gebhart/patrepeval huggingface dataset:
An analysis of the accuracy of Langevin and molecular dynamics algorithms (1988)

Abstract Analytic expressions for mean squared positions and velocities of a harmonic oscillator are derived for Langevin dynamics algorithms valid in the high and low friction limits, and for the Verlet algorithm. For typical values of the parameters, errors in the positions are small. However, if the velocity is defined by the usual Verlet form, kinetic energies (and therefore calculated temperatures) can be in error by several per cent for the Langevin algorithms. If the Bunger-Brooks-Karplus algorithm is used to calculate positions, a simple redefinition of the velocity results greatly in improved kinetic energies. In addition, due to cancellation of errors in the velocities and the positions, the correct virial is obtained. The effect of including the force derivative in diffusive algorithms is examined. Positional and velocity averages are calculated for the Verlet algorithm for arbitrary initial conditions, and errors in the total energy and virial are analysed. Connection is made with the Langevin algorithms, and it is shown for harmonic oscillators that different definitions of the velocity are required to optimally calculate the temperature, pressure, and total energy, respectively.
Terahertz photomixing with diode lasers in low-temperature-grown GaAs (1995)

Recent optical heterodyne measurements with distributed-Bragg-reflector diode-laser pumps demonstrate that low-temperature-grown (LTG) GaAs photomixers will be useful in a compact all-solid-state terahertz source. Electrical 3 dB bandwidths as large as 650 GHz are measured in mixers with low electrode capacitance. These bandwidths appear to be independent of pump-laser wavelength over the range 780–850 nm. Shorter wavelength pumping results in a significant reduction of the bandwidth. The best LTG-GaAs photomixers are used to generate coherent continuous-wave output radiation at frequencies up to 5 THz.
Selective production of interferon-alpha subtypes by cultured peripheral blood mononuclear cells and lymphoblastoid cell lines. (1992)

The biological significance of the existence of multiple interferon-alpha (IFN-alpha) subtypes is unknown but may represent a finely tuned mechanism whereby different subtypes are produced in response to different stimuli. To investigate the expression of individual IFN-alpha subtypes, polyclonal antipeptide antisera designed to react with all IFN-alpha subtypes, or with a particular subtype, IFN-alpha 2 or IFN-alpha 4, have been produced. In this study we demonstrate the utility of these antisera for the detection, using indirect immunofluorescence staining, of intracellular IFN-alpha produced by human peripheral blood mononuclear cells (PBMC) and lymphoblastoid cells. Secreted IFN-alpha was also investigated by bioassay and a sandwich radioimmunoassay (RIA), using two monoclonal antibodies (mAb) and specific for IFN-alpha 4. The PBMC were shown to produce IFN reactive with all three polyclonal antisera, after stimulation with Sendai virus. The lymphoblastoid cells also produced IFN, including IFN-alpha 2, but IFN-alpha 4 was not detected either intracellularly, by immunofluorescence, or in the medium, by sandwich RIA. The immunofluorescence studies also demonstrate that in the absence of viral stimulation IFN-alpha is found in the cytoplasm of PBMC and lymphoblastoid cells but not secreted in detectable levels. The finding that two lymphoblastoid cell lines do not produce the subtype IFN-alpha 4 raises important questions as to whether other cell lines and cell types produce IFN-alpha subtypes selectively, and whether individual IFN-alpha subtypes have different roles in human physiology and pathology.
Dinaphtho[1,2-<i>b</i>:2′,1′-<i>d</i>]chalcogenophenes: Comprehensive Investigation of the Effect of the Chalcogen Atoms in the Phenacene-Type π-Electronic Cores (2013)

We report dinaphtho[1,2-b:2′,1′-d]chalcogenophenes as a new class of highly potential p-type semiconductors. As the result of comprehensive investigations including computational studies based on single-crystal structures successfully determined by X-ray analysis, the impacts of the chalcogen atoms are substantially manifested in their molecular orbitals, crystal packing structures, charge-transporting properties, and the device performances at the end. Among them, dinaphtho[1,2-b:2′,1′-d]thiophene and dinaphtho[1,2-b:2′,1′-d]selenophene achieved a hole mobility of up to 1.6 and 2.0 cm2 V–1 s–1, respectively, accompanied by an Ion/Ioff ratio as high as 104–105 in their single-crystal organic field-effect transistors. Such high performances are attributed to the large orbital coefficient on the chalcogen atoms and the ideal packing structures induced by chalcogen-bridged W-shaped molecules.
Integrating ethics and science in the International HapMap Project (2004)

Genomics resources that use samples from identified populations raise scientific, social and ethical issues that are, in many ways, inextricably linked. Scientific decisions about which populations to sample to produce the HapMap, an international genetic variation resource, have raised questions about the relationships between the social identities used to recruit participants and the biological findings of studies that will use the HapMap. The sometimes problematic implications of those complex relationships have led to questions about how to conduct genetic variation research that uses identified populations in an ethical way, including how to involve members of a population in evaluating the risks and benefits posed for everyone who shares that identity. The ways in which these issues are linked is increasingly drawing the scientific and ethical spheres of genomics research closer together.
Chemical modification and characterization of poly(ethylene terephthalate) surfaces for collagen immobilization (2013)

Abstract The functionalization of poly(ethylene terephthalate) (PET) surface films by reactions with multifunctional amines such as triethylenetetramine (TETA), and tetraethylenepentamine (TEPA) was investigated. For the functionalization of PET films surface we used a new way of treatment, a “sandwich model”. Physical-chemical properties of functionalized PET films were analysed. Qualitative and quantitative determination of the introduced amine groups were examined by means of Fourier Transform Infrared Attenuated Total Reflexion (FTIR — ATR), X-ray photoelectron spectroscopy (XPS), and potentiometric titration. Gained wetting properties were determined by using contact angle measurements and thoroughly analysed by acid-base approach. In addition, surface topography was investigated by atomic force microscopy (AFM). The amount of the introduced amino groups after TETA incorporation has been found to be two times higher as compared to TEPA. Wetting properties were significantly improved after aminolysis. Surface free energy was higher for PET — TETA treated film than that observed for PET — TEPA treated which is in accordance with titration results. The collagen immobilization onto PET treated films was evidenced by using AFM and subsequently by using XPS.
Immunity Provided by Colonized Enteric Bacteria (1986)

Floral organisms influence the host's immunological activities not only in the mucosal barrier system but also systemically. Using“unnatural”animals, i.e., monoassociated mice, we attempted to explore the stimulatory effect of intestinally colonized floral organisms. These gnotobiotic mice exhibited specific immune response against associated bacteria probably through the intestinal mucosal membrane. IgA antibody to the colonized bacteria was detected in the secretion. In addition, it was suggested that the specific response accompanied a production ofIgA unrelated to the stimulating antigen. Cell mediated immunity to the colonized bacterial antigen could be detected by the footpad reaction as well as the macrophage migration inhibition test with peritoneal exudate cells after monoassociation. These findings suggest that non-specific resistance to invading microorganisms or other noxious agents may be operative through floral organisms in both mucosal and systemic fashions.
Merger mania - politics before patients? (1999)

The recent spate of mergers is part of the latest attempt to improve the NHS through reorganisation. But are the expected benefits being delivered? Is patient care really going to improve? And has anyone accurately assessed the cost?
Towards better program obfuscation (2016)

As a common practice in software development, program obfuscation aims at deterring reverse engineering and malicious attacks on released source or binary code. Owning ample obfuscation techniques, we have relatively little knowledge on how to most effectively use them. The biggest challenge lies in identifying the most useful combination of these techniques. We propose a unified framework to automatically generate and optimize obfuscation based on an obscurity language model and a Monte Carlo Markov Chain (MCMC) based search algorithm. We further instantiate it for JavaScript programs and developed the Closure* tool. Compared to the well-known Google Closure Compiler, Closure* outperforms its default setting by 26%. For programs which have already been well obfuscated, Closure* can still outperform by 22%.
Tactical Decision Making for Lane Changing with Deep Reinforcement Learning (2017)

In this paper, we consider the problem of autonomous lane changing for self driving vehicles in a multi-lane, multi-agent setting. We present a framework that demonstrates a more structured and data efficient alternative to end-to-end complete policy learning on problems where the high-level policy is hard to formulate using traditional optimization or rule based methods but well designed low-level controllers are available. Our framework uses deep reinforcement learning solely to obtain a high-level policy for tactical decision making, while still maintaining a tight integration with the low-level controller, thus getting the best of both worlds. We accomplish this with Q-masking, a technique with which we are able to incorporate prior knowledge, constraints, and information from a low-level controller, directly in to the learning process thereby simplifying the reward function and making learning faster and data efficient. We provide preliminary results in a simulator and show our approach to be more efficient than a greedy baseline, and more successful and safer than human driving.
Maternal Viral Load, Zidovudine Treatment, and the Risk of Transmission of Human Immunodeficiency Virus Type 1 from Mother to Infant (1996)

A high maternal plasma concentration of virus is a risk factor for the transmission of HIV-1 from an untreated mother to her infant. The reduction in such transmission after zidovudine treatment is only partly explained by the reduction in plasma levels of viral RNA. To prevent HIV-1 transmission, initiating maternal treatment with zidovudine is recommended regardless of the plasma level of HIV-1 RNA or the CD4+ count.
Asymmetric Dimethylarginine Causes Hypertension and Cardiac Dysfunction in Humans and Is Actively Metabolized by Dimethylarginine Dimethylaminohydrolase (2003)

This study defines the cardiovascular effects of a systemic increase in ADMA in humans. These are similar to changes seen in diseases associated with ADMA accumulation. Finally, our data also indicate that ADMA is metabolized by DDAHs extensively in humans in vivo.
Challenges in portable RF transceiver design (1996)

As wireless products such as cellular phones become an everyday part of people's lives, the need for higher performance at lower costs becomes even more important. Overcoming the challenges involved in the design of radio-frequency (RF) transceivers can help meet this need. This article provides an overview of RF electronics in portable transceivers and describes design issues as well as current work toward achieving both high performance and low cost. To understand the implications in the design of RF integrated circuits (ICs) we look at the properties of the mobile communications environment. We then study receiver and transmitter architectures and their viability in present IC technologies. An example of an RF transceiver is given and the design of transceiver building blocks is discussed. We conclude by looking at future directions in RF design.
Characterization of <i>Vibrio cholerae</i> RyhB: the RyhB Regulon and Role of <i>ryhB</i> in Biofilm Formation (2005)

Vibrio cholerae encodes a small RNA with homology to Escherichia coli RyhB. Like E. coli ryhB, V. cholerae ryhB is negatively regulated by iron and Fur and is required for repression of genes encoding the superoxide dismutase SodB and multiple tricarboxylic acid cycle enzymes. However, V. cholerae RyhB is considerably longer (>200 nucleotides) than the E. coli RNA (90 nucleotides), and it regulates the expression of a variety of genes that are not known to be regulated by RyhB in E. coli, including genes involved in motility, chemotaxis, and biofilm formation. A mutant with a deletion in ryhB had reduced chemotactic motility in low-iron medium and was unable to form wild-type biofilms. The defect in biofilm formation was suppressed by growing the mutant in the presence of excess iron or succinate. The wild-type strain showed reduced biofilm formation in iron-deficient medium, further supporting a role for iron in normal biofilm formation. The ryhB mutant was not defective for colonization in a mouse model and appeared to be at a slight advantage when competing with the wild-type parental strain. Other genes whose expression was influenced by RyhB included those encoding the outer membrane porins OmpT and OmpU, several iron transport systems, and proteins containing heme or iron-sulfur clusters. These data indicate that V. cholerae RyhB has diverse functions, ranging from iron homeostasis to the regulation of biofilm formation.
Allosteric Activation of PTEN Phosphatase by Phosphatidylinositol 4,5-Bisphosphate (2003)

Phosphatase and tensin homologue deleted on chromosome 10 (PTEN) is a tumor suppressor that is lost in many human tumors and encodes a phosphatidylinositol phosphate phosphatase specific for the 3-position of the inositol ring. Here we report a novel mechanism of PTEN regulation. Binding of di-C8-phosphatidylinositol 4,5-P2 (PI(4,5)P2) to PTEN enhances phosphatase activity for monodispersed substrates, PI(3,4,5)P3 and PI(3,4)P2. PI(5)P also is an activator, but PI(4)P, PI(3,4)P2, and PI(3,5)P2 do not activate PTEN. Activation by exogenous PI(4,5)P2 is more apparent with PI(3,4)P2 as a substrate than with PI(3,4,5)P3, probably because hydrolysis of PI(3,4)P2 yields PI(4)P, which is not an activator. In contrast, hydrolysis of PI(3,4,5)P3 yields a potent activator, PI(4,5)P2, creating a positive feedback loop. In addition, neither di-C4-PI(4,5)P2 nor inositol trisphosphate-activated PTEN. Hence, the interaction between PI(4,5)P2 and PTEN requires specific, ionic interactions with the phosphate groups on the inositol ring as well as hydrophobic interactions with the fatty acid chains, likely mimicking the physiological interactions that PTEN has with the polar surface head groups and the hydrophobic core of phospholipid membranes. Mutations of the apparent PI(4,5)P2-binding motif in the PTEN N terminus severely reduced PTEN activity. In contrast, mutation of the C2 phospholipid-binding domain had little effect on PTEN activation. These results suggest a model in which a PI(4,5)P2 monomer binds to PTEN, initiates an allosteric conformational change and, thereby, activates PTEN independent of membrane binding.
Applying video sensor networks to nearshore environment monitoring (2003)

Environmental monitoring is an important emerging application area for pervasive computing. We describe shore-based sensing using standard video cameras and measurement techniques for important variables such as wave and ocean current conditions. We apply networked sensors for monitoring environmentally sensitive beaches and nearshore coastal oceans. We give some steps to improve the Argus video sensor network's functionality to quantify the time-space characteristics of the imaged world. We also discuss future system architectures, on the basis of the experience with a sensor network that have already deployed.
Bioluminescence Activity of Coelenterazine Analogues after Incorporation into Recombinant Apoaequorin (1993)

Abstract Of twenty-seven synthetic analogues of coelenterazine tested for bioluminescence activity with recombinant apoaequorin, eleven showed activity, but the best activity was obtained with celenterazine incorporated into wild type apoaequorin and into apoaequorin with all three cystein residues replaced by serine.
Computer based analyses of the 5'-flanking regions of selected genes involved in the nucleotide excision repair complex. (2000)

We have previously observed that the mRNA of selected genes involved in nucleotide excision repair appear to be coordinately expressed in human tissues from patients with ovarian cancer, testicular cancer, malignant brain tumors, and other malignancies. Such genes include ERCC1, XPA, XPB, XPD, XPF, and XPG. Coordinate mRNA expression appears to be most impressive in non-malignant tissues. We therefore began to explore possible reasons why such coordinate expression should occur. DNA sequences for the above noted genes were obtained from GeneBank. Two different software programs were applied to the DNA sequence, to the area 5' to the start of exon I of each gene. Analyses were performed by computer. The length of the 5' area assessed, was based on previous reports that determined what portion of the genomic sequence comprised the 5' UTR of the promoter of the respective gene. Based on this approach, potential DNA binding sites for no less than three dozen proteins, were identified in the 5'-flanking region of each of the NER genes studied. For each gene, potential binding sites for activator proteins and for repressor proteins were identified. The 5'-flanking regions for each gene noted above, had binding sites in common for 14 proteins with transcription modulatory activity. Eleven of these proteins are known for activator activity; two are reported to have repressor activity, and one has both repressor and activator function. These data suggest a possible molecular basis for the previously observed coordinate mRNA expression of selected NER genes in human tissue specimens.
Viruses and diarrhoea - where are we now? (1993)

Viruses are important causes of diarrhoea, with the major mortality occurring in the poor tropical overcrowded parts of the world. A successful vaccine, to rotavirus at least, may be developed, but how widely it would be used is uncertain. Even if successful, it would not remove all virus-associated diarrhoea and vomiting any more than a successful influenza vaccine would remove all viral respiratory disease. Perhaps the one aspect that needs most attention is the host. It is evident that not all infections lead to disease and that this is not simply related to the amount of virus in the faeces. This could be an indicator of the amount of damage--more virus coming from more infected cells--but there appear to be similar amounts of virus in "normal" stools as in diarrhoeal ones. Why is it then that some host, some babies, and not others have diarrhoea and vomiting? Is there an important, and as yet unrecognized, difference? If there is and it can be identified, then finding how to induce it or increase it in young babies could be as effective as a vaccine.
Erythropoietin production after renal denervation or beta-adrenergic blockade (1976)

The ability of either beta-adrenergic blockade or bilateral renal denervation to alter erythropoietin (ESF) production in rabbits exposed to hypobaric hypoxia was studied. ESF elaboration during 5 h of exposure to hypoxia was not affected by beta-blockade, but was markedly reduced by prior surgical denervation of both kidneys. After 18 h of hypoxia plasma ESF levels in renal denervated rabbits did not differ significantly from those of sham-operated controls. Previous studies have shown that ESF production during this more prolonged exposure to hypoxia was significantly inhibited by some beta-adrenergic blocking agents. Combined renal denervation and beta-blockade were more effective than renal denervation alone in attenuating ESF production during 5 h of exposure to hypoxia. However, ESF elaboration during 18 h of hypoxia was significantly greater in animals with combined denervation and beta-blockade than in control rabbits. These results suggest the existence of two distinct mechanisms for ESF production in rabbits exposed to hypobaric hypoxia.
Current Concepts and Treatments of Schizophrenia (2018)

Schizophrenia is a debilitating mental illness which involves three groups of symptoms, i.e., positive, negative and cognitive, and has major public health implications. According to various sources, it affects up to 1% of the population. The pathomechanism of schizophrenia is not fully understood and current antipsychotics are characterized by severe limitations. Firstly, these treatments are efficient for about half of patients only. Secondly, they ameliorate mainly positive symptoms (e.g., hallucinations and thought disorders which are the core of the disease) but negative (e.g., flat affect and social withdrawal) and cognitive (e.g., learning and attention disorders) symptoms remain untreated. Thirdly, they involve severe neurological and metabolic side effects and may lead to sexual dysfunction or agranulocytosis (clozapine). It is generally agreed that the interactions of antipsychotics with various neurotransmitter receptors are responsible for their effects to treat schizophrenia symptoms. In particular, several G protein-coupled receptors (GPCRs), mainly dopamine, serotonin and adrenaline receptors, are traditional molecular targets for antipsychotics. Comprehensive research on GPCRs resulted in the exploration of novel important signaling mechanisms of GPCRs which are crucial for drug discovery: intentionally non-selective multi-target compounds, allosteric modulators, functionally selective compounds and receptor oligomerization. In this review, we cover current hypotheses of schizophrenia, involving different neurotransmitter systems, discuss available treatments and present novel concepts in schizophrenia and its treatment, involving mainly novel mechanisms of GPCRs signaling.
A Fast Algorithm for Competitive Recommendation Marketing Strategy (2016)

The development of social networks changes the way of information diffusion and the means of selling and buying. In this paper we study the problem of online promoting for a product with limited budget in the competitive propagation social networks, we called this problem competitive recommendation marketing strategy (CRM). The key of CRM problem is to find out a fixed number of target nodes as the original recommended nodes (by giving them free or discount samples) of our product, that can maximize the diffusion range and number of adoptions in the competitive propagation models. We first introduce two kind of competitive information propagation models called Competitive Independent Cascade model (CIC model) and Competitive Linear Threshold model (CLT model). Then we demonstrate the submodular property of CRM problem in CIC and CLT moels. Finally, we give greedy and fast heuristic algorithms for this problem. Experiment results show the efficiency of our algorithm.
ChemInform Abstract: The Role of Co in Unsupported Co‐Mo Sulfides in the Hydrodesulfurization of Thiophene. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.