gebhart/patrepeval huggingface dataset:
Identification of the OXA-48 Carbapenemase Family by Use of Tryptic Peptides and Liquid Chromatography-Tandem Mass Spectrometry (2019)

Phenotypic detection of the OXA-48-type class D β-lactamases in <i>Enterobacteriaceae</i> is challenging. We describe a rapid (less than 90 min) assay for the identification of OXA-48 family carbapenemases in subcultured bacterial isolates based on a genoproteomic approach. Following <i>in silico</i> trypsin digestion to ascertain theoretical core peptides common to the OXA-48 family, liquid chromatography-tandem mass spectrometry (LC-MS/MS) data-dependent acquisition was used to identify candidate peptide markers. Two peptides were selected based on performance characteristics: ANQAFLPASTFK, a core peptide common to all 12 OXA-48 family β-lactamase members, and YSVVPVYQEFAR, a highly specific peptide common to 11 of 12 OXA-48 family proteins providing the basis for an LC-MS/MS multiple reaction monitoring assay. An accuracy assessment was performed that included 98 isolates, 26 of which were OXA-48 positive. Two additional specificity assessments were performed including a mixture of isolates positive for OXA-48, KPC, NDM, VIM, and IMP carbapenemases. A combination of expert rules and expert judgment was applied by blinded operators to identify positive isolates. All isolates containing an OXA-48 family carbapenemase across all three test sets were correctly identified with no false positives, demonstrating 100% sensitivity (95% confidence interval [CI], 91.2% to 100%) and 100% specificity (95% CI, 96.2% to 100%) for the assay. These findings provide a framework for an LC-MS/MS-based method for the direct detection of OXA-48 family carbapenemases from cultured isolates that may have utility in predicting carbapenem resistance and tracking hospital outbreaks of OXA-48-carrying organisms.
Performance of Frenchbean at different dates of sowing and plant densities in Telangana region of Andhra Pradesh (2010)

Field experiments were conducted during rabi seasons of 200405, 2005–06 and 2006–07 in sandy loam soil to study the performance of Frenchbean (rajmash) at different dates of sowing and plant densities. The results revealed that significantly higher number of pods/plant, number of seeds/pod, 100-seed weight (g) and seed yield (kg ha−1) were recorded when Frenchbean is sown during the second fortnight of October to first week of November. Further, sowing Frenchbean at 30 x 10 cm spacing was found to produce optimum plant density for recording significantly higher seed yields over wider spacings in the Telangana region of Andhra Pradesh.
Phase behavior and phase separation in blends of a liquid crystalline polymer and an amorphous polymer containing hydrogen-bonding interaction (1998)

The phase behavior and thermally induced phase separation in blends of poly{styrene-co-[p-(2,2,2-trifluoro-1-hydroxy-1-trifluoromethyl)ethyl-α-methylstyrene]} (PS(OH)) and a thermotropic liquid crystalline polymer (LCP) were studied by optical microscopy (OM), infrared spectroscopy (IR) and time-resolved light scattering (TRLS). PS(OH) contains strong proton-donating groups —C(CF3)2OH, and the LCP is poly[p-(tert-butyl)phenylene fumarate] (PBPF), which is soluble in common solvents. For blends of PS(OH)/PBPF, the miscible region was found only at high PBPF compositions and low temperature due to intermolecular hydrogen bonding between —C(CF3)2OH groups of PS(OH) and the phenolic OH end-groups of PBPF according to IR. The PS(OH)/PBPF blend undergoes phase separation via spinodal decomposition (SD) during isothermal annealing in the two-phase regime of phase diagram. The SD yielded unique Vv and Hv scattering patterns, which can be attributed to regular periodic phase-separated structures composed of an anisotropic phase and an isotropic phase. Preliminary studies on the SD process by TRLS showed that the phase separation spontaneously occurs at a certain time, that might be associated with the presence of the LCP.
AgIn: measuring the landscape of CpG methylation of individual repetitive elements (2016)

Abstract Motivation: Determining the methylation state of regions with high copy numbers is challenging for second-generation sequencing, because the read length is insufficient to map reads uniquely, especially when repetitive regions are long and nearly identical to each other. Single-molecule real-time (SMRT) sequencing is a promising method for observing such regions, because it is not vulnerable to GC bias, it produces long read lengths, and its kinetic information is sensitive to DNA modifications. Results: We propose a novel linear-time algorithm that combines the kinetic information for neighboring CpG sites and increases the confidence in identifying the methylation states of those sites. Using a practical read coverage of ∼30-fold from an inbred strain medaka (Oryzias latipes), we observed that both the sensitivity and precision of our method on individual CpG sites were ∼93.7%. We also observed a high correlation coefficient (R = 0.884) between our method and bisulfite sequencing, and for 92.0% of CpG sites, methylation levels ranging over [0,1] were in concordance within an acceptable difference 0.25. Using this method, we characterized the landscape of the methylation status of repetitive elements, such as LINEs, in the human genome, thereby revealing the strong correlation between CpG density and hypomethylation and detecting hypomethylation hot spots of LTRs and LINEs. We uncovered the methylation states for nearly identical active transposons, two novel LINE insertions of identity ∼99% and length 6050 base pairs (bp) in the human genome, and 16 Tol2 elements of identity &gt;99.8% and length 4682 bp in the medaka genome. Availability and Implementation: AgIn (Aggregate on Intervals) is available at: https://github.com/hacone/AgIn Contact: ysuzuki@cb.k.u-tokyo.ac.jp or moris@cb.k.u-tokyo.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online.
A Self-Assembled Nanofiber Catalyst for Ester Hydrolysis (2007)

Catalytic particles based on supramolecular systems have demonstrated significant improvement in the field of catalysis. In this work, histidine-functionalized self-assembling peptide amphiphiles (PAs) were synthesized in order to form self-assembly high-aspect-ratio nanofibers with internal order that can present imidazolyl groups capable of ester hydrolysis. Self-assembly of the molecules making up the catalytic particle was studied by transmission electron microscopy and circular dichroism. The reactive sites were designed with histidine residues to catalyze the hydrolysis of 2,4-dinitrophenyl acetate (DNPA). Enzymatic hydrolysis of DNPA was observed in the presence of the nanofibers by UV−vis spectroscopy and the Michaelis−Menten enzyme kinetics model. Significantly faster hydrolysis rate was observed in the presence of self-assembled nanofibers relative to spherical aggregates expected to have less order as well as single molecule catalysts.
Fire Resistance Tests for Fluids and Lubricants — Their Limitations and Misapplication (1996)

A large number of tests are currently available for assessing the fire resistance of functional fluids and lubricants. Since it is extremely difficult to simulate fire conditions for fluids in laboratory tests, the main use for the different methods is a comparative assessment of the various fluids. The fluids in commercial use, where fire resistance is a critical feature, can be divided into those which depend on water for their performance and non-aqueous fluids, where the fire resistance depends on the chemical composition. Ideally a fire resistance test should be capable of assessing the behaviour of all candidate fluids on an equal basis, but because the two groups of fluids behave in totally different ways comparison in most tests is not valid. Although some tests suffer from indifferent precision or are unable to satisfactorily discriminate one type of fluid from another (within the same group), many rank the fluids in approximately the same order and therefore do not provide any additional information. The introduction of two new spray ignition tests which enable all the different fluids to be compared under similar conditions is a major step forward. These tests, however, cannot simulate a condition where the water content of aqueous fluids can volatilise and leave behind a flammable residue. As a result, for the minimum assessment of the behaviour of both groups of fluid it is advisable to obtain both spray ignition test performance and performance in a ‘hot surface’ test.
Towards understanding the symmetry of human ears: A biometric perspective (2010)

In this paper, an analysis of the symmetry of human ears is presented. Such an analysis is essential in order to understand the possibility of matching the left and right ears of an individual, or to reconstruct portions of the ear that may be occluded in a surveillance video. Ear symmetry is assessed geometrically using symmetry operators and Iannarelli's measurements, where the contribution of individual ear regions to the overall symmetry of the ear is studied. Next, to assess the ear symmetry (or asymmetry) from a biométrie recognition system perspective, several experiments were conducted on the WVU Ear Database. Our experiments suggest the existence of some degree of symmetry in the human ears that can perhaps be systematically exploited in the design of commercial ear recognition systems. At the same time, the degree of asymmetry it offers may be used in designing effective fusion schemes that combine the face information with the two ears.
High Density Solenoidal Series Pair Symmetric Inductors and Transformers (2014)

A high density symmetric inductor using a novel combination of solenoidal wound series stacked spirals is proposed in this paper. Series stacking in the individual sections increases overall inductance density, while solenoidal winding pushes the quality factors ( <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Q</i> ) to higher frequencies. The proposed inductor achieves more than 65% improvement in peak- <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Q</i> value and 100% higher peak- <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Q</i> frequency and self resonance frequency, while occupying 20% lesser area when compared with a standard symmetric inductor with crossovers. Implemented in a high resistivity 0.18 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="TeX">\(\mu \) </tex-math></inline-formula> m CMOS silicon-on-insulator process with dual-thick metal stack, the proposed inductor achieves 70-nH inductance and a <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Q</i> of 11.3 operating at 1.6 GHz within <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="TeX">\(250\times 250\) </tex-math></inline-formula> <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="TeX">\(\mu \) </tex-math></inline-formula> m <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="TeX">\(^2\) </tex-math></inline-formula> area. This translates to a record figure-of-merit of 12.2, which is highest in air core symmetric inductor literature. Further, the proposed inductor configuration is extended to realize a planar transformer with very high turns ratio of 9.25 using only two metals.
Wound research funding from alternative sources of federal funds in 2012 (2014)

Chronic wounds represent a major healthcare burden, costing $25 billion annually, and are associated with high mortality. We previously reported that cutaneous wound healing represented only 0.1% ($29.8 million) of the National Institutes of Health budget. This current study focuses on quantifying the contribution by federal agencies other than the National Institutes of Health for fiscal year 2012. Federal databases including USA Spending, Veterans Affairs, Tracking Accountability in Government Grants Systems, Health Services Research Projects in Progress, and Patient-Centered Outcomes Research Institute, were searched for individual projects addressing wound healing. Twenty-seven projects were identified, totaling funding of $16,588,623 (median: $349,856). Four sponsor institutions accounted for 74% of awarded funds: Department of the Army, National Science Foundation, Department of Veterans Affairs, and Agency for Healthcare Research & Quality. Research projects and cooperative agreements comprised 44% and 37% of awarded grants. New applications and continuing projects represented 52% and 37%. Wound healing represented 0.15% of total medical research funded by the non-National Institutes of Health federal sector. Compared with potential impact on US public health, federal investment in wound research is exiguous. This analysis will draw attention to a disproportionately low investment in wound research and its perils to American public health.
IDENTIFICATION AND CLONING OF AMPLIFIED FRAGMENT LENGTH POLYMORPHISM MARKERS LINKED TO THE MATING TYPE LOCUS OF <i>CHLAMYDOMONAS REINHARDTII</i> (CHLOROPHYTA) (2001)

Amplified fragment length polymorphism (AFLP) markers have been widely used to generate molecular maps of plant species, including crops and cereals. We report on a useful protocol to identify AFLPs from Chlamydomonas reinhardtii Dangeard with digoxigenin labeled primers. Although Chlamydomonas has a small genome with a high GC content, we could detect polymorphic bands that led to the identification of several AFLP markers linked to the mating type locus of Chlamydomonas. Three of these markers were isolated from the gel, reamplified, and cloned. The clones were sequenced, and the insertion of the correct fragment was verified in AFLP gels and in Southern blots. One marker showed sequence identity to parts of the fus1 gene, known to be unique in the plus mating type. We also converted some of the AFLP markers into sequence tagged site markers, which allows a fast and convenient screening of progeny of crosses. This procedure will be a useful and fast alternative to the conventional generation of maps for the positional cloning of genes from Chlamydomonas.
Conversion of the straight-run gasoline fraction of high-paraffin oil on a zeolite catalyst (2011)

The conversion of the straight-run gasoline fraction of high-paraffin crude oil into the high-octane gasoline over niobium-zirconium-aluminosilicate catalyst with the ZSM-5 zeolite structure has been studied. The influence of the process conditions on the yield, composition, and performance characteristics of the product gasoline has been shown. It has been found that in the presence of the catalyst, the required quality of gasoline can be reached by varying the process conditions. Using ammonia thermal desorption and differential thermal analysis techniques, data on the acid characteristics of the zeolite catalyst and the amount of coke formed on its surface during the conversion of straight-run gasoline have been obtained. The catalyst operation stability in the model reaction of methanol-to-hydrocarbons conversion has been estimated.
Protein engineering of Aspergillus awamori glucoamylase to increase its pH optimum (1998)

To increase the pH optimum of glucoamylase (GA), five mutations-S411G, S411A, S411C, S411H and S411D--were designed to destabilize the carboxylate ion form of Glu400, the catalytic base, by removing or weakening the hydrogen bond between Ser411 and Glu400, and thereby raising its pK. The substitution of alanine, histidine and aspartate were also designed to study the additional effects of polarity and both positive and negative charges, respectively. S411G GA had catalytic efficiencies like those of wild-type GA for isomaltose, maltose and maltoheptaose hydrolysis at pH 4.4, while S411A and S411C GAs had 54-74% and S411H and S411D GAs had only about 6-12% of wild-type catalytic efficiencies. All five mutations increased the pH optimum in the enzyme-substrate complex, mainly by raising pK1 values. S411A is the best performing and most industrially promising of the pH mutants isolated to date. S411A GA increased the pH optimum by 0.8 units for both maltose and maltoheptaose hydrolysis while maintaining a high level of activity and catalytic efficiency. In hydrolysis of 28% DE 10 maltodextrin, S411A GA had a pH optimum of 7 compared with pH 5.6 for wild-type GA, and had higher initial rates of glucose production than wild-type GA at all pH values tested above pH 6.6.
The asymmetry in idiotype-isotype expression in the response to phosphocholine is due to divergence in the expressed repertoires of Lyb-5+ and Lyb-5- B cells. (1983)

The X-linked CBA/N immune defect was used to investigate the roles of Lyb-5- and Lyb-5+ B cells in the memory response to PC-KLH (phosphocholine-conjugated keyhole limpet hemocyanin). (CBA/N X BALB/c)F1 (CB) male mice express the xid mutation and thereby lack the Lyb-5+ B cell subset, whereas their female littermates are normal and express both Lyb-5+ and Lyb-5- B cells. After priming with PC-conjugated hemocyanin (PC-Hy) in complete Freund's adjuvant, female B cells produce three phenotypic sets of PC-KLH-specific antibody. The first set (group I) is dominated by T15+, IgM, IgA, and IgG3, PC-specific antibodies. The second subset (group II) is specific for phenylphosphocholine (PPC), and is dominated by T15-, IgG1, and IgG2 antibodies. The third set (group III) recognizes an epitope(s) composed of both the PPC hapten and carrier determinants. PC-Hy-primed B cells from immune defective CB male mice produce the same number of IgG1 and IgG2 plaque-forming cells (PFC) as do PC-Hy-primed normal female cells, and these PFC are also predominantly T15- and PPC specific (group II). In addition, a significant amount of group III IgG1 and IgG2 antibody is observed in the immune defective male response. In contrast to female B cells, immune defective male B cells produce a low IgM, IgA, and IgG3 memory response that is not composed of PC-specific (group I) antibodies; in fact, most of these antibodies arise from group III precursors and are not inhibited by either PC or PPC. PC-specific antibodies usually represent less than 25% of the anti-PC-KLH response in immune defective mice; however, these PC-specific antibodies are predominantly T15-. These data suggest that the Lyb-5-B cells in both normal and immune defective mice produce the T15-, IgG1, and IgG2 antibodies that dominate the secondary immune response to PC-KLH, and that the Lyb-5+ B cells produce the T15+, IgM, IgA, and IgG3 portion of the secondary response in normal mice. This hypothesis was confirmed by priming normal mice with the R36a strain of Streptococcus pneumoniae or with PC-Hy in saline. These forms of PC-antigen prime only the Lyb-5+ B cell subset. The adoptive transfer of these two B cell sources results in an anti-PC-KLH response that is T15 dominant and totally PC inhibitable.(ABSTRACT TRUNCATED AT 400 WORDS)
Phenotypic effects of membrane protein overexpression in <i>Saccharomyces cerevisiae</i> (2006)

Large-scale protein overexpression phenotype screens provide an important complement to the more common gene knockout screens. Here, we have targeted the so far poorly understood Saccharomyces cerevisiae membrane proteome and report growth phenotypes for a strain collection overexpressing approximately 600 C-terminally tagged integral membrane proteins grown both under normal and three different stress conditions. Although overexpression of most membrane proteins reduce the growth rate in synthetic defined medium, we identify a large number of proteins that, when overexpressed, confer specific resistance to various stress conditions. Our data suggest that regulation of glycosylphosphatidylinositol anchor biosynthesis and the Na(+)/K(+) homeostasis system constitute major downstream targets of the yeast PKA/RAS pathway and point to a possible connection between the early secretory pathway and the cells' response to oxidative stress. We also have quantified the expression levels for >550 membrane proteins, facilitating the choice of well expressing proteins for future functional and structural studies.
FPGA based re-configurable wireless sensor network protocol (2008)

Recent advances in wireless communications and micro-electronics have enabled the development of low-cost wireless sensor networks. In this paper, a reconfigurable wireless sensor network platform for reliable detection and quick reporting of random and temporary events is being described. Bluetooth, which has the key features like low cost, low power and robustness, is used to establish the communication between the sensor nodes. To have the advantage of multi-hop routing and easy expansion of the network, tree topology is used. Altera's Cyclone Field Programmable Gate Array (FPGA) device, equipped with a configurable )IOS II soft-core is used as a sensor node. The main features of the network are re-configurability, programmability and scalability.
Voluntary activation failure contributes more to plantar flexor weakness than antagonist coactivation and muscle atrophy in chronic stroke survivors (2010)

The contributions of nervous system muscle activation and muscle atrophy to poststroke weakness have not been evaluated together in the same subject. Maximal voluntary contraction (MVC) torque, voluntary activation (twitch interpolation), and electromyographic (EMG) amplitude were determined bilaterally in the plantar flexors of seven chronic stroke survivors (40-63 yr, 24-51 mo poststroke). Volumes of the plantar flexor muscles were determined bilaterally with magnetic resonance imaging (MRI). The mean (±SD) contralesional (paretic) MVC torque was less than one-half of the ipsilesional leg: 56.7 ± 57.4 vs. 147 ± 35.7 Nm (P = 0.006). Contralesional voluntary activation was only 48 ± 36.9%, but was near complete in the ipsilesional leg, 97 ± 1.9% (P = 0.01). The contralesional MVC EMG amplitude (normalized to the maximum M-wave peak-to-peak amplitude) of the gastrocnemii and soleus were 36.0 ± 28.5 and 36.0 ± 31.0% of the ipsilesional leg. Tibialis anterior (TA) EMG coactivation was not different between the contralesional (23.2 ± 24.0% of TA MVC EMG) and ipsilesional side (12.3 ± 5.7%) (P = 0.24). However, TA EMG coactivation was excessive (71%) in one subject and accounted for ~8% of her weakness based on the estimated antagonist torque. Relative (%ipsilesional leg) plantar flexor and gastrocnemii volumes were 88 ± 6% (P = 0.004) and 76 ± 15% (P = 0.01), respectively. Interlimb volume differences of the soleus, deep plantar flexors, and peronei were not significant. Preferred walking speed (0.83 ± 0.33 m/s) was related to the contralesional MVC torque (r(2) = 0.57, P = 0.05, N = 7), but the two subjects with the greatest weakness walked faster than three others. Our findings suggest that plantar flexor weakness in mobile chronic stroke survivors reflects mostly voluntary activation failure, with smaller contributions from antagonist activity and atrophy.
Protection of 3D Object Visual Representations (2006)

In this paper, we describe a new framework for watermarking 3D objects via their contour information. Unlike most conventional 3D object watermarking techniques, for which both insertion and extraction of the mark are performed on the object itself (3D/3D approach), we propose an asymmetric 3D/2D procedure. The goal of our work is to retrieve information (originally hidden in the apparent 3D silhouette of the object) from resulting images or videos having used the synthetic object, thus protecting the visual representations of the object. After developing theoretical and practical key-points of this 3D object watermarking scheme, we present the results of some preliminary experiments
Le dieu inconnu du chapitre VIII de la Satire sur l'apothéose de Claude (1951)

info:eu-repo/semantics/published