gebhart/patrepeval huggingface dataset:
Characteristics of High Efficiency Dye-Sensitized Solar Cells (2006)

Impedance spectroscopy was applied to investigate the characteristics of dye-sensitized nanostructured TiO2 solar cells (DSC) with high efficiencies of light to electricity conversion of 11.1% and 10.2%. The different parameters, that is, chemical capacitance, steady-state transport resistance, transient diffusion coefficient, and charge-transfer (recombination) resistance, have been interpreted in a unified and consistent framework, in which an exponential distribution of the localized states in the TiO2 band gap plays a central role. The temperature variation of the chemical diffusion coefficient dependence on the Fermi-level position has been observed consistently with the standard multiple trapping model of electron transport in disordered semiconductors. A Tafel dependence of the recombination resistance dependence on bias potential has been rationalized in terms of the charge transfer from a distribution of surface states using the Marcus model of electron transfer. The current-potential curve of the solar cells has been independently constructed from the impedance parameters, allowing a separate analysis of the contribution of different resistive processes to the overall conversion efficiency.
Angiotensin II Induces c-fos mRNA in Aortic Smooth Muscle (1989)

Vasoconstrictors such as angiotensin II (Ang II) play an important role in the pathogenesis of hypertension. These agonists may be responsible for the abnormal vascular smooth muscle cell (VSMC) growth seen in hypertension, either indirectly as a consequence of elevating blood pressure or directly as a result of receptor-mediated effects on VSMC growth. To investigate whether Ang II might directly initiate or modulate some of the "early" genetic programs associated with growth in VSMC, the expression of the proto-oncogene c-fos was studied in cultured rat aortic VSMC. Ang II rapidly induced the accumulation of c-fos mRNA, with maximal levels occurring at approximately 30 min. Induction of c-fos mRNA by Ang II was concentration-dependent, with a maximal response at 100 nM. Ang II induction of c-fos mRNA was blocked by its competitive inhibitor, [sarcosine 1,isoleucine 8]angiotensin II. Induction of c-fos mRNA was not dependent upon Ang II-stimulated intracellular alkalinization or activation of Na+/H+ exchange, but was dependent upon mobilization of intracellular Ca2+ and protein kinase C activation. Epidermal growth factor, a VSMC mitogen, also induced c-fos mRNA in VSMC, but by a mechanism different from that of Ang II. These results demonstrate that the vasoconstrictor hormone Ang II induces in VSMC one of the earliest genes, c-fos, associated with the proliferative response.
Mechanical and thermal behaviour of flexible food packaging polymeric films materials under high pressure/temperature treatments (2008)

Abstract The effect of high‐pressure processing on mechanical and thermal properties of four complex packaging materials (polyethylene/ethylene vinyl alcohol/ polyethylene: PE/EVOH/PE; metallized polyester/polyethylene: PETmet/PE; polyester/polyethylene: PET/PE; polypropylene SiOx recovered: PPSiOx) was studied. Pouches of the different materials containing distilled water or olive oil as food simulants, as well as empty ones, were subjected to 400 MPa for 30 min, at temperatures of 20 or 60°C. Delamination and wrinkling were a general consequence of the high‐pressure processing of multilayer polymeric systems. However, no significant changes were observed regarding the mechanical properties of PE containing laminates after pressurization. PPSiOx underwent significant modifications as SiOx completely broke down. Neither thermal property was affected by pressure, as it was the processing temperature that induced tempering effects on the crystallization behaviour of polymeric components. Only PE/EVOH/PE, when in contact with water as a simulant, presented a decrease in the melting point temperature. Copyright © 2008 John Wiley &amp; Sons, Ltd.
Gabapentin and pregabalin, but not morphine and amitriptyline, block both static and dynamic components of mechanical allodynia induced by streptozocin in the rat (1999)

A single injection of streptozocin (50 mg/kg, i.p.) led to the development of static and dynamic allodynia in the rat. The two responses were detected, respectively, by application of pressure using von Frey hairs or lightly stroking the hind paw with a cotton bud. Static allodynia was present in the majority of the animals within 10 days following streptozocin. In contrast, dynamic allodynia took almost twice as long to develop and was only present in approximately 60% of rats. Morphine (1-3 mg/kg, s.c.) and amitriptyline (0.25-2.0 mg/kg, p.o.) dose-dependently blocked static allodynia. However, neither of the compounds was effective against dynamic allodynia. In contrast, gabapentin (10-100 mg/kg, p.o.) and the related compound pregabalin (3-30 mg/kg, p.o.) dose-dependently blocked both types of allodynia. However, the corresponding R-enantiomer (10-100 mg/kg, p.o.) of pregabalin, was found to be inactive. The intrathecal administration of gabapentin dose-dependently (1-100 microg/animal) blocked both static and dynamic allodynia. In contrast, administration of similar doses of gabapentin into the hind paw failed to block these responses. It is suggested that in this model of neuropathic pain dynamic allodynia is mediated by A beta-fibres and the static type involves small diameter nociceptive fibres. These data suggest that gabapentin and pregabalin possess a superior antiallodynic profile than morphine and amitriptyline, and may represent a novel class of therapeutic agents for the treatment of neuropathic pain.
Efficient Deterministic Replay of Multithreaded Executions in a Managed Language Virtual Machine (2015)

Shared-memory parallel programs are inherently nondeterministic, making it difficult to diagnose rare bugs and to achieve deterministic execution. Existing multithreaded record & replay approaches have serious limitations such as relying on custom hardware, handling only data-race-free executions, or slowing programs by an order of magnitude. Furthermore, language virtual machines (VMs) such as Java VMs (JVMs) introduce various sources of nondeterminism that thwart demonstrating deterministic replay.
XML (1998)

article Free Access Share on XML: not a silver bullet, but a great pipe wrench Authors: Tommie Usdin Mulberry Technologies, Inc., Rockville, MD Mulberry Technologies, Inc., Rockville, MDView Profile , Tony Graham Mulberry Technologies, Inc., Rockville, MD Mulberry Technologies, Inc., Rockville, MDView Profile Authors Info & Claims StandardViewVolume 6Issue 3Sept. 1998 pp 125–132https://doi.org/10.1145/324042.324049Online:01 September 1998Publication History 6citation998DownloadsMetricsTotal Citations6Total Downloads998Last 12 Months5Last 6 weeks2 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Temperature-sensitive, protoplast-forming os-1 varient of Neurospora- a few tricks. (1982)

Temperature-sensitive, protoplast-forming os-1 varient of Temperature
Measuring cereblon as a biomarker of response or resistance to lenalidomide and pomalidomide requires use of standardized reagents and understanding of gene complexity (2013)

Cereblon, a member of the cullin 4 ring ligase complex (CRL4), is the molecular target of the immunomodulatory drugs (IMiDs) lenalidomide and pomalidomide and is required for the antiproliferative activity of these agents in multiple myeloma (MM) and immunomodulatory activity in T cells. Cereblon's central role as a target of lenalidomide and pomalidomide suggests potential utility as a predictive biomarker of response or resistance to IMiD therapy. Our studies characterized a cereblon monoclonal antibody CRBN65, with high sensitivity and specificity in Western analysis and immunohistochemistry that is superior to commercially available antibodies. We identified multiple cereblon splice variants in both MM cell lines and primary cells, highlighting challenges with conventional gene expression assays given this gene complexity. Using CRBN65 antibody and TaqMan quantitative reverse transcription polymerase chain reaction assays, we showed lack of correlation between cereblon protein and mRNA levels. Furthermore, lack of correlation between cereblon expression in MM cell lines and sensitivity to lenalidomide was shown. In cell lines made resistant to lenalidomide and pomalidomide, cereblon protein is greatly reduced. These studies show limitations to the current approaches of cereblon measurement that rely on commercial reagents and assays. Standardized reagents and validated assays are needed to accurately assess the role of cereblon as a predictive biomarker.
A σ 32 mutant with a single amino acid change in the highly conserved region 2.2 exhibits reduced core RNA polymerase affinity (1997)

sigma32, the product of the rpoH gene in Escherichia coli, provides promoter specificity by interacting with core RNAP. Amino acid sequence alignment of sigma32 with other sigma factors in the sigma70 family has revealed regions of sequence homology. We have investigated the function of the most highly conserved region, 2.2, using purified products of various rpoH alleles. Core RNAP binding analysis by glycerol gradient sedimentation has revealed reduced core RNAP affinity for one of the mutant sigma32 proteins, Q80R. This reduced core interaction is exacerbated in the presence of sigma70, which competes with sigma32 for binding of core RNAP. When a different but more conserved amino acid was introduced at this position by site-directed mutagenesis (Q80N), this mutant sigma factor still displayed a significant reduction in its core RNAP affinity. Based on these results, we conclude that at least one specific amino acid in region 2.2 is involved in core RNAP interaction.
n-type doping of highly tetrahedral diamond-like amorphous carbon (1993)

The ability to control the electrical resistivity of semiconducting tetrahedral amorphous carbon (ta-C) films is reported. Phosphorus is incorporated during film growth from a plasma formed with a cathodic vacuum arc by using a phosphorus-containing carbon cathode. By changing the P content in the cathode from 0-1% mass the room temperature resistivity of the films can be changed from 107 Omega cm to 5 Omega cm. Electron energy-loss spectroscopy shows that incorporation of P does not change the amorphous tetrahedral nature of the carbon films deposited by the vacuum arc method.
Andreev reflection in nanoscale metal-superconductor devices (1994)

Computer simulation is used to study Andreev reflection in nanoscale normal-metal--superconductor devices. Back-focusing of hole waves through quantum point contacts is demonstrated. The electron-hole conversion efficiency is shown to depend on the diffraction of the electron wave at the quantum point contact.
The phenomena of spin-filter tunnelling (2007)

The spin filtering phenomenon allows one to obtain highly spin-polarized charge carriers generated from nonmagnetic electrodes using magnetic tunnel barriers. The exponential dependence of tunnel current on the tunnel barrier height is operative here. The magnetic, semiconducting europium chalcogenide compounds have strikingly demonstrated this effect. The possibility of employing ferrites and other methods opens the potential for display of this phenomenon at room temperature, which can be expected to lead to huge progress in spin injection and detection in semiconductors. But first, extremely challenging material-related issues have to be addressed. This review covers the field.
Structural Basis of CXCR4 Sulfotyrosine Recognition by the Chemokine SDF-1/CXCL12 (2008)

Stem cell homing and breast cancer metastasis are orchestrated by the chemokine stromal cell-derived factor 1 (SDF-1) and its receptor CXCR4. Here, we report the nuclear magnetic resonance structure of a constitutively dimeric SDF-1 in complex with a CXCR4 fragment that contains three sulfotyrosine residues important for a high-affinity ligand-receptor interaction. CXCR4 bridged the SDF-1 dimer interface so that sulfotyrosines sTyr7 and sTyr12 of CXCR4 occupied positively charged clefts on opposing chemokine subunits. Dimeric SDF-1 induced intracellular Ca2+ mobilization but had no chemotactic activity; instead, it prevented native SDF-1-induced chemotaxis, suggesting that it acted as a potent partial agonist. Our work elucidates the structural basis for sulfotyrosine recognition in the chemokine-receptor interaction and suggests a strategy for CXCR4-targeted drug development.
Cleavage of growth differentiation factor 15 (GDF15) by membrane type 1‐matrix metalloproteinase abrogates GDF15‐mediated suppression of tumor cell growth (2007)

Growth differentiation factor 15 (GDF15), a transforming growth factor (TGF)-beta superfamily member, has been cloned from a placenta cDNA library as a gene product that has promoted activation of pro-matrix metalloproteinase (MMP)2 mediated by membrane type (MT)1-MMP. Expression of MT1-MMP in HEK293T cells caused cleavage of the GDF15 mature form at N(252)-M(253) to produce a 6-kDa C-terminal fragment. Treatment of MCF7 cells with GDF15 induced activation of p53 and enhanced expression of p21, which was abrogated by MT1-MMP expression. GDF15 mRNA synthesis was also shown to be induced by treatment of cells with GDF15. Treatment of MCF7 cells with GDF15 caused suppression of cell proliferation. However, proliferation of MCF7 cells transfected with the MT1-MMP gene was not affected by GDF15 treatment, but was suppressed in the presence of the MMP inhibitor BB94. HT1080 cells transfected with the GDF15 gene, which endogenously express MT1-MMP, synthesize a high-level GDF15 precursor form and a low-level mature form, and treatment of cells with BB94 enhanced production of the GDF15 mature form. Consistent with GDF15 production, HT1080 cells transfected with the GDF15 gene proliferated almost equally with control cells, and addition of BB94 effectively suppressed growth of HT1080 cells transfected with the GDF15 gene concomitant with the accumulation of the GDF15 mature form, but not control cells. These results suggest that MT1-MMP contributes to tumor cell proliferation through the cleavage of GDF15, which down-regulates cell proliferation by inducing activation of p53 and p21 synthesis.
The Minimal Set of Genetic Alterations Required for Conversion of Primary Human Fibroblasts to Cancer Cells in the Subrenal Capsule Assay (2005)

Based on previous studies, a minimal set of genetic alterations that is required to convert normal human fibroblasts into cancer cells has been defined. Essential roles for telomere maintenance and alterations in phosphatase 2A activity were inferred from experiments in which tumorigenicity was tested by injecting cells under the skin of immunodeficient mice. However, in the present experiments, the combination of SV40 large T antigen and activated Ras, without hTERT or SV40 small t antigen, was sufficient to convert nine different primary human fibroblast cell strains to a fully malignant state. The malignant behavior of the cells was demonstrated by growth of the cells into invasive tumors when the cells were injected beneath the kidney capsule of immunodeficient mice. Lung metastases and circulating tumor cells were also detected. These tumors were not immortal; cells entered crisis, from which they could be rescued by expression of hTERT. However, the same cell populations were not tumorigenic when they were injected under the skin. In this site, tumorigenicity required the expression of hTERT and SV40 small t antigen as well as SV40 large T antigen and Ras. The cellular pathways targeted by SV40 large T antigen (p53 and pRb) and those targeted by activated Ras represent a minimal set of genetic alterations required for the conversion of normal human fibroblasts into cancer cells.
RNA tetraloops as minimalist substrates for aminoacylation (1992)

Previous work established that seven-base-pair hairpin microhelices with sequences based on the acceptor stems of alanine, glycine, methionine, and histidine tRNAs can be aminoacylated specifically with their cognate amino acids. To obtain "minimalist" substrates with fewer base pairs, we took advantage of the high thermodynamic stability of RNA tetraloop motifs that are found in ribosomal RNAs. We show here that rationally designed RNA tetraloops with as few as four base pairs are substrates for aminoacylation. Major nucleotide determinants for recognition by the class II synthetases were incorporated into each of the respective tetraloop substrates, resulting in specific aminoacylation by the alanine, glycine, and histidine tRNA synthetases. An analysis of the kinetics of aminoacylation shows that, for the alanine system, the majority of the transition-state stabilization provided by the synthetase-tRNA interaction is reproduced by the interaction of the synthetase with nucleotides in its minimalist tetraloop substrate. In an extension of this work, we also observed specific aminoacylation with the class I methionine tRNA synthetase of RNA tetraloops based on sequences in the acceptor stem of methionine tRNA. Thus, the results demonstrate four different examples where specific aminoacylation is directed by sequences/structures contained in less than half of a turn of an RNA helix.
Tumor-infiltrating immune repertoires captured by single-cell barcoding in emulsion (2017)

Abstract Tumor-infiltrating lymphocytes (TILs) are critical to anti-cancer immune responses, but their diverse phenotypes and functions remain poorly understood and challenging to study. We therefore developed a single-cell barcoding technology for deep characterization of TILs without the need for cell-sorting or culture. Our emulsion-based method captures full-length, natively paired B-cell and T-cell receptor (BCR and TCR) sequences from lymphocytes among millions of input cells. We validated the method with 3 million B-cells from healthy human blood and 350,000 B-cells from an HIV elite controller, before processing 400,000 cells from an unsorted dissociated ovarian adenocarcinoma and recovering paired BCRs and TCRs from over 11,000 TILs. We then extended the barcoding method to detect DNA-labeled antibodies, allowing ultra-high throughput, simultaneous protein detection and RNA sequencing from single cells.
dBug: Systematic Evaluation of Distributed Systems (2018)

This paper presents the design, implementation and evaluation of “dBug” – a tool that leverages manual instrumentation for systematic evaluation of distributed and concurrent systems. Specifically, for a given distributed concurrent system, its initial state and a workload, the dBug tool systematically explores possible orders in which concurrent events triggered by the workload can happen. Further, dBug optionally uses the partial order reduction mechanism to avoid exploration of equivalent orders. Provided with a correctness check, the dBug tool is able to verify that all possible serializations of a given concurrent workload execute correctly. Upon encountering an error, the tool produces a trace that can be replayed to investigate the error. We applied the dBug tool to two distributed systems – the Parallel Virtual File System (PVFS) implemented in C and the FAWN-based key-value storage (FAWN-KV) implemented in C++. In particular, we integrated both systems with dBug to expose the non-determinism due to concurrency. This mechanism was used to verify that the result of concurrent execution of a number of basic operations from a fixed initial state meets the high-level specification of PVFS and FAWN-KV. The experimental evidence shows that the dBug tool is capable of systematically exploring behaviors of a distributed system in a modular, practical, and effective manner.
Protein-Protein Interactions in the Bacteriophage T4 Replisome (2003)

The bacteriophage T4 replication complex is composed of eight proteins that function together to replicate DNA. This replisome can be broken down into four basic units: a primosome composed of gp41, gp61, and gp59; a leading strand holoenzyme composed of gp43, gp44/62, and gp45; a lagging strand holoenzyme; and a single strand binding protein polymer. These units interact further to form the complete replisome. The leading and lagging strand polymerases are physically linked in the presence of DNA or an active replisome. The region of interaction was mapped to an extension of the finger domain, such that Cys-507 of one subunit is in close proximity to Cys-507 of a second subunit. The leading strand polymerase and the primosome also associate, such that gp59 mediates the contact between the two complexes. Binding of gp43 to the primosome complex causes displacement of gp32 from the gp59.gp61.gp41 primosome complex. The resultant species is a complex of proteins that may allow coordinated leading and lagging strand synthesis, helicase DNA unwinding activity, and polymerase nucleotide incorporation.
Site-Selective Azaindole Arylation at the Azine and Azole Rings via N-Oxide Activation (2009)

Subjection of N-methyl 6- and 7-azaindole N-oxides to a Pd(OAc)2/DavePhos catalyst system enables regioselective direct arylation of the azine ring. Following deoxygenation, 7-azaindole substrates undergo an additional regioselective azole direct arylation event in good yield.
Design limitations of highly parallel free-space optical interconnects based on arrays of vertical cavity surface-emitting laser diodes, microlenses, and photodetectors (1994)

We utilize a novel diffraction formalism to study the crosstalk effect in a highly parallel free-space optical interconnect based on two-dimensional arrays of surface-emitting laser diodes, microlenses, and photodetectors. The diffraction induced crosstalk between adjacent laser diodes in each detector to the system limitations is investigated. Optimum design rules and formulas are given for the first time, to include the relation of channel packaging density and interconnect length to the design parameters of the optical interconnect components. The design formulas developed here yield an optimum detector size and indicate a tradeoff between channel packaging density and interconnect length. The feasibility of such a free-space interconnect with a channel packaging density of 3460 channels/cm/sup 2/ and 2.0 cm interconnection length is determined using typical parameters of detector radius from /spl sim/5 to /spl sim/45 /spl mu/m, lens radius of 85 /spl mu/m, and laser diode radius of /spl sim/5 pm operating at wavelength 0.67 pm for signal-to-noise ratio above 17 dB. Some experiments were conducted to measure the diffraction induced crosstalk and optical link efficiency.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>