gebhart/patrepeval huggingface dataset:
High-Throughput, Signature-Tagged Mutagenic Approach To Identify Novel Virulence Factors of Yersinia pestis CO92 in a Mouse Model of Infection (2015)

The identification of new virulence factors in Yersinia pestis and understanding their molecular mechanisms during an infection process are necessary in designing a better vaccine or to formulate an appropriate therapeutic intervention. By using a high-throughput, signature-tagged mutagenic approach, we created 5,088 mutants of Y. pestis strain CO92 and screened them in a mouse model of pneumonic plague at a dose equivalent to 5 50% lethal doses (LD50) of wild-type (WT) CO92. From this screen, we obtained 118 clones showing impairment in disseminating to the spleen, based on hybridization of input versus output DNA from mutant pools with 53 unique signature tags. In the subsequent screen, 20/118 mutants exhibited attenuation at 8 LD50 when tested in a mouse model of bubonic plague, with infection by 10/20 of the aforementioned mutants resulting in 40% or higher survival rates at an infectious dose of 40 LD50. Upon sequencing, six of the attenuated mutants were found to carry interruptions in genes encoding hypothetical proteins or proteins with putative functions. Mutants with in-frame deletion mutations of two of the genes identified from the screen, namely, rbsA, which codes for a putative sugar transport system ATP-binding protein, and vasK, a component of the type VI secretion system, were also found to exhibit some attenuation at 11 or 12 LD50 in a mouse model of pneumonic plague. Likewise, among the remaining 18 signature-tagged mutants, 9 were also attenuated (40 to 100%) at 12 LD50 in a pneumonic plague mouse model. Previously, we found that deleting genes encoding Braun lipoprotein (Lpp) and acyltransferase (MsbB), the latter of which modifies lipopolysaccharide function, reduced the virulence of Y. pestis CO92 in mouse models of bubonic and pneumonic plague. Deletion of rbsA and vasK genes from either the Δlpp single or the Δlpp ΔmsbB double mutant augmented the attenuation to provide 90 to 100% survivability to mice in a pneumonic plague model at 20 to 50 LD50. The mice infected with the Δlpp ΔmsbB ΔrbsA triple mutant at 50 LD50 were 90% protected upon subsequent challenge with 12 LD50 of WT CO92, suggesting that this mutant or others carrying combinational deletions of genes identified through our screen could potentially be further tested and developed into a live attenuated plague vaccine(s).
Overview of Serum Uric Acid Treatment Targets in Gout: Why Less Than 6 mg/dL? (2016)

Gout is a progressive, painful, debilitating form of inflammatory arthritis. It is caused by factors that elevate the concentration of serum uric acid (sUA), leading to hyperuricemia (sUA >6.8 mg/dL). Continued elevated sUA can result in monosodium urate (MSU) crystal deposition in joints and soft tissues, and can cause acute and chronic inflammation. The prevalence of hyperuricemia and gout has increased over the last few decades, likely due to an aging population, changes in lifestyles and diet, and an increase in gout-associated comorbidities. Untreated or improperly treated gout can lead to chronic manifestation of the disease, including persistent inflammation, increased number of flares, development of tophi, and structural joint damage. Data show that even when patients are asymptomatic, ongoing inflammation and subsequent damage occurs locally at the joint and systemically. The aim of long-term treatment of gout is to reduce sUA levels to <6 mg/dL, which is below the saturation point of MSU (6.8 mg/dL), to inhibit formation of new crystals and to promote dissolution of existing crystals. Gout treatment should improve disease outcomes by eliminating gout flares, inducing long-term resolution of tophi, and more effectively managing comorbidities, many of which are associated with hyperuricemia. A number of studies have demonstrated that treating to the target of <6 mg/dL, by using effective therapies to lower sUA, results in reduction in the incidence of gout flares as well as shrinkage and eventual disappearance of tophi. Gout is often poorly managed due to a number of factors including lack of physician and patient adherence to treatment guidelines. Patients need to be educated about their diagnosis and management of the disease, such as the influence of diet and the importance of compliance with long-term treatment. With treatment, regular sUA monitoring, and patient adherence, gout is a curable disease.
Human Embryonic Stem Cell Lines and Their Use in International Research (2009)

Research in human pluripotent stem cells, including human embryonic stem cells (hESC) and human induced pluripotent stem cells (hiPSC), is one of the most dynamic research fields. Despite the high public attention, especially for hESC research, there is only scattered information on the number of hESC lines and the degree, dynamics, and diversification of their use on a global level. In this study we present data on the current number of publicly disclosed hESC lines, on the extent and impact of experimental work involving hESCs, and on the use of specific hESC lines in international research. The results are based on the evaluation of nearly 1,000 research papers published by the end of 2008, which describe experimental work on hESCs, and of a comprehensive database of published hESC lines. The average impact of hESC research papers is high at 7.422, with a predominance of research output by the United States. Of at least 1,071 original hESC lines derived up to November 2009 at 87 institutions in 24 countries, only a fraction is thoroughly characterized. Our data show the global predominance of a few hESC lines in research, but also reveal remarkable country-specific differences. Comparison of hESC and hiPSC application did not show a diminished role for hESC research, but rather revealed that, up to this time, both fields continue to expand, exist independently, and partially overlap.
Infrared Method for <i>In Situ</i> Studies of Polymer/Surfactant Adsorption on Silica Powders from Aqueous Solution (2003)

This article presents a general infrared spectroscopic method that enables the monitoring of the adsorption of surfactants and polyelectrolytes on high surface area silica particles from aqueous solution. The method is based on the use of a ZnSe internal reflection element (IRE) coated with a layer of titania particles. The titania surface is the converted to silica using atomic layer deposition with sequential addition of an amine catalyst, gaseous SiCl4, and water vapor. A minimum of three cycles is needed to produce a surface that mimics silica, as evidenced by the reaction of hexamethyldisilazane and zeta potential measurements. It is shown that the silicacoated titania particles on the ZnSe crystals are stable to flowing aqueous solutions below pH = 8 and can be used to study the dynamics of polymer/surfactant adsorption on silica.
Molting Single Comb White Leghorns with the Use of the Lupron Depot® Formulation of Leuprolide Acetate (1994)

Reproductive tract regression and cessation of egg production was induced in 80-wk-old Hy-Line W36 strain hens by an i.m. injection of Lupron Depot at a dose calculated to release 60 micrograms of leuprolide acetate (LA)/kg of BW for 30 d, by restriction of feed intake (FR) for 28 d, or by total feed deprivation (FD) for 7 d followed by feed restriction for 21 d. Egg production in LA and FD groups dropped to 24 and 19% in the first 7 d after initiation of the treatments and to 3.5 and 0% in the 2nd wk. Production of the FR group dropped to 38% during the 1st wk and to 1.7% in the 2nd wk. Production of both nutritionally deprived groups remained near zero through the 5th wk, whereas it increased to 8.2% in the LA group at that time. Hens injected with LA reached 50% production at about 37 vs 45 d for both nutritionally deprived groups. Egg production of control groups remained unchanged during this time. Shell characteristics did not differ significantly among the molted groups throughout most of the 16 wk of the experiment. However shell weight and shell weight per unit surface area of eggs from LA-treated hens were significantly (P < or = .05) lower than those of FR, but not FD, hens at several times. Mean values for shell characteristics of eggs from unmolted hens were significantly lower than those of molted hens. There were no differences in albumen quality between any of the groups at any time.(ABSTRACT TRUNCATED AT 250 WORDS)
New directions in covert malware modeling which exploit white-listing (2007)

Zero-day attacks - especially those that hide the attack exploit by using code obfuscation and encryption - remain a formidable challenge to existing network defenses. Many techniques have been developed that can address known attacks and similar new attacks that may arise in the future. Some methods, like Earlybird and Polygraph, focus on string-based content prevalence in payloads; others focus on the presence of particular I386 instructions, e.g., Sigfree counts the number of ldquousefulrdquo instructions in each request. For both types of systems, a white-listing mechanism, in which some strings or instructions are regarded as innocuous, is necessary to avoid a high false positive rate associated with common content such as URL addresses and peer-to-peer traffic. In this paper, we explore a more sophisticated attack model that not only makes malcode payloads look like nominal ones, but which is also assumed to be both aware of and exploitative of the white-listing itself in forming a Trojan mechanism. In other words, the malware attempts to embed its malcode into the prevalent content that is normally white-listed. If the malcode is encrypted, the attacker will also attempt to obfuscate its plain-text decryption code as much as possible. Both current string-based and instructionbased systems will likely fail to detect such attacks. We propose a comprehensive IDS model in the paper and discuss some potential defensive mechanisms against such attack.
Boosting Cu2ZnSnS4 solar cells efficiency by a thin Ag intermediate layer between absorber and back contact (2014)

In this work, 20 nm Ag is deposited on Mo coated soda lime glass prior to Cu2ZnSnS4 absorber deposition to improve the back contact and therefore enhance solar cell efficiency. This thin coating is found to inhibit the formation of SnS2, MoS2, and other defects especially voids at the back contact; therefore, reduces the series resistance and recombination leading to substantially higher short circuit current density (JSC), fill factor, open circuit voltage (VOC), and efficiency in comparison to the controlled non-coating Mo, though the former results in lower material crystallinity.
Animal Fiber Analysis Using Imaging Techniques (2000)

The assessment of fiber scale height is known to be a key ingredient in animal fiber analysis, particularly when quantifying speciality fiber/wool blends. This paper ex plores the potential role of imaging techniques in scale height measurement. High magnification fiber images are captured from a SEM, and imaging techniques are applied and critically evaluated. A systematic, semi-automatic image capture, pro cessing, and analysis approach enables measurement of scale height and scale pattern features for two specific animal fiber types and the creation of information databases. Linear discriminant statistical techniques allow assessment of database integrity and the implementation of "unknown" fiber classification strategies. Adding scale height data to scale pattern data improves database integrity and permits correct classification of a larger proportion of "unknowns."
Automatic evaluation of sentence fluency (2004)

In the machine translation (MT) system, how to evaluate the sentence fluency of the translation results is an important research topic. Most of the current methods are based on the similarity of output words compared with the reference translations, which don't specially address the evaluation of the sentence fluency according to the syntactic structure. This paper proposes a statistical approach to the problem, which is based on the n-gram language model and reference-independent. Our approach is a beneficial compensation to the reference-dependent methods and has better robustness than those methods based on the syntactic analysis. The preliminary experimental results indicate that the approach basically reflects the reality of human's judgment.
Studio on demand by distributed video production over ATM (1996)

This paper presents an overview on the European ACTS project named “Distributed Video Production (DVP)”. Central to the DVP project are distributed pilot applications for professional digital video production over ATM broadband networks (LAN and WAN). The DVP project investigates the quality of service (QoS) requirements of broadcasters for several forms of distributed video production and runs a series of trials of distributed virtual studios (“studio on demand”), distributed rehearsals and remote video editing and retrieval. Additionally, this paper reports on two initial tests with a German public broadcaster and the German Telekom. The DVP project partners are GMD and about 20 broadcasters, computer and video equipment manufacturers, and video production companies.
Gö 6976, a selective inhibitor of protein kinase C, is a potent antagonist of human immunodeficiency virus 1 induction from latent/low-level-producing reservoir cells in vitro. (1993)

Human immunodeficiency virus (HIV-1) infection is followed by a period of latency or a low-level-persistent (LLP) state that results in an asymptomatic infection of the host. Productive viral expression may be triggered by a variety of activators including mitogens, antigens, and cytokines. Protein kinase C (PKC) has been shown to be important in the intracellular cascade of signals induced by such activators. With U1 and ACH-2 cell lines representative of an HIV-1 postintegration state, the effect of Gö 6976, a synthetic inhibitor of PKC was tested. Gö 6976 is a nonglycosidic indolocarbazole found to potently inhibit HIV-1 induction by Bryostatin 1, tumor necrosis factor alpha, and interleukin 6. Gö 6976 effectively blocks viral transcription induced by Bryostatin 1 or tumor necrosis factor alpha that leads to the inhibition of intracellular viral protein synthesis and viral shedding. Gö 6976 also blocks interleukin 6-mediated posttranscriptional induction of viral proteins. The IC50 of Gö 6976 shows a 12- to 60-fold more potent effect than for H-7, another PKC inhibitor with a similar mechanism. The inhibitory effect is reduced when Gö 6976 is not added before or within 1 hr of induction by the potent PKC activator Bryostatin 1. However, U1 cells can be grown for long periods in a nontoxic concentration of Gö 6976 (300 nM), which confers virtual inhibition of HIV-1 induction without the development of resistance. Results indicate that inhibition of HIV-1 proviral induction from latent/low-level-producing infectious states with potent PKC inhibitors like Gö 6976 may represent an additional and promising antiviral approach.
In vivo MRI visualization of different cell populations labeled with PARACEST agents (2012)

Conventional T1- or T2-MRI contrast agents do not allow to track the distribution of different cell populations simultaneously because the effects of relaxation enhancers are additive. Herein, it is shown that paramagnetic chemical exchange saturation transfer agents offer the opportunity to visualize different cell populations in vitro and in vivo by 1H-MRI. Yb- and Eu-HPDO3A complexes have been used to label murine macrophages (J774.A1) and melanoma cells (B16-F10), respectively. By selective irradiation of the highly-shifted OH resonances of the two chemical exchange saturation transfer agents, it has been shown that tracking of the two cell types is possible. These PARAmagnetic Chemical Exchange Saturation Transfer agents have a tremendous potential for clinical translation as they share the same stability and in vivo pharmacokinetic properties of Gd-HPDO3A (ProHance®), which is a widely used clinically approved MRI agent.
Engineering and use of <sup>32</sup>P‐labeled human recombinant interleukin‐11 for receptor binding studies (2002)

Human interleukin-11 (hIL-11) is a pleiotropic cytokine that is involved in numerous biological activities such as hematopoiesis, osteoclastogenesis, neurogenesis and female fertility. IL-11 is obviously a key reagent to study the IL-11 receptors. However, conventional radio-iodination techniques lead to a loss of IL-11 bioactivity. Here, we report the construction and the production of a new recombinant human IL-11 (FP Delta IL-11). In this molecule, a specific phosphorylation site (RRASVA) has been introduced at the N-terminus of rhIL-11. It can be specifically phosphorylated by bovine heart protein kinase and accordingly, easily radiolabeled with (32)P. A high radiological specific activity (250,000 c.p.m x ng(-1) of protein) was obtained with the retention of full biological activity of the protein. The binding of (32)P-labeled FP Delta IL-11 to Ba/F3 cells stably transfected with plasmids encoding human IL-11 receptors alpha and beta chains (IL-11R alpha and gp130) was specific and saturable with a high affinity as determined from Scatchard plot analysis. Availability of this new ligand should prompt further studies on IL-11R structure, expression and regulation.
Physics and Instrumentation of Diagnostic Medical Ultrasound (1990)

Nature of Ultrasound. Propagation in Tissue. Beam Shapes and Transducers. A-Scan Instruments. Static B-Scan. Real-Time Scanners. M-Mode. Other Scanners and Probes. Measurement of Size. Doppler Ultrasound Physics and Instruments. Doppler Ultrasound Measurement. Digital Storage, Scan Converters and Data Processing. Image Artifacts. Performance Checks. Bioeffects, Dosimetry and Safety. Appendices. Bibliography. Index.
Chymotrypsin C mutations in chronic pancreatitis (2011)

Chronic pancreatitis is a persistent inflammatory disorder characterized by destruction of the pancreatic parenchyma, maldigestion, and chronic pain. Mutations in the chymotrypsin C (CTRC) gene encoding the digestive enzyme CTRC have been shown to increase the risk of chronic pancreatitis in European and Asian populations. Here, we review the biochemical properties and physiological functions of human CTRC, summarize the functional defects associated with CTRC mutations, and discuss mechanistic models that might explain the increased disease risk in carriers.
Factors Influencing the Kinetics of the Alkaline Depolymerisation of Poly(ethylene terephthalate). I: The Effect of Solvent (1996)

The effect of solvent on the kinetics of the alkaline depolymerisation of poly(ethylene terephthalate) (PET) has been investigated. The process was found to be first-order with respect to hydroxide ion concentration, and the activation energy for the reaction in water was found to be 69 ± 13 kJ mol−1 (95% confidence limits). This is higher than the reported activation energy in the homogeneous molten state depolymerisation, but lower than the reported activation energies for the neutral solid-state heterogeneous hydrolysis. The choice of solvent plays an important role in the alkaline depolymerisation process; strong solvent–polymer interactions can facilitate the depolymerisation by causing swelling to mitigate diffusion constraints, and strong solvent–solvent interaction can enhance the nucleophilicity of the hydroxide ion. However, the first-order kinetic behaviour with respect to [NaOH] has been shown to be applicable over a limited range in some solvent systems, the limitation being due to ion-pairing which leads to reduced activity of the hydroxide ion.
Dimensional structure and diagnostic specificity of the Frankfurt Complaint Questionnaire (1997)

The Frankfurt Complaint Questionnaire (FCQ) is a widely used method to investigate non-psychotic subjective experiences of schizophrenics. Less is known about its dimensional structure. Therefore, principal components analyses (PCA) were conducted with the FCQ data of 505 schizophrenics and 187 alcoholics. Furthermore, results of a former analysis using item-to-item comparisons between schizophrenics and alcoholics were examined. PCA yielded two factors called 'dysphoric concomitants of severe illness particularly impairing concentration' and 'subjective experiences of perceptual uncertainties'. Neither of the factors was specific to schizophrenia. The item comparisons suggest that only a group of eight FCQ items (subscale 'FCQ-S') is specific to schizophrenia while ten items ('FCQ-A') are related more to alcoholism. The validity of FCQ-S and FCQ-A was confirmed: schizophrenics reached high scores in FCQ-S and low scores in FCQ-A; alcoholics scored high in FCQ-A and low in FCQ-S; schizophrenics with an additional alcohol disorder scored high in both of the subscales. It is concluded that direct group comparisons seem to be promising for the identification of non-psychotic subjective phenomena which are characteristic for schizophrenia.
Microstructure and thermal properties of ethylene‐(vinyl acetate) copolymer/rectorite nanocomposites (2005)

Abstract Ethylene‐(vinyl acetate) copolymer (EVA)/rectorite nanocomposites were prepared by direct melt extrusion of EVA and organo‐rectorite. The microstructures and thermal properties of EVA nanocomposites were characterized by X‐ray diffraction (XRD), scanning electron microscopy (SEM), solid‐state nuclear magnetic spectroscopy, positron annihilation spectroscopy, thermal gravimetric analysis (TGA) and dynamic mechanical analysis techniques. XRD pattern and SEM images show that the intercalated structure is formed and rectorite is finely dispersed in EVA matrix. When organoclay content of the hybrid increases to 7.5 wt%, or pristine rectorite was used instead of organoclay, the crystallization behavior of EVA nanocomposite changes greatly and the ratio of the monoclinic to orthorhombic crystal increases significantly. The relative fractional free volume of the nanocomposite decreases with the increasing organo‐rectorite content, and the values of damping factor (tan δ) for all nanocomposites are lower than that of pure EVA. These facts illuminate that intercalated structure restricts the segment motion and mobilization of polymer chain. TGA results of EVA nanocomposites in air indicate that deacylation of EVA is accelerated because of the catalytic effect and the thermal degradation of the main chain is delayed owing to the barrier effect of silicate layers. Copyright © 2005 Society of Chemical Industry
γ-Guanidinobutyraldehyde Dehydrogenase of <i>Vicia faba</i> Leaves (1984)

gamma-Guanidinobutyraldehyde dehydrogenase was purified 27-fold in 40% yield from extracts of Vicia faba leaves. High specificity exist only for gamma-guanidinobutyraldehyde and gamma-aminobutyraldehyde; the K(m) value was 3.4 micromolar for gamma-guanidinobutyraldehyde, 25 micromolar for gamma-aminobutyraldehyde, and 84 micromolar (case of gamma-guanidinobutyraldehyde) for NAD, respectively. The enzyme had a molecular weight of approximately 83,000. Optimal pH and temperature for activity were 9.5 and 45 degrees C, respectively. The enzyme was inhibited strongly by p-chloromercuribenzoate, N-ethylmaleimide, and zincon (2-carboxy-2'-hydroxy-5'-sulfoformazylbenzene).