gebhart/patrepeval huggingface dataset:
Regulation of the calcitonin/calcitonin gene-related peptide gene by cell-specific synergy between helix-loop-helix and octamer-binding transcription factors (1993)

The calcitonin/calcitonin gene-related peptide (CGRP) gene is transcribed in thyroid C-cells and a subset of neurons. We have localized sequences required for cell-specific enhancement of calcitonin/CGRP transcription in rat thyroid C-cell lines. An 18-base pair element approximately 1 kilobase pair upstream of the transcriptional start site stimulated expression of a luciferase reporter gene 50-fold in 44-2C C-cells. There was less than 2-fold stimulation in HeLa and Rat-1 cells, which do not express the endogenous calcitonin/CGRP gene. The enhancer contains potential binding sites for helix-loop-helix (HLH) and octamer transcription factors based on sequence homologies. The functional significance of these sites was shown by point mutations in the HLH and octamer motifs and by separation of the two motifs, all of which decreased enhancer activity greater than 10-fold. The involvement of HLH proteins was further shown by co-expression of the mammalian achaete-scute homologue-1 HLH protein, which activated the enhancer severalfold in HeLa cells. Electrophoretic mobility shift analyses revealed several DNA-protein complexes containing HLH and octamer-binding proteins. One octamer-binding complex (OB1) most likely contains the ubiquitous Oct-1 protein, whereas a second complex (OB2) was cell-specific. In contrast to OB1, OB2 had lower affinity for a consensus octamer motif, and its DNA binding was not affected by addition of antiserum that recognizes Oct-1 and Oct-2 proteins. In addition, we observed a large complex that appears to contain both an HLH protein and OB2. These results demonstrate that calcitonin/CGRP enhancer activity is controlled by a cell-specific synergistic activation involving HLH and octamer-binding factors.
Engineered Pullulan–Collagen Composite Dermal Hydrogels Improve Early Cutaneous Wound Healing (2010)

New strategies for skin regeneration are needed to address the significant medical burden caused by cutaneous wounds and disease. In this study, pullulan-collagen composite hydrogel matrices were fabricated using a salt-induced phase inversion technique, resulting in a structured yet soft scaffold for skin engineering. Salt crystallization induced interconnected pore formation, and modification of collagen concentration permitted regulation of scaffold pore size. Hydrogel architecture recapitulated the reticular distribution of human dermal matrix while maintaining flexible properties essential for skin applications. In vitro, collagen hydrogel scaffolds retained their open porous architecture and viably sustained human fibroblasts and murine mesenchymal stem cells and endothelial cells. In vivo, hydrogel-treated murine excisional wounds demonstrated improved wound closure, which was associated with increased recruitment of stromal cells and formation of vascularized granulation tissue. In conclusion, salt-induced phase inversion techniques can be used to create modifiable pullulan-collagen composite dermal scaffolds that augment early wound healing. These novel biomatrices can potentially serve as a structured delivery template for cells and biomolecules in regenerative skin applications.
BK Polyomavirus Genotypes Represent Distinct Serotypes with Distinct Entry Tropism (2013)

BK polyomavirus (BKV) causes significant urinary tract pathogenesis in immunosuppressed individuals, including kidney and bone marrow transplant recipients. It is currently unclear whether BKV-neutralizing antibodies can moderate or prevent BKV disease. We developed reporter pseudoviruses based on seven divergent BKV isolates and performed neutralization assays on sera from healthy human subjects. The results demonstrate that BKV genotypes I, II, III, and IV are fully distinct serotypes. While nearly all healthy subjects had BKV genotype I-neutralizing antibodies, a majority of subjects did not detectably neutralize genotype III or IV. Surprisingly, BKV subgenotypes Ib1 and Ib2 can behave as fully distinct serotypes. This difference is governed by as few as two residues adjacent to the cellular glycan receptor-binding site on the virion surface. Serological analysis of mice given virus-like particle (VLP)-based BKV vaccines confirmed these findings. Mice administered a multivalent VLP vaccine showed high-titer serum antibody responses that potently cross-neutralized all tested BKV genotypes. Interestingly, each of the neutralization serotypes bound a distinct spectrum of cell surface receptors, suggesting a possible connection between escape from recognition by neutralizing antibodies and cellular attachment mechanisms. The finding implies that different BKV genotypes have different cellular tropisms and pathogenic potentials in vivo. Individuals who are infected with one BKV serotype may remain humorally vulnerable to other BKV serotypes after implementation of T cell immunosuppression. Thus, prevaccinating organ transplant recipients with a multivalent BKV VLP vaccine might reduce the risk of developing posttransplant BKV disease.
Immunoreactive prostate‐specific antigen in lung tumors (1995)

Prostate-specific antigen (PSA) is a glycoprotein produced by the epithelial cells of the prostate. PSA is currently used clinically to diagnose and monitor prostate carcinoma. In previous work we have demonstrated that 30% of breast tumors and, more rarely other tumors, contain significant amounts of PSA. PSA appears to be a favorable prognostic indicator in breast cancer. Here, using a sensitive assay, we demonstrated for the first time that lung adenocarcinomas and squamous cell carcinomas also contain PSA. PSA in lung tumor extracts was present mainly in its 33 KDa form (free PSA), at levels measurable by commercial methods. The presence of PSA was associated more closely with male patients and adenocarcinomas. The physiological role of PSA in lung tissue and the prognostic significance of PSA in lung cancer remain to be determined. These and our previous data as well as reports by other groups support the view that PSA is a ubiquitous biochemical marker of steroid hormone action.
In-Situ Diagnosis of Formation Characteristics in Horizontal Wells (2003)

Abstract We present a method of estimating the distribution of permeability along the length of a liner-completed horizontal well from measurements of well flowing pressure at multiple points along the path of flow in the wellbore. We do not model the deployment mechanism of the sensors, although in principle this can be achieved with stinger completions. The method applies to flow under constant-rate conditions and yields estimates of permeability along well trajectory in the principal directions normal to well path. Therefore, estimates of horizontal permeability perpendicular to well orientation and vertical permeability can be obtained for the gridblocks intersected by the well. Estimation accuracy, however, improves when the geometric mean of the normal permeabilities is obtained, as opposed to their individual values. This permeability group is what governs the influx into the wellbore. We neglect the effect of skin, but the method can be used to invert for a piecewise well index coefficient, that is proportional to the permeability group and inversely proportional to skin. Therefore, the method can generate the longitudinal profile of a parametric group that represents the quality of the formation and the integrity of completion. The quality of the inversion is governed by the spatial density of measurements, accuracy of measurements, knowledge of wellbore hydraulics, and knowledge of the relative permeability characteristics of the formation. We obtain fair estimation of wellbore-gridblock permeability distribution for a five-node pressure configuration in a 2000 ft horizontal well experiencing 60 psi pressure drop (10,000 STB/day), given realistic bands of uncertainty associated with the governing parameters, including measurement drift, and errors in liner roughness, and relative permeability exponent. Also, the inversion can be rendered insensitive to knowledge of the reservoir permeability field through a far-field scaling technique. Therefore, good estimates of the near-wellbore permeability profile can be obtained with highly uncertain knowledge of the reservoir permeability field. This is important as the technique can be applied not only to early-time but also late-time data. We illustrate the application of the multipoint pressure method through a series of examples and discuss its potential as an interventionless method of well diagnosis, for estimation of both flux and permeability distribution in high-angle completions.
Stimulation of Collagen Synthesis by Insulin and Proteoglycan Accumulation by Ascorbate in Bovine Keratocytes In Vitro (2006)

The results of this study indicate that the accumulation of lumican and keratocan depends in part on the level of collagen synthesis and its hydroxylation. The interaction of lumican and keratocan with the stably folded triple helix provided by hydroxylation may also serve to stabilize these proteoglycans.
Simultaneous Enhancement of Thermostability and Catalytic Activity of Phospholipase A <sub>1</sub> by Evolutionary Molecular Engineering (2000)

The thermal stability and catalytic activity of phospholipase A(1) from Serratia sp. strain MK1 were improved by evolutionary molecular engineering. Two thermostable mutants were isolated after sequential rounds of error-prone PCR performed to introduce random mutations and filter-based screening of the resultant mutant library; we determined that these mutants had six (mutant TA3) and seven (mutant TA13) amino acid substitutions. Different types of substitutions were found in the two mutants, and these substitutions resulted in an increase in nonpolar residues (mutant TA3) or in differences between side chains for polar or charged residues (mutant TA13). The wild-type and mutant enzymes were purified, and the effect of temperature on the stability and catalytic activity of the enzymes was investigated. The melting temperatures of the TA3 and TA13 enzymes were increased by 7 and 11 degrees C, respectively, compared with the melting temperature of the wild-type enzyme. Thus, we found that evolutionary molecular engineering was an effective and efficient approach for increasing thermostability without compromising enzyme activity.
Fungicidal Activity of Plant Saponin CAY-1 for Fungi Isolated from Diseased<i>Vitis</i>Fruit and Stems (2008)

Members of 10 fungal genera were isolated from diseased grape berries and stems collected in a local vineyard. These fungi were identified as <i>Alternaria</i> sp.<i>, Aspergillus japonicus, Cladosporium cladosporioides</i>, <i>Colletotrichum</i> sp., <i>Curvularia brachyspora</i>, <i>Epicoccum purpurascens, Greeneria uvicola, Nigrospora sphaerica, Trichoderma</i> sp., <i>Penicillium sclerotiorum</i> and <i>P. thomii</i>. CAY-1, a fungicidal saponin in cayenne pepper (<i>Capsicum frutescens</i>) was significantly (<i>p</i> ≤ 0.05) lethal to the germinating (incubated 8 hr) but not the nongerminated (0 hr incubation) conidia of all the fungi except <i>Alternaria</i> and <i>E. purpurascens</i> at concentrations greater than 7.5 μM. CAY-1 was ineffective against the conidia of all the isolated fungi incubated 24 hr prior to mixing with the saponin. Results show that, in vitro, CAY-1 is lethal to these fungi only during their early germination cycle.
A Hybrid Magnetostrictive Propellant Management Device for Active Slosh Damping in Spacecraft (2015)

This disclosure includes a hybrid magneto-active membrane, which can be used as part of a Magneto-active Propellant Management Device (MAPMD), to actively control free surface effects of liquid materials, such as fuels, and to reduce fuel slosh. The disclosed MAPMD merges aspects of a diaphragm membrane with a magneto-active inlay to control the membrane during in-flight conditions.
Model for gain dynamics inerbium-doped fibre amplifiers (1996)

A simple model is presented for characterising the dynamic gain of an erbium-doped fibre amplifier (EDFA). The time dependent gain is described by a single ordinary differential equation for an EDFA with arbitrary number of signal channels with arbitrary power levels and propagation directions. The simulation results agree with experimental data.
FakeNewsNet: A Data Repository with News Content, Social Context, and Spatiotemporal Information for Studying Fake News on Social Media (2020)

Social media has become a popular means for people to consume and share the news. At the same time, however, it has also enabled the wide dissemination of <i>fake news</i>, that is, news with intentionally false information, causing significant negative effects on society. To mitigate this problem, the research of fake news detection has recently received a lot of attention. Despite several existing computational solutions on the detection of fake news, the lack of comprehensive and community-driven fake news data sets has become one of major roadblocks. Not only existing data sets are scarce, they do not contain a myriad of features often required in the study such as <i>news content</i>, <i>social context</i>, and <i>spatiotemporal information</i>. Therefore, in this article, to facilitate fake news-related research, we present a fake news data repository <i>FakeNewsNet</i>, which contains two comprehensive data sets with diverse features in <i>news content</i>, <i>social context</i>, and <i>spatiotemporal information</i>. We present a comprehensive description of the FakeNewsNet, demonstrate an exploratory analysis of two data sets from different perspectives, and discuss the benefits of the FakeNewsNet for potential applications on fake news study on social media.
Effect of charge and aerodynamic properties of particles on electrified fabric filtration (1985)

An electrical-single particle aerodynamic relaxation time (E-SPART) analyzer employs a laser Doppler velocimeter for measuring motion of charged particles in an applied oscillatory electric field in order to simultaneously measure the aerodynamic diameter and electrostatic charge on a single particle. A modification has been made to incorporate both acoustic excitation and a DC electric field for simultaneous measurement of the aerodynamic diameter and electrical charge of particles so that measurement of particle size is possible even for uncharged particles. Other modifications include use of a frequency counting technique for measuring the drift velocity of the particle, thereby determining the particle charge, use of a Millikan apparatus only for calibrating electrical charge above q = 4, and optimization of the operation of the aerosol generator and an electrostatic charger for calibration. The analyzer optics are being modified for determining particle size down to 0.1 microns in diameter. Experimental data on particle size and charge measurement obtained after stabilizing the operating temperature of the phase locked loop demodulator are presented. (LEW)
ChemInform Abstract: Selective Catalytic Oxidation of Glycerol: Perspectives for High Value Chemicals (2011)

Abstract Review: 96 refs.
SPAACE IV: Self-Properties for an Autonomous &#x00026; Autonomic Computing Environment &#150; Part IV A Newish Hope (2010)

Self-* properties, or ¿selfware¿, refers to current and emerging behaviours exhibited by systems that are considered to be ¿autonomic¿ or inspired by another view of self-management. We describe some emerging properties, which may range from self-adjusting to self-destruction. We describe the architecture required to create self-ware and discuss the relationship between autonomicity and autonomicity, and document some additional autonomic constructs inspired for next generation Space Exploration Systems.
Calf Bioimpedance Spectroscopy for Determination of Dry Weight in Hemodialysis Patients: Effects on Hypertension and Left Ventricular Hypertrophy (2013)

We conclude that attainment of dry weight assessed by cBIS tends to reduce left ventricular mass and blood pressure while antihypertensive medication remains unchanged. While the study was underpowered, its results provide an important hypothesis generating data basis for the design of larger studies.
A preliminary transcriptome map of non-small cell lung cancer. (2002)

We constructed a genome-wide transcriptome map of non-small cell lung carcinomas based on gene-expression profiles generated by serial analysis of gene expression (SAGE) using primary tumors and bronchial epithelial cells of the lung. Using the human genome working draft and the public databases, 25,135 nonredundant UniGene clusters were mapped onto unambiguous chromosomal positions. Of the 23,056 SAGE tags that appeared more than once among the nine SAGE libraries, 11,156 tags representing 7,097 UniGene clusters were positioned onto chromosomes. A total of 43 and 55 clusters of differentially expressed genes were observed in squamous cell carcinoma and adenocarcinoma, respectively. The number of genes in each cluster ranged from 18 to 78 in squamous cell carcinomas and from 20 to 165 in adenocarcinomas. The size of these clusters varied from 1.8 Mb to 65.5 Mb in squamous cell carcinomas and from 1.6 Mb to 98.1 Mb in adenocarcinomas. Overall, the clusters with genes over-represented in tumors had an average of 3-4-fold increase in gene expression compared with the normal control. In contrast, clusters of genes with reduced expression had about 50-65% of the gene expression level compared with the normal. Examination of clusters identified in squamous cell lung cancer suggested that 9 of 15 clusters with overexpressed genes and 13 of 28 clusters with underexpressed genes were concordant with previously reported cytogenetic, comparative genomic hybridization or loss of heterozygosity studies. Therefore, at least a portion of the gene clusters identified via the transcriptome map most likely represented the transcriptional or genetic alterations occurred in the tumors. Integrating chromosomal mapping information with gene expression profiles may help reveal novel molecular changes associated with human lung cancer.
Formation and magnetic properties of Fe-B-Si amorphous alloys (1979)

The magnetic properties and crystallization temperatures of alloys in the ternary Fe-B-Si system are reported. The Curie temperature increases slightly on replacement of boron by silicon. This results in a sharp ridge of relatively constant room-temperature saturation magnetization extending from Fe <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">80</inf> B <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">20</inf> to Fe <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">82</inf> B <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">12</inf> Si <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</inf> . The coercivity exhibits a broad minimum, both before and after stress relief annealing, in the region around Fe <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">81</inf> B <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">15</inf> Si <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</inf> and extending at least to Fe <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">77</inf> B <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">13</inf> Si <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">10</inf> . The crystallization temperature increases with increasing silicon and with decreasing iron and boron. The alloys with silicon are generally easier to prepare in the amorphous state than the binary Fe-B alloys. Thus for the highest saturation magnetization alloy combined with ease of preparation, stability, and lowest losses, the alloys between Fe <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">81</inf> B <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">17</inf> Si <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> and Fe <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">82</inf> B <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">12</inf> Si <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</inf> are preferred.
A machine learning based demand charge management solution (2017)

In contrast with battery storages installed by distribution network operators (DNOs) which are responsible to shave the daily peaks, behind the meter energy managements systems (BTM-EMSs) are mostly installed by the commercial/industrial units to minimize the maximum demand peak over a billing period. Therefore, the daily optimization frameworks used in DNO side battery storages could not be applied to control BTM battery storages due to unnecessary degradation of the battery storages. As an alternative, two-layer control frameworks could be applied in BTM applications in which the minimum achievable of the maximum peak value in the next month (called demand charge threshold (DCT)) is determined in the monthly layer, and the daily layer schedules battery charge and discharge to realize the predetermined DCT. However, the unpredicted behavior of individual electricity loads in coming month casts a shadow over the functionality of such two layer demand charge management solutions(DCMS). In this paper, a novel two-layer DCMS is proposed in which, the monthly layer forecasts the near optimal DCT value for the next month based on the behavior of the load DCT values in the last few months. In the absence of the long history of the load profile, the similar DCT profiles of the other loads available in the data set are used to construct the DCT forecast model. The efficiency of the proposed approach is validated through the simulation studies on the real value load data.
Active zone protein CAST is a component of conventional and ribbon synapses in mouse retina (2006)

CAST is a novel cytomatrix at the active zone (CAZ)-associated protein. In conventional brain synapses, CAST forms a large molecular complex with other CAZ proteins, including RIM, Munc13-1, Bassoon, and Piccolo. Here we investigated the distribution of CAST and its structurally related protein, ELKS, in mouse retina. Immunofluorescence analyses revealed that CAST and ELKS showed punctate signals in the outer and inner plexiform layers of the retina that were well-colocalized with those of Bassoon and RIM. Both proteins were found presynaptically at glutamatergic ribbon synapses, and at conventional GABAergic and glycinergic synapses. Moreover, immunoelectron microscopy revealed that CAST, like Bassoon and RIM, localized at the base of synaptic ribbons, whereas ELKS localized around the ribbons. Both proteins also localized in the vicinity of the presynaptic plasma membrane of conventional synapses in the retina. These results indicated that CAST and ELKS were novel components of the presynaptic apparatus of mouse retina.
Persistent GB Virus C Infection and Survival in HIV-Infected Men (2004)

GBV-C viremia was significantly associated with prolonged survival among HIV-positive men 5 to 6 years after HIV seroconversion, but not at 12 to 18 months, and the loss of GBV-C RNA by 5 to 6 years after HIV seroconversion was associated with the poorest prognosis. Understanding the mechanisms of interaction between GBV-C and HIV may provide insight into the progression of HIV disease.