gebhart/patrepeval huggingface dataset:
Reannotation of <i>Shewanella oneidensis</i> Genome (2003)

As more and more complete bacterial genome sequences become available, the genome annotation of previously sequenced genomes may become quickly outdated. This is primarily due to the discovery and functional characterization of new genes. We have reannotated the recently published genome of Shewanella oneidensis with the following results: 51 new genes have been identified, and functional annotation has been added to the 97 genes, including 15 new and 82 existing ones with previously unassigned function. The identification of new genes was achieved by predicting the protein coding regions using the HMM-based program GeneMark.hmm. Subsequent comparison of the predicted gene products to the non-redundant protein database using BLAST and the COG (Clusters of Orthologous Groups) database using COGNITOR provided for the functional annotation.
Bright organic electroluminescent devices with double-layer cathode (1993)

Electroluminescent devices were fabricated using a diamine derivative and tris (8-quinolinolato) aluminum (III) complex as the hole transport layer and the emitting layer, respectively. The glass substrate/anode/hole transport layer/emitting layer/cathode cells structure was employed. The anode was indium-tin-oxide (ITO) transparent electrode, and the cathode was a double layer consisting of first layer of Mg or Li and the second layer of Ag. Intense bright green emission with luminance of 40400 cd/m/sup 2/ was achieved at 18-V with a current density of 330 mA/cm/sup 2/ for the cell with the Al complex doped with 1 mol.% of coumarin 6 and Li/Ag as the cathode.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A Chinese Postman Problem Based on DNA Computing (2002)

DNA computing is a novel method for solving a class of intractable computational problems, in which the computing can grow exponentially with the problem size. Up to now, many accomplishments have been achieved to improve its performance and increase its reliability. A Chinese Postman Problem has been solved by means of molecular biology techniques in the paper. A small graph was encoded in molecules of DNA, and the "operations" of the computation were performed with standard protocols and enzymes. This work represents further evidence for the ability of DNA computing to solve NP-complete search problems.
A high throughput system for the evaluation of protein kinase C inhibitors based on Elk1 transcriptional activation in human astrocytoma cells. (1999)

Protein kinase C (PKC) designates a family of kinases that regulate many essential functions including cell growth and differentiation. The tight regulation of PKC activity is crucial for maintaining normal cellular proliferation and excessive activity leads to abnormal or uncontrolled cell growth. Recent reports indicate that malignant glioma cell lines express 100 to 1000-fold higher PKC activity when compared to non-neoplastic astrocytes. This high activity correlates well with the proliferation of tumor cells in vitro. We recently reported on the anti-proliferative properties of selective PKC inhibitors on the growth of U-373MG human astrocytoma cell line, and their ability to block mitogen-activated protein (MAP) kinase pathway activated by substance P (SP) neuropeptide receptor signaling via a PKC-dependent mechanism. Therefore, inhibiting PKC activity by selective PKC inhibitors may present a promising approach for improving astroglial brain tumor therapy. For this purpose, we constructed a high throughput model cell system to evaluate the efficacy of PKC inhibitors. This system is based on the measurement of light production in U-373MG cells stably transfected with the luciferase reporter gene whose expression depends on the transcriptional activation of GAL4-Elk1 fusion protein by enzyme components of the MAP kinase pathway and the upstream activation of PKC (PKC activation-->MAP kinases-->GAL4-Elk1 phosphorylation-->luciferase expression-->luciferase activity). In brief, we have demonstrated that the PKC activator 12-O-tetradecanoyl phorbol 13-acetate (TPA)-induced luciferase activity in this cell system is mediated via the MAP kinase pathway and can be blocked in the presence of MEK1 selective inhibitors (PD 098059 or U0126). We also demonstrated that TPA-induced luciferase activity in U-373MG stable clones can be blocked by PKC inhibitors (CGP 41251, Go 6976, and GF 109203X) in a concentration dependent manner. In contrast, epidermal growth factor (EGF)-induced luciferase activity, which is independent of PKC activation (Ras-->Raf-1-->MEK1-->MAP kinases-->GAL4-Elk1 phosphorylation-->luciferase expression-->luciferase activity) can only be blocked using a selective EGF receptor inhibitor (AG 1478). In conclusion, we have constructed a model cell system for the high throughput screening and identification of PKC inhibitors potentially active against astrocytoma cells in culture.
Calendar Access Protocol (CAP) (2005)

The Calendar Access Protocol (CAP) described in this memo permits a
Calendar User (CU) to utilize a Calendar User Agent (CUA) to access an
iCAL-based Calendar Store (CS). At the time of this writing, three
vendors are implementing CAP, but it has already been determined that
some changes are needed. In order to get implementation experience,
the participants felt that a CAP specification is needed to preserve
many years of work. Many properties in CAP which have had many years
of debate, can be used by other iCalendar protocols. This memo defines
an Experimental Protocol for the Internet community.
Analysis of a Wavelength-Scaled Array (WSA) Architecture (2010)

Wavelength-scaled array architectures use scaled elements to achieve ultrawideband performance with significantly fewer overall radiators than traditional ultrawideband arrays based on a single element type. Compared to a conventional ultrawideband array with 8:1 bandwidth, a wavelength-scaled array that uses elements of three different sizes creates an aperture with fewer than 16% of the original element count, i.e., 6.4-times fewer elements, and by extension a comparable reduction in electronics required to feed the array. In this paper, a study of an asymmetric wavelength-scaled array architecture is presented for finite arrays of offset-centered dual-polarized flared-notch radiators. The unique element transitions within the finite array structure are modeled via a non-matching grid Domain Decomposition-Finite Element Method that allows for rigorous impedance and radiation pattern prediction of full-sized wavelength-scaled arrays. This design study shows that the wavelength-scaled array has comparable performance to traditional ultrawideband arrays in terms of VSWR, radiation patterns, array mismatch efficiency, and cross-polarization levels.
Improving Parallel Write by Node-Level Request Scheduling (2009)

In a cluster of multiple processors or cpu-cores, many processes may run on each compute node. Each process tends to issue contiguous I/O requests for snapshot, checkpointing or so, however, if large number of processes enter the I/O phase at the same time, the requests from the same process may be interrupted by the requests of other processes. Then, the I/O nodes receive these requests as non-contiguous way. This interleaved access pattern causes performance degradation in parallel file systems. In order to overcome the problem, we have designed the gather-arrange-scatter (GAS) I/O architecture, for optimizing the parallel write performance. The GAS is an architecture for capturing write operations, buffering them in the memory, and scheduling them to reduce I/O cost at I/O nodes. The scheduling is done per compute node, and the requests are sent to the remote disks in parallel. In this paper, after introducing the GAS architecture in detail, its efficiency and scalability are evaluated using the NAS Parallel Benchmark BTIO. GAS is 5.2%faster than ROMIO collective I/O on PVFS2 in BTIO with 16 nodes/64 processes, and 34.9% faster than MPI noncollective I/O in the same configuration.
GluR2‐free α‐amino‐3‐hydroxy‐5‐methyl‐4‐isoxazolepropionate receptors intensify demyelination in experimental autoimmune encephalomyelitis (2007)

We adopted a genetic approach to test the importance of edited GluR2-free, Ca(2+)-permeable, alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionate (AMPA) receptors in the pathophysiology of experimental autoimmune encephalomyelitis, an inflammatory demyelinative disorder resembling multiple sclerosis. Initial studies showed that oligodendroglial lineage cells from mice lacking functional copies of the gene encoding the GluR3 AMPA receptor subunit (Gria3) had a diminished capacity to assemble edited GluR2-free AMPA receptors, and were resistant to excitotoxicity in vitro. Neurological deficits and spinal cord demyelination elicited by immunization with myelin oligodendrocyte glycoprotein peptide were substantially milder in these Gria3 mutant mice than in their wild-type littermates. These results support the hypothesis that oligodendroglial excitotoxicity mediated by AMPA receptors that do not contain edited GluR2 subunits contributes to demyelination in experimental autoimmune encephalomyelitis, and suggest that inhibiting these Ca(2+)-permeable AMPA receptors would be therapeutic in multiple sclerosis.
Phage release from biofilm and planktonic<i>Staphylococcus aureus</i>cells (2005)

The ability of pathogenic staphylococci to form biofilms facilitates colonization and the development of chronic infections. Therapy is hampered by the high tolerance of biofilms towards antibiotic treatment and the immune system. We found evidence that lysogenic Staphylococcus aureus cells in a biofilm and in planktonic cultures spontaneously release phages into their surroundings. Phages were detected over a much longer period in biofilm cultures than in planktonic supernatants because the latter were degraded by secreted proteases. Phage release in planktonic and biofilm cultures was artificially increased by adding mitomycin C. Two morphologically distinct phages in the S. aureus strain used in this work were observed by electron microscopy. We postulate that phage-release is a frequent event in biofilms. The resulting lysis of cells in a biofilm might promote the persistence and survival of the remaining cells, as they gain a nutrient reservoir from their dead and lysed neighboring cells. This might therefore be an early differentiation and apoptotic mechanism.
VGE - A Service-Oriented Grid Environment for On-Demand Supercomputing (2005)

In this paper, we present the Vienna Grid Environment, a service-oriented grid infrastructure based on standard Web services technologies. VGE automates the provision of HPC applications as grid services for on-demand super-computing and simplifies the construction of client-side applications. As a key distinguishing feature, VGE supports a flexible QoS negotiation model which enables clients to negotiate dynamically, and on a case-by-case basis, QoS guarantees on execution time and price with potential service providers. The VGE service provision framework is currently utilized in the context of the EU Project GEMSS, which focuses on the provision of advanced medical simulation services by means of a grid infrastructure.
Droop improvement in blue InGaN/GaN multiple quantum well light-emitting diodes with indium graded last barrier (2011)

Blue InGaN/GaN multiple quantum well light-emitting diodes with the conventional and graded last barriers (GLB) are numerically investigated. When the last GaN barrier is replaced by a linearly graded InxGa1 − xN barrier with increasing indium composition in the growth direction, the forward voltage is reduced from 3.60 V to 3.25 V, and the efficiency droop is improved from 36% to 13%. Simulation results indicate that these improvements can be attributed to the formation of a deep potential well in the GLB which enhances the electron confinement and improves the hole injection efficiency.
Evidence for the Presence of a Guanine Quadruplex Forming Region within a Polypurine Tract of the Hypoxia Inducible Factor 1α Promoter (2005)

The promoter of the hypoxia inducible factor 1 alpha (HIF-1alpha) gene has a polypurine/polypyrimidine tract (-65 to -85) overlapping or adjacent to several putative transcription factor binding sites, and we found that mutagenesis of this region diminished basal HIF-1alpha expression. Oligonucleotides representing this region of the HIF-1alpha promoter were analyzed by electrophoretic mobility shift, chemical probing, circular dichroism, and DNA polymerase arrest assays. The guanine-rich strand was found to form a parallel, unimolecular quadruplex in the presence of potassium that was further stabilized by two known quadruplex binding compounds, the cationic porphyrin TmPyP4 and the natural product telomestatin, while TmPyP2, a positional isomer of TmPyP4, did not stabilize quadruplex formation. These data suggest that a quadruplex structure may form in a region of the HIF-1alpha promoter that regulates basal HIF-1alpha expression.
Glucocorticoid receptor in prostate epithelia is not required for corticosteroid-induced epithelial hyperproliferation in the mouse prostate (2014)

Sustained administration of corticosterone induces prostate hyperplasia, which is mediated via GR expressed predominantly in the stroma. Thus GR mediated actions in the prostate may have significant cell-specific effects that could be utilized for more rational therapeutic approaches in prostate cancer treatment. This also illustrates the paracrine hormonal mechanisms in prostate pathophysiology.
Construction of a Fully Synthetic Human scFv Antibody Library with CDR3 Regions Randomized by a Split-Mix-Split Method and Its Application (2008)

The randomization scheme of hypervariable region takes crucial role in construction of a synthetic antibody library. The codon bias and inevitable 'stop' codon of conventional 'NNK' and 'NNS' codons limit their applications. Here we report a split-mix-split DNA synthesis method that can control over the amino acid composition and distribution of randomized sequences effectually. A fully synthetic human antibody library with a diversity of 1.56 x 10(9) was successfully generated with complementarity determining region 3 (CDR3) randomized by this strategy. Sequencing analysis indicated that >60% of colonies had completely correct scFv genes and the amino acid composition and distribution were designed well in accordance. The utility was demonstrated by screening of scFv clones against BHL (anti-CD3 x anti-ovarian carcinoma bispecific antibody). These results proved the feasibility of the split-mix-split DNA randomization strategy in library construction and site-directed mutagenesis.
The Value of the Designated Market Maker (2007)

Abstract The proliferation of electronic limit order books operating without dealers raises questions regarding the need for intermediaries with affirmative obligations to maintain markets. We develop a simple model of dealer participation and test it using a sample of less liquid firms that trade on the Paris Bourse. The results indicate that firms with designated dealers exhibit better market quality, and that younger firms, smaller firms, and less volatile firms choose a designated dealer. Around the announcement of dealer introduction, stocks experience an average cumulative abnormal return of nearly 5% that is positively correlated with improvements in liquidity. Overall, these findings emphasize the potential benefits of designing better market structures, even within electronic limit order books, and suggest that purely endogenous liquidity provision may not be optimal for all securities.
Cross-Modality Attention with Semantic Graph Embedding for Multi-Label Classification (2020)

Multi-label image and video classification are fundamental yet challenging tasks in computer vision. The main challenges lie in capturing spatial or temporal dependencies between labels and discovering the locations of discriminative features for each class. In order to overcome these challenges, we propose to use cross-modality attention with semantic graph embedding for multi-label classification. Based on the constructed label graph, we propose an adjacency-based similarity graph embedding method to learn semantic label embeddings, which explicitly exploit label relationships. Then our novel cross-modality attention maps are generated with the guidance of learned label embeddings. Experiments on two multi-label image classification datasets (MS-COCO and NUS-WIDE) show our method outperforms other existing state-of-the-arts. In addition, we validate our method on a large multi-label video classification dataset (YouTube-8M Segments) and the evaluation results demonstrate the generalization capability of our method.
Feature-based pronunciation modeling for speech recognition (2004)

We present an approach to pronunciation modeling in which the evolution of multiple linguistic feature streams is explicitly represented. This differs from phone-based models in that pronunciation variation is viewed as the result of feature asynchrony and changes in feature values, rather than phone substitutions, insertions, and deletions. We have implemented a flexible feature-based pronunciation model using dynamic Bayesian networks. In this paper, we describe our approach and report on a pilot experiment using phonetic transcriptions of utterances from the Switchboard corpus. The experimental results, as well as the model's qualitative behavior, suggest that this is a promising way of accounting for the types of pronunciation variation often seen in spontaneous speech.
Specific binding of estrogen receptor to the estrogen response element. (1989)

Gene transfer studies have shown that estrogen regulation of specific genes is mediated by estrogen response elements (ERE). We report that binding of the estrogen receptor to the ERE can be detected by a gel retardation (band shift) assay. This binding interaction was highly sequence and receptor specific. Methylation interference analysis showed that the ERE contact sites of estrogen receptor displayed a perfect twofold rotational symmetry. This is compatible with estrogen receptor binding to the ERE as a head-to-head dimer.
Atypical PKC ζ is activated by ceramide, resulting in coactivation of NF-κb/JNK kinase and cell survival (1999)

Both protein kinase C (PKC) and ceramide play a critical role in cell signaling, but the relationship between PKC and ceramide is unclear. Low concentrations of ceramide were observed to transiently stimulate PKC zeta activity in vitro and in vivo, whereas high doses of ceramide lead to inhibition of PKC zeta. Inhibition of activity was accompanied by enhanced binding of the negative regulator, Par4 to PKC zeta. Treatment of PC12 cells with low doses of ceramide promoted survival in serum-free media and activation of nuclear factor-KB, whereas higher doses (>2.5 microM) resulted in cell death. Overexpression of either aPKC isoform, PKC zeta or iota, resulted in enhanced survival of PC12 cells at high doses of ceramide and in ceramide-stimulated Jun N-terminal kinase (JNK), without any apparent effect on mitogen-activated kinase. These findings support a role for ceramide-induced PKC zeta activity in the control of cell survival signaling via a pathway that also activates JNK kinase.
Quality factors of MEMS gyros and the role of thermoelastic damping (2003)

In this paper, we present new experimental data illustrating the importance of thermoelastic damping in MEMS resonant sensors. We have used MEMS gyroscopes to demonstrate that both the choice of materials and variations in device design can lead to significant differences in the measured Quality (Q) factors of the device. These differences in Q factor can be explained by including the contribution of thermoelastic damping (TED), which varies strongly between the different silicon etch-stop compositions used in this study. Known damping mechanisms such as fluid damping, anchor damping, and electronics damping are minimized and held fixed in this experiment so that materials effects can be isolated.
Modeling Conflicts of Heterogeneous Traffic at Urban Uncontrolled Intersections (1998)

The behavior of traffic in the heterogeneous environment of an urban uncontrolled intersection is complex and difficult to model. The present study describes the methodology of simulating the traffic flow and thereby estimating the number of conflicts in varying traffic flow conditions. The arrival pattern of vehicles was represented by a multivariate distribution to generate input to the simulation model. The model was validated externally, using field observed data, and was found to predict the number of conflicts well. As an illustration of usefulness of the model, variation of conflict rate (the probability of a vehicle's getting involved in conflict) due to variation in traffic volume and the proportion of right-turning traffic has been quantified. Under the prevailing traffic composition and turning movements, the conflict rate is estimated to lie in the range of 0.66–0.70, 0.79–0.84, and 0.80–0.87 for intersection volumes of 2,000, 2,500, and 3,000 vehicles per hour, respectively. Issues related to the applicability of the proposed model are briefly discussed.
Interobserver and Intraobserver Reproducibility with Volume Dynamic Contrast Enhanced Computed Tomography (DCE-CT) in Gastroesophageal Junction Cancer (2016)

The purpose of this study was to assess inter- and intra-observer reproducibility of three different analytic methods to evaluate quantitative dynamic contrast-enhanced computed tomography (DCE-CT) measures from gastroesophageal junctional cancer. Twenty-five DCE-CT studies with gastroesophageal junction cancer were selected from a previous longitudinal study. Three radiologists independently reviewed all scans, and one repeated the analysis eight months later for intraobserver analysis. Review of the scans consisted of three analysis methods: (I) Four, fixed small sized regions of interest (2-dimensional (2D) fixed ROIs) placed in the tumor periphery, (II) 2-dimensional regions of interest (2D-ROI) along the tumor border in the tumor center, and (III) 3-dimensional volumes of interest (3D-VOI) containing the entire tumor volume. Arterial flow, blood volume and permeability (k(trans)) were recorded for each observation. Inter- and intra-observer variability were assessed by Intraclass Correlation Coefficient (ICC) and Bland-Altman statistics. Interobserver ICC was excellent for arterial flow (0.88), for blood volume (0.89) and for permeability (0.91) with 3D-VOI analysis. The 95% limits of agreement were narrower for 3D analysis compared to 2D analysis. Three-dimensional volume DCE-CT analysis of gastroesophageal junction cancer provides higher inter- and intra-observer reproducibility with narrower limits of agreement between readers compared to 2D analysis.