gebhart/patrepeval huggingface dataset:
Evolution of type C viral genes: preservation of ancestral murine type C viral sequences in pig cellular DNA. (1975)

Domestic pigs (Sus scrofa) and other members of the family Suidae have multiple copies of type C viral gene sequences in the cellular DNA of all their tissues. Partially homologous viral gene sequences are also found in cellular DNA of rodents, particularly Muridae. The results lead to the conclusion that type C viral genes were introduced into the Suidae lineage as a result of trans-species infection by an ancestral xenotropic murine virus. The rate of evolution of the virogene sequences in the pig appears to be much slower than that of genes that have remained in the rodent lineage; this may be a consequence of transfer from a shorter-lived animal (the rodent) to a longer-lived one (the pig). We estimate the time of gene transmission as 5-10 million years ago and conclude that the present-day porcine type C virogenes most closely approximate the viral genes as they were several million years ago in the rodent lineage.
The oxidation of CO on RuO2(110) at room temperature (2001)

RuO 2 (110) surfaces were prepared by exposing Ru(0001) to 107 L of O2 at 700 K. Postexposure of O2 at 300 K resulted in an additional oxygen species (O-cus) adsorbed on coordinatively unsaturated Ru atoms (Ru-cus). The surface was then exposed to CO at 300 K and studied by thermal desorption spectroscopy (TDS) and high-resolution electron energy loss spectroscopy (HREELS). It is demonstrated that CO is oxidized at 300 K through reaction with both the O-cus as well as with surface O-atoms held in bridge positions (O-bridge). Although—at room temperature—CO adsorbs intermediately on the Ru-cus atoms, it is stable only at the Ru atoms underneath the O-bridge after the latter has been reacted off. At room temperature only surface oxygen takes part in the CO oxidation and the oxygen-depleted surface can be restored by O2 exposure, so that under steady-state flow conditions an oxygen-deficient surface will exist whose stoichiometry will be determined by the ratio of partial pressures.
Micro- and nanomechanical sensors for environmental, chemical, and biological detection (2007)

Micro- and nanoelectromechanical systems, including cantilevers and other small scale structures, have been studied for sensor applications. Accurate sensing of gaseous or aqueous environments, chemical vapors, and biomolecules have been demonstrated using a variety of these devices that undergo static deflections or shifts in resonant frequency upon analyte binding. In particular, biological detection of viruses, antigens, DNA, and other proteins is of great interest. While the majority of currently used detection schemes are reliant on biomarkers, such as fluorescent labels, time, effort, and chemical activity could be saved by developing an ultrasensitive method of label-free mass detection. Micro- and nanoscale sensors have been effectively applied as label-free detectors. In the following, we review the technologies and recent developments in the field of micro- and nanoelectromechanical sensors with particular emphasis on their application as biological sensors and recent work towards integrating these sensors in microfluidic systems.
Robust Lane Detection for Video-Based Navigation Systems (2007)

Lane detection from a live video captured in a moving vehicle is an important issue for autonomous vehicles and video-based navigation systems. In this paper, we present a novel idea for robust lane detection and lane color recognition. More specifically, a framework for robust lane detection is presented. Then, a novel idea to reduce illumination effects is presented. Lastly, SVM approach is presented to recognize lane color robustly for various lighting conditions including shadow, backlight, sunset, and so on. By combining information from navigation database, it is possible to decide if we are in the leftmost, middle, or the rightmost lane, which allows us to provide more realistic navigation information to drivers. Simulation results are provided to show the robustness of the proposed idea.
Erythropoietin Protects the Kidney against the Injury and Dysfunction Caused by Ischemia-Reperfusion (2004)

Erythropoietin (EPO) is upregulated by hypoxia and causes proliferation and differentiation of erythroid progenitors in the bone marrow through inhibition of apoptosis. EPO receptors are expressed in many tissues, including the kidney. Here it is shown that a single systemic administration of EPO either preischemia or just before reperfusion prevents ischemia-reperfusion injury in the rat kidney. Specifically, EPO (300 U/kg) reduced glomerular dysfunction and tubular injury (biochemical and histologic assessment) and prevented caspase-3, -8, and -9 activation in vivo and reduced apoptotic cell death. In human (HK-2) proximal tubule epithelial cells, EPO attenuated cell death in response to oxidative stress and serum starvation. EPO reduced DNA fragmentation and prevented caspase-3 activation, with upregulation of Bcl-X(L) and XIAP. The antiapoptotic effects of EPO were dependent on JAK2 signaling and the phosphorylation of Akt by phosphatidylinositol 3-kinase. These findings may have major implications in the treatment of acute renal tubular damage.
Cells Engineered to Produce Acetylcholine: Therapeutic Potential for Alzheimer's Diseasea (1993)

Alzheimer's disease (AD) is a debilitating disorder of the central nervous system which may affect up to 50% of the population over the age of 85 years. The etiology of AD is unknown and there is currently no cure for the disease. Well-documented losses in cholinergic and other neurotransmitter systems have provided a focal point for attempting pharmacological interventions in AD to ameliorate some of the cognitive deficits that occur. However, current systemic strategies have met with limited success. An alternative strategy, that has been pursued in animal models of neurodegenerative disease, is to augment neurotransmitter function within the brain through tissue transplantation. Such implants have an advantage over conventional drug therapies in that the cells can be precisely placed within compromised areas of the brain. We have pursued a strategy of designing cells, through the use of molecular biology techniques, to produce neurotrophic factors and neurotransmitters. Recently, we developed a primary fibroblast cell line that was genetically modified to express choline acetyltransferase (ChAT). In vitro, these cells produced and released acetylcholine at levels that varied with the amount of choline in the culture media. When implanted into the hippocampus of rats, the in vivo microdialysis technique revealed that the ChAT-expressing fibroblasts continued to produce and release acetylcholine after grafting. Most importantly, the levels of acetylcholine synthesized by the cells could be regulated by the localized infusion of choline in the vicinity of the grafts. These results confirmed previous work which indicated that engineered fibroblasts provide an effective delivery vehicle of different substances to the brain. While the intracerebral implantation of genetically modified cells will not cure AD, the continuing development of this strategy may ultimately provide a powerful approach for ameliorating the devastating cognitive impairments which are a hallmark of this disease.
Pict: A Programming Language Based on the Pi-Calculus (2000)

The &amp;amp;pi;-calculus offers an attractive basis for concurrent programming. It is small, elegant, and well studied, and supports (via simple encodings) a wide range of high-level constructs including data structures, higher-order functional programming, concurrent control structures, and objects. Moreover, familiar type systems for the &amp;amp;lambda;-calculus have direct counterparts in the &amp;amp;pi;-calculus, yielding strong, static typing for a high-level language using the &amp;amp;pi;-calculus as its core. This paper describes Pict, a strongly-typed concurrent programming language constructed in terms of an explicitly-typed &amp;amp;pi;-calculus core language.
The central role of T cells in rheumatoid arthritis. (2008)

Rheumatoid arthritis (RA) is one of the most common chronic inflammatory syndromes. As such, RA is often considered the prototype disease for defining both the molecular and pathological basis of immune-mediated chronic inflammatory disease, and for validating targeted therapies. The immunogenetics of RA suggest a key role for aberrant pathways of T-cell activation in the initiation and/or perpetuation of disease. In the T-cell activation process, CD4+ T-cells are engaged by antigenic peptide fragments in a complex with HLA class II molecules, in addition to co-stimulatory molecules, such as CD80/CD86, expressed on the surface of professional antigen presenting cells. The strongest evidence supporting a role for CD4+ T cells in disease pathogenesis is the association between RA and HLA-DRB1; however, the functional role of this association has yet to be defined. Susceptibility to RA may also be linked with several RA-associated allelic variants of genes, especially PTPN22, but also CTLA4, IL2RA, IL-2RB, STAT4, PTPN2 and PADI4, many of which encode molecules directly implicated in pathways of T-cell activation.The presence of inflammatory infiltrates, such as follicular structures, in the synovial membrane provides compelling evidence of ongoing immune reactions in moderate to severe RA. These structures likely play a key role in T cell - B cell cooperation and the local generation of specific autoantibodies; as such, chronically activated synovial T cells represent key cellular targets for therapy. Evidence also supports a role for T-helper (Th) cells, Th17 cells, and impaired CD4+CD25(hi) regulatory T cell (Treg) function in the pathogenesis of RA. In addition to discussing a range of issues regarding T-cell activation in RA, this review describes how therapeutic modulation of T-cell function, as opposed to profound immunosuppression or immunodepletion, has been associated with better disease outcomes in clinical trials. Ultimately, elucidation of the distinct effects of co-stimulation modulation with abatacept on T cells should provide key insights into understanding how to restore immune homeostasis in patients with RA.
A phase I study of the androgen signaling inhibitor ARN-509 in patients with metastatic castration-resistant prostate cancer (mCRPC). (2012)

4548 Background: ARN-509 is a novel small molecule AR antagonist that impairs AR nuclear translocation and binding to DNA, inhibiting tumor growth and promoting apoptosis, with no partial agonist activity. (Clegg et al., 2012) We conducted a phase I trial to assess safety, pharmacokinetics (PK), and determine the recommended phase II dose (RP2D). Methods: Eligible patients with mCRPC received ARN-509 orally on a continuous daily dosing schedule. Seven doses (30, 60, 90, 120, 180, 240, and 300 mg) were tested using standard 3x3 dose escalation criteria. Once drug concentrations were achieved that met or exceeded optimal levels predicted preclinically, an additional 2 dose levels were tested to further confirm the safety margin of ARN-509 (390 and 480 mg). Anti-tumor activity was assessed by PSA, radiographic responses, and FDHT-PET imaging. Results: Thirty patients were enrolled. The most common grades 1-2 treatment-related adverse events were fatigue (38%), nausea (29%), and pain (24%). There was only 1 treatment-related grade 3 adverse event (abdominal pain) at 300 mg, possibly related to a higher pill burden. PK was shown to be linear and dose-dependent. At 12 weeks, 42% of patients have had ≥ 50% PSA declines. Eleven (37%) patients have discontinued the study due to progression, with the longest patient still on study for more than 16 months. FDHT-PET imaging demonstrated AR blockade at 4 weeks across multiple dose levels. Conclusions: In this phase I study, ARN-509 was shown to be safe and well tolerated with linear PK. Based on promising activity across all dose levels and pharmacodynamic evidence of AR antagonism, an optimal biologic dose of 240 mg daily was selected for phase II investigation. DOD/PCF PCCTC trial sponsored by Aragon Pharmaceuticals.
The ACM conference on the history of personal workstations (1986)

ACM held a conference on the history of personal workstations at Palo Alto, CA on January 9-10, 1986. There were presentations by thirteen pioneering researchers, primarily from projects funded by ARPA at MIT, the Stanford Research Institute, and the Xerox Palo Alto Research Center. The participants described their motivation, the systems they developed and the goals of the organizations where they worked. This paper summarizes and discusses the conference.
Passivation properties of RST silicon ribbon by single SiNx:H or double a-Si:H/SiNx:H layer and solar cells (2008)

International audience
Pressure And Thermal Modeling Of Rocket Launches (1995)

Report presents mathematical model for use in designing rocket-launching stand. Predicts pressure and thermal environment, as well as thermal responses of structures to impinging rocket-exhaust plumes. Enables relatively inexperienced analyst to determine time-varying distributions and absolute levels of pressure and heat loads on structures.
Reciprocal Autocrine and Paracrine Regulation of Growth of Mesenchymal and Alveolar Epithelial Cells from Fetal Lung (1986)

The regulation of DNA synthesis in 19 day rat fetal lung epithelial (alveolar type II) and mesenchymal (fibroblast) cells by protein growth factors has been studied. In each case a single growth factor is capable of stimulating 3H-thymidine incorporation into DNA: platelet-derived growth factor in the case of the alveolar type II cell and epidermal growth factor in the case of the fetal lung fibroblast. We hypothesize that these results indicate that the type II cell endogenously produces progression activities (i.e., epidermal growth factor-like and somatomedin-like activity) while the fibroblast produces competence (i.e., platelet-derived growth factor-like) and progression (i.e., somatomedin-like activity). The latter is in keeping with previous observations with skin fibroblasts. To test the above hypothesis, the effect of fetal lung fibroblast-derived conditioned media upon the growth of fetal alveolar type II cells has been determined. The results indicate that, indeed, such media contain competence activity for this cell type. The mitogenic activity was further characterized as heat-sensitive, trypsin-sensitive, and has an apparent molecular weight of 30,000 Daltons. It is not synthesized by 19 day fetal liver, kidney or skin fibroblasts and its synthesis is higher in lung fibroblasts isolated from 19 day fetuses as compared to those isolated on day 16 or day 22.
Real-time GDP forecasting in the euro area (2002)

Paper presented at the Cepr-Bocconi University Workshop 'Understanding the Structure of the European Business Cycle', Milan, 11 June 2002, and at the Fall Meeting of the Project LINK, Bologna, 7-11 October 2002
Stable hamster-mouse hybridomas producing IgG and IgM hamster monoclonal antibodies of defined specificity. (1983)

Specific antibody-secreting hybridomas have been obtained by fusing Syrian or Armenian hamster (Mesocricetus auratus or Cricetulus migratorius) spleen cells with mouse myeloma cells. The hamsters were immunized to mouse cytolytic T lymphocytes. Hybrids were selected either by an indirect binding assay using an 125I-monoclonal antibody (MAb) reactive with hamster kappa-chains or by their ability to block T cell-mediated cytolysis. Three hybridoma clones were obtained that secreted intact IgM-like and IgG-like hamster MAb as shown by SDS-PAGE. The clones were stable as shown by subcloning. Two MAb recognized antigens of wide tissue distribution; the third bound specifically to T lymphocytes, gave strong inhibition of T cell-mediated cytolysis, and immunoprecipitated the Lyt-2,3 molecule.
From PGF(2alpha)-isopropyl ester to latanoprost: a review of the development of xalatan: the Proctor Lecture. (2001)

From PGF(2alpha)-isopropyl ester to latanoprost: a review of the development of xalatan: the Proctor Lecture
Characterization of vesicles, containing an acylated oligopeptide, released by human colon adenocarcinoma cells (1989)

RNA-containing vesicles, recovered from the supernatant of high-density cell samples of human colon carcinoma, produce a high-resolution 1H NMR spectrum of lipids characterized by isotropic tumbling; these vesicles contain large amounts of triglycerides and cholesterol esters. Both findings have strict analogies to what is displayed by the proteolipid complexes isolated from the sera of tumor-bearing patients [(1985) Proc. Natl. Acad. Sci. USA 82, 3455-3459; (1986) FEBS Lett. 203, 164-168]. Lipid analysis and enzymatic tests indicate that these vesicles are selected micromaps of plasma membranes, analogous to those that can be recovered from culture media in which tumor cells are grown [(1985) Dev. Biol. 3, 33-57]. Peculiar lipids, an acylated oligopeptide and a modified phospholipid, are also present in the vesicles.
A modified Volterra series approach for nonlinear dynamic systems modeling (2002)

This paper describes a modeling approach for nonlinear dynamic systems based on a modified Volterra series; by comparing the truncation error of this series with that of the classical Volterra one, we outlined that, under the assumption of short-term nonlinear memory effects, the modified series enables a single-fold nonlinear convolution integral to be adopted also in the presence of strong nonlinearities. The measurement-based identification of the first terms of the modified Volterra series is described; experimental and simulation results which confirm the theoretical considerations are also provided.
Evaluation and utilization of beam simulation codes for the SNS ion source and low energy beam transport development (2008)

Beam simulation codes PBGUNS, SIMION, and LORENTZ-3D were evaluated by modeling the well-diagnosed SNS base line ion source and low energy beam transport (LEBT) system. Then, an investigation was conducted using these codes to assist our ion source and LEBT development effort which is directed at meeting the SNS operational and also the power-upgrade project goals. A high-efficiency H(-) extraction system as well as magnetic and electrostatic LEBT configurations capable of transporting up to 100 mA is studied using these simulation tools.
Improved Methods for the Structural Analysis of the Amylose-Rich Fraction from Rice Flour (2006)

Cooking and sensory properties of rice are largely determined by the amylose content and structure. For relationships between functional and structural properties, a more accurate method to determine the structure of amylose is required. Here we calibrate size exclusion chromatography (SEC) columns, using Mark-Houwink parameters for linear starch and pullulan standards, to obtain the true molecular weight distribution of linear starch. When the molecular weight distribution is reported relative to pullulan, rather than the actual molecular weight which is readily obtained from universal calibration, it is seen that the molecular weights of longer amylose chains are greatly underestimated. We validate the SEC method to enable the measurement of the hydrodynamic volume distribution of the starch by examining reproducibility and recovery. Analysis of the starch in the sample pre- and post-SEC shows that 20% of the carbohydrate is not recovered. Comparison of the weight-average degree of polymerization, X(w), of (undebranched) starch of pre- and post-SEC is made using iodine binding as well as Berry plots of data from multi-angle laser light scattering (MALLS). These both show that current SEC techniques for starch analysis lead to significant loss of high molecular weight material. Indeed, for the systems studied here, the values for X(w) after SEC are about three times lower than those before SEC. Iodine-starch complexes of pre- and post-SEC samples reveals that the SEC techniques give reliable data for the amylose fraction but not for amylopectin. We address reports in the literature suggesting that the conventional isoamylase method for debranching starch would lead to incomplete debranching and thus incorrect molecular weight distributions. However, it is shown using (1)H NMR that isoamylase can completely debranch the amylose (to within the detection limit of 0.5%), and by SEC that successive incubation with isoamylase, alpha-amylase, and beta-amylase can degrade the amylose-rich fraction completely to maltose. We develop a method to obtain a hot water soluble fraction (HWSF), rich in undamaged amylose molecules, directly from rice flour, avoiding the structural degradation of previous techniques. With appropriate sample handling, the formation of associations between starch chains is minimized. With the combination of calibrated and validated SEC methods, and an improved extraction of amylose from rice, the X(w) for both HWSF and debranched HWSF are found to be much larger than has previously been reported.
Boolean operations of 2-manifolds through vertex neighborhood classification (1986)

A topologically complete set operations algorithm for planar polyhedral Z-manifold objects is described; that is, under the assumption that all numerical tests required can be correctly evaluated, the algorithm is capable of solving all “special cases." The central component of the algorithm is a module here called the vertex neighborhood classifier . By virtue of the classifier, the various special cases can be reduced into a collection of classification problems involving a pair of coincident vertices. The classifier works by means of decision rules that guarantee the topological consistency and regularity of the resulting polyhedron. If the result is not a 2-manifold, a relaxed polyhedron will be produced.
Short communication: Modulation of the small intestinal microbial community composition over short-term or long-term administration with Lactobacillus plantarum ZDY2013 (2016)

The small intestinal (SI) microbiota has an essential role in the maintenance of human health. However, data about the indigenous bacteria in SI as affected by probiotics are limited. In our study, the short-term and long-term effects of a probiotic candidate, Lactobacillus plantarum ZDY2013, on the SI microbiota of C57BL/6J mice were investigated by the Illumina HiSeq (Novogene Bioinformatics Technology Co., Ltd., Tianjin, China) platform targeting the V4 region of the 16S rDNA. A total of 858,011 sequences in 15 samples were read. The α diversity analysis revealed that oral administration with L. plantarum ZDY2013 for 3 wk led to a significant increase in the richness and diversity of the SI bacterial community. Principal coordinate analysis and unweighted pair-group method with arithmetic means analysis showed a clear alteration in the SI microbiota composition after 3 wk of L. plantarum ZDY2013 treatment, although these changes were not found 6 wk after ceasing L. plantarum ZDY2013 administration. Species annotation showed that the dominant phyla in SI microbiota were Firmicutes, Bacteroidetes, Proteobacteria, and Verrucomicrobia. Interestingly, operational taxonomic unit cluster analysis showed that administration with L. plantarum ZDY2013 for 3 wk significantly increased the abundance of Proteobacteria, but decreased that of Bacteroidetes. Linear discriminant analysis coupled with effect size identified 18 bacterial taxa (e.g., Ruminococcus spp. and Clostridium spp.) that overgrew in the SI microbiota of the mice administered with L. plantarum ZDY2013 for 3 wk, and most of them belonged to the phyla Bacteroidetes and Proteobacteria. However, only one bacterial taxon (e.g., Nocardioides spp.) was over-represented in the SI microbiota of mice 6 wk after L. plantarum ZDY2013 administration. Overall, this study shows that oral administration with probiotic results in an important but transient alteration in the microbiota of SI.