gebhart/patrepeval huggingface dataset:
Quality control for translational biomedical informatics (2009)

Translational biomedical informatics is the application of computational methods to facilitate the translation of basic biomedical science to clinical relevance. An example of this is the multi-step process in which large-scale microarray-based discovery experiments are refined into reliable clinical tests. Unfortunately, the quality of microarray data is a major issue that must be addressed before microarrays can reach their full potential as a clinical molecular profiling tool for personalized and predictive medicine. A new methodology, titled caCORRECT, has been developed to replace or augment existing microarray processing technologies, in order to improve the translation of microarray data to clinical relevance. Results of validation studies show that caCORRECT is able to improve the mean accuracy of microarray gene expression by as much as 60%, depending on the magnitude and size of artifacts on the array surface. As part of a case study to demonstrate the widespread usefulness of caCORRECT, the entire pipeline of biomarker discovery has been executed for the clinical problem of classifying Renal Cell Carcinoma (RCC) specimens into appropriate subtypes. As a result, we have discovered and validated a novel two-gene RT-PCR assay, which has the ability to diagnose between the Clear Cell and Oncocytoma RCC subtypes with near perfect accuracy. As an extension to this work, progress has been made towards a quantitative quantum dot immunohistochemical assay, which is expected to be more clinically viable than a PCR-based test.
Prevalence and spectrum of rheumatic diseases associated with proteinase 3‐antineutrophil cytoplasmic antibodies (ANCA) and myeloperoxidase‐ANCA (2001)

ANCA testing is useful due to its high sensitivity and specificity, especially for cANCA/PR3-ANCA in WG. We found a divergence in the disease spectrum between PR3- and MPO-ANCA-positive patients, characterized by higher DEI and extrarenal manifestations in the PR3-ANCA group. MPO-ANCA was rarely found in WG and was associated with less organ involvement.
Application of soil venting at a large scale: A data and modeling analysis (1990)

Soil venting will be applied at a demonstration scale to a site at the Idaho National Engineering Laboratory which is contaminated with carbon tetrachloride and other organic vapors. The application of soil venting at the site is unique in several aspects including scale, geology, and data collection. The containmented portion of the site has a surface area of over 47,000 square meters (12 acres) and the depth to the water table is approximately 180 meters. Migration of contaminants through the entire depth of the vadose zone is evidenced by measured levels of chlorinated solvents in the underlying aquifer. The geology of the site consists of a series of layered basalt flows interspersed with sedimentary interbeds. The depth of the vadose zone, the nature of fractured basalt flows, and the degree of contamination all tend to make drilling difficult and expensive. Because of the scale of the site, extent of contamination, and expense of drilling, a computer model has been developed to simulate the migration of the chlorinated solvents during plume growth and cleanup. The demonstration soil venting operation has been designed to collect pressure drop and plume migration data to assist with calibration of the transport model. The model will then be used to help design a cost-effective system for site cleanup which will minimize the drilling required. This paper discusses mathematical models which have been developed to estimate the growth and eventful cleanup of the site. 12 refs., 4 figs.
The Effect of Chlorine on PAH, Soot, and Tar Yields From a Jet Stirred/Plug Flow Reactor System (1992)

Abstract The effect of Cl on polycyclic aromatic hydrocarbon (PAH), soot, and tar yields from fuel rich combustion is studied using a jet-stirred reactor close-coupled with a plug flow reactor system (JSR/PFR). The JSR provides input to the PFR from the fuel rich (φJSR = 2.2) combustion of C2H4/O2/N2, and chlorine is introduced into this stream at the PFR inlet via addition of CH3Cl (φPFR = 2.3). This experimental condition is compared to second condition where C2H4 is added (φPFR = 2.3) to the PFR in lieu of CH3Cl. PAH yields are seen to increase under both conditions at early PFR residence limes, while coming to an equilibrium value, or even decreasing in concentration at the end of the PFR. However, the yield of cyclopenta(cd)pyrene, a major human and bacterial cell mutagen, is suppressed with Cl present by as much as 90% near the end of the PFR, while benzo(a)pyrene, a major human carcinogen, shows a decrease in yield of about 25%. Tar (defined as total CH2Cl2 soluble material) is split into a low molecular weight fraction (128 amu to 226 amu), and a high molecular weight fraction (greater than 226 amu). The low molecular weight fraction shows behavior similar to representative individual PAH from that fraction, whereas twice as much high molecular weight tar is produced in the CH3,Cl injection case. While soot production increases with time for both cases, accelerated soot growth occurred when CH3Cl was added. These data indicate an increase in the ability of soot to capture high molecular weight PAH when Cl is present. Key Words: PAHtarsootchlorineCH3Clmutagens.
Design of a ceramic dielectric resonator for NMR microimaging at 14.1 tesla (2008)

Abstract Radiofrequency coil design for magnetic resonance becomes increasingly challenging at high magnetic field strengths due to resonator dimensions being a significant fraction of the electromagnetic wavelength, as well as the increased radiative and component losses intrinsic to higher frequencies. In this article an inductively fed dual‐disk ceramic dielectric resonator was constructed from barium strontium titanate, which has a high relative permittivity of 323, for operation at 600 MHz (14.1 tesla). The design is very simple, avoids wavelength issues, uses high Q‐materials, and has the additional advantage of being able to change the resonator's effective diameter. Preliminary images show a significantly higher signal‐to‐noise than obtained using a similarly‐sized conventional saddle coil. © 2008 Wiley Periodicals, Inc. Concepts Magn Reson Part B (Magn Reson Engineering) 33B: 109–114, 2008
Fabrication of Flexible pH-Responsive Agarose/Succinoglycan Hydrogels for Controlled Drug Release (2021)

Agarose/succinoglycan hydrogels were prepared as pH-responsive drug delivery systems with significantly improved flexibility, thermostability, and porosity compared to agarose gels alone. Agarose/succinoglycan hydrogels were made using agarose and succinoglycan, a polysaccharide directly isolated from <i>Sinorhizobium meliloti</i>. Mechanical and physical properties of agarose/succinoglycan hydrogels were investigated using various instrumental methods such as rheological measurements, attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopic analysis, X-ray diffraction (XRD), and field-emission scanning electron microscopy (FE-SEM). The results showed that the agarose/succinoglycan hydrogels became flexible and stable network gels with an improved swelling pattern in basic solution compared to the hard and brittle agarose gel alone. In addition, these hydrogels showed a pH-responsive delivery of ciprofloxacin (CPFX), with a cumulative release of ~41% within 35 h at pH 1.2 and complete release at pH 7.4. Agarose/succinoglycan hydrogels also proved to be non-toxic as a result of the cell cytotoxicity test, suggesting that these hydrogels would be a potential natural biomaterial for biomedical applications such as various drug delivery system and cell culture scaffolds.
Valve‐Enabled Sample Preparation and RNA Amplification in a Coffee Mug for Zika Virus Detection (2018)

Abstract The recent outbreaks of Zika virus (ZIKV) infection represent a public health challenge. Rapid, cost‐effective, and reliable diagnostic tools for ZIKV detection at the point of care (POC) are highly desirable, especially for resource‐limited nations. To address the need, we have developed an integrated device to achieve sample‐to‐answer ZIKV detection. The device features innovative ball‐based valves enabling the storage and sequential delivery of reagents for virus lysis and a paper‐based unit for RNA enrichment and purification. The paper unit is placed in a commercially available coffee mug that provides a constant temperature for reverse transcription loop‐mediated isothermal amplification (RT‐LAMP), followed by colorimetric detection by naked eye or a cellphone camera. Using the device, we demonstrated the reproducible detection of ZIKV in human urine and saliva samples.
Simple recurrent networks as generalized hidden Markov models with distributed representations (2002)

Proposes simple recurrent neural networks as probabilistic models for representing and predicting time-sequences. The proposed model has the advantage of providing forecasts that consist of probability densities instead of single guesses of future values. It turns out that the model can be viewed as a generalized hidden Markov model with a distributed representation. The authors devise an efficient learning algorithm for estimating the parameters of the model using dynamic programming. The authors present some very preliminary simulation results to demonstrate the potential capabilities of the model. The present analysis provides a new probabilistic formulation of learning in simple recurrent networks.
Computation of Fresnel integral by Fractional Fourier Transform methods (2015)

Fractional Fourier Transform (FrFT) is the generalization of the ordinary Fourier Transform (FT) and a subclass of the Linear Canonical Transform (LCT). FrFT is used in many fields, where ordinary FT has already found applications, such as signal processing, optics, telecommunications, noise filtering, beamforming, and solution of differential equations.
Bone and mineral metabolism in the androgen-resistant (testicular feminized) male rat (1993)

Androgens have important effects on bone in vivo, possibly by direct activation of the androgen receptors in osteoblasts. To test this hypothesis, calcium homeostasis, bone mass, and bone turnover were evaluated in mature (4-month-old) androgen-resistant (testicular feminized, TFM) male rats. Data were compared with data from both female and male littermates of the same age and strain. Compared to normal males, TFM had similar serum testosterone, twofold higher estradiol and estrone, and sixfold higher androstenedione concentrations. Compared to normal females, TFM rats showed lower estradiol but also elevated concentrations of androstenedione and estrone. Despite similar free 1,25-(OH)2D3 concentrations, both TFM and male rats maintained higher serum calcium and phosphate concentrations than their female littermates. Serum IGF-I concentrations in TFM rats were decreased compared to male rats (-12%) or female rats (-27%). Serum osteocalcin concentrations, however, were twofold higher in TFM rats than in females but not significantly different from males. Femoral length, diameter, and cortical thickness were intermediate between those of males and females. The cancellous bone density of the femur and cancellous bone volume of the proximal metaphysis of the tibia, however, were not significantly different between groups. The ash weight of the tibia was also not significantly different, and the ash weight of the four distal lumbar vertebrae ranged between male and female values. Bone mechanical properties as measured by torsional strength and energy absorption of the femur were lower in TFM than in females but not different from males.(ABSTRACT TRUNCATED AT 250 WORDS)
Paenungulata: a comparison of the hemoglobin sequences from elephant, hyrax, and manatee. (1986)

Inspection of the amino acid differences among hemoglobin sequences of a wide range of mammalian species suggested that at alpha 19, alpha 110, alpha 111, beta 23, beta 44, and beta 56, synapomorphies group manatee (Trichechus inungius, Sirenia), Indian and African elephant (Elephas maximus and Loxodonta africana, Proboscidea), and rock hyrax (Procavia habessinica, Hyracoidea) into a monophyletic clade. Results obtained by parsimony analysis provide evidence for this grouping--and thus support for the genealogical validity of Simpson's superorder Paenungulata, which contains as the extant orders Proboscidea, Sirenia, and Hyracoidea. All of the 39 most, or nearly most, parsimonious of 10,395 trees constructed from a tandemly combined alpha- and beta-hemoglobin sequence for 103 vertebrate species (of which 79 were mammals from 16 extant orders), depicted Paenungulata as one of the most anciently separated branches of Eutheria. It was found on examining thousands of alternative trees that to not group Proboscidea, Hyracoidea, and Sirenia in a monophyletic clade required at least four additional substitutions.
Nutrient Intakes by Young Children in a Prospective Randomized Trial of a Low-Saturated Fat, Low-Cholesterol Diet (1997)

A recent article in theArchivesby investigators in the Department of Pediatrics at the University of Turku, Turku, Finland,<sup>1</sup>is the third in a series describing the results of the Special Turku Coronary Risk Factor Intervention Baby Project (STRIP) which investigated the results of feeding infants and children low-fat diets.<sup>1-3</sup>The rationale for this study seems to be the unproved assumption that significant atherosclerosis begins at birth and that dietary intervention in infancy will have a major effect on the risk of coronary heart disease in later life. Because the crucial event in clinically marked atherogenesis is the formation of the raised plaque, which does not begin until puberty in boys and much later in girls, the assumption underlying STRIP seems groundless. In fact the Pathobiological Determinants of Atherosclerosis in Youth Research Group<sup>4</sup>study, which documented arterial plaque development in male subjects 15 to 34 years
R2C2 (2015)

Rack-scale computers, comprising a large number of micro-servers connected by a direct-connect topology, are expected to replace servers as the building block in data centers. We focus on the problem of routing and congestion control across the rack's network, and find that high path diversity in rack topologies, in combination with workload diversity across it, means that traditional solutions are inadequate. We introduce R2C2, a network stack for rack-scale computers that provides flexible and efficient routing and congestion control. R2C2 leverages the fact that the scale of rack topologies allows for low-overhead broadcasting to ensure that all nodes in the rack are aware of all network flows. We thus achieve rate-based congestion control without any probing; each node independently determines the sending rate for its flows while respecting the provider's allocation policies. For routing, nodes dynamically choose the routing protocol for each flow in order to maximize overall utility. Through a prototype deployed across a rack emulation platform and a packet-level simulator, we show that R2C2 achieves very low queuing and high throughput for diverse and bursty workloads, and that routing flexibility can provide significant throughput gains.
One-Pot Synthesis of 2,5-Disubstituted Oxazoles (2007)

Reported is a concise one-pot three-step amidation, Pd-catalyzed acylation, and cycloisomerization procedure for the synthesis of 1-(hetero)aryl-2-[2-(hetero)aryloxazol-5-yl] ethanones from propargyl amine and acid chlorides in moderate to good overall yields. Anhydrides may be used as replacements of acid chlorides in the first step allowing access to 2-trifluoromethyl derivatives; carbonylative Sonogashira coupling can be used equally well in the second step. The structures have been confirmed by X-ray crystal structure analysis of one of the products.
In Vitro Bacterial Interference in the Nasopharynx of Otitis Media–Prone and Non–Otitis Media–Prone Children (2000)

The nasopharyngeal flora of N-OMP children contains more aerobic and anaerobic organisms with interfering capability and less potential pathogens than that of OMP children.
Misalignment Resilient, Near Field Wireless Power Transfer (WPT) Antennas using Anchor Shape (2019)

In this paper, a near-field coupled resonator antenna element is presented for power transfer applications. We propose an anchor shaped geometry that represents a combination of electric dipole and magnetic loop to realize stronger coupling over misaligned distances between the source and receiver antenna. The resonator was prototyped on textile substrate for wearable applications. A full-wave simulation of the power transfer efficiency is presented and compared with single-loop of the same size. The lateral misalignments are studied, and it is demonstrated that anchor-shaped resonators offer 80-90 % power transfer efficiency for misalignments as large as 70% of antenna lateral size. Simulation studies and measurement results are presented.
Clinical Utilization of Injectable Collagen (1983)

The applications for an injectable, highly purified form of calfhide collagen (Zyderm Collagen Implant) were first described by Knapp et al in 1977. Since that time, the material has undergone evaluation in a nationwide clinical trial in which 728 physicians participated under a cooperative protocol. In these trials--which culminated in marketing clearance by the Food and Drug Administration--over 5,000 patients were treated for a variety of soft-tissue depressions resulting from surgery, atrophy, acne, viral pox, and aging. We participated in the clinical trial and have used injectable collagen in our practices since 1977 when the material was undergoing evaluation in California. We have treated over 400 patients with injectable collagen for a variety of facial cutaneous defects. The material has proved to be an effective tool for correction of certain soft-tissue defects not previously amenable to correction, and a useful surgical adjunct. Simplicity and safety are its major advantages. The persistence of correction afforded by injectable collagen is variable, but the majority of our patients have maintained improvement twelve or more months since the end of treatment. Hence we believe that there is a definite role for injectable collagen but that its long-term persistence must still be confirmed. This paper represents our state-of-the-art assessment of injectable collagen after six years of personal experience.
An 11.2-Gb/s LVDS Receiver With a Wide Input Range Comparator (2014)

Cameras and image sensors have recently been installed in many portable devices. An image processor and a transceiver are also adopted in multimedia system-on-a-chip to handle the data from the image sensor. A wide input range and flexible data bandwidth are needed for the serial link receiver to deal with various sensor specifications. This paper presents an 11.2-Gb/s low-voltage differential signaling (LVDS) receiver for various portable devices that employ a LVDS system for data transmission between an image sensor and a processor. The designed LVDS receiver has 16 data channels and four clock channels. All the channels are selectively turned on or off, depending on the application. The proposed comparator used for the input driver of the receiver has a rail-to-rail input range and 60 mV of minimum input swing level. The clock dividing ratio and the data de-serializing factor of the proposed receiver are also programmable to deal with various color depths of image sensors. The designed LVDS receiver is fabricated in a 0.13-μm CMOS process, occupying 4-4 mm, with a 7.24-mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> core. Power consumption is 77.38 mW, when every channel is turned on.
ChemInform Abstract: A KINETIC AND MECHANISTIC STUDY OF THE FORMATION OF SULFINATO IRIDIUM(III) COMPLEXES BY OXIDATIVE ADDITION REACTIONS (1978)

Abstract Die Geschwindigkeiten der Reaktion . 2. Ordnung der trans‐Komplexe (I) mit den Sulfonylchloriden (II) "in Benzol wurden bestimmt.
The Reaction of 1-Alkynes with Organometallic Compounds. II. The Relationship between Decomposition Potentials of Grignard Reagents and Their Relative Reactivity Towards Terminal Acetylens (1955)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Reaction of 1-Alkynes with Organometallic Compounds. II. The Relationship between Decomposition Potentials of Grignard Reagents and Their Relative Reactivity Towards Terminal AcetylensRaymond E. Dessy, C.A. Hollingsworth, and John H. WotizCite this: J. Am. Chem. Soc. 1955, 77, 16, 4410Publication Date (Print):August 1, 1955Publication History Published online1 May 2002Published inissue 1 August 1955https://doi.org/10.1021/ja01621a068RIGHTS & PERMISSIONSArticle Views70Altmetric-Citations3LEARN 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 InReddit PDF (148 KB) Get e-Alerts Get e-Alerts
Molecular Basis of Substrate Recognition in D‐3‐Hydroxybutyrate Dehydrogenase from Pseudomonas putida (2006)

D-3-Hydroxybutyrate dehydrogenase from Pseudomonas putida (EC 1.1.1.30) belongs to the family of short-chain dehydrogenases/reductases (SDRs). It catalyzes the reversible and stereospecific oxidation of D-3-hydroxybutyrate (D-3-HB) to acetoacetate with the aid of NAD(+) as coenzyme. This study contributes to understanding the mechanism and the high specificity of this enzyme towards its negatively charged and hydrophilic substrate. Sequence comparison of 44 bacterial HBDHs shows the residues Gln91, His141, Lys149, Lys192, and Gln193 to be strictly conserved. Site-directed mutagenesis of these amino acids to alanine and subsequent kinetic characterization of the mutated enzymes provides insight into the importance of these residues for substrate recognition and catalysis. Docking studies and molecular-dynamics simulations based on a three-dimensional structure model of a complex between P. putida HBDH and its coenzyme obtained by comparative molecular modeling were performed and provided deeper insight into the binding of the ligands at the molecular level. They show the residues Gln91, His141, Gln193, and, in particular, Lys149 to be involved in a hydrogen-bonding network with the carboxylate group of the substrate.
Computational modelling of human induced pluripotent stem cell derived cardiomyocytes (2012)

Human induced pluripotent stem cell cardiomyocytes (hiPSC-CMs) offer a new in vitro model to study cardiac cell properties and develop and test drugs. Anyway tThe high times and costs of the induction and differentiation process make interesting the use of in silico models to understand the hiPS-CM electrophysiology and response to pharmacological tools. We developed a hiPSC-CM action potential (AP) model, based on a variety of published experimental data, reproducing the main features of ventricular-like hiPSC-CMs: spontaneous firing activity, AP morphology and response to common current blockers.