gebhart/patrepeval huggingface dataset:
Facile Solid-Phase Synthesis of Peptide-p-Nitroanilide (pNA) Analog Containing Conjugates Using a Novel Wang or Rink Amide Resin (2011)

Proteases play a key role in literally all biological processes, and are of great interest, especially to the pharmaceutical industry. Colorimetric based Peptide-p-Nitroanilide conjugates (peptide-pNAs), with absorbance at approximately 408 nm, have historically been and are still widely used substrates for the study of protease activity. The preparation of peptide-pNA however, presents several technical challenges. Firstly, the amino group of pNA has a low nucleophilic property due to the electron-withdrawing effect of the nitro group. Secondly, the poor solubility of a p-nitroanilide intermediate and lastly, coupling in solution phase by DCC, azide or active ester, commonly used techniques are not effective. Here we report the development of two novel supports for facile solid phase peptide syntheses, namely, Wang-resin and Rink Amide-resin conjugated with a pNA analog, 5-amino-2-nitrobenzoic acid (Anb5,2). Based on a paper by Hojo, et al. in which they described the introduction of Anb5,2 to a p-methylbenzhydrylamine (MB) resin; we successfully coupled Anb5,2 to either Wang or Rink Amide resin using the TBTU method in the presence of p-dimethylaminopyridine (DMAP). Anb5,2-Wang or Rink Rmide resin is then coupled to a Fluorenylmethyloxycarbonyl (Fmoc) containing amino acid. Peptide synthesis can subsequently proceed using Fmoc synthesis strategy. The use of this pNA analog containing resins circumvents the tehcnical difficulties stated above. These resins also greatly facilitates the synthesis of peptide-pNA-like chromogenic substrates for protease research.
Bone marrow cells from myelodysplastic syndromes show altered immunophenotypic profiles that may contribute to the diagnosis and prognostic stratification of the disease: A pilot study on a series of 56 patients (2010)

Assessment of immunophenotypic abnormalities of maturing/mature BM cells allows an efficient discrimination between MDS and both normal and reactive BM, once the number and degree of severity of the abnormalities detected are simultaneously scored. Interestingly, progressively higher IS were found among patients with MDS with adverse prognostic features and shorter overall survival.
Reactions of dicarbonyl compounds with β-ketoglutaric acid: synthesis of 4-hydroxy-3,4-diphenylcyclopent-2-enone-2-carboxylic acid (1977)

Reaction of β-ketoglutaric acid with benzil in ethanolic KOH furnished the 1:1 adduct 7. Hydrolysis and partial decarboxylation gave the monoacid 8, the structure of which was erroneously reported to be 5 in the earlier literature.[Formula: see text]
Resilient hosting in a continuously available virtualized environment (2008)

In this paper, we describe continuously available services and application hosting on the Events/IBM.comt Infrastructure (EI)—a continuously available virtualized environment based on three active data centers that has demonstrated 100-percent availability for many premier Web sites, including www.ibm.com. The environment consists of simultaneously active paths spanning three geographically diverse data centers. We describe techniques for automated rapid scaling and continuous availability using IBM WebSphere® clustering, IBM DB2™ replication, load balancing, virtualized network infrastructure components, and IBM System p® virtualization capabilities. We explore best practices for deploying application releases and updates, applying fix packs, and updating hardware and perating systems, all without interrupting service. In addition, we discuss how to troubleshoot and synchronize the vast flows of a multipath redundant solution. Finally, we describe the requirements that dictate continuously available hosting solutions and modifications to our multisite approach for use in fewer data centers. Application of the topics in this paper has resulted in continuous service with no planned or unplanned interruptions over many years of application hosting within the EI.
Predicting the shapes of bones at a joint: application to the shoulder (2007)

This paper presents a novel method to explore the intrinsic morphological correlation between the bones of a shoulder joint (humerus and scapula). To model this correlation, canonical correlation analysis (CCA) is used. We also propose a technique to predict a three-dimensional (3D) bone shape from its adjoining segment at a joint based on partial least squares regression (PLS). The high dimensional 3D surface information of a bone is represented by a few variables using principal component analysis, which also captures the pattern of variability of the shapes in our datasets. Our results show that the humerus set and scapula set have highly linear morphological relationship and that the correlation information can be used as a classifier. In this study, primate shoulder bone datasets were categorised into two clusters: great apes (including humans) and monkeys. A leave one out experiment was performed to test the robustness of this prediction method. The prediction behaviour using this method shows statistically significantly better results than using the mean shape from the training set.
Utilizing Drilling Data and Machine Learning in Real-Time Prediction of Poisson's Ratio (2023)

Abstract Rock elastic properties influence drilling performance, estimation of in-situ stresses, and hydraulic fracturing design. Therefore, having complete and accurate information on rock properties is essential. While those properties are conventionally measured experimentally or using well logs, this work proposes to estimate the Poisson's ratio (PR) from parameters available while drilling. Various machine learning techniques were employed, such as artificial neural network (ANN), support vector machine (SVM), and random forest (RF). The dataset utilized contains more than 5800 data points, each of them has a value of PR and six drilling parameters such as rate of penetration (ROP), rotary speed (RPM), and weight on bit (WOB). The dataset was divided into three parts, two were fed to the algorithms for training and testing the models, while the last group (around half of the dataset) was hidden to be used to validate the models later. The models had a good fit with the actual PR values with correlation coefficients as high as 0.99 and errors as low as 1%. Among the used algorithms, ANN and RF yielded the best accuracy in all datasets with no significant difference between the training and the validation performance which indicate good generalization without an overfitting problem. Using drilling data to predict rock mechanical parameters allows building a complete geomechanical model at an early time. It also saves the time and cost associated with laboratory tests.
Glutathione prevents N -methyl-d-aspartate receptor-mediated neurotoxicity (1991)

N-methyl-D-aspartate(NMDA) antagonists afford possible therapeutic modalities for stroke, trauma, and various neurodegenerative conditions thought to be mediated by excessive stimulation of NMDA receptors in the brain. To date, however, no drug has been demonstrated to be a safe NMDA antagonist at a dosage necessary for neuroprotection. In the present study, we use an in-vitro preparation to show that glutathione is capable of attenuating neuronal damage mediated by NMDA receptor activation. Both oxidized and reduced glutathione are protective, and an extracellular mechanism of action on the NMDA receptor-channel complex is suggested.
A preliminary investigation of conductive immiscible polymer blends as sensor materials (2000)

Abstract This paper discusses the feasibility of the application of conductive immiscible polymer blends as sensor materials for detection of organic liquid solvents. Immiscible polymer blends of polypropylene (PP), nylon 6 (Ny6) and carbon black (CB) have been used to produce a series of electrically conductive filaments by a capillary rheometer process. In these immiscible blends, PP serves as a semi‐crystalline matrix and Ny6 as the semi‐crystalline dispersed phase. The enhancement of conductivity in these blends is due to the attraction of CB to Ny6 and localization of CB particles at the PP/Ny6 interface, giving rise to conductive networks. The dc electrical resistivity of extruded filaments, produced at different shear levels, is found to be sensitive to various organic liquid solvents. The shear rate at which the filaments are produced has an important effect on the PP/Ny6/CB filament's sensitivity. The compositions studied were close to the double‐percolation structure believed to perform best as sensor materials. In addition, it seems that the PP/Ny6 interface plays a major role in the sensing process. Liquid contact/drying cycling of the filaments indicates stabilization of the sensitivity change making the sensing process reversible.
Adenosine Stimulates Human Sperm Motility via A2 Receptors (1993)

The effects of adenosine and its analogues on human sperm motility were studied using a transmembrane migration method. Specific binding sites for adenosine in human sperm were also investigated. Adenosine and 5'-N-ethylcarboxamidoadenosine (NECA) stimulated human sperm motility with similar efficacies and the maximal amplitudes of motility increases were both about 70%. 3,7-Dimethyl-1-propargylxanthine (DMPX), a potent A2 antagonist, competitively antagonized NECA-induced motility stimulation. Successively higher concentrations of DMPX shifted the dose-response curve of NECA to the right in a nearly parallel fashion. Dipyridamole, an inhibitor of adenosine uptake, does not reduce the ability of adenosine to stimulate human sperm motility. In radioligand-binding studies, adenosine A1 selective analogues, cyclopentyl-1,3-dipropylxanthine and 1-methyl-2-phenylethyl adenosine, have little competitive effect on [3H]NECA binding in human sperm membrane. These results provide evidence that adenosine enhances human sperm motility via adenosine A2 receptors on the surface of sperm membranes.
A Phenome-Based Functional Analysis of Transcription Factors in the Cereal Head Blight Fungus, Fusarium graminearum (2011)

Fusarium graminearum is an important plant pathogen that causes head blight of major cereal crops. The fungus produces mycotoxins that are harmful to animal and human. In this study, a systematic analysis of 17 phenotypes of the mutants in 657 Fusarium graminearum genes encoding putative transcription factors (TFs) resulted in a database of over 11,000 phenotypes (phenome). This database provides comprehensive insights into how this cereal pathogen of global significance regulates traits important for growth, development, stress response, pathogenesis, and toxin production and how transcriptional regulations of these traits are interconnected. In-depth analysis of TFs involved in sexual development revealed that mutations causing defects in perithecia development frequently affect multiple other phenotypes, and the TFs associated with sexual development tend to be highly conserved in the fungal kingdom. Besides providing many new insights into understanding the function of F. graminearum TFs, this mutant library and phenome will be a valuable resource for characterizing the gene expression network in this fungus and serve as a reference for studying how different fungi have evolved to control various cellular processes at the transcriptional level.
PHYTOTHERAPY PHARMACOPHORES FOR MAJOR CELLULAR DRUG TARGETS (2015)

This chapter examines the use of computational determination of pharmacophores to illustrate and predict interactions of active constituents of phytotherapies with novel drug targets. Pharmacophore models have been generated and manipulated to restrict findings to target compounds with specific properties, such as chemical structure in the case of some morphinan-based AChE inhibitors, or activity for new anticonvulsant medications. The use of multiple pharmacophore models in parallel screening has been shown to be advantageous for in silico high throughput screening for targets with numerous binding conformations or for compounds that potentially target multiple targets. As a simple yet valuable tool, there are many opportunities for which pharmacophore modeling can be utilized in the search for lead active compounds in the drug discovery process. For this reason, a variety of case studies are presented in the chapter as potential phytotherapies for the treatment of disease.
Methods for the stereoselective cis-cyanohydroxylation and -carboxyhydroxylation of olefins (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMethods for the stereoselective cis-cyanohydroxylation and -carboxyhydroxylation of olefinsAlan P. Kozikowski and Maciej AdamczCite this: J. Org. Chem. 1983, 48, 3, 366–372Publication Date (Print):February 1, 1983Publication History Published online1 May 2002Published inissue 1 February 1983https://pubs.acs.org/doi/10.1021/jo00151a017https://doi.org/10.1021/jo00151a017research-articleACS PublicationsRequest reuse permissionsArticle Views1850Altmetric-Citations158LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Genome-wide annotation and functional identification of aphid GLUT-like sugar transporters (2014)

The gut enhanced expression of ApST4, and the transport specificity of its product is consistent with ApST4 functioning as a gut glucose/fructose transporter. Here, we hypothesize that both ApST3 (reported previously) and ApST4 (reported here) function at the gut interface to import glucose and fructose from the gut lumen.
Evolution of UMTS toward high-speed downlink packet access (2003)

An expanded effort is under way to support the evolution of the Universal Mobile Telecommunications System (UMTS) standard to meet the rapidly developing needs associated with wireless data applications. A new, shared channel — the high-speed downlink shared channel (HS-DSCH) — provides support to packet-switched high-speed data users. A number of performance-enhancing technologies are included in the high-speed downlink packet access (HSDPA) system to ensure high peak and average packet data rates while supporting circuit-switched voice and packet data on the same carrier. Lucent Technologies took a pivotal role in specifying many of these techniques, including adaptive modulation and coding (AMC), hybrid automatic repeat request (HARQ), and fat-pipe scheduling. In this paper, we provide system-level simulations results to indicate the achievable performance and capacity with these advanced technologies. We also discuss HSDPA protocol architecture along with the uplink and downlink control channel design and performance. We conclude with a discussion of potential enhancements for the future.
NEW EVALUATION METHOD OF PS-ANCHOR FORCE BY USING MAGNETIC SENSOR AND ITS APPLICATION IN A LARGE UNDERGROUND POWERHOUSE CAVERN (2008)

大規模地下空洞の維持管理には施設全体の総合的評価が必要とされる．本研究では，空洞周辺岩盤の健全性を評価する際に検討する項目として，PSアンカーの軸力に着目した．導入力を固定するためにナットが用いられている場合，磁歪法を用いてその表面に存在する応力を計測し，間接的にアンカー軸力を推定することができる．まず，室内試験によりナットの残留応力を計測し，それが十分に小さいことを確かめた．次に，軸力を作用させた状態でのナット表面の応力を計測し，両者の関係を調べた．この関係を用いて，実際の地下発電所空洞で計測したPSアンカーナットの応力からその軸力を推定し，それを検証した．その結果，磁歪法から推定した軸力は十分な精度を有していることが分かり，今後の大規模地下空洞の健全性評価を合理化できる可能性を確認できた．
(Methoxymethylidene)dimethylazanium tetraphenylborate acetonitrile monosolvate (2014)

In the cation of the title salt, C4H10NO(+)·C24H20B(-)·C2H3N, the C-N bond lengths are 1.2864 (16), 1.4651 (17) and 1.4686 (16) Å, indicating double- and single-bond character, respectively. The C-O bond length of 1.2978 (15) Å shows double-bond character, pointing towards charge delocalization within the NCO plane of the iminium ion. C-H⋯π inter-actions are present between the methine H atom and two of the phenyl rings of the tetra-phenyl-borate ion. The latter forms an aromatic pocket in which the cation is embedded. The iminium ion is further connected through a C-H⋯N hydrogen bond to the aceto-nitrile mol-ecule. This leads to the formation of a two-dimensional supramolecular pattern along the bc plane.
Multiobjective Optimization Paradigm for Toroidal Inductors With Spatially Tuned Permeability (2020)

Spatially tuning core permeability of an electromagnetic device enables superior performance. A permeability profile can be heuristically selected to improve the flux distribution in a device with a given geometry, but in order to fully leverage the capacity of spatial dependent permeability engineering, the geometry and the permeability should be optimized simultaneously. The work in this article herein presented sets forth a multiphysics design optimization paradigm that includes the permeability profile tuning in the context of both inductor and converter design. This approach enables the determination of Pareto optimal fronts consisting of a set of optimal solutions against competing objectives (e.g., mass and loss) under imposed constraints. To this end, computationally efficient analytical solutions of the heat transfer and electromagnetic formulations are derived for toroidal inductors, which are validated with finite-element analysis-based simulations. The software implemented in MATLAB 2018b is available online as an attachment to this article.
Determining Design Wind Loads for Work Zone Traffic-Control Devices (2004)

Proper traffic control and delineation are critical to achieving safety in work zones. In addition to being crashworthy, a barricade or temporary sign support should have the ability to withstand anticipated service loads. If a barricade or temporary sign support fails or overturns, it cannot perform its intended function and the safety of the work zone may be compromised. Currently, no guidance is provided on the service loads that should be used in the design of these work zone devices. Recommendations are provided for design wind loads for work zone traffic-control devices. The results from field trials indicate that truck-induced wind loading is not a critical design issue for barricades and barricades with signs. The recommendations are thus based on an analytical determination of design wind speeds associated with different recurrence intervals that correspond to the duration of work zone activities. Analytical case studies are presented for two common barricade designs, with consideration given to both structural capacity and overturn. Guidance on the amount of ballast required to prevent overturn is provided as a function of wind speed, barricade length, and sign mounting height.
Pharmacological properties of the PI3 kinase (PI3K) inhibitors PI-540 and PI-620 (2008)

AACR Annual Meeting-- Apr 12-16, 2008; San Diego, CA

LB-149 

The PI3K pathway is highly deregulated in cancer and has been the focus of much drug discovery effort in the last decade. We have previously reported the pyridofuropyrimidine PI-103 as a potent inhibitor of p110α, p110β and p110δ(1). PI-103 inhibits cancer cell proliferation consistent with pathway modulation but has pharmaceutical limitations such as poor solubility and significant metabolism in liver microsomal incubations. Here we report the improved pharmacological properties of the thienopyrimidine PI3K inhibitors. PI-540 and PI-620 that show a similar in vitro profile to that of PI-103. Submicromolar efficacy was observed in U87MG glioblastoma cells, PC3 prostate carcinoma, Detroit 562 squamous cell carcinoma , IGROV-1 ovarian carcinoma and human endothelial cells (HUVEC). In the human glioblastoma U87MG, all 3 compounds showed similar pathway modulation in the multiplexed electroluminescent immunoassay (Mesoscale Discovery; see Table). PI-540 and PI-620 showed improved solubility (>100μM) when compared with PI-103 ( 30 for PI-540 and PI-620; compared to 1 for PI-103. PI-540 and PI-620 showed significant antitumour efficacy in the U87MG glioblastoma and SKOV3 ovarian carcinoma xenograft models with T/C of 66 and 60 for PI-540 at 100mg/kg uid and PI-620 at 25mg/kg bid respectively. In addition to growth inhibition in vitro and in vivo, a significant antiangiogenic effect was observed. This series of PI3K inhibitors shows considerable potential for cancer treatment. This work was funded by Cancer Research UK and by Piramed Ltd. 1. Raynaud et al., Cancer Research 67;12:5840, 2007.

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E-cadherin regulates MAL-SRF-mediated transcription in epithelial cells (2010)

Epithelial junctions are dynamically and functionally linked to the actin cytoskeleton, and their disassembly is a key event during physiological and pathological processes. We recently showed that epithelial disintegration facilitates transcriptional activation via Rac, G-actin, MAL (also known as MRTF) and serum response factor (SRF). Here, we investigate which specific component of the epithelial junction is essential for this MAL-SRF-mediated transcription. The Ca(2+)-dependent dissociation of polarised epithelial cells depleted of ZO proteins - which form adherens junctions (AJs) but completely lack tight junctions (TJs) - fully activated SRF. By contrast, AGS gastric adenocarcinoma epithelial cells, which form TJs but are deficient in E-cadherin, and therefore also in AJs, failed to activate SRF. The introduction of wild-type E-cadherin in AGS cells restored AJ formation and MAL-SRF inducibility. To gain further insight into the membrane-proximal signalling, AGS cells were stably transfected with E-cadherin-alpha-catenin fusions. Despite restored formation of cell-cell contacts containing the nectin-afadin complex and p120-catenin, these cells did not activate SRF upon junction dissociation, suggesting that signal transmission depends on the C-terminal tail of E-cadherin. We conclude that the dissociation of intercellular E-cadherin interactions from AJs, and signals originating from the C-terminal region covering the beta-catenin-binding site of E-cadherin, are essential for transcriptional activation via Rac, MAL and SRF, whereas TJs are not involved.
Modeling of unbalanced multiphase buck converters with applications to voltage regulator module control (2005)

Multiple parallel-input parallel-output low-output voltage converters serve high-current high-slew rate loads, often using current mode control to achieve tight output voltage regulation. One way to enhance slew rate performance is to combine unbalanced phases: a low inductance converter in parallel with one or more conventional phases can deliver fast slews without altering low-frequency performance. An unbalanced combination is facilitated by combining conventional current-mode controls with sensorless current mode (SCM) controls; The dynamic properties resulting from using equal and unequal filter inductances for parallel converters are investigated for a 12 V to 1.5 V 100 A VRM.