gebhart/patrepeval huggingface dataset:
Folding Very Short Peptides Using Molecular Dynamics (2006)

Peptides often have conformational preferences. We simulated 133 peptide 8-mer fragments from six different proteins, sampled by replica-exchange molecular dynamics using Amber7 with a GB/SA (generalized-Born/solvent-accessible electrostatic approximation to water) implicit solvent. We found that 85 of the peptides have no preferred structure, while 48 of them converge to a preferred structure. In 85% of the converged cases (41 peptides), the structures found by the simulations bear some resemblance to their native structures, based on a coarse-grained backbone description. In particular, all seven of the beta hairpins in the native structures contain a fragment in the turn that is highly structured. In the eight cases where the bioinformatics-based I-sites library picks out native-like structures, the present simulations are largely in agreement. Such physics-based modeling may be useful for identifying early nuclei in folding kinetics and for assisting in protein-structure prediction methods that utilize the assembly of peptide fragments.
One-Factor-at-a-Time versus Designed Experiments (1999)

Abstract Many engineers and scientists perform one-factor-at-a-time (OFAT) experiments. They will continue to do so until they understand the advantages of designed experiments over OFAT experiments, and until they learn to recognize OFAT experiments so they can avoid them. A very effective way to illustrate the advantages of designed experiments, and to show ways in which OFAT experiments present themselves in real life, is to introduce real examples of OFAT experiments and then demonstrate why a designed experiment would have been better. Three engineering examples of OFAT experiments are presented, as well as designed experiments that would have been better. The three examples have been successfully used in an industrial workshop and can also be used in academic courses.
Straggler Detection in Parallel Computing Systems through Dynamic Threshold Calculation (2016)

Cloud computing systems face the substantial challenge of the Long Tail problem: a small subset of straggling tasks significantly impede parallel jobs completion. This behavior results in longer service response times and degraded system utilization. Speculative execution, which create task replicas at runtime, is a typical method deployed in large-scale distributed systems to tolerate stragglers. This approach defines stragglers by specifying a static threshold value, which calculates the temporal difference between an individual task and the average task progression for a job. However, specifying static threshold debilitates speculation effectiveness as it fails to consider the intrinsic diversity of job timing constraints within modern day Cloud computing systems. Capturing such heterogeneity enables the ability to impose different levels of strictness for replica creation while achieving specified levels of QoS for different application types. Furthermore, a static threshold also fails to consider system environmental constraints in terms of replication overheads and optimal system resource usage. In this paper we present an algorithm for dynamically calculating a threshold value to identify task stragglers, considering key parameters including job QoS timing constraints, task execution characteristics, and optimal system resource utilization. We study and demonstrate the effectiveness of our algorithm through simulating a number of different operational scenarios based on real production cluster data against state-of-the-art solutions. Results demonstrate that our approach is capable of creating 58.62% less replicas under high resource utilization while reducing response time up to 17.86% for idle periods compared to a static threshold.
Graphene-Based Non-Noble-Metal Catalysts for Oxygen Reduction Reaction in Acid (2011)

Non-noble-metal catalysts based on Fe–N–C moieties have shown promising oxygen reduction reaction (ORR) activity in proton exchange membrane fuel cells (PEMFCs). In this study, we report a facile method to prepare a Fe–N–C catalyst based on modified graphene (Fe–N–rGO) from heat treatment of a mixture of Fe salt, graphitic carbon nitride (g-C3N4), and chemically reduced graphene (rGO). The Fe–N–rGO catalyst was found to have pyridinic N-dominant heterocyclic N (40% atomic concentration among all N components) on the surface and have an average Fe coordination of ∼3 N (Fe–N3,average) in bulk. Rotating disk electrode measurements revealed that Fe–N–rGO had high mass activity in acid and exhibited high stability at 0.5 V at 80 °C in acid over 70 h, which was correlated to low H2O2 production shown from rotating ring disk electrode measurements.
Deep Soil Mixing at the Jackson Lake Dam (1989)

The Jackson Lake Dam was constructed in 1917 in the Grand Teton National Park near Jackson, Wyoming. The dam was a hydraulic fill placed on a natural alluvium and outwash foundation. The Bureau of Reclamation (Burec) determined that the dam and its foundation would be susceptible to liquefaction and failure during a potential earthquake; a series of contracts was let to remove and replace the dam with a compacted fill and to improve the dam's foundation to depths of up to 110 feet (33 meters). After considering a number of options, the Burec selected deep soil mixing (DSM) as the method to improve the subsoils and to install an upstream cut-off wall. The DSM method appears to have great promise as a method for creating deep foundations, retaining walls, areal soil improvement and even underwater foundations.
<i>Déjà vu</i>? A decade of research on language laboratories, television and video in language learning (2009)

The developments in the last ten years in the form of DVD, streaming video, video on demand, interactive television and digital language laboratories call for an assessment of the research into language teaching and learning making use of these technologies and the learning paradigms underpinning them. This paper surveys research on language teaching and learning using these and older technologies since 1999, and maps out some pointers for future research. The evidence suggests that research on video and language learning using DVD and other recent technologies is already well established, bringing out a number of issues for further study. In contrast, research-led implementation of the enhanced functionality of digital language laboratories is hardly in its infancy and much language laboratory use is marginal at best.
The complement receptor 3, CR3 (CD11b/CD18), on T lymphocytes: activation-dependent up-regulation and regulatory function (2001)

The complement receptor 3 (CR3; CD11b/CD18) is present exclusively on leukocytes, particularly on NK cells, monocytes and polymorphonuclear neutrophils. Approximately 10% of peripheral T lymphocytes and, as we found now mainly CD8(+) cells, expressed CD11b. Upon stimulation, however, expression of CD11b was up-regulated also on CD4(+) cells. Stimulation of T cells either by cross-linked anti-CD3 and IL-2 or by mononuclear cells and mitogen yielded up to 28% CD11b(+) T cells. The majority of CD11b(+) T cells also expressed CD56. T cell lines established from healthy donors were also found to express CR3. When restimulated up to 90% of cells became positive for CD11b making those cells an ideal tool for studying the functional role of CD11b. Antibodies to CD11b and bona fide ligands for the complement receptor inhibited the anti-CD3-induced T cell proliferation and as well as IL-2 release. In contrast, proliferation of a CD11b(-) T cell line was not inhibited. Taken together, our data indicate an activation-dependent expression of the complement receptor on T cells and suggest a regulatory function.
Quantitative x‐ray studies of order in amorphous and crystalline polymers. Quantitative x‐ray determination of crystallinity in polyethylene (1951)

Abstract Various quantitative scattering relationships for polymers have been examined experimentally in order to test their validity as assumptions in the x‐ray determination of crystallinity. These are ( a ) the proportionality between the scattered intensity and the pt value of the specimen ( p is the density and t the thickness of the material), ( b ) the relationship between equal pt values for two different specimens of the same material and the corresponding scattering masses in the beam, ( c ) the scattering from equal masses of a polymer in the amorphous or crystalline states, and ( d ) the values of the total scattered intensity from equal masses of different polymers. It has been demonstrated, at least in the case of polyethylene, that the percentage of crystalline material in a polycrystalline polymer can be determined quantitatively by means of x‐ray diffraction methods. The method used in this study, viz. , a comparison of the amorphous scattering from the sample with that from a completely amorphous sample, has been applied to an investigation of the temperature variation of crystallinity in unstretched and stretched polyethylene. The comparison between the x‐ray and density results for the case of the unstretched material has been pointed out. The technique has also permitted a determination of the orientation of the crystallites. By means of these methods, it has been shown that the x‐ray diffraction results are in essential agreement with previous stress‐birefringence data on stretched polyethylene; and that the nature of the stretchng process is different at high and at low elongations.
Observer variation inhistopathological diagnosis andgrading of cervical intraepithelial neoplasia (1989)

To assess thevariability amonghistopathologists indiagnosing andgrading cervical intraepithelial neoplasia eight experienced histopathologists based atdifferent hospitals examined thesamesetof100 consecutive colposcopic cervical biopsy specimens andassigned themintooneofsixdiagnostic categories. Thesewerenormal squamous epithelium, non-neoplastic squamousproliferations, cervical intraepithelial neoplasia grades I,II,andIII, and other. Thehistopathologists weregivencurrently accepted criteria fordiagnosing andgrading cervical intraepithelial neoplasia andaskedtomarktheir degree ofconfidence about their decision onavisual linear analogue scale provided. Thedegree ofagreementbetween thehistopathologists wascharacterisedbykappastatistics, whichshowedanoverall pooragreement (unweighted kappa0.358). Agreementbetween observers wasexcellent forinvasive lesions, moderately goodforcervical intraepithelial neoplasia gradeIII,andpoorforcervical intraepithelial neoplasia grades IandII(unweighted kappa0-832, 0*496, 0-172, and0-175, respectively); thekappavalueforallgrades ofcervical intraepithelial neoplasia takentogether was0-660. The mostimportant source ofdisagreement layinthe distinction ofreactive squamous proliferations from cervical intraepithelial neoplasia grade I.Thehistopathologists wereconfident indiagnosing cervical intraepithelial neoplasia gradeIIIandinvasive carcinoma(other) butnotasconfident indiagnosing cervical intraepithelial neoplasia grades IandIIand glandular atypia (other). Experienced histopathologists showconsiderable interobserver variability ingrading cervical intraepithelial neoplasia andmoreimportantly indistinguishing between reactive squamous proliferations andcervical intraepithelial neoplasia grade I.Itis suggested thatthethree grade division ofcervical intraepithelial neoplasia should beabandoned anda borderline category introduced that entails follow up without treatment.
Intrahypothalamic corticotropin-releasing factor elevates gastric bicarbonate and inhibits stress ulcers in rats (1990)

The effects of intrahyopthalamic microinfusions of corticotropin-releasing factor (CRF) on gastric bicarbonate, acid, and pepsin content and on cold restraint-induced gastric lesion formation were tested in three experiments. Bilateral microinfusions of CRF into the hypothalamic ventromedial nucleus (0.86 nmol/rat) significantly increased both gastric bicarbonate concentration and total bicarbonate output. These effects were observed irrespective of whether rats were pretreated with the acid antisecretory drug omeprazole. In nonomeprazole-pretreated rats, CRF microinfusions also significantly reduced acid secretion and raised pH. The increase in bicarbonate content accounted for half of the observed decrease in acid output, suggesting that CRF microinfusions activated separable bicarbonate-stimulating and acid-inhibiting hypothalamic systems. In non-omeprazole-pretreated rats, CRF microinfusions significantly increased serum gastrin, whereas pepsin output was unchanged. Gastric mucosal damage produced by 4 h of cold restraint was significantly diminished by CRF microinfusion into the ventromedial hypothalamus. These data demonstrate that ventromedial hypothalamic microinfusions of CRF increase bicarbonate content, decrease gastric acid content, and confer protection against cold restraint-induced gastric mucosal damage. Hypothalamic CRF neuronal terminals and receptors may be involved in the central regulation of gastric bicarbonate secretion as well as acid secretion.
Comparison of the live-attenuated Japanese encephalitis vaccine SA14 -14-2 strain with its pre-attenuated virulent parent SA14 strain: similarities and differences in vitro and in vivo (2016)

Japanese encephalitis virus (JEV) is the main cause of acute viral encephalitis, primarily affecting children and young adults in the Asia-Pacific region. JEV is a vaccine-preventable pathogen, with four types of JE vaccine licensed in different regions of the world. To date, the most common JEV strain used in vaccine development and production is SA14-14-2, an attenuated strain derived from its wild-type parental strain SA14. In this study, we directly compared the phenotypic and genotypic characteristics of SA14 and SA14-14-2 to determine the biological and genetic properties associated with their differential virulence. In susceptible BHK-21 cells, SA14-14-2 grew slightly more slowly and formed smaller plaques than SA14, but unlike SA14, it showed almost no expression of the viral protein NS1', the product of a conserved predicted RNA pseudoknot-mediated ribosomal frameshift. In weanling ICR mice, SA14-14-2 was highly attenuated in terms of both neuroinvasiveness and neurovirulence, with its median lethal doses invariably over five logs higher than those of SA14 when inoculated intramuscularly and intracerebrally. Interestingly, the neurovirulence of SA14-14-2 was dependent on mouse age, with the 1- to 7-day-old mice being highly susceptible and the 14- to 21-day-old mice becoming resistant to intracerebral inoculation. At the genome level, SA14-14-2 differed from SA14 by 57 nucleotides, including one silent G-to-A substitution at position 3599 within the predicted RNA pseudoknot for NS1' synthesis; of the 57 differences, 25 resulted in amino acid substitutions. Our data pave the way for the development of new genetically modified JE vaccines.
Rap1 Is Activated by Erythropoietin or Interleukin-3 and Is Involved in Regulation of β1 Integrin-mediated Hematopoietic Cell Adhesion (2001)

The CrkL adaptor protein is involved in signaling from the receptor for erythropoietin (Epo) as well as interleukin (IL)-3 and activates beta(1) integrin-mediated hematopoietic cell adhesion through its interaction with C3G, a guanine nucleotide exchange factor for Rap1. We demonstrate here that Epo as well as IL-3 activates Rap1 in an IL-3-dependent hematopoietic cell line, 32D, expressing the Epo receptor. The cytokine-induced activation of Rap1 was augmented in cells that inducibly overexpress CrkL or C3G. The CrkL-mediated enhancement of cell adhesion was inhibited by expression of a dominant negative mutant of Rap1, Rap1A-17N, whereas an activated mutant of Rap1, Rap1A-63E, activated beta(1) integrin-dependent adhesion of hematopoietic cells. In 32D cells, Rap1 was also activated by phorbol 12-myristate 13-acetate and ionomycin, which also enhanced cell adhesion to fibronectin, whereas, an inhibitor of phospholipase C, inhibited both cytokine-induced activation of Rap1 and cell adhesion. It was also demonstrated that Rap1 as well as CrkL is involved in signaling from the EpoR endogenously expressed in a human leukemic cell line, UT-7. These results suggest that Epo and IL-3 activate Rap1 at least partly through the CrkL-C3G complex as well as through additional pathways most likely involving phospholipase Cgamma and strongly implicate Rap1 in regulation of beta(1) integrin-mediated hematopoietic cell adhesion.
Combination of Bortezomib, Melphalan, Prednisone and Thalidomide (VMPT) for Relapsed Multiple Myeloma: Results of a Phase I/II Clinical Trial. (2006)

Abstract BACKGROUND: In newly diagnosed patients, the addition of thalidomide or bortezomib (Velcade™) to the standard oral melphalan/prednisone combination significantly increased response rate and event-free survival. In this multicenter, open-label, non randomized, phase I/II trial, the safety/efficacy profile of the 4 drug combination, bortezomib (Velcade™), melphalan, prednisone, and thalidomide (VMPT) was evaluated in patients with relapsed/refractory myeloma. METHODS: Bortezomib was administered by IV bolus on days 1, 4, 15, 22 at three dose levels: in the first cohort (10 patients) at 1.0 mg/m2; in the second cohort (10 patients) at 1.3 mg/m2and in the third cohort (10 patients) at 1.6 mg/m2. Oral melphalan was administered at 6 mg/m2 on days 1–5, oral prednisone at 60 mg/m2 on days 1–5. Thalidomide was delivered at 50 mg on days 1–35. Each course was repeated every 35 days for a total of 6 courses. RESULTS: Thirty patients, median age 66 years (range 38–79), with relapsed or refractory myeloma were enrolled. Fourteen patients received VMPT as second line of therapy, 16 as third line. Twenty patients received prior autologous transplant, 10 conventional chemotherapy and 9 thalidomide-based regimens. After a median of 6 courses, 20 patients (67%) achieved a partial response (PR) including 13 patients (43%) who achieved at least a very good partial response (VGPR). Among patients who received VMPT as second line treatment, the PR rate was 79%, and the immunofixation negative complete response rate 36%. The 1-year progression-free survival was 61%, and the 1-year survival from study entry was 84%. Grade 3 non-hematological adverse events included: infections (5 patients), fatigue (1), vasculitis (1) and peripheral neuropathy (2); no grade 4 toxicities were recorded. CONCLUSIONS: Initial results showed that VMPT is an effective salvage therapy with a high proportion of responses. Toxicities were manageable. The incidence of neurotoxicities was unexpectedly low.
Levitation Forces, Relaxation and Magnetic Stiffness of Melt-Quenched YBa<sub>2</sub>Cu<sub>3</sub>O<sub>x</sub> (1990)

Measurements of levitation forces on melt-quenched and free sintered YBa 2 Cu 3 O x superconductors show that melt-quenched samples produce forces from 96-170% higher than sintered specimens. The force increases are correlated with higher magnetization values for the melt-quenched material. Similar increases in the magnetic stiffness were also measured. Vertical levitation force relaxation showed less than 5% decrease in one hour. These results have important favorable implications for application to superconducting bearings.
Formation of vapor bubbles in nonpolar liquids initiated by current pulses (2002)

The electrical conduction of purified nonpolar liquids with point-plane electrode geometry was studied as a function of various parameters. For negative polarity of the point, a pulse regime has been observed which bears a great similarity to the TRICHEL pulses occurring in air, with the exception of a lack of pressure dependence. At atmospheric pressure, bubble formation was correlated with current pulse. The generation and dynamics of the bubble are studied as a function of various parameters: injected energy, hydrostatic pressure (up to 12 MPa), and the nature of the liquid (cyclohexane, n-pentane, n-decane, iso-octane, and tetramethylsilane).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Affinity chromatography of the muscarinic acetylcholine receptor. (1983)

A novel compound, 3-(2'-aminobenzhydryloxy)-tropane (ABT), and an ABT-agarose gel were synthesized and used for the purification of solubilized muscarinic receptors. ABT had a high affinity with an apparent dissociation constant (Kd) of 7 nM for the muscarinic receptors solubilized from the porcine brain by digitonin. An ABT-agarose gel was prepared by coupling ABT with epoxy-activated Sepharose 6B, and the degree of substitution to the gel was determined to be 4-5 mumol/ml of the gel by UV absorption spectrum. During affinity chromatography using 10 ml of the ABT-agarose gel and 100 ml of the digitonin-solubilized preparation, 70% of muscarinic receptors were adsorbed to the gel, in marked contrast with the adsorption of only 2% of proteins. Approximately 25% of muscarinic receptors applied to the gel were eluted biospecifically with 1 mM muscarinic ligands. The purified fraction showed a high affinity for [3H]quinuclidinyl benzylate with a Kd of 0.4 nM and similar specificity for muscarinic ligands to that of unpurified soluble receptors. The protein concentration of the purified fraction was too low to be determined accurately, but very approximately a purification of 10(3)-fold was indicated.
Oxidative stress and the molecular biology of antioxidant defenses. (1997)

The oxygen paradox - biochemistry of active oxygen redox regulation by the HIV-1 TAT transcritional factor oxidative damage to DNA and its repair the antioxidative stress in eukaryotes transcriptional regulators of oxidative stress responses oxidative stress, gene expression and the aging process superoxide dismutases in bacteria and pathogen protists superoxide dismutase - studies in the yeast saccharomyces cerevisiae molecular genetics of superoxide dismutases in plants bacterial catalases biochemistry, molecular biology and cell biology of yeast and fungal catalases catalases in plants - gene structure, properties, regulation and expression the structure of catalases mediation of signal transduction by oxidants the oxidative burst and its roles in signal transduction and response of stressed plants the NADPH oxidase of leukocytes osicative burst-mediated defense responses in plant disease resistance gluta-thione reductase - regulation and role in oxidative stress oxidative stress in mitochondria oxygen metabolism and electron transport in photosynthesis ascorbate peroxidase and monodehydroscorbate reducatase - key enzymes for hydrogen peroxide-scavenging system in plants oxidandants, antioxidants and aging reactive oxygen and apoptosis role of sod in neurodegenerative disease free radicals - dietary advantages and disadvantages defense against photooxidative damage in plants air pollution and free radical protection responses of plants.