gebhart/patrepeval huggingface dataset:
Identifying Authorship by Byte-Level N-Grams: The Source Code Author Profile (SCAP) Method. (2007)

Source code author identification deals with identifying the most likely author of a computer program, given a set of predefined author candidates. There are several scenarios where digital evidence of this kind plays a role in investigation and adjudication, such as code authorship disputes, intellectual property infringement, tracing the source of code left in the system after a cyber attack, and so forth. As in any identification task, the disputed program is compared to undisputed, known programming samples by the predefined author candidates. We present a new approach, called the SCAP (Source Code Author Profiles) approach, based on byte-level n-gram profiles representing the source code author’s style. The SCAP method extends a method originally applied to natural language text authorship attribution; we show that an n-gram approach also suits the characteristics of source code analysis. The methodological extension includes a simplified profile and a less complicated, but more effective, similarity measure. Experiments on data sets of different programming-language (Java or C++) and commented/commentless code demonstrate the effectiveness of these extensions. The SCAP approach is programming-language independent. Moreover, the SCAP approach deals surprisingly well with cases where only a limited amount of very short programs per programmer is available for training. Finally, it is also demonstrated that SCAP effectiveness persists even in the absence of comments in the source code, a condition usually met in cyber-crime cases. 1. The Forensic Significance of Source Code Nowadays, in a wide variety of legal cases it is important to identify the author of a usually limited piece of programming code. Such situations include cyber attacks in the form of viruses, Trojan horses, logic bombs, fraud, and credit card cloning, code authorship disputes, and intellectual property infringement. Identifying the authorship of malicious or stolen source code in a reliable way has become a primary goal for digital investigators (Spafford and Weeber 1993). Please see Appendix 1 for a legal analysis of the forensic significance of source code.
An All D-Amino Acid Opioid Peptide with Central Analgesic Activity from a Combinatorial Library (1994)

A synthetic combinatorial library containing 52,128,400 D-amino acid hexapeptides was used to identify a ligand for the mu opioid receptor. The peptide, Ac-rfwink-NH2, bears no resemblance to any known opioid peptide. Simulations using molecular dynamics, however, showed that three amino acid moieties have the same spatial orientation as the corresponding pharmacophoric groups of the opioid peptide PLO17. Ac-rfwink-NH2 was shown to be a potent agonist at the mu receptor and induced long-lasting analgesia in mice. Analgesia produced by intraperitoneally administered Ac-rfwink-NH2 was blocked by intracerebroventricular administration of naloxone, demonstrating that this peptide may cross the blood-brain barrier.
Development of a Novel Silyl Ether Linker for Solid-Phase Organic Synthesis1 (1996)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTDevelopment of a Novel Silyl Ether Linker for Solid-Phase Organic Synthesis1Terri L. Boehm and H. D. Hollis ShowalterView Author Information Chemistry Department, Parke-Davis Pharmaceutical Research, Division of Warner-Lambert Company, Ann Arbor, Michigan 48105 Cite this: J. Org. Chem. 1996, 61, 19, 6498–6499Publication Date (Web):September 20, 1996Publication History Received2 July 1996Published online20 September 1996Published inissue 1 January 1996https://doi.org/10.1021/jo961242dCopyright © 1996 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views909Altmetric-Citations111LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit Read OnlinePDF (92 KB) Get e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Aldehydes,Aromatic compounds,Ethers,Ketones,Organic polymers Get e-Alerts
The function neutralizing anti-TrkA antibody MNAC13 reduces inflammatory and neuropathic pain (2007)

Nerve growth factor (NGF) is involved in pain transduction mechanisms and plays a key role in many persistent pain states, notably those associated with inflammation. On this basis, both the NGF ligand and its receptor TrkA (tyrosine kinase A) represent an eligible target for pain therapy. Although the direct involvement of NGF in pain modulation is well established, the effect of a direct functional block of the TrkA receptor is still unknown. In this study, we have demonstrated that MNAC13, the only anti-TrkA monoclonal antibody for which function neutralizing properties have been clearly shown both in vitro and in vivo, induces analgesia in both inflammatory and neuropathic pain models, with a surprisingly long-lasting effect in the latter. The formalin-evoked pain licking responses are significantly reduced by the MNAC13 antibody in CD1 mice. Remarkably, treatment with the anti-TrkA antibody also produces a significant antiallodynic effect on neuropathic pain: repeated i.p. injections of MNAC13 induce significant functional recovery in mice subjected to sciatic nerve ligation, with effects persisting after administration. Furthermore, a clear synergistic effect is observed when MNAC13 is administered in combination with opioids, at doses that are not efficacious per se. This study represents a direct demonstration that neutralizing antibodies directed against the TrkA receptor may display potent analgesic effects in inflammatory and chronic pain.
Circulating Nucleosomes Predict the Response to Chemotherapy in Patients with Advanced Non–Small Cell Lung Cancer (2004)

Circulating nucleosomes in combination with oncological biomarkers are valuable for the early estimation of the efficacy of chemotherapy in patients with lung cancer.
Electrical characterization of protein molecules by a solid-state nanopore (2007)

The authors measured ionic current blockages caused by protein translocation through voltage-biased silicon nitride nanopores in ionic solution. By calculating the mean amplitude, time duration, and the integral of current blockages, they estimated the relative charge and size of protein molecules at a single molecule level. The authors measured the change in protein charge of bovine serum albumin (BSA) protein induced by pH variation. They also confirmed that BSA molecules indeed traverse nanopores using an improved chemiluminescent analysis. They demonstrated that a larger protein fibrinogen could be distinguished from BSA by a solid-state nanopore measurement.
Rifampicin has a Profound Effect on the Pharmacokinetics of Oral S‐Ketamine and Less on Intravenous S‐Ketamine (2012)

Low-dose ketamine is currently used in several acute and chronic pain conditions as an analgesic. Ketamine undergoes extensive metabolism and is thus susceptible to drug-drug interactions. We examined the effect rifampicin, a well-known inducer of many cytochrome P450 (CYP) enzymes and transporters, on the pharmacokinetics of intravenous and oral S-ketamine in healthy volunteers. Eleven healthy volunteers were administered in randomized order 600 mg rifampicin or placebo orally for 6 days in a four-session paired cross-over study. On day 6, S-ketamine was administered intravenously (0.1 mg/kg) in the first part of the study and orally (0.3 mg/kg) in the second part. Plasma concentrations of ketamine and norketamine were measured up to 24 hr and behavioural and analgesic effects up to 12 hr. Rifampicin treatment decreased the mean area under the plasma ketamine concentration-time curve extrapolated to infinity (AUC (0-∞)) of intravenous and oral S-ketamine by 14% (p = 0.005) and 86% (p < 0.001), respectively. Rifampicin decreased greatly the peak plasma concentration of oral S-ketamine by 81% (p < 0.001), but shortened only moderately the elimination half-life of intravenous and oral S-ketamine. Rifampicin decreased the ratio of norketamine AUC (0-∞) to ketamine AUC (0-∞) after intravenous S-ketamine by 66%, (p < 0.001) but increased the ratio by 147% (p < 0.001) after the oral administration of S-ketamine. Rifampicin profoundly reduces the plasma concentrations of ketamine and norketamine after oral administration of S-ketamine, by inducing mainly its first-pass metabolism.
A hierarchical approach to protein molecular evolution (1999)

Biological diversity has evolved despite the essentially infinite complexity of protein sequence space. We present a hierarchical approach to the efficient searching of this space and quantify the evolutionary potential of our approach with Monte Carlo simulations. These simulations demonstrate that nonhomologous juxtaposition of encoded structure is the rate-limiting step in the production of new tertiary protein folds. Nonhomologous "swapping" of low-energy secondary structures increased the binding constant of a simulated protein by approximately 10(7) relative to base substitution alone. Applications of our approach include the generation of new protein folds and modeling the molecular evolution of disease.
Solid texturing of complex surfaces (1985)

Texturing is an effective method of simulating surface detail at relatively low cost. Traditionally, texture functions have been defined on the two-dimensional surface coordinate systems of individual surface patches. This paper introduces the notion of "solid texturing". Solid texturing uses texture functions defined throughout a region of three-dimensional space. Many nonhomogeneous materials, including wood and stone, may be more realistically rendered using solid texture functions. In addition, solid texturing can easily be applied to complex surface which are difficult to texture using two-dimensional texture functions. The paper gives examples of solid texture functions based on Fourier synthesis, stochastic texture models, projections of two-dimensional textures, and combinations of other solid textures.
Self-Organized GaN Quantum Wire UV Lasers (2003)

Quantum wire lasers are generally fabricated through complex overgrowth processes with molecular beam epitaxy. The material systems of such overgrown quantum wires have been limited to Al−Ga−As−P, which leads to emission largely in the visible region. We describe a simple, one-step chemical vapor deposition process for making quantum wire lasers based on the Al−Ga−N system. A novel quantum-wire-in-optical-fiber (Qwof) nanostructure was obtained as a result of spontaneous Al−Ga−N phase separation at the nanometer scale in one dimension. The simultaneous excitonic and photonic confinement within these coaxial Qwof nanostructures leads to the first GaN-based quantum wire UV lasers with a relatively low threshold.
Oncoretroviral gene transfer to NOD/SCID repopulating cells using three different viral envelopes (2002)

The best conditions for transduction and engraftment of CB SRCs were obtained with GALV-pseudotyped vectors using serum-free conditions.
A Simple Route to Metal Nanodots and Nanoporous Metal Films (2002)

High density arrays of chromium (Cr) and layered gold/chromium (Au/Cr) nanodots and nanoholes in metal films were fabricated by evaporation onto nanoporous templates produced by the self-assembly of poly(styrene-b-methyl methacrylate) (P(S-b-MMA)) diblock copolymers. The cylindrical microdomains of the asymmetric block copolymer were oriented normal to the surface by balancing interfacial interactions of the blocks with the substrate. By selectively removing either the minor or major component, nanoporous films of PS or nanoscopic posts of PS could be produced. Thus, a template, comprising an array of hexagonally packed pores in a PS matrix or PS posts, was easily fabricated. Evaporation of Cr and Au onto the template, followed by sonication and UV degradation of the PS, left Cr or Au/Cr nanodots or a nanoporous metallic film.
Analysis of narcotic analgesic usage in the treatment of postoperative pain (1983)

We reviewed 526 medical records of surgical patients and interviewed 81 of these patients. We also sent questionnaires to house staff (57 of 97 responded) and nurses (70 of 142 responded) involved in the care of these patients. A substantial number of patients suffered at least moderate pain during the postoperative period despite analgesic medication. Patients received 70% of the maximal ordered analgesic dose in the first 24 hours. Physicians prescribed drugs in doses that were often inadequate and to be given at inflexible intervals. The optimal doses and duration of action of meperidine, as judged by the house staff and nurses, did not agree with the accepted pharmacologic profile of this drug. (<i>JAMA</i>1983;250:926-929)
The effects of recombinant human granulocyte‐colony stimulating factor on vascular dysfunction and splanchnic ischaemia‐reperfusion injury (1997)

1. The aim of our study was to investigate the effects of recombinant human granulocyte-colony stimulating factor in a rat model of splanchnic ischaemia-reperfusion injury. 2. Male anaesthetized rats were subjected to clamping of the splanchnic arteries for 45 min. This surgical procedure resulted in an irreversible state of shock (splanchnic artery occlusion shock. SAO shock). Sham operated animals were used as controls. Survival rate, serum tumour necrosis factor-alpha (TNF-alpha), neutrophil count, bone marrow myeloid precursor cells, myeloperoxidase activity (MPO; studied as a quantitative means to assess leukocyte accumulation), mean arterial blood pressure and the responsiveness of aortic rings to phenylephrine (PE, 1 nM-10 microM) were studied. 3. SAO shocked rats had a decreased survival rate (0% at 4 h of reperfusion, while sham shocked rats survived more than 4 h), increased serum levels of TNF-alpha (201 +/- 10 u ml-1; sham shocked rats = undetectable), neutropenia, enhanced MPO activity in the ileum (0.11 +/- 0.06 u x 10(-3) g-1 tissue; sham shocked rats = 0.02 +/- 0.001 u x 10(-3) g-1 tissue) and in the lung (1.5 +/- 0.2 u x 10(-3) g-1 tissue; sham shocked rats = 0.19 +/- 0.05 u x 10(-3) g-1 tissue) and unchanged bone marrow myeloid precursor cells. Furthermore aortic rings from shocked rats showed a marked hyporeactivity to PE. 4. Administration of recombinant human granulocyte colony stimulating factor (rh G-CSF; 5, 10 and 20 micrograms kg-1 5 min following the release of occlusion) increased in a dose-dependent manner survival rate (90% at 4 h of reperfusion with the dose of 20 u x 10(-3) g kg-1), reduced serum TNF-alpha (13 +/- 5 u ml-1) and MPO activity in the ileum (0.065 +/- 0.002 u x 10(-3) g-1 tissue) and in the lung (0.7 +/- 0.03 microgram kg-1 tissue), improved neutropenia and mean arterial blood pressure but did not modify bone marrow myeloid progenitor cells. Furthermore rh G-CSF, either in vivo or in vitro (200 nM for 1 h in the organ bath), restored to control values the hyporeactivity to PE. Finally rh G-CSF potently inhibited the activity of inducible nitric oxide synthase in peritoneal macrophages activated with endotoxin. 5. Our results suggest that rh G-CSF protects against splanchnic ischaemia reperfusion injury by a mechanism(s) that does not depend upon its haematopoietic effects.
Human Immunodeficiency Virus Type-1 Reverse Transcriptase (1996)

Mutations were made in recombinant human immunodeficiency virus type-1 reverse transcriptase (RT) by substituting methionine 184 with alanine (M184A) or valine (M184V), and steady-state and pre-steady-state kinetic constants were determined. The Km values of M184A RT for dNTPs were larger than those of wt RT for RNA-directed synthesis; the kcat values of M184A RT for processive or distributive synthesis were similar. In contrast to M184A RT, the Km and kcat values of M184V RT for dNTP substrates were similar to those of wt RT. The Ki values of M184V RT for 1-beta-L-nucleoside analogs were increased 30-500-fold relative to wt RT for both RNA- and DNA-directed synthesis. The Kd and kp values of wt RT and M184V RT for dCTP and cis-5-fluoro-1-[2-(hydroxymethyl)-1, 3-oxathiolan-5-yl]cytosine 5'-triphosphate (1-beta-L-FTCTP) were estimated from pre-steady-state kinetics for single nucleotide incorporation. The Kd value of M184V RT for 1-beta-L-FTCTP was 19-fold greater than that of wt RT; the kpvalues of the two enzymes were similar. These results support the hypothesis that methionine 184 in the highly conserved YMDD region of wt RT participates in the binding of the nucleoside (analog) 5'-triphosphate.
Structure and inhibition of EV-D68, a virus that causes respiratory illness in children (2015)

Enterovirus D68 (EV-D68) is a member of Picornaviridae and is a causative agent of recent outbreaks of respiratory illness in children in the United States. We report here the crystal structures of EV-D68 and its complex with pleconaril, a capsid-binding compound that had been developed as an anti-rhinovirus drug. The hydrophobic drug-binding pocket in viral protein 1 contained density that is consistent with a fatty acid of about 10 carbon atoms. This density could be displaced by pleconaril. We also showed that pleconaril inhibits EV-D68 at a half-maximal effective concentration of 430 nanomolar and might, therefore, be a possible drug candidate to alleviate EV-D68 outbreaks.
Direct Growth of Bilayer Graphene on SiO2 Substrates by Carbon Diffusion through Nickel (2011)

Here we report a transfer-free method of synthesizing bilayer graphene directly on SiO(2) substrates by carbon diffusion through a layer of nickel. The 400 nm nickel layer was deposited on the top of SiO(2) substrates and used as the catalyst. Spin-coated polymer films such as poly(methyl methacrylate), high-impact polystyrene or acrylonitrile-butadiene-styrene, or gas-phase methane were used as carbon sources. During the annealing process at 1000 °C, the carbon sources on the top of the nickel decomposed and diffused into the nickel layer. When cooled to room temperature, bilayer graphene was formed between the nickel layer and the SiO(2) substrates. The nickel films were removed by etchants, and bilayer graphene was then directly obtained on SiO(2), eliminating any transfer process. The bilayer nature of the obtained graphene films on SiO(2) substrates was verified by Raman spectroscopy and transmission electron microscopy. The Raman spectroscopy mapping over a 100 × 100 μm(2) area indicated that the obtained graphene is high-quality and bilayer coverage is approximately 70%.
Heterocyclic Amides:  Inhibitors of Acyl-CoA:Cholesterol O-Acyl Transferase with Hypocholesterolemic Activity in Several Species and Antiatherosclerotic Activity in the Rabbit (1996)

A series of heterocyclic amides were synthesized and evaluated as inhibitors of acyl-CoA: cholesterol O-acyltransferase (ACAT) in vitro and for cholesterol lowering in cholesterol-fed rats. Compounds were evaluated for cell-based macrophage ACAT inhibition, bioactivity, and adrenal toxicity. Candidates were selected for evaluation in cholesterol-fed dogs and, ultimately, the injured cholesterol-fed rabbit model of atherosclerosis. The heterocyclic amides potently inhibited rabbit liver ACAT (IC50's = 0.014-0.11 microM), and the majority of compounds significantly lowered plasma cholesterol (42-68%) in an acute cholesterol-fed rat model at 3 mg/kg. The most efficacious compounds in the rat were evaluated for bioactivity in vivo and arterial ACAT inhibition in a cell-based macrophage ACAT assay. Two highly bioactive analogs, (+/-)-2-(3-dodecylisoxazol-5-yl)-2-phenyl-N-(2,4,6-trimethoxypheny l) acetamide (13a) and (+/-)-2-(5-dodecylisoxazol-3-yl)-2-phenyl-N-(2,4,6-trimethoxypheny l) acetamide (16a), were selected for further study and were found to be nontoxic in a guinea pig model of adrenal toxicity. Compounds 13a and 16a lowered total cholesterol in the cholesterol-fed rat, rabbit, and dog models of pre-established hypercholesterolemia. Compound 13a in the injured cholesterol-fed rabbit model of atherosclerosis was effective in slowing the development of cholesteryl ester-rich thoracic aortic lesions, reducing lesion coverage by 53% at a dose of 1 mg/kg.
Logarithm of odds (lods) for linkage in complex inheritance. (1996)

Lod scores provide a method to unify linkage tests based on identity by descent and identity in marker state while permitting selection of the most informative individuals through their disease-related phenotypes and markers in relatives. After parametric lods are reviewed, a nonparametric approach that depends on a single logistic parameter beta is introduced. Lods for parents tested or unknown are derived, multiple pairwise mapping is presented, and power is shown to be good even for moderately small values of beta. Comparison of parametric and nonparametric approaches (yet to be made) will provide for polygenes the efficiency and reliability that lod scores gave to mapping of major loci 40 years ago.
Vibrio cholerae iron transport: haem transport genes are linked to one of two sets of tonB, exbB, exbD genes (1998)

Vibrio cholerae was found to have two sets of genes encoding TonB, ExbB and ExbD proteins. The first set (tonB1, exbB1, exbD1) was obtained by complementation of a V. cholerae tonB mutant. In the mutant, a plasmid containing these genes permitted transport via the known V. cholerae high-affinity iron transport systems, including uptake of haem, vibriobactin and ferrichrome. When chromosomal mutations in exbB1 or exbD1 were introduced into a wild-type V. cholerae background, no defect in iron transport was noted, indicating the existence of additional genes that can complement the defect in the wild-type background. Another region of the V. cholerae chromosome was cloned that encoded a second functional TonB/Exb system (tonB2, exbB2, exbD2). A chromosomal mutation in exbB2 also failed to exhibit a defect in iron transport, but a V. cholerae strain that had chromosomal mutations in both the exbB1 and exbB2 genes displayed a mutant phenotype similar to that of an Escherichia coli tonB mutant. The genes encoding TonB1, ExbB1, ExbD1 were part of an operon that included three haem transport genes (hutBCD), and all six genes appeared to be expressed from a single Fur-regulated promoter upstream of tonB1. A plasmid containing all six genes permitted utilization of haem by an E. coli strain expressing the V. cholerae haem receptor, HutA. Analysis of the hut genes indicated that hutBCD, which are predicted to encode a periplasmic binding protein (HutB) and cytoplasmic membrane permease (HutC and HutD), were required to reconstitute the V. cholerae haem transport system in E. coli. In V. cholerae, the presence of hutBCD stimulated growth when haemin was the iron source, but these genes were not essential for haemin utilization in V. cholerae.