gebhart/patrepeval huggingface dataset:
Sterylglucoside Catabolism in Cryptococcus neoformans with Endoglycoceramidase-related Protein 2 (EGCrP2), the First Steryl-β-glucosidase Identified in Fungi (2014)

Cryptococcosis is an infectious disease caused by pathogenic fungi, such as Cryptococcus neoformans and Cryptococcus gattii. The ceramide structure (methyl-d18:2/h18:0) of C. neoformans glucosylceramide (GlcCer) is characteristic and strongly related to its pathogenicity. We recently identified endoglycoceramidase-related protein 1 (EGCrP1) as a glucocerebrosidase in C. neoformans and showed that it was involved in the quality control of GlcCer by eliminating immature GlcCer during the synthesis of GlcCer (Ishibashi, Y., Ikeda, K., Sakaguchi, K., Okino, N., Taguchi, R., and Ito, M. (2012) Quality control of fungus-specific glucosylceramide in Cryptococcus neoformans by endoglycoceramidase-related protein 1 (EGCrP1). J. Biol. Chem. 287, 368-381). We herein identified and characterized EGCrP2, a homologue of EGCrP1, as the enzyme responsible for sterylglucoside catabolism in C. neoformans. In contrast to EGCrP1, which is specific to GlcCer, EGCrP2 hydrolyzed various β-glucosides, including GlcCer, cholesteryl-β-glucoside, ergosteryl-β-glucoside, sitosteryl-β-glucoside, and para-nitrophenyl-β-glucoside, but not α-glucosides or β-galactosides, under acidic conditions. Disruption of the EGCrP2 gene (egcrp2) resulted in the accumulation of a glycolipid, the structure of which was determined following purification to ergosteryl-3β-glucoside, a major sterylglucoside in fungi, by mass spectrometric and two-dimensional nuclear magnetic resonance analyses. This glycolipid accumulated in vacuoles and EGCrP2 was detected in vacuole-enriched fraction. These results indicated that EGCrP2 was involved in the catabolism of ergosteryl-β-glucoside in the vacuoles of C. neoformans. Distinct growth arrest, a dysfunction in cell budding, and an abnormal vacuole morphology were detected in the egcrp2-disrupted mutants, suggesting that EGCrP2 may be a promising target for anti-cryptococcal drugs. EGCrP2, classified into glycohydrolase family 5, is the first steryl-β-glucosidase identified as well as a missing link in sterylglucoside metabolism in fungi.
<i>N</i>-(2,3,5,6-Tetrafluoropyridyl)sulfoximines: synthesis, X-ray crystallography, and halogen bonding (2020)

<italic>N</italic>-(Tetrafluoropyridyl)sulfoximines are obtained from<italic>N</italic>H-sulfoximines and pentafluoropyridine under solution-based or mechanochemical conditions, and the solid-state structures of 26 products have been determined by X-ray diffraction analysis.
Complex ac susceptibility studies of the disordered molecular based magnets V(TCNE)<i>x</i>: Role of spinless solvent (1993)

The effect of different spinless solvents on the magnetism of V(TCNE)x⋅y(solvent) (TCNE=tetracyanoethylene) is studied by temperature (T) dependent ac susceptibility above 2.3 K. Though V(TCNE)x⋅y(CH2Cl2) has a critical temperature Tc ∼400 K, for V(TCNE)x⋅y(C4H8O), Tc ∼205 K and the coercive field is reduced, while for V(TCNE)x⋅y(CH3CN), Tc ∼140 K or below and a spin glass phase exists below a spin freezing temperature of Tf∼7–15 K. The variations with solvent are suggested to be due to spin dilution and random anisotropy introduced by the spinless solvents.
Algorithm design (1987)

The quest for efficiency in computational methods yields not only fast algorithms, but also insights that lead to elegant, simple, and general problem-solving methods.
Cell transplantation for Huntington's disease. (1992)

This text is a comprehensive review of research into animal models and humans with HD from neurochemical, neuroanatomical and behavioural perspectives. It focuses on neural transplantation studies in rodent and primate models of HD. Studies demonstrating that foetal brain tissue transplants can reverse the neurodegenerative and behavioural pathology of HD animal models are presented. In addition, the final section discusses recent clinical studies on the advantages, future directions and ethical considerations of cell transplantation for HD.
The OSPF NSSA Option (1994)

This document describes a new optional type of OSPF area, somewhat humorously referred to as a not-so-stubby area (or NSSA). NSSAs are similar to the existing OSPF stub area configuration option but have the additional capability of importing AS external routes in a limited fashion.
Depolymerization of lignocellulosic biomass to fuel precursors: maximizing carbon efficiency by combining hydrolysis with pyrolysis (2010)

In this paper we study the carbon efficiency of combining hydrolysis and pyrolysis processes using maple wood as a feedstock. A two-step hydrolysis of maple wood in batch reactors, that consisted of a thermochemical pretreatment in water followed by enzymatic hydrolysis, achieved an 88.7 wt% yield of glucose and an 85 wt% yield of xylose as liquid streams. The residue obtained was 80 wt% lignin. A combination of TGA and pyroprobe studies was used for the pyrolysis of pure maple wood, hemicellulose-extracted maple wood, and the lignin residue from the hydrolysis of maple wood. Pyrolysis of raw maple wood produced 67 wt% of condensable liquid products (or bio-oils) that were a mixture of compounds including sugars, water, phenolics, aldehydes, and acids. Pyrolysis of hemicellulose-extracted maple wood (the solid product after pretreatment of maple wood) showed similar bio-oil yields and compositions to raw maple wood while pyrolysis of the lignin residue (the final solid product of enzymatic hydrolysis) produced only 44.8 wt% of bio-oil. The bio-oil from the lignin residue is mostly composed of phenolics such as guaiacol and syringol compounds. Catalytic fast pyrolysis (CFP) of maple wood, hemicellulose-extracted maple wood, and lignin residue produced 18.8, 16.6 and 10.1 wt% aromatic products, respectively. Three possible options for the integration of hydrolysis with pyrolysis processes were evaluated based on their material and carbon balances: Option 1 was the pyrolysis/CFP of raw maple wood, option 2 combined hemicellulose extraction by hydrolysis with pyrolysis/CFP of hemicellulose-extracted maple wood, and option 3 combined the two-step hydrolysis of hemicellulose and cellulose sugar extraction with pyrolysis/CFP of the lignin residue. It was found that options 1, 2, and 3 all have similar overall carbon yields for sugars and bio-oils of between 66 and 67%.
Efficacy and safety of RTS,S/AS01 malaria vaccine with or without a booster dose in infants and children in Africa: final results of a phase 3, individually randomised, controlled trial (2020)

The efficacy and safety of the RTS,S/AS01 candidate malaria vaccine during 18 months of follow-up have been published previously. Herein, we report the final results from the same trial, including the efficacy of a booster dose.
Transcriptional control of the nuo operon which encodes the energy-conserving NADH dehydrogenase of Salmonella typhimurium (1995)

The 14 nuo genes encode the subunits of the type I (energy-conserving) NADH dehydrogenase, a key component of the respiratory chain. Salmonella typhimurium, like Escherichia coli, has two enzymes that can oxidize NADH and transfer electrons to ubiquinone, but only the type I enzyme translocates protons across the membrane to generate a proton motive force. Cells with the type I enzyme are energetically more efficient; the role of the type II enzyme (encoded by ndh) is not established, but it may function like a relief valve to allow more rapid NADH recycling. Here, we have investigated transcription of the nuo gene cluster, primarily in S. typhimurium. Studies with polar insertion mutants demonstrate that these genes are arranged as a single, large operon that is expressed from a complex promoter region upstream of nuoA. The DNA sequence of the promoter region was determined, and primer extension analysis of nuo transcripts was used to map four major RNA 5' ends to this region. A set of lac operon fusions to various DNA segments from the nuo promoter region was also constructed. Analysis of these fusions confirmed the presence of at least two nuo promoters. Mutations in the global regulatory genes arcA, oxrA (fnr), crp, cya, and katF were tested for effects on expression of the nuo operon. However, none of the mutations tested had a large effect on expression of type I NADH dehydrogenase.
Aryl Hydrocarbon Receptor Nuclear Translocator/Hypoxia-inducible Factor-1β Plays a Critical Role in Maintaining Glucose-stimulated Anaplerosis and Insulin Release from Pancreatic β-Cells (2010)

The metabolic pathways that are involved in regulating insulin secretion from pancreatic β-cells are still incompletely understood. One potential regulator of the metabolic phenotype of β-cells is the transcription factor aryl hydrocarbon receptor nuclear translocator (ARNT)/hypoxia-inducible factor (HIF)-1β. ARNT/HIF-1β levels are profoundly reduced in islets obtained from type 2 diabetic patients. However, no study to date has investigated key pathways involved in regulating insulin release in β-cells that lack ARNT/HIF-1β. In this study, we confirm that siRNA-mediated knockdown of ARNT/HIF-1β inhibits glucose-stimulated insulin secretion. We next investigated the metabolic consequence of the loss of ARNT/HIF-1β knockdown. We demonstrate that β-cells with reduced ARNT/HIF-1β expression levels exhibit a 31% reduction in glycolytic flux without significant changes in glucose oxidation or the ATP:ADP ratio. Metabolic profiling of β-cells treated with siRNAs against the ARNT/HIF-1β gene revealed that glycolysis, anaplerosis, and glucose-induced fatty acid production were down-regulated, and all are key events involved in glucose-stimulated insulin secretion. In addition, both first and second phase insulin secretion in islets were significantly reduced after ARNT/HIF-1β knockdown. Together, our data suggest an important role for ARNT/HIF-1β in anaplerosis, and it may play a critical role in maintaining normal secretion competence of β-cells.
Asymptomatic individuals – risk stratification in the prevention of coronary heart disease (2001)

The report of the World Health Organization Expert Committee on Prevention of Coronary Heart Disease considered that a comprehensive action for coronary heart disease (CHD) prevention has to include three components:
3D Photogrammetry Point Cloud Segmentation Using a Model Ensembling Framework (2020)

The US Army is paying increased attention to the development of rapid three-dimensional (3D) reconstruction using photogrammetry and unmanned aerial vehicle (UAV) technologies for creating virtual environments and simulations in areas of interest. The ability of the intelligence community, mission commanders, and front-line soldiers to understand their deployed physical environment in advance is critical in the planning and rehearsal phases of any military operation. In order to achieve various simulation capabilities such as destruction operations, route planning, and explosive-standoff distances computation among others, reconstructed 3D data needs to be properly attributed. In this paper, we introduce a model ensembling framework for segmenting a 3D photogrammetry point cloud into top-level terrain elements (i.e., ground, human-made objects, and vegetation). Preprocessing and postprocessing methods were designed to overcome the data segmentation challenges posed by photogrammetric data-quality issues. A large UAV-based photogrammetric database was created for validation purposes. The designed model ensembling framework was compared with existing point cloud segmentation algorithms, and it outperformed other algorithms and achieved the best F1-score. Because the ultimate goal of segmenting a photogrammetric-generated point cloud is to create realistic virtual environments for simulation. Qualitative results for creating virtual environments using the segmented data are also discussed in this paper.
Cholelithiasis in children in a Chinese hospital: report of 52 cases. (1984)

Over a period of 22 years (1958-1980), 52 children with cholelithiasis were treated in the Hunan Medical College Hospital in Ghangsha, China. Enteric helminthiasis is a common endemic disease in China and the countries of the Far East. Common in this region also is biliary ascariasis, which can precipitate an abdominal emergency in children. Both these conditions make differentiation of primary acute cholecystitis from the acute cholecystitis that is a complication of biliary ascariasis difficult in children. But, whatever the etiology of the disease, cholelithiasis was confirmed in all 52 children, an incidence of 1:62.4 the frequency of this disease in adults, or eight times higher than that which occurs in Western countries. Table 1 shows the distribution according to sex and age in our patients.
Principal Components Analysis of Cointegrated Time Series (2017)

This paper considers the analysis of cointegrated time series using principal components methods. These methods have the advantage of neither requiring the normalisation imposed by the triangular error correction model, nor the specification of a finite order vector autoregression. An asymptotically efficient estimator of the cointegrating vectors is given, along with tests for cointegration and tests of certain linear restrictions on the cointegrating vectors. An illustrative application is provided.
Allelic Loss of Chromosome 16q in Endometrial Cancer: Correlation with Poor Prognosis of Patients and Less Differentiated Histology (1996)

Deletion of certain chromosomal regions can be demonstrated in malignant cells. Chromosome 16q is one of the regions where allelic loss is frequently detected in carcinoma of the breast and many other tumors, suggesting that gene(s) which retard tumor growth may exist here. To elucidate the clinicopathological significance of chromosome 16q, loss of heterozygosity (LOH) was investigated using microsatellite polymorphism analysis in 58 patients with endometrial lesions (50 with endometrial carcinoma and 8 who had hyperplasia with or without atypia). When 11 regions of chromosome 16q were examined, LOH was found in 20 patients with carcinoma (40%) and none of the patients with hyperplasia. The tumors of 9 of the 20 patients (45%) showed total loss of 16q, while the others (55%) showed partial deletion. Tumors with LOH were histologically less differentiated than those without LOH (P = 0.038, chi2 test). Patients with tumors showing LOH of 16q had a worse prognosis than those without LOH according to Kaplan-Meier survival analysis (P=0.0158, log-rank test). In addition, LOH of 16q showed a significant relationship to prognosis by Cox regression analysis. Deletion mapping of 16q demonstrated that two regions (16q22.1 and 16q22.2-23.1) were frequently involved. Patients with 16q22.1 LOH had a poorer prognosis than those with intact 16q22.1 (P=0.0003, log-rank test). These findings suggest that gene(s) of which defect is possibly related to the aggressiveness of endometrial cancer are localized on a limited region of 16q that includes 16q22.1.
Improved growth uniformity in molecular-beam epitaxy: Alternative strategies (1992)

We use computer modeling to evaluate alternative strategies for the improvement of molecular-beam epitaxy (MBE) growth uniformity. Using GaAs growth in a V80H MBE system as an example, we evaluate the effect of shifting the effusion cell away from the substrate on layer uniformity, Ga melt temperature, and yield. Four different crucible systems are compared. We find that, for the V80H system, pulling back a straight wall crucible brings substantial uniformity improvement only when the crucible orifice is capped with an annular disk. This modification is not necessary for a conical crucible or straight wall crucible with a conical insert. The increase in the cell operating temperature due to the pull back is found to be about 50 °C for a 10 cm cell shift for all the crucible designs. Depending on the cell, such a shift can improve layer uniformity over a 3 in. wafer by up to a factor of 5.
Fungicide Effects on Thatch Depth, Thatch Decomposition Rate, and Growth of Kentucky Bluegrass<sup>1</sup> (1985)

Abstract Development of improved management strategies for controlling thatch on tuifgrasses is limited by an incomplete understanding of thatch biology. Mechanisms whereby fungicides cause thatch to accumulate in turfgrass were investigated, by evaluating the influences of fungicides on rates of tissue production and thatch decomposition. Fourteen fungicides, one nematicide, and five mixed‐fungicide programs were applied repeatedly (up to nine times annually), over a 4‐yr period, to a field‐grown Kentucky bluegrass ( Poa pratensis L.) turf on a soil of the fine, illitic mesic family of Glossoboric Hapludalfs. Measurements were made of thatch depths, root and leaf clipping weights, shear strength of sod, and decomposition rates for thatch implanted into the turfs. Compounds that caused thatch to become deeper ( p = 0.05) than in the nontreated control included benomyl, cadmium succinate, fenamiphos, iprodione, and mancozeb. Treatments in which these pesticides were used were characterized by sod shear strengths greater ( p = 0.05) than in the control. Thatch accumulations were related mostly to the amounts of roots in the surface 4 cm. None of the studied fungicides significantly ( p = 0.10) reduced the apparent rate of thatch decomposition. Fungicides in this study therefore appeared to induce thatchiness in Kentucky bluegrass by increasing the rates of root and rhizome production and not by reducing the rate of litter decomposition.
Isolation and Characterization of the Human Gene Homologous to the Drosophila Headcase (hdc) Gene in Chromosome Bands 6q23-q24, a Region of Common Deletion in Human Pancreatic Cancer (2001)

Deletions of the long arm of chromosome 6 (6q) are one of the most common chromosomal abnormalities in multiple human malignancies. Previously, we have identified three commonly deleted regions on 6q (6q21, 6q23-q24, and 6q26) in pancreatic cancer by loss of heterozygosity studies, suggesting the presence of one or more tumor suppressor genes on this chromosome arm. Using a combination of database search and cDNA library screening, we successfully isolated a transcript from 6q24. This mRNA encodes a protein consisting of 543 amino acids with homology to the Drosophila headcase (hdc) gene and, thus, is designated as hHDC. Northern analysis identified a ubiquitously expressed 5.6-kb transcript. Seventeen (81%) of 21 pancreatic cancer cell lines and four (80%) of five renal cell carcinoma cell lines showed low level expression, suggesting that the hHDC gene may play an important role in some human cancers.
Horizontal transfer of penicillin-binding protein genes in penicillin-resistant clinical isolates of Streptococcus pneumoniae. (1989)

Resistance to penicillin in clinical isolates of Streptococcus pneumoniae has occurred by the development of altered penicillin-binding proteins (PBPs) that have greatly decreased affinity for the antibiotic. We have investigated the origins of penicillin-resistant strains by comparing the sequences of the transpeptidase domain of PBP2B from 6 penicillin-sensitive and 14 penicillin-resistant strains. In addition we have sequenced part of the amylomaltase gene from 2 of the sensitive and 6 of the resistant strains. The sequences of the amylomaltase gene of all of the strains and of the PBP2B gene of the penicillin-sensitive strain show that S. pneumoniae is genetically very uniform. In contrast the PBP2B genes of the penicillin-resistant strains show approximately equal to 14% sequence divergence from those of the penicillin-sensitive strains and the development of penicillin resistance has involved the replacement, presumably by transformation, of the original PBP2B gene by a homologous gene from an unknown source. This genetic event has occurred on at least two occasions, involving different sources, to produce the two classes of altered PBP2B genes found in penicillin-resistant strains of S. pneumoniae. There is considerable variation among the PBP2B genes of the resistant strains that may have arisen by secondary transformation events accompanied by mismatch repair subsequent to their original introductions into S. pneumoniae.
Transparent, Nanostructured Silk Fibroin Hydrogels with Tunable Mechanical Properties (2015)

Silk fibroin from the <i>Bombyx mori</i> caterpillar has been processed into many material forms, with potential applications in areas ranging from optoelectronics to tissue engineering. As a hydrogel, silk fibroin has been engineered as a substrate for the regeneration of soft tissues where hydration and mechanical compatibility are necessary. Current fabrication of silk fibroin hydrogels produces microstructured materials that lack transparency and limits the ability to fully exploit the hydrogel form. Transparency is the main characteristic of some human tissues (e.g., cornea) where silk fibroin in the film format has shown potential as scaffolding material, however, lacking the necessary hydration and successful attachment of cells without biochemical functionalization. Additionally, detection using light is an important method to translate information for instruction, sensing, and visualization of biological entities and light sensitive molecules. Here, we introduce a method for the fabrication of transparent silk hydrogels by driving the formation of nanostructures in the silk fibroin material. These nanostructures are formed by exposing silk solution (concentration below 15 mg/mL) to organic solvents that induce the amorphous to crystalline transition of the protein and indeed the sol-gel transition of the material. We have also explored a process to modulate the mechanical properties of silk fibroin hydrogel within the physiological range by controlling the amount of metal ions present in the protein structure. Nanostructured silk fibroin hydrogels are biocompatible and allow for attachment and proliferation of human dermal fibroblasts without any biochemical functionalization. In addition, seeding of human cornea epithelial cells (HCECs) on the hydrogel surface results in the formation of an epithelium, which does not alter the gels' transparency and shows biological properties that challenge the performances of HCECs seeded in collagen hydrogels, the current standard material for the engineering of corneal tissue.
Field distortion caused by magnetization tolerances of permanent magnets (1993)

Factors contributing to distortion of the field generated by permanent magnets, such as fabrication and material tolerances, are analyzed using the harmonic series expansion of the magnetostatic potential. The power spectrum is influenced by the number of discrete blocks and the number of layers of the magnetic structure. Ferromagnetic plates, acting as spatial filters inserted in the magnetic structure, reduce the distortions due to magnetization tolerances by approximately 60%.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Immobilization of enzymes on slowly soluble carriers (1977)

The preparation and some properties of microspheres composed of oxidized polysaccharides and some vinyl polymers are described. The microspheres contain immobilized enzyme and can be slowly solubilized in water solutions, thereby releasing active a enzyme into the surrounding medium. The kinetic characteristics of the immobilized enzyme bound with a fragment of matrix after complete solubilization are unchanged, but the enzyme exhibits high thermostability. These preparations could have a wide range of medical applications, e.g., to form a drug "depot" directly in an affected organ.