gebhart/patrepeval huggingface dataset:
Threonine dehydratases of Corynebacterium glutamicum with altered allosteric control: their generation and biochemical and structural analysis (1994)

Threonine dehydratase is the key enzyme in L-isoleucine synthesis, since it is allosterically feedback-inhibited by L-isoleucine. With the aim of obtaining regulatorily altered mutants of the threonine dehydratase of Corynebacterium glutamicum, amino acids were specifically exchanged and a new biological system of mutant selection was developed, based on the intoxication of Escherichia coli by ketobutyrate, which is the dehydratase reaction product. A collection of 19 mutant enzymes was generated and genetically and biochemically characterized comprising a whole range of regulatorily and catalytically altered enzymes. Of particular interest is the mutant Val-323-Ala, which is characterized by the fact that the L-isoleucine inhibition is entirely abolished so that the enzyme is always present in a relaxed, high-activity state. Correspondingly, the Hill coefficient is 1.4, in contrast to the value of 3.4 characteristic of the wild-type enzyme. Another peculiar mutant generated is the double mutant His-278-Arg-Leu-351-Ser. Here, again, L-isoleucine no longer inhibits catalytic activity, but the effector still promotes major structural changes of the protein, as ascertained from the L-isoleucine-dependent loss of pyridoxal-5'-phosphate from this mutant enzyme. Further enzymes obtained are reduced in L-isoleucine inhibition to a varying degree. Detailed studies on the structure of the enzyme revealed a partially very high similarity of the secondary structure to the mechanistically identical beta-subunit of the tryptophan synthase. This provides further indications concerning the localization of the regulatory and catalytic domain of the threonine dehydratase.
Harnessing Nonlinearity: Predicting Chaotic Systems and Saving Energy in Wireless Communication (2004)

We present a method for learning nonlinear systems, echo state networks (ESNs). ESNs employ artificial recurrent neural networks in a way that has recently been proposed independently as a learning mechanism in biological brains. The learning method is computationally efficient and easy to use. On a benchmark task of predicting a chaotic time series, accuracy is improved by a factor of 2400 over previous techniques. The potential for engineering applications is illustrated by equalizing a communication channel, where the signal error rate is improved by two orders of magnitude.
Energy transfer: a spectroscopic ruler. (1967)

Electronic excitation energy transfer as function of distance measured, noting energy transfer process use as spectroscopic ruler
Transcranial Focused Ultrasound to the Thalamus Is Associated with Reduced Extracellular GABA Levels in Rats (2012)

The ability to modulate region-specific brain activity, along with the present evidence of the ability to modulate neurotransmission, demonstrates the potential utility of FUS as a completely new non-invasive therapeutic modality.
Electron‐specimen interactions in low‐voltage scanning electron microscopy (1993)

Abstract Measurements of the electron range R, and the backscattering coefficient η and the secondary electron yield δ at normal and tilted incidence for different elements show characteristic differences for electron energies in the range of 0.5 to 5 keV, compared with energies larger than 5 keV. The backscattering coefficient does not increase monotonically with increasing atomic number; for example, the secondary electron yield shows a lesser increase with increasing tilt angle. This can be confirmed in back‐scattered electron (BSE) and secondary electron (SE) micrographs of test specimens. The results are in rather good agreement with Monte Carlo simulations using elastic Mott cross‐sections and a continuous‐slowing‐down model with a Rao Sahib‐Wittry approach for the stopping power at low electron energies. Therefore, this method can be used to calculate quantities of BSE and SE emission, which need a larger experimental effort. Calculations of the angular distribution of BSEs show an increasing intensity with increasing atomic number at high takeoff angles than expected from a cosine law that describes the angular characteristics at high electron energies. When simulating the energy distribution of BSEs, the continuous‐slowing‐down model should be substituted by using an electron energy‐loss spectrum (EELS) that considers plasmon losses and inner‐shell ionizations individually (single‐scattering‐function model). The EELS can be approached via the theory for aluminium or from EELS spectra recorded in a transmission electron microscope for other elements. Measurements of electron range Rα E n of 1 to 10 keV electrons are obtained from transmission experiments with thin films of known mass thickness. In agreement with other authors the exponent n is lower than at higher electron energies.
The Initial Step of the Glycerolipid Pathway (2001)

The initial step of phospholipid biosynthesis in yeast is carried out through the acylation of glycerol 3-phosphate (G-3-P) and dihydroxyacetone phosphate by stereospecific sn-1 acyltransferases. Here we report the identification of two key fatty acyltransferases of the glycerolipid biosynthesis pathway in Saccharomyces cerevisiae. Disruption of the open reading frame YBL011w, corresponding to a gene previously identified as a choline transporter suppressor (SCT1), resulted in a substantial decrease of total cellular G-3-P acyltransferase activity. A yeast strain disrupted at the open reading frame YKR067w, which encodes a protein closely related to Sct1p, also exhibited a dramatic reduction in G-3-P acyltransferase activity. Molecular characterizations of the genes revealed that a missense mutation in YKR067w accounted for a defect in the activities of the G-3-P acyltransferase in the yeast mutant strain TTA1. Heterologous expression of YKR067w in Escherichia coli further confirmed its enzyme activity. These results indicate that YKR067w and YBL011w, designated herein as GAT1 and GAT2(SCT1), respectively, are yeast G-3-P acyltransferase genes. Furthermore, biochemical results are presented to show that both Gat1p and Gat2p(Sct1p) are G-3-P/dihydroxyacetone phosphate dual substrate-specific sn-1 acyltransferases. The fatty acyl specificity of Gat1p is similar to that of the mammalian microsomal G-3-P acyltransferase, as it can effectively utilize a broad range of fatty acids as acyl donors. In contrast, Gat2p(Sct1p) displayed preference toward 16-carbon fatty acids. The most notable of the altered phospholipid compositions of the gat1Delta and gat2(sct1)Delta strains are a decreased phosphatidic acid pool and an increased phosphatidylserine/phosphatidylinositol ratio. This did not appear to affect the mutants as no growth defect was found. However, null mutations of both GAT1 and GAT2(SCT1) are synthetically lethal to yeast.
Aromatase Inhibitors in Breast Cancer: An Update (2002)

Aromatase inhibitors have important roles in optimal management of postmenopausal patients with hormone-responsive metastases in both the adjuvant and advanced-disease settings.
Recombinant Interferon-τ Regulates Secretion of Two Bovine Endometrial Proteins (1993)

Conceptus-derived interferon-tau (IFN-tau) has been implicated in the process of maternal recognition of pregnancy in the bovine. This type I IFN interacts with a uterine receptor complex to elicit secondary maternal responses, one of which is secretion of uterine proteins. We investigated the effects of pregnancy and recombinant (r) bovine (bo) IFN-tau (10(7) antiviral units/mg) on secreted proteins by cultured bovine endometrial explants. Explants were cultured for 24 h with [3H]leucine and dialyzed medium analyzed by one- and two-dimensional SDS polyacrylamide gel electrophoresis (PAGE) and fluorography. In one-dimensional PAGE experiments, endometrium representing early pregnancy (days 16-21) and the estrous cycle (days 16-19) was cultured in the presence of 5 nM rboIFN-tau and showed an increase (two- to five-fold) in secretion of 12- and 28-kD proteins. Further examination of these proteins by using two-dimensional PAGE indicated that the 12-kD protein was basic (pI > or = 7.5), whereas the 28-kD protein was acidic (pI approximately 5.0). Isoelectric focusing in the acidic range revealed that the 28-kD protein was composed of several isoelectric variants (pI 4.5-5.5). Although the functions of these secretory proteins are currently unknown, they serve as useful markers for IFN action and may act as secondary signals to protect the early developing conceptus.
Artificial Muscles from Fishing Line and Sewing Thread (2014)

The high cost of powerful, large-stroke, high-stress artificial muscles has combined with performance limitations such as low cycle life, hysteresis, and low efficiency to restrict applications. We demonstrated that inexpensive high-strength polymer fibers used for fishing line and sewing thread can be easily transformed by twist insertion to provide fast, scalable, nonhysteretic, long-life tensile and torsional muscles. Extreme twisting produces coiled muscles that can contract by 49%, lift loads over 100 times heavier than can human muscle of the same length and weight, and generate 5.3 kilowatts of mechanical work per kilogram of muscle weight, similar to that produced by a jet engine. Woven textiles that change porosity in response to temperature and actuating window shutters that could help conserve energy were also demonstrated. Large-stroke tensile actuation was theoretically and experimentally shown to result from torsional actuation.
Characterization of an immune response. (2005)

The characterization of any detected antibodies provides detailed information that can be critical to understanding the significance of an immune response. The BIAcore immunoassay provides a straightforward means of characterizing many aspects of the immune response including antibody concentration, specificity, binding affinity, and the presence of isotypes. One important aspect of the immune response is determination of neutralizing capability, which requires a biological assay. The ultimate clinical significance of an immune response can only be fully understood when data from antibody characterization are coupled with clinical data from the patient. Some of the factors that can contribute to the clinical significance of an immune response are: (i) magnitude of the immune response (concentration of antibodies detected); (ii) duration of the immune response (continuous antibody production or sporadic and not sustained); (iii) correlation with any adverse events; (iv) correlation with a change in pharmacokinetics (either mediating sustained circulation or enhanced clearance of the drug); (v) biological neutralization of the drug; (vi) biological neutralization of an endogenous protein. Full characterization of the immune response requires the incorporation of antibody assays, pharmacokinetic assays, and clinical data.
Standardized endpoint definitions for transcatheter aortic valve implantation clinical trials: a consensus report from the Valve Academic Research Consortium (2011)

Although consensus criteria will invariably include certain arbitrary features, an organized multidisciplinary process to develop specific definitions for TAVI clinical research should provide consistency across studies that can facilitate the evaluation of this new important catheter-based therapy. The broadly based consensus endpoint definitions described in this document may be useful for regulatory and clinical trial purposes.
Natural and synthetic video in MPEG-4 (2002)

The ISO MPEG Committee, after successful completion of the MPEG-1 and the MPEG-2 standards, has recently completed the Committee Draft for MPEG-4, its third standard. MPEG-4 is designed to be an object-based standard for multimedia coding. The visual part of the standard specifies coding of both natural and synthetic video. The MPEG-4 visual standard supports coding of natural video not only in a conventional manner (using frames) but also as a collection of arbitrary shape objects (using video object planes). Further, it supports functionalities such as spatial and temporal scalability, both conventional and with arbitrary shape objects. It also supports error resilient coding for delivery of coded video on error prone channels. MPEG-4 visual standard also supports coding of synthetic video which includes still texture maps used in 3D graphics models, mesh geometry for object animation, and parameters for facial animation.
Computer-aided detection (CADe) and diagnosis (CADx) system for lung cancer with likelihood of malignancy (2016)

From our preliminary results, we believe that our system is promising for clinical applications assisting radiologists in the detection and diagnosis of lung cancer.
Keap1 Mutations and Nrf2 Pathway Activation in Epithelial Ovarian Cancer (2011)

Resistance to platinum-based chemotherapy develops in the majority of patients with epithelial ovarian cancer (EOC). Platinum compounds form electrophilic intermediates that mediate DNA cross-linking and induce double-strand DNA breaks. Because the cellular response to electrophilic xenobiotics is partly mediated by Keap1-Nrf2 pathway, we evaluated the presence of Kelch-like ECH-associated protein 1 (Keap1) mutations and NF-E2-related factor 2 (Nrf2) pathway activation in EOC and correlated these with platinum resistance and clinical outcome. Nrf2 immunohistochemistry revealed nuclear localization (a surrogate of pathway activation) in over half of EOC patient specimens examined, with more common occurrence in the clear cell EOC subtype. Quantitative real-time PCR revealed that Nrf2 target genes were upregulated in tumors with nuclear positivity for Nrf2. Microarray analysis also showed upregulation of Nrf2 target genes in clear cell EOCs compared with other EOC subtypes. In addition, Keap1 sequence analysis revealed genetic mutations in 29% of clear cell samples and 8% of nonclear cell tumors. RNAi-mediated knockdown of Keap1 was associated with Nrf2 pathway activation and resistance to carboplatin in vitro. Importantly, patients with evidence of Nrf2 pathway activation had fewer complete clinical responses to platinum-based therapy, were enriched for platinum resistance, and had shorter median overall survival compared with those who did not show evidence of Nrf2 pathway activation. Our findings identify Keap1 mutations in EOC and they suggest a previously unrecognized role for the Keap1-Nrf2 pathway in mediating chemotherapeutic responses in this disease.
Source Detection and Separation in Power Plant Process Monitoring: Application of the Bootstrap (2006)

We consider source enumeration and identification in the context of monitoring the cooling circuit of a pressurized-water-reactor (PWR) nuclear plant. We employ a linear instantaneous-mixture to describe the system. We use the Gerschgorin radii of the transformed covariance matrix of the data to detect the number of sources. In particular, we illustrate the advantage of employing the boot-strap in a scenario where no or little a priori knowledge is available on the statistical properties of the measured data. A specific denoising procedure is also applied to the data to alleviate the effect of small variations of the noise power over the sensors, and allow a more accurate source separation. The results show the potential of both Gerschgorin-based detection and the bootstrap in practice.
Suppression of human pancreatic cancer cell proliferation by AGN194204, an RXR-selective retinoid (2004)

Retinoids may be useful agents for the treatment of pancreatic cancer. However, retinoic acid receptor (RAR)selective retinoids produce unwanted side effects. In contrast, retinoid X receptor (RXR)-selective retinoids produce fewer side effects; however, it was not known whether RXR-selective retinoids could reduce pancreatic tumor cell proliferation. In the present study, the novel RXR-selective retinoid, AGN194204, was compared with that of other retinoids for the ability to suppress pancreatic cancer cell proliferation. We treated various pancreatic cancer cell lines with receptor-selective ligands and cytotoxic agents and monitored the effects on cell proliferation, markers of apoptosis and cell cycle. Our results indicate that AGN194204, at concentrations 410 nM, inhibits proliferation of MIA PaCa-2 and BxPC-3 cells but not the proliferation of AsPC-1 cells. Moreover, in BxPC-3 and MIA PaCa-2 cells, AGN194204 was 10EE100 times more effective than RAR-selective retinoids. AGN194204dependent suppression of MIA PaCa-2 cell proliferation is associated with reduced cyclin E and cyclin-dependent kinase 6 (cdk6) level, but cyclin D1, cdk2 and cdk4 content is not altered. In addition, p27 level increases 2-fold. The RXR-selective antagonist, AGN195393, reverses the AGN194204-dependent growth inhibition and the decline in cyclin E and cdk6 levels. In contrast, these changes are not reversed by treatment with the RAR antagonist, AGN193109. AGN194204 did not appear to alter cell apoptosis as measured by change in cleavage of procaspase-3, -8 or -9. We also examined the effects AGN194204 co-treatment with cytotoxic agents. Treatment of MIA PaCa-2 cells with AGN194204 cisplatin, gemcitabine, 5-flurouracil, interferon (IFN)a or IFNg resulted in an additive but not synergistic reduction in MIA PaCa-2 cell number. These results indicate that AGN194204, an RXR-selective retinoid, is a more effective inhibitor of pancreatic cell proliferation than the RAR-selective retinoids, and further indicate that AGN194204 produces an additive reduction in cell number when given with other agents. Our results suggest that RXR-selective ligands, which are less toxic than RAR-selective ligands, may be suitable agents for the treatment of pancreatic cancer.
Profile control of plastic sheet in an industrial polymer processing process (1998)

Abstract A control system was developed using a two‐degree of freedom control structure with four input variables in the feedforward, and two inputs, the screw rotation speed and the gap of the forming roller, in the feedback loop. The feedforward signals were predetermined from first principles and the operators' heuristic rules for each changeover operation and prepared in a database. At the end of each changeover operation, the values in the database were rewritten by evaluating control performance. The magnitude of the true dead time changed as the production rate was changed. The rate of sampling and control action in the feedback control was adapted in each changeover operation so that the changing time delay was always expressed by a one‐sampling‐step time delay in the discrete models and dealt with by the controller robustness against parameter uncertainty. The developed control system was applied to an actual industrial plastic sheet production line and allowed one to easily perform the changeover operation and reduce material consumption.
Influence of exogenously generated oxidant species on myocardial function (1986)

Oxygen-derived free radicals (OFR) have been implicated as mediators of tissue injury in various disease states. Their participation in myocardial injury due to ischemia-reperfusion has also been suggested. To characterize the mechanical dysfunction associated with OFR-induced injury, we studied alterations in isometric contractions of rat papillary muscle at 28 degrees C. A purine-xanthine oxidase system was used to generate OFR. Neither purine nor xanthine oxidase alone had significant effects on rest or active tension, duration of the contraction, or peak rates of tension development or decline. In contrast, their combination resulted in a reduction of active tension to 38% of base-line values without alteration in rest tension. This reduction was largely due to a decline in the peak rate of tension development. When catalase or superoxide dismutase was introduced into the bath prior to the generation of OFR, catalase but not superoxide dismutase offered essentially complete functional protection. These results substantiate that impaired myocardial function can result from exposure to OFR. In this case the active radicals appear to be either peroxides or hydroxyl and not superoxide. These observations provide a basis for understanding the functional protection afforded ischemic myocardium by OFR scavenging enzymes.
Expansion of immunoregulatory macrophages by granulocyte-macrophage colony-stimulating factor derived from a murine mammary tumor. (1990)

Using an immunogenic nonmetastatic murine mammary adenocarcinoma (D1-DMBA-3) induced in BALB/c mice by dimethylbenzanthracene, we have previously shown that splenocytes from tumor bearers have depressed lymphocyte responses to mitogens and antigens, including tumor-associated antigens. In addition, they display decreased natural killer and T-cell cytotoxic activities. Macrophages from tumor-bearing mice appear to be responsible for the suppression of T- and B-cell responses to concanavalin A, lipopolysaccharide, and tumor-associated antigens observed in tumor bearers. The appearance of these macrophages in the spleen tightly parallels the progressive growth of the tumor and the concomitant immunosuppression. Simultaneously high levels of macrophage progenitors were observed in blood, bone marrow, lung, and liver. A significant increase of colony-stimulating activity of the granulocyte-macrophage lineage was detected in the sera from tumor-bearing mice. Higher levels of this colony-stimulating activity (CSA) were detected in tumor cystic fluid as compared with the levels in serum. A tumor cell line established in vitro from the D1-DMBA-3 in vivo tumor produces high levels of a factor with CSA in culture supernatant fluids. Partial purification of the CSA from the tumor cell line supernatants was achieved using CentriCell ultrafiltration and SephacrylS-300 chromatography. These studies revealed that the molecular weight of the colony-stimulating-like factor is 32,000 to 35,000. The morphology of the colonies obtained in cultures using this factor is similar to that of the colonies that develop in the presence of granulocyte-macrophage colony-stimulating factor (GM-CSF) but not with macrophage colony-stimulating factor (M-CSF). CSA from tumor cell supernatants was neutralized by antiserum to GM-CSF but not with anti-M-CSF or anti-granulocyte colony-stimulating factor (G-CSF). Macrophages from bone marrow or peritoneal exudates from normal mice cultured with tumor supernatant for 2 to 3 days strongly inhibit normal splenocyte responses to concanavalin A and lipopolysaccharide. The data suggest that the tumor releases a GM-CSF that alters the hemopoietic system and induces or expands macrophages, which exert a suppressive function on the immune system of tumor-bearing mice.
Dynamic Organization of Search Results Using the UMLS (1997)

This paper describes an approach that addresses this need by automatically grouping the results of a broad search into meaningful categories based on the user&amp;apos;s query. This approach combines the main benefit of clustering techniques with the main benefit of classification techniques by taking advantage of the domain knowledge present in the UMLS. I present a preliminary evaluation that demonstrates that a categorization produced by this approach corresponds reasonably well to a physician &amp;apos;s categorization.