gebhart/patrepeval huggingface dataset:
Simulation Analysis of Conduction Block in Myelinated Axons Induced by High-Frequency Biphasic Rectangular Pulses (2006)

Nerve conduction block induced by high-frequency biphasic rectangular pulses was analyzed using a lumped circuit model of the myelinated axon based on Frankenhaeuser-Huxley (FH) equations. At the temperature of 37 degrees C, axons of different diameters (2-20 microm) can be blocked completely at supra-threshold intensities when the stimulation frequency is above 10 kHz. However, at stimulation frequencies between 6 kHz and 9 kHz, both nerve block and repetitive firing of action potentials can be observed at different stimulation intensities. When the stimulation frequency is below 6 kHz, nerve block does not occur regardless of stimulation intensity. Larger diameter axons have a lower threshold intensity to induce conduction block. When temperature is reduced from 37 degrees C to 20 degrees C, the lowest frequency to completely block large axons (diameters 10-20 microm) decreased from 8 kHz to 4 kHz. This simulation study can guide future animal experiments as well as optimize stimulation waveforms for electrical nerve block in clinical applications.
Nonreductive Enantioselective Ring Opening of <i>N</i>‐(Methylsulfonyl)dicarboximides with Diisopropoxytitanium α,α,α′,α′‐Tetraaryl‐1,3‐dioxolane‐4,5‐dimethanolate (1996)

Abstract The bicyclic and tricyclic meso‐N ‐(methylsulfonyl)dicarboximides 1a–f are converted enantioselectively to isopropyl [(sulfonamido)carbonyl]‐carboxylates 2a–f by diisopropoxytitanium TADDOLate (75–92% yield; see Scheme 3 ). The enantiomer ratios of the products are between 86:14 and 97:3, and recrystallization from CH 2 Cl 2 /hexane leads to enantiomerically pure sulfonamido esters 2 ( Scheme 3 ). The enantioselectivity shows a linear relationship with the enantiomer excess of the TADDOL employed ( Fig.3 ). Reduction of the ester and carboxamide groups (LiAlH 4 ) and additional reductive cleavage of the sulfonamido group ( Red‐Al ) in the products 2 of imide‐ring opening gives hydroxy‐sulfonamides 3 and amino alcohols 4 , respectively ( Scheme 4 ). The absolute configuration of the sulfonamido esters 2 is determined by chemical correlation (with 2a,b ; Scheme 6 ), by the X‐ray analysis of the camphanate of 3e ( Fig. 1 ), and by comparative 19 F‐NMR analysis of the Mosher esters of the hydroxy‐sulfonamides 3 ( Table 1 ). A general proposal for the assignment of the absolute configuration of primary alcohols and amines of Formula HXCH 2 CHR 1 R 2 , X = O, NH, is suggested (see 11 in Table 1 ). It follows from the assignment of configuration of 2 that the Re carbonyl group of the original imide 1 is converted to an isopropyl ester group. This result is compatible with a rule previously put forward for the stereochemical course of reactions involving titanium TADDOLate activated chelating electrophiles ( 12 in Scheme 7 ). A tentative mechanistic model is proposed ( 13 and 14 in Scheme 7 ).
The challenge of selecting protein kinase assays for lead discovery optimization (2008)

BACKGROUND: Protein kinases represent one of the most promising groups of drug targets owing to their involvement in such pathological conditions as cancer, inflammatory diseases, neural disorders, and metabolism problems. In the last few years, numerous pharmaceutical and biotech companies have established kinase high-throughput screening (HTS) programs, and the reagent and service industries for kinase assay platforms, kits, and profiling services have begun to thrive. OBJECTIVE: The plethora of different assay formats available today poses a great challenge to scientists who want to select a technology that will be cost efficient, convenient to use, and have low false positive and false negative rates. METHODS: In the current review, we summarize the most commonly used kinase assay methods in the drug discovery process, present the advantages and disadvantages of each of these methods, and discuss the challenges of discovering kinase inhibitors by using these technologies. CONCLUSIONS: The decision of selecting the assay formats for HTS or service platform for profiling should take into account not only the final goals of the screens but also the limitation of resources.
Interference of globin genes with biomarker discovery for allograft rejection in peripheral blood samples (2007)

Microarray technology is a powerful tool in the discovery of new biomarkers for disease. After solid organ transplantation, where the detection of rejection is usually made on invasive biopsies, it could be hypothesized that noninvasive transcriptional profiling of peripheral blood will reveal rejection-specific expression patterns from circulating immune cells. However, in kidney transplant rejection, the analysis of gene expression data in whole blood has proven difficult for detecting significant genes specific for acute graft rejection. Previous studies have demonstrated that the abundance of globin genes in whole blood may mask the underlying biological differences between whole blood samples. In the present study, we compared the gene expression profiles of peripheral blood of nine stable renal allograft recipients with seven matched patients having an ongoing acute renal transplant rejection, using four different protocols of preparation, amplification, and synthesis of cRNA or cDNA and hybridization on the Affymetrix platform. We demonstrated that the globin reduction method is not sufficient to unmask clinically relevant rejection-specific transcriptome profiles in whole blood. Applying an additional mathematical depletion of the globin genes improves the efficacy of globin reduction but cannot remove the confounding influence of globin gene hybridization. Sampling of peripheral blood leukocytes alone, without the confounding influence of globin mRNA, provides sensitive and specific peripheral signatures for graft rejection, with many of these signals overlapping with rejection-driven tissue (kidney)-specific signatures from matched biopsies. Similar applications may exist for array-based biomarker discovery for other diseases associated with changes in leukocyte trafficking, activation, or function.
Synthesis of some steroidal esters of .alpha.-amino acids (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of some steroidal esters of .alpha.-amino acidsLucas Lapatsanis, Christos Profilis, and Panayotis CatsoulacosCite this: J. Chem. Eng. Data 1980, 25, 3, 287–289Publication Date (Print):July 1, 1980Publication History Published online1 May 2002Published inissue 1 July 1980https://pubs.acs.org/doi/10.1021/je60086a037https://doi.org/10.1021/je60086a037research-articleACS PublicationsRequest reuse permissionsArticle Views84Altmetric-Citations9LEARN 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
ADAMTS-5: The story so far (2008)

The recent discovery of ADAMTS-5 as the major aggrecanase in mouse cartilage came as a surprise. A great deal of research had focused on ADAMTS-4 and much less was known about the regulation, expression and activity of ADAMTS-5. Two years on, it is still not clear whether ADAMTS-4 or ADAMTS-5 is the major aggrecanase in human cartilage. On the one hand there are in vitro studies using siRNA, neutralising antibodies and immunoprecipitation with anti-ADAMTS antibodies that suggest a significant role for ADAMTS-4 in aggrecanolysis. On the other hand, ADAMTS-5 (but not ADAMTS-4)-deficient mice are protected from cartilage erosion in models of experimental arthritis, and recombinant human ADAMTS-5 is substantially more active than ADAMTS-4. The activity of both enzymes is modulated by C-terminal processing, which occurs naturally in vivo. The most interesting finding to emerge from our comparison of ADAMTS-5 and ADAMTS-4 is that in terms of gene regulation, these two enzymes are the antitheses of each other. In most cases, ADAMTS-5 is constitutively expressed in human chondrocytes and synovial fibroblasts, whereas ADAMTS-4 expression is induced by proinflammatory cytokines. This paper reviews the data on ADAMTS-5 so far. It represents a snapshot in time of a field that is fast-moving and very exciting.
Single Crystal X-ray Diffraction Studies of Carbon Dioxide and Fuel-Related Gases Adsorbed on the Small Pore Scandium Terephthalate Metal Organic Framework, Sc<sub>2</sub>(O<sub>2</sub>CC<sub>6</sub>H<sub>4</sub>CO<sub>2</sub>)<sub>3</sub> (2009)

The adsorption behavior of the microporous scandium terephthalate Sc2(O2CC6H4CO2)3 for small fuel-related molecules has been measured. The structure shows an adsorption capacity for N2 and CO2 of 6.5 mmol g(-1) and is able to take up straight chain hydrocarbons. The mechanism of adsorption of CO2, CH4, and C2H6 has been determined by single crystal synchrotron X-ray diffraction at approximately 230 K. Adsorption of CO2 at 235 K and 1 bar pressure and H2 at 80 K and 0.25 bar results in each case in a symmetry change from orthorhombic Fddd to monoclinic C2/c through tilts in the terephthalate linkers. CO2 molecules take up different sites in the two symmetrically different channels that result from this symmetry change. The structure remains orthorhombic in 9 bar of CH4 and 5 bar of C2H6, and the adsorption sites are located. CH4 and C2H6 are observed to adopt sites within the channels, and C2H6 is also observed to adopt adsorption sites between phenyl groups in the channel walls, suggesting that the structure is sufficiently flexible to allow diffusion of small molecules between adjacent channels.
Unraveling the Gain Mechanism in High Performance Solution‐Processed PbS Infrared PIN Photodiodes (2015)

High gain and low dark current solution‐processed colloidal PbS quantum dots infrared (IR) PIN photodetectors with IR sensitivity up to 1500 nm are demonstrated. The low dark current is due to the P‐I‐N structure with both electron and hole blockers. The high gain in our IR photodiodes is due to the enhancement of electron tunneling injection through the 1,1‐bis[(di‐4‐tolylamino) phenyl]cyclohexane (TAPC) electron blocker under IR illumination resulting from a distorted electron blocking barrier in the presence of photo‐generated holes trapped in the TAPC electron blocker. It is further found that the trap states in the TAPC layer are generated by the Ag atoms penetrated in the TAPC layer during the thermal evaporation process. The resulting photodetectors have a high detectivity value of 7 × 10 13 Jones, which is even higher than that of a commercial InGaAs photodiode.
The emergence of networking abstractions and techniques in TinyOS (2004)

The constraints of sensor networks, an emerging area of network research, require new approaches in system design. We study the evolution of abstractions and techniques in TinyOS, a popular sensor network operating system. Examining CVS repositories of several research institutions that use TinyOS, we trace three areas of development: single-hop networking, multi-hop networking, and network services. We note common techniques and draw conclusions on the emerging abstractions as well as the novel constraints that have shaped them. 1.
Capping DNA with DNA (2000)

Twelve classes of deoxyribozymes that promote an ATP-dependent "self-capping" reaction were isolated by in vitro selection from a random-sequence pool of DNA. Each deoxyribozyme catalyzes the transfer of the AMP moiety of ATP to its 5'-terminal phosphate group, thereby forming a 5',5'-pyrophosphate linkage. An identical DNA adenylate structure is generated by the T4 DNA ligase during enzymatic DNA ligation. A 41-nucleotide class 1 deoxyribozyme requires Cu(2+) as a cofactor and adopts a structure that recognizes both the adenine and triphosphate moieties of ATP or dATP. The catalytic efficiency for this DNA, measured at 10(4) M(-1) x min(-1) using either ATP or dATP as substrate, is similar to other catalytic nucleic acids that use small substrates. Chemical probing and site-directed mutagenesis implicate the formation of guanine quartets as critical components of the active structure. The observation of ATP-dependent "self-charging" by DNA suggests that DNA could be made to perform the reactions typically associated with DNA cloning, but without the assistance of protein enzymes.
A Fully Automatic Deep Learning System for COVID-19 Diagnostic and Prognostic Analysis (2020)

Abstract Coronavirus disease 2019 (COVID-19) has spread globally, and medical resources become insufficient in many regions. Fast diagnosis of COVID-19, and finding high-risk patients with worse prognosis for early prevention and medical resources optimization is important. Here, we proposed a fully automatic deep learning system for COVID-19 diagnostic and prognostic analysis by routinely used computed tomography. We retrospectively collected 5372 patients with computed tomography images from 7 cities or provinces. Firstly, 4106 patients with computed tomography images and gene information were used to pre-train the DL system, making it learn lung features. Afterwards, 1266 patients (924 with COVID-19, and 471 had follow-up for 5+ days; 342 with other pneumonia) from 6 cities or provinces were enrolled to train and externally validate the performance of the deep learning system. In the 4 external validation sets, the deep learning system achieved good performance in identifying COVID-19 from other pneumonia (AUC=0.87 and 0.88) and viral pneumonia (AUC=0.86). Moreover, the deep learning system succeeded to stratify patients into high-risk and low-risk groups whose hospital-stay time have significant difference (p=0.013 and 0.014). Without human-assistance, the deep learning system automatically focused on abnormal areas that showed consistent characteristics with reported radiological findings. Deep learning provides a convenient tool for fast screening COVID-19 and finding potential high-risk patients, which may be helpful for medical resource optimization and early prevention before patients show severe symptoms. Take-home message Fully automatic deep learning system provides a convenient method for COVID-19 diagnostic and prognostic analysis, which can help COVID-19 screening and finding potential high-risk patients with worse prognosis.
A New Strategy for Neurochemical Photodelivery:  Metal−Ligand Heterolytic Cleavage (2003)

A new strategy to build caged-compounds is presented. The approach is based on heterolytic photocleavage of a metal-ligand bond in a coordination compound. A ruthenium polypyridine complex, containing the neurocompound 4-amino pyridine (4AP) is used as the core of the phototrigger. The biomolecule is released by irradiation with visible light (>480 nm). The liberated 4AP promotes the activation of a leech neuron by means of blocking its K+ channels. The syntesis, characterization, and the inherent advantages of this method are discussed.
Methods to reduce radiation from split ground plane structures [packaging] (2003)

Methods to reduce radiation from split-ground planes are examined using FDTD analysis. While differential lines and RF chokes to prove to be reasonable solutions, using a corrugated slot is shown to be the simplest and most effective measure.
1.25-Gb/s burst-mode receiver ICs with quick response for PON systems (2005)

This paper describes burst-mode receiver ICs with quick response for 1.25-Gb/s optical access networks. In a point-to-multipoint fiber access system, such as a passive optical network (PON) system, the receiver should be able to handle burst-data packets with different amplitudes. In burst-mode transmission, a receiver with a quick response is desired for high efficiency in data transmission. In addition, high sensitivity is also required for such a shared access system. To achieve a quick response and high sensitivity at the same time, a transimpedance amplifier (TIA) with three gain modes has been designed. The use of a hysteresis comparator enables fast gain mode switching. A limiting amplifier with feed-forward auto-offset compensation (AOC) is also used for quick response to burst data. These circuit techniques require no external adjustment. Using these design techniques, optical receiver ICs were fabricated in SiGe-BiCMOS technology. The optical receiver built with the ICs exhibits a settling time of under 20 bits and a sensitivity of -30 dBm with wide dynamic range of over 26 dB using a p-i-n photodiode (PD) for burst-mode optical input at 1.25 Gb/s. These fast-response receiver chips improve the data transmission efficiency. The use of a conventional p-i-n PD and the freedom from external adjustment make it possible to build an inexpensive receiver.
A Token-Based Access Control System for RDF Data in the Clouds (2010)

The Semantic Web is gaining immense popularity-and with it, the Resource Description Framework (RDF)broadly used to model Semantic Web content. However, access control on RDF stores used for single machines has been seldom discussed in the literature. One significant obstacle to using RDF stores defined for single machines is their scalability. Cloud computers, on the other hand, have proven useful for storing large RDF stores, but these system slack access control on RDF data to our knowledge. This work proposes a token-based access control system that is being implemented in Hadoop (an open source cloud computing framework). It defines six types of access levels and an enforcement strategy for the resulting access control policies. The enforcement strategy is implemented at three levels: Query Rewriting, Embedded Enforcement, and Post processing Enforcement. In Embedded Enforcement, policies are enforced during data selection using MapReduce, whereas in Post-processing Enforcement they are enforced during the presentation of data to users. Experiments show that Embedded Enforcement consistently outperforms Post processing Enforcement due to the reduced number of jobs required.
Consensus outlier detection in survival analysis using the rank product test (2018)

Abstract Survival analysis is a well known technique in the medical field. The identification of individuals whose survival time is too short or to long given their profile, assumes great importance for the detection of new prognostic factors. The study of these outlying observations have gained increasing relevancy with the availability of high-throughput molecular and clinical data for large cohorts of patients. Several methods for outlier detection in survival data have been proposed, which include the analysis of the residuals, the measurement of the concordance c-index, and methods based on quantile regression for censored data. However, different results are obtained depending on the type of method used. In order to solve the disparity of results we proposed to apply the Rank Product test. A simulated dataset, and two clinical datasets were used to illustrate our proposed consensus outlier detection method, one from myeloma disease and the other from The Cancer Genome Atlas (TCGA) ovarian cancer. Finally, the Rank Product with multiple testing corrections was performed in order to identify which observations have the highest rank amongst the methods considered. Our results illustrate the potential of this consensus approach for the automated retrieval of outliers and also the identification of biomarkers associated with survival in large datasets.
MHTP-a multimedia high-speed transport protocol (2003)

In considering transport layer protocols for multimedia applications in high-speed networks, several chacteristics of multimedia applications have to be considered. These characteristics include high-speed transmission capability, real-time constraints, and large bandwidth required by applications, and packet loss of some percentage is acceptable in some multimedia applications. A transport layer protocol for high-speed multimedia applications, namely MHTP (multimedia high-speed transport protocol), is proposed to resolve problems in interworking multimedia systems using high-speed networks.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Motility of Metal Nanoparticles in Silicon and Induced Anisotropic Silicon Etching (2008)

Abstract The autonomous motion behavior of metal particles in Si, and the consequential anisotropic etching of silicon and production of Si nanostructures, in particular, Si nanowire arrays in oxidizing hydrofluoric acid solution, has been systematically investigated. It is found that the autonomous motion of metal particles (Ag and Au) in Si is highly uniform, yet directional and preferential along the [100] crystallographic orientation of Si, rather than always being normal to the silicon surface. An electrokinetic model has been formulated, which, for the first time, satisfactorily explains the microscopic dynamic origin of motility of metal particles in Si. According to this model, the power generated in the bipolar electrochemical reaction at a metal particle's surface can be directly converted into mechanical work to propel the tunneling motion of metal particles in Si. The mechanism of pore and wire formation and their dependence on the crystal orientation are discussed. These models not only provide fundamental interpretation of metal‐induced formation of pits, porous silicon, and silicon nanowires and nanopores, they also reveal that metal particles in the metal/Si system could work as a self‐propelled nanomotor. Significantly, it provides a facile approach to produce various Si nanostructures, especially ordered Si nanowire arrays from Si wafers of desired properties.
Selective hydrogenation of 5-hydroxymethylfurfural to 2,5-bis-(hydroxymethyl)furan using Pt/MCM-41 in an aqueous medium: a simple approach (2014)

An effective method was developed to obtain a very high yield of BHMF (98%) <italic>via</italic> hydrogenation of HMF in water.
Design and Validation of a Laboratory System for Measurement of Volatilized Ammonia (2011)

The design of laboratory systems for studying ammonia (NH 3 ) released from fertilizers varies widely, and few designs have been tested to determine the accuracy and precision in measuring NH 3 loss. A standard volatilization system design is needed for reliable and comparable studies of NH 3 volatilization from N fertilizer. The objectives of this study are: (i) to describe the design of a system capable of controlling air flow rate and temperature for laboratory measurement of NH 3 volatilized from N fertilizers; and (ii) assess the system's efficiency and variation in recovering NH 3 lost from NH 4 Cl applied to an alkaline sand media. The system is comprised of individual chambers for soil and fertilizer, where temperature can be varied from room temperature to ∼32°C; humidity is maintained near saturation, air flow rate can be varied, and acid traps are used to capture volatilized NH 3 . Two initial trials (I and II) were conducted at an N rate of 90 kg N ha −1 using air flow rates of 2.00 and 1.00 L min −1 and trapping acid volumes of 50 and 100 mL, respectively. A third trial was conducted at 30°C. A fourth trial (IV) was performed using a range of N application rates (25–250 kg N ha −1 ). The system recovered 89.3 to 97.1% of the N applied over all four trials and provided accurate and repeatable results under the conditions tested. Rapid, precise comparisons of NH 3 volatilization losses from N fertilizers under laboratory conditions can be made with this system.