gebhart/patrepeval huggingface dataset:
Introducing an Implicit Membrane in Generalized Born/Solvent Accessibility Continuum Solvent Models (2002)

A new empirical approach to model the solvent effects in protein−membrane complexes is proposed. The generalized Born (GB) approximation is extended by including an implicit membrane (IM) in the calculation of the electrostatic contribution to the solvation free energy (GB/IM model). In addition, nonpolar solvation energy terms are calculated on the basis of the solvent-accessible surface approximation including the effect of membrane (SA/IM model). The generalized Born−solvent-accessible surface area (GBSA) model with implicit membrane (GBSA/IM) is implemented in the CHARMm package and is applicable for energy calculations and molecular dynamics simulations. The potential of the new method for studying large molecular systems is demonstrated with the example of two transmembrane proteins, bacteriorhodopsin and rhodopsin. The results show a clear directional asymmetry of the solvation energy during translocation of the proteins through the membrane, which is suggested to be an alternative explanation of the known “positive-inside” rule. The method is also tested in nanosecond molecular dynamics (MD) simulations of the influenza virus HA2 (1:20) fusion peptide. Interestingly, when starting from two different initial positions of peptide, during the 3 ns runs, the helical fragment consistently adopts a tilted (∼20−25°) orientation with respect to the membrane in very close agreement with the known electron paramagnetic resonance (EPR) data. We also found an excellent agreement between the pKs of the N-terminal amino group computed for the final MD structures and the known NMR titration data.
(Invited) Heterogeneously Integrated III-V on Silicon Lasers (2014)

Silicon photonics has generated an outstanding interest for optical telecommunications and inter/intra-chip interconnects in microelectronic systems. This platform can address a wide range of applications from very short distance data communication to long haul optical transmission. Silicon-based compounds are commonly used in commercial optical waveguide devices for applications such as passive optical interconnects and biomedical sensors. However, the integration of lasers together with Si integrated photonics-electronic circuits has proved to be much more challenging. The complexity lies in the fact that silicon is a poor light-emitting material due to its indirect energy bandgap. A particularly promising approach is based on molecular bonding of III-V materials on top of a patterned Si-on-insulator (SOI) substrate. Hybrid Si/III-V lasers are then realized following a collective fabrication procedure, enabling complex photonic integrated systems onto the silicon platform. In this communication, we describe the hybrid platform and we present the recent advances on III-V/Si lasers and transmitters.
Complementary Role of CD4+ T Cells and Secondary Lymphoid Tissues for Cross-presentation of Tumor Antigen to CD8+ T Cells (2003)

MHC class I-restricted tumor antigens can be presented to CD8+ T cells by two distinct pathways: via direct and indirect presentation. The relative contribution of these two pathways toward the initial activation of tumor antigen-specific CD8+ T cells and their subsequent tumor rejection is still vigorously debated. Using a tumor model able to dissect the relative contributions of direct and indirect presentation, we show unequivocally the inefficiency of direct presentation and the essential requirement of indirect presentation for the priming of naive tumor antigen-specific T cells leading to tumor rejection. Moreover, we characterize the essential environment under which indirect presentation occurs, and find efficient cross-priming of tumor-specific CD8+ T cells in the complete absence of secondary lymphoid tissues. The independence of this process from local lymph nodes is compromised, however, in the absence of CD4+ T cell help. Therefore, our paper demonstrates that effective immune protection against tumors requires the cross-priming of CD8+ T cells under conditions that require either CD4+ T cell help, or draining lymph nodes.
Control of Osteoclast Differentiation (1998)

The osteoclast is the primary bone-resorbing cell and is derived from the monocyte/macrophage lineage. Bipotent osteoclast precursors, which can form both osteoclasts and monocyte-macrophages, proliferate and differentiate to become unipotent post-mitotic committed osteoclast precursors. These post-mitotic committed precursors fuse to form the multinucleated osteoclast, which is then activated to resorb bone. A variety of soluble and membrane-bound factors play a critical role in regulating osteoclast formation, including growth factors, systemic hormones, and cells in the marrow microenvironment, such as osteoblasts and marrow stromal cells. Cell-to-cell interactions are important in both the formation and activity of the osteoclast. Recent molecular biological studies have identified transcription factors, such as c-fos and PU.1, which are required for osteoclast differentiation. In this review, we discuss the phenotypic changes that are induced as the cells mature from bipotent early precursors to mature osteoclasts; factors that have been identified that are involved in this process; and the role of marrow stromal cells and osteoblasts in osteoclast differentiation.
Dedication to excellence - project management : women in mining (2014)

Gerhard Hope talks to senior process engineer Alecia Sewlal from Consulmet about her first successful stint at project management in Africa.
<title>High-concentration collection and remote delivery of sunlight with fiber optic minidishes</title> (1999)

A new approach to the efficient collection and remote delivery of concentrated solar energy is proposed. The system's building block is a miniature (e.g., 0.2 m diameter) dish which concentrates sunlight into a single optical fiber. A number of mini-dishes comprise a module from which the optical fibers transport bundled power to a remote receiver. A second-stage nonimaging concentrator can boost flux levels to those approaching the thermodynamic limit and can be performed either in each individual dish or collectively in one or more larger devices at the entrance to the remote receiver. There are substantial advantages in efficiency, compactness, reduced mechanical loads, and ease of fabrication and installation relative to conventional solar designs. The design exploits the availability of low- attenuation optical fibers of high numerical aperture, as well as the practical advantages of mass producing highly accurate very small parabolic dishes. Designs for maximum efficiency attaining collection efficiencies as high as 80%, and maximum-concentration designs realizing flux levels of 30,000 suns, are achievable.
Identification of a Domain Containing B-Cell Epitopes in Hepatitis C Virus E2 Glycoprotein by Using Mouse Monoclonal Antibodies (1999)

Evidence from clinical and experimental studies of human and chimpanzees suggests that hepatitis C virus (HCV) envelope glycoprotein E2 is a key antigen for developing a vaccine against HCV infection. To identify B-cell epitopes in HCV E2, six murine monoclonal antibodies (MAbs), CET-1 to -6, specific for HCV E2 protein were generated by using recombinant proteins containing E2t (a C-terminally truncated domain of HCV E2 [amino acids 386 to 693] fused to human growth hormone and glycoprotein D). We tested whether HCV-infected sera were able to inhibit the binding of CET MAbs to the former fusion protein. Inhibitory activity was observed in most sera tested, which indicated that CET-1 to -6 were similar to anti-E2 antibodies in human sera with respect to the epitope specificity. The spacial relationship of epitopes on E2 recognized by CET MAbs was determined by surface plasmon resonance analysis and competitive enzyme-linked immunosorbent assay. The data indicated that three overlapping epitopes were recognized by CET-1 to -6. For mapping the epitopes recognized by CET MAbs, we analyzed the reactivities of CET MAbs to six truncated forms and two chimeric forms of recombinant E2 proteins. The data suggest that the epitopes recognized by CET-1 to -6 are located in a small domain of E2 spanning amino acid residues 528 to 546.
Poly(ester urethane)s Consisting of Poly[(R)-3-hydroxybutyrate] and Poly(ethylene glycol) as Candidate Biomaterials:  Characterization and Mechanical Property Study (2005)

Poly(ester urethane)s with poly[(R)-3-hydroxybutyrate] (PHB) as the hard and hydrophobic segment and poly(ethylene glycol) (PEG) as the soft and hydrophilic segment were synthesized from telechelic hydroxylated PHB (PHB-diol) and PEG using 1,6-hexamethylene diisocyanate as a nontoxic coupling reagent. Their chemical structures and molecular characteristics were studied by gel permeation chromatography, 1H NMR, and Fourier transform infrared spectroscopy. Results of differential scanning calorimetry and X-ray diffraction indicated that the PHB segment and PEG segment in the poly(ester urethane)s formed separate crystalline phases with lower crystallinity and a lower melting point than those of their corresponding precursors, except no PHB crystalline phase was observed in those with a relatively low PHB fraction. Thermogravimetric analysis showed that the poly(ester urethane)s had better thermal stability than their precursors. The segment compositions were calculated from the two-step thermal decomposition profiles, which were in good agreement with those obtained from 1H NMR. Water contact angle measurement and water swelling analysis revealed that both surface hydrophilicity and bulk hydrophilicity of the poly(ester urethane)s were enhanced by incorporating the PEG segment into PHB polymer chains. The mechanical properties of the poly(ester urethane)s were also assessed by tensile strength measurement. It was found that the poly(ester urethane)s were ductile, while natural source PHB is brittle. Young's modulus and the stress at break increased with increasing PHB segment length or PEG segment length, whereas the strain at break increased with increasing PEG segment length or decreasing PHB segment length.
A distinct cyclin A is expressed in germ cells in the mouse (1996)

In this paper, the existence of two A-type cyclins in the mouse is demonstrated. In the adult mouse, the expression of cyclin A1, which has greatest sequence identity with Xenopus cyclin A1, is restricted to germ cells. In contrast cyclin A2, which has greatest sequence identity with human cyclin A and Xenopus cyclin A2, is expressed in all tissues analysed. In order to explore the function of cyclin A1 in germ cells, its expression during the meiotic cell cycle and its associated kinase subunits have been characterised in the testis. The levels of cyclin A1 mRNA rise dramatically in late pachytene spermatocytes and become undetectable soon after completion of the meiotic divisions; thus its expression is cell cycle regulated. In lysates of germ cells from adult testes, cyclin A1 is present in p13suc1 precipitates, and cyclin A1 immunoprecipitates possess histone H1 kinase activity. Three kinase partners of cyclin A1 were identified: p34cdc2, a polypeptide of 39 x 10(3) M(r) that is related to p33cdk2 and, in lesser quantities, p33cdk2. Cyclin A1 was also detected in oocytes; in metaphase I and metaphase II oocytes, a proportion of the cyclin A1 colocalises with the spindle, possibly suggestive of a functional interaction. These data indicate that mammalian germ cells contain cyclin A1-dependent kinases that either act as a substitute for, or in addition to, the cyclin A2-dependent kinases characterised in somatic tissues.
Specific quantification of trichoderma reesei cellulases in reconstituted mixtures and its application to cellulase–cellulose binding studies (1994)

Specific quantifications of the major cellulolytic components of the Trichoderma reesei enzyme complex, i.e., endoglucanases I and III and cellobiohydrolases I and II, are described and, employing a defined mixture of these four cellulases reconstituted according to the composition of the native Trichoderma cellulase complex, used to determine the binding of each individual component onto filter paper. During substrate degradation by this enzyme mixture, the specific adsorption of each individual cellulase gradually increases and no preferential binding of one enzyme component in any particular phase of cellulose hydrolysis is found. T. reesei cellobiohydrolases I and II admixed with endoglucanases I and III represent a "full-value" cellulase system that is capable of degrading semicrystalline cellulose efficiently. In comparison with the crude Trichoderma enzyme complex, almost identical adsorption properties and similar hydrolytic efficiency are found for the reconstituted mixture. (c) 1994 John Wiley & Sons, Inc.
Engineered E. coli That Detect and Respond to Gut Inflammation through Nitric Oxide Sensing (2012)

Advances in synthetic biology now allow for the reprogramming of microorganisms to execute specific tasks. Here, we describe the development of an engineered strain of E. coli capable of sensing and responding to the presence of a mammalian inflammatory signal. The synthetic gene regulatory circuit is designed to permanently alter gene expression in response to the well characterized inflammatory signal nitric oxide. The detection of nitric oxide initiates the expression of a DNA recombinase, causing the permanent activation of a DNA switch. We demonstrate that E. coli containing this synthetic circuit respond to nitric oxide from both chemical and biological sources, with permanent DNA recombination occurring in the presence of nitric oxide donor compounds or inflamed mouse ileum explants. In the future, this synthetic genetic circuit will be optimized to allow E. coli to reliably detect and respond to inflammation in vivo.
Spectral efficiency of a multitone frequency hopping system for personal communication systems (2002)

Different spread spectrum techniques have been proposed for future mobile radio systems. The two main methods of spreading the spectrum have been to use either a direct sequence spreading or a frequency hopping spreading. The authors analyze an alternative multiple access scheme, multitune frequency hopping. The choice of frequencies is made randomly with the constraint that each frequency is not used more than once in each cell. With this random channel allocation one can avoid both frequency planning and intra-cell interference. Other advantages are frequency diversity, frequency interleaving and no problems regarding time dispersion. For a given minimum transmission quality constraint the authors define, a spectral efficiency measure. Further, they derive the spectral efficiency of the proposed system when a pilot tone MPSK modulation has been used. Even though they transmit a pilot tone for each used frequency, the resulting spectral efficiency of the proposed system compares favorably with other proposals for future mobile radio systems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Fibrates: no ACCORD on their use in the treatment of dyslipidaemia (2010)

Fenofibrate and bezafibrate are reasonable second-line therapies for dyslipidaemia and in diabetes. They are safe in combination therapy with statins but add little endpoint benefit except possibly in patients with a significant degree of atherogenic dyslipidaemia (high triglycerides and low HDL-cholesterol). The benefits of fibrates on microvascular disease remain to be fully explored.
Design and development of a peptide-based adiponectin receptor agonist for cancer treatment (2011)

ADP 355 is a first-in-class adiponectin receptor agonist. Its biological activity, superior stability in biological fluids as well as acceptable toxicity profile indicate that the peptidomimetic represents a true lead compound for pharmaceutical development to replace low adiponectin levels in cancer and other malignancies.
Effects of Renal Sympathetic Denervation on 24-hour Blood Pressure Variability (2012)

In patients with therapy-refractory arterial hypertension, RDN leads to significant reductions of BP variability. Effects of RDN on BP variability over 24 h were more pronounced than on average levels of BP.
Next generation sequence analysis for mitochondrial disorders (2009)

Our study indicates that the use of next generation sequencing technology holds great promise as a tool for screening mitochondrial disorders. The availability of a comprehensive molecular diagnostic tool will increase the capacity for early and rapid identification of mitochondrial disorders. In addition, the proposed approach has the potential to identify new mutations in candidate genes, expanding and redefining the spectrum of causative genes responsible for mitochondrial disorders.
Tissue and species distribution of mRNA encoding two ADP-ribosylation factors, 20-kDa guanine nucleotide binding proteins (1989)

Cholera toxin catalyzed ADP-ribosylation of Gs alpha, the stimulatory guanine nucleotide binding protein of the adenylyl cyclase system, is enhanced by approximately 20-kDa guanine nucleotide binding proteins, termed ADP-ribosylation factors or ARFs. ARF is an allosteric activator of the A1 catalytic protein of the toxin. Bovine ARF cDNA clones, ARF-1 isolated from adrenal (Sewell & Kahn, 1988) and ARF-2B from retina (Price et al., 1988), exhibit nucleotide and deduced amino acid sequences that are 80% and 96% identical, respectively, in the coding region. To determine tissue and species distribution of ARF-like mRNAs, bovine ARF-2B and human ARF-1 cDNAs and 30- or 48-base oligonucleotide probes that distinguish between ARF-1 and ARF-2B cDNAs in coding and 3'-untranslated regions were used for Northern analysis of poly(A+) RNA from different tissues and species. On the basis of hybridization with specific oligonucleotide probes, all bovine tissues contained mRNAs of 1.7 and 2.1 kb that were related to ARF-1 and ARF-2B, respectively. Northern analysis of brain poly(A+) RNA from different species with ARF-2B and ARF-1 cDNAs at low stringency demonstrated several bands varying in size from 0.9 to 3.7 kb. A 1.7-kb band consistently hybridized with an ARF-1 30-base coding-region probe but not with a probe for the 3'-untranslated region. Similar ARF-2B oligonucleotide probes did not hybridize with rat, mouse, rabbit, or human brain mRNA. Cleavage of ARF-2B cDNA with PvuII generated two fragments, one containing coding and the other 3'-noncoding region.(ABSTRACT TRUNCATED AT 250 WORDS)
Cross Linking of Human Platelet Membrane Aminophospholipids:Changes Induced by Thrombin (1977)

The proximity of the aminophospholipids, phosphatidylethanolamine (PE) and phosphatidyl-serine (PS), in platelet membranes was probed with difluorodinitrobenzene (D) which reacts with and cross-links aminophospholipids when they are less than 5 A° apart. D can penetrate intact cells and labels lipids on either side of the membrane bilayer. The incubation of mixtures of pure PE and PS can result in the formation of the following derivatives: PE-D-PE, PE-D-PS, PE-D, PS-D-PS, PS-D. Following incubation of washed platelets with D, lipids and derivatives were extracted, separated by thin-layer chromatography, and quantitated by lipid phosphorus. The incubation of platelets with D (125μM) for 2 hours resulted in derivatization of 49% PE and 34.6%PS. When platelets were treated with thrombin (0.1U/ml) for 5 minutes prior to incubation with D, 71.4% PE and 53.8% PS reacted. Results are shown in Table; %PE(PS)=% total platelet PE(PS). In controls significant amounts of only PE-D-PE and PE-D-PS were detected and thus are intimately associated within platelet membranes. In thrombin-treated platelets significant amounts of PS-D-PS were formed which did not occur in controls. However, there was no increase in PE-D-PE and PE-D-PS. Also, in thrombin-treated platelets additional PE and PS reacted but were not close enough to be cross-linked. The study indicates that incubation of platelets with thrombin results in the unmasking or rearrangement of specific compartments of PE and PS within platelet membranes which may be critical for platelet hemostatic activities.
Cross-correlation frequency resolved optical gating analysis of broadband continuum generation in photonic crystal fiber: simulations and experiments (2002)

Numerical simulations are used to study the temporal and spectral characteristics of broadband supercontinua generated in photonic crystal fiber. In particular, the simulations are used to follow the evolution with propagation distance of the temporal intensity, the spectrum, and the cross-correlation frequency resolved optical gating (XFROG) trace. The simulations allow several important physical processes responsible for supercontinuum generation to be identified and, moreover, illustrate how the XFROG trace provides an intuitive means of interpreting correlated temporal and spectral features of the supercontinuum. Good qualitative agreement with preliminary XFROG measurements is observed.
Robust H 2 control (1991)

In order to examine whether the false consensus bias applied to psychologically disturbed adolescents, outpatients at a rural mental health center who described themselves as very depressed or suicidal, and nondisturbed teenagers (who had no history of psychological treatment and were not at that time seeking psychological treatment), were asked to read a newspaper article about either a child's suicidal or viral illness death. Both groups of adolescents, like adults in previous research, viewed the suicidal child and the surviving family more negatively than they did the child and survivors of a viral illness death. Further, consistent with the false consensus hypothesis, adolescent clients viewed either child as more psychologically disturbed than did nonclients. Also, clients, as compared to nonclients, viewed both parents as more psychologically disturbed prior to either child's death. Results somewhat support the hypothesis of a false consensus bias which operates for depressed, suicidal adolescents when they view the tragedy of a child's death, but not when they are making recommendations about psychological help for the surviving family. Results are interpreted as suggesting that adolescent outpatients either view therapy as not particularly beneficial or as not particularly appropriate for bereaved individuals.
Low-power task scheduling for multiple devices (2000)

Power management saves power by shutting down idle devices. These devices often serve requests from concurrently running tasks. Ordering task execution can adjust the lengths of idle periods and exploit better opportunities for power management. This paper presents an on-line low-power scheduling algorithm for multiple devices. Simulations show that it can save up to 33% power and reduce 40% state-transition delays. This algorithm is robust under imperfect knowledge of future requests and timing constraints; therefore, it is applicable to interactive systems.
Antisense and RNA interference approaches to target validation in pain research. (2004)

In recent years numerous potential new targets for the development of novel drugs to treat chronic pain have been identified. Antisense strategies provide a straightforward approach to validate and further analyze their function. Furthermore, they offer the possibility of investigating a single member of a closely related family of proteins that cannot be easily targeted using small-molecule pharmacological tools. The recent discovery that short double-stranded RNA molecules can be employed to induce RNA interference in mammalian systems has opened exciting new roads for functional genomics. Gene silencing by small interfering RNAs has been demonstrated in neurons, and several targets involved in pain perception have been addressed. Furthermore, promising in vivo results have recently been obtained with small interfering RNAs.