gebhart/patrepeval huggingface dataset:
Forge (2013)

Domain-specific languages provide a promising path to automatically compile high-level code to parallel, heterogeneous, and distributed hardware. However, in practice high performance DSLs still require considerable software expertise to develop and force users into tool-chains that hinder prototyping and debugging. To address these problems, we present Forge, a new meta DSL for declaratively specifying high performance embedded DSLs. Forge provides DSL authors with high-level abstractions (e.g., data structures, parallel patterns, effects) for specifying their DSL in a way that permits high performance. From this high-level specification, Forge automatically generates both a naïve Scala library implementation of the DSL and a high performance version using the Delite DSL framework. Users of a Forge-generated DSL can prototype their application using the library version, and then switch to the Delite version to run on multicore CPUs, GPUs, and clusters without changing the application code. Forge-generated Delite DSLs perform within 2x of hand-optimized C++ and up to 40x better than Spark, an alternative high-level distributed programming environment. Compared to a manually implemented Delite DSL, Forge provides a factor of 3-6x reduction in lines of code and does not sacrifice any performance. Furthermore, Forge specifications can be generated from existing Scala libraries, are easy to maintain, shield DSL developers from changes in the Delite framework, and enable DSLs to be retargeted to other frameworks transparently.
Dependence of electric double layer capacitance on electrolyte ion for carbon electrolyte interface (2007)

The effect of the kind of electrolyte ions and carbon surface on electric double layer capacitance was investigated using graphitized carbon black (GCB), multi-walled carbon nanotube (MWCNT), or activated carbon (ACF) as active material and (C2H5) 4NBF4, (C4H9) 4NBF4, (C6H13) 4NBF4, (C2H5) 4NCF3SO3, or (C2H5) 4N (CF3SO2) 2N as electrolyte salt for propylene carbonate solution. The GCB and MWCNT, which have no or less microporosity, showed no dependence of the capacitance on the kinds of the electrolyte ions. This suggests that the capacitance is not related to the size of ions adsorbed on carbon surface in the absence of micropores. In the case of the ACF, the smaller capacitances were observed when bulkier ions adsorbing/desorbing. This tendency was more prominent for narrower micropore width, which can be explained by the ion sieving effect of micropores.
Characterisation of a linear binding site for a monoclonal antibody to hepatitis B core antigen (1991)

The complete amino acid (aa) sequence of the hepatitis B virus (HBV) core protein (HBcAg), ayw subtype, was synthesized as decapeptides with five overlapping aas. The peptides were tested for reactivity with monoclonal antibodies (mAbs) to HBcAg (35/312, 37/275, and 7/275). All the mAbs specifically inhibited human anti-HBc by cross competition in assays for anti-HBc and anti-HBe. The mAb 35/312 recognised a peptide covering residues 76-85 of the HBcAg sequence. The other two mAbs did not react specifically with any linear peptide, suggesting discontinuous epitopes for these mAbs. The linear sequence EDPASR at residues 77-82 was found to constitute the epitope for mAb 35/312 when fine mapping the binding site. The most essential aas for mAb 35/312 were found to be the DP at residues 79-80, when peptides were synthesized where the aas at 77-83, were substituted by the other 19 aas. Since the mAb 35/312 inhibits the binding of human anti-HBc positive sera, which are known to recognise an SDS labile epitope, the sequence 77-82 might be a part of a larger discontinuous epitope. Alternatively the mAb 35/312 blocks the binding of human anti-HBc by steric hindrance.
Deep-learning-based electrical noise removal for localized spectral optoacoustic contrast in deep tissue (2021)

Image contrast in multispectral optoacoustic tomography can be reduced by electrical noise. We present a deep learning method to remove electrical noise from optoacoustic signals and thereby significantly enhance morphological and spectral contrast.
Improved running performance in hot humid conditions following whole body precooling (1997)

On two separate occasions, eight subjects controlled speed to run the greatest distance possible in 30 min in a hot, humid environment (ambient temperature 32 degrees C, relative humidity 60%). For the experimental test (precooling), exercise was preceeded by cold-water immersion. Precooling increased the distance run by 304 +/- 166 m (P < 0.05). Precooling decreased the pre-exercise rectal and mean skin temperature by 0.7 degrees C and 5.9 degrees C, respectively (P < 0.05). Rectal and mean skin temperature were decreased up to 20 and 25 min during exercise, respectively (P < 0.05). Mean body temperature decreased from 36.5 +/- 0.1 degrees C to 33.8 +/- 0.2 degrees C following precooling (P < 0.05) and remained lower throughout exercise (P < 0.01) and at the end of exercise (by 0.8 degrees C; P < 0.05). The rate of heat storage at the end of exercise increased from 113 +/- 45 to 249 +/- 55 W.m-2 (P < 0.005). Precooling lowered the heart rate at rest (13%), 5 (9%), and 10 min (10%) exercise (P < 0.05) and increased the end of exercise blood lactate from 4.9 +/- 0.5 to 7.4 +/- 0.9 mmol.L-1 (P < 0.01). The VO2 at 10 and 20 min of exercise and total body sweating are not different between tests. In conclusion, water immersion precooling increased exercise endurance in hot, humid conditions with an enhanced rate of heat storage and decreased thermoregulatory strain.
Molecular Approach for Improving the Stability of Insecticidal Nematodes (2002)

Our overall goal is to improve insecticidal nematodes by genetically engineering strains capable of entering an enhanced state of dormancy that provides improved stability. Objectives: 1. Clone and sequence tps-l homologue from Steinernema carpocapsae. (Revised: A failure to isolate the tps gene group from Steinernema precipitated a redirection to identifying other genes involved in insecticidal nematode desiccation process.) 2. Incorporate cloned tps-l gene into S. carpocapsae to obtain overexpression, thereby, enhancing desiccation tolerance. (Revised: Other stress genes in addition to tps-l genes were cloned and efforts at expression in S. carpocapsae were conducted) 3. Characterize the transgenic strains. No other biological control agent offers more impressive attributes than insecticidal nematodes. However, their potential is limited by the bane of nearly all biological control agents: poor stability. This leads to inadequate shelf-life and ultimately reduced field efficacy. Nematode storage is based on desiccation, yet insecticidal species are only capable of partial desiccation termed quiescent anhydrobiosis. Overwhelming evidence has shown that when the disaccharide compound trehalose is elevated in anhydrobiotic organisms such as yeast, plants, and nematodes it enables these organisms the ability to survive environmental stresses i.e., desiccation. Armed with this information our goal was to improve insecticidal nematodes stability by engineering trehalose overexpression.
Body MR imaging at 3T: basic considerations about artifacts and safety (2011)

Three Tesla magnetic resonance (MR) imaging scanners have been seeing steadily increasing use recently as hardware has matured and pulse sequences have become more optimized for a higher field strength. This increase in popularity has been more pronounced for neurologic and musculoskeletal imaging than for body imaging, however, due to the fact that 3T imaging with the larger field of view required for the torso tends to be more susceptible to artifacts and energy absorption limits than the imaging of smaller body parts.
Absolute quantum yield for understanding upconversion and downshift luminescence in PbF2:Er3+,Yb3+ crystals (2023)

The search for new materials capable of efficient upconversion continues to attract attention. In this work, a comprehensive study of the upconversion luminescence in PbF<sub>2</sub>:Er<sup>3+</sup>,Yb<sup>3+</sup> crystals with different concentrations of Yb<sup>3+</sup> ions in the range of 2 to 7.5 mol% (Er<sup>3+</sup> concentration was fixed at 2 mol%) was carried out. The highest value of upconversion quantum yield (<i>ϕ</i><sub>UC</sub>) 5.9% (at 350 W cm<sup>-2</sup>) was found in the PbF<sub>2</sub> crystal doped with 2 mol% Er<sup>3+</sup> and 3 mol% Yb<sup>3+</sup>. Since it is not always easy to directly measure <i>ϕ</i><sub>UC</sub> and estimate the related key figure of merit parameter, saturated photoluminescence quantum yield (<i>ϕ</i><sub>UCsat</sub>), a method to reliably predict <i>ϕ</i><sub>UCsat</sub> can be useful. Judd-Ofelt theory provides a convenient way to determine the radiative lifetimes of the excited states of rare-earth ions based on absorption measurements. When the luminescence decay times after direct excitation of a level are also measured, <i>ϕ</i><sub>UCsat</sub> for that level can be calculated. This approach is tested on a series of PbF<sub>2</sub>:Er<sup>3+</sup>,Yb<sup>3+</sup> crystals. Good agreement between the estimates obtained as above and the directly experimentally measured <i>ϕ</i><sub>UCsat</sub> values is demonstrated. In addition, three methods of Judd-Ofelt calculations on powder samples were tested and the results were compared with Judd-Ofelt calculations on single crystals, which served as the source of the powder samples. Taken together, the results presented in our work for PbF<sub>2</sub>:Er<sup>3+</sup>,Yb<sup>3+</sup> crystals contribute to a better understanding of the UC phenomena and provide a reference data set for the use of UC materials in practical applications.
Ivar Asbjörn Følling (2010)

Ivar Asbjorn Folling (1888–1973)



Dr. Asbjorn Folling, a Norwegian biochemist and physician, first published the description of phenylketonuria (PKU) as a cause of mental retardation in 1934.1 Moreover, this study reported a laboratory test to confirm this metabolic disease, which was later determined to be an autosomal recessive metabolic disorder. Subsequent work by other investigators would determine that diet modification would drastically improve the outcome and prevent the onset of mental retardation. The discovery of PKU was a fundamentally important discovery for the fields of biochemistry, genetics, metabolism, and medicine.

Phenylketonuria (PKU) is a genetic disorder due to the inability to metabolize the amino acid phenylalanine. This is due to mutations leading to a deficiency in the enzyme phenylalanine hydroxylase. The disease occurs in approximately 1 in 10,000 children,2 and the prevalence is slightly higher among people of Irish and West Scottish descent.2 Some have suggested an ecologic advantage of heterozygotes, protecting them from the negative health consequences of consuming moldy food, as the wet climates of Ireland and West Scotland have a higher risk of mold contamination.3

Born Ivar Asbjorn Folling on August 23, 1888, he was raised on a farm in northern Norway. He was the youngest of five children.4,5 The farm was located eight miles from the nearest town of Steinkjer and 50 miles from the Trondheim. Starting at the age of five, he …
Isolation and Characterization of Some Oxidation Products Associated with Oxidized Flavor (1955)

Oxidized flavor is a troublesome defect in some dairy products. The work of Thurston and Barnhart Swanson and Sommer In this paper the expression "oxidized flavor ''~ consequently refers to the defect resulting from the partial oxidation of the milk phospholipids.
Aging, emotional states, and memory (1993)

These findings indicate that aging modulates the relation between emotional state and memory functions, and they are consistent with the hypothesis that the elderly are more vulnerable than the young to the adverse effects of negative emotional states on memory. Therefore, even in normal elderly individuals without diagnosable psychopathology, negative affective states (such as anxiety and depression) may interfere with memory functioning.
The Effects of Cocaine on Different Redox Forms of Cysteine and Homocysteine, and on Labile, Reduced Sulfur in the Rat Plasma Following Active versus Passive Drug Injections (2013)

The aim of the present studies was to evaluate cocaine-induced changes in the concentrations of different redox forms of cysteine (Cys) and homocysteine (Hcy), and products of anaerobic Cys metabolism, i.e., labile, reduced sulfur (LS) in the rat plasma. The above-mentioned parameters were determined after i.p. acute and subchronic cocaine treatment as well as following i.v. cocaine self-administration using the yoked procedure. Additionally, Cys, Hcy, and LS levels were measured during the 10-day extinction training in rats that underwent i.v. cocaine administration. Acute i.p. cocaine treatment increased the total and protein-bound Hcy contents, decreased LS, and did not change the concentrations of Cys fractions in the rat plasma. In turn, subchronic i.p. cocaine administration significantly increased free Hcy and lowered the total and protein-bound Cys concentrations while LS level was unchanged. Cocaine self-administration enhanced the total and protein-bound Hcy levels, decreased LS content, and did not affect the Cys fractions. On the other hand, yoked cocaine infusions did not alter the concentration of Hcy fractions while decreased the total and protein-bound Cys and LS content. This extinction training resulted in the lack of changes in the examined parameters in rats with a history of cocaine self-administration while in the yoked cocaine group an increase in the plasma free Cys fraction and LS was seen. Our results demonstrate for the first time that cocaine does evoke significant changes in homeostasis of thiol amino acids Cys and Hcy, and in some products of anaerobic Cys metabolism, which are dependent on the way of cocaine administration.
Mutations of the RET proto-oncogene in the multiple endocrine neoplasia type 2 syndromes and Hirschsprung disease (1994)

Distinct point mutations in the RET proto-oncogene are the cause of the inherited multiple endocrine neoplasia type 2 syndromes (MEN 2), and the congenital gut disorder Hirschsprung disease. The site and type of these mutations suggests that they have differing effects on the activity of the receptor tyrosine kinase encoded by RET. The normal function of the RET receptor tyrosine kinase has yet to be determined. However, this has been investigated by the inactivation of the RET gene in transgenic mice. The developmental abnormalities apparent in these mice, together with the observation that the major tissues affected in MEN 2 and Hirschsprung disease have a common origin in the embryonal neural crest, suggest that RET encodes a receptor for a developmental regulator involved in the genesis of a variety of neural crest derivatives, and in the organogenesis of the kidney.
Variation in morphology of gold nanoparticles synthesized by the spontaneous reduction of aqueous chloroaurate ions by alkylated tyrosine at a liquid–liquid and air–water interface (2004)

We demonstrate the formation of gold nanocrystals of different morphologies using alkylated tyrosine (AT) as a reducing agent at a liquid–liquid and air–water interface. The reduction of aqueous chloroaurate ions occurs in a single step wherein the AT molecule plays the multifunctional role of a phase transfer, reducing and capping agent. Gold nanoparticles formed at the air–water interface are very thin, flat sheet or ribbon-like nanostructures, which are highly oriented in the (111) direction. On the other hand, reduction of aqueous chloroaurate ions at a liquid–liquid interface by AT molecules present in the organic phase yielded nanoparticles having predominantly spherical morphology but with no specific crystallographic orientation. The difference in morphology of the nanoparticles may be due to the different orientational and translational degrees of freedom of the AT molecules and gold ions at these two interfaces. The AT-capped gold nanoparticles were characterized by UV-vis spectroscopy, transmission electron microscopy (TEM), X-ray diffraction (XRD), and nuclear magnetic resonance spectroscopy ( 1H NMR), while the LB films of flat gold sheets were also studied by X-ray photoemission spectroscopy (XPS).
Isolation and characterization of the glutaminyl cyclases from Solanum tuberosum and Arabidopsis thaliana: implications for physiological functions (2007)

Glutaminyl cyclases (QCs) catalyze the formation of pyroglutamic acid at the N-terminus of several peptides and proteins. On the basis of the amino acid sequence of Carica papaya QC, we identified cDNAs of the putative counterparts from Solanum tuberosum and Arabidopsis thaliana. Upon expression of the corresponding cDNAs from both plants via the secretory pathway of Pichia pastoris, two active QC proteins were isolated. The specificity of the purified proteins was assessed using various substrates with different amino acid composition and length. Highest specificities were observed with substrates possessing large hydrophobic residues adjacent to the N-terminal glutamine and for fluorogenic dipeptide surrogates. However, compared to Carica papaya QC, the specificity constants were approximately one order of magnitude lower for most of the QC substrates analyzed. The QCs also catalyzed the conversion of N-terminal glutamic acid to pyroglutamic acid, but with approximately 10(5)- to 10(6)-fold lower specificity. The ubiquitous distribution of plant QCs prompted a search for potential substrates in plants. Based on database entries, numerous proteins, e.g., pathogenesis-related proteins, were found that carry a pyroglutamate residue at the N-terminus, suggesting QC involvement. The putative relevance of QCs and pyroglutamic acid for plant defense reactions is discussed.
Inner and Outer Scalings in Rough Surface Turbulent Boundary Layers (2005)

The incompressible, zero-pressure-gradient turbulent boundary layer is investigated in light of the effect of the Reynolds number and surface roughness. The experimental data from various researchers has been collected and analyzed in order to study the effect of the roughness on the inner and outer flow. The scalings of George and Castillo (GC) (1997) for the mean velocity profiles and Reynolds stresses are used for the analysis and compared with the results of the classical scalings. Moreover, the true asymptotic profile (self-preserving) solution for the velocity deficit profiles is found when the profiles are normalized by the Zagarola/Smits (1998) scaling, U∞δ /δ. This scaling successfully removes the effects of the Reynolds number, the upstream conditions, and the roughness from the outer flow. Similarly, the classical scaling, uτ , tends to remove the effects from the outer flow but not in the inner region. However, it will be shown that as the roughness parameter, k, increases beyond k ≈ 28 or less, the Reynolds stresses and velocity profiles are influenced in the outer flow by roughness. This limit corresponds to the lower limit of the outer region of a boundary layer, thus the outer flow is affected by roughness beyond this limit. However, for the inner layer, the Reynolds stresses are sensitive to values of the roughness parameter, k ≈ 0.4 while the velocity profiles are affected for values of about k ≈ 17.
Solubility of recombinant Src homology 2 domains expressed in E. colican be predicted by TANGO (2014)

Solubility of recombinant proteins expressed in E.coli can be predicted by TANGO, an algorithm developed to determine the aggregation propensity of peptides. Targeted mutations representing corresponding amino acids in similar protein domains may increase solubility of recombinant proteins.
3D point cloud segmentation using GIS (2021)

In this paper we propose an approach to perform semantic segmentation of 3D point cloud data by importing the geographic information from a 2D GIS layer (OpenStreetMap). The proposed automatic procedure identifies meaningful units such as buildings and adjusts their locations to achieve best fit between the GIS polygonal perimeters and the point cloud. Our processing pipeline is presented and illustrated by segmenting point cloud data of Trinity College Dublin (Ireland) campus constructed from optical imagery collected by a drone.
Active Learning for Inference and Regeneration of Applications that Access Databases (2020)

We present K onure , a new system that uses active learning to infer models of applications that retrieve data from relational databases. K onure comprises a domain-specific language (each model is a program in this language) and associated inference algorithm that infers models of applications whose behavior can be expressed in this language. The inference algorithm generates inputs and database contents, runs the application, then observes the resulting database traffic and outputs to progressively refine its current model hypothesis. Because the technique works with only externally observable inputs, outputs, and database contents, it can infer the behavior of applications written in arbitrary languages using arbitrary coding styles (as long as the behavior of the application is expressible in the domain-specific language). K onure also implements a regenerator that produces a translated Python implementation of the application that systematically includes relevant security and error checks.
Electrophilic Activation of Lewis Base Complexes of Borane with Trityl Tetrakis(pentafluorophenyl)borate (2007)

Borenium ions do not accumulate under the conditions of hydride abstraction from Lewis base borane complexes (L·BH3) using trityl cation because subsequent rapid reaction with L·BH3 occurs to form B−H−B bonds. The hydride-bridged cations are sufficiently stabilized to resist abstraction of the remaining hydride by excess trityl cation; however, reversible cleavage of the 3c2e bond does take place to release borenium ion equivalents, as evidenced by interaction with weak nucleophiles.
ChemInform Abstract: Palladium‐Catalyzed Cross‐Coupling Reaction of Organometalloids Through Activation with Fluoride Ion (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Depletion of bronchus-associated lymphoid tissue associated with lung allograft rejection. (1988)

Pulmonary infections remain one of the major complications of lung transplantation. The bronchus-associated lymphoid tissue (BALT) forms a local immune system that normally protects the lung from infection. The effects of lung transplantation and lung allograft rejection on the BALT were examined using immunoperoxidase techniques. The BALT was evaluated by quantifying the number of immunoglobulin-bearing plasma cells in the lamina propria of sections of trachea and mainstem bronchus. Sections of donor mainstem bronchus from 2 patients with allograft rejection were compared with sections of native trachea from these same patients, and with sections of mainstem bronchus from 2 transplanted lungs without rejection and 20 controls. Lung allografts from the 2 patients with rejection had a marked depletion of submucosal IgA-bearing and IgG-bearing plasma cells. Two sets of transplanted lungs without evidence of rejection showed only a mild reduction of the BALT. The depletion of BALT associated with allograft rejection may contribute to the increased incidence of pulmonary infections seen in these patients.