gebhart/patrepeval huggingface dataset:
Deep AutoRegressive Networks (2013)

We introduce a deep, generative autoencoder capable of learning hierarchies of distributed representations from data. Successive deep stochastic hidden layers are equipped with autoregressive connections, which enable the model to be sampled from quickly and exactly via ancestral sampling. We derive an efficient approximate parameter estimation method based on the minimum description length (MDL) principle, which can be seen as maximising a variational lower bound on the log-likelihood, with a feedforward neural network implementing approximate inference. We demonstrate state-of-the-art generative performance on a number of classic data sets: several UCI data sets, MNIST and Atari 2600 games.
Identification of mutations in p53 that affect its binding to SV40 large T antigen by using the yeast two‐hybrid system (1993)

The tumor suppressor p53 protein binds to the products of several viral oncogenes, including SV40 large T antigen. We reconstructed the p53-T antigen interaction in the yeast two-hybrid system, a genetic assay that uses the reconstitution of the activity of a transcriptional activator to detect protein-protein interactions. Using mutants of T antigen known to be defective in binding to p53, we demonstrate that the two-hybrid system is more sensitive than immunoprecipitation in the detection of weak interactions. We mutagenized the murine p53 gene and screened in the yeast assay for decreased reporter gene expression indicative of the failure of p53 to bind T antigen. This screen identified 34 p53 mutants, almost all of which contain at least one mutation in the conserved domains frequently found mutated in human cancers. These results support the idea that the function of the wild-type p53 protein requires residues involved in binding to T antigen, and indicate that this approach may be generally applicable in the analysis of protein-protein interactions.
The Largest Eigenvalue of Sparse Random Graphs (2003)

We prove that for all values of the edge probability p(n) the largest eigenvalue of a random graph G(n, p) satisfies almost surely:
Inducing chalcogenide phase change with ultra-narrow carbon nanotube heaters (2009)

Carbon nanotube (CNT) heaters with sub-5 nm diameter induce highly localized phase change in Ge2Sb2Te5 (GST) chalcogenide. A significant reduction in resistance of test structures is measured as the GST near the CNT heater crystallizes. Effective GST heating occurs at currents as low as 25 μA, significantly lower than in conventional phase change memory with metal electrodes (0.1–0.5 mA). Atomic force microscopy reveals nucleation sites associated with phase change in GST around the CNT heater. Finite element simulations confirm electrical characteristics consistent with the experiments, and reveal the current and phase distribution in GST.
Esophageal Cancer (2003)

Cancers arising from the esophagus, including the gastroesophageal junction, are relatively uncommon in the United States — the lifetime risk of this cancer is 0.8 percent for men and 0.3 percent for women, and it increases with age. The presentation is insidious; at diagnosis, more than 50 percent of patients have either unresectable cancer or radiographically visible metastases, rendering management problematic. This review discusses the pathogenesis of esophageal cancer, as well as the clinical presentation, treatment, and prognosis.
Stereoselective terminal functionalization of small peptides for catalytic asymmetric synthesis of unnatural peptides (2004)

The asymmetric phase-transfer catalytic alkylation of peptides has been achieved by the use of designed C(2)-symmetric chiral quaternary ammonium bromide 1 as catalyst. Excellent stereoselectivities were uniformly observed in the alkylation with a variety of alkyl halides and the efficiency of the transmission of stereochemical information was not affected by the side-chain structure of the preexisting amino acid residues. This method also enables an asymmetric construction of noncoded alpha,alpha-dialkyl-alpha-amino acid residues at the peptide terminal. Since this chirality can be efficiently transferred to the adjacent amino acid moiety, our approach provides a general procedure not only for the highly stereoselective terminal functionalization of peptides but also for the sequential asymmetric construction of unnatural oligopeptides, which should play a vital role in the peptide-based drug discovery process.
Site-directed mutagenesis of conserved amino acids in the alpha subunit of toluene dioxygenase: potential mononuclear non-heme iron coordination sites (1996)

The terminal oxygenase component of toluene dioxygenase from Pseudomonas putida F1 is an iron-sulfur protein (ISP(TOL)) that requires mononuclear iron for enzyme activity. Alignment of all available predicted amino acid sequences for the large (alpha) subunits of terminal oxygenases showed a conserved cluster of potential mononuclear iron-binding residues. These were between amino acids 210 and 230 in the alpha subunit (TodC1) of ISP(TOL). The conserved amino acids, Glu-214, Asp-219, Tyr-221, His-222, and His-228, were each independently replaced with an alanine residue by site-directed mutagenesis. Tyr-266 in TodC1, which has been suggested as an iron ligand, was treated in an identical manner. To assay toluene dioxygenase activity in the presence of TodC1 and its mutant forms, conditions for the reconstitution of wild-type ISP(TOL) activity from TodC1 and purified TodC2 (beta subunit) were developed and optimized. A mutation at Glu-214, Asp-219, His-222, or His-228 completely abolished toluene dioxygenase activity. TodC1 with an alanine substitution at either Tyr-221 or Tyr-266 retained partial enzyme activity (42 and 12%, respectively). In experiments with [14C]toluene, the two Tyr-->Ala mutations caused a reduction in the amount of Cis-[14C]-toluene dihydrodiol formed, whereas a mutation at Glu-214, Asp-219, His-222, or His-228 eliminated cis-toluene dihydrodiol formation. The expression level of all of the mutated TWO proteins was equivalent to that of wild-type TodC1 as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blot (immunoblot) analyses. These results, in conjunction with the predicted amino acid sequences of 22 oxygenase components, suggest that the conserved motif Glu-X3-4,-Asp-X2-His-X4-5-His is critical for catalytic function and the glutamate, aspartate, and histidine residues may act as mononuclear iron ligands at the site of oxygen activation.
Controlling Release From pH-Responsive Microcapsules (2013)

We report a microfluidic approach to produce monodisperse pH-responsive microcapsules with precisely controlled release behavior. The solid microcapsule shells are composed of a biocompatible pH-responsive polymer and robustly encapsulate an active material; however, when exposed to a trigger pH, the shells degrade and ultimately release the microcapsule contents. We control the trigger pH by using polymers that dissolve at different pH values. We independently control the time at which the microcapsule contents are released by carefully controlling the shell thickness. Moreover, we independently control the rate at which the encapsulated contents are released by making hybrid shells composed of a mixture of a pH-responsive polymer and varying proportions of another, solid, pH-unresponsive polymer. This enables us to achieve monodisperse microcapsules that robustly encapsulate an active material, only releasing it when exposed to a desired pH, after a prescribed time delay, and at a prescribed rate.
Immunomagnetic separation as an alternative to enrichment broths for Salmonella detection (1993)

One hundred and twenty foodstuffs were tested for the enrichment of Salmonella species by immunoseparation. The foodstuffs covered six groups: raw chicken, prawns, skimmed milk powder, herbs and spices, cocoa powder and animal feed. Half of the food samples were spiked with one Salmonella species: Salm. ealing, Salm. enteritidis, Salm. give, Salm. typhimurium or Salm. virchow. Comparison of Salmonella recovery with standard methods (selenite cystine broth, tetrathionate broth and Rappaport‐Vassiliadis broth) was carried out. Immunoseparation gave similar numbers of true positives to the standard enrichment methods in a short time period. Only immunoseparation isolated Salmonella species from spiked garlic granules demonstrating the possible recovery of sublethally injured cells.
Variation in Sensitivity to Photoperiod Among Early Maturing Soybean Strains1 (1972)

Two experiments were conducted to identify soybean [ Glycine max (L.) Merrill] strains that were nonsensitive to photoperiod for possible use as parental lines in a breeding program. Twelve soybean varieties were subjected to photoperiods of 12, 16, 20 and 24 hours in growth cabinets. The number of days from planting until first flower was increased by long photoperiods in all but 1 of 12 varieties. Early maturing varieties were less sensitive to photoperiod than were later varieties. for this reason, 111 soybean strains from Maturity Group 00 were grown in a controlled‐environment room at photoperiods of 12, 22, 23 and 24 hours. In approximately 70% of these strains the length of time from planting to flowering was unaffected by photoperiod.
Too Much Waste: A Proposal for Change in the Government's Effort to Clean Up the Nation (1995)

Under the language of the acts, Congress granted the power to enforce their provisions to the President, who in turn delegated this power to the EPA.27.This Note focuses on TSD facilities because RCRA requirements applicable to TSD facilities are much more
REVIEW: Genetically selected Marchigian Sardinian alcohol‐preferring (msP) rats: an animal model to study the neurobiology of alcoholism (2006)

The present article provides an up-to-date review summarizing almost 18 years of research in genetically selected Marchigian Sardinian alcohol-preferring (msP) rats. The results of this work demonstrate that msP rats have natural preference for ethanol characterized by a spontaneous binge-type of drinking that leads to pharmacologically significant blood ethanol levels. This rat line is highly vulnerable to relapse and presentation of stimuli predictive of alcohol availability or foot-shock stress can reinstate extinguished drug-seeking up to 8 months from the last alcohol experience. The msP rat is highly sensitive to stress, shows an anxious phenotype and has depressive-like symptoms that recover following ethanol drinking. Interestingly, these animals have an up-regulated corticotrophin releasing factor (CRF) receptor 1 system. Clinical studies have shown that alcoholic patients often drink ethanol in the attempt to self-medicate from negative affective states and to search for anxiety relief. We propose that msP rats represent an animal model that largely mimics the human alcoholic population that due to poor ability to engage in stress-coping strategies drink ethanol as a tension relief strategy and for self-medication purposes.
Epidemiology of Alzheimer's Disease (1992)

Journal Article Epidemiology of Alzheimer's Disease Get access Monique M. B. Breteler, Monique M. B. Breteler Department of Epidemiology and Biostatistics, Erasmus University Medical SchoolRotterdam, The Netherlands Dr. M. M. B. Breteler, Department of Epidemiology and Biostatistics, Erasmus University Medical School, P.O. Box 1738, 3000 DR Rotterdam, The Netherlands Search for other works by this author on: Oxford Academic PubMed Google Scholar Jules J. Claus, Jules J. Claus Department of Epidemiology and Biostatistics, Erasmus University Medical SchoolRotterdam, The Netherlands Search for other works by this author on: Oxford Academic PubMed Google Scholar Cornelia M. van Duijn, Cornelia M. van Duijn Department of Epidemiology and Biostatistics, Erasmus University Medical SchoolRotterdam, The Netherlands Search for other works by this author on: Oxford Academic PubMed Google Scholar Lenore J. Launer, Lenore J. Launer Department of Epidemiology and Biostatistics, Erasmus University Medical SchoolRotterdam, The Netherlands Search for other works by this author on: Oxford Academic PubMed Google Scholar Albert Hofman Albert Hofman Department of Epidemiology and Biostatistics, Erasmus University Medical SchoolRotterdam, The Netherlands Search for other works by this author on: Oxford Academic PubMed Google Scholar Epidemiologic Reviews, Volume 14, Issue 1, 1992, Pages 59–82, https://doi.org/10.1093/oxfordjournals.epirev.a036092 Published: 01 March 1992 Article history Received: 29 November 1991 Published: 01 March 1992 Revision received: 09 July 1992
Effect of Temperature on Microstructure and Mechanical Properties of 316L Stainless Steel Brazed Joints (2011)

The effects of brazing temperature on microstructure and mechanical properties of vacuum brazed joints of 316L stainless steel were studied. Choose three soldering temperature. After soldering, observed the microstructure, element distribution, microhardness and shear strength of welding clearance. The results show that the welding temperature for 940 °C, the brazing clearance organization mainly by Ni-Cr-P phase composition. Joint performance is poor, element can't get enough spread. P element does not spread easily, mainly in the brazing clearance; Cr element can spread along the grain boundary into mother material; the ability of spread of Ni elements is less than the Cr element. While welding temperature of 970 °C, the shear strength is the highest, and the comprehensive performance is the best.
D‐amino acid levels in human physiological fluids (1993)

Plasma, urine, cerebrospinal fluid (CSF), and amniotic fluid were examined to determine whether free D-amino acids were present and if so at what levels. It was found that D-amino acids exist in all physiological fluids tested, but that their level varied considerably. The lowest levels of D-amino acids were usually found in amniotic fluid or CSF (almost always < 1% of the corresponding L-amino acid). The highest levels were found in urine (usually tenth percent to low percent levels). Pipecolic acid seemed to be different from the other amino acids tested in that it was excreted primarily as the D-enantiomer (often > 90%). Correspondingly high levels of D-pipecolic acid were not found in plasma. Some of the trends found in this work seemed to be analogous to those found in a recent rodent study.
Photofrin Uptake in the Tumor and Normal Tissues of Patients Receiving Intraperitoneal Photodynamic Therapy (2006)

Some selectivity is found in Photofrin uptake between tumor and normal tissues of the peritoneal cavity, but absolute differences in drug uptake relative to toxicity-limiting normal tissues (intestine) are small. This narrow differential in drug selectivity likely contributes to a narrow window in therapeutic application, which has been previously reported.
Highlighting Interleukin-36 Signalling in Plaque Psoriasis and Pustular Psoriasis (2017)

Plaque psoriasis and pustular psoriasis are overlapping, but distinct, disorders. The therapeutic response to biologics supports the pivotal role of the tumour necrosis alpha (TNF-?)/ interleukin (IL)-23/IL-17/IL-22 axis in the pathogenesis of these disorders. Recently, functional activation of the IL-36 receptor (IL-36R) was discovered to be another driving force in the pathogenesis of psoriasis. This was first highlighted by the discovery that a loss-of-function mutation of the IL-36R antagonist (IL-36Ra) causes pustular psoriasis. Although the TNF-?/IL-23/IL-17/IL-22 axis and the functional activation of IL-36R are fundamentally involved in plaque psoriasis and pustular psoriasis, respectively, the 2 pathways are closely related and mutually reinforced, resulting in full-blown clinical manifestations. This review summarizes current topics on how IL-36 agonists (IL-36?, IL-36?, IL-36?) signal IL-36R, the pathological expression of IL-36 agonists and IL-36Ra in plaque and pustular psoriatic lesions, and the cross-talk between the TNF-?/IL-23/IL-17/IL-22 axis and the functional activation of IL-36R in the epidermal milieu.
Endothelial function and cardiovascular disease: Effects of quercetin and wine polyphenols (2006)

Endothelial dysfunction is an early pathophysiological feature and independent predictor of poor prognosis in most forms of cardiovascular diseases. Epidemiological studies report an inverse association between dietary flavonoid consumption and mortality from cardiovascular diseases. In the present paper, we review the effects of flavonoids, especially quercetin and wine polyphenols, on endothelial function and dysfunction and its potential protective role in hypertension, ischemic heart disease and stroke. In vitro studies show that flavonoids may exert multiple actions on the NO-guanylyl cyclase pathway, endothelium-derived hyperpolarizing factor(s) and endothelin-1 and protect endothelial cells against apoptosis. In vivo, flavonoids prevent endothelial dysfunction and reduce blood pressure, oxidative stress and end-organ damage in hypertensive animals. Moreover, some clinical studies have shown that flavonoid-rich foods can improve endothelial function in patients with hypertension and ischemic heart disease. Altogether, the available evidence indicates that quercetin and wine polyphenols might be of therapeutic benefit in cardiovascular diseases even though prospective controlled clinical studies are still lacking.
Asymmetric Hollow Nanorod Formation through a Partial Galvanic Replacement Reaction (2009)

An asymmetric single hollow structure was generated from Ag-Au-Ag heterometal nanorods by a partial galvanic replacement reaction for the first time. The C(2)-symmetry breaking took place because of the random generation of a single pit on only one end of the silver domain at an early stage of the reaction. Careful control of the reaction kinetics could also yield a double-hollow structure on both ends of the silver domain. The resulting single- and double-hollow nanorods exhibited characteristic extinctions in the near-IR range.
Aggregates Are the Biologically Active Units of Endotoxin (2004)

For the elucidation of the very early steps of immune cell activation by endotoxins (lipopolysaccharide, LPS) leading to the production and release of proinflammatory cytokines the question concerning the biologically active unit of endotoxins has to be addressed: are monomeric endotoxin molecules able to activate cells or is the active unit represented by larger endotoxin aggregates? This question has been answered controversially in the past. Inspired by the observation that natural isolates of lipid A, the lipid moiety of LPS harboring its endotoxic principle, from Escherichia coli express a higher endotoxic activity than the same amounts of the synthetic E. coli-like hexaacylated lipid A (compound 506), we looked closer at the chemical composition of natural isolates. We found in these isolates that the largest fraction was hexaacylated, but also significant amounts of penta- and tetraacylated molecules were present that, when administered to human mononuclear cells, may antagonize the induction of cytokines by biologically active hexaacylated endotoxins. We prepared separate aggregates of either compound 506 or 406 (tetraacylated precursor IVa), mixed at different molar ratios, and mixed aggregates containing both compounds in the same ratios. Surprisingly, the latter mixtures showed higher endotoxic activity than that of the pure compound 506 up to an admixture of 20% of compound 406. Similar results were obtained when using various phospholipids instead of compound 406. These observations can only be understood by assuming that the active unit of endotoxins is the aggregate. We further confirmed this result by preparing monomeric lipid A and LPS by a dialysis procedure and found that, at the same concentrations, only the aggregates were biologically active, whereas the monomers showed no activity.
Alternatively spliced forms in the cytoplasmic domain of the human growth hormone (GH) receptor regulate its ability to generate a soluble GH-binding protein. (1996)

The mechanism underlying the generation of soluble growth hormone binding protein (GHBP) probably differs among species. In rats and mice, it involves an alternatively spliced mRNA, whereas in rabbits, it involves limited proteolysis of the membrane-bound growth hormone receptor (GHR). In humans, this latter mechanism is favored, as no transcript coding for a soluble GHR has been detected so far. To test this hypothesis, we analyzed COS-7 cells transiently expressing the full-length human (h) GHR and observed specific GH-binding activity in the cell supernatants. Concomitantly, an alternatively spliced form in the cytoplasmic domain of GHR, hGHR-tr, was isolated from several human tissues. hGHR-tr is identical in sequence to hGHR, except for a 26-bp deletion leading to a stop codon at position 280, thereby truncating 97.5% of the intracellular domain of the receptor protein. When compared with hGHR, hGHR-tr showed a significantly increased capacity to generate a soluble GHBP. Interestingly, this alternative transcript is also expressed in liver from rabbits, mice, and rats, suggesting that, in these four species, proteolysis of the corresponding truncated transmembrane GHR is a common mechanism leading to GHBP generation. These findings support the hypothesis that GHBP may at least partly result from alternative splicing of the region encoding the intracellular domain and that the absence of a cytoplasmic domain may be involved in increased release of GHBP.
8-Substituted guanosine and 2'-deoxyguanosine derivatives as potential inducers of the differentiation of Friend erythroleukemia cells (1985)

A variety of 8-substituted guanosine and 2'-deoxyguanosine derivatives were synthesized and tested as inducers of the differentiation of Friend murine erythroleukemia cells in culture. The most active agents in the guanosine series were 8-substituted-N(CH3)2, -NHCH3, -NH2, -OH, and -SO2CH3, which caused 68, 42, 34, 33, and 30% of erythroleukemia cells to attain benzidine positivity, a functional measure of maturation, at concentrations of 5, 1, 0.4, 5, and 5 mM, respectively. The 8-OH derivative of the 2'-deoxyguanosine series produced comparable activity, causing 62% benzidine-positive cells at a level of 0.2 mM. These findings indicate that 8-substituted analogues of guanosine and 2'-deoxyguanosine have the potential to terminate leukemia cell proliferation through conversion to end-stage differentiated cells.
On the synchronization and display of multiple full-motion video streams (2002)

A study is made of workstation architectures that permit several video windows to be displayed simultaneously. The transmission from each video source to the workstation display must be synchronized with the scan of the display, otherwise aberrations such as discontinuities in moving objects will be visible. This paper shows why the traditional master-slave techniques will not work and discusses how to correctly synchronize these streams.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Strong Resistance of Oligo(phosphorylcholine) Self-Assembled Monolayers to Protein Adsorption (2006)

In this work, we demonstrate the strong resistance of oligo(phosphorylcholine) (OPC) self-assembled monolayers (SAMs) to protein adsorption and cell adhesion. OPC SAMs were characterized using X-ray photoelectron spectroscopy (XPS), and protein adsorption was measured using a surface plasmon resonance (SPR) sensor. Results are compared with those of phosphorylcholine (PC) SAMs. Despite the existence of negative charge on OPC SAMs and the simple synthesis procedure of OPC thiols, OPC SAMs resist protein adsorption as effectively as or better than PC SAMs formed from highly purified PC thiols. The ease of their preparation and the effectiveness of their function make OPC SAMs an attractive alternative for creating nonfouling surfaces.