronounced Ca(2+) elevations with an EC(50) around 1 nm. When the extracellular [Ca(2+)] was reduced to a submicromolar concentration, the EC(50) was increased 100-fold. Similarly, the inositol 1,4,5-trisphosphate production in the presence of 1 mm external Ca(2+) was about 2 orders of magnitude more sensitive to orexin-A stimulation than in low extracellular Ca(2+). The shift in the potency was not caused by depletion of intracellular Ca(2+) but by a requirement of extracellular Ca(2+) for production of inositol 1,4,5-trisphosphate. Fura-2 experiments with the "Mn(2+)-quench technique" indicated a direct activation of a cation influx pathway by OX(1) receptor independent of Ca(2+) release or pool depletion. Furthermore, depolarization of the cells to +60 mV, which almost nullifies the driving force for Ca(2+) entry, abolished the Ca(2+) response to low concentrations of orexin-A. The results thus suggest that OX(1) receptor activation leads to two responses, (i) a Ca(2+) influx and (ii) a direct stimulation of phospholipase C, and that these two responses converge at the level of phospholipase C where the former markedly enhances the potency of the latter.
The Antiviral Effect of Zidovudine and Ribavirin in Clinical Trials and the Use of p24 Antigen Levels as a Virologic Marker (1989)

The inhibition of viremia and p24 core antigenemia in patients infected with human immunodeficiency virus (HIV) was evaluated in separate multicenter, double-blind, placebo-controlled trials of zidovudine and ribavirin. Of 29 patients (14 with AIDS and 15 with AIDS-related complex [ARC]) enrolled in the zidovudine study, 16 received 250 mg of zidovudine every 4 h and 13 received placebo. No difference in HIV isolation from peripheral blood was observed at 20 w in treated versus placebo groups (79% vs. 82%). In patients tolerating zidovudine, mean p24 antigen levels dropped to 8.2% +/- 8.1% of their baseline values, whereas in placebo recipients mean p24 antigen levels declined to 61.3% +/- 40.8% of their baseline values (P less than .005). In the ribavirin study, patients with ARC treated with either 800 mg or 600 mg ribavirin daily or with placebo showed no consistent reduction in p24 antigenemia or decrease in HIV isolation. These data indicate that decline in p24 antigenemia can be a useful virologic marker in evaluation of new antiretroviral drugs.
Migration of Additives in Polyolefin Films Characterized by AFM (2010)

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.
Efficacy of the Dietary Supplement S-Adenosyl-L-Methionine (2001)

Consumers should be instructed to avoid unmonitored consumption of this dietary supplement until sufficient discussion has taken place with their primary healthcare provider. Although there exists significant potential for therapeutic application of SAMe, its uncertain risk profile precludes definitive recommendation at this time. Healthcare providers and consumers should likely temper their enthusiasm for this dietary supplement until sufficient information becomes available.
3D nanostructures fabricated by advanced stencil lithography (2016)

This letter reports on a novel fabrication method for 3D metal nanostructures using high-throughput nanostencil lithography. Aperture clogging, which occurs on the stencil membranes during physical vapor deposition, is leveraged to create complex topographies on the nanoscale. The precision of the 3D nanofabrication method is studied in terms of geometric parameters and material types. The versatility of the technique is demonstrated by various symmetric and chiral patterns made of Al and Au.
Isolation of GD3 synthase gene by expression cloning of GM3 alpha-2,8-sialyltransferase cDNA using anti-GD2 monoclonal antibody. (1994)

For the isolation of ganglioside GD3 synthase (EC 2.4.99.8) cDNA, we developed an expression cloning approach that used an anti-GD2 monoclonal antibody for selection. A host recipient cell line that we have named KF3027-Hyg5 was also utilized. This cell line expresses high levels of GM2 as well as GM3 but no GD3 or GD2 and was constructed from mouse B16 melanoma cells transfected with the polyoma large tumor antigen gene (KF3027) and the previously cloned beta-1,4-N-acetylgalactosaminyltransferase (EC 2.4.1.92) cDNA. Four rounds of transfection, monoclonal antibody 3F8 panning, and Hirt extraction resulted in the isolation of two cDNA clones, transfection of which directed the expression of GD3 in KF3027 and B16 melanoma cells and GD3 and GD2 in KF3027-Hyg5 cells. The cDNA contained a 1650-bp insert and a single open reading frame. The deduced amino acid predicted a type II membrane topology consisting of cytoplasmic (14 aa), transmembrane (18 aa), and catalytic (309 aa) domains. The sequence also predicted the presence of a sialyl motif similar to that found in the other sialyltransferases cloned so far. As expected, mRNA of this gene (2.6 kb) was strongly expressed in human melanoma lines.
Multiple HLA Epitopes Contribute to Type 1 Diabetes Susceptibility (2013)

Disease susceptibility for type 1 diabetes is strongly associated with the inheritance of specific HLA alleles. However, conventional allele frequency analysis can miss HLA associations because many alleles are rare. In addition, disparate alleles that have similar peptide-binding sites, or shared epitopes, can be missed. To identify the HLA shared epitopes associated with diabetes, we analyzed high-resolution genotyping for class I and class II loci. The HLA epitopes most strongly associated with susceptibility for disease were DQB1 A(57), DQA1 V(76), DRB1 H(13), and DRB1 K(71), whereas DPB1 YD(9,57), HLA-B C(67), and HLA-C YY(9,116) were more weakly associated. The HLA epitopes strongly associated with resistance were DQB1 D(57), DQA1 Y(80), DRB1 R(13), and DRB1 A(71). A dominant resistance phenotype was observed for individuals bearing a protective HLA epitope, even in the presence of a susceptibility epitope. In addition, an earlier age of disease onset correlated with significantly greater numbers of susceptibility epitopes and fewer resistance epitopes (P < 0.0001). The prevalence of both DQ and DR susceptibility epitopes was higher in patients than in control subjects and was not exclusively a result of linkage disequilibrium, suggesting that multiple HLA epitopes may work together to increase the risk of developing diabetes.
Improved Plagiarism Detection Algorithm Based on Abstract Syntax Tree (2013)

Statements with conditionals are widely used in C, C++ and java, such as if and while statements and they are easy to plagiarize by adjusting the logical structure of the corresponding statements. However, the existing relative algorithms and tools cannot effectively detect code plagiarism of these statements. This paper puts forward an improved code plagiarism detection algorithm based on abstract syntax tree. The algorithm calculates the hash value for each node of the abstract syntax tree, and compares the hash values node by node. Based on this, it analyzes the if-statement plagiarism, as if-statements are representative in the statements with conditionals, and puts forward the corresponding detection schemes in order to detect plagiarism effectively. After that, with the results of many experiments, the algorithm is proved effective on detecting if-statement plagiarisms.
Properties of spontaneous growth hormone secretory bursts and half-life of endogenous growth hormone in boys with idiopathic short stature. Genentech Collaborative Group (1992)

We analyzed endogenous GH secretory dynamics and MCRs by a novel quantitative deconvolution technique in 20 boys with idiopathic short stature (ISS) and 35 boys of normal stature in Tanner stage I of puberty. We tested the null hypotheses that 1) ISS is not associated with any alterations in the frequency, mass, amplitude, or duration of spontaneous GH secretory bursts and/or the 24-h GH production rate; and 2) the half-life of endogenous GH is not altered in ISS. The boys with ISS had a mean (+/- SEM) bone age of 8.0 +/- 0.42 yr and a chronological age of 10 +/- 0.50 yr. The latter was similar to the chronological (and bone) age of the normal boys of 9.8 +/- 0.23 (and 9.3 +/- 0.34) yr. Mean height SD scores were significantly lower in ISS boys, viz. -2.7 +/- 0.15 in ISS vs. +0.34 +/- 0.13 in normal boys (P less than 0.001). Plasma insulin-like growth factor-I concentrations were similar in the two groups, as were (24-h) mean serum GH concentrations, viz. 3.5 +/- 0.29 micrograms/L in ISS and 4.1 +/- 0.49 micrograms/L in normal boys (P = NS). Deconvolution analysis revealed that the mean number of GH secretory events per 24 h was similar in normal and ISS boys, viz. 9.6 +/- 0.76 (normal) vs. 8.4 +/- 0.55 (ISS), and that there was no significant difference in mean GH interburst intervals. The amplitude, mass, and duration of computer-resolved GH secretory bursts also did not differ in normal and ISS boys. The half-lives of endogenous GH were estimated to be 16 +/- 0.77 min in the ISS and 18 +/- 0.93 min in the control boys (P = NS). The calculated daily GH secretion rate per unit distribution volume was not significantly reduced in ISS, i.e. 194 +/- 19 micrograms/L.day in ISS vs. 177 +/- 19 micrograms/L.day in control boys. Moreover, daily GH secretion rates corrected for body mass index (weight/height2) in the twp groups were not significantly different. In summary, the present cohort of boys with ISS manifested no significant alterations in GH secretory burst frequency, duration, mass, or amplitude or in the half-life of endogenous GH compared to normal boys in Tanner stage I of pubertal development. Indeed, whether daily GH secretion rates are expressed per unit distribution volume or per unit body mass index, groups of boys with ISS and normal height controls secrete similar total amounts of GH. We conclude that the overall dynamics of GH secretion and clearance in boys with ISS considered as a whole cannot be distinguished readily from physiological patterns observed in prepubertal boys of normal height.
Tolerance of transformed cotton to glufosinate (2001)

Field experiments from 1997 to 1999 examined cotton cv. ‘Coker 312’ that was genetically transformed to tolerate glufosinate. None of the glufosinate treatments caused visible injury to the glufosinate-tolerant cotton, but treatments were lethal to nontransformed or nonexpressing cotton. No glufosinate treatment adversely affected plant height at maturity, total number of nodes, bolls per plant, or boll positions. Glufosinate applications of 0.6 kg ha−1 made at eight stages of growth, ranging from cotyledon stage to 50% open boll, did not adversely affect yield or fiber quality as measured by micronaire or fiber length and strength. Sequential glufosinate applications up to four stages of growth from the zero- to one-leaf stage to the 14- to 15-leaf stage or individual glufosinate applications at 3.3 kg ha−1 made at the two- to three-leaf stage of growth also did not adversely affect yield or fiber quality. Overall yields in these studies were low relative to normal Texas Southern High Plains cotton yield because these studies were conducted using a Coker 312 parental line, which is generally a poor performer in this region. This research indicated that the transformation events for glufosinate tolerance in cotton were successful and the glufosinate-tolerance gene was expressed throughout the growing season. Transformation and field testing of other cotton varieties are needed to improve varietal performance on the Texas Southern High Plains.
Massively Parallel Recording of Unit and Local Field Potentials With Silicon-Based Electrodes (2003)

Parallel recording of neuronal activity in the behaving animal is a prerequisite for our understanding of neuronal representation and storage of information. Here we describe the development of micro-machined silicon microelectrode arrays for unit and local field recordings. The two-dimensional probes with 96 or 64 recording sites provided high-density recording of unit and field activity with minimal tissue displacement or damage. The on-chip active circuit eliminated movement and other artifacts and greatly reduced the weight of the headgear. The precise geometry of the recording tips allowed for the estimation of the spatial location of the recorded neurons and for high-resolution estimation of extracellular current source density. Action potentials could be simultaneously recorded from the soma and dendrites of the same neurons. Silicon technology is a promising approach for high-density, high-resolution sampling of neuronal activity in both basic research and prosthetic devices.
Choosing Reporter-Quencher Pairs for Efficient Quenching Through Formation of Intramolecular Dimers (2006)

Fluorescent energy transfer within dual-labeled oligonucleotide probes is widely used in assays for genetic analysis. Nucleic acid detection/amplification methods, such as real-time polymerase chain reaction, use dual-labeled probes to measure the presence and copy number of specific genes or expressed messenger RNA. Fluorogenic probes are labeled with both a reporter and a quencher dye. Fluorescence from the reporter is only released when the two dyes are physically separated via hybridization or nuclease activity. Fluorescence resonance energy transfer (FRET) is the physical mechanism that is most often cited to describe how quenching occurs. We have found that many dual-labeled probes have enhanced quenching through a nonFRET mechanism called static quenching. Static quenching, which is also referred to as contact quenching, can occur even in “linear” oligonucleotide probes that have no defined secondary structure to bring the reporter and quencher pair into proximity. When static quenching accompanies FRET quenching, the background fluorescence of probes is suppressed. This chapter describes how to pair reporter and quencher dyes for duallabeled probes to maximize both FRET and static quenching. Data comparing various reporter-quencher pairs is presented as well as protocols for evaluation and optimization of the probes.
Orthogonal Forward Selection and Backward Elimination Algorithms for Feature Subset Selection (2004)

Sequential forward selection (SFS) and sequential backward elimination (SBE) are two commonly used search methods in feature subset selection. In the present study, we derive an orthogonal forward selection (OFS) and an orthogonal backward elimination (OBE) algorithms for feature subset selection by incorporating Gram-Schmidt and Givens orthogonal transforms into forward selection and backward elimination procedures, respectively. The basic idea of the orthogonal feature subset selection algorithms is to find an orthogonal space in which to express features and to perform feature subset selection. After selection, the physically meaningless features in the orthogonal space are linked back to the same number of input variables in the original measurement space. The strength of employing orthogonal transforms is that features are decorrelated in the orthogonal space, hence individual features can be evaluated and selected independently. The effectiveness of our algorithms to deal with real world problems is finally demonstrated.
Low‐Voltage SOI CMOS VLSI Devices and Circuits (2002)

Preface. Acknowlegments. Introduction. SOI CMOS Devices--Part I. SOI CMOS Devices--Part II. Fundamentals of SOI CMOS Circuits. SOI CMOS Digital Circuits. SOI CMOS Analog Circuits. PD SOI-Technology SPICE Models. Index.
Processing of Switch Transcripts Is Required for Targeting of Antibody Class Switch Recombination (1998)

Antibody class switching is mediated by somatic recombination between switch regions of the immunoglobulin heavy chain gene locus. Targeting of recombination to particular switch regions is strictly regulated by cytokines through the induction of switch transcripts starting 5' of the repetitive switch regions. However, switch transcription as such is not sufficient to target switch recombination. This has been shown in mutant mice, in which the I-exon and its promoter upstream of the switch region were replaced with heterologous promoters. Here we show that, in the murine germline targeted replacement of the endogenous gamma1 promoter, I-exon, and I-exon splice donor site by heterologous promoter and splice donor sites directs switch recombination in activated B lymphocytes constitutively to the gamma1 switch region. In contrast, switch recombination to IgG1 is inhibited in mutant mice, in which the replacement does not include the heterologous splice donor site. Our data unequivocally demonstrate that targeting of switch recombination to IgG1 in vivo requires processing of the Igamma1 switch transcripts. Either the processing machinery or the processed transcripts are involved in class switch recombination.
Big Data, Big Challenges (2014)

Summary form only given. Big data analytics is the process of examining large amounts of data of a variety of types (big data) to uncover hidden patterns, unknown correlations and other useful information. Its revolutionary potential is now universally recognized. Data complexity, heterogeneity, scale, and timeliness make data analysis a clear bottleneck in many biomedical applications, due to the complexity of the patterns and lack of scalability of the underlying algorithms. Advanced machine learning and data mining algorithms are being developed to address one or more challenges listed above. It is typical that the complexity of potential patterns may grow exponentially with respect to the data complexity, and so is the size of the pattern space. To avoid an exhaustive search through the pattern space, machine learning and data mining algorithms usually employ a greedy approach to search for a local optimum in the solution space, or use a branch-and-bound approach to seek optimal solutions, and consequently, are often implemented as iterative or recursive procedures. To improve efficiency, these algorithms often exploit the dependencies between potential patterns to maximize in-memory computation and/or leverage special hardware (such as GPU and FPGA) for acceleration. These lead to strong data dependency, operation dependency, and hardware dependency, and sometimes ad hoc solutions that cannot be generalized to a broader scope. In this talk, I will present some open challenges faced by data scientist in biomedical fields and the current approaches taken to tackle these challenges.
Naloxone Inhibits Gastric Emptying in the Rat (1999)

Naloxone is generally considered to be a pure antagonist, but it may produce several behavioral effects, such as hyperalgesia or stimulation of respiration.We studied the effect of naloxone on gastric emptying and gastrointestinal transit in rats. Six to eight Wistar rats (200-250 g) were used for each experiment. Either saline or naloxone (0.01-10 mg/kg) was injected intraperitoneally at 0 min. At 30 min, radiolabeled saline or milk 1 mL was infused into the stomach. At 60 min, gastric emptying and gastrointestinal transit were calculated by measuring the radioactivity in the gastrointestinal tract. Naloxone significantly inhibited gastric emptying of saline (P = 0.002) and of milk (P < 0.05), but not the gastrointestinal transit of either (P > 0.05). Gastric emptying of saline showed a significant peak (P < 0.05) in the dose-response curve at 0.7 mg/kg. Therefore, naloxone significantly inhibits gastric emptying of saline and milk, but not the gastrointestinal transit of either. Implications: Although naloxone is generally considered to be a pure opioid receptor antagonist, it delays gastric emptying of saline or milk, as does morphine in the rat. However, it is uncertain from our results whether naloxone inhibited gastric emptying by antagonizing the effects of endogenous opioids. (Anesth Analg 1999;88:204-8)
[Crystalline modifications and polymorphism changes during drug manufacture]. (2002)

More than half of the pharmaceutical compounds exhibit polymorphism or pseudopolymorphism, e.g., they exist as more than one crystalline structure (true polymorphs, hydrates, solvates) or as more or less amorphous products. As such, they show at the solid state different physicochemical properties (melting point, transition point, plasticity, solubility, hygroscopicity, chemical reactivity), which in turn may affect the technological and biopharmaceutical properties of active ingredients or excipients (compactibility, dissolution rate, bioavailability, pharmacological activity, stability). When considering a chemically well-defined compound, one may find one or another crystalline state or polymorphic form according to the source or batch considered. One may also observe changes in technological or biopharmaceutical properties that are due to polymorphic transformations arising from the mechanical or heat treatment or from the environmental conditions (solvent-mediated reactions, desolvation) undergone by the product or the dosage form. The present article presents the fundamental aspects related to the above-mentioned phenomena and reviews both classical and recent examples from the literature reporting transformations during milling or grinding, tabletting, preparation of drug suspensions, granulation, dissolution or release tests, stability trials, spray drying, freeze-drying or preparation of adsorbates or complexes.
Recorded and Expected Mortality Among the Navajo, with Special Reference to Cancer (1956)

Journal Article Recorded and Expected Mortality Among the Navajo, with Special Reference to Cancer Get access Robert L. Smith, M.D., Robert L. Smith, M.D. Search for other works by this author on: Oxford Academic PubMed Google Scholar Clarence G. Salsbury, M.D., Clarence G. Salsbury, M.D. Search for other works by this author on: Oxford Academic PubMed Google Scholar Alexander G. Gilliam, M.D. Alexander G. Gilliam, M.D. Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 17, Issue 1, July 1956, Pages 77–89, https://doi.org/10.1093/jnci/17.1.77 Published: 01 July 1956 Article history Received: 23 February 1956 Published: 01 July 1956