gebhart/patrepeval huggingface dataset:
Rational Design of High Performance Conjugated Polymers for Organic Solar Cells (2012)

The research on the polymer based solar cells (PSCs) has attracted increasing amount of attention in recent years and great progresses have been made in the field of bulk heterojunction (BHJ) polymer solar cells since its inception in 1995. The power conversion efficiency (PCE) has increased from 1% in the 1990s to over 9% just recently. These great advances are mainly fueled by the development of conjugated polymers used as the electron-donating materials in BHJ solar cells. My research was focused on the rational design of those conjugated polymers. And first we investigated the positioning effect of alkyl side chains on the properties of conjugated polymers and find the best attaching position where high molecular weight and good solubility of conjugated polymers can be achieved without introducing large steric hindrance. Then, we proposed and demonstrated a weak donor-strong acceptor designing strategy to construct donor-acceptor type polymers with controlled energy levels. With those strategy to increase molecular weight, solubility and to control energy levels, we designed and synthesized several weak donor based conjugated polymers with solubilizing chains. Those polymers exhibited low HOMO levels, good solubility and molecular weight, thus high Voc and high PCE over 5% were obtained. Since most of the conjugated polymers developed so far have high-lying LUMO levels than desired LUMO, we developed some strong acceptor units to decrease the LUMO level of conjugated polymers. Combined with the methods we developed, conjugated polymers with high molecular weight, good solubility and near ideal energy levels were synthesized and they exhibit excellent PCE over 6%. In addition, by introducing fluorine atoms into conjugated backbone, we successfully created polymers with both low-lying HOMO and LUMO levels. Although band gap of this polymer is not ideal, large short circuit current (Jsc), open circuit voltage (Voc) and fill factor (FF) can still be obtained. Amazing PCE over 7% was demonstrated, which is among the best performances for polymer solar cells.
Dendritic Cell Function Can Be Modulated through Cooperative Actions of TLR Ligands and Invariant NKT Cells (2007)

The quality of signals received by dendritic cells (DC) in response to pathogens influences the nature of the adaptive response. We show that pathogen-derived signals to DC mediated via TLRs can be modulated by activated invariant NKT (iNKT) cells. DC maturation induced in vivo with any one of a variety of TLR ligands was greatly improved through simultaneous administration of the iNKT cell ligand alpha-galactosylceramide. DC isolated from animals treated simultaneously with TLR and iNKT cell ligands were potent stimulators of naive T cells in vitro compared with DC from animals treated with the ligands individually. Injection of protein Ags with both stimuli resulted in significantly improved T cell and Ab responses to coadministered protein Ags over TLR stimulation alone. Ag-specific CD8(+) T cell responses induced in the presence of the TLR4 ligand monophosphoryl lipid A and alpha-galactosylceramide showed faster proliferation kinetics, and increased effector function, than those induced with either ligand alone. Human DC exposed to TLR ligands and activated iNKT cells in vitro had enhanced expression of maturation markers, suggesting that a cooperative action of TLR ligands and iNKT cells on DC function is a generalizable phenomenon across species. These studies highlight the potential for manipulating the interactions between TLR ligands and iNKT cell activation in the design of effective vaccine adjuvants.
Solution Structure of a Cisplatin-Induced DNA Interstrand Cross-Link (1995)

The widely used antitumor drug cis-diamminedichloroplatinum(II) (cisplatin or cis-DDP) reacts with DNA, cross-linking two purine residues through the N7 atoms, which reside in the major groove in B-form DNA. The solution structure of the short duplex [d(CAT-AGCTATG)]2 cross-linked at the GC:GC site was determined by nuclear magnetic resonance (NMR). The deoxyguanosine-bridging cis-diammineplatinum(II) lies in the minor groove, and the complementary deoxycytidines are extrahelical. The double helix is locally reversed to a left-handed form, and the helix is unwound and bent toward the minor groove. These findings were independently confirmed by results from a phase-sensitive gel electrophoresis bending assay. The NMR structure differs markedly from previously proposed models but accounts for the chemical reactivity, the unwinding, and the bending of cis-DDP interstrand cross-linked DNA and may be important in the formation and repair of these cross-links in chromatin.
The Effects of RPM and Recycle on Separation Efficiency in a Clinical Blood Cell Centrifuge (1987)

A COBE blood cell centrifuge, model 2997 with a single stage channel, was modified to allow computer controlled sampling, and to allow recycle of red blood cells (RBCs) and plasma streams using bovine whole blood. The effects of recycle of the packed RBC and plasma product streams, and of the centrifuge RPM on platelet and white blood cell (WBC) separation efficiencies were quantified using a central composite factorial experimental design. These data were then fit using second order models. Both the model for the WBC separation efficiency and the model for the platelet separation efficiency predict that RPM has the greatest effect on separation efficiency and that RBC and plasma recycle have detrimental effects at moderate to low RPM, but have negligible impact on separation efficiency at high RPM.
Efficient and effective metasearch for a large number of text databases (1999)

Metasearch engines can be used to facilitate ordinary users for retrieving information from multiple local sources (text databases). In a metasearch engine, the contents of each local database is represented by a representative. Each user query is evaluated against the set of representatives of all databases in order to determine the appropriate databases to search. When the number of databases is very large, say in the order of tens of thousands or more, then a traditional metasearch engine may become inefficient as each query needs to be evaluated against too many database representatives. Furthermore, the storage requirement on the site containing the metasearch engine can be very large. In this paper, we propose to use a hierarchy of database representatives to improve the efficiency. We provide an algorithm to search the hierarchy. We show that the retrieval effectiveness of our algorithm is the same as that of evaluating the user query against all database representatives. We also show that our algorithm is efficient. In addition, we propose an alternative way of allocating representatives to sites so that the storage burden on the site containing the metasearch engine is much reduced.
Morphometric Analysis of Macular Photoreceptors and Ganglion Cells in Retinas With Retinitis Pigmentosa (1992)

There have been a number of histopathologic studies of retinas that were taken post mortem from patients with retinitis pigmentosa (RP), but few have addressed the question of transneuronal degeneration of ganglion cells secondary to photoreceptor death. We studied sectioned maculae that were obtained from 41 patients with different genetic forms of RP: autosomal dominant (n = 11); X-linked (n = 9); and simplex (n = 21). We also studied sectioned maculae that were taken from 20 age-matched normal subjects. We counted cell bodies in the photoreceptor and ganglion cell layers at 100-microns (0.35 degrees) intervals from the foveola to 1500-microns eccentricity and compared the mean cell counts among each group with RP. Each RP type had significantly fewer (P < .05) photoreceptors than those of the control group at each 100-microns interval. At eccentricities of 700 to 1500 microns, the retinas with X-linked and autosomal dominant RP had significantly fewer (P < .05) ganglion cells than those of the control group; the simplex RP mean ganglion cell counts were significantly lower (P < .05) than those of the control group, from 1000 to 1500 microns. The mean photoreceptor and ganglion cell counts had a .43 correlation (P < .001) in the zone of 700 to 1500 microns, consistent with transneuronal ganglion cell degeneration. Current experimental attempts to restore vision in diseased retinas by simulating or replacing photoreceptors are based on the premise that ganglion cells are retained after photoreceptor death. Our findings support this assumption.
Detection of procalcitonin (PCT) in healthy controls and patients with local infection by a sensitive ILMA. (2002)

The new PCT assay is 30 times more sensitive than the established routine assay LUMItest PCT, thus allowing for the first time PCT detection in healthy individuals. First results indicate that the assay is suitable to differentiate local bacterial infections from other non-infectious diseases.
Novel Control of S Phase of the Cell Cycle by Ubiquitin-conjugating Enzyme H7 (2008)

Timely degradation of regulatory proteins by the ubiquitin proteolytic pathway (UPP) is an established paradigm of cell cycle regulation during the G2/M and G1/S transitions. Less is known about roles for the UPP during S phase. Here we present evidence that dynamic cell cycle-dependent changes in levels of UbcH7 regulate entrance into and progression through S phase. In diverse cell lines, UbcH7 protein levels are dramatically reduced in S phase but are fully restored by G2. Knockdown of UbcH7 increases the proportion of cells in S phase and doubles the time to traverse S phase, whereas UbcH7 overexpression reduces the proportion of cells in S phase. These data suggest a role for UbcH7 targets in the completion of S phase and entry into G2. Notably, UbcH7 knockdown was coincident with elevated levels of the checkpoint kinase Chk1 but not Chk2. These results argue that UbcH7 promotes S phase progression to G2 by modulating the intra-S phase checkpoint mediated by Chk1. Furthermore, UbcH7 levels appear to be regulated by a UPP. Together the data identify novel roles for the UPP, specifically UbcH7 in the regulation of S phase transit time as well as in cell proliferation.
Idiopathic Dilated Cardiomyopathy in Dogs: Survival and Prognostic Indicators (1995)

To further define the prognosis and identify clinical findings predictive for survival in dogs with dilated cardiomyopathy (DCM), we performed Kaplan Meier survival analysis of 37 dogs with idiopathic DCM. Survival analysis showed that the 50% probability of survival occurred at 2.3 months. Probability of survival at 1 year was 37.5% and at 2 years was 28%. Bivariate Cox proportional hazard ratios identified pleural effusion and pulmonary edema, both signs of congestive heart failure, as independent prognostic indicators for dogs with DCM (P < .01). Hazard ratios for these prognostic indicators were 2.354 and 3.291, respectively. Multivariate Cox stepwise regression identified pleural effusion, left ventricular free-wall thickening fraction, ventricular ectopy, and weight loss as significant prognostic indicators for dogs with DCM. Because of the retrospective nature of this study, the effects of different drug treatments were not evaluated. The type of cardiac-related death, progressive failure versus sudden death, was not addressed in this study and requires further evaluation.
The role of theloxPspacer region in PI site-specific recombination (1986)

The lox-Cre site-specific recombination system of bacteriophage P1 is comprised of a site on the DNA where recombination occurs called loxP, and a protein, Cre, which mediates the reaction. The loxP site is 34 base pairs (bp) in length and consists of two 13 bp inverted repeats separated by an 8 bp spacer region. Previously it has been shown that the cleavage and strand exchange of recombining loxP sites occurs within this spacer region. We report here an analysis of various base substitution mutations within the spacer region of loxP, and conclude the following: Homology is a requirement for efficient recombination between recombining loxP sites. There is at least one position within the spacer where a base change drastically reduces recombination even when there is homology between the two recombining loxP sites. When two loxP sites containing symmetric spacer regions undergo Cre-mediated recombination in vitro, the DNA between the sites undergoes both excision and inversion with equal frequency.
Distinct Binding and Immunogenic Properties of the Gonococcal Homologue of Meningococcal Factor H Binding Protein (2013)

Neisseria meningitidis is a leading cause of sepsis and meningitis. The bacterium recruits factor H (fH), a negative regulator of the complement system, to its surface via fH binding protein (fHbp), providing a mechanism to avoid complement-mediated killing. fHbp is an important antigen that elicits protective immunity against the meningococcus and has been divided into three different variant groups, V1, V2 and V3, or families A and B. However, immunisation with fHbp V1 does not result in cross-protection against V2 and V3 and vice versa. Furthermore, high affinity binding of fH could impair immune responses against fHbp. Here, we investigate a homologue of fHbp in Neisseria gonorrhoeae, designated as Gonococcal homologue of fHbp (Ghfp) which we show is a promising vaccine candidate for N. meningitidis. We demonstrate that Gfhp is not expressed on the surface of the gonococcus and, despite its high level of identity with fHbp, does not bind fH. Substitution of only two amino acids in Ghfp is sufficient to confer fH binding, while the corresponding residues in V3 fHbp are essential for high affinity fH binding. Furthermore, immune responses against Ghfp recognise V1, V2 and V3 fHbps expressed by a range of clinical isolates, and have serum bactericidal activity against N. meningitidis expressing fHbps from all variant groups.
RNA-Directed DNA Polymerase and Virus-Induced Leukemia in Mice (1973)

Rifamycin antibiotics, which inhibit RNA-directed DNA polymerase of Rauscher leuckemia virus, prevent the leukemogenic activity of the virus, and the effect of leukemogenesis correlates with the magnitude of inhibition of the purified enzyme. This inhibition of enzyme activity by rifamycin SV derivatives is due to a relatively tight binding between the enzymes and the inhibitors, yet the binding can be reversed by nonionic detergent. The results of this study suggest that RNA-directed DNA polymerase is essential for induction of leukemia by exogenous virus and correlate with the previous observation that the same derivatives block viral transformation in vitro.
Angiotensin II type 2 receptors mediate inhibition of mitogen-activated protein kinase cascade and functional activation of SHP-1 tyrosine phosphatase (1997)

Angiotensin II type 2 (AT2) receptors are involved in the inhibition of cell proliferation as well as in apoptosis and neuronal differentiation, through intracellular signalling pathways that remain poorly defined. The present study examines the effect of AT2-receptor stimulation on growth-factor-induced pathways leading to the activation of mitogen-activated protein (MAP) kinases. In N1E-115 neuroblastoma cells, AT2 receptors inhibit the activity of MAP kinases induced by serum as well as by epidermal growth factor. The inhibitory effect of angiotensin II (Ang II) is rapid and transient, and affects both ERK1 and ERK2 (extracellular signal-related protein kinase) isoforms of the enzyme. AT2-mediated MAP kinase inactivation is not sensitive to pertussis toxin or okadaic acid, but involves a vanadate-sensitive protein tyrosine phosphatase (PTP). Expression of MAP kinase phosphatase-1 (MKP-1) is not significantly modified upon AT2-receptor activation, and insensitivity to actinomycin D also rules out transcriptional induction of other MKPs as a possible mechanism for AT2-mediated inactivation of MAP kinases. In addition, we report here that both in N1E-115 cells and in Chinese hamster ovary cells expressing recombinant human AT2 receptors, Ang II rapidly stimulates the catalytic activity of SHP-1, a soluble PTP that has been implicated in termination of signalling by cytokine and growth-factor receptors. These findings thus demonstrate functional negative cross-talk between heptahelical AT2 receptors and receptor tyrosine kinases, and suggest that SHP-1 tyrosine phosphatase is an early transducer of the AT2 receptor signalling pathway.
Flux through Citrate Synthase Limits the Growth of EthanologenicEscherichia coliKO11 during Xylose Fermentation (2002)

Previous studies have shown that high levels of complex nutrients (Luria broth or 5% corn steep liquor) were necessary for rapid ethanol production by the ethanologenic strain Escherichia coli KO11. Although this strain is prototrophic, cell density and ethanol production remained low in mineral salts media (10% xylose) unless complex nutrients were added. The basis for this nutrient requirement was identified as a regulatory problem created by metabolic engineering of an ethanol pathway. Cells must partition pyruvate between competing needs for biosynthesis and regeneration of NAD(+). Expression of low-K(m) Zymomonas mobilis pdc (pyruvate decarboxylase) in KO11 reduced the flow of pyruvate carbon into native fermentation pathways as desired, but it also restricted the flow of carbon skeletons into the 2-ketoglutarate arm of the tricarboxylic acid pathway (biosynthesis). In mineral salts medium containing 1% corn steep liquor and 10% xylose, the detrimental effect of metabolic engineering was substantially reduced by addition of pyruvate. A similar benefit was also observed when acetaldehyde, 2-ketoglutarate, or glutamate was added. In E. coli, citrate synthase links the cellular abundance of NADH to the supply of 2-ketoglutarate for glutamate biosynthesis. This enzyme is allosterically regulated and inhibited by high NADH concentrations. In addition, citrate synthase catalyzes the first committed step in 2-ketoglutarate synthesis. Oxidation of NADH by added acetaldehyde (or pyruvate) would be expected to increase the activity of E. coli citrate synthase and direct more carbon into 2-ketoglutarate, and this may explain the stimulation of growth. This hypothesis was tested, in part, by cloning the Bacillus subtilis citZ gene encoding an NADH-insensitive citrate synthase. Expression of recombinant citZ in KO11 was accompanied by increases in cell growth and ethanol production, which substantially reduced the need for complex nutrients.
CryptosporidiumOocysts in a Water Supply Associated with a Cryptosporidiosis Outbreak (2002)

An outbreak of cryptosporidiosis occurred in and around Clitheroe, Lancashire, in northwest England, during March 2000. Fifty-eight cases of diarrhea with Cryptosporidium identified in stool specimens were reported. Cryptosporidium oocysts were identified in samples from the water treatment works as well as domestic taps. Descriptive epidemiology suggested that drinking unboiled tap water in a single water zone was the common factor linking cases. Environmental investigation suggested that contamination with animal feces was the likely source of the outbreak. This outbreak was unusual in that hydrodynamic modeling was used to give a good estimate of the peak oocyst count at the time of the contamination incident. The oocysts' persistence in the water distribution system after switching to another water source was also unusual. This persistence may have been due to oocysts being entrapped within biofilm. Despite the continued presence of oocysts, epidemiologic evidence suggested that no one became ill after the water source was changed.
Molecular Mechanisms of Membrane Perturbation by Antimicrobial Peptides and the Use of Biophysical Studies in the Design of Novel Peptide Antibiotics (2005)

Antibiotic resistant bacterial strains represent a global health problem with a strong social and economic impact. Thus, there is an urgent need for the development of antibiotics with novel mechanisms of action. There is currently an extensive effort to understand the mode of action of antimicrobial peptides which are considered as one alternative to classical antibiotics. The main advantage of this class of substances, when considering bacterial resistance, is that they rapidly, within minutes, kill bacteria. Antimicrobial peptides can be found in every organism and display a wide spectrum of activity. Hence, the goal is to engineer peptides with an improved therapeutic index, i.e. high efficacy and target specificity. For the rational design of such novel antibiotics it is essential to elucidate the molecular mechanism of action. Biophysical studies have been performed using to a large extent membrane model systems demonstrating that there are distinctive different mechanisms of bacterial killing by antimicrobial peptides. One can distinguish between peptides that permeabilize and/or disrupt the bacterial cell membrane and peptides that translocate through the cell membrane and interact with a cytosolic target. Lantibiotics exhibit specific mechanisms, e.g. binding to lipid II, a precursor of the peptidoglycan layer, either resulting in membrane rupture by pore formation or preventing cell wall biosynthesis. The classical models of membrane perturbation, pore formation and carpet mechanism, are discussed and related to other mechanisms that may lead to membrane dysfunction such as formation of lipid-peptide domains or membrane disruption by formation of non-lamellar phases. Emphasis is on the role of membrane lipid composition in these processes and in the translocation of antimicrobial peptides.
A Survey on Technologies for Implementing Sensor Networks for Power Delivery Systems (2007)

The task of monitoring asset status and optimizing asset utilization for the T&D industry, given millions of assets and hundreds of thousands of miles of power lines distributed geographically over millions of square miles, seems particularly challenging if not impossible. Given the traditionally high cost of sensing and communications, the grid has minimal 'smarts' with much of the intelligence located at major substations. Dramatic reductions in sensor, computing and communications costs, coupled with significant performance enhancements has raised the possibility of realizing widely and massively distributed sensor networks (SNs) to monitor utility asset status. Under NEETRAC funding, a survey was conducted to review existing sensor technologies and products, and to estimate the possibility of extending these to realize distributed SNs. Possible applications for such SNs were also explored, as was the issue of cost point at which such networks would become commercially viable. This paper provides an overview of the highlights from the detailed survey that was conducted, and identifies 'gaps' in currently available sensor technologies, both from a performance and cost point.