gebhart/patrepeval huggingface dataset:
Diagnostic performance of amplified Mycobacterium tuberculosis direct test with cerebrospinal fluid, other nonrespiratory, and respiratory specimens (1996)

The Gen-Probe Amplified Mycobacterium tuberculosis Direct Test (MTD) was adapted to be used for cerebrospinal fluid (CSF) and a large variety of other nonrespiratory specimens. Standardized with artificially spiked dilution series of CSF, the modified MTD procedure consists of (i) increasing the amount of sample 10-fold, (ii) pretreating the specimen with a detergent, and (iii) increasing the amplification time from 2 to 3 h. Performance of MTD in a clinical mycobacteriology laboratory was tested over an extended period of time, involving a total of 322 nonrespiratory as well as 1,117 respiratory specimens from 998 patients. Results from MTD were compared with those from microscopy, culture, analysis of tuberculostearic acid by gas-liquid chromatography-mass spectrometry (CSF only), and the final clinical diagnosis. When MTD results were compared with resolved data, the sensitivity, specificity, and positive and negative predictive values for MTD were 93.1, 97.7, 90.0, and 98.5%, respectively, for nonrespiratory specimens and 86.6, 96.4, 76.8, and 98.1%, respectively, for respiratory specimens. Our data demonstrate that (i) MTD is a robust, highly sensitive and specific technique for the rapid detection of M. tuberculosis complex in all types of clinical specimens, (ii) there was no statistically significant difference (P > 0.005) in sensitivity and specificity for nonrespiratory compared with respiratory specimens, and (iii) repeating all MTDs which yield a result between 30,000 and 200,000 relative light units would help prevent a large number of false positives and, thus, enhance test specificity.
Increased Specificity of Serodiagnosis of Chagas' Disease by Detection of Antibody to the 72- and 90-Kilodalton Glycoproteins of Trypanosoma cruzi (1987)

Journal Article Increased Specificity of Serodiagnosis of Chagas' Disease by Detection of Antibody to the 72- and 90-Kilodalton Glycoproteins of Trypanosoma cruzi Get access Louis V. Kirchhoff, Louis V. Kirchhoff Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland; and the Department of Internal Medicine, Universidade Federal de Goiás, Goiânia, Goiás, Brazil Please address requests for reprints to Dr. Louis V. Kirchhoff, Division of Infectious Diseases, Department of Medicine, University of Iowa, Iowa City, Iowa 52242. Search for other works by this author on: Oxford Academic PubMed Google Scholar Albert A. Gam, Albert A. Gam Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland; and the Department of Internal Medicine, Universidade Federal de Goiás, Goiânia, Goiás, Brazil Search for other works by this author on: Oxford Academic PubMed Google Scholar Renald d'A Gusmao, Renald d'A Gusmao Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland; and the Department of Internal Medicine, Universidade Federal de Goiás, Goiânia, Goiás, Brazil Search for other works by this author on: Oxford Academic PubMed Google Scholar Robert S. Goldsmith, Robert S. Goldsmith Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland; and the Department of Internal Medicine, Universidade Federal de Goiás, Goiânia, Goiás, Brazil Search for other works by this author on: Oxford Academic PubMed Google Scholar Jofre M. Rezende, Jofre M. Rezende Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland; and the Department of Internal Medicine, Universidade Federal de Goiás, Goiânia, Goiás, Brazil Search for other works by this author on: Oxford Academic PubMed Google Scholar Anis Rassi Anis Rassi Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland; and the Department of Internal Medicine, Universidade Federal de Goiás, Goiânia, Goiás, Brazil Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Infectious Diseases, Volume 155, Issue 3, March 1987, Pages 561–564, https://doi.org/10.1093/infdis/155.3.561 Published: 01 March 1987 Article history Received: 19 March 1986 Revision received: 26 August 1986 Published: 01 March 1987
Sumoylation of eukaryotic elongation factor 2 is vital for protein stability and anti‐apoptotic activity in lung adenocarcinoma cells (2011)

By screening mouse monoclonal antibody libraries for Kelch repeats, we serendipitously identified monoclonal antibodies to eukaryotic elongation factor 2 (eEF2). Interestingly, eEF2 was highly expressed in lung adenocarcinoma (LADC), but not in the neighboring non-tumor lung tissue. Normally, eEF2 is involved in the peptidyl-tRNA translocation during protein synthesis. Overexpression of eEF2 would implicate an association with disease progression of LADC. In the present study, we investigated the prognostic significance of eEF2 in patients with LADC. Expression of eEF2 was detected by immunoblotting, immunohistochemistry and confocal immunofluorescence microscopy. Our results show that patients with high eEF2 expression had a significantly higher incidence of early tumor recurrence (67.8%vs 18.2%, P = 0.016), and a significantly worse prognosis (P < 0.001). In an in vitro study, silencing of eEF2 expression increased mitochondrial elongation, cellular autophagy and cisplatin sensitivity. Moreover, eEF2 was sumoylated in LADC cells, and eEF2 sumoylation correlated with drug resistance. These results suggest that eEF2 is an anti-apoptotic marker in LADC. However, biological function and involvement of eEF2 in the disease progression of LADC require further studies.
Reconfigurable Architectures for Low Complexity Software Radio Channelizers using Hybrid Filter Banks (2006)

The flexibility of a software-defined radio (SDR) depends on its capability to operate in multi-standard wireless communication environments. The most computationally intensive part of the digital front end of an SDR receiver is the channelizer, which extracts multiple narrowband signals from a wideband input signal. The compatibility of the channnelizer with different communications standard is guaranteed by its reconfigurability. Low power and high-speed are the two other desirable characteristics of a channelizer. This paper presents a combinational architecture based on discrete Fourier transform filter bank and quadrature mirror filter bank trees for realizing a reconfigurable low complexity high-speed channelizer. Our hybrid channelizer has an additional complexity of 38% over the quadrature mirror filter bank, but the delay of the former is reduced by 94% when compared to the latter. Thus the proposed channelizer architecture offers a better trade-off between the complexity and delay
Designer Natriuretic Peptides (2009)

Designer natriuretic peptides (NPs) are novel hybrid peptides that are engineered from the native NPs through addition, deletion, or substitution of amino acid(s) with a goal toward optimization of pharmacological actions while minimizing undesirable effects. In this article, selected peptides that were designed in our laboratory are reviewed, and future directions for research and development of designer NPs are discussed.
MicroRNA Dysregulation in Cutaneous Squamous Cell Carcinoma (2019)

Cutaneous squamous cell carcinoma (CSCC) is the second most frequent cancer in humans and it can be locally invasive and metastatic to distant sites. MicroRNAs (miRNAs or miRs) are endogenous, small, non-coding RNAs of 19-25 nucleotides in length, that are involved in regulating gene expression at a post-transcriptional level. MicroRNAs have been implicated in diverse biological functions and diseases. In cancer, miRNAs can proceed either as oncogenic miRNAs (onco-miRs) or as tumor suppressor miRNAs (oncosuppressor-miRs), depending on the pathway in which they are involved. Dysregulation of miRNA expression has been shown in most of the tumors evaluated. MiRNA dysregulation is known to be involved in the development of cutaneous squamous cell carcinoma (CSCC). In this review, we focus on the recent evidence about the role of miRNAs in the development of CSCC and in the prognosis of this form of skin cancer.
Sex differences in and effects of estrogen on oxytocin receptor messenger ribonucleic acid expression in the ventromedial hypothalamus. (1995)

In situ hybridization techniques were used in the present study to detect hypothalamic expression of the oxytocin receptor (OR) gene. Binding studies have localized OR to various brain regions and have detected a high density of receptors in the ventromedial hypothalamus (VMH), a documented target of estrogen action. This study was designed to compare levels of OR messenger RNA (mRNA) in the VMH of male and female rats and to study the effects of estrogen treatment on mRNA levels in the VMH of female rats. After cloning a rat OR gene from a genomic testes library, a probe was generated for use in in situ hybridization assays to evaluate sex differences in OR mRNA expression in the VMH. In addition, ovariectomized females were treated with estrogen, and VMH OR mRNA expression was compared with that in ovariectomized or intact females. The results of these studies showed that male rats expressed higher levels of OR mRNA in the VMH than females. Estrogen-treated ovariectomized females exhibited significantly greater expression in the VMH than either oil-treated or intact females. These results support binding studies that have shown oxytocin binding in the VMH to be regulated by gonadal steroids and suggest that estrogen may either directly or indirectly regulate transcription of the OR gene.
Coil design considerations for deep-brain transcranial magnetic stimulation (dTMS) (2008)

Deep-brain transcranial magnetic stimulation (dTMS) could provide new, non-invasive therapeutic options for various psychiatric and neurological disorders. Figures of merit (FoMs) are proposed to evaluate and compare dTMS coil designs. These FoMs characterize the depth of electric field penetration, scalp stimulation, focality, and energy. Two coil configurations potentially suitable for dTMS are analyzed: circular crown coil and C-core coil. These coils have significantly less attenuation of the electric field strength in depth, compared to conventional TMS coils. In the limiting case as the coil dimensions become large relative to the head, the electric field decay in depth becomes linear, which indicates that, at best, the electric field attenuation is directly proportional to the depth of the target. The charge density and heating induced in the brain are at safe levels, but the risk of unintended neuromodulation and seizures with dTMS has to be evaluated further. Preliminary simulation results suggest that the crown coil has the best overall performance for dTMS. Finally, synchronous firing of all TMS coil elements appears more effective at stimulating deep neurons than is sequential firing.
HIGH-PRESSURE LASER ACTION IN 13 GASES WITH TRANSVERSE EXCITATION (1971)

Laser action has been achieved in 13 gases at high pressures using pulsed transverse excitation. A total of 149 wavelengths from 0.8 to 28μ was observed. Pulse lengths were found to lie in the range 0.2–5μsec. Several gases operate at atmospheric pressure and above and promise to give very high power outputs.
Switched-capacitor second-order noise-shaping coder (1983)

The rapid development of digital processing in the fields of instrumentation, control and communications has generated a good deal of research into simple, easily integrable, high-resolution A/D converters. Given the significant promise such converters offer for future application, a switched-capacitor version of a second-order noise-shaping coder intended for high-resolution conversion has been realised. This coder has been used successfully to produce a PCM signal.
Cost of Neuromodulation Therapies for Overactive Bladder: Percutaneous Tibial Nerve Stimulation Versus Sacral Nerve Stimulation (2012)

Percutaneous tibial nerve stimulation and sacral nerve stimulation are safe, effective neuromodulation therapies for overactive bladder. In this economic model percutaneous tibial nerve stimulation had substantially lower cost. An additional 1% of patients would remain on therapy at 2 years if sacral nerve stimulation were used rather than percutaneous tibial nerve stimulation but the average cost per additional patient would be more than $500,000.
The third wave of myotome colonization by mitotically competent progenitors: regulating the balance between differentiation and proliferation during muscle development (2001)

The myotome is formed by a first wave of pioneer cells originating from the entire dorsomedial region of epithelial somites and a second wave that derives from all four lips of the dermomyotome but generates myofibers from only the rostral and caudal edges. Because the precedent progenitors exit the cell cycle upon myotome colonization, subsequent waves must account for consecutive growth. In this study, double labeling with CM-DiI and BrdU revealed the appearance of a third wave of progenitors that enter the myotome as mitotically active cells from both rostral and caudal dermomyotome edges. These cells express the fibroblast growth factor (FGF) receptor FREK and treatment with FGF4 promotes their proliferation and redistribution towards the center of the myotome. Yet, they are negative for MyoD, Myf5 and FGF4, which are, however, expressed in myofibers. The proliferating progenitors first appear around the 30-somite stage in cervical-level myotomes and their number continuously increases, making up 85% of total muscle nuclei by embryonic day (E)4. By this stage, generation of second-wave myofibers, which also enter from the extreme lips is still under way. Formation of the latter fibers peaks at 30 somites and progressively decreases with age until E4. Thus, cells in these dermomyotome lips generate simultaneously distinct types of muscle progenitors in changing proportions as a function of age. Consistent with a heterogeneity in the cellular composition of the extreme lips, MyoD is normally expressed in only a subset of these epithelial cells. Treatment with Sonic hedgehog drives most of them to become MyoD positive and then to become myofibers, with a concurrent reduction in the proportion of proliferating muscle precursors.
Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM) (2011)

Abstract Motivation: A critical task in high-throughput sequencing is aligning millions of short reads to a reference genome. Alignment is especially complicated for RNA sequencing (RNA-Seq) because of RNA splicing. A number of RNA-Seq algorithms are available, and claim to align reads with high accuracy and efficiency while detecting splice junctions. RNA-Seq data are discrete in nature; therefore, with reasonable gene models and comparative metrics RNA-Seq data can be simulated to sufficient accuracy to enable meaningful benchmarking of alignment algorithms. The exercise to rigorously compare all viable published RNA-Seq algorithms has not been performed previously. Results: We developed an RNA-Seq simulator that models the main impediments to RNA alignment, including alternative splicing, insertions, deletions, substitutions, sequencing errors and intron signal. We used this simulator to measure the accuracy and robustness of available algorithms at the base and junction levels. Additionally, we used reverse transcription–polymerase chain reaction (RT–PCR) and Sanger sequencing to validate the ability of the algorithms to detect novel transcript features such as novel exons and alternative splicing in RNA-Seq data from mouse retina. A pipeline based on BLAT was developed to explore the performance of established tools for this problem, and to compare it to the recently developed methods. This pipeline, the RNA-Seq Unified Mapper (RUM), performs comparably to the best current aligners and provides an advantageous combination of accuracy, speed and usability. Availability: The RUM pipeline is distributed via the Amazon Cloud and for computing clusters using the Sun Grid Engine (http://cbil.upenn.edu/RUM). Contact: ggrant@pcbi.upenn.edu; epierce@mail.med.upenn.edu Supplementary Information:The RNA-Seq sequence reads described in the article are deposited at GEO, accession GSE26248.
Highly Efficient Green‐Light‐Emitting Diodes Based on CdSe@ZnS Quantum Dots with a Chemical‐Composition Gradient (2009)

Highly efficient green-light-emitting diodes (LEDs) based on [email protected] quantum dots (QDs) with a chemical-composition gradient are demonstrated. Through the moderate control of QD coverage in multilayered devices, excellent device performance has been achieved. The color-saturated green-light emission (see figure for Commission Internationale de l'Eclairage (CIE) co-ordinates) is mainly from the QD layers (more than 99% of total emission). Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
The Pharmacokinetics and Safety of Deuterated-Tetrabenazine (P07.210) (2013)

OBJECTIVE: To compare the pharmacokinetics (PK) of deuterated-tetrabenazine (SD-809) and tetrabenazine (TBZ) and their respective metabolites.
Microeeonomics in Context (2006)

Neva Goodwin / Julie A. Nelson / Frank Ackerman / Thomas Weisskopt: Microeeonomics in Context* ISBN 0-618-34599-X, Boston: Houghton Mifflin Company, 2005, $79.56 What a pleasure to find an introductory microeconomics textbook that's written to support - rather than hinder - a comprehensive introduction to microeconomics! At last, a book that takes seriously the contributions of the household and the environment, emphasizes human wellbeing rather than GDP, discusses market structures as they are visible to students rather than as non-existent idealized types, explains something of the spectrum of schools of economics thought, includes historical and institutional context AND retains the core of the neoclassical analytical framework in a wellwritten, accessible textbook format! In the nearly fifteen years that I've been teaching, I have found textbooks to be increasingly, frustratingly focused on the sterile mind games that perhaps intrigue their authors: If the world were not as it is, but like this instead, and then we changed that and that, this would happen! Or, perhaps worse, the texts seem driven by the political winds, and geared toward a one-size fits all market. Early in my teaching career, I found myself in an argument with the author of a widely used principles text, who had come to town to reclaim his turf after learning that my department would no longer buy his book en masse, but shift to a policy of allowing each faculty member to select his or her own text. Having heard, I suppose, that I had been instrumental in that decision, his associates called me several times to let me know that I could have lunch with the author! When I declined, the author dropped by my office in person to see why I didn't want to order his book. When I told him that it was important to me to use a text that substantively treated issues of income distribution, poverty, discrimination and unpaid work, he grew angry, saying that he cared about these topics - and indeed, he used to publish on poverty - but that people didn't care about them anymore, so he couldn't include them. I found it astounding that an economist would resent the idea that people might use their market power to purchase what they wanted, and appalling that anyone would neglect the issue of poverty in introductory economics, not because it had been eradicated but because no-one wanted to talk about that anymore. I find that my students do want to talk about poverty, and discrimination and whether the Third World can develop in the present context. They want to know how human development and capacities, as understood by Amartya Sen and the United Nations Development Programme, can be facilitated as a goal of economic policy. They want to know if our economic system is compatible with valuing the environment. They want to find out why child care workers, who spend their time nurturing people and the future, earn so much less than people who organize corporate buyouts, creating no value at all? …
How to Make Analog-to-Information Converters Work in Dynamic Spectrum Environments With Changing Sparsity Conditions (2017)

Compressed sensing (CS) analog to information converters (AICs) offer key benefits for signal reception or detection when the input signal is sparse. So far AICs have been demonstrated in environments with controlled input signal conditions and with fixed sparsity levels. This paper investigates how to make AICs effectively operate in dynamic environments with changing signal conditions and thus changing sparsity levels. We focus on RF spectrum scanning, where signals or interferers need to be detected across a wide dynamic RF spectrum, but the presented concepts are widely applicable for low-pass and band-pass CS AICs. The number of measurements and hence the number of branches required in a CS RF front end scales with the sparsity level, i.e. the number of signals that need to be detected. In practice this leads to excessively large silicon area for more than a few signals (e.g., six). We introduce the time-segmented quadrature analog-to-information converter (TS-QAIC), a scalable architecture for signal detection in dynamically changing spectrum environments. While our TS-QAIC prototype implements a fixed number of hardware branches, we experimentally demonstrate adaptive thresholding and adaptive time segmentation to adjust its signal detection capability to the sparsity level of the input signal.
Expression of T cell receptor genes in human B cells. (1986)

We analyzed the transcription and rearrangement of the T cell antigen receptor (Ti) genes Ti alpha and Ti beta in human B cell, T cell, and myeloid cell lines, as well as in purified tonsillar B and T cells. All four B cell lines examined, as well as one of two myeloid cell lines, expressed low levels of truncated Ti beta transcripts, as did freshly purified tonsillar B cells. Two of the B cell lines and one of the myeloid lines also expressed truncated Ti alpha transcripts, while tonsillar B cells did not. Sequence analysis of cDNA clones from a B cell line demonstrated that these truncated Ti alpha and Ti beta transcripts were composed of unrearranged J and C gene segments. Comparison of cDNA clones from T and B cells suggests that D alpha genes or N regions contribute to the formation of Ti alpha transcripts in T cells but not in B cells. None of the B cell or myeloid cell lines in this study showed evidence of Ti beta gene rearrangements by Southern blotting. Our data, and other studies of gene rearrangements in human tumors, demonstrate that the level of Ti beta transcriptional activity and the frequency of Ti beta gene rearrangements are correlated in all cell types examined. Thus, our data support the accessibility model of antigen receptor gene rearrangement, whereby the susceptibility of gene segments to recombination enzymes is correlated with their transcriptional activity.