gebhart/patrepeval huggingface dataset:
Serum Metabolomics Reveals Irreversible Inhibition of Fatty Acid β-Oxidation through the Suppression of PPARα Activation as a Contributing Mechanism of Acetaminophen-Induced Hepatotoxicity (2009)

Metabolic bioactivation, glutathione depletion, and covalent binding are the early hallmark events after acetaminophen (APAP) overdose. However, the subsequent metabolic consequences contributing to APAP-induced hepatic necrosis and apoptosis have not been fully elucidated. In this study, serum metabolomes of control and APAP-treated wild-type and Cyp2e1-null mice were examined by liquid chromatography-mass spectrometry (LC-MS) and multivariate data analysis. A dose-response study showed that the accumulation of long-chain acylcarnitines in serum contributes to the separation of wild-type mice undergoing APAP-induced hepatotoxicity from other mouse groups in a multivariate model. This observation, in conjunction with the increase of triglycerides and free fatty acids in the serum of APAP-treated wild-type mice, suggested that APAP treatment can disrupt fatty acid beta-oxidation. A time-course study further indicated that both wild-type and Cyp2e1-null mice had their serum acylcarnitine levels markedly elevated within the early hours of APAP treatment. While remaining high in wild-type mice, serum acylcarnitine levels gradually returned to normal in Cyp2e1-null mice at the end of the 24 h treatment. Distinct from serum aminotransferase activity and hepatic glutathione levels, the pattern of serum acylcarnitine accumulation suggested that acylcarnitines can function as complementary biomarkers for monitoring the APAP-induced hepatotoxicity. An essential role for peroxisome proliferator-activated receptor alpha (PPARalpha) in the regulation of serum acylcarnitine levels was established by comparing the metabolomic responses of wild-type and Ppara-null mice to a fasting challenge. The upregulation of PPARalpha activity following APAP treatment was transient in wild-type mice but was much more prolonged in Cyp2e1-null mice. Overall, serum metabolomics of APAP-induced hepatotoxicity revealed that the CYP2E1-mediated metabolic activation and oxidative stress following APAP treatment can cause irreversible inhibition of fatty acid oxidation, potentially through suppression of PPARalpha-regulated pathways.
Bacteriophage T4 multiplication in a glucose-limited <i>Escherichia coli</i> biofilm (2001)

An Escherichia coli K-12 biofilm was grown at a dilution rate of 0.028 h -1 for 48 h in a glucose-limited chemostat coupled to a modified Robbins' device to determine its susceptibility to infection by bacteriophage T4. Bacteriophage T4 at a multiplicity of infection (MOI) of 10 caused a log reduction in biofilm density (expressed as colony forming units (CFU) per cm 2 ) at 90 min postinfection. After 6 h, a net decrease and equilibrium in viral titer was seen. When biofilms were exposed to T4 phage at a MOI of 100, viral titer doubled after 90 min. After 6 h, viral titers (expressed as plaque forming units (PFU) per cm 2 ) stabilized at levels approximately one order of magnitude higher than seen at a MOI of 10. Scanning confocal laser microscopy images also indicated disruption of biofilm morphology following T4 infection with the effects being more pronounced at a MOI of 100 than at a MOI of 10. These results imply that biofilms under carbon limitation can act as natural reservoirs for bacteriophage and that bacteriophage can have some influence on biofilm morphology.Key words: bacteriophage T4, biofilm, biofilm morphology, bacteriophage ecology, carbon limitation.
The FliP and FliR proteins of <i>Salmonella typhimurium</i>, putative components of the type III flagellar export apparatus, are located in the flagellar basal body (1997)

Most of the structural components of the flagellum of Salmonella typhimurium are exported through a flagellum-specific pathway, which is a member of the family of type III secretory pathways. The export apparatus for this process is poorly understood. A previous study has shown that two proteins, about 23 and 26 kDa in size and of unknown genetic origin, are incorporated into the flagellar basal body at a very early stage of flagellar assembly. In the present study, we demonstrate that these basal body proteins are FliP (in its mature form after signal peptide cleavage) and FliR respectively. Both of these proteins have homologues in other type III secretion systems. By placing a FLAG epitope tag on FliR and the MS-ring protein FliF and immunoblotting isolated hook basal body complexes with anti-FLAG monoclonal antibody, we estimate (using the FLAG-tagged FliF as an internal reference) that the stoichiometry of FliR is fewer than three copies per basal body. An independent estimate of stoichiometry was made using data from an earlier quantitative radiolabelling analysis, yielding values of around four or five subunits per basal body for FliP and around one subunit per basal body for FliR. Immunoelectron microscopy using anti-FLAG antibody and gold-protein A suggests that FliR is located near the MS ring. We propose that the flagellar export apparatus contains FliP and FliR and that this apparatus is embedded in a patch of membrane in the central pore of the MS ring.
Umbilical cord matrix stem cells trophic ability and use as a drug delivery vehicle for treatment of melanomas (2012)

Melanoma is caused by uncontrolled growth of melanocytes, which can lead to a progressive form of malignant melanoma with limited treatment options. Stem cells have previously demonstrated a trophic ability to melanoma, which could be used as an anti‐cancer delivery system. Interferon‐β (IFN‐β) has been used as an anti‐cancer drug in previous studies. Our aim was to use umbilical cord matrix stem cells (UCMSC) loaded with IFN‐β (UCMSC‐IFN‐β) as drug delivery vehicles for melanoma treatment. To investigate the trophic ability of UCMSC towards B16F10 melanoma cells, we plated B16F10 melanoma cells at increasing concentrations in the bottom of a transwell plate and UCMSC's plated in the top of transwells. After 24 hours, the number of UCMSC's showing trophic ability was counted. All the experiments were replicated three times. To investigate the anti‐cancer ability of UCMSC‐IFN‐β on B16F10 melanoma cells, we plated B16F10 melanoma cells at increasing concentrations in the bottom of a transwell plate. UCMSC and UCMSC‐IFN‐β were then plated in the top of the transwells. After 48 hours, the number of B16F10 melanoma cells both alive and dead was counted. All the experiments were replicated three times. This in vitro study shows that as melanoma cells concentration increased, the amount of UCMSC migration increased as well. The second study showed that wells with UCMSC‐IFN‐β had higher amounts of dead B16F10 melanoma cells as compared to the control wells with UCMSC. These results indicate the trophic ability of UCMSC's and the use as a drug delivery vehicle through the anti‐cancer ability of UCMSC‐IFN‐β. Grant Funding Source : A.T. Still University Graduate Program
Chemical vapor deposition of diamond on an adamantane-coated sapphire substrate (2014)

Continuous diamond thin films can be grown on sapphire substrates by microwave plasma chemical vapor deposition utilizing a pretreatment of adamantane dip coating on the substrate for enhanced nucleation.
New anticancer agents: chiral isomers of ethyl 5-amino-1,2-dihydro-2-methyl-3-phenylpyrido[3,4-b]pyrazine-7-carbamate (1989)

Racemic ethyl 5-amino-1,2-dihydro-2-methyl-3-phenylpyrido[3,4-b]pyrazine-7- carbamate (1a) has shown antitumor activity in a variety of in vivo experiments. The preparation of the R and S isomers gave compounds with significant differences in potency in several biological tests.
Source Address Verification Architecture Problem Statement (2007)

This document outlines the problems that the Source Address
Verification Architecture (SAVA) initiative plans to solve. It
examines the current state in the internet, looks at current best
practices, and discusses why the current approaches are unlikely to
ever solve the problem of IP address spoofing. It also discusses some
of the problems that SAVA should NOT attempt to solve.
ErsatzPasswords (2015)

In this work we present a simple, yet effective and practical, scheme to improve the security of stored password hashes, rendering their cracking detectable and insuperable at the same time. We utilize a machine-dependent function, such as a physically unclonable function (PUF) or a hardware security module (HSM) at the authentication server to prevent off-site password discovery, and a deception mechanism to alert us if such an action is attempted. Our scheme can be easily integrated with legacy systems without the need of any additional servers, changing the structure of the hashed password file or any client modifications. When using the scheme the structure of the hashed passwords file, etc/shadow or etc/master.passwd, will appear no different than in the traditional scheme.1 However, when an attacker exfiltrates the hashed passwords file and tries to crack it, the only passwords he will get are the ersatzpasswords --- the "fake passwords". When an attempt to login using these ersatzpasswords is detected an alarm will be triggered in the system. Even with an adversary who knows about the scheme, cracking cannot be launched without physical access to the authentication server. The scheme also includes a secure backup mechanism in the event of a failure of the hardware dependent function. We discuss our implementation and provide some discussion in comparison to the traditional authentication scheme.
Distinguishing isobaric phosphated and sulfated carbohydrates by coupling of mass spectrometry with gas phase vibrational spectroscopy (2014)

An original application of the coupling of mass spectrometry with vibrational spectroscopy, used for the first time to discriminate isobaric bioactive saccharides with sulfate and phosphate functional modifications, is presented. Whereas their nominal masses and fragmentation patterns are undifferentiated by sole mass spectrometry, their distinctive OH stretching modes at 3595 cm(-1) and 3666 cm(-1), respectively, provide a reliable spectroscopic diagnostic for distinguishing their sulfate or phosphate functionalization. A detailed analysis of the 6-sulfated and 6-phosphated d-glucosamine conformations is presented, together with theoretical scaled harmonic spectra and anharmonic spectra (VPT2 and DFT-based molecular dynamics simulations). Strong anharmonic effects are observed in the case of the phosphated species, resulting in a dramatic enhancement of its phosphate diagnostic mode.
Compact CPW-to Microstrip transition design for MMIC packaging (2006)

In MMIC circuit design, the transitions and interconnects are essential components for integration and packaging [1-3]. However, the conventional distributed type transition circuits will result in great loss owing to their huge size, most especially in medium and low frequency band. In this paper, a new CPW-to-microstrip transition design based on lumped element circuits is proposed. The optimized design can achieve a return loss of less than 10 dB from 3 to 14 GHz and insertion loss of less than ldB from 3 to 14 GHz.
Detection of Elevated Plasma Levels of Epidermal Growth Factor Receptor Before Breast Cancer Diagnosis among Hormone Therapy Users (2010)

Applying advanced proteomic technologies to prospectively collected specimens from large studies is one means of identifying preclinical changes in plasma proteins that are potentially relevant to the early detection of diseases such as breast cancer. We conducted 14 independent quantitative proteomics experiments comparing pooled plasma samples collected from 420 estrogen receptor-positive (ER(+)) breast cancer patients ≤17 months before their diagnosis and matched controls. Based on the more than 3.4 million tandem mass spectra collected in the discovery set, 503 proteins were quantified, of which 57 differentiated cases from controls with a P value of <0.1. Seven of these proteins, for which quantitative ELISA assays were available, were assessed in an independent validation set. Of these candidates, epidermal growth factor receptor (EGFR) was validated as a predictor of breast cancer risk in an independent set of preclinical plasma samples for women overall [odds ratio (OR), 1.44; P = 0.0008] and particularly for current users of estrogen plus progestin (E + P) menopausal hormone therapy (OR, 2.49; P = 0.0001). Among current E + P users, the EGFR sensitivity for breast cancer risk was 31% with 90% specificity. Whereas the sensitivity and specificity of EGFR are insufficient for a clinically useful early detection biomarker, this study suggests that proteins that are elevated preclinically in women who go on to develop breast cancer can be discovered and validated using current proteomic technologies. Further studies are warranted to examine the role of EGFR and to discover and validate other proteins that could potentially be used for early detection of breast cancer.
Caveolins as tumour markers in lung cancer detected by combined use of cDNA and tissue microarrays (2004)

To identify new potential diagnostic markers for lung cancer, the expression profiles of 37 lung tumours were analysed using cDNA arrays. Seven samples were from small-cell lung cancer (SCLC), two from large-cell neuroendocrine tumours (LCNEC), and 28 from other non-small-cell lung cancers (mainly squamous cell cancer and adenocarcinoma). Principal component analysis and the permutation test were used to detect differences in the gene expression profiles and a set of genes was found that distinguished high-grade neuroendocrine carcinomas (SCLC and LCNEC) from other lung cancers. In addition, several genes, such as caveolin-1 (CAV1) and caveolin-2 (CAV2), were constantly deregulated in all types of tumour sample, compared with normal tissue. The expression of these two genes was investigated further at the protein level on a tissue microarray containing tumours from 161 patients and normal tissues. Immunostaining for CAV1 was negative in 48% of tumours, whereas 28% of the tumours did not express CAV2. Lack of CAV1 protein expression was not caused by methylation or mutation. In stage I adenocarcinomas, CAV2 protein expression correlated with shorter survival. In conclusion, the present study was able to identify genes that have not previously been implicated in lung cancer by the combined use of two different array techniques. Some of these genes may provide novel diagnostic markers for lung cancer.
Performance Evaluation of the GCR Block ACK Mechanism in IEEE 802.11aa Networks (2013)

With the growing demand for multimedia services, video streams have become major traffic sources\nin the Internet. However, it is challenging to transmit multimedia streams over IEEE 802.11 Wireless\nLocal Area Networks (WLANs) with high performance and reliability. As a solution to improve\nsystem efficiency, a new standard, 802.11aa, is introduced to provide much more reliable\nand robust transfer of video stream by introducing several new service features. In this thesis,\nwe analyze the performance of the Groupcast with Retries (GCR) Block ACK scheme as one of\nthe most important features in this standard based on Markov chain models. The properties of\ngroupcast service and block acknowledgement will be merged together in our model. Besides, we\ntake into account the memory feature of the wireless channel and extend it into multi-receivers\nin accordance with the standard. In particular, the proposed model is built on fixed block size,\na type of communication technique in which the block size is kept as fixed during transmission.\nFurthermore, the lost position of a packet in the block is taken into consideration for in-depth\nanalysis.\nNumerical results show that under the groupcast with constant retry limit and fixed block size\ntransmission mechanism, the network throughput will be reduced with the growing number of\nreceiving terminals. Compared with the throughput result for the variable block size mechanism\nobtained from our previous study, we found that with the increasing number of stations, the\nperformance of the fixed block size mechanism is much more stable with respect to the number\nof stations and channel memory property. However, the variable block size transmission scheme\nexhibits much better throughput performance when the number of stations is small.
The Shaker Bomb. A New Laboratory Tool for Studying Thermal Processes (1958)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Shaker Bomb. A New Laboratory Tool for Studying Thermal ProcessesJohn W. Payne, Carl W. Streed, and Eric R. KentCite this: Ind. Eng. Chem. 1958, 50, 1, 47–52Publication Date (Print):January 1, 1958Publication History Published online1 May 2002Published inissue 1 January 1958https://pubs.acs.org/doi/10.1021/ie50577a031https://doi.org/10.1021/ie50577a031research-articleACS PublicationsRequest reuse permissionsArticle Views31Altmetric-Citations2LEARN 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 options Get e-Alerts
MODELING FLUID FLOW IN OIL RESERVOIRS (2005)

▪ Abstract Efficiently and accurately solving the equations governing fluid flow in oil reservoirs is very challenging because of the complex geological environment and the intricate properties of crude oil and gas at high pressure. We present these challenges and review successful and promising solution approaches. We discuss in detail the modeling of fluid flow in reservoirs with strongly varying rock properties. This requires subgrid-scale models that accurately represent the flow physics due to fine-scale fluctuations. A second focus is on the complex multiphase, multicomponent systems that describe miscible gas injection processes for enhanced oil recovery and CO 2 sequestration.
Electricity-Free Amplification and Detection for Molecular Point-of-Care Diagnosis of HIV-1 (2014)

In resource-limited settings, the lack of decentralized molecular diagnostic testing and sparse access to centralized medical facilities can present a critical barrier to timely diagnosis, treatment, and subsequent control and elimination of infectious diseases. Isothermal nucleic acid amplification methods, including reverse transcription loop-mediated isothermal amplification (RT-LAMP), are well-suited for decentralized point-of-care molecular testing in minimal infrastructure laboratories since they significantly reduce the complexity of equipment and power requirements. Despite reduced complexity, however, there is still a need for a constant heat source to enable isothermal nucleic acid amplification. This requirement poses significant challenges for laboratories in developing countries where electricity is often unreliable or unavailable. To address this need, we previously developed a low-cost, electricity-free heater using an exothermic reaction thermally coupled with a phase change material. This heater achieved acceptable performance, but exhibited considerable variability. Furthermore, as an enabling technology, the heater was an incomplete diagnostic solution. Here we describe a more precise, affordable, and robust heater design with thermal standard deviation <0.5°C at operating temperature, a cost of approximately US$.06 per test for heater reaction materials, and an ambient temperature operating range from 16°C to 30°C. We also pair the heater with nucleic acid lateral flow (NALF)-detection for a visual readout. To further illustrate the utility of the electricity-free heater and NALF-detection platform, we demonstrate sensitive and repeatable detection of HIV-1 with a ß-actin positive internal amplification control from processed sample to result in less than 80 minutes. Together, these elements are building blocks for an electricity-free platform capable of isothermal amplification and detection of a variety of pathogens.
A dataflow toolkit for visualization (1990)

A toolkit known as apE is presented. Originally, this was an acronym for animation production environment, but apE has become known as a software designed for more than just animation. Previous work is briefly reviewed, and the processing of designing the system is discussed. Common elements in building any graphics system as well as elements particular to building a large system are examined. The design and construction of apE 1.1 and apE 2.0 are described. The policy governing the distribution of apE and the advantages of academic software development are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A Perhaps "Politically Incorrect" Solution to the Very Real Problem of Grade Inflation (2004)

Few would disagree that grade inflation is a major problem at colleges and universities across the country. In this article, I argue that a significant contributing factor-perhaps the single most important factor-has been the institution of the now almost universal practice of administering anonymous, multiple-choice student evaluations of instruction at the end of most courses. I argue that the process has been examined incorrectly from a short-term perspective-whether there is a correlation between the grades an instructor gives and instructor evaluations in a particular course. The problem must be addressed from a much broader academic cultural perspective.
Human epidermal growth factor receptor 2 testing in invasive breast cancer: should histological grade, type and oestrogen receptor status influence the decision to repeat testing? (2015)

Mandatory repeat HER2 testing of grade 3 HER2-negative carcinomas is not appropriate. This is particularly true if repeat testing is performed after borderline negative amplification in the core biopsy or in HER2-negative heterogeneous carcinomas.