gebhart/patrepeval huggingface dataset:
A Point Mutation Converts Dihydroneopterin Aldolase to a Cofactor-Independent Oxygenase (2006)

Dihydroneopterin aldolase (DHNA) catalyzes the conversion of 7,8-dihydroneopterin (1) to 6-hydroxymethyl-7,8-dihydropterin (4) in the folate biosynthetic pathway. Substitution of a conserved tyrosine residue at the active site of DHNA by phenylalanine converts the enzyme to a cofactor-independent oxygenase, which generates mainly 7,8-dihydroxanthopterin (6) rather than 4. 6 is generated via the same enol intermediate as in the wild-type enzyme-catalyzed reaction, but this species undergoes an oxygenation reaction to form 6. The conserved tyrosine residue plays only a minor role in the formation of the enol reaction intermediate but a critical role in the protonation of the enol intermediate to form 4.
Roles of temperature, solvent, M/L ratios and anion in preparing complexes containing a Himta ligand (2016)

Nine new complexes based on the Himta ligand were hydrothermally synthesized and structurally characterized. A systematic and comprehensive investigation of four influence factors on some complex architectures was carried out.
E‐cadherin expression in human epithelial ovarian cancer and normal ovary (1997)

The ovarian surface epithelium (OSE) is the origin of the majority of human ovarian cancers.These adenocarcinomas are characterized by initial local growth followed by spreading into the peritoneal cavity at later stages of tumor progression.The cell-adhesion molecule E-cadherin (E-cad) plays an important role in maintaining tissue integrity.Disappearance or impaired function of E-cad have often been associated with tumor formation and invasion in vivo and in vitro.The cell-specific expression of E-cad was investigated in normal human ovaries (n 5 12), in benign (n 5 5) and borderline (n 5 4) ovarian epithelial tumors and in adenocarcinomas of different stages and histological grades (n 5 18), by immunohistochemistry and immunoblotting.An ovarian cancer cell line (NIH-OVCAR3) was used as a reference.The epithelial origin of the cells was confirmed with cytokeratin (AE1/AE3) staining.In normal ovaries, the expression of E-cad was limited to inclusion cysts or deep clefts lined with OSE, whereas no staining of the OSE could be demonstrated at the surface of the ovary.In contrast, benign and borderline tumors uniformly expressed E-cad.This was observed in malignant tumors of all stages despite their degree of differentiation.E-cad was also present in metastasis from such tumors.The cell-specific expression of E-cad in inclusion cysts of normal ovaries and in epithelial layers of borderline tumors indicates a role for E-cad in the early events of the progression to a malignant phenotype.E-cad was not downregulated in later stages of ovarian cancer progression.Int.
Large-scale 3D point cloud representations via graph inception networks with applications to autonomous driving (2019)

We present a novel graph-neural-network-based system to effectively represent large-scale 3D point clouds with the applications to autonomous driving. Many previous works studied the representations of 3D point clouds based on two approaches, voxelization, which causes discretization errors and learning, which is hard to capture huge variations in large-scale scenarios. In this work, we combine voxelization and learning: we discretize the 3D space into voxels and propose novel graph inception networks to represent 3D points in each voxel. This combination makes the system avoid discretization errors and work for large-scale scenarios. The entire system for large-scale 3D point clouds acts like the blocked discrete cosine transform for 2D images; we thus call it the point cloud neural transform (PCT). We further apply the proposed PCT to represent real-time LiDAR sweeps produced by self-driving cars and the PCT with graph inception networks significantly outperforms its competitors.
Associations between the CDKN2A/B, ADTRP and PDGFD Polymorphisms and the Development of Coronary Atherosclerosis in Japanese Patients (2014)

The present study confirmed the association between CDKN2A/B and CAD and identified a different associated risk allele of ADTRP. PDGFD was found to exhibit a gender-specific association with CAD. The combination of multiple risk alleles may be associated with a higher risk of CAD.
Ultrathin Film Organic Transistors: Precise Control of Semiconductor Thickness via Spin‐Coating (2012)

Construction of ultrathin film organic transistors is an important challenge towards deeper understanding of the charge transport mechanism and multifunctional applications. We report on precise thickness control of ultrathin films of several organic semiconductors by using a simple spin-coating approach. Ultrathin film, n-channel organic transistors with mobilities well over 1.0 cm(2) V(-1) s(-1) have been realized and their potential in high-sensitivity gas sensing and other applications is demonstrated.
Thermotaxis navigation behavior (2014)

This chapter describes four different protocols used to assay thermotaxis navigation behavior of single, or populations of, C. elegans hermaphrodites on spatial thermal gradients within the physiological temperature range (15-25°C). A method to assay avoidance of noxious temperatures is also described.
PINK1-parkin pathway of mitophagy protects against contrast-induced acute kidney injury via decreasing mitochondrial ROS and NLRP3 inflammasome activation (2019)

Contrast-induced acute kidney injury (CI-AKI) occurs in more than 30% of patients after intravenous iodinated contrast media and causes serious complications, including renal failure and mortality. Recent research has demonstrated that routine antioxidant and alkaline therapy failed to show benefits in CI-AKI patients with high risk for renal complications. Mitophagy is a mechanism of selective autophagy, which controls mitochondrial quality and mitochondrial reactive oxygen species (ROS) through degradation of damaged mitochondria. The role of mitophagy and its regulation of apoptosis in CI-AKI are poorly understood. In this study, we demonstrated that mitophagy was induced in renal tubular epithelial cells (RTECs) during CI-AKI, both in vivo and in vitro. Meanwhile, contrast media-induced mitophagy was abolished when silencing PINK1 or PARK2 (Parkin), indicating a dominant role of the PINK1-Parkin pathway in mitophagy. Moreover, mitochondrial damage, mitochondrial ROS, RTEC apoptosis, and renal injury under contrast exposure were more severe in PINK1- or PARK2-deficient cells and mice than in wild-type groups. Functionally, PINK1-Parkin-mediated mitophagy prevented RTEC apoptosis and tissue damage in CI-AKI through reducing mitochondrial ROS and subsequent NLRP3 inflammasome activation. These results demonstrated that PINK1-Parkin-mediated mitophagy played a protective role in CI-AKI by reducing NLRP3 inflammasome activation.
Inactivation of Representative Species of Entomopathogenic Viruses, a Bacterium, Fungus, and Protozoan by an Ultraviolet Light Source (1977)

Four entomopathogenic viruses and one each of an entomopathogenic bacterium, fungus, and protozoan were inactivated when exposed to ultraviolet light; the half-life was less than 4 h in every instance. Relative ranking in stability of the entomopathogens was as follows: B. thuringiensis Berliner > Nomuraea rileyi (Farlow) Samson > entomopox Virus > nucleopolyhedrosis virus = cytoplasmic polyhedrosis virus > Vairimorpha (= Nosema ) necatrix (Kramer) > granulosis virus.
Potential Symbiosis-Specific Genes Uncovered by Sequencing a 410-Kilobase DNA Region of the <i>Bradyrhizobium japonicum</i> Chromosome (2001)

The physical and genetic map of the Bradyrhizobium japonicum chromosome revealed that nitrogen fixation and nodulation genes are clustered. Because of the complex interactions between the bacterium and the plant, we expected this chromosomal sector to contain additional genes that are involved in the maintenance of an efficient symbiosis. Therefore, we determined the nucleotide sequence of a 410-kb region. The overall G+C nucleotide content was 59.1%. Using a minimum gene length of 150 nucleotides, 388 open reading frames (ORFs) were selected as coding regions. Thirty-five percent of the predicted proteins showed similarity to proteins of rhizobia. Sixteen percent were similar only to proteins of other bacteria. No database match was found for 29%. Repetitive DNA sequence-derived ORFs accounted for the rest. The sequenced region contained all nitrogen fixation genes and, apart from nodM, all nodulation genes that were known to exist in B. japonicum. We found several genes that seem to encode transport systems for ferric citrate, molybdate, or carbon sources. Some of them are preceded by -24/-12 promoter elements. A number of putative outer membrane proteins and cell wall-modifying enzymes as well as a type III secretion system might be involved in the interaction with the host.
Radioprotection of cells in culture by WR-2721 and derivatives: form of the drug responsible for protection. (1988)

Studies of V79-171 cells were undertaken to determine what extracellular or intracellular derivative of the drug WR-2721 is associated with radioprotection. The effect of preincubation at 23 +/- 1 degree C with WR-2721, and with derivatives of WR-2721 produced in medium containing alkaline phosphatase, upon survival of cells following subsequent gamma-irradiation was examined. It was established that WR-2721, WR-1065, WR-33278, WRSSCys, and other disulfide forms produced by reactions of WR-1065 with the medium do not provide significant protection when present only extracellularly. Protection was found to correlate with cellular levels of the thiol form of the drug (WR-1065) but not with the cellular level of the disulfide forms of WR-1065. Similar results were obtained with HeLa, Me-180, Ovary 2008, HT-29/SP-1d, and Colo 395 cell lines showing that human tumor cell lines behave in the same fashion as the V79-171 nontumorigenic hamster diploid cell line. None of the drug forms produced significant cytotoxicity under the conditions used. It was concluded that it is the cellular level of WR-1065 at the time of irradiation which determines protection. The results are consistent with protection mechanisms involving scavenging of hydroxyl radicals, hydrogen atom transfer to DNA radicals, depletion of oxygen near DNA, enhancement of rapid biochemical repair processes, or some combination of these mechanisms.
Trehalose 6-phosphate is indispensable for carbohydrate utilization and growth in <i>Arabidopsis thaliana</i> (2003)

Genes for trehalose metabolism are widespread in higher plants. Insight into the physiological role of the trehalose pathway outside of resurrection plant species is lacking. To address this lack of insight, we express Escherichia coli genes for trehalose metabolism in Arabidopsis thaliana, which manipulates trehalose 6-phosphate (T6P) contents in the transgenic plants. Plants expressing otsA [encoding trehalose phosphate synthase (TPS)] accumulate T6P whereas those expressing either otsB [encoding trehalose phosphate phosphatase (TPP)] or treC [encoding trehalose phosphate hydrolase (TPH)] contain low levels of T6P. Expression of treF (encoding trehalase) yields plants with unaltered T6P content and a phenotype not distinguishable from wild type when grown on soil. The marked phenotype obtained of plants accumulating T6P is opposite to that of plants with low T6P levels obtained by expressing either TPP or TPH and consistent with a critical role for T6P in growth and development. Supplied sugar strongly inhibits growth of plants with reduced T6P content and leads to accumulation of respiratory intermediates. Remarkably, sugar improves growth of TPS expressors over wild type, a feat not previously accomplished by manipulation of metabolism. The data indicate that the T6P intermediate of the trehalose pathway controls carbohydrate utilization and thence growth via control of glycolysis in a manner analogous to that in yeast. Furthermore, embryolethal A. thaliana tps1 mutants are rescued by expression of E. coli TPS, but not by supply of trehalose, suggesting that T6P control over primary metabolism is indispensable for development.
Two-Phase Relative Permeability Prediction Using a Linear Regression Model (2000)

Abstract In the absence of laboratory measured data or in the case when a more general representation of fluid flow in a reservoir is needed, empirical relative permeability correlations become useful. These correlations will also apply to simulation studies which require adjustments to the relative permeability values to account for grid effects. A linear regression model approach is employed to develop prediction equations for water-oil, gas-oil, gas-water, and gas-condensate relative permeability from experimental data. Use of the SPE CD-ROM has allowed a rapid and thorough data retrieval for this study; 416 sets of relative permeability data were obtained from published literature and various industry sources. Improved equations were developed for water-oil and gas-oil systems based on formation type and wettability. Additionally, general equations for gas-condensate and gas-water systems were formulated. Craig’s rule for determining the rock wettability has been modified to cover a wider range of relative permeability data currently available. Available data has increased significantly since the last published work in this area. The prediction equations are compared with previously published correlations where possible.
Assessment of laboratory assays to measure rivaroxaban – an oral, direct factor Xa inhibitor (2010)

Although there is no need for routine coagulation monitoring with rivaroxaban--an oral, direct factor Xa inhibitor--a haemostasis assay might be valuable to measure its pharmacodynamic effects. This study aimed to find assays, among those commercially available, to measure rivaroxaban pharmacodynamics. Several global conventional clotting tests, as well as clotting or chromogenic assays to measure anti-factor Xa activity, were studied. A thrombin generation test using calibrated automated thrombogram was also done. Tests were performed with the indirect factor Xa inhibitor fondaparinux for comparison. A concentration-dependent prolongation of prothrombin time (PT), dilute PT, and activated partial thromboplastin time was observed with rivaroxaban. The results varied depending on the reagents. This variability cannot be standardised with the international normalised ratio system commonly used for vitamin K antagonists. Using a standard calibration curve, PT test results can be expressed in plasma concentrations of rivaroxaban rather than PT seconds or ratio. Standard methods for HepTest and two-step prothrombinase-induced clotting time (PiCT) resulted in a paradoxical response, with low concentrations of rivaroxaban reducing clotting times. This was not observed with shorter incubation times, or when antithrombin-deficient (immunodepleted) plasma was used. The chromogenic tests found a dose-dependent relationship between anti-factor Xa activity and rivaroxaban concentration. Modified specific factor Xa chromogenic assays are being further investigated. One-step PiCT and HepTest with shortened incubation times, as well as the widely available PT assay (using a rivaroxaban calibrator) could be useful to monitor the pharmacodynamic effects of rivaroxaban accurately. Finally, all clotting and chromogenic assays showed a concentration-dependent effect induced by rivaroxaban.
Sub‐100‐nanometre resolution in total internal reflection fluorescence microscopy (2008)

Combining total internal reflection fluorescence microscopy with structured illumination allows optical wide-field imaging with sub-100-nanometre resolution. We present a novel objective-launch set-up for standing wave illumination that takes advantage of a tunable transmission diffraction grating and transparent phase shifters actuated by electro-active polymers to control the excitation pattern in three dimensions. Image acquisition is completed in less than 1 s. To reconstruct the extended image spectrum, we apply a new apodization function that results in a lateral resolution of 89 nm for green emission wavelength.
Reengineering C++ Component Models via Automatic Program Transformation (2006)

Automated program transformation holds promise for a variety of software life cycle endeavors, particularly where the size of legacy systems makes code analysis, re-engineering, and evolution difficult and expensive. But constructing highly scalable transformation tools supporting modern languages in full generality is itself a painstaking and expensive process. This cost can be managed by developing a common transformation system infrastructure re-useable by derived tools that each address specific tasks, thus leveraging the infrastructure costs. This paper describes the design maintenance system (DMS), a practical, commercial program analysis and transformation system, and discusses how it was employed to construct a custom modernization tool being applied to a large C++ industrial avionics system. The tool transforms components developed in a 1990's-era component style to a more modern CORBA-like component framework, preserving functionality.
Wideband subarray design for 5G an antenna arrays (2016)

There is a global trend towards migrating to millimeter wave frequencies in the fifth generation of mobile communications (5G) to further enhance the available capacity and data rates. Antenna arrays are usually applied to overcome the innate high path loss at the millimeter wave (mmW) frequency band. Moreover, the use of subarrays decreases design complexity and system cost. The goal of this paper is to present a design of a wideband subarray at the frequency range from 28 GHz to 32 GHz, i.e. the frequency range applied for Local Multipoint Distribution Service (LMDS), to be used in the antenna array design of next generation mobile networks. The proposed subarray consists of four radiating elements of proximity coupled stacked patch antennas. The unit-cell is first designed, fabricated and tested, which confirms the wideband coverage along the required band. The proposed subarray achieves a simulated gain that ranges between 11.1 dB and 12 dB along the frequency band from 28 GHz to 32 GHz. The impedance bandwidth and the 1-dB gain bandwidth are 30% and 21.2%, respectively.
A Scalable Algorithm for Placement of Virtual Clusters in Large Data Centers (2012)

We consider the problem of placing virtual clusters, each consisting of a set of heterogeneous virtual machines (VM) with some interrelationships due to communication needs and other dependability-induced constraints, onto physical machines (PM) in a large data center. The placement of such constrained, networked virtual clusters, including compute, storage, and networking resources is challenging. The size of the problem forces one to resort to approximate and heuristics-based optimization techniques. We introduce a statistical approach based on importance sampling (also known as cross-entropy) to solve this placement problem. A straightforward implementation of such a technique proves inefficient. We considerably enhance the method by biasing the sampling process to incorporate communication needs and other constraints of requests to yield an efficient algorithm that is linear in the size of the data center. We investigate the quality of the results of using our algorithm on a simulated system, where we study the effects of various parameters on the solution and performance of the algorithm.
Human thyroglobulin reference material (CRM 457). 2nd Part: Physicochemical characterization and certification. (1996)

This report describes the characterization of a purified human thyroglobulin (Tg) reference material, and details the procedures used in its certification. The purified Tg is intended to be used as a primary reference material to establish calibration of working serum based reference material for immunoassay procedures. The programme involved the participation of 15 European laboratories and one laboratory from the United States. The physicochemical characterization showed by polyacrylamide gel electrophoresis and immunoblotting that the purified Tg had for the major part the expected molecular size of 660 kDa with traces of lower molecular forms. The amino acid composition was close to that demonstrated for the cDNA and the content of iodine was in keeping with a moderately to highly iodinated Tg. The mass concentration in reference material RM 457 is certified to be (0.324 +/- 0.018) g/L on the basis of protein determined by the Lowry method and supported by nitrogen determination, absorbance measurement, and amino acid analysis. This reference material is considered the first step towards decreasing the interlaboratory variability between Tg methods of measurement.
Tunable Mechanical Stability and Deformation Response of a Resilin-Based Elastomer (2011)

Resilin, the highly elastomeric protein found in specialized compartments of most arthropods, possesses superior resilience and excellent high-frequency responsiveness. Enabled by biosynthetic strategies, we have designed and produced a modular, recombinant resilin-like polypeptide bearing both mechanically active and biologically active domains to create novel biomaterial microenvironments for engineering mechanically active tissues such as blood vessels, cardiovascular tissues, and vocal folds. Preliminary studies revealed that these recombinant materials exhibit promising mechanical properties and support the adhesion of NIH 3T3 fibroblasts. In this Article, we detail the characterization of the dynamic mechanical properties of these materials, as assessed via dynamic oscillatory shear rheology at various protein concentrations and cross-linking ratios. Simply by varying the polypeptide concentration and cross-linker ratios, the storage modulus G' can be easily tuned within the range of 500 Pa to 10 kPa. Strain-stress cycles and resilience measurements were probed via standard tensile testing methods and indicated the excellent resilience (>90%) of these materials, even when the mechanically active domains are intercepted by nonmechanically active biological cassettes. Further evaluation, at high frequencies, of the mechanical properties of these materials were assessed by a custom-designed torsional wave apparatus (TWA) at frequencies close to human phonation, indicating elastic modulus values from 200 to 2500 Pa, which is within the range of experimental data collected on excised porcine and human vocal fold tissues. The results validate the outstanding mechanical properties of the engineered materials, which are highly comparable to the mechanical properties of targeted vocal fold tissues. The ease of production of these biologically active materials, coupled to their outstanding mechanical properties over a range of compositions, suggests their potential in tissue regeneration applications.
Does BERT Understand Sentiment? Leveraging Comparisons Between Contextual and Non-Contextual Embeddings to Improve Aspect-Based Sentiment Models (2020)

When performing Polarity Detection for different words in a sentence, we need to look at the words around to understand the sentiment. Massively pretrained language models like BERT can encode not only just the words in a document but also the context around the words along with them. This begs the questions, "Does a pretrain language model also automatically encode sentiment information about each word?" and "Can it be used to infer polarity towards different aspects?". In this work we try to answer this question by showing that training a comparison of a contextual embedding from BERT and a generic word embedding can be used to infer sentiment. We also show that if we finetune a subset of weights the model built on comparison of BERT and generic word embedding, it can get state of the art results for Polarity Detection in Aspect Based Sentiment Classification datasets.