gebhart/patrepeval huggingface dataset:
Comparative Genomics of Atypical Enteropathogenic Escherichia coli from Kittens and Children Identifies Bacterial Factors Associated with Virulence in Kittens (2020)

Typical enteropathogenic <i>Escherichia coli</i> (tEPEC) is a leading cause of diarrhea and associated death in children worldwide. Atypical EPEC (aEPEC) lacks the plasmid encoding bundle-forming pili and is considered less virulent, but the molecular mechanism of virulence is poorly understood. We recently identified kittens as a host for aEPEC where intestinal epithelial colonization was associated with diarrheal disease and death. The purposes of this study were to (i) determine the genomic similarity between kitten aEPEC and human aEPEC isolates and (ii) identify genotypic or phenotypic traits associated with virulence in kitten aEPEC. We observed no differences between kitten and human aEPEC in core genome content or gene cluster sequence identities, and no distinguishing genomic content was observed between aEPEC isolates from kittens with nonclinical colonization (NC) versus those with lethal infection (LI). Variation in adherence patterns and ability to aggregate actin in cultured cells mirrored descriptions of human aEPEC. The aEPEC isolated from kittens with LI were significantly more motile than isolates from kittens with NC. Kittens may serve as a reservoir for aEPEC that is indistinguishable from human aEPEC isolates and may provide a needed comparative animal model for the study of aEPEC pathogenesis. Motility seems to be an important factor in pathogenesis of LI associated with aEPEC in kittens.
Inhibitory Effects of Trospium Chloride on Cytochrome P450 Enzymes in Human Liver Microsomes (1999)

Trospium chloride, an atropine derivative used for the treatment of urge incontinence, was tested for inhibitory effects on human cytochrome P450 enzymes. Metabolic activities were determined in liver microsomes from two donors using the following selective substrates: dextromethorphan (CYP2D6), denitronifedipine (CYP3A4), caffeine (CYP1A2), chlorzoxazone (CYP2E1), S-(+)-mephenytoin (CYP2C19), S-(-)-warfarin (CYP2C9) and coumarin (CYP2A6). Incubations with each substrate were carried out without a possible inhibitor and in the presence of trospium chloride at varying concentrations (37-3000 microM) at 37 degrees in 0.1 M KH2PO4 buffer containing up to 3% DMSO. Metabolite concentrations were determined by high-performance liquid chromatography (HPLC) in all cases except CYP2A6 where direct fluorescence spectroscopy was used. First, trospium chloride IC50 values were determined for each substrate at respective K(M) concentrations. Trospium chloride did not show relevant inhibitory effects on the metabolism of most substrates (IC50 values considerably higher than 1 mM). The only clear inhibition was seen for the CYP2D6-dependent high-affinity O-demethylation of dextromethorphan, where IC50 values of 27 microM and 44 microM were observed. Therefore, additional dextromethorphan concentrations (0.4-2000 microM) were tested. Trospium chloride was a competitive inhibitor of the reaction with Ki values of 20 and 51 microM, respectively. Thus, trospium chloride has negligible inhibitory effects on CYP3A4, CYP1A2, CYP2E1, CYP2C19, CYP2C9 and CYP2A6 activity but is a reasonably potent inhibitor of CYP2D6 in vitro. Compared to therapeutic trospium chloride peak plasma concentrations below 50 nM, the 1000-times higher competitive inhibition constant Ki however suggests that inhibition of CYP2D6 by trospium chloride is without any clinical relevance.
ChemInform Abstract: 6‐ AND 8Π‐RING CYCLIZATION REACTIONS OF 2‐OXAHEPTATRIENYL DIPOLES: SYNTHESIS OF 3‐VINYL‐2,3‐DIHYDROFURANS AND 2,3(6,7)‐DIHYDROOXEPINS (1981)

Abstract Die (E)‐Butadienyloxirane (IIIa) entstehen durch Knoevenagel‐Kondensation des Aldehyds (I) mit den Malonsäurederivaten (II) (Ausb. 40‐45%) und anschließender Epoxidation mit m‐Chlor‐perbenzoe‐ bzw. Trifluorperessigsäure.
Superconductivity in a New Oxide System of Eu-La-Ce-Cu-O (1989)

A Ce-doped Eu-La-Cu-O system was confirmed to be superconducting by the observation of the Meissner effect. Compounds with the nominal compositions of Eu 2- x - y La y Ce x CuO 4-δ ( x =0.1 to 0.2, and y =0.8 to 1.4) were prepared by sintering the constituent metal oxide powders in a stream of Ar. The XRD pattern of the compounds primarily exhibited the T'-phase (Nd 2 CuO 4 ) structure. The measurements of resistivity and susceptibility indicate that the samples have T c onset in the range of 11 K to 18 K.
Design of Self-Sampling Based ASK Demodulator for Implantable Microsystem (2006)

In most of bioimplantable or wireless sensor network systems, ASK is one of the most commonly used schemes to modulate the baseband signal with reference to the intermediate or even the carrier frequency. In this study, a novel demodulator architecture is proposed. It is based on a simple self-sampling scheme which is a truly low-cost high-efficiency implementation and has excellent ability to work on a very small difference (0.15 V) between the two modulated levels, which represent the binary '0' and '1' separately. The results show the presented type can be designed to fit the operation carrier for the special need and has a quite area efficiency than the ever published similar works due to its existent digital benefit. In addition, a comforting robustness is also demonstrated under different process variations. According to the merits mentioned above, both the chip cost and the complexity in the design of on-chip voltage regulator for stable DC extraction are greatly reduced. This design has been verified and realized by using a TSMC (Taiwan Semiconductor Manufacturing Company) 0.18- <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">μ</i> m 1P6M standard CMOS technology.
Adsorption of Methane, Nitrogen, Carbon Dioxide, and Their Binary Mixtures on Dry Activated Carbon at 318.2 K and Pressures up to 13.6 MPa (2003)

A detailed experimental study has been made of the adsorption of pure methane, nitrogen, carbon dioxide, and their binary mixtures on dry activated carbon (Filtrasorb 400, 12 × 40 mesh, Calgon Carbon) at 318.2 K and pressures up to 13.6 MPa. The mixture measurements were made at nominal feed-gas compositions of 20, 40, 60, and 80 mol %. The mixture data clearly elucidate the competitive nature of the individual-component adsorption from the mixtures. Measurements were made using a volumetric technique, coupled with gas chromatographic analysis of the equilibrium gas-phase compositions. Error propagation analysis reveals the expected average experimental uncertainties in the amount adsorbed of 2% for pure methane and nitrogen and 6% for CO2. For the mixture measurements, the uncertainties are estimated to be about 3% for the total adsorption, while the individual-component uncertainties vary from 0.02 to 0.2 mmol/g activated carbon, depending on the mixture composition. The data were correlated using the two-dimensional Zhou−Gasem−Robinson equation of state model. The model fits the pure-component adsorption data within their experimental uncertainties, whereas the total and individual-component adsorptions in the binary systems are represented within one to two times the expected experimental uncertainties. As an additional benefit, the good agreement between the present data and those of Humayun and Tomasko for pure carbon dioxide (using two very different experimental techniques) suggests that these data provide a useful reference for benchmarking new experimental apparatus/techniques intended for the high-pressure adsorption measurements of supercritical gases.
Effect of Different Suture Materials on Cartilage Reshaping (2009)

Cartilaginous folds created using PDS are comparable to those created using nylon and are significantly better than monocryl and plain catgut materials. On this animal model, it appears that permanent suture material is not required to maintain a long lasting cartilaginous fold as long as the suture material holds the fold in shape for a certain period of time.
Computational methods for scaffold hopping (2012)

Abstract It is not uncommon in drug discovery that the core fragment, typically called scaffold, of a molecule with an interesting biological activity cannot be developed further because of issues related to intellectual property, physicochemical properties, metabolic stability, or toxicity, to name only a few reasons. In this situation, it is desirable to replace this molecule with another having a different chemical connectivity, but similar shape and pharmacophore features enabling it to interact in the same way with the target as the original molecule. Such a replacement is called scaffold hopping. Several ligand‐based virtual screening and scoring methods supporting the identification of novel ligands starting from known ligands and, if known, their bound conformation, are available. Scaffold hopping capability has been demonstrated for pharmacophore searches, field‐ and shape‐based similarity searches, alignment free similarity searches using three‐dimensional (3D)‐ or connectivity‐based descriptors, and fragment‐based methods. Although for many methods successful prospective uses have been reported, rigorous systematic benchmarking of scaffold hopping is still challenging due to the lacking consensus in the definition of a scaffold. Despite their drawbacks, computational scaffold extraction methods have been frequently used in approximate benchmarks for scaffold hopping. In many systematic retrospective studies, connectivity‐based methods were shown to be at least equally effective as 3D methods, especially when the conformations of the reference structures were generated with a conformer generator. However, in prospective comparison studies, especially when a hypothesis of the 3D binding conformation was available and used, often 3D methods were found to give superior results. © 2012 John Wiley &amp; Sons, Ltd. This article is categorized under: Computer and Information Science &gt; Chemoinformatics
Amino Acid Metabolism and Water Transport Across the Seawater Eel Intestine (1988)

ABSTRACT To elucidate how intracellular L-alanine enhances water transport across the seawater eel intestine, effects of various metabolic inhibitors were examined. The L-alanine-induced water flux was inhibited by amino-oxyacetate, an inhibitor of aminotransferase. After blocking the synthesis of pyruvate from L-alanine with this drug, water transport was stimulated with pyruvate, whose effects were inhibited by oxythiamine, an inhibitor of pyruvate dehydrogenase. 2,4-Dinitro-phenol (DNP) also inhibited the effects of L-alanine. Furthermore, L-alanine enhanced ouabain-sensitive O2 consumption in this tissue, and the enhancement in O2 consumption preceded that in the transepithelial potential difference (PD) and the net water flux. These results indicate that L-alanine is metabolized through the citric acid cycle to produce ATP, and that a metabolic product stimulates ion and water transport. L-Glutamine also seems to be metabolized just like L-alanine because: L-glutamine acted from inside the enterocyte; DNP inhibited the effects of L-glutamine; neither of the effects of L-glutamine and L-alanine were additive but they were mutually complementary; L-glutamine also enhanced ouabain-sensitive O2 consumption; and the increment in O2 consumption preceded that in the PD and the net water flux. The effects of L-glutamine on the PD and the net water flux depended on glutamine concentration and the concentration-response curve was of the Michaelis-Menten type, indicating that the rate of L-glutamine uptake into the enterocyte limits the overall rate of L-glutamine metabolism. A regulatory role of amino acids for ion and water transport is discussed.
Temperature Sensor Using Quartz Tuning Fork Resonator (1986)

Summary This paper describes the development of a temperature sensor based on a temperature-sensitive quartz resonator. The resonator was fabricated using photolithography and anisotropic etching. The optimum cut of the crystal and optimum resonator orientation on the wafer were determined - taking into account the anisotropic etching properties of the crystal - to give a large temperature coefficient of frequency consistent with small equivalent series resistance. The tuning fork temperature sensor operates over a wide range of temperature (from 4.2K to 250OC). After the temperature sensor was cycled between O°C and 4.2K, hysteresis in the temperature characteristic was only 0.005K at OOC. The quartz temperature sensor is quite compact -- it is mounted in a hermetic case only 3 mm in diameter.
3D Steerable Biopsy Needle with a Motorized Manipulation System and Ultrasound Tracking to Navigate inside Tissue (2020)

Needle insertion techniques have been used in several minimally invasive procedures for diagnostic and therapeutic purposes. For example, in tissue biopsy, a small sample of suspicious tissue is extracted using percutaneous needles for further analysis. A clinically significant biopsy sample is a definitive factor in cancer diagnosis; therefore, precise placement of the needle tip at target location is necessary. However, it is often challenging to guide and track the needle in a desired path to reach the target precisely, while avoiding sensitive organs or large arteries. Needle steering has been an active field of research in the past decade. Researchers have introduced passive and active needles to improve navigation and targeting inside the tissue. This work introduces a novel active steerable biopsy needle capable of bending inside the tissue in multiple directions. The needle is equipped with a biopsy mechanism to extract suspicious tissue. A motorized manipulation system is developed and programmed to pull the cable tendons and control the needle deflection inside tissue. To show the feasibility of the design concept, the active needle manipulation in air and in a tissue-mimicking phantom is evaluated. An average angular deflection of about 12.40 ∘ and 11.34 ∘ in three principal directions is realized in air and phantom tissue, respectively, which is expected to assist in breast cancer biopsy. A robot-assisted ultrasound tracking method is also proposed to track the active needle tip inside the phantom tissue in real time. It is shown that using this method, the needle tip can be tracked in real time with an average and maximum tracking error of [Formula: see text][Formula: see text]mm and [Formula: see text][Formula: see text]mm, respectively.
Tachykinin antagonists and capsaicin‐induced contraction of the rat isolated urinary bladder: evidence for tachykinin‐mediated cotransmission (1991)

1. The possible involvement of tachykinins (TKs) in the contraction produced by capsaicin in the rat isolated urinary bladder was addressed on the hypothesis that co-release of substance P (SP) and neurokinin A (NKA) occurs from sensory nerve terminals. 2. A low concentration of SP (30 nM) produced a rapid contraction which faded to baseline within 10 min. A low concentration of NKA (10 nM) produced a slowly developing contraction which was still evident at 10 min. Capsaicin (1 microM) produced a rapid phasic response and a tonic response (late response to capsaicin). Co-administration of SP and NKA mimicked the response to capsaicin more than each TK alone. 3. Fading of the response to SP was not caused by receptor desensitization and was partially prevented by peptidase inhibitors. 4. Spantide (3 microM) selectively antagonized the SP-induced contraction while L-659,877 (3-10 microM) or MEN 10,376 (10-30 microM) which are NK2 receptor selective antagonists selectively blocked the response to NKA. Co-administration of spantide and L-659,877 inhibited the response to both SP and NKA by an amount not greater than that produced by each antagonist alone. 5. Spantide selectively reduced the peak response to capsaicin, while leaving the late response unaffected. L-659,877 (3 microM) and MEN 10,376 (10 microM) selectively inhibited the late response to capsaicin while, at higher concentrations, also reduced the peak response to capsaicin. Co-administration of spantide and L-659,877 reduced the peak response to capsaicin more than that produced by each antagonist alone. 6. Bombesin (10 nM) produced a tonic contraction similar to that induced by NKA. The response to bombesin was not affected by spantide, L-659,877 or MEN 10,376. 7 P2. purinoceptor desensitization by repeated administration of alpha,betal-methylene ATP depressed the twitch response to electrical stimulation of postganglionic nerves but did not affect the peak or the late response to capsaicin. 8. We conclude that multiple TKs are coreleased by capsaicin in the rat bladder and mediate the capsaicin-induced contraction by activating both NKI and NK2 receptors. Endogenous TK with preferential affinity for the NK, receptor (putatively SP) are selectively involved in the peak response to capsaicin while endogenous TK with preferential affinity for the NK2 receptor (putatively NKA) are selectively involved in the late response to capsaicin and partly contribute to the peak response. These findings provide pharmacological evidence for tachykinin-mediated cotransmission in the rat urinary bladder. ATP is unlikely to be involved in the efferent function of capsaicin-sensitive sensory nerves in the rat bladder.
icuARM-An ICU Clinical Decision Support System Using Association Rule Mining (2013)

The rapid development of biomedical monitoring technologies has enabled modern intensive care units (ICUs) to gather vast amounts of multimodal measurement data about their patients. However, processing large volumes of complex data in real-time has become a big challenge. Together with ICU physicians, we have designed and developed an ICU clinical decision support system icuARM based on associate rule mining (ARM), and a publicly available research database MIMIC-II (Multi-parameter Intelligent Monitoring in Intensive Care II) that contains more than 40,000 ICU records for 30,000+patients. icuARM is constructed with multiple association rules and an easy-to-use graphical user interface (GUI) for care providers to perform real-time data and information mining in the ICU setting. To validate icuARM, we have investigated the associations between patients' conditions such as comorbidities, demographics, and medications and their ICU outcomes such as ICU length of stay. Coagulopathy surfaced as the most dangerous co-morbidity that leads to the highest possibility (54.1%) of prolonged ICU stay. In addition, women who are older than 50 years have the highest possibility (38.8%) of prolonged ICU stay. For clinical conditions treatable with multiple drugs, icuARM suggests that medication choice can be optimized based on patient-specific characteristics. Overall, icuARM can provide valuable insights for ICU physicians to tailor a patient's treatment based on his or her clinical status in real time.
Megakaryocytopoiesis and granulopoiesis after murine cytomegalovirus infection. (1984)

Thrombopoiesis and granulopoiesis following murine cytomegalovirus infection were investigated by studying changes in megakaryocytes, megakaryocyte and granulocyte-macrophage progenitor cells, and spleen colony-forming cells. The soft gel in vitro culture system was used to assay for megakaryocyte and granulocyte-macrophage progenitor cells in marrow and spleen. Murine cytomegalovirus produced a mild thrombocytopenia to 90% of control values 1 day after infection at a time when marrow megakaryocyte levels were normal, suggesting a mild direct toxic effect of the virus on platelets. A reduction of megakaryocytes, megakaryocyte and granulocyte-macrophage progenitor cells, and spleen colony-forming cells to 40% to 60% of control values occurred within 24 to 48 hours of infection in association with an additional decrease in platelets to 58% of control levels on day 4. In vitro inoculation of marrow cell cultures with murine cytomegalovirus also resulted in a reduction of megakaryocyte- and granulocyte-macrophage colony-forming cells within 24 to 48 hours, suggesting that murine cytomegalovirus-induced thrombocytopenia and granulocytopenia may be in part caused by direct infection of precursor cells. The recovery of cells in the spleen was followed by a striking seven- to 10-fold increase in spleen colony-forming cells and megakaryocyte and granulocyte-macrophage progenitor cells in the spleen. These marked increases followed significant increases in spleen cell production of colony-stimulating activities within 2 days of murine cytomegalovirus infection, suggesting that hematopoietic cell recovery is mediated by increased local production of colony-stimulating activities in the spleen.
Effects of murine norovirus infection on a mouse model of diet-induced obesity and insulin resistance. (2010)

Murine norovirus (MNV) is prevalent in SPF mouse facilities in the United States, and we currently lack sufficient data to determine whether it should be eliminated. It is generally accepted that the virus does not cause clinical symptoms in immuno-competent mice. However, we previously reported that MNV infection alters the phenotype of a mouse model of bacteria-induced inflammatory bowel disease in part through its effects on dendritic cells. The tropism of MNV toward macrophages and dendritic cells makes MNV a potential intercurrent variable in murine models of macrophage-driven inflammatory diseases, such as obesity, insulin resistance, and atherosclerosis. Therefore, we determined whether MNV infection altered obesity and insulin resistance phenotypes in C57BL/6 mice, a widely used model of diet-induced obesity. We found that MNV did not alter weight gain, food intake, and glucose metabolism in this model, but it did induce subtle changes in lymphoid tissue. Further studies using other models of metabolic diseases are needed to provide additional information on the potential role this 'subclinical' virus might have on disease progression in mouse models of inflammatory diseases.
Anaerobic Fish Spoilage by Bacteria I. Biochemical Changes in Herring Extracts (1979)

Water extracts of herring fillets were used as laboratory model substrates for the study of anaerobic bacterial spoilage of fish stored in bulk. The organisms studied ( Enterobacter sp., str. NTHC 151, Proteus sp., str. NTHC 153, and Aeromonas sp., str. NTHC 154) were selected for by an enrichment method designed to isolate the bacteria having the highest anaerobic growth yields in these herring extracts. The extracts were then inoculated with pure cultures of the bacteria and incubated anaerobically at 15°C. Chemical analyses of the extracts were carried out at the start and at the end of the incubation period. The compounds determined accounted for 88% of total carbon and 93% of total nitrogen of the sterile extracts. Ribose (free and bound), free hexoses and lactate were the main substrates for the growth of the bacteria. These compounds were converted to acetate and CO 2 ; hydrogen liberated by these processes was used for the quantitative reduction of trimethylamine oxide to trimethylamine. Fermentation balances support the contention that the biochemical changes observed represent the quantitative dominating chemical events in the herring extracts as a result of the development of the spoilage bacteria.