gebhart/patrepeval huggingface dataset:
Gold deposition from a scanning tunneling microscope tip (1991)

We have demonstrated that a gold scanning tunneling microscope (STM) tip can be used as a miniature solid-state emission source for directly depositing nanometer-size gold structures. The process has been demonstrated in ultrahigh vacuum on gold substrates, and in air on gold and platinum substrates. Studies made in air suggest that the process is fast, repeatable, and field-induced. The emission mechanism is believed to be field evaporation of tip atoms, which is enhanced by the close proximity of the substrate. The technique has been used to write several thousand features with no apparent degradation of the tip’s ability to write. Elevated and room temperature studies show the written structures to be stable over periods of weeks, in contrast to some previous STM measurements of gold self-diffusion.
Amino acid copolymer-specific IL-10-secreting regulatory T cells that ameliorate autoimmune diseases in mice (2008)

IL-10-secreting regulatory T cell lines specific to glatiramer acetate [poly(Y,E,A,K)n] or poly(Y,F,A,K)n have been established from the enlarged spleen and lymph nodes that result from copolymer treatment of SJL mice in which experimental autoimmune encephalomyelitis was induced by PLP139-151. These CD4+CD25+T cell lines secrete high levels of IL-10 and IL-13 but only small amounts of IL-4 and virtually no TGF-beta, IL-17, IL-6, IFN-gamma, or TNF-alpha. Their phenotypes are particularly characterized by the absence of Foxp3 and the presence of two TNFR family members, CD30 and GITR. The lines proliferated specifically to the immunizing copolymers but were autoantigen-nonspecific, in that the same T cell line could suppress autoimmunity induced by three different autoantigens in SJL mice, i.e., PLP139-151(EAE), MBP85-99 (EAE), and bovine peripheral nerve myelin (experimental autoimmune neuritis), indicating they function by bystander suppression.
Design of arrayed-waveguide gratings using hybrid Fourier-Fresnel transform techniques (1999)

We describe how transform techniques may be applied to the design of arrayed-waveguide gratings (AWG's). A hybrid Fourier-Fresnel transform model indicates that a flat AWG router passband over 30% of the device free-spectral range (FSR) is feasible. Minimized passband ripple is achieved by applying a subparabolic phase-profile (phase-exponent P=1.82) to the Fourier plane of the AWG. Simulations of a complex-apodized AWG with passband 3 dB width increased from 1 to 12 nm, with a near-trapezoidal amplitude response, and band-edge group delay of 70 ps reduced to 10 ps are presented for a device with a FSR of 40 nm.
Inhibitory Effect of 2′-Substituted Nucleosides on Hepatitis C Virus Replication Correlates with Metabolic Properties in Replicon Cells (2005)

Nucleosides have been widely used in the treatment of viral diseases, but relatively few have been identified as inhibitors of hepatitis C virus (HCV). The modified ribonucleosides, 2'-C-methyl-adenosine and 2'-O-methyl-cytidine, are potent inhibitors of HCV replication which specifically target the NS5B polymerase. Herein, a more extensive characterization of the effect of these compounds upon HCV replication in subgenomic replicons is reported. A highly selective antireplicative effect induced by the nucleosides in replicon-containing cell lines was maintained during an exponential growth period with potencies which paralleled the reduction of both positive- and negative-strand RNA replication. Moreover, the inhibitory effect closely correlated with the intrinsic metabolic properties of differing replicon clonal lines. Interestingly, while 2'-C-methyl-adenosine elicited similar inhibitory potencies in different cell lines, 2'-O-methyl-cytidine was found to be inactive in one replicon cell line tested, although the corresponding triphosphates comparably inhibited the in vitro activity of replication complexes isolated from these cells and the activity of NS5B polymerase using synthetic templates. The lack of antireplicative effect, attributed to poor intracellular conversion of the 2'-O-methyl-cytidine nucleoside to the active 5'-triphosphate, was reversed using a monophosphate prodrug. Thus, although replicon cells are useful for evaluating the effect of inhibitors upon HCV replication, these findings have important implications for their use in the identification and characterization of nucleosides and other chemotherapeutic agents requiring cellular metabolism.
WNTS and WNT receptors as therapeutic tools and targets in human disease processes (2006)

The body of scientific literature linking Wnts and Wnt-associated proteins to human disease processes continues to grow in parallel with new discoveries from basic science laboratories that further characterize the elaborate cellular events following the binding of Wnts to their receptors. While Wnt-mediated signaling has long been known to play a major role in human carcinogenesis, accumulating evidence indicates that Wnts are also important mediators of inflammation and recovery from injury. The binding of secreted Wnt ligands to their receptors offers an attractive and accessible target for therapeutic regulation of these signaling pathways. Several promising preliminary studies have already addressed potential avenues for the manipulation of Wnt signaling in disease processes. This review will focus on disease processes involving the regulation of Wnt signaling at the level of Wnt binding to its target receptors. Wnt proteins, Wnt receptors, and secreted Wnt inhibitors are attractive as potential therapeutic agents and targets due to their extracellular location. In addition, since Wnt signaling results in a diverse array of downstream intracellular events, many of which are not fully understood, the targeting of this pathway at the most upstream site of pathway activation also provides a strategic advantage for therapy. As the list of Wnt-related diseases continues to grow, advances in our understanding of the biochemical and molecular mechanisms underlying Wnt signaling may ultimately translate into innovative ways to treat Wnt-related disease processes in patients.
Alpha-interferon inhibits the development of diabetes in NOD mice. (1998)

The NOD mouse is a model of human IDDM, which is characterized by a cell-mediated autoimmune process resulting in spontaneous diabetes. Alpha-interferon (IFN-alpha) is thought to play a pathogenic role in this autoimmune process. We report that recombinant alpha-interferon (rIFN-alpha) administration decreases the development of spontaneous diabetes and the passive transfer of diabetes in NOD mice. Spontaneous diabetes was inhibited by IFN-alpha in a dose-dependent fashion. A dose of as little as 20 x 10(3) U inhibited diabetes development, while a dose of 100 x 10(3) U potently prevented diabetes (14% incidence vs. 70% incidence in control mice). Even at the termination of the experiment, nondiabetic mice administered rIFN-alpha maintained normal glucose tolerance. Islet inflammation was 65% lower in the pancreases of rIFN-alpha mice. rIFN-alpha administration decreased anti-islet effector cell bioactivity of spleen cells without inducing generalized immunosuppression. Passive transfer experiments demonstrated that the decreased anti-islet effector cell activity was not a direct action of rIFN-alpha on these cells. In conclusion, rIFN-alpha potently and paradoxically prevents diabetes by indirectly decreasing anti-islet effector cell activity and in turn the development of insulitis without inducing generalized immunosuppression. This work, which goes against our current understanding of the role of rIFN-alpha in autoimmunity, may have significant implications to further our understanding of the pathogenesis of IDDM and to further the development of novel modes to prevent the disease.
Harm reduction and tobacco: a new opportunity or a step too far? (2013)

Purpose – The paper aims to describe the public health potential and legal status of electronic cigarettes (e‐cigarettes) and Swedish snus. The author evaluates claims made for and against tobacco harm reduction.
Enabling trusted software integrity (2002)

Preventing execution of unauthorized software on a given computer plays a pivotal role in system security. The key problem is that although a program at the beginning of its execution can be verified as authentic, while running, its execution flow can be redirected to externally injected malicious code using, for example, a buffer overflow exploit. Existing techniques address this problem by trying to detect the intrusion at run-time or by formally verifying that the software is not prone to a particular attack.We take a radically different approach to this problem. We aim at intrusion prevention as the core technology for enabling secure computing systems. Intrusion prevention systems force an adversary to solve a computationally hard task in order to create a binary that can be executed on a given machine. In this paper, we present an exemplary system--SPEF--a combination of architectural and compilation techniques that ensure software integrity at run-time. SPEF embeds encrypted, processor-specific constraints into each block of instructions at software installation time and then verifies their existence at run-time. Thus, the processor can execute only properly installed programs, which makes installation the only system gate that needs to be protected. We have designed a SPEF prototype based on the ARM instruction set and validated its impact on security and performance using the MediaBench suite of applications.
Angiongenesis: a new theory for endometriosis (1998)

Excessive endometrial angiogenesis is proposed as an important mechanism in the pathogenesis of endometriosis. Evidence is reviewed for the hypothesis that the endometrium of women with endometriosis has an increased capacity to proliferate, implant and grow in the peritoneal cavity. Data is summarized indicating that the endometrium of patients with endometriosis shows enhanced endothelial cell proliferation. Results are also reviewed indicating that the cell adhesion molecule integrin alphavbeta3 is expressed in more blood vessels in the endometrium of women with endometriosis when compared with normal women. Taken together, these results provide evidence for increased endometrial angiogenesis in women with endometriosis when compared with normal subjects. Endometriosis is one of the family of angiogenic diseases. Other angiogenic diseases include solid tumours, rheumatoid arthritis, psoriasis and diabetic retanopathy. Excessive endometrial angiogenesis suggests novel new medical treatments for endometriosis aimed at the inhibition of angiogenesis.
Inhaled Insulin Using the AERx Insulin Diabetes Management System in Healthy and Asthmatic Subjects (2003)

After inhaling insulin using the AERx iDMS, asthmatic subjects absorbed less insulin than healthy subjects, resulting in less reduction of serum glucose. No effects on airway reactivity were observed. Diabetic patients with asthma may need to inhale more insulin than patients with normal respiratory function in order to achieve similar glycemic control.
IgG antibodies to chlamydial and mycoplasma infection plus C-reactive protein related to poor outcome in unstable angina. (1998)

These findings suggest a pathophysiologically based relationship between infective and inflammatory processes related to poor clinical outcome during the in-hospital stay in the setting of unstable angina patients.
Microbial Prevalence, Diversity and Abundance in Amniotic Fluid During Preterm Labor: A Molecular and Culture-Based Investigation (2008)

The amniotic cavity of women in preterm labor harbors DNA from a greater diversity of microbes than previously suspected, including as-yet uncultivated, previously-uncharacterized taxa. The strength, temporality and gradient with which these microbial sequence types are associated with preterm delivery support a causal relationship.
Erratum: ‘‘Electron Hall mobility of n-GaN’’ [Appl. Phys. Lett. 66, 1972 (1995)] (1995)

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Rigidified multivalent lactose molecules and their interactions with mammalian galectins: a route to selective inhibitors (2003)

New and rigid multivalent lactose molecules were prepared. The structures contain lactose-2-aminothiazoline units at the periphery that were formed from a cyclisation of the thiourea sulphur onto the triple bond of the spacer. The lactosides were evaluated as inhibitors against lectin binding in a solid phase inhibition assay. In this assay the glycoprotein asialofetuin was immobilized onto the surface of microtiter plate wells, mimicking cell surface presentation, while mammalian galectins-1, -3 or -5 were in solution. Between the three galectins, the folding pattern and sequence are closely related but the topology of presentation of the carbohydrate recognition domains differs. Strong multivalency effects were observed for the tetravalent lactoside in the inhibition of galectin-3 binding with enhancements of almost 4300-fold compared to lactose. Remarkable selectivity was obtained in the inhibition since relative potencies of the tetravalent lactoside with the proto type galectins-1 and -5 did not exceed a factor of 143 relative to lactose. The binding of the lactosides to galectin-3 was also studied by fluorescence spectroscopy with all components in solution. These studies showed no multivalency effects in the inherent binding affinities.
Long-term weight control study I (weeks 0 to 34) (1992)

To investigate the value of anorexiant medications as an adjunct to other forms of weight control therapy, we studied 121 people in a 34-week, double-blind clinical trial of 60 mg extended-release fenfluramine plus 15 mg phentermine resin versus placebo added to behavior modification, caloric restriction, and exercise. Participants weighed 130% to 180% (154% +/- 1.2%, mean +/- SEM) of ideal body weight (1983 Metropolitan Life tables) and were in good health. By week 34, participants receiving active medication lost an average of 14.2 +/- 0.9 kg, or 15.9% +/- 0.9% of initial weight (n = 58), versus a loss of 4.6 +/- 0.8 kg or 4.9% +/- 0.9% of initial weight by subjects taking placebo (n = 54; p less than 0.001). On visual analog scales, participants rated fenfluramine plus phentermine as more helpful than placebo (50.3 +/- 0.5 versus 20.3 +/- 0.3) and not bothersome (fenfluramine plus phentermine, 17.4 +/- 0.3 versus 13.5 +/- 0.2). Blood pressure decreased and pulse remained unchanged in both groups. Dry mouth was the most common adverse effect in subjects receiving fenfluramine plus phentermine; all adverse effects decreased after 4 weeks. Only nine participants left the study in the first 34 weeks. Two subjects from each group left the study as a result of adverse effects. Overall, fenfluramine plus phentermine used in conjunction with behavior modification, caloric restriction, and exercise aided weight loss and continued to be efficacious for 34 weeks.
Stress Proteins and Tolerance to Focal Cerebral Ischemia (1996)

Stress proteins are induced after a variety of neuronal injuries. The inducible 72-kDa heat shock protein (hsp70) is a stress protein that protects neurons from glutamate toxicity in vitro. Hsp70 has also been proposed to underlie the phenomenon of ischemic tolerance whereby brief sublethal intervals of global ischemia protect the hippocampus from subsequent lethal prolonged ischemia. To determine if the phenomenon of tolerance occurs in cortex after focal ischemia, the rat middle cerebral artery (MCA) was occluded by the suture method. Three 10-min intervals of transient ischemia (3 x 10-isc) separated by 45-min periods of reperfusion made up the most effective paradigm of preconditioning ischemia studied, and substantially reduced the volume of infarction 72 h after subsequent 100-min MCA occlusion. This approach induced protection if the interval between the 3 x 10-isc and the 100-min ischemia was 2, 3, or 5 days but not 1 or 7 days. Three 10-min intervals of transient ischemia alone produced minimal histological changes in the cortex at 72 h. Moreover, there were no significant changes in regional cerebral blood flow in the tolerant regions at 72 h after 3 x 10-isc before or during MCA occlusion. To explore the role of stress proteins in the induction of tolerance, expression of hsp70 and the glucose-regulated proteins grp75 and grp78 were studied. Samples from tolerant regions of the brain that had undergone preconditioning ischemia were evaluated at 1, 2, 3, 5, 7, and 14 days after 3 x 10-isc by Western blot analysis. The time course of hsp70 expression most closely correlated with tolerance. Hsp70 protein expression increased during times when tolerance was present (at 2-5 days) but did not increase thereafter (at 7 and 14 days). However, hsp70 was also increased before tolerance was present (at 1 day). Immunocytochemistry showed that hsp70 protein was expressed in neurons in the tolerant regions 24 h after 3 x 10-isc and was expressed in both neurons and glia after 72 h. Although immunocytochemistry suggested that there was increased neuronal expression of grp75 and grp78, no significant differences were found in protein expression as determined by Western blot before (at 1 day), during (at 2-5 days), and after (at 7 days and thereafter) tolerance. Thus, the time course of grp75 and grp78 expression did not correlate with that of tolerance. This model of ischemic tolerance is a useful method by which mechanisms of endogenous neuroprotection may be explored.
Oral Corticosteroid Use in Exacerbations of Asthma (2015)

Exacerbations of asthma are treated with oral corticosteroid medications which are associated with various adverse effects that impact negatively on patient adherence. Historically oral corticosteroid use has been associated with weight gain, increased appetite and dietary intake, though new evidence suggests that these effects are not associated with short term use. Impaired response to oral corticosteroids is also an issue in some patients due to steroid resistance. A new study suggests that inflammometry can be used to guide patient selection for oral corticosteroid therapy to improve responses. While oral corticosteroids remain the mainstay of treating asthma exacerbations, clinicians should give consideration to using inflammometry for patient selection and providing guidance on the likelihood and management of adverse effects. Keywords: Asthma, environmental exposure, inflammation, OCS therapy, oral corticosteroid, short-term OCS.
Lymphotoxin activation by human T-cell leukemia virus type I-infected cell lines: role for NF-kappa B (1990)

Human T-cell leukemia virus type I (HTLV-I)-infected T-cell lines constitutively produce high levels of biologically active lymphotoxin (LT; tumor necrosis factor-beta) protein and LT mRNA. To understand the regulation of LT transcription by HTLV-I, we analyzed the ability of a series of deletions of the LT promoter to drive the chloramphenicol acetyltransferase (CAT) reporter gene in HTLV-I-positive MT-2 cells. The smallest LT promoter fragment (-140 to +77) that was able to drive CAT activity contained a site that was similar to the immunoglobulin kappa-chain NF-kappa B-binding site. Since the HTLV-I tax gene activates the nuclear form of NF-kappa B, this finding suggested a possible means of HTLV-I activation of LT production. We found that the LT kappa B-like site specifically formed a complex with NF-kappa B-containing nuclear extract from MT-2, C81-66-45, and other activated T cells. Mutation of the LT kappa B site in the context of the LT promoter (-293 to +77) (mutant M1) reduced the ability of the promoter to drive the CAT gene in HTLV-I-infected and noninfected human T-cell lines. These data suggest a general role for NF-kappa B activation in the induction of LT gene transcription. Activation of LT in HTLV-I-infected cells may explain the pathology associated with HTLV-I infection, including the hypercalcemia that is prevalent in adult T-cell leukemia.
Effects of spin-orbit interactions on tunneling via discrete energy levels in metal nanoparticles (1999)

The presence of spin-orbit scattering within an aluminum nanoparticle affects measurements of the discrete energy levels within the particle by (1) reducing the effective g factor below the free-electron value of 2, (2) causing avoided crossings as a function of magnetic field between predominantly spin-up and predominantly spin-down levels, and (3) introducing magnetic-field-dependent changes in the amount of current transported by the tunneling resonances. All three effects can be understood in a unified fashion by considering a simple Hamiltonian. Spin-orbit scattering from 4% gold impurities in superconducting aluminum nanoparticles produces no dramatic effect on the superconducting gap at zero magnetic field, but we argue that it does modify the nature of the superconducting transition in a magnetic field.
Comparison of three next-generation sequencing platforms for metagenomic sequencing and identification of pathogens in blood (2014)

The analytical sensitivity of all three platforms approaches that of standard qPCR assays. Although all platforms were able to detect pathogens at the levels tested, there were several noteworthy differences. The Roche-454 Titanium platform produced consistently longer reads, even when compared with the latest chemistry updates for the PGM platform. The MiSeq platform produced consistently greater depth and breadth of coverage, while the Ion Torrent was unequaled for speed of sequencing. None of the platforms were able to verify a single nucleotide polymorphism responsible for antiviral resistance in an Influenza A strain isolated from the 2009 H1N1 pandemic. Overall, the benchtop platforms perform well for identification of pathogens from a representative clinical sample. However, unlike identification, characterization of pathogens is likely to require higher titers, multiple libraries and/or multiple sequencing runs.
Engineered Human IgG Antibodies with Longer Serum Half-lives in Primates (2004)

The neonatal Fc receptor (FcRn) plays an important role in regulating the serum half-lives of IgG antibodies. A correlation has been established between the pH-dependent binding affinity of IgG antibodies to FcRn and their serum half-lives in mice. In this study, molecular modeling was used to identify Fc positions near the FcRn binding site in a human IgG antibody that, when mutated, might alter the binding affinity of IgG to FcRn. Following mutagenesis, several IgG2 mutants with increased binding affinity to human FcRn at pH 6.0 were identified at Fc positions 250 and 428. These mutants do not bind to human FcRn at pH 7.5. A pharmacokinetics study of two mutant IgG2 antibodies with increased FcRn binding affinity indicated that they had serum half-lives in rhesus monkeys approximately 2-fold longer than the wild-type antibody.
Copy number and the stability of 2-micron circle-based artificial plasmids of Saccharomyces cerevisiae (1984)

The copy number and stability of artificial 2-micron circle-based plasmids have been accurately measured in [Cir+] and [Cir0] strains of Saccharomyces cerevisiae. We conclude that (i) instability and copy number vary greatly from plasmid to plasmid; (ii) instability and copy number are negatively correlated--that is, high copy number is associated with low instability; (iii) it is difficult to reconcile this variability with a strict and direct system of copy number control; (iv) instabilities are much higher than expected from random partition and the observed copy numbers: this may imply partition which is less efficient than random. Even so, (v) the partitioning of 2-micron circle-like plasmids is more efficient than that of ARS-based plasmids, which hints at the existence of a system for the (inefficient) distribution of 2-micron circles.