gebhart/patrepeval huggingface dataset:
Selection and grouping of herds in international genetic evaluation of daughter performance records (2002)

Although international dairy sire evaluations have traditionally been calculated by reanalyzing national EBV data, recent research has focused on direct analysis of individual animal performance records from participating countries. The latter approach offers several theoretical advantages, including relaxation of the assumption that all herds within a country use the same production system and freedom from “phantom” genotype by environment interactions that are actually artifacts of differences in genetic evaluation systems between countries. Previous research in our laboratory has focused on estimation of genetic correlations between countries using individual performance records in a sire model, as well as methodology for grouping herds across country borders (according to management variables) for the purpose of genetic evaluation.
Adsorption and Reactions of C6Hydrocarbons at High Pressures on Pt(111) Single-Crystal Surfaces Studied by Sum Frequency Generation Vibrational Spectroscopy:  Mechanisms of Isomerization and Dehydrocyclization ofn-Hexane (2004)

The adsorption geometries and surface reactions of various C(6) hydrocarbons (n-hexane, 2-methylpentane, 3-methylpentane, and 1-hexene) adsorbed on Pt(111) were investigated using sum frequency generation (SFG) surface vibrational spectroscopy. The adsorptions and reactions were carried out in 1.5 Torr of C(6) hydrocarbons in the absence and presence of excess hydrogen (15 Torr) and in the temperature range 296-453 K. At 296 K and in the presence of excess hydrogen, n-hexane and 3-methylpentane adsorbed molecularly on Pt(111) mostly in "flat-lying" geometries. Upon heating the sample up to 453 K, the molecules underwent dehydrogenation to form new surface species in "standing-up" geometries, such as hexylidyne and metallacyclic species. However, 2-methylpentane and 1-hexene were dehydrogenated to metallacyclobutane and hexylidyne, respectively, at 296 K in the presence of excess hydrogen. The dehydrogenated species remained unreacted on the surface upon heating the sample up to 453 K. The absence of excess hydrogen enhanced dehydrogenation of n-hexane and 3-methylpentane to form pi-allyl c-C(6)H(9) and metallacyclohexane, respectively, at 296 K. Upon heating to 453 K, the pi-allyl c-C(6)H(9) species underwent irreversible dehydrogenation, while hexylidyne and metallacyclic species remained unreacted. On the basis of these results, the mechanisms for catalytic isomerization and dehydrocyclization of n-hexane, which are the important "reforming" reactions to produce high-octane fuels over platinum, were discussed.
Gefitinib or Chemotherapy for Non–Small-Cell Lung Cancer with Mutated EGFR (2010)

First-line gefitinib for patients with advanced non-small-cell lung cancer who were selected on the basis of EGFR mutations improved progression-free survival, with acceptable toxicity, as compared with standard chemotherapy. (UMIN-CTR number, C000000376.)
The Sbi Protein Is a Multifunctional Immune Evasion Factor of Staphylococcus aureus (2011)

The second immunoglobulin-binding protein (Sbi) of Staphylococcus aureus has two N-terminal domains that bind the Fc region of IgG in a fashion similar to that of protein A and two domains that can bind to the complement protein C3 and promote its futile consumption in the fluid phase. It has been proposed that Sbi helps bacteria to avoid innate immune defenses. By comparing a mutant defective in Sbi with mutants defective in protein A, clumping factor A, iron-regulated surface determinant H, and capsular polysaccharide, it was shown that Sbi is indeed an immune evasion factor that promotes bacterial survival in whole human blood and the avoidance of neutrophil-mediated opsonophagocytosis. Sbi is present in the culture supernatant and is also associated with the cell envelope. S. aureus strains that expressed truncates of Sbi lacking N-terminal domains D1 and D2 (D1D2) or D3 and D4 (D3D4) or a C-terminal truncate that was no longer retained in the cell envelope were analyzed. Both the secreted and envelope-associated forms of Sbi contributed to immune evasion. The IgG-binding domains contributed only when Sbi was attached to the cell, while only the secreted C3-binding domains were biologically active.
Chromatic Plasmonic Polarizers for Active Visible Color Filtering and Polarimetry (2012)

Color filters are widely used in color displays, optical measurement devices, and imaging devices. Conventional color filters have usually only one fixed output color. However developing active color filters with controllable color output can lead to more compact and sophisticated color filter-based devices and applications. Recent progress in nanotechnology and new knowledge of the interaction of light with metal nanostructures allow us to capture and control light better than ever. Here we use it to fabricate active color filters, based on arrays of metallic optical nanoantennas that are tailored to interact with light at visible frequencies via excitation of localized surface plasmons. This interaction maps the polarization state of incident white light to visible color. Similarly, it converts unpolarized white light to chromatically polarized light. We experimentally demonstrate a wide range of applications including active color pixels, chromatically switchable and invisible tags, and polarization imaging based on these engineered colored metasurfaces.
Qualitative health research via the Internet: practical and methodological issues (2002)

Electronic mail (email) has become a ubiquitous form of global communication. Much of this discourse concerns the experience of health and illness. As it is stored and accessible via the Internet, it is then available for qualitative analysis by health researchers. In particular, researchers can employ document analysis methods using Internet communication such as email posts and archives. This paper outlines ways in which such research could proceed, including locating potential research sites and collecting and analysing data. In addition, the advantages and disadvantages of using documentary analysis of Internet communication in qualitative health research are explored.
Influence of Subchronic Intake of Melatonin at Various Times of the Day on Fatigue and Hormonal Levels: A Placebo‐Controlled, Double‐Blind Trial (1989)

In a double-blind study, melatonin (50 mg) or placebo was administered daily to 25 subjects at 9 am or 7 pm for 1 week. Self-rated fatigue as evaluated by the Stanford Sleepiness Scale (SSS) was significantly increased during the 3 hours following melatonin intake in the morning, whereas, after administration in the evening, no difference between melatonin and placebo could be distinguished. Sleep onset latency slightly decreased in both melatonin groups without reaching statistical significance. No cumulative effects on sleep or behavior were observed. Twelve pituitary and peripheral hormones measured under baseline and partly (in the evening groups) under stimulated conditions before and after the trial did not change. The two most important conclusions are that: 1) the sedative potency of exogenous melatonin depends on the daily time of administration; and 2) the high pharmacological doses used for acute sedation do not seem to have cumulative effects after prolonged application.
pH‐Responsive Supramolecular Nanovalves Based on Cucurbit[6]uril Pseudorotaxanes (2008)

An open and closed case: pH-controllable nanovalves that operate in water have been produced by attaching [2]pseudorotaxanes to the surface of mesoporous silica nanoparticles. The nanovalves are able to contain guest molecules (rhodamine B, red circles) within the nanopores at acidic and neutral pH values but release them on command when the pH value is raised (see picture). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2008/z705211_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Epigenetic Hierarchy Governing Nestin Expression (2009)

Nestin is an intermediate filament protein expressed specifically in neural stem cells and progenitor cells of the central nervous system. DNA demethylation and histone modifications are two types of epigenetic modifications working in a coordinate or synergistic manner to regulate the expression of various genes. This study investigated and elucidated the epigenetic regulation of Nestin gene expression during embryonic differentiation along the neural cell lineage. Nestin exhibits differential DNA methylation and histone acetylation patterns in Nestin-expressing and nonexpressing cells. In P19 embryonic carcinoma cells, activation of Nestin expression is mediated by both trichostatin A and 5-aza-2'-deoxycytidine treatment, concomitant with histone acetylation, but not with DNA demethylation. Nestin transcription is also mediated by treatment with retinoic acid, again in the absence of DNA demethylation. Thus, histone acetylation is sufficient to mediate the activation of Nestin transcription. This study proposed that the regulation of Nestin gene expression can be used as a model to study the epigenetic regulation of gene expression mediated by histone acetylation, but not by DNA demethylation.
Pharmacological modulation of photodynamic therapy with hematoporphyrin derivative and light. (1987)

The interactions between photodynamic therapy (PDT) with hemotoporphyrin derivative (HPD) and treatment with cytotoxic drugs have been examined using both an in vitro tissue culture assay and an in vivo transplantable mouse tumor assay. Adriamycin (0.5-4.0 mg/kg) administered with HPD and at the time of irradiation potentiated the photodynamic effect, doubling the duration of tumor control. Adriamycin administered after PDT was not as effective. Methotrexate (0.2 mg/kg) also potentiated the tumor response to PDT. The other cytotoxic agents tested, cyclophosphamide, thiotepa, vincristine, and 5-fluorouracil, did not result in significant increases in tumor responses at the doses tested. In contrast to the effects observed in vivo, Adriamycin inhibited the photodynamic destruction of Raji or Lewis lung carcinoma cells in vitro, in part by reducing the uptake of HPD. Methotrexate had no effect on either the uptake of HPD or the efficacy of photodynamic destruction of Raji cells in vitro. The discrepancy between the in vitro and in vivo results implies that the interaction between PDT and other pharmacological agents cannot be assessed in vitro.
Dual roles of ATM in the cellular response to radiation and in cell growth control. (1996)

The gene mutated in ataxia-telangiectasia (AT) patients, denoted ATM, encodes a putative protein or lipid kinase. To elucidate the functions of ATM, we disrupted the mouse ATM gene through homologous recombination in mice. Consistent with cellular defects of AT patients, the ATM-/- cells are hypersensitive to gamma-irradiation and defective in cell-cycle arrest following radiation, correlating with a defective up-regulation of p53. In addition, ATM-/- mouse thymocytes are more resistant to apoptosis induced by gamma-irradiation than normal thymocytes. ATM-/- fibroblasts are inefficient in G1 to S-phase progression following serum stimulation and senesce after only a few passages in culture. They have an increased constitutive level of p21CP1/WAF1. The ATM protein is therefore critical both for cellular responses to ionizing radiation and for normal cell-cycle progression. ATM+/- fibroblasts and thymocytes showed intermediately defective responses to irradiation but no growth defect, suggesting that the increased cancer risk of AT heterozygotes could be attributable to poor checkpoint function.
A Novel Human-Based Receptor Antagonist of Sustained Action Reveals Body Weight Control by Endogenous GLP-1 (2010)

Ex-4 (9-39)a is a well characterized GLP-1 receptor antagonist that suffers from two notable limitations, its nonhuman amino acid sequence and its relatively short in vivo duration of action. Comparable N-terminal shortening of human GLP-1 lessens agonism but does not provide a high potency antagonist. Through a series of GLP-1/Ex-4 hybrid peptides, the minimal structural changes required to generate a pure GLP-1-based antagonist were identified as Glu16, Val19, and Arg20, yielding an antagonist of approximately 3-fold greater in vitro potency compared with Ex-4 (9-39)a. The structural basis of antagonism appears to result from stabilization of the α helix combined with enhanced electrostatic and hydrophobic interactions with the extracellular domain of the receptor. Site-specific acylation of the human-based antagonist yielded a peptide of increased potency as a GLP-1 receptor antagonist and 10-fold greater selectivity relative to the GIP receptor. The acylated antagonist demonstrated sufficient duration of action to maintain inhibitory activity when administered as a daily subcutaneous injection. The sustained pharmacokinetics and enhanced human sequence combine to form an antagonist optimized for clinical study. Daily administration of this antagonist by subcutaneous injection to diet-induced obese mice for 1 week caused a significant increase in food intake, body weight, and glucose intolerance, demonstrating endogenous GLP-1 as a relevant hormone in mammalian energy balance in the obese state.
A Novel Technique for Improving Hardware Trojan Detection and Reducing Trojan Activation Time (2011)

Fabless semiconductor industry and government agencies have raised serious concerns about tampering with inserting hardware Trojans in an integrated circuit supply chain in recent years. Most of the recently proposed Trojan detection methods are based on Trojan activation to observe either a faulty output or measurable abnormality on side-channel signals. Time to activate a hardware Trojan circuit is a major concern from the authentication standpoint. This paper analyzes time to generate a transition in functional Trojans. Transition is modeled by geometric distribution and the number of clock cycles required to generate a transition is estimated. Furthermore, a dummy scan flip-flop insertion procedure is proposed aiming at decreasing transition generation time. The procedure increases transition probabilities of nets beyond a specific threshold. The relation between circuit topology, authentication time, and the threshold is carefully studied. The simulation results on s38417 benchmark circuit demonstrate that, with a negligible area overhead, our proposed method can significantly increase Trojan activity and reduce Trojan activation time.
Flexible, polyimide-based neural interfaces (1999)

Micromachining technologies were established to fabricate microelectrode arrays and devices for interfacing parts of the central or peripheral nervous system in case of neuronal disorders. The devices were part of a neural prosthesis that allows simultaneous multichannel recording and multisite stimulation of neurons. Overcoming the brittle mechanics of silicon devices and challenging housing demands close to the nerve, we established a process technology to fabricate light-weighted and highly flexible polyimide based devices with integrated interconnects. A new assembling technique-the microflex interconnection (MFI)-has been applied for the connection of the flexible microsystems to silicon microelectronics. In this paper, we present different shapes and applications of the flexible electrodes. The discussion is focused on electrode properties and the hybrid assembly of a fully implantable neural prosthesis.
Zinc fixation preserves flow cytometry scatter and fluorescence parameters and allows simultaneous analysis of DNA content and synthesis, and intracellular and surface epitopes (2010)

Zinc salt-based fixation (ZBF) has proved advantageous in histochemical analyses conducted on intact tissues but has not been exploited in flow cytometry procedures that focus on quantitative analysis of individual cells. Here, we show that ZBF performs equally well to paraformaldehyde in the preservation of surface epitope labeling and forward and side scatter parameters as measured by flow cytometry. ZBF-fixed mouse epithelial keratinocytes exhibit a staining pattern for the surface markers Sca-1, CD34 and alpha6 integrin that is highly analogous to live cells. Furthermore, ZBF also preserves DNA allowing subsequent quantitative PCR analysis or labeling for incorporation of the thymidine analog EdU following surface and intracellular epitope staining. Finally, ZBF treatment allows for long-term storage of labeled cells with little change in these parameters. Thus, we present a protocol for zinc salt fixation of cells that allows for the simultaneous analysis of DNA and intracellular and cell surface proteins by flow cytometry.
Identification of a receptor/G-protein contact site critical for signaling specificity and G-protein activation. (1995)

Each G protein-coupled receptor recognizes only a distinct subset of the many structurally closely related G proteins expressed within a cell. How this selectively is achieved at a molecular level is not well understood, particularly since no specific point-to-point contact sites between a receptor and its cognate G protein(s) have been identified. In this study, we demonstrate that a 4-aa epitope on the m2 muscarinic acetylcholine receptor, a prototypical Gi/o-coupled receptor, can specifically recognize the C-terminal 5 aa of alpha subunits of the Gi/o protein family. The m2 receptor residues involved in this interaction are predicted to be located on one side of an alpha-helical receptor region present at the junction between the third intracellular loop and the sixth transmembrane domain. Coexpression studies with hybrid m2/m3 muscarinic receptors and mutant G-protein alpha q subunits showed that the receptor/G-protein contact site identified in this study is essential for coupling specificity and G-protein activation.
In vitro and in vivo study of phloretin‐induced apoptosis in human liver cancer cells involving inhibition of type II glucose transporter (2008)

Phloretin (Ph), a natural product found in apples and pears with glucose transporter (GLUT) inhibitory activity, exerts antitumor effects. However, little is known about its effects on human liver cancer. The purpose of this study is to test the cytotoxic effects of Ph on HepG2 cells and to identify the underlying molecular pathways. Human hepatocellular carcinoma specimens and HepG2 show a high level of GLUT2 transporter activity in the cell membrane. Real-time PCR and MTT assays demonstrate that Ph-induced cytotoxicity correlates with the expression of GLUT2. Flow cytometry and DNA fragmentation studies show that 200 microM Ph induces apoptosis in HepG2, which was reversed by glucose pretreatment. GLUT2 siRNA knockdown induced HepG2 apoptosis, which was not reversed by glucose. Western blot analysis demonstrates that both intrinsic and extrinsic apoptotic pathways in addition to Akt and Bcl-2 family signaling pathways are involved in Ph-induced cell death in HepG2 cells. Furthermore, using flow cytometry analysis, a mitochondrial membrane potential assay and Western blot analysis, we show that cytochalasin B, a glucose transport inhibitor, enhances the Ph-induced apoptotic effect on HepG2 cells, which was reversed by pretreatment with glucose. Furthermore, we found significant antitumor effects in vivo by administering Ph at 10 mg/kg intraperitoneally to severe combined immune deficiency mice carrying a HepG2 xenograft. A microPET study in the HepG2 tumor-bearing mice showed a 10-fold decrease in (18)F-FDG uptake in Ph-treated tumors compared to controls. Taken together, these results suggest that Ph-induced apoptosis in HepG2 cells involves inhibition of GLUT2 glucose transport mechanisms.
Non-Hodgkinʼs lymphoma (1995)

The incidence of non-Hodgkin's lymphoma continues to rise. Molecular events in lymphocytes from individuals without lymphoma are found with increasing age and may represent early changes toward malignant transformation. Molecular, immunophenotypic, and histologic data have been used to propose a new classification system and several new entities have been identified. Localized, low-grade non-Hodgkin's lymphoma can be cured by radiotherapy, whereas patients with extensive disease experience a continuous remitting course. The effect of high-dose regimens is yet to be determined. Current therapy cures less than 50% of patients with advanced aggressive lymphoma and randomized multi-institutional trials using several regimens have shown similar outcomes. The addition of high-dose therapy to patients in remission may offer a survival advantage to a high-risk subset. Late complications of myeloablative therapy, including myelodysplasia and leukemia, are being increasingly recognized. A significant advance in the treatment of posttransplantation lymphoproliferative disorders using donor T cells was made and future applications of this approach are anticipated.
A Specification Language for Agents Observable Behavior. (2002)

Abstract|One of the main issues in the engineering ofmulti-agent systems is to give a precise semantics to agentcommunicative acts, by specifying how agent interactionswith the environment a ect and are a ected by the agentinner status { namely, by the decisions it takes and by itsperception of the world. In this paper, we tackle this prob-lem by modelling agents as observable sources, that is, asproactive and autonomous abstractions manifesting an ob-servable status and dynamics, and allowing external enti-ties to perceive and alter it. Based on this idea, an ab-stract language for specifying agents observable behaviouris presented, providing the designer with a tool for pre-cisely characterising the relationship between agents inter-nal aspects and agents collaborative aspects. We claim thatthis language can be the basis for a successful engineeringmethodology for agent-based systems where the concept ofobservation is taken as a foundational issue.Index Terms|Agent Communication Languages, AgentArchitectures, Formal Speci cation Languages, Agent-Oriented Software Engineering
Template‐Free Synthesis, Controlled Conversion, and CO Oxidation Properties of CeO2 Nanorods, Nanotubes, Nanowires, and Nanocubes (2008)

Abstract A general large‐scale synthesis of single‐crystalline and uniform CeO 2 nanorods was first realized without templates by a precipitation method at room temperature and pressure. Such nanorods have an aspect ratio of ca. 3 nm with a diameter of ca. 8 nm and a large BET specific area of 128.2 m 2 /g. On the basis of this, the controlled conversion of the as‐prepared nanorods into nanotubes, nanowires, and nanocubes through hydrothermal reactions has been realized. Further experimental results show that the growth of nanorods is a function of the base concentration, temperature, and time. In addition, particle size measurements demonstrate that the primary nanorods grow by Ostwald ripening. It is found that CeO 2 growth is faster at higher base concentration and temperature due to the accelerated ripening. During the synthesis, the formation of Ce(OH) 3 intermediate species and their transformation into CeO 2 have been dynamically demonstrated and are regarded as the key factors responsible for the evolution of shape. The CO oxidation properties of CeO 2 nanorods, nanowires, nanotubes, and nanocubes were investigated, and CeO 2 nanotubes have the best performance due to the large BET surface area and the novel inner surface. In addition, CeO 2 nanorods aged for 9 d also have an excellent catalytic performance for CO oxidation due to the exposed crystal surface (110) of CeO 2 . (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2008)