gebhart/patrepeval huggingface dataset:
Enzymatic Synthesis of 3-Deoxy-d-manno-octulosonate 8-Phosphate, 3-Deoxy-d-altro-octulosonate 8-Phosphate, 3,5-Dideoxy-d-gluco(manno)-octulosonate 8-Phosphate by 3-Deoxy-d-arabino-heptulosonate 7-Phosphate Synthase (1998)

The phenylalanine-sensitive 3-deoxy-d-arabino-heptulosonate 7-phosphate (DAH 7-P) synthase (phe), a key enzyme involved in the biosynthesis of the aromatic amino acid phenylalanine, expressed by the Escherichia coli gene aroG, which catalyzes the condensation of d-erythrose 4-phosphate with phosphoenolpyruvate (PEP) to give DAH 7-P, was cloned into the expression vector pT7-7 for overexpression in E. coli. Purified enzyme from this expression system was used to demonstrate that DAH 7-P synthase (phe) also catalyses the aldol-type condensation of PEP with the 5-carbon analogues d-arabinose 5-phosphate, d-ribose 5-phosphate, and 2-deoxy-d-ribose 5-phosphate to yield 3-deoxy-d-manno-octulosonate 8-phosphate, 3-deoxy-d-altro-octulosonate 8-phosphate, and 3,5-dideoxy-d-gluco(manno)-octulosonate 8-phosphate, respectively, as determined by 1H NMR and other standard analytical methods. The kinetic parameters, Km and Vmax, for these reactions were determined. The 3- and 6-carbon phosphorylated monosaccharides, d,l-glyceraldehyde 3-phosphate and d-glucose 6-phosphate, as well as the nonphosphorylated 5-carbon analogues d-arabinose 5-phosphate, d-ribose 5-phosphate, and 2-deoxy-d-ribose 5-phosphate were not substrates.
The intrinsic tensile behavior of the matrix of bovine articular cartilage and its variation with age. (1980)

To study the age dependence of the uniaxial tensile behavior of bovine articular cartilage, 216 specimens of articular cartilage from the patellofemoral joint were grouped into two age categories: those from joints with growth plates present (open physes) and those from joints without growth plates (no physes). We prepared standard, dumbbell-shaped test specimens from the three ultrastructural zones of the tissue: the superficial tangential zone, the middle zone, and the deep zone. As was done in the early works of Kempson et al. and of Woo et all., we prepared specimens whose long axes were either parallel or perpendicular to the axis of the local split line on the joint surface. In these tensile tests we observed a profound difference between the two age groups in terms of the variations in the tensile properties related to the depth below the surface. With increasing distance from the articular surface, the tensile strength and stiffness increased in the open-physis group and decreased in the no-physis group. Directional dependence of the tensile response was manifested by increased stiffness and strength of the samples oriented parallel to the split-line axis when compared with the samples oriented perpendicular to it. Distortion of the initially flat, straight-sided portion of the gauge section was observed in most of the 216 specimens immediately after the application of tensile strains. This effect casts serious doubts on all previous measurements of cross-sectional dimensional changes. At present, we believe that this distortion occurs because articular cartilage is an inhomogeneous, layered material. We also observed that cartilage exudes substantial amounts of its interstitial fluid when the applied tensile strain becomes large. These two effects create serious problems in assessing the true volumetric changes and the material properties of cartilage specimens during uniaxial tension experiments.
Local Secretion of IFN-γ Induces an Antitumor Response (1999)

Previously we described that the adoptive transfer of tumor-infiltrating lymphocytes (TIL) + interleukin-2 (IL-2) leads to eradication of established methylcholanthrene (MCA)-105 fibrosarcoma pulmonary metastases in a congenic murine model. The in vivo efficacy of TIL was associated with their ability to secrete interferon-gamma (IFN-gamma), and to a lesser extent granulocyte-macrophage colony-stimulating factor. The local secretion of these cytokines resulted in recruitment of naive host immune cells to the tumor and eventually in a successful host antitumor immune response. In the present study, to further evaluate the role of IFN-gamma in the induction of a host antitumor immune response, we compared the treatment efficacy of adoptively transferred T cells and IFN-gamma gene transfected tumor cells (MCA-105/IFN-gamma) as delivery systems of IFN-gamma. Treatment with TIL-IL-2 or irradiated MCA-105/IFN-gamma induced a similar reduction in pulmonary metastases of MCA-105 tumor. In contrast, irradiated wild-type MCA-105 or TIL from IFN-gamma gene knockout mice did not cause tumor eradication. MCA-105 tumor-bearing mice treated with MCA-205/IFN-gamma showed a partial reduction in the number of pulmonary metastases. Histologically, lungs of successfully treated mice showed that initially activated macrophages expressing inducible nitric oxide synthase (iNOS) and dendritic cells infiltrated the tumor bed. Subsequently, CD4+ and CD8+ T cells infiltrated tumors. The therapeutic efficacy of IFN-gamma transfected tumor cells was eliminated when either CD4+ T cells or CD8+ T cells were depleted. These results suggest that local secretion of IFN-gamma induces a tumor-specific host antitumor immune response mediated through activated macrophages, dendritic cells, and tumor-specific T cells. This may be a common component of successful immunotherapy.
Proline-Catalyzed One-Step Asymmetric Synthesis of 5-Hydroxy-(2E)-hexenal from Acetaldehyde (2001)

For the first time, the L-proline-catalyzed direct asymmetric self-aldolization of acetaldehyde is described affording (+)-(5S)-hydroxy-(2E)-hexenal 2 with ee's ranging from 57 to 90%. Further transformations of 2 into synthetically valuable building blocks are presented. A mechanism for the formation of 2 is proposed.
Effects of Bifidobacterium sp fermented milk ingested with or without inulin on colonic bifidobacteria and enzymatic activities in healthy humans. (1996)

Administration of BFM substantially increases the proportion of bifidobacteria in the colonic flora, but the concurrent administration of inulin does not enhance this effect.
New Directions in Cardiac Transplantation (2006)

More than three decades of clinical experience in cardiac transplantation resulted in the spread of the procedure worldwide with a wealth of knowledge and advancements. Developments included liberalization of recipient and donor selection criteria, improved surgical techniques, novel immunosuppressive drugs and protocols, new rejection surveillance techniques, and better understanding of the pathophysiology of cardiac allograft vasculopathy to direct interventions for prevention and treatment.
The SH2-containing 5'-inositol phosphatase (SHIP) is tyrosine phosphorylated after Fc gamma receptor clustering in monocytes. (1999)

Current models of Fc gamma R signal transduction in monocytes describe a molecular cascade that begins upon clustering of Fc gamma R with the phosphorylation of critical tyrosine residues in the cytoplasmic domains of Fc gamma RIIa or the gamma-chain subunit of Fc gamma RI and Fc gamma RIIIa. The cascade engages several other tyrosine-phosphorylated molecules, either enzymes or adapters, to manifest ultimately an array of biological responses, including phagocytosis, cell killing, secretion of a variety of inflammatory mediators, and activation. Continuing to assess systematically the molecules participating in the cascade, we have found that the SH2-containing 5'-inositol phosphatase (SHIP) is phosphorylated on tyrosine early and transiently after Fc gamma R clustering. This molecule in other systems, such as B cells and mast cells, mediates an inhibitory signal. We find that clustering of either Fc gamma RIIa or Fc gamma RI is effective in inducing SHIP phosphorylation, that SHIP binds in vitro to a phosphorylated immunoreceptor tyrosine-based activation motif, peptide from the cytoplasmic domain of Fc gamma RIIa in activation-independent fashion, although SHIP binding increases upon cell activation, and that Fc gamma RIIb and Fc gamma RIIc are not responsible for the observed SHIP phosphorylation. These findings prompt us to propose that SHIP inhibits Fc gamma R-mediated signal transduction by engaging immunoreceptor tyrosine-based activation motif-containing cytoplasmic domains of Fc gamma RIIa and Fc gamma RI-associated gamma-chain.
Enhanced proliferation, invasion, and epithelial-mesenchymal transition of nicotine-promoted gastric cancer by periostin (2011)

Periostin is a nicotine target gene in gastric cancer and plays a role in gastric cancer cell growth, invasion, drug resistance, and EMT facilitated by nicotine.
Structural flexibility of carbon nanotubes (1996)

We report high resolution electron microscope (HREM) observations and atomistic simulations of the bending of single and multi-walled carbon nanotubes under mechanical duress. Single and multiple kinks are observed at high bending angles. Their occurrence is quantitatively explained by the simulations, which use a realistic many-body potential for the carbon atoms. We show that the bending is fully reversible up to very large bending angles, despite the occurrence of kinks and highly strained tube regions. This is due to the remarkable flexibility of the hexagonal network, which resists bond breaking and bond switching up to very high strain values.
Detailed Studies of a High-Capacity Electrode Material for Rechargeable Batteries, Li2MnO3−LiCo1/3Ni1/3Mn1/3O2 (2011)

Lithium-excess manganese layered oxides, which are commonly described by the chemical formula zLi(2)MnO(3)-(1-z)LiMeO(2) (Me = Co, Ni, Mn, etc.), are of great importance as positive electrode materials for rechargeable lithium batteries. In this Article, Li(x)Co(0.13)Ni(0.13)Mn(0.54)O(2-δ) samples are prepared from Li(1.2)Ni(0.13)Co(0.13)Mn(0.54)O(2) (or 0.5Li(2)MnO(3)-0.5LiCo(1/3)Ni(1/3)Mn(1/3)O(2)) by an electrochemical oxidation/reduction process in an electrochemical cell to study a reaction mechanism in detail before and after charging across a voltage plateau at 4.5 V vs Li/Li(+). Changes of the bulk and surface structures are examined by synchrotron X-ray diffraction (SXRD), X-ray absorption spectroscopy (XAS), X-ray photoelectron spectroscopy (XPS), and time-of-flight secondary ion mass spectroscopy (SIMS). SXRD data show that simultaneous oxygen and lithium removal at the voltage plateau upon initial charge causes the structural rearrangement, including a cation migration process from metal to lithium layers, which is also supported by XAS. This is consistent with the mechanism proposed in the literature related to the Li-excess manganese layered oxides. Oxygen removal associated with the initial charge on the high voltage plateau causes oxygen molecule generation in the electrochemical cells. The oxygen molecules in the cell are electrochemically reduced in the subsequent discharge below 3.0 V, leading to the extra capacity. Surface analysis confirms the formation of the oxygen containing species, such as lithium carbonate, which accumulates on the electrode surface. The oxygen containing species are electrochemically decomposed upon second charge above 4.0 V. The results suggest that, in addition to the conventional transition metal redox reactions, at least some of the reversible capacity for the Li-excess manganese layered oxides originates from the electrochemical redox reaction of the oxygen molecules at the electrode surface.
Sirt1 protects against high-fat diet-induced metabolic damage (2008)

The identification of new pharmacological approaches to effectively prevent, treat, and cure the metabolic syndrome is of crucial importance. Excessive exposure to dietary lipids causes inflammatory responses, deranges the homeostasis of cellular metabolism, and is believed to constitute a key initiator of the metabolic syndrome. Mammalian Sirt1 is a protein deacetylase that has been involved in resveratrol-mediated protection from high-fat diet-induced metabolic damage, but direct proof for the implication of Sirt1 has remained elusive. Here, we report that mice with moderate overexpression of Sirt1 under the control of its natural promoter exhibit fat mass gain similar to wild-type controls when exposed to a high-fat diet. Higher energy expenditure appears to be compensated by a parallel increase in food intake. Interestingly, transgenic Sirt1 mice under a high-fat diet show lower lipid-induced inflammation along with better glucose tolerance, and are almost entirely protected from hepatic steatosis. We present data indicating that such beneficial effects of Sirt1 are due to at least two mechanisms: induction of antioxidant proteins MnSOD and Nrf1, possibly via stimulation of PGC1alpha, and lower activation of proinflammatory cytokines, such as TNFalpha and IL-6, via down-modulation of NFkappaB activity. Together, these results provide direct proof of the protective potential of Sirt1 against the metabolic consequences of chronic exposure to a high-fat diet.
Adipose tissue dysfunction tracks disease progression in two Huntington's disease mouse models (2009)

In addition to the hallmark neurological manifestations of Huntington's disease (HD), weight loss with metabolic dysfunction is often observed in the later stages of disease progression and is associated with poor prognosis. The mechanism for weight loss in HD is unknown. Using two mouse models of HD, the R6/2 transgenic and CAG140 knock-in mouse strains, we demonstrate that adipose tissue dysfunction is detectable at early ages and becomes more pronounced as the disease progresses. Adipocytes acquire a 'de-differentiated' phenotype characterized by impaired expression of fat storage genes. In addition, HD mice exhibit reduced levels of leptin and adiponectin, adipose tissue-derived hormones that regulate food intake and glucose metabolism. Importantly, some of these changes occur prior to weight loss and development of some of the characteristic neurological symptoms. We demonstrate that impaired gene expression and lipid accumulation in adipocytes can be recapitulated by expression of an inducible mutant huntingtin transgene in an adipocyte cell line and that mutant huntingtin inhibits transcriptional activity of the PGC-1alpha co-activator in adipocytes, which may contribute to aberrant gene expression. Thus, our findings indicate that mutant huntingtin has direct detrimental effects in cell types other than neurons. The results also indicate that circulating adipose-tissue-derived hormones may be accessible markers for HD prognosis and progression and suggest that adipose tissue may be a useful therapeutic target to improve standard of life for HD patients.
Prostaglandin as a Mediator of Bone Resorption Induced by Experimental Tooth Movement in Rats (1980)

Administration of indomethacin inhibited the appearance of osteoclasts and bone resorption induced by experimental tooth movement in rats. Effects were limited to groups injected within 12 h after treatment. Prostaglandin E1 or E2 solutions injected in gingiva lying near the upper first molar caused the appearance of osteoclasts and bone resorption.
THE DESIGN OF A NEW LETTER CHART FOR MEASURING CONTRAST SENSITIVITY (1988)

Summary-I. A consideration of methods for assessing contrast sensitivity leads to the conclusion that, for a clinical test, letters are more suitable than gratings. 2. A letter chart is described in which letters decrease in contrast but not in size. The letters are arranged in groups of three; successive groups decrease in contrast by a factor of IfJ2 from a very high contrast down to a contrast below the threshold of normal observers. A subject&amp;apos;s threshold is taken to be the lowest contrast for which at least two letters in a group are correctly reported. 3. A mathematical model of the observer and the chart-testing procedure has been used to predict how the accuracy and repeatability of the test score depend on the parameters of the chart and observer. This reveals that even a low probability of misreporting supra threshold letters will seriously bias the test score if the passing criterion is strict, requiring correct report of all letters in each group, but will have little effect if the passing criterion is less strict. This effect of the passing criterion may explain Rubin&amp;apos;s [Clin. Vision Sci. 2, No. I (1987)] finding that the new test, which uses a lenient criterion, has excellent test-retest reliability, much higher than the Ginsburg [Am. J. Optom. Physiol. Opt. 61,403-407 (1984)] chart with its strict criterion. Key words-Contrast sensitivity; letter sensitivity; contrast sensitivity test; clinical testing; charts.
Comparative biochemical properties of p21 ras molecules coded for by viral and cellular ras genes (1982)

In earlier studies, we molecularly cloned a normal cellular gene, c-rasH-1, homologous to the v-ras oncogene of Harvey murine sarcoma virus (v-rasH). By ligating a type c retroviral promotor to c-rasH-1, we could transform NIH 3T3 cells with the c-rasH-1 gene. The transformed cells contained high levels of a p21 protein coded for by the c-rasH-1 gene. In the current studies, we have purified extensively both v-rasH p21 and c-rasH p21 and compared the in vivo and in vitro biochemical properties of both these p21 molecules. The p21 proteins coded for by v-rasH and c-rasH-1 shared certain properties: each protein was synthesized as a precursor protein which subsequently became bound to the inner surface of the plasma membrane; each protein was associated with guanine nucleotide-binding activity, a property which copurified with p21 molecules on a high-pressure liquid chromatography molecular sizing column. In some other properties, the v-rasH and c-rasH p21 proteins differed. In vivo, approximately 20 to 30% of v-rasH p21 molecules were in the form of phosphothreonine-containing pp21 molecules, whereas in vivo only a minute fraction of c-rasH-1 p21 contained phosphate, and this phosphate was found on a serine residue. v-rasH pp21 molecules with an authentic phosphothreonine peptide could be synthesized in vitro in an autophosphorylation reaction in which the gamma phosphate of GTP was transferred to v-rasH p21. No autophosphorylating activity was associated with purified c-rasH-1 p21 in vitro. The results indicate a major qualitative difference between the p21 proteins coded for by v-rasH and c-rasH-1. The p21 coded for by a mouse-derived oncogenic virus, BALB murine sarcoma virus, resembled the p21 coded for by c-rasH-1 in that it bound guanine nucleotides but did not label appreciably with 32Pi. The forms of p21 coded for by other members of the ras gene family were compared, and the results indicate that the guanine nucleotide-binding activity is common to p21 molecules coded for by all known members of the ras gene family.
Spatially Resolved Modeling of Microstructurally Complex Battery Architectures (2007)

Recently, batteries with interpenetrating electrode architectures have been proposed which have the potential to outperform classical designs. These electrode structures are highly percolating particle distributions with short diffusion distances. One of the main advantages with respect to classic rocking chair battery designs is the decrease of the ohmic losses and localized joule-heating, while simultaneously delivering higher power densities and specific energies closer to the theoretical ideal. In the present paper, the rocking chair lithium-ion battery architecture is taken as a point of reference to explore two variations of a three-dimensional battery concept. The first microstructure possesses a highly branched tortuous positive electrode particle distribution, and the second architecture corresponds to a topology with perfectly ordered branches of positive electrode materials. Both architectures outperform the classic rocking chair design by a factor of five for intermediate discharge rates and by 37% for high discharge rates; however, branch ordering has the advantage of improving the macroscopic discharge time by 18% for discharge rates of 4C or higher. Simulations show that the power density of a rechargeable battery can be engineered by maximizing the electrochemical driving force for intercalation while decreasing the characteristic transport distances of the material components. Additionally, the analyzed devices greatly diminish the possibility of salt precipitation during discharge due to removal of microstructure limitations in the classic design. Results also show that for the interpenetrating architectures, when lithium plating and fracture fatigue do occur, they initiate at the tips of the branches of anode material, particularly in those regions that are closer to the electrode phase of opposite polarity. Increasing branch tortuosity induces lithium depletion at the back ohmic contact of the positive electrode at high discharge rates.
Genetic circuit design automation (2016)

Computation can be performed in living cells by DNA-encoded circuits that process sensory information and control biological functions. Their construction is time-intensive, requiring manual part assembly and balancing of regulator expression. We describe a design environment, Cello, in which a user writes Verilog code that is automatically transformed into a DNA sequence. Algorithms build a circuit diagram, assign and connect gates, and simulate performance. Reliable circuit design requires the insulation of gates from genetic context, so that they function identically when used in different circuits. We used Cello to design 60 circuits forEscherichia coli(880,000 base pairs of DNA), for which each DNA sequence was built as predicted by the software with no additional tuning. Of these, 45 circuits performed correctly in every output state (up to 10 regulators and 55 parts), and across all circuits 92% of the output states functioned as predicted. Design automation simplifies the incorporation of genetic circuits into biotechnology projects that require decision-making, control, sensing, or spatial organization.
Coronary artery disease following bone marrow transplantation. (1989)

A 19-year-old woman died suddenly 30 months after allogeneic bone marrow transplantation for refractory leukemia. On postmortem examination severe coronary artery disease and acute myocardial infarction were found. The patient had previously been given chemotherapy including daunorubicin for treatment of her leukemia. She received high dose cyclophosphamide and total body irradiation (1260 cGy) for her transplant. Diffuse chronic graft-versus-host disease, mainly affecting skin, subsequently developed, and was resistant to various therapies. The possible association of coronary artery disease and allogeneic bone marrow transplantation is discussed.
An advanced mixed user domestic satellite system architecture (1980)

A domestic satellite system architecture that can efficiently and economically accommodate a wide variety of disparate user classes is described and a baseline system configuration identified. With such a technique, both the efficiency of TDMA operation and the operational terminal flexibility of FDMA can be simultaneously achieved.
Sensor fusion-based line detection for unmanned navigation (2010)

We propose an algorithm of reliable detection of line for unmanned navigation of mobile robots using sensor fusion. To detect the distance and the angle between the robot and the line, we use a vision sensor system and a laser range finder (LRF). Each sensor system runs its own extended Kalman filter (EKF) to estimate the distance and orientation of the line. The vision system processes images being captured using well-known edge detection algorithms, and the LRF detects the line using the measurement of the intensity of the laser beam reflected. However, depending on the condition of the road and ambient light, each sensor gives us wrong measurement of the line or sometimes completely fails to detect it. To resolve such uncertainty, we develop a simple and easy-to-implement sensor fusion algorithm that uses weighted sum of the output of each EKF, and it gives us more reliable estimate of the distance and orientation of the line than each measurement/estimator system.