gebhart/patrepeval huggingface dataset:
Delayed Inflammatory Response to Primary Pneumonic Plague Occurs in Both Outbred and Inbred Mice (2006)

Yersinia pestis is the causative agent of plague, a disease that can manifest as either bubonic or pneumonic plague. An interesting feature of plague is that it is a rapidly progressive disease, suggesting that Y. pestis either evades and/or suppresses the innate immune response to infection. Therefore, the early host response during the course of primary pneumonic plague was investigated in two mouse strains, the outbred strain CD1 and the inbred strain C57BL/6. A comparative analysis of the course of disease in these two strains of mice indicated that they are susceptible to intranasal Y. pestis CO92 infection and have similar 50% lethal doses and kinetics of infection with respect to colonization of the lung, liver, and spleen. Significantly, in both strains of mice, robust neutrophil recruitment to the lungs was not observed until 48 h after infection, suggesting that there was a delay in inflammatory cell recruitment to the site of infection. In addition, proinflammatory cytokines (interleukin-6 [IL-6], tumor necrosis factor alpha, gamma interferon, IL-12p70, monocyte chemoattractant protein 1) and chemokines (KC, MIP-2) in the bronchoalveolar lavage fluids were not readily detected until 48 h after infection, which coincided with the increase in polymorphonuclear leukocyte (PMN) recruitment to the lungs. In comparison, CD1 mice with gram-negative pneumonia caused by Klebsiella pneumoniae exhibited strong inflammatory responses early in infection, with PMNs comprising the majority of the cells in the bronchoalveolar lavage fluid 24 h postinfection, indicating that PMN recruitment to the lungs could occur earlier in this infection than in Y. pestis infection. Together, our results indicate that there is a delay in the recruitment of neutrophils to the lungs in the mouse model of primary plague pneumonia that correlates with delayed expression of proinflammatory cytokines and chemokines in both outbred and inbred mice.
Newer antihypertensive drugs (1995)

We review three new classes of antihypertensive drugs: imidazolines, monatepil, and neutral endopeptidase inhibitors. Imidazolines are a new generation of central acting drugs. Because of their greater affinity for imidazoline receptors rather than alpha 2-adrenoreceptors, they cause less fatigue and dry mouth than the older central acting drugs. Monatepil is a single drug with both calcium antagonist and peripheral alpha 1-antagonist properties. This agent not only lowers blood pressure but also lowers serum cholesterol, an effect mediated by its alpha-antagonism, and has anti-lipid peroxidation properties. Monatepil might become an effective antiatherosclerosis drug. Neutral endopeptidase inhibitors lower blood pressure by inhibiting the metabolism of atrial natriuretic peptide and other vasoactive peptides.
Clinical Manifestations of Sarin Nerve Gas Exposure (2003)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
Discovery of a New Class of Potent, Selective, and Orally Bioavailable CRTH2 (DP2) Receptor Antagonists for the Treatment of Allergic Inflammatory Diseases (2008)

A novel chemical class of potent chemoattractant receptor-homologous expressed on Th2 lymphocytes (CRTH2 or DP2) antagonists is reported. An initial and moderately potent spiro-indolinone compound ( 5) was found during a high-throughput screening campaign. Structure-activity relationship (SAR) investigation around the carboxylic acid group revealed that changes in this part of the molecule could lead to a reversal of functional activity, yielding weakly potent agonists. SAR investigation of the succinimide functional group led to the discovery of several single-digit nanomolar antagonists. The potency of these compounds was confirmed in a human eosinophil chemotaxis assay. Moreover, compounds ( R)- 58 and ( R)- 71 were shown to possess pharmacokinetic properties suitable for development as an orally bioavailable drug.
A noninstrumented quantitative test system and its application for determining cholesterol concentration in whole blood (1990)

A novel noninstrumented technology has been developed for quantifying analytes of clinical interest in biological fluids. Application of this technology is exemplified by the development of a quantitative cholesterol test with performance equivalent to state-of-the-art instrumented methods. The assay chemistry combines two separate processes located in different areas of a test strip: enzymatic action on serum cholesterol to produce hydrogen peroxide (5 x 10 mm enzyme reagent pad) and quantification of the hydrogen peroxide (5 x 70 mm measurement region). Color bands are formed in the measurement area through the use of a redox-coupled indicator system. The height of the color band on the strip is directly proportional to the sample cholesterol concentration. A one-step cassette contains all components necessary to run the test and includes blood filtration and automatic sample measurement, so that unmeasured finger-stick whole-blood specimens can be analyzed by the non-technically trained user. The test is complete in less than 15 min, is read visually like a thermometer, and gives results that are in excellent correlation with established instrumented methods.
Statistical Tools to Analyze Continuous Glucose Monitor Data (2009)

Continuous glucose monitors (CGMs) generate data streams that are both complex and voluminous. The analyses of these data require an understanding of the physical, biochemical, and mathematical properties involved in this technology. This article describes several methods that are pertinent to the analysis of CGM data, taking into account the specifics of the continuous monitoring data streams. These methods include: (1) evaluating the numerical and clinical accuracy of CGM. We distinguish two types of accuracy metrics-numerical and clinical-each having two subtypes measuring point and trend accuracy. The addition of trend accuracy, e.g., the ability of CGM to reflect the rate and direction of blood glucose (BG) change, is unique to CGM as these new devices are capable of capturing BG not only episodically, but also as a process in time. (2) Statistical approaches for interpreting CGM data. The importance of recognizing that the basic unit for most analyses is the glucose trace of an individual, i.e., a time-stamped series of glycemic data for each person, is stressed. We discuss the use of risk assessment, as well as graphical representation of the data of a person via glucose and risk traces and Poincaré plots, and at a group level via Control Variability-Grid Analysis. In summary, a review of methods specific to the analysis of CGM data series is presented, together with some new techniques. These methods should facilitate the extraction of information from, and the interpretation of, complex and voluminous CGM time series.
Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis (2020)

We provide a single-cell atlas of idiopathic pulmonary fibrosis (IPF), a fatal interstitial lung disease, by profiling 312,928 cells from 32 IPF, 28 smoker and nonsmoker controls, and 18 chronic obstructive pulmonary disease (COPD) lungs. Among epithelial cells enriched in IPF, we identify a previously unidentified population of aberrant basaloid cells that coexpress basal epithelial, mesenchymal, senescence, and developmental markers and are located at the edge of myofibroblast foci in the IPF lung. Among vascular endothelial cells, we identify an ectopically expanded cell population transcriptomically identical to bronchial restricted vascular endothelial cells in IPF. We confirm the presence of both populations by immunohistochemistry and independent datasets. Among stromal cells, we identify IPF myofibroblasts and invasive fibroblasts with partially overlapping cells in control and COPD lungs. Last, we confirm previous findings of profibrotic macrophage populations in the IPF lung. Our comprehensive catalog reveals the complexity and diversity of aberrant cellular populations in IPF.
GeneXpert Captures Unstable Methicillin-Resistant Staphylococcus aureus Prone to Rapidly Losing the mecA Gene (2010)

A cefoxitin-susceptible Staphylococcus aureus strain was identified by the Cepheid GeneXpert as methicillin-resistant S. aureus (MRSA). This strain was highly unstable and rapidly lost SCCmec upon subculturing in vitro, indicating that unstable MRSA is best detected by gene amplification-based methods.
Resistivity and dissipation in pulsar magnetospheres (2012)

Abstract Current models of pulsar magnetospheres typically assume either a complete absence of plasma or abundant ideal plasma filling the magnetosphere in order to compute the field structure. The latter condition is thought to be closer to reality, but we know of a number of pulsars in which the ideal conditions break down, resulting in dissipation and high-energy emission. In this work we formulate a resistive force-free scheme that allows us to consider the effects of resistive plasma and accelerating fields on the magnetospheric structure. We run numerical simulations to construct a family of resistive solutions that smoothly bridges the gap between the vacuum and the force-free magnetosphere solutions. We further provide a self-consistent model for the spin-down of intermittent pulsars, pulsars which appear to transition between radio-loud and radio-quiet states with different spin-down rates. Finally, we present models for high-energy emission from reconnecting current sheets in Gamma-ray pulsars.
THE VASCULAR REACTION OF TUBULAR BONE TO ISCHAEMIA IN PERIPHERAL OCCLUSIVE VASCULAR DISEASE (1960)

1. Twenty-five lower limbs, amputated above the knee for senile atherosclerosis with peripheral gangrene, have been investigated radiologically and histologically to determine the vascular patterns in ischaemic bone with particular reference to the tibia. These have been contrasted with the patterns found in non-atherosclerotic tubular bone. 2. The principal changes are the development of a diffuse vascularisation of compact and spongy bone; a widening of Haversian spaces which come to contain a variable number of sinusoidal blood vessels; and an increasing periosteal participation in cortical nutrition which is related to the severity and chronicity of the ischaemic process. 3. Views on the normal blood supply of long bones are discussed, and evidence is presented for regarding this as discrete and end-arterial in nature; in particular it is suggested that the normal cortex has a wholly medullary, centrifugal, arterial supply.
Explicit identification and implicit recognition of facial emotions: I. Age effects in males and females across 10 decades (2008)

A number of psychiatric and neurological disorders are characterized by impairments in facial emotion recognition. Recognition of individual emotions has implicated limbic, basal ganglionic, and frontal brain regions. Since these regions are also implicated in age-related decline and sex differences in emotion processing, an understanding of normative variation is important for assessing deficits in clinical groups. An internet-based test ("WebNeuro") was administered to 1,000 healthy participants (6 to 91 years, 53% female) to assess explicit identification of basic expressions of emotion (happiness, sadness, fear, anger, disgust, neutral). A subsequent implicit recognition condition was based on a priming protocol, in which explicit identification provided the "study" phase. Responses were most accurate for happiness and slowest for fear in the explicit condition, but least accurate for happiness and fastest for fear in the implicit condition. The effects of age, by contrast, showed a similar pattern for both explicit and implicit conditions, following a nonlinear distribution in which performance improved from childhood through adolescence and early adulthood and declined in later adulthood. Females were better than males at explicit identification of fear in particular. These findings are consistent with the priority of threat-related signals, but indicate opposing biases depending on whether emotion processing is conscious or nonconscious. The lifespan trends in emotion processing over 10 decades point to an interaction of brain-based (maturation, stability, and then atrophy of cortical and subcortical systems) and experiential contributing factors. These findings provide a robust normative platform for assessing clinical groups.
Correlates of protection induced by live Aro−Salmonella typhimurium vaccines in the murine typhoid model (1997)

Live attenuated salmonella vaccines generally confer better protection than killed vaccines. The immune responses in BALB/c mice elicited by immunization with a live attenuated Aro Salmonella typhimurium vaccine given orally, intravenously or subcutaneously were compared with those elicited by killed whole-cell vaccines (acetone or heat-treated) given subcutaneously. Live vaccines given by all routes elicited higher interleukin-2 (IL-2) and interferon-gamma (IFN-gamma) responses in spleen cells against an alkali-treated whole-cell salmonella lysate than did killed vaccines. Live and killed vaccines elicited high total antibody levels to smooth lipopolysaccharide (LPS) (enzyme-linked immunosorbent assay), but all live vaccine regimes elicited higher IgG2a, suggesting a Th1 response. Oral and intravenous vaccination with live organisms elicited IgA against smooth LPS which subcutaneous vaccination with live or killed salmonellae failed to evoke. Western blots using rough whole-cell lysates showed that all vaccines elicited a varied anti-protein response; however, all groups immunized with live organisms recognized three unidentified bands of MW 52,000, 46,000 and 18,000 which were consistently absent in groups immunized with killed organisms. The results indicate that immunization with live aroA salmonellae elicited a Th1 type of response, including bystander T-cell help to LPS, and a response to proteins not seen in mice that received killed vaccines.
Finding common sequence and structure motifs in a set of RNA sequences. (1997)

We present a computational scheme to search for the most common motif, composed of a combination of sequence and structure constraints, among a collection of RNA sequences. The method uses a simplified version of the Sankoff algorithm for simultaneous folding and alignment of RNA sequences, but maintains tractability by constructing multi-sequence alignments from pairwise comparisons. The overall method has similarities to both CLUSTAL and CONSENSUS, but the core algorithm assures that the pairwise alignments are optimized for both sequence and structure conservation. Example solutions, and comparisons with other approaches, are provided. The solutions include finding consensus structures identical to published ones.
Temporal and spatial evolution of a laser induced plasma from a steel target (2002)

Temporally and spatially resolved measures of emission lines by a photomultiplier and shadow images by a frame camera were used to study the dynamical evolution of different elements in a steel plume in air produced by a Q-switched Nd:Yag laser.
Highly Purified Lipoteichoic Acid fromStaphylococcus aureusInduces Procoagulant Activity and Tissue Factor Expression in Human Monocytes but Is a Weak Inducer in Whole Blood: Comparison with Peptidoglycan (2004)

Lipoteichoic acid from Staphylococcus aureus was a potent inducer of procoagulant activity in isolated mononuclear cells but not in whole blood. In contrast, staphylococcal peptidoglycan showed equal levels of potency in isolated mononuclear cells and whole blood, suggesting that peptidoglycan is an important inducer of procoagulant activity in severe sepsis involving gram-positive bacteria.
Extending assembly of short DNA sequences to handle error (2007)

http://152.2.15.114/~labweb/VCAKE
Compiler-based prefetching for recursive data structures (1996)

Software-controlled data prefetching offers the potential for bridging the ever-increasing speed gap between the memory subsystem and today's high-performance processors. While prefetching has enjoyed considerable success in array-based numeric codes, its potential in pointer-based applications has remained largely unexplored. This paper investigates compiler-based prefetching for pointer-based applications---in particular, those containing recursive data structures. We identify the fundamental problem in prefetching pointer-based data structures and propose a guideline for devising successful prefetching schemes. Based on this guideline, we design three prefetching schemes, we automate the most widely applicable scheme ( greedy prefetching ) in an optimizing research compiler, and we evaluate the performance of all three schemes on a modern superscalar processor similar to the MIPS R10000. Our results demonstrate that compiler-inserted prefetching can significantly improve the execution speed of pointer-based codes---as much as 45% for the applications we study. In addition, the more sophisticated algorithms (which we currently perform by hand, but which might be implemented in future compilers) can improve performance by as much as twofold. Compared with the only other compiler-based pointer prefetching scheme in the literature, our algorithms offer substantially better performance by avoiding unnecessary overhead and hiding more latency.
Channel estimation for ultra-wideband communications (2002)

This paper deals with channel estimation in ultra-wideband communications operating in a multipath environment and in the presence of multiaccess interference. The channel parameters are the attenuations and delays incurred by the signal echoes along the propagation paths. Time-hopping modulation with binary symbols is assumed. The estimation method is based on the maximum-likelihood criterion and is applied to two different scenarios: either with known symbols (DA estimation) or with unknown symbols (NDA estimation). The effects of the estimation errors on the performance of a RAKE receiver are assessed by simulation by comparing the receiver bit-error rate with either perfect channel estimates or imperfect estimates as obtained from the proposed algorithms. The results show that the degradations are tolerable as long as the number of users is limited. They also show that the DA method has an edge over the NDA in that it can handle a larger number of users for a fixed degradation. The number of users that can be accommodated in practice is found for some values of the system parameters.
A High-avidity WT1-reactive T-Cell Receptor Mediates Recognition of Peptide and Processed Antigen but not Naturally Occurring WT1-positive Tumor Cells (2016)

Wilms tumor gene 1 (WT1) is an attractive target antigen for cancer immunotherapy because it is overexpressed in many hematologic malignancies and solid tumors but has limited, low-level expression in normal adult tissues. Multiple HLA class I and class II restricted epitopes have been identified in WT1, and multiple investigators are pursuing the treatment of cancer patients with WT1-based vaccines and adoptively transferred WT1-reactive T cells. Here we isolated an HLA-A*0201-restricted WT1-reactive T-cell receptor (TCR) by stimulating peripheral blood lymphocytes of healthy donors with the peptide WT1:126-134 in vitro. This TCR mediated peptide recognition down to a concentration of ∼0.1 ng/mL when pulsed onto T2 cells as well as recognition of HLA-A*0201 target cells transfected with full-length WT1 cDNA. However, it did not mediate consistent recognition of many HLA-A*0201 tumor cell lines or freshly isolated leukemia cells that endogeneously expressed WT1. We dissected this pattern of recognition further and observed that WT1:126-134 was more efficiently processed by immunoproteasomes compared with standard proteasomes. However, pretreatment of WT1 tumor cell lines with interferon gamma did not appreciably enhance recognition by our TCR. In addition, we highly overexpressed WT1 in several leukemia cell lines by electroporation with full-length WT1 cDNA. Some of these lines were still not recognized by our TCR suggesting possible antigen processing defects in some leukemias. These results suggest WT1:126-134 may not be a suitable target for T-cell based tumor immunotherapies.
HIV-1 TAR RNA: The Target of Molecular Interactions Between the Virus and its Host (2005)

HIV-1 TAR RNA is the binding site of the viral protein Tat, the trans-activator of the HIV-1 LTR. It is present at the 5' end of all HIV-1 spliced and unspliced mRNAs in the nucleus as well as in the cytoplasm. It has a highly folded stem-bulge-loop structure, which also binds cellular proteins to form ribonucleoprotein complexes. The Tat-Cyclin T1-CDK9 complex is the main component in the trans-activation of HIV-1 and its affinity for TAR is regulated through Tat acetylation by histone acetyl transferases. Recent studies show that this complex is able to recruit other cellular partners to mediate efficient transcriptional elongation. TRBP, PKR and La bind directly to the TAR RNA structure and influence translation of HIV-1 in either positive or negative manners. Some mutations in TAR RNA severely impair HIV-1 trans-activation, translation and viral production, showing its functional importance. The overexpression or suppression of several TAR RNA-binding proteins has a strong impact on viral replication pointing out their major role in the viral life cycle. TAR RNA has been the target of drug development to inhibit viral replication. Recent data using small molecules or RNA-based technologies show that acting on the TAR RNA or on its viral and cellular binding factors effectively decreases virion production.