gebhart/patrepeval huggingface dataset:
Characterizing the metabolic phenotype: A phenotype phase plane analysis (2001)

Genome-scale metabolic maps can be reconstructed from annotated genome sequence data, biochemical literature, bioinformatic analysis, and strain-specific information. Flux-balance analysis has been useful for qualitative and quantitative analysis of metabolic reconstructions. In the past, FBA has typically been performed in one growth condition at a time, thus giving a limited view of the metabolic capabilities of a metabolic network. We have broadened the use of FBA to map the optimal metabolic flux distribution onto a single plane, which is defined by the availability of two key substrates. A finite number of qualitatively distinct patterns of metabolic pathway utilization were identified in this plane, dividing it into discrete phases. The characteristics of these distinct phases are interpreted using ratios of shadow prices in the form of isoclines. The isoclines can be used to classify the state of the metabolic network. This methodology gives rise to a "phase plane" analysis of the metabolic genotype-phenotype relation relevant for a range of growth conditions. Phenotype phase planes (PhPPs) were generated for Escherichia coli growth on two carbon sources (acetate and glucose) at all levels of oxygenation, and the resulting optimal metabolic phenotypes were studied. Supplementary information can be downloaded from our website (http://epicurus.che.udel.edu).
Training neural network with genetic algorithms for forecasting the stock price index (2002)

The paper combines genetic algorithms (GA) with neural network (NN). It trains NN with GA and then predicts the stock price index with the trained network. By learning the special stock knowledge, it can find out the modes and relationship hidden in the abstract data. It can help shareholders and investment agencies to make wise decisions in the stock market so as to get more profits. The primary data are from Shanghai Stock Exchange from March 29, 1994 to August 1, 1994. The imitation result shows that the network is fit for short time prediction and it has high precision.
Inflamed Adipose Tissue (2007)

The metabolic syndrome is associated with a dysregulated adipose tissue; in part a consequence of adipose cell enlargement and the associated infiltration of macrophages. Adipose cell enlargement leads to a proinflammatory state in the cells with reduced secretion of adiponectin and with increased secretion of several cytokines and chemokines including interleukin (IL)-6, IL-8, and MCP-1. MCP-1 has been shown to play an important role for the associated recruitment of macrophages into the adipose tissue. The increased release of cytokines leads to an impaired differentiation of the preadipocytes with reduced lipid accumulation and induction of adiponectin, thus promoting ectopic lipid storage. In particular tumor necrosis factor (TNF) alpha, but also IL-6, has been shown to induce these effects in preadipocytes and this is associated with an increased Wnt signaling maintaining the cells in an undifferentiated and proinflammatory state. The proinflammatory state in the adipose tissue also leads to a local insulin resistance including an impaired inhibitory effect of insulin on FFA release. The insulin resistance further supports the proinflammatory state because insulin, by itself, is both antilipolytic and antiinflammatory by antagonizing cytokine-induced activation of STAT signaling.
Building towards precision medicine: empowering medical professionals for the next revolution (2016)

A new paradigm in disease classification, diagnosis and treatment is rapidly approaching. Known as precision medicine, this new healthcare model incorporates and integrates genetic information, microbiome data, and information on patients' environment and lifestyle to better identify and classify disease processes, and to provide custom-tailored therapeutic solutions. In spite of its promises, precision medicine faces several challenges that need to be overcome to successfully implement this new healthcare model. In this paper we identify four main areas that require attention: data, tools and systems, regulations, and people. While there are important ongoing efforts for addressing the first three areas, we argue that the human factor needs to be taken into consideration as well. In particular, we discuss several studies that show how primary care physicians and clinicians in general feel underequipped to interpret genetic tests and direct-to-consumer genomic tests. Considering the importance of genetic information for precision medicine applications, this is a pressing issue that needs to be addressed. To increase the number of professionals with the necessary expertise to correctly interpret the genomics profiles of their patients, we propose several strategies that involve medical curriculum reforms, specialist training, and ongoing physician training.
Monitoring of Transplanted Liver Health by Quantification of Organ-Specific Genomic Marker in Circulating DNA from Receptor (2014)

Determination of a SRY gene in a female recipient's serum is a clear and specific biomarker of donated organs and may give us important information about graft health in a short period of time by a non-expensive technique. This approach may permit clinicians to maintain a close follow up of the transplanted patient.
Determination of Absolute Sound Levels and Acoustic Absorption Coefficients by Thermocouple Probes—Experiment (1954)

A stable, readily constructable thermocouple probe has been developed for determining absolute sound levels in ultrasonic fields in liquid media. This paper includes criteria for design of such probes and a discussion of experimental measurements made with such a device. It is a consequence of the method that if the sound intensity at an appropriate size thermocouple junction imbedded in an absorbing medium is known the acoustic absorption coefficient of the material can be determined. The method thus makes possible the determination of absorption coefficients of minute quantities of material. The probe consists of a thermocouple imbedded in a sound absorbing medium which closely matches in density and sound velocity the medium in which the sound level is to be determined. In use the transducer which generates the acoustic field is exctied to generate sound pulses with a rectangular envelope. The initial time rate of change of the temperature at the thermocouple junction is determined. In addition to the measurement of the temperature change, the calculation of the absolute sound intensity requires only a knowledge of the absorption coefficient of the imbedding material and its heat capacity per unit volume at the temperature at which the measurements are made. The experimental results include a comparison of the sound level determined by a thermocouple probe and a determination by radiation pressure methods. The values obtained by the two methods agree within the uncertainty of the experimental measurements.
Comparison of HRV parameters derived from photoplethysmography and electrocardiography signals (2015)

Heart rate variability (HRV) has become a useful tool in analysis of cardiovascular system in both research and clinical fields. HRV has been also used in other applications such as stress level estimation in wearable devices. HRV is normally obtained from ECG as the time interval of two successive R waves. Recently PPG has been proposed as an alternative for ECG in HRV analysis to overcome some difficulties in measurement of ECG. In addition, PPG-HRV is also used in some commercial devices such as modern optical wrist-worn heart rate monitors. However, some researches have shown that PPG is not a surrogate for heart rate variability analysis. In this work, HRV analysis was applied on beat-to-beat intervals obtained from ECG and PPG in 19 healthy male subjects. Some important HRV parameters were calculated from PPG-HRV and ECG-HRV. Maximum of PPG and its second derivative were considered as two methods for obtaining the beat-to-beat signals from PPG and the results were compared with those achieved from ECG-HRV. Our results show that the smallest error happens in SDNN and SD2 with relative error of 2.46% and 2%, respectively. The most affected parameter is pNN50 with relative error of 29.89%. In addition, in our trial, using the maximum of PPG gave better results than its second derivative.
8×8 Space and Wavelength Selective Cross-connect for Simultaneous Dynamic Multi-wavelength Routing (2013)

We demonstrate the first monolithic 8-input, 8-output WDM-compliant cross-connect with nanosecond programmable path provisioning between each input and output. Multiple data channels are simultaneously demonstrated for all eight outputs with penalty as low as 1.7dB.
Changes in Wool Low-Sulfur and High-Sulfur Protein Components Following Chemical Defleecing (1981)

The changes in the protein composition of wool following suppression of wool growth by mimosine and cyclophosphamide have been examined. Polyacrylamide gel electrophoresis of high-sulfur and low-sulfur protein fractions isolated from wool grown before and after a chemical defleecing treatment showed that the same protein components were present but in different proportions, and that even after three months the protein composition had not reverted to pretreatment composition. These variations in protein composition along the wool fiber could be important as they may alter the physicochemical and textile processing properties of wool grown after chemical defleecing.
Thermotolerance and cell death are distinct cellular responses to stress: dependence on heat shock proteins (1999)

We tested the hypothesis that heat shock protein (Hsp) induction and cell death are mutually exclusive responses to stress. Despite activation of heat shock transcription factor 1 at temperatures ranging from 40 to 46 degrees C, Hsp72 and Hsp27 were not induced above 42 degrees C. Moreover, cells underwent apoptosis at 44 degrees C and necrosis at 46 degrees C, with mitochondrial cytochrome c release at both temperatures. However, only apoptosis was associated with caspase activation. Treatment of cells with z-VAD-fmk prior to heat shock at 44 degrees C failed to restore Hsp induction despite inhibition of heat-induced apoptosis. Furthermore, accumulation of Hsps after incubation at 42 degrees C rendered the cells resistant to apoptosis. These results suggest that lack of Hsp induction is the cause rather than the consequence of cell death.
Combination Megestrol Acetate, Oxandrolone, and Dietary Advice Restores Weight in Human Immunodeficiency Virus (2004)

Prolonged combination therapy with megestrol acetate, oxandrolone, and dietary advice could reverse weight loss and low BMI associated with incomplete viral suppression and improve physical health.
cDNA sequence of human transforming gene hst and identification of the coding sequence required for transforming activity. (1987)

The hst gene was originally identified as a transforming gene in DNAs from human stomach cancers and from a noncancerous portion of stomach mucosa by DNA-mediated transfection assay using NIH3T3 cells. cDNA clones of hst were isolated from the cDNA library constructed from poly(A)+ RNA of a secondary transformant induced by the DNA from a stomach cancer. The sequence analysis of the hst cDNA revealed the presence of two open reading frames. When this cDNA was inserted into an expression vector containing the simian virus 40 promoter, it efficiently induced the transformation of NIH3T3 cells upon transfection. It was found that one of the reading frames, which coded for 206 amino acids, was responsible for the transforming activity.
Ribonucleoside cyclic 3′,5′-phosphoramidates: synthesis, stereochemistry, and conversion into ribonucleoside cyclic 3′,5′-phosphorothioates and -[18O]phosphates (1987)

Base- and O2′-protected nucleoside cyclic 3′,5′-phosphates (1) react with aniline in the presence of triphenylphosphine–carbon tetrachloride to give the nucleoside cyclic 3′,5′-phosphoranilidates (2), which after separation into individual diastereoisomers are converted in stereoretentive manner into the corresponding nucleoside cyclic 3′,5′-phosphorothioates (3). Isotopomers of adenosine cyclic 3′,5′-[18O] phosphates (9a) are prepared via two independent routes: (a) reaction of adenosine cyclic 3′,5′-phosphoranilidates (2a) with sodium hydride–[18O]benzaldehyde (retention) or (b) acid-catalysed hydrolysis of adenosine cyclic 3′,5′-N,N-dimethylphosphoramidates (10a)(inversion).Adenosine cyclic 3′,5′-phosphoranilidothioates (Sp)-(23) and (Rp)-(23), prepared via cyclisation of the corresponding 5′-[O-(4-nitrophenyl)phosphoranilidothioates](22), have been converted into P-achiral adenosine cyclic 3′,5′-phosphorodithioate (26).
Identification of glycoproteins specific to biotrophic intracellular hyphae formed in the Colletotrichum lindemuthianum‐bean interaction (1994)

Monoclonal antibodies (MAbs) specific for intracellular for hyphae (IH, i.e. infection vesicles and primary hyphae). Appressoria/germ tubes and conidia of Colletotrichum lindemuthianum (Sace, & Magn.) Briosi & Cav. isolated from infected leaves of Phaseolus vulgoria L. were obtained using a co-immunization procedure. One of the MAhs; UB25, bound specifically to IH in immunofluorescence immunogold and Western blot assays: it showed no affinity for conidia, conidial germ tubes, appressoria or appressorial germ tubes growing in vitro, of for any plant components. Immunogold labeling of infected tissue prepared by high pressure freezing, freeze-substitution and low temperature embedding showed that the UB25 antigen was present in the interfacial matri surrounding IH and in the fungal wall. The antigen was confined to infection vesicles and primary hyphae in contact with host protoplast and could not be detected in primary hyphae growing in intercellular spaces. UB25 recognizes a protein epitope present in a set of N-linked glycoproteins. These glycoproteins are expressed at an early stage of intracellular development, suggesting a possible role in biotrophy or recognition.
Hydration Repulsion between Carbohydrate Surfaces Mediated by Temperature and Specific Ions (2016)

Stabilizing colloids or nanoparticles in solution involves a fine balance between surface charges, steric repulsion of coating molecules, and hydration forces against van der Waals attractions. At high temperature and electrolyte concentrations, the colloidal stability of suspensions usually decreases rapidly. Here, we report a new experimental and simulation discovery that the polysaccharide (dextran) coated nanoparticles show ion-specific colloidal stability at high temperature, where we observed enhanced colloidal stability of nanoparticles in CaCl2 solution but rapid nanoparticle-nanoparticle aggregation in MgCl2 solution. The microscopic mechanism was unveiled in atomistic simulations. The presence of surface bound Ca(2+) ions increases the carbohydrate hydration and induces strongly polarized repulsive water structures beyond at least three hydration shells which is farther-reaching than previously assumed. We believe leveraging the binding of strongly hydrated ions to macromolecular surfaces represents a new paradigm in achieving absolute hydration and colloidal stability for a variety of materials, particularly under extreme conditions.
N-terminus of M2 protein could induce antibodies with inhibitory activity against influenza virus replication (2003)

New influenza vaccines have been designed based on the fact that the extracellular domain of M2 protein (M2e) is nearly invariant in all influenza A strains. To clarify which exact region of M2e could induce antibodies with inhibitory activities against influenza virus replication, four overlapping peptides covering M2e were synthesized and then coupled to the carrier protein bovine serum albumin through the cysteine of the peptides. After a vaccination course, all these four peptide vaccines could induce high levels of rabbit antibodies with predefined peptide specificity (antibody dilution: 1:6400-1:25600). Besides, the anti-N-terminal antibodies (AS2) reacted strongly with M2e, and reacted weakly with the middle part and C-terminus of M2e. The MDCK assay for cytopathic effect proved that antibodies recognizing the N-terminus of M2e could obviously inhibit replication of influenza A virus (A/wuhan/359/95) and influenza B virus (B/wuhan/321/99) in vitro in a dose-dependent manner, while antibodies recognizing the middle part and the C-terminus of M2e did not show such significant inhibitory activities. Sequence analysis indicates that the first nine N-terminal amino acid residues of M2e are extremely conservative. Just this region containing the first nine amino acid residues could induce antibodies with inhibitory activity against influenza A and influenza B virus replication, suggesting that the N-terminus of M2e may contain an epitope that could induce inhibitory antibodies against influenza virus replication in vitro.
Type-Specialized Serialization with Sharing (2005)

In this paper we present an implementation of a Standard ML combinator library for serializing and deserializing data structures. The combinator library supports serialization of cyclic data structures and sharing. It generates compact serialized values, both due to sharing, but also due to type specialization. The library is type safe in the sense that a type specialized serializer can be applied only to values of the specialized type. In the paper, we demonstrate how programmer control provided by the combinator library can lead to efficient serializers compared to how values are serialized with generic serializers supported by traditional language implementations.
Exploitation of host cell signaling machinery: activation of macrophage phosphotyrosine phosphatases as a novel mechanism of molecular microbial pathogenesis (2000)

Intracellular pathogens, particularly those that target host mononuclear phagocytes, have evolved strategies to either evade or inhibit cellular mechanisms of host defense. Mycobacterium tuberculosis and Leishmania donovani exemplify a diverse group of microorganisms that have developed the ability to invade and replicate within host macrophages, leading to disease expression. Recent studies have suggested that the pathogenesis of intracellular infection may involve interference with host cell signaling. Drawing upon examples from in vitro models that focused on M. tuberculosis and L. donovani, we review evidence that activation of host cell phosphotyrosine phosphatases may contribute to pathogenesis. A leading candidate appears to be the Src homology 2 domain containing phosphotyrosine phosphatase SHP-1, the activation of which may contribute to the development of infection and disease progression.
Identification of genomic targets downstream of p38 mitogen-activated protein kinase pathway mediating tumor necrosis factor-α signaling (2007)

Inhibition of p38 MAPK suppresses the expression of proinflammatory cytokines such as TNF-alpha and IL-1 beta in macrophages and fibroblast-like synoviocytes (FLS). However, there have been no genomewide studies on the gene targets of p38 MAPK signaling in synoviocytes. Microarray technology was applied to generate a comprehensive analysis of all genes regulated by the p38 MAPK signaling pathway in FLS. Gene expression levels were measured with Agilent oligonucleotide microarrays. Four independent sets of mRNA modulated by TNF-alpha and vehicle were used to measure the change of gene expression due to TNF-alpha, and three experiments were done to ascertain the effect of SB-203580, a p38 MAPK inhibitor, on TNF-alpha-induced genes. Microarray data were validated by RT-quantitative polymerase chain reaction. One hundred forty-one significantly expressed genes were more than twofold upregulated by TNF-alpha. Thirty percent of these genes were downregulated by the p38 inhibitor SB-203580, whereas 67% of these genes were not significantly changed. The SB-203580-inhibited genes include proinflammatory cytokines such as interleukins and chemokines, proteases including matrix metallopeptidases, metabolism-related genes such as cyclooxygenases and phosphodiesterase, genes involved in signal transduction, and genes encoding for transcription factors, receptors, and transporters. Approximately one-third of the TNF-alpha-induced genes in FLS are regulated by the p38 MAPK signal pathway, showing that p38 MAPK is a possible target for suppressing proinflammatory gene expressions in rheumatoid arthritis.
Protein translocation across the endoplasmic reticulum. I. Detection in the microsomal membrane of a receptor for the signal recognition particle. (1982)

Salt-extracted microsomal membranes (K-RM) contain an activity that is capable of releasing the signal recognition particle (SRP)-mediated elongation arrest of the synthesis of secretory polypeptides (Walter, P., and G. Blobel, 1981, J. Cell Biol., 91:557-561). This arrest-releasing activity was shown to be a function of an integral microsomal membrane protein, termed the SRP receptor (Gilmore, R., P. Walter, and G. Blobel, 1982, J. Cell Biol., 95:470-477). We attempted to solubilize the arrest-releasing activity of the SRP receptor by mild protease digestion of K-RM using either trypsin or elastase. We found, however, that neither a trypsin, nor an elastase "solubilized" supernatant fraction exhibited the arrest-releasing activity. Only when either the trypsin- or elastase-derived supernatant fraction was combined with the trypsinized membrane fraction, which by itself was also inactive, was the arrest-releasing activity restored. Release of the elongation arrest was followed by the translocation of the secretory protein across the microsomal membrane and the removal of the signal peptide. Thus, although we have been unable to proteolytically sever the arrest-releasing activity from K-RM and thereby to uncouple the release of the elongation arrest from the process of chain translocation, we have been able to proteolytically dissect and reconstitute the arrest-releasing activity. Furthermore, we found that the arrest-releasing activity of the SRP receptor can be inactivated by alkylation of K-RM with N-ethylmaleimide.
A study of psychiatric comorbidity after traumatic limb amputation: A neglected entity (2017)

A substantial proportion of amputees had alarming sign of depression, suicidal ideation, and PTSD. Thus, there is a need to form liaison between surgical treatment providers and psychiatrists and psychologists to manage psychiatric comorbidity in amputees.
Velocity inversion using a variable reference (1985)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 1985Velocity inversion using a variable referenceAuthors: Jack K. CohenFrank G. HaginJack K. CohenCenter for Wave Phenomena, Colorado School of Mines and Frank G. HaginCenter for Wave Phenomena, Colorado School of Mineshttps://doi.org/10.1190/1.1892651 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail FiguresReferencesRelatedDetails SEG Technical Program Expanded Abstracts 1985ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 1985 Pages: 643 publication data© 1985 Copyright © 1985 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished: 07 Mar 2005 CITATION INFORMATION Jack K. Cohen and Frank G. Hagin, (1985), "Velocity inversion using a variable reference," SEG Technical Program Expanded Abstracts : 341-343. https://doi.org/10.1190/1.1892651 Plain-Language Summary PDF DownloadLoading ...