gebhart/patrepeval huggingface dataset:
Adaptation of the Endogenous Salmonella enterica Serovar Typhi clyA -Encoded Hemolysin for Antigen Export Enhances the Immunogenicity of Anthrax Protective Antigen Domain 4 Expressed by the Attenuated Live-Vector Vaccine Strain CVD 908- htrA (2004)

Bacterial live-vector vaccines aim to deliver foreign antigens to the immune system and induce protective immune responses, and surface-expressed or secreted antigens are generally more immunogenic than cytoplasmic constructs. We hypothesize that an optimum expression system will use an endogenous export system to avoid the need for large amounts of heterologous DNA encoding additional proteins. Here we describe the cryptic chromosomally encoded 34-kDa cytolysin A hemolysin of Salmonella enterica serovar Typhi (ClyA) as a novel export system for the expression of heterologous antigens in the supernatant of attenuated Salmonella serovar Typhi live-vector vaccine strains. We constructed a genetic fusion of ClyA to the reporter green fluorescent protein and showed that in Salmonella serovar Typhi CVD 908-htrA, the fusion protein retains biological activity in both domains and is exported into the supernatant of an exponentially growing live vector in the absence of detectable bacterial lysis. The utility of ClyA for enhancing the immunogenicity of an otherwise problematic antigen was demonstrated by engineering ClyA fused to the domain 4 (D4) moiety of Bacillus anthracis protective antigen (PA). A total of 11 of 15 mice immunized intranasally with Salmonella serovar Typhi exporting the protein fusion manifested fourfold or greater rises in serum anti-PA immunoglobulin G, compared with only 1 of 16 mice immunized with the live vector expressing cytoplasmic D4 (P = 0.0002). In addition, the induction of PA-specific gamma interferon and interleukin 5 responses was observed in splenocytes. This technology offers exceptional versatility for enhancing the immunogenicity of bacterial live-vector vaccines.
A RAPID ASSESSMENT OF SKILLS IN YOUNG CHILDREN WITH AUTISM (2004)

Educational interventions based on the principles of behavior analysis are highly effective for establishing skills in young children with autism. As a first step in program development, the child's current skill level is determined by evaluating performance on tasks drawn from a preestablished curriculum. However, few specific guidelines have been delineated for conducting these skills assessments or interpreting the results. In this study, we evaluated an efficient methodology for conducting skills assessments. Six children who had been diagnosed with autism participated. The relative efficacy of two assessment packages--one containing several reinforcement procedures and one containing several potentially effective prompts--was evaluated across two to three skills for each child using multiple baseline and reversal designs. Results suggested that the methodology was useful for matching targeted skills to appropriate interventions.
Impact of Cytomegalovirus in Organ Transplant Recipients in the Era of Antiviral Prophylaxis (2006)

Late CMV disease is an important clinical problem in liver transplant recipients who receive antiviral prophylaxis, and is strongly and independently associated with mortality. Strategies to prevent late CMV disease are warranted.
Experiments on not ‘‘hearing the shape’’ of drums (1994)

We present an experimental test of the theorem of isospectral domains which states that certain pairs of planar domains have identical spectra for eigenvalues of the Laplacian operator or the Helmholtz wave equation. The experiments employ thin microwave cavities shaped in the form of two different domains known to be isospectral. We verify the equality of at least 54 of the measured low-lying eigenvalues to a few parts in ${10}^{4}$. We also obtain the eigenfunctions experimentally, and confirm that two nonisometric transformations connect isospectral eigenfunction pairs. An analysis in terms of periodic orbits using the trace formula is also carried out, and shown to be an alternative confirmation of isospectrality.
The origin of high efficiency in low-temperature solution-processable bilayer organometal halide hybrid solar cells (2013)

This work reports a study into the origin of the high efficiency in solution-processable bilayer solar cells based on methylammonium lead iodide (CH3NH3PbI3) and [6,6]-phenyl-C61-butyric acid methyl ester (PC61BM). Our cell has a power conversion efficiency (PCE) of 5.2% under simulated AM 1.5G irradiation (100 mW cm−2) and an internal quantum efficiency of close to 100%, which means that nearly all the absorbed photons are converted to electrons and are efficiently collected at the electrodes. This implies that the exciton diffusion, charge transfer and charge collection are highly efficient. The high exciton diffusion efficiency is enabled by the long diffusion length of CH3NH3PbI3 relative to its thickness. Furthermore, the low exciton binding energy of CH3NH3PbI3 implies that exciton splitting at the CH3NH3PbI3/PC61BM interface is very efficient. With further increase in CH3NH3PbI3 thickness, a higher PCE of 7.4% could be obtained. This is the highest efficiency attained for low temperature solution-processable bilayer solar cells to date.
Experimental study of the influence of edge roughness on magnetization switching in Permalloy nanostructures (2004)

Rectangular Permalloy nanostructures with different edge roughness, but the same average width, were fabricated by controlled variations in the exposure conditions of an electron-beam lithography process. The average widths that were studied ranged from 200 to 640 nm. Structures were characterized individually using magneto-optical Kerr effect single-structure nanomagnetometry and scanning electron microscopy on the same structure. Increased edge roughness caused increased coercivity, except for 200-nm-wide structures. Large edge roughness doubled the coercivity of wide (&amp;gt;600nm) structures. The coercivity of nominally identical structures (same roughness amplitude) differed by up to 20 Oe, suggesting that the specific edge profile influences magnetic switching.
Flexible and Safe Resolution of File Conflicts, (1994)

In this paper we describe the support provided by the Coda File System for transparent resolution of conflicts arising from concurrent updates to a file in different network partitions. Such partitions often occur in mobile computing environments. Coda provides a framework for invoking customized pieces of code called application-specific resolvers (asrs) that encapsulate the knowledge needed for file resolution. If resolution succeeds, the user notices nothing more than a slight performance delay. Only if resolution fails does the user have to resort to manual repair. Our design combines a rule-based approach to ASR selection with transactional encapsulation of ASR execution. This paper shows how such an approach leads to flexible and efficient file resolution without loss of security or robustness.
Blockade of the epidermal growth factor receptor signaling by a novel tyrosine kinase inhibitor leads to apoptosis of endothelial cells and therapy of human pancreatic carcinoma. (2000)

We determined whether down-regulation of the epidermal growth factor-receptor (EGF-R) signaling pathway by oral administration of a novel EGF-R tyrosine kinase inhibitor (PKI166) alone or in combination with gemcitabine (administered i.p.) can inhibit growth and metastasis of human pancreatic carcinoma cells implanted into the pancreas of nude mice. Therapy beginning 7 days after orthotopic injection of L3.6pl human pancreatic cancer cells reduced the volume of pancreatic tumors by 59% in mice treated with gemcitabine only, by 45% in those treated with PKI166 only, and by 85% in those given both drugs. The combination therapy also significantly inhibited lymph node and liver metastasis, which led to a significant increase in overall survival. EGF-R activation was significantly blocked by therapy with PKI166 and was associated with significant reduction in tumor cell production of VEGF and IL-8, which in turn correlated with a significant decrease in microvessel density and an increase in apoptotic endothelial cells. Collectively, our results demonstrate that oral administration of an EGF-R tyrosine kinase inhibitor decreased growth and metastasis of human pancreatic cancer growing orthotopically in nude mice and increased survival. The therapeutic effects were mediated in part by inhibition of tumor-induced angiogenesis attributable to a decrease in production of proangiogenic molecules by tumor cells and increased apoptosis of tumor-associated endothelial cells.
Photolabeling of Glu-129 of the S-1 subunit of pertussis toxin with NAD (1989)

UV irradiation was shown to induce efficient transfer of radiolabel from nicotinamide-labeled NAD to a recombinant protein (C180 peptide) containing the catalytic region of the S-1 subunit of pertussis toxin. Incorporation of label from [3H-nicotinamide]NAD was efficient (0.5 to 0.6 mol/mol of protein) relative to incorporation from [32P-adenylate]NAD (0.2 mol/mol of protein). Label from [3H-nicotinamide]NAD was specifically associated with Glu-129. Replacement of Glu-129 with glycine or aspartic acid made the protein refractory to photolabeling with [3H-nicotinamide]NAD, whereas replacement of a nearby glutamic acid, Glu-139, with serine did not. Photolabeling of the C180 peptide with NAD is similar to that observed with diphtheria toxin and exotoxin A of Pseudomonas aeruginosa, in which the nicotinamide portion of NAD is transferred to Glu-148 and Glu-553, respectively, in the two toxins. These results implicate Glu-129 of the S-1 subunit as an active-site residue and a potentially important site for genetic modification of pertussis toxin for development of an acellular vaccine against Bordetella pertussis.
Modeling Organic Surfaces with Self‐Assembled Monolayers (1989)

Abstract The interfacial properties of organic materials are of critical importance in many applications, especially the control of wettability, adhesion, tribology, and corrosion. The relationships between the microscopic structure of an organic surface and its macroscopic physical properties are, however, only poorly understood. This short review presents a model system that has the ease of preparation and the structural definition required to provide a firm understanding of interfacial phenomena. Long‐chain thiols, HS(CH 2 ) n X, adsorb from solution onto gold and form densely packed, oriented monolayers. By varying the terminal functional group, X, of the thiol, organic surfaces can be created having a wide range of structures and properties. More complex systems can be constructed by coadsorbing two or more thiols with different terminal functional groups or with different chain lengths onto a common gold substrate. By these techniques, controlled degrees of disorder can be introduced into model surfaces. We have used these systems to explore the relationships between the microscopic structure of the monolayers on a molecular and supramolecutar scale and their macroscopic properties. Wettability is a macroscopic interfacial property that has proven of particular interest.
The Cosmc connection to the Tn antigen in cancer (2014)

The Tn antigen is a tumor-associated carbohydrate antigen that is not normally expressed in peripheral tissues or blood cells. Expression of this antigen, which is found in a majority of human carcinomas of all types, arises from a blockage in the normal O-glycosylation pathway in which glycans are extended from the common precursor GalNAcα1-O-Ser/Thr (Tn antigen). This precursor is generated in the Golgi apparatus on newly synthesized glycoproteins by a family of polypeptide α-N-acetylgalactosaminyltransferases (ppGalNAcTs) and then extended to the common core 1 O-glycan Galβ1-3GalNAcα1-O-Ser/Thr (T antigen) by a single enzyme termed the T-synthase (core 1 β3-galactosyltransferase or C1GalT). Formation of the active form of the T-synthase requires a unique molecular chaperone termed Cosmc, encoded by Cosmc on the X-chromosome (Xq24 in humans, Xc3 in mice). Cosmc resides in the endoplasmic reticulum (ER) and prevents misfolding, aggregation, and proteasome-dependent degradation of newly synthesized T-synthase. Loss of expression of active T-synthase or Cosmc can lead to expression of the Tn antigen, along with its sialylated version Sialyl Tn antigen as observed in several cancers. Both genetic and epigenetic pathways, in addition to potential metabolic regulation, can result in abnormal expression of the Tn antigen. Engineered expression of the Tn antigen by disruption of either C1GalT (T-syn) or Cosmc in mice is associated with a tremendous range of pathologies and engineered expression of the Tn antigen in mouse embryos leads to embryonic death. Studies indicate that many membrane glycoproteins expressing the Tn antigen and/or truncated O-glycans may be dysfunctional, due to degradation and/or misfolding. Thus, expression of normal O-glycans is associated with health and homeostasis whereas truncation of O-glycans, e.g. the Tn and/or Sialyl Tn antigens is associated with cancer and other pathologies.
Experimental antitumor activity of taxotere (RP 56976, NSC 628503), a taxol analogue. (1991)

Taxotere (RP 56976; NSC 628503; N-debenzoyl-N-tert-butoxycarbonyl-10-deacetyl taxol) is a new microtubule stabilizing agent. It is obtained by semisynthesis from a noncytotoxic precursor extracted from the needles of the tree, Taxus baccata L. Taxotere was evaluated for antitumor activity against a variety of transplantable tumors of mice. Taxotere had no marked schedule dependency and was found active by the i.v. and the i.p. routes. Upon i.v. administration, 9 of 11 tumor models tested responded to Taxotere. B16 melanoma was found highly sensitive to Taxotere, with a tumor growth inhibition of 0% and a 3.0 log10 tumor cell kill at the maximum tolerated dose. In the same trial, taxol produced only a 1.1 log10 tumor cell kill at the maximum tolerated dose. Taxotere cured early stage pancreatic ductal adenocarcinoma 03 (6 of 6 cures) and colon adenocarcinoma 38 (7 of 7 cures). It also effected greater than 80% complete regressions of advanced stage disease with both tumors. Taxotere was active against early and advanced stage colon adenocarcinoma 51, with 2.3 and 1.7 log10 cell kill, respectively. Four other tumors responded to a lesser extent: Lewis lung (5.5% tumor growth inhibition), Glasgow osteogenic sarcoma (27.2% tumor growth inhibition), L1210 and P388 leukemias (70 and 54% increase in life span, respectively). Because of its good preclinical activity and its unique mechanism of action, Taxotere has entered Phase I clinical trials.
Localization of breakpoints by polymerase chain reactions in Burkitt's lymphoma with 8;14 translocations (1990)

Translocations involving chromosomes 8 and 14 in Burkitt's lymphoma (BL) often involve the switch mu (Smu) region on chromosome 14, which contains multiple repeats. This has enabled us to use the polymerase chain reaction (PCR) to detect breakpoints that involve this region on chromosome 14 and the c-myc gene on chromosome 8. Using pairs of flanking primers, each pair including one annealing to repeat sequences within the switch region and one of three primers from the c-myc region (first intron, 3', or 5' flanking sequence of the first exon of c-myc), we have been able to amplify DNA fragments containing the corresponding breakpoint regions from chromosome 14 in both cell lines and biopsied tumor samples. The definitive demonstration of sequences from both chromosomes in these fragments permitted the confirmation of the presence of a translocation. Because of the sensitivity of PCR, we were able to localize breakpoints in samples containing as few as 1 neoplastic cell in 10(8) cells. PCR provides a valuable tool for the detection of 8;14 chromosomal translocations, which should prove to be of value in diagnosis and molecular epidemiologic studies, as well as providing a means of detecting minimal disease.
Enhanced Expression and Activation of the Alternative Oxidase during Infection of Arabidopsis withPseudomonas syringae pv tomato1 (1999)

Cyanide-resistant ("alternative") respiration was studied in Arabidopsis during incompatible and compatible infection with Pseudomonas syringae pv tomato DC3000. Total leaf respiration increased as the leaves became necrotic, as did the cyanide-resistant component that was sensitive to salicylhydroxamic acid. Infiltration of leaves with an avirulent strain rapidly induced alternative oxidase (AOX) mRNA, whereas the increase was delayed in the compatible combination. The increase in mRNA correlated with the increase in AOX protein. Increased expression was confined to the infected leaves, in contrast to the pathogenesis-related protein-1, which was induced systemically. Virtually all of the AOX protein was in the reduced (high-activity) form. Using transgenic NahG and mutant npr1-1 and etr1-1 plants, we established that the rapid induction of the AOX was associated with necrosis and that ethylene, but not salicylic acid, was required for its induction. Increased pyruvate levels in the infected leaves suggested that increased substrate levels were respired through the alternative pathway; however, in the control leaves and the infected leaves, respiration was not inhibited by salicylhydroxamic acid alone. Increased respiration appeared to be associated primarily with symptom expression rather than resistance reactions.
Up-Regulation of Endothelial Delta-like 4 Expression Correlates with Vessel Maturation in Bladder Cancer (2006)

DLL4 expression is associated with vascular differentiation in bladder cancer; thus, targeting DLL4 may be a novel antiangiogenic therapy.
High-speed vertical-cavity surface emitting laser (1993)

Planar, gain-guided vertical-cavity surface-emitting lasers (VCSELs) with a modulation bandwidth of 14 GHz are described. This bandwidth is reached at a drive current of only 8 mA. The intrinsic bandwidth of these devices is estimated to be greater than 50 GHz. Nonlinear light-current characteristics of these lasers may lead to a high level of nonlinear harmonic distortion of the high-frequency output. It is shown that the relative intensity of the second-harmonic response decreases rapidly at higher drive currents, in agreement with a phenomenological model based on the DC characteristics of the laser.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Porphyrin Architectures Bearing Functionalized Xanthene Spacers (2002)

A modular synthetic strategy for the construction of cofacial porphyrin architectures bearing hydrogen-bond synthons on a xanthene platform is presented. The convergent approach is based on a xanthene aldehyde-ester building block that is easily obtainable on a multigram scale with minimal purification. Treatment of this xanthene derivative with a variety of aryl aldehydes and pyrrole under standard Lindsey conditions affords a family of meso-substituted porphyrins bearing a single functionalized xanthene spacer. Direct modification of the hydrogen-bond synthon after macrocyclization proceeds smoothly to furnish porphyrin systems with a variety of cofacial functionalities (e.g., carboxylic acid, ester, amide). Porphyrins bearing two trans-functionalized xanthene spacers are prepared by the MacDonald [2 + 2] condensation of the xanthene aldehyde-ester with readily available 5-aryl-substituted dipyrromethanes such as 5-mesityldipyrromethane to afford the pure alpha,alpha- and alpha,beta-porphyrin atropisomers after chromatographic separation. The versatility of this synthetic method offers intriguing opportunities for the use of these and related templates for the study of proton-coupled activation of small molecules.
Involvement of Poly(ADP-ribose) Polymerase-1 and XRCC1/DNA Ligase III in an Alternative Route for DNA Double-strand Breaks Rejoining (2004)

The efficient repair of DNA double-strand breaks (DSBs) is critical for the maintenance of genomic integrity. In mammalian cells, the nonhomologous end-joining process that represents the predominant repair pathway relies on the DNA-dependent protein kinase (DNA-PK) and the XRCC4-DNA ligase IV complex. Nonetheless, several in vitro and in vivo results indicate that mammalian cells use more than a single end-joining mechanism. While searching for a DNA-PK-independent end-joining activity, we found that the pretreatment of DNA-PK-proficient and -deficient rodent cells with an inhibitor of the poly(ADP-ribose) polymerase-1 enzyme (PARP-1) led to increased cytotoxicity of the highly efficient DNA double-strand breaking compound calicheamicin gamma1. In addition, the repair kinetics of the DSBs induced by calicheamicin gamma1 was delayed both in PARP-1-proficient cells pretreated with the PARP-1 inhibitor and in PARP-1-deficient cells. In order to get new insights into the mechanism of an alternative route for DSBs repair, we have established a new synapsis and end-joining two-step assay in vitro, operating on DSBs with either nuclear protein extracts or recombinant proteins. We found an end-joining activity independent of the DNA-PK/XRCC4-ligase IV complex but that actually required a novel synapsis activity of PARP-1 and the ligation activity of the XRCC1-DNA ligase III complex, proteins otherwise involved in the base excision repair pathway. Taken together, these results strongly suggest that a PARP-1-dependent DSBs end-joining activity may exist in mammalian cells. We propose that this mechanism could act as an alternative route of DSBs repair that complements the DNA-PK/XRCC4/ligase IV-dependent nonhomologous end-joining.
Multilevel codes: theoretical concepts and practical design rules (1999)

This paper deals with 2/sup l/-ary transmission using multilevel coding (MLC) and multistage decoding (MSD). The known result that MLC and MSD suffice to approach capacity if the rates at each level are appropriately chosen is reviewed. Using multiuser information theory, it is shown that there is a large space of rate combinations such that MLC and full maximum-likelihood decoding (MLD) can approach capacity. It is noted that multilevel codes designed according to the traditional balanced distance rule tend to fall in the latter category and, therefore, require the huge complexity of MLD. The capacity rule, the balanced distances rules, and two other rules based on the random coding exponent and cutoff rate are compared and contrasted for practical design. Simulation results using multilevel binary turbo codes show that capacity can in fact be closely approached at high bandwidth efficiencies. Moreover, topics relevant in practical applications such as signal set labeling, dimensionality of the constituent constellation, and hard-decision decoding are emphasized. Bit interleaved coded modulation, proposed by Caire et al. (see ibid., vol.44, p.927-46, 1998), is reviewed in the context of MLC. Finally, the combination of signal shaping and coding is discussed. Significant shaping gains are achievable in practice only if these design rules are taken into account.