gebhart/patrepeval huggingface dataset:
High Concentration Capture Probes Enhance Massively Parallel Sequencing Assays (2016)

To the Editor:

Targeted capture of genomic regions by oligonucleotide (oligo)1 probes, followed by massively parallel sequencing (MPS) enables consistent sequencing reactions (1). However, some regions of interest have poor depth of coverage (DOC) (defined as <50× in our laboratory) to no DOC after capture, leading to incomplete analysis of genes and, possibly, false negative test results (2). One strategy for improvement is to supplement the original capture reagent with a higher concentration of oligo probes specifically targeting regions with poor coverage (“spike-in”) (3–5). However, a detailed description of the spike-in method has not been published. Here, we describe the application of spike-in on the development of a clinical MPS panel for laboratories using capture and seeking to improve gene coverage.

We developed a custom capture SeqCap EZ panel (Roche Nimblegen) targeting 339 pediatric disease-related genes [1102 514 target nucleotides (TNs) contained within 6094 target regions (TRs), with TRs defined as exons ± the flanking 5 base pairs]. To characterize TRs with poor DOC, DNA libraries created from 12 human blood samples (Kapa Biosystems) were multiplexed (250 ng/sample; 4 samples/run), captured, and sequenced on a MiSeq® instrument (Illumina) via paired-end, 2×151 base pair reads, generating approximately 8 million total reads per sample. Alignment (allowing for multiply mapped reads) and variant calling were done using NextGENe® v2.3.4 (SoftGenetics).

For these samples, the average DOC was 607× (range, …
A comparison of multicarrier PWM strategies for cascaded and neutral point clamped multilevel inverters (2002)

Analytical solutions of pulse width modulation (PWM) strategies for multilevel neutral point clamped (NPC) and cascaded inverters are presented. These solutions show that the alternative phase opposition disposition (APOD) PWM strategy for NPC inverters produces the same spectral components as the phase shifted carrier PWM (PSCPWM) strategy for cascaded inverters, when the carrier frequencies are adjusted to achieve the same number of total switch transitions for each inverter over one fundamental cycle. From this understanding, a method is proposed to apply the harmonically superior phase disposition (PD) PWM strategy for NPC inverters to cascaded inverters, to achieve improved harmonic performance for the modulation of cascaded inverters. Both theoretical and experimental results confirming this understanding are presented.
Antileishmanial Activity of Parthenolide, a Sesquiterpene Lactone Isolated from <i>Tanacetum parthenium</i> (2004)

The in vitro activity of parthenolide against Leishmania amazonensis was investigated. Parthenolide is a sesquiterpene lactone purified from the hydroalcoholic extract of aerial parts of Tanacetum parthenium. This isolated compound was identified through spectral analyses by UV, infrared, (1)H and (13)C nuclear magnetic resonance imaging, DEPT (distortionless enhancement by polarization transfer), COSY (correlated spectroscopy), HMQC (heteronuclear multiple-quantum coherence), and electron spray ionization-mass spectrometry. Parthenolide showed significant activity against the promastigote form of L. amazonensis, with 50% inhibition of cell growth at a concentration of 0.37 microg/ml. For the intracellular amastigote form, parthenolide reduced by 50% the survival index of parasites in macrophages when it was used at 0.81 microg/ml. The purified compound showed no cytotoxic effects against J774G8 macrophages in culture and did not cause lysis in sheep blood when it was used at higher concentrations that inhibited promastigote forms. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis with gelatin as the substrate showed that the enzymatic activity of the enzyme cysteine protease increased following treatment of the promastigotes with the isolated compound. This finding was correlated with marked morphological changes induced by parthenolide, such as the appearance of structures similar to large lysosomes and intense exocytic activity in the region of the flagellar pocket, as seen by electron microscopy. These results provide new perspectives on the development of novel drugs with leishmanicidal activities obtained from natural products.
Recent progress in the chemistry of the monoterpenoid indole alkaloids (1997)

J. E. Saxton, Nat. Prod. Rep., 1997, 14, 559 DOI: 10.1039/NP9971400559
Seismic wave extrapolation using lowrank symbol approximation (2012)

ABSTRACT We consider the problem of constructing a wave extrapolation operator in a variable and possibly anisotropic medium. Our construction involves Fourier transforms in space combined with the help of a lowrank approximation of the space‐wavenumber wave‐propagator matrix. A lowrank approximation implies selecting a small set of representative spatial locations and a small set of representative wavenumbers. We present a mathematical derivation of this method, a description of the lowrank approximation algorithm and numerical examples that confirm the validity of the proposed approach. Wave extrapolation using lowrank approximation can be applied to seismic imaging by reverse‐time migration in 3D heterogeneous isotropic or anisotropic media.
A reconfigurable mesh reflector antenna (1989)

Describes a novel method for controlling the coverage pattern of a spacecraft antenna. An offset mesh reflector is proposed with reconfiguration achieved by means of adjustment to forces applied at control points on the reflector surface. Synthesis software has been developed and this is demonstrated for typical regional coverage patterns. A model of the mesh based on a network of springs is used and this has been successfully verified following precision mechanical measurements using an 85 cm diameter reflector. Gold-plated molybdenum mesh has been chosen so that the antenna can be tested electrically at a frequency of 10 GHz.
Combatting resistance in intensive care: the multimodal approach of the Spanish ICU “Zero Resistance” program (2015)

This article is one of ten reviews selected from the Annual Update in Intensive Care and Emergency Medicine 2015 and co-published as a series in Critical Care. Other articles in the series can be found online at http://ccforum.com/series/annualupdate2015. Further information about the Annual Update in Intensive Care and Emergency Medicine is available from http://www.springer.com/series/8901.
Insight into New Potential Targets for the Treatment of Overactive Bladder and Detrusor Overactivity (2012)

Although overactive bladder (OAB) and detrusor overactivity (DO) are not synonyms, they share therapeutic options and partially underlying physiopathological mechanisms. The aim of this overview is to give insight into new potential targets for the treatment of OAB and DO. A narrative review was done in order to reach this goal. Ageing, pelvic floor disorders, hypersensitivity disorders, morphologic bladder changes, neurological diseases, local inflammations, infections, tumors and bladder outlet obstruction may alter the normal voluntary control of micturition, leading to OAB and DO. The main aim of pharmacotherapy is to restore normal control of micturition, inhibiting the emerging pathological involuntary reflex mechanism. Therapeutic targets can be found at the levels of the urothelium, detrusor muscles, autonomic and afferent pathways, spinal cord and brain. Increased expression and/or sensitivity of urothelial-sensory molecules that lead to afferent sensitization have been documented as a possible pathogenesis of OAB. Targeting afferent pathways and/or bladder smooth muscles by modulating activity of ligand receptors and ion channels could be effective to suppress OAB.
Direct polymerase chain reaction detection of Campylobacter jejuni and Campylobacter coli in raw milk and dairy products (1993)

A polymerase chain reaction (PCR) method designed to sensitively detect and identify Campylobacter jejuni and Campylobacter coli without the need for isolating and culturing strains is described. The intergenic sequence between the flagellin genes flaA and flaB was amplified and characterized with a triple primer or seminested primer approach. A total of 50 bacterial strains, 27 of C. jejuni and C. coli and 23 of other species, were tested, giving no false-positive or false-negative results. The detection limit as determined by ethidium bromide staining of amplification products on agarose gels was 10 bacteria or less in artificially contaminated water, milk, and soft cheese samples with the seminested primer PCR assay. As an application of the PCR system, a set of 93 samples of milk and other dairy products was screened for the presence of C. jejuni and C. coli. We identified six positive samples (6.5%), while none were found with a conventional culture method.
Effects of Various Rejuvenator Sealer Materials on Rheological Properties of Aged SBS Modified Asphalt (2014)

In recent years, using rejuvenator sealer materials (RSMs) to recover the performance of aged asphalt on the pavement is becoming more and more popular. In this paper, four different RSMs were made and applied to rejuvenate the aged asphalt which experienced a PAV 20H process. Then the dynamic rheological characteristics of different binders were tested by the dynamic shear rheometer (DSR).The results indicated that the four RSM can recover the stress relaxation and fatigue factor of aged asphalt. But the rutting parameter decreased with the introduction of four RSMs.
Modeling of Soft Poroelastic Tissue in Time-Harmonic MR Elastography (2008)

Elastography is an emerging imaging technique that focuses on assessing the resistance to deformation of soft biological tissues in vivo. Magnetic resonance elastography (MRE) uses measured displacement fields resulting from low-amplitude, low-frequency (10 Hz-1 kHz) time-harmonic vibration to recover images of the elastic property distribution of tissues including breast, liver, muscle, prostate, and brain. While many soft tissues display complex time-dependent behavior not described by linear elasticity, the models most commonly employed in MRE parameter reconstructions are based on elastic assumptions. Further, elasticity models fail to include the interstitial fluid phase present in vivo. Alternative continuum models, such as consolidation theory, are able to represent tissue and other materials comprising two distinct phases, generally consisting of a porous elastic solid and penetrating fluid. MRE reconstructions of simulated elastic and poroelastic phantoms were performed to investigate the limitations of current-elasticity-based methods in producing accurate elastic parameter estimates in poroelastic media. The results indicate that linearly elastic reconstructions of fluid-saturated porous media at amplitudes and frequencies relevant to steady-state MRE can yield misleading effective property distributions resulting from the complex interaction between their solid and fluid phases.
Analysis of recombinant cytokines in human body fluids by immunoaffinity capillary electrophoresis (1998)

An immunoaffinity capillary electrophoresis (ICE) system for rapidly quantifying recombinant cytokines in human body fluids has been developed. Cytokines within biological fluids were labeled with a red light emitting fluorochrome and injected into the capillary. Selected cytokines were captured by immobilized antibodies on the internal surface of the capillary, and held while unbound materials were purged. The cytokines were then eluted electrophoretically in acidic buffer. Individual cytokine peaks were detected by on-line laser-induced fluorescence detection coupled to a computerized fiber-optic spectrometer, and analyzed by integration of the eluted peaks. The comparison of the results of ICE to routine assays used for these cytokines demonstrates that ICE provides a fast and accurate procedure for defining these cytokines in complex biological samples. Immunoaffinity separations can be used for any material to which a specific antibody can be raised, making this procedure applicable to a wide range of molecules of biomedical interest.
A Low Phase Noise Oscillator Principled on Transformer-Coupled Hard Limiting (2013)

Reduced phase noise conversion in a monolithic oscillator suitable for basestation applications is realized by hard limiting and subsequently restoring the resonating waveform. Overdriven transistors hard limit the drain voltage swing and it is shown analytically that this desensitizes the oscillation phase to circuit noise. A pair of tuned, 1:2 step-up transformers in the feedback path restore the fundamental frequency component with sufficient gain to overdrive the transistors forming the oscillator core, with greater selectivity than an equivalent LC tank. The 8 GHz, 65 nm CMOS oscillator prototype targeting the GSM-900 base-station specification consumes 32 mA from 1.5 V. Normalized to 915 MHz, the phase noise measured at 1 MHz offset is -147.7 dBc/Hz, validating predictions from theory and simulation. The measured frequency pushing is less than 16 MHz/V.
Role of trimethylaluminum on the zirconocene-methylaluminoxane-catalyzed polymerization of ethylene (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRole of trimethylaluminum on the zirconocene-methylaluminoxane-catalyzed polymerization of ethyleneS. Srinivasa Reddy, G. Shashidhar, and S. SivaramCite this: Macromolecules 1993, 26, 5, 1180–1182Publication Date (Print):March 1, 1993Publication History Published online1 May 2002Published inissue 1 March 1993https://pubs.acs.org/doi/10.1021/ma00057a044https://doi.org/10.1021/ma00057a044research-articleACS PublicationsRequest reuse permissionsArticle Views287Altmetric-Citations47LEARN 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
Treatment of Diarrhea Caused by <i>Cryptosporidium parvum:</i> A Prospective Randomized, Double‐Blind, Placebo‐Controlled Study of Nitazoxanide (2001)

A prospective randomized, double-blind, placebo-controlled study was conducted in 50 adults and 50 children from the Nile delta of Egypt, to evaluate the efficacy of nitazoxanide in treating diarrhea caused by Cryptosporidium parvum. Nitazoxanide was administered in 500-mg doses twice daily for 3 days in adults and adolescents, in 200-mg doses twice daily for 3 days in children aged 4-11 years, and in 100-mg doses twice daily for 3 days in children aged 1-3 years. At 7 days after initiation of therapy, diarrhea had resolved in 39 (80%) of the 49 patients in the nitazoxanide treatment group, compared with 20 (41%) of 49 in the placebo group (P<.0001). Diarrhea was resolved in most patients receiving nitazoxanide within 3 or 4 days of treatment initiation. Nitazoxanide treatment reduced the duration of both diarrhea (P<.0001) and oocyst shedding (P<.0001).
Effects of ionic strength on the regulation of Na/H exchange and K-Cl cotransport in dog red blood cells. (1995)

Dog red cell membranes contain two distinct volume-sensitive transporters: swelling-activated K-Cl cotransport and shrinkage-activated Na/H exchange. Cells were prepared with intracellular salt concentration and weight percentage of cell water (%cw) varied independently by transient permeabilization of the cell membrane to cations. The dependence of transporter-mediated Na and K influxes upon %cw and upon extracellular salt concentration (c(ext)) was measured in cells so prepared. It was found that the critical value of %cw at which transporters are activated, called the set point, is similar for the two transporters, and that the set points for the two transporters decrease similarly with increasing extracellular salt concentration. These findings suggest a common mechanism of regulation of these two transporters. Cellular Na, K, and Cl concentrations were measured as functions of %cw and c(ext). Using these data together with data from the literature for other solute concentrations, empirical expressions were developed to describe the dependence of the intracellular concentrations of all significant small molecule electrolytes, and therefore the intracellular ionic strength, upon %cw and c(ext). A mechanistic model for the dependence of the set point of an individual transporter upon intracellular ionic strength is proposed. According to this model, the set point represents a critical extent of association between the transporter and a postulated soluble regulatory protein, called regulator. Model functions are presented for the calculation of the thermodynamic activity of regulator, and hence extent of regulator-transporter association, as a function of total intracellular protein concentration (or %cw) and ionic strength. The experimentally observed dependence of set point %cw on c(ext) are simulated using these functions and the empirical expressions described above, together with reasonable but not uniquely determined values of model parameters.
Effects of intraperitoneal and intracerebroventricular injection of crocin on acute corneal pain in rats (2010)

In this study, the effects of intraperitoneal (i.p.) and intracerebroventricular (i.c.v.) injection of crocin in separate and combined treatments with i.p. injections of morphine (an opioid receptor agonist) and naloxone (an opioid receptor antagonist) were investigated on acute corneal pain in rats. Acute corneal pain was induced by local application of a drop of 5 M NaCl solution on the corneal surface. The number of eye wipes was taken as a pain response, and counted during the first 30 s. Crocin injected i.p. and i.c.v. and morphine injected i.p. significantly (p < 0.05) decreased the number of eye wipes. Morphine (i.p.)-induced antinociception was significantly (p < 0.05) increased by the systemically and centrally injected crocin. The antinociceptive effects induced by i.p. and i.c.v. injections of crocin were not reversed by i.p. injection of naloxone. These findings indicated that both crocin and morphine attenuated hypertonic saline-induced corneal pain. The opioid receptors may not be involved in the analgesic mechanism of crocin.
Active suspension control using a novel strut and active filtered feedback: design and implementation (2003)

An active suspension control approach is designed for a quarter-vehicle suspension system using a filtered feedback control scheme and a novel compressible fluid suspension system. Analysis of feedback for the mechanical subsystem shows that motions of the sprung mass above and below the wheel frequency can be mitigated using skyhook damping plus active filtering of spring and damping coefficients. The frequency-dependent filtering is accomplished through an outer control loop that generates the target strut force, plus an inner force control loop. Performance of the active suspension control is demonstrated in simulations.
Sol−Gel Materials as Efficient Enzyme Protectors:  Preserving the Activity of Phosphatases under Extreme pH Conditions (2005)

By entrapment in (surfactant modified) silica sol-gel matrixes, alkaline phosphatase (AlP) -- naturally with optimum activity at pH 9.5 -- was kept functioning at extreme acidic environments as low as pH 0.9, and acid phosphatase (AcP) -- naturally with optimum activity at pH 4.5 -- was kept functioning at extreme alkaline environments, up to pH 13.0. Propositions are offered as to the origin of the ability of the matrixes to provide such highly efficient protection and as to the origin of the synergetic enhancing effect when both the silica and the surfactants are used as a combined entrapping environment. It was found that the protectability of the enzymes against harsh pH values is dependent on the nature of the surfactant.
The Digital and Electronic Revolution in Social Work: Rethinking the Meaning of Ethical Practice (2012)

The recent and dramatic emergence of digital and other electronic technology in social work—such as online counseling, video counseling, avatar therapy, and e-mail therapy—has tested and challenged the profession's longstanding and widely accepted perspectives on the nature of both clinical relationships and core ethics concepts. These developments have transformed key elements of social work practice and require critical examination of the meaning and application of relevant ethical concepts in diverse cultures. This article explores pertinent ethical implications related to social workers' commitment to clients; privacy/confidentiality; client self-determination and professional paternalism; informed consent; and professional–client boundaries and dual relationships. The author discusses the need for social workers to re-examine time-honored ethics concepts and explore their implications for the profession's ethical standards pertaining to the practitioner–client relationship.
The GreenCut2 Resource, a Phylogenomically Derived Inventory of Proteins Specific to the Plant Lineage (2011)

The plastid is a defining structure of photosynthetic eukaryotes and houses many plant-specific processes, including the light reactions, carbon fixation, pigment synthesis, and other primary metabolic processes. Identifying proteins associated with catalytic, structural, and regulatory functions that are unique to plastid-containing organisms is necessary to fully define the scope of plant biochemistry. Here, we performed phylogenomics on 20 genomes to compile a new inventory of 597 nucleus-encoded proteins conserved in plants and green algae but not in non-photosynthetic organisms. 286 of these proteins are of known function, whereas 311 are not characterized. This inventory was validated as applicable and relevant to diverse photosynthetic eukaryotes using an additional eight genomes from distantly related plants (including Micromonas, Selaginella, and soybean). Manual curation of the known proteins in the inventory established its importance to plastid biochemistry. To predict functions for the 52% of proteins of unknown function, we used sequence motifs, subcellular localization, co-expression analysis, and RNA abundance data. We demonstrate that 18% of the proteins in the inventory have functions outside the plastid and/or beyond green tissues. Although 32% of proteins in the inventory have homologs in all cyanobacteria, unexpectedly, 30% are eukaryote-specific. Finally, 8% of the proteins of unknown function share no similarity to any characterized protein and are plant lineage-specific. We present this annotated inventory of 597 proteins as a resource for functional analyses of plant-specific biochemistry.
[The clinical significance of changes in immunological function of T lymphocyte in severe burn patients with sepsis]. (2007)

The immunological function of T lymphocyte in severely burn patients with sepsis is depressed persistently. Apoptosis of T lymphocyte may participate in the pathological process of cell immunological disorder induced by sepsis.