gebhart/patrepeval huggingface dataset:
Identification of an Atypical Grb2 Carboxyl-terminal SH3 Domain Binding Site in Gab Docking Proteins Reveals Grb2-dependent and -independent Recruitment of Gab1 to Receptor Tyrosine Kinases (2000)

The Gab family of docking proteins is phosphorylated in response to various growth factors and cytokines and serves to recruit multiple signaling proteins. Gab1 acts downstream from the Met-hepatocyte growth factor receptor, and Gab1 overexpression promotes Met-dependent morphogenesis of epithelial cells. Recruitment of Gab1 to Met or epidermal growth factor (EGF) receptors requires a receptor-binding site for the Grb2 adapter protein and a proline-rich domain in Gab1, defined as the Met-binding domain. To determine the requirement for Grb2 in Gab1 recruitment, we have mapped two Grb2 carboxyl-terminal SH3 domain binding sites conserved in Gab1 and related protein Gab2. One corresponds to a canonical Grb2-binding motif, whereas the second, located within the Gab1 Met-binding domain, requires the proline and arginine residues of an atypical PXXXR motif. The PXXXR motif is required but not sufficient for Grb2 binding, whereas an extended motif, PX3RX2KPX7PLD, conserved in Gab proteins as well as the Grb2/Gads-docking protein, Slp-76, efficiently competes binding of Grb2 or Gads adapter proteins. The association of Gab1 with Grb2 is required for Gab1 recruitment to the EGF receptor but not the Met receptor. Hence different mechanisms of Gab1 recruitment may reflect the distinct biological functions for Gab1 downstream from the EGF and Met receptors.
Characterization of cerebral hemodynamic phases following severe head trauma: hypoperfusion, hyperemia, and vasospasm (1997)

The extent and timing of posttraumatic cerebral hemodynamic disturbances have significant implications for the monitoring and treatment of patients with head injury. This prospective study of cerebral blood flow (CBF) (measured using 133Xe clearance) and transcranial Doppler (TCD) measurements in 125 patients with severe head trauma has defined three distinct hemodynamic phases during the first 2 weeks after injury. The phases are further characterized by measurements of cerebral arteriovenous oxygen difference (AVDO[2]) and cerebral metabolic rate of oxygen (CMRO[2]). Phase I (hypoperfusion phase) occurs on the day of injury (Day 0) and is defined by a low CBF calculated from cerebral clearance curves integrated to 15 minutes (mean CBF 32.3 +/- 2 ml/100 g/minute), normal middle cerebral artery (MCA) velocity (mean V[MCA] 56.7 +/- 2.9 cm/second), normal hemispheric index ([HI], mean HI 1.67 +/- 0.11), and normal AVDO(2) (mean AVDO[2] 5.4 +/- 0.5 vol%). The CMRO, is approximately 50% of normal (mean CMRO(2) 1.77 +/- 0.18 ml/100 g/minute) during this phase and remains depressed during the second and third phases. In Phase II (hyperemia phase, Days 1-3), CBF increases (46.8 +/- 3 ml/100 g/minute), AVDO(2) falls (3.8 +/- 0.1 vol%), V(MCA) rises (86 +/- 3.7 cm/second), and the HI remains less than 3 (2.41 +/- 0.1). In Phase III (vasospasm phase, Days 4-15), there is a fall in CBF (35.7 +/- 3.8 ml/100 g/minute), a further increase in V(MCA) (96.7 +/- 6.3 cm/second), and a pronounced rise in the HI (2.87 +/- 0.22). This is the first study in which CBF, metabolic, and TCD measurements are combined to define the characteristics and time courses of, and to suggest etiological factors for, the distinct cerebral hemodynamic phases that occur after severe craniocerebral trauma. This research is consistent with and builds on the findings of previous investigations and may provide a useful temporal framework for the organization of existing knowledge regarding posttraumatic cerebrovascular and metabolic pathophysiology.
Estimating effective population size or mutation rate using the frequencies of mutations of various classes in a sample of DNA sequences. (1994)

Mutations resulting in segregating sites of a sample of DNA sequences can be classified by size and type and the frequencies of mutations of different sizes and types can be inferred from the sample. A framework for estimating the essential parameter theta = 4Nu utilizing the frequencies of mutations of various sizes and types is developed in this paper, where N is the effective size of a population and mu is mutation rate per sequence per generation. The framework is a combination of coalescent theory, general linear model and Monte-Carlo integration, which leads to two new estimators theta xi and theta eta as well as a general Watterson's estimator theta K and a general Tajima's estimator theta tau. The greatest strength of the framework is that it can be used under a variety of population models. The properties of the framework and the four estimators theta K, theta tau, theta xi and theta eta are investigated under three important population models: the neutral Wright-Fisher model, the neutral model with recombination and the neutral Wright's finite-islands model. Under all these models, it is shown that theta xi is the best estimator among the four even when recombination rate or migration rate has to be estimated. Under the neutral Wright-Fisher model, it is shown that the new estimator theta xi has a variance close to a lower bound of variances of all unbiased estimators of theta which suggests that theta xi is a very efficient estimator.
An Architecture for Object Replication in Distributed Systems (1996)

In this paper we present an architecture for developing replicated objects in object oriented distributed systems. The architecture is however general and the concepts can be adapted to non-object oriented distributed systems. The architecture specifies the main requirements for developing replicated objects in distributed systems, namely: the replicated object representation, the replicated object development and management mechanism, and the replica consistency protocol. For achieving these requirements the architecture specifies a hierarchy of objects and the inheritance and functional relationship among these objects. All the management functions of replicated objects are encapsulated in a manager object. An application object inherits these functionalities from the manager object. This object replication architecture will greatly reduce the complexity of the development of replicated objects in distributed systems. We also developed an efficient replica consistency algorithm that ...
XSLT and XPath Optimization (2004)

Recent releases of Saxon support XQuery 1.0 as well as XSLT 2.0. However, the XQuery processor is an in-memory processor, not a database query engine. Optimizing database queries is an entirely different art, because it relies so heavily on rearranging queries to exploit persistent indexes. An in-memory processor does not have this opportunity, because the only indexes available are those that are constructed transiently for the duration of a transformation or query.
Decoding the Complex Free Radical Cascade by Using a DNA Framework‐Based Artificial DNA Encoder (2021)

DNA-based molecular communications (DMC) are critical for regulating biological networks to maintain stable organismic functions. However, the complicated, time-consuming information transmission process involved in genome-coded DMC and the limited, vulnerable decoding activity generally lead to communication impairment or failure, in response to external stimuli. Herein, we present a conceptually innovative DMC strategy mediated by the DNA framework-based artificial DNA encoder. With the free-radical cascade as a proof-of-concept study, the artificial DNA encoder shows active sensing and real-time actuation, in situ and broad free radical-decoding efficacy, as well as robust resistance to environmental noise. It can also block undesirable short-to-medium-range communications between free radicals and inflammatory networks, leading to a synergistic anti-obesity effect. The artificial DNA encoder-based DMC may be generalized to other communication systems for a variety of applications.
Ultrasonic locating devices for central venous cannulation: meta-analysis (2003)

Evidence supports the use of two dimensional ultrasonography for central venous cannulation.
Dosimetry of 131I-labeled 81C6 monoclonal antibody administered into surgically created resection cavities in patients with malignant brain tumors. (1999)

At the maximum tolerated dose of 3700 MBq 131I-labeled 81C6 MAb, the absorbed doses to the SCRC interface and ROIs of 1 and 2 cm thickness were estimated to be 1180, 71 and 39 Gy, respectively. The estimated average absorbed dose to the brain was 6.5 Gy. There was no neurological toxicity and minimal hematologic toxicity at this maximum tolerated administration level.
Exploiting Linear Structure Within Convolutional Networks for Efficient Evaluation (2014)

We present techniques for speeding up the test-time evaluation of large convolutional networks, designed for object recognition tasks. These models deliver impressive accuracy but each image evaluation requires millions of floating point operations, making their deployment on smartphones and Internet-scale clusters problematic. The computation is dominated by the convolution operations in the lower layers of the model. We exploit the linear structure present within the convolutional filters to derive approximations that significantly reduce the required computation. Using large state-of-the-art models, we demonstrate we demonstrate speedups of convolutional layers on both CPU and GPU by a factor of 2x, while keeping the accuracy within 1% of the original model.
Adaptive correction of deterministic models to produce probabilistic forecasts (2012)

Abstract. This paper considers the correction of deterministic forecasts given by a flood forecasting model. A stochastic correction based on the evolution of an adaptive, multiplicative, gain is presented. A number of models for the evolution of the gain are considered and the quality of the resulting probabilistic forecasts assessed. The techniques presented offer a computationally efficient method for providing probabilistic forecasts based on existing flood forecasting system output.
Comparative study of papaverine plus phentolamine versus prostaglandin E1 in erectile dysfunction. (1997)

One ml. 30 mg./ml. papaverine plus 0.5 mg./ml. phentolamine has the same efficacy and equal prolonged erection rate as 1 ml. 30 micrograms./ml. prostaglandin E1 but the latter agent induces significantly more pain.
Solid-state vibrational spectroscopy. Part IV. A vibrational and differential scanning calorimetry study of the polymorphism of sodium and potassium sulphates (1975)

The polymorphism of sodium and potassium sulphates has been studied using differential scanning calorimetry (d.s.c.) and vibrational spectroscopy. For Na2[SO4] the d.s.c. study has yielded enthalpy changes for the various phase transitions. The polymorphs have distinct Raman spectra whereas the i.r. spectra do not show such distinct differences. The phase-transition temperature of K2[SO4] is outside the range of the d.s.c. instrument, but the vibrational spectra indicate that K2[SO4], unlike Na2[SO4], does not exist in a metastable phase on cooling below the transition temperature.
Hypermethylation of the <i>TSLC1</i> Gene Promoter in Primary Gastric Cancers and Gastric Cancer Cell Lines (2002)

The TSLC1 (tumor suppressor in lung cancer-1) gene is a novel tumor suppressor gene on chromosomal region 11q23.2, and is frequently inactivated by concordant promoter hypermethylation and loss of heterozygosity (LOH) in non-small cell lung cancer (NSCLC). Because LOH on 11q has also been observed frequently in other human neoplasms including gastric cancer, we investigated the promoter methylation status of TSLC1 in 10 gastric cancer cell lines and 97 primary gastric cancers, as well as the corresponding non-cancerous gastric tissues, by bisulfite-SSCP analysis followed by direct sequencing. Allelic status of the TSLC1 gene was also investigated in these cell lines and primary gastric cancers. The TSLC1 promoter was methylated in two gastric cancer cell lines, KATO-III and ECC10, and in 15 out of 97 (16%) primary gastric cancers. It was not methylated in non-cancerous gastric tissues, suggesting that this hypermethylation is a cancer-specific alteration. KATO-III and ECC10 cells retained two alleles of TSLC1, both of which showed hypermethylation, associated with complete loss of gene expression. Most of the primary gastric cancers with promoter methylation also retained heterozygosity at the TSLC1 locus on 11q23.2. These data indicate that bi-allelic hypermethylation of the TSLC1 promoter and resulting gene silencing occur in a subset of primary gastric cancers.
Lymphangiogenesis in tumors: What do we know? (2003)

Lymphangiogenesis, the growth of new lymphatic vessels, has long been regarded as a putative efficient pathway to neoplastic metastization. However, until recently consistent data regarding reliable lymphatic endothelial cell markers were lacking. Moreover, the presence of new formed lymphatic vessels was considered a largely disputable concept. Now, this scenario has changed significantly, owing to consistent reports describing novel lymphatic endothelial cell (LEC) markers, the demonstration of new formed lymphatic vessels within the bulk of the tumor in animal models and human neoplasms, and the characterization of the VEGF-C/VEGFR-3 pathway. We herein review the major breakthroughs in the field of lymphangiogenesis, with special emphasis on novel and reliable LEC markers, such as prox-1, LYVE-1, and podoplanin, as well as on the pathological assessment of lymphangiogenesis as a putative prognostic factor for human neoplasms.
Oligonucleotide probes based on 16S rRNA sequences for the identification of four <i>Azospirillum</i> species (1995)

Partial sequences of the 16S rRNA molecules of nine strains belonging to four Azospirillum species were used to design species-specific oligonucleotide probes. Azospirillum strains sequences were analyzed and three homologous fragments containing 16 nucleotides were determined. These three probes were found to be characteristic of A. lipoferum (Al), A. irakense (Ai), and A. brasilense/amazonense species (Aba) and of few nontarget organisms. The specificity of these three probes was tested both against sequences in the GenBank data base and in numerous colony hybridization experiments. As a few non-target organisms hyridized with the different Azospirillum probes, the use of these probes in bulk soil hybridization is not permitted. However, their use together with specific isolation techniques is validated.
Heterogeneous Silicon III-V Photonic Integrated Circuits (2015)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text J. Bowers, "Heterogeneous Silicon III-V Photonic Integrated Circuits," in Optical Fiber Communication Conference, OSA Technical Digest (online) (Optica Publishing Group, 2015), paper W1B.1. Export Citation BibTex Endnote (RIS) HTML Plain Text Get Video Citation alert Save article
Effect of Planting Density on the Growth and Yield of Ligusticum chuanxiong Hort. (1994)

This experiment was conducted to study the effect of growth characteristics and yield by different planting density on Ligusticum chuanxiong Hort.Number of stem, leaf and branch on main stem were plant reduced by increasing the plant density. Stem height was showed the highest at planting density, but diameter did not show significant difference at different planting density. Stem number in of field area showed negative correlation with leaf number and branch number on main stem. The height of first branched node became longer by increasing stem number, leaf number and branch number on stem in of field area. Rhizome yield showed negative correlation with stem number and leaf number per plant, but showed positive with stem number in of field area leaf number and branch number of main stem. Root and rhizome weight per plant decreased by increasing planting density, but root and rhizome yield in of field area were increased by high planting density.
TAPRAV: An interactive analysis tool for exploring workload aligned to models of task execution (2007)

Pupillary response is a valid indicator of mental workload and is being increasingly leveraged to identify lower cost moments for interruption, evaluate complex interfaces, and develop further understanding of psychological processes. Existing tools are not sufficient for analyzing this type of data, as it typically needs to be analyzed in relation to the corresponding task’s execution. To address this emerging need, we have developed a new interactive analysis tool, TAPRAV. The primary components of the tool include; (i) a visualization of pupillary response aligned to the corresponding model of task execution, useful for exploring relationships between these two data sources; (ii) an interactive overview + detail metaphor, enabling rapid inspection of details while maintaining global context; (iii) synchronized playback of the video of the user’s screen interaction, providing awareness of the state of the task; and (iv) interaction supporting discovery driven analysis. Results from a user study showed that users are able to efficiently interact with the tool to analyze relationships between pupillary response and task execution. The primary contribution of our tool is that it demonstrates an effective visualization and interaction design for rapidly exploring pupillary response in relation to models of task execution, thereby reducing the analysis effort.
Effect of temperature variation during post exposure bake on 193 nm chemically amplified resist simulation (2002)

We measured the temperature change of 193 nm chemically amplified resist during post exposure bake and investigated the effects of these variations on photoresist (PR) simulation. The effects of the variations were studied for various baking and cooling methods. The effective PEB time was determined by considering the temperature variation during PEB. The effective PEB times were used in simulation and the resulting PR profiles were compared with the experimental results. The resulting profiles showed a significant variation in line width depending on bake conditions. Careful PEB temperature consideration is necessary since the resulting line width is strongly dependent on the resist temperature rising and cooling rate. The effective bake time with proper consideration of the temperature change during PEB should be used in the simulation to depict experimental profile correctly.
[Use of biomanagement methods to combined medical rehabilitation of patients with hypertensive disease]. (2009)

The biomanagement technique finds wide application in practical medicine, e.g. in rehabilitation of patients with psychosomatic pathology. Results of combined rehabilitative treatment with the use of bioacoustic psychocorrection was assessed in patients with hypertensive disease. It was shown that normalization of CNS functional state by means of bioacoustic psychocorrection improves vegetative regulation of cardiovascular activity, corrects AP, reduces its variability and the degree of nocturnal fall, decreases peripheral vascular resistance, and increases efficiency of rehabilitative treatment.
Infrared Luminescence from Bismuth-Doped Silica Glass (2001)

A new infrared luminescence from bismuth-doped silica glass is discovered. Spectroscopic properties of this glass are different from those of previously reported Bi 2+ - or Bi 3+ -doped glasses or crystals. Its luminescence spectrum is wide (full-width at half maximum; about 200 nm), with the peak at 1140 nm with 500 nm excitation. Absorption bands exist between the visible and near-infrared region. The lifetime of bismuth-doped silica glass is 630 µs at room temperature, which is longer than the lifetimes of Bi 3+ luminescence reported previously.
Calgranulin expression in inflammatory dermatoses (1989)

We have used monoclonal antibodies to study the expression of calgranulins by keratinocytes in inflammatory dermatoses. Calgranulins are intracellular calcium binding proteins which have inflammatory cytokine activity and are composed of at least two different chains, calgranulin A and B. Antibody CF 145 and CF 557 identify calgranulin A and B, respectively. MAC 387 recognizes a molecule probably containing both calgranulins. Keratinocytes in normal skin did not contain these molecules. The keratinocytes in 52 cases of different inflammatory dermatoses showed expression of both calgranulin chains in lesional but not in non-lesional skin. Keratinocytes in inflammatory dermatoses therefore express an intracellular calcium binding protein which has cytokine activity.
Mechanisms of HDA6-mediated rRNA gene silencing: suppression of intergenic Pol II transcription and differential effects on maintenance versus siRNA-directed cytosine methylation (2010)

The Arabidopsis histone deacetylase HDA6 is required to silence transgenes, transposons, and ribosomal RNA (rRNA) genes subjected to nucleolar dominance in genetic hybrids. In nonhybrid Arabidopsis thaliana, we show that a class of 45S rRNA gene variants that is normally inactivated during development fails to be silenced in hda6 mutants. In these mutants, symmetric cytosine methylation at CG and CHG motifs is reduced, and spurious RNA polymerase II (Pol II) transcription occurs throughout the intergenic spacers. The resulting sense and antisense spacer transcripts facilitate a massive overproduction of siRNAs that, in turn, direct de novo cytosine methylation of corresponding gene sequences. However, the resulting de novo DNA methylation fails to suppress Pol I or Pol II transcription in the absence of HDA6 activity; instead, euchromatic histone modifications typical of active genes accumulate. Collectively, the data reveal a futile cycle of unregulated transcription, siRNA production, and siRNA-directed DNA methylation in the absence of HDA6-mediated histone deacetylation. We propose that spurious Pol II transcription throughout the intergenic spacers in hda6 mutants, combined with losses of histone deacetylase activity and/or maintenance DNA methylation, eliminates repressive chromatin modifications needed for developmental rRNA gene dosage control.
Local degradation of selectively oxidized AlGaAs/AlAs distributed Bragg reflectors in lateral-injection vertical-cavity surface-emitting lasers (2000)

We show the local degradation of a selectively oxidized top distributed Bragg reflector (DBR) in a lateral-junction vertical-cavity surface-emitting laser (LJ-VCSEL) working at room temperature in continuous-wave operation. The measurements were carried out by a scanning microluminescence system used in reflection mode. The injection of a few milliamps in continuous-wave operation at room temperature in the LJ-VCSEL induces damage both in the DBRs and in the active area. The submicron resolution maps of the reflected laser intensity, recorded from the top surface of the LJ-VCSEL, show a strong local change in the top DBR reflectivity before and after current injection. The μ-photoluminescence map, recorded after the device failure, shows that the radiative recombination is strongly decreased in the damaged area of the device.