gebhart/patrepeval huggingface dataset:
Cloud-MAQ: The cloud-enabled scalable whole genome reference Assembly application (2010)

Biology problems are in general NP-hard that demands tremendous resource both in terms of time and computing resources. Most of the computing systems developed for quantifying biological objects suffer from such limitations. MAQ (Mapping and Assembly with Quality) is one such popular bioinformatics system developed for whole genome reference assembly - it is designed to handle the challenges related to short sequence reads generated by Illumina sequencing machines, and can support a maximum read length of 63 nucleotides. MAQ is not multithreaded or many core ready - it runs on single CPU and does not scale. Therefore, as the data size increases, it fails to scale efficiently and requires a supercomputer to perform the assembly within a desired time. In this paper we report Cloud-MAQ that uses the cloud computing paradigm to address the NP-hard related challenges of whole genome reference assembly. Through Hadoop and the cloud paradigm MAQ is made parallel and scalable. Also, MAQ functionality has been enhanced to support recent reads from Illumina that are of 76 nucleotides. This cloud-enabled Cloud-MAQ increases the performance of MAQ reference assembly multi-fold.
From Martí to Walsh: voices of children's poetry in Latin America (1995)

The results suggest that eye diseases, especially glaucoma, restrain the mobility of older people in many different ways. It is important to further explore the impact of eye disease on mobility in this population, to develop interventions that could help affected older adults maintain their independence.
<title>New telescope concept for space communication</title> (1990)

The design concept of an optical transmit-receive antenna telescope developed in the framework of the ESA SILEX program is presented. SILEX involves optical communication between satellites in GEO, using semiconductor laser diodes operating at 825 nm as the light source. The telescope requirements include entrance diameter 250 mm, exit pupil 8 mm, acquisition FOV 8500 microrad, communication FOV 2000 microrad, angular magnification -31.25, retroreflection 3 microW/sq m nm or less, stray light 1.05 microW/sq m nm or less, and alignment stability 10 years with no refocusing in orbit. The present compact two-mirror configuration employs the glass-ceramic Zerodur for all of the major components (primary mirror/baseplate, secondary mirror, tube, front ring, and ocular) for a total mass of only 5760 g. The prototype manufacturing process gave surface errors of 25 nm rms-WF for the primary and 15 nm rms-WF for the secondary.
The Non-phagocytic Route of Collagen Uptake (2011)

The degradation of collagens, the most abundant proteins of the extracellular matrix, is involved in numerous physiological and pathological conditions including cancer invasion. An important turnover pathway involves cellular internalization and degradation of large, soluble collagen fragments, generated by initial cleavage of the insoluble collagen fibers. We have previously observed that in primary mouse fibroblasts, this endocytosis of collagen fragments is dependent on the receptor urokinase plasminogen activator receptor-associated protein (uPARAP)/Endo180. Others have identified additional mechanisms of collagen uptake, with different associated receptors, in other cell types. These receptors include β1-integrins, being responsible for collagen phagocytosis, and the mannose receptor. We have now utilized a newly developed monoclonal antibody against uPARAP/Endo180, which down-regulates the receptor protein level on treated cells, to examine the role of uPARAP/Endo180 as a mediator of collagen internalization by a wide range of cultured cell types. With the exception of macrophages, all cells that proved capable of efficient collagen internalization were of mesenchymal origin and all of these utilized uPARAP/Endo180 for their collagen uptake process. Macrophages internalized collagen in a process mediated by the mannose receptor, a protein belonging to the same protein family as uPARAP/Endo180. β1-Integrins were found not to be involved in the endocytosis of soluble collagen, irrespectively of whether this was mediated by uPARAP/Endo180 or the mannose receptor. This further distinguishes these pathways from the phagocytic uptake of particulate collagen.
Structure and properties of oblique-deposited magnetic thin films (1987)

Structural characterizations of angle-of-incidence CoNi films using electron microscopy are reported. Both fixed-angle-of-incidence and continuous-variation-of-incidence films are included. The tangent rule is found to be valid at high oblique angle. The easy axis as measured from the torque curve and angular variation of coercivity in a 170-nm film deposited at 75° is about 15° inclined to the film plane, whereas the columnar axis is about 30°. A weak c-axis texture exists as revealed by the electron diffraction study. The c-axis texture in the continuous-variation-of-incidence films with and without oxygen is not detected by electron diffraction.
p<i>‐Hydroxyphenylacetate decarboxylase from </i>Clostridium difficile (2001)

The human pathogenic bacterium Clostridium difficile is a versatile organism concerning its ability to ferment amino acids. The formation of p-cresol as the main fermentation product of tyrosine by C. difficile is unique among clostridial species. The enzyme responsible for p-cresol formation is p-hydroxyphenylacetate decarboxylase. The enzyme was purified from C. difficile strain DMSZ 1296(T) and initially characterized. The N-terminal amino-acid sequence was 100% identical to an open reading frame in the unfinished genome of C. difficile strain 630. The ORF encoded a protein of the same size as the purified decarboxylase and was very similar to pyruvate formate-lyase-like proteins from Escherichia coli and Archaeoglobus fulgidus. The enzyme decarboxylated p-hydroxyphenylacetate (K(m) = 2.8 mM) and 3,4-dihydroxyphenylacetate (K(m) = 0.5 mM). It was competitively inhibited by the substrate analogues p-hydroxyphenylacetylamide and p-hydroxymandelate with K(i) values of 0.7 mM and 0.48 mM, respectively. The protein was readily and irreversibly inactivated by molecular oxygen. Although the purified enzyme was active in the presence of sodium sulfide, there are some indications for an as yet unidentified low molecular mass cofactor that is required for catalytic activity in vivo. Based on the identification of p-hydroxyphenylacetate decarboxylase as a novel glycyl radical enzyme and the substrate specificity of the enzyme, a catalytic mechanism involving ketyl radicals as intermediates is proposed.
IN VITRO STUDY OF UREASE/AlaDH ENZYME SYSTEM ENCAPSULATED INTO HUMAN ERYTHROCYTES AND RESEARCH INTO ITS MEDICAL APPLICATIONS (2002)

In our system, urease/AlaDH have been encapsulated within erythrocytes by using slow dialysis methods. Urea is decomposed into ammonia and bicarbonate and the ammonia released is converted into alanine by reacting pyruvate under the catalytic action of AlaDH. It is very important for our that products are formed quickly but the ammonia is not connected definetely. For this aim, urease/AlaDH we encapsulated using different enzyme activity ratio (0.5:1.5; 0.5:2.5; 0.25:1.25 U/U urease/AlaDH). The activities of enzyme systems, encapsulation yield, McV, McH, and McHc were measured for each sample. Investigated results suggest that loaded enzyme systems can be used as potential carrier systems for the removal of high levels of urea from blood.
Vacuum Headspace Method in Aroma Research:  Flavor Chemistry of Yellow Passion Fruits (1998)

The volatile flavor components of yellow passion fruits have been isolated using four different isolation techniques. The most representative and typical extract was obtained by vacuum headspace sampling and subsequent liquid−liquid extraction of the aqueous phase. This vacuum headspace concentrate was prefractionated by medium-pressure adsorption chromatography on silica gel. Approximately 180 components were identified in the LC fractions of yellow passion fruit flavor for the first time. Of these compounds, 14 components have not previously been reported as naturally occurring flavor ingredients. Moreover, 47 sulfur-containing volatiles were identified in yellow passion fruits after enrichment by preparative multidimensional capillary gas chromatography; 35 of these components are reported to be present in the tropical fruit flavor for the first time, and 23 of these sulfur-bearing compounds have not been previously reported as constituents of food flavors and are therefore new natural components. In addition, the enantiomeric distributions of several chiral flavor substances were determined by enantioselective multidimensional gas chromatography. Keywords: Yellow passion fruit flavor; comparison of sampling techniques; vacuum headspace method; sulfur volatiles; enantio-MDGC
A Device for Measuring Stress-Strain Behavior of Low-Modulus Textiles Under Uniform Radial Straining1 (1974)

This paper describes a strain tester that stretches a knitted fabric or other low-modulus material such that the strain at any point in the specimen is uniform in any planar direction. Radial strain is produced by expanding the perimeter of a circular sample radially. Uniform radial strain is of interest in testing the effects of chemical or other treatments on knitted materials which undergo minimal yarn-loop sliding during use. The apparatus is attachable to a standard tensile tester which records the cumulative stress-strain curve. Force-deformation curves and unrecovered-strain data are given for three patterned jersey knits.
<i>HRD4/NPL4</i> Is Required for the Proteasomal Processing of Ubiquitinated ER Proteins (2001)

We isolated a temperature-sensitive mutant, hrd4-1, deficient in ER-associated degradation (ERAD). The HRD4 gene was identical to NPL4, a gene previously implicated in nuclear transport. Using a diverse set of substrates and direct ubiquitination assays, our analysis revealed that HRD4/NPL4 is required for a poorly characterized step in ERAD after ubiquitination of target proteins but before their recognition by the 26S proteasome. Our data indicate that this lack of proteasomal processing of ubiquitinated proteins constitutes the primary defect in hrd4/npl4 mutant cells and explains the diverse set of hrd4/npl4 phenotypes. We also found that each member of the Cdc48p-Ufd1p-Npl4p complex is individually required for ERAD.
Manufacturability of a Printed Resistance-Based Multiplexing Scheme for Smart Drug Packaging (2016)

The efficacy of drug plans can critically depend on patient's adherence to a prescribed intake schedule. Detection of the rupture of blisters in drug packages through circuits printed on the package allows medical practitioners to monitor patient's compliance. In the current state of the art, each blister is overprinted with a conductive track and their rupture is detected by a dedicated pin in a reusable integrated circuit (IC) that records and communicates the results. In this paper, we are reporting on the development of a smart drug package based on the multiplexed detection of printed resistive tracks monitored by an IC with a reduced number of pins, which lowers the cost and the complexity of components and assembly. Using a generalized formalism, it is shown how manufacturing tolerances limit the achievable multiplexing factor. Tests with our chosen screen printing technique allow us to conclude that a factor of 3 is achievable. This was verified by the design and the fabrication of a multiplexed 28-blister package and corresponding interrogation system. A detailed analysis reveals the limits of the technique and points to factors that may reduce variability, and the robustness of the technique is demonstrated by environmental and mechanical tests. This technique is shown to be a viable way of reducing the complexity of integration of printed and conventional electronics.
Is there any physiological role for gonadotrophin oligosaccharide heterogeneity in humans? (2001)

Heterogeneity of gonadotrophin oligosaccharides caused either by pharmacological intervention or which occurs naturally during normal physiological changes is well documented. Recent advances in structure determination of oligosaccharides has to some extent led to a better appreciation of how oligosaccharide heterogeneity may affect protein folding, stability, measurement and modulation of receptor binding. Here it is discussed how carbohydrate structure can impact upon gonadotrophin structure and function. It is well documented that oligosaccharides can serve as a cognate site for protein binding. One functional aspect of gonadotrophin glycosylation heterogeneity is the modulation of receptor binding affinity, yielding partially agonistic glycoforms. Carbohydrate heterogeneity is problematic for a clinical chemist if immunochemical assays are sensitive to heterogeneity. However, even measurements made without such interference may not accurately reflect the biological activity that is a collective result of all isoforms in the circulation, and perhaps of the genotype of each individual. Moreover, oligosaccharide heterogeneity may affect heterodimer stability, therefore, biological activity and immunochemical activity, not to mention clearance. It seems reasonable to conclude that from a biochemical point of view, oligosaccharide heterogeneity is of considerable importance. However, accurate measurement of isoforms in blood, and appropriate in-vitro bioassays that are insensitive to matrix effects are needed to define the physiological significance of each glycoform, and thereby better define target therapeutics and interpret diagnostic results.
Development of chromaffin cells depends on MASH1 function (2002)

The sympathoadrenal (SA) cell lineage is a derivative of the neural crest (NC), which gives rise to sympathetic neurons and neuroendocrine chromaffin cells. Signals that are important for specification of these two types of cells are largely unknown. MASH1 plays an important role for neuronal as well as catecholaminergic differentiation. Mash1 knockout mice display severe deficits in sympathetic ganglia, yet their adrenal medulla has been reported to be largely normal suggesting that MASH1 is essential for neuronal but not for neuroendocrine differentiation. We show now that MASH1 function is necessary for the development of the vast majority of chromaffin cells. Most adrenal medullary cells in Mash1(-/-) mice identified by Phox2b immunoreactivity, lack the catecholaminergic marker tyrosine hydroxylase. Mash1 mutant and wild-type mice have almost identical numbers of Phox2b-positive cells in their adrenal glands at embryonic day (E) 13.5; however, only one-third of the Phox2b-positive adrenal cell population seen in Mash1(+/+) mice is maintained in Mash1(-/-) mice at birth. Similar to Phox2b, cells expressing Phox2a and Hand2 (dHand) clearly outnumber TH-positive cells. Most cells in the adrenal medulla of Mash1(-/-) mice do not contain chromaffin granules, display a very immature, neuroblast-like phenotype, and, unlike wild-type adrenal chromaffin cells, show prolonged expression of neurofilament and Ret comparable with that observed in wild-type sympathetic ganglia. However, few chromaffin cells in Mash1(-/-) mice become PNMT positive and downregulate neurofilament and Ret expression. Together, these findings suggest that the development of chromaffin cells does depend on MASH1 function not only for catecholaminergic differentiation but also for general chromaffin cell differentiation.
A 0.4-μm/sup 2/ self-aligned contactless memory cell technology suitable for 256-Mbit flash memories (2002)

This paper describes advanced self-aligned contactless memory-cell technology with sector erase and programming operations for a single power supply 256-Mbit flash memory. Using new self-aligned field-isolation technology and a deep punch-through stopper while minimizing the thermal budget of memory-cell fabrication process, 0.40-/spl mu/m/sup 2/ cells based on 0.25-/spl mu/m CMOS processes are fabricated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Assessing heterogeneity of lesion enhancement kinetics in dynamic contrast-enhanced MRI for breast cancer diagnosis (2010)

The current study investigates the feasibility of using texture analysis to quantify the heterogeneity of lesion enhancement kinetics in order to discriminate malignant from benign breast lesions. A total of 82 biopsy-proven breast lesions (51 malignant, 31 benign), originating from 74 women subjected to dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) were analysed. Pixel-wise analysis of DCE-MRI lesion data was performed to generate initial enhancement, post-initial enhancement and signal enhancement ratio (SER) parametric maps; these maps were subsequently subjected to co-occurrence matrix texture analysis. The discriminating ability of texture features extracted from each parametric map was investigated using a least-squares minimum distance classifier and further compared with the discriminating ability of the same texture features extracted from the first post-contrast frame. Selected texture features extracted from the SER map achieved an area under receiver operating characteristic curve of 0.922 +/- 0.029, a performance similar to post-initial enhancement map features (0.906 +/- 0.032) and statistically significantly higher than for initial enhancement map (0.767 +/- 0.053) and first post-contrast frame (0.756 +/- 0.060) features. Quantifying the heterogeneity of parametric maps that reflect lesion washout properties could contribute to the computer-aided diagnosis of breast lesions in DCE-MRI.
Local built-in potential on grain boundary of Cu(In,Ga)Se2 thin films (2004)

We report on a direct measurement of two-dimensional potential distribution on the surface of photovoltaic Cu(In,Ga)Se2 thin films using a nanoscale electrical characterization of scanning Kelvin probe microscopy. The potential measurement reveals a higher surface potential or a smaller work function on grain boundaries of the film than on the grain surfaces. This demonstrates the existence of a local built-in potential on grain boundaries, and the grain boundary is positively charged. The local built-in potential on the grain boundary is expected to increase the minority-carrier collection area from one to three dimensional. In addition, a work function decrease induced by Na on the film surface was observed.
Efficient sensor network based acoustic localization (2011)

Sensor networks, constructed from a large number of inexpensive devices can be used to provide accurate and robust acoustic localization services. A consistency-based fusion method, which can be utilized for Time Difference of Arrival (TDOA) measurements has recently been proposed. The fusion algorithm is able to find the global optimum with good accuracy, but the location estimator is not optimal. In this paper an enhanced consistency-based fusion is proposed for TDOA localization, with improved performance, as real measurement results show. The performance of the proposed method is close to the Cramer-Rao lower bound, as illustrated by simulation results.
Performance Impacts of Nerve Agents and Their Pharmacological Countermeasures (2002)

Nerve agents are some of the most toxic compounds known to man and, as suggested by their name, have pronounced effects on central and peripheral nervous system function. In addition, several of the drugs used as pharmacological countermeasures to reverse the potentially life-threatening physiological effects of nerve agents themselves have potent effects on a variety of neurobehavioral functions. This article reviews the toxicological and neurobehavioral effects of exposure to nerve agents and their medical treatment compounds, giving particular emphasis to their impacts on performance and behavior, both immediate and long-term. As such, this review touches on a number of major related topics, primarily pharmacological and toxico-logical. Where possible, more in-depth discussions of these topics have been cited for the interested reader. The toxicology and pharmacology of the nerve agents and the respective medical treatment drugs are addressed separately, representing distinctly different pharmacological classes of compounds and producing distinctly different effects on the central nervous system and performance. Both animal and human data have been evaluated for this review. Although animal data provide a valuable adjunct to the human reports, the majority of studies cited here describe the effects of these compounds in humans. Where it was thought necessary for clarification or elaboration, animal studies have been cited, but these represent only a small subset of this vast literature.
A Study on Cost and Returns of Indigenous Dairy Products in Meerut City of Western Uttar Pradesh (2009)

The present study was carried out during 1999 to know the milk utilization, Investment pattern and economics of large varieties of Khoa and Channa based sweets manufactured by halwaies In Meerut city of Western Uttar Pradesh. It was found that the average milk utilization per unit was about 204 litres/day with the Initial fixed investment of Rs. 1.72 and 0.38 lakhs in owned and rented shops, respectively. Besides that, the average working capital required for dally expenses was Rs. 2772.0 per day which was positively related to the size of unit. The total manufacturing costs of Khoa and Channa based sweets decreased marginally with increase in size of production. Among these products, share of profit was highest from Kalakand (25.89 per cent) in Khoa based and Rasgolla(57.35 per cent) among Channa based.
Investigation to Simulation of Regenerative Braking for Parallel Hydraulic Hybrid Vehicles (2009)

Parallel hydraulic hybrid vehicles (PHHV) have the potential of improving fuel economy by operating the engine in the optimum efficiency range and making use of regenerative braking during deceleration. Based on the analysis of the characteristics of braking in the city drive cycle and high power density of hydraulic hybrid vehicles, a new regenerative braking strategy tailored specially for PHHV was proposed to improve the fuel economy. The simulation results shown that hydraulic regenerative braking strategy reasonably distributed the hydraulic regenerative braking torque and traditional friction braking torque, effectively regenerated braking energy of the vehicle under the premise of safety brake and improved the braking performance.
A bridge network for the precise measurement of direct capacitance (1957)

For measurements by substitution only, the balance of a transformer bridge network can be made independent of capacitance and conductance from either terminal of the specimen to earth. In the network proposed in the paper both oscillator and detector have one terminal connected to earth. The network is particularly useful for measuring capacitances of less than 100μμF in the presence of stray capacitances to earth. It can be used at frequencies between about 4c/s and 20Mc/s; at frequencies up to about 1Mc/s it is suitable for work of the highest precision.
<title>Continuous processing of acoustic data for land mine detection</title> (2002)

Methods for processing continuously acquired data using an Acoustic/Seismic system are described. Data were acquired from 80-300 Hz. Two independent chains of processing were pursued. In one chain, pre-processing and normalization were followed by shape feature extraction using eccentricity and minor axis length. In another chain, Independent Component Analysis was used to generate image templates. The results were combined using piecewise linear discriminants. Probabilities of detection of 97.5% and 100% with false alarm rates of 0.01 and 0.03 were achieved on training and validation sets, respectively.