gebhart/patrepeval huggingface dataset:
Coordinate up-regulation of hypoxia inducible factor (HIF)-1alpha and HIF-1 target genes during multi-stage epidermal carcinogenesis and wound healing. (2000)

Both carcinogenesis and wound healing proceed through stages of proliferation and tissue remodeling. Here, using either a model of multistage epidermal carcinogenesis in K14-HPV16 transgenic mice or creation of full-thickness back wounds in nontransgenic mice, we determined patterns of expression of hypoxia inducible factor (HIF)-1alpha, and three targets of the heterodimeric transcription factor HIF-1, glucose transporter (GLUT)-1, phosphoglycerate kinase (PGK)-1, and vascular endothelial growth factor (VEGF) in skin. Neither HIF-1alpha, GLUT-1, PGK-1, nor VEGF mRNA was detectable in unwounded nontransgenic skin. In epidermal carcinogenesis, HIF-1alpha, GLUT-1, PGK-1, and VEGF mRNAs were just detectable in early-stage hyperplasia, markedly increased in high-grade epidermal chest dysplasias, and further increased in invasive squamous carcinomas. In neoplastic skin, HIF-1alpha, GLUT-1, and PGK-1 mRNAs localized in the basal and immediate suprabasal epidermal layers, whereas VEGF mRNA was predominantly expressed in the more superior spinous and granular epidermal layers. Immediately after wounding, HIF-1alpha, GLUT-1, and PGK-1 mRNAs were detectable in basal keratinocytes at the wound edge. Expression of all three genes increased to maximum levels in reepithelializing basal keratinocytes and then diminished to near undetectable levels after wound epithelialization. Although VEGF mRNA similarly increased and decreased during wound healing, its expression pattern was more punctate; the most intense hybridization signals were detected in the upper spinous and granular layers of reepithelializing keratinocytes and in dermal cells morphologically similar to macrophages. These data suggest stage-specific and spatio-temporal control of HIF-1alpha and HIF-1 target gene expression in both multistage epithelial carcinogenesis and wound healing.
Photosynthesis gene superoperons in purple nonsulfur bacteria: the tip of the iceberg? (1992)

The purple, nonsulfur phototrophic bacterium Rhodobacter capsulatus has recently been found to contain several pigment biosynthetic operons that exhibit marked transcription read through into downstream operons that encode polypeptide components of photosynthetic pigment-protein complexes. This phenomenon has been found to be phenotypically significant for adaptation to changes in environmental conditions, and the term superoperon has been proposed to describe this sort of coupled transcriptional arrangement. We summarize the data that led to recognition of this novel transcriptional arrangement and suggest that superoperons might be more prevalent in prokaryotes than has heretofore been recognized. Key words: superoperons, overlapping transcription units, photosynthesis genes.
A 12 b 128 MSample/s ADC with 0.05 LSB DNL (2002)

This analog-to-digital converter uses integrated dither, dynamic element matching, and output data scrambling to achieve SFDR of 85dB and DNL below 0.05LSB at l28MSample/s. This compares to about 0.5LSB DNL for slower 12b converters. The basic two-step flash architecture is shown. The /spl plusmn/0.25V input is amplified to /spl plusmn/1V and held in the track-and-hold circuit when the input clock rises. The 32 comparators in ADC1 produce an approximation that switches the 32 matched current sources in the main DAC. The residue is formed and amplified in the summer to /spl plusmn/0.5V and is converted by ADC2, an 8b folding-and-interpolating flash ADC. To allow low clock rates, there is no analog pipelining, and all analog settling from the track-to-hold transition to latching the result in ADC2 takes only 4.4ns. The ADC1 and ADC2 results added together form the 12b output. The total signal-to-data-output delay is slightly more than two cycles due to digital pipelining.
4β-Hydroxywithanolide E from Physalis peruviana (golden berry) inhibits growth of human lung cancer cells through DNA damage, apoptosis and G2/M arrest (2010)

In this study, we demonstrated that golden berry-derived 4betaHWE is a potential DNA-damaging and chemotherapeutic agent against lung cancer.
Strategies to Minimize Frac Spacing and Stimulate Natural Fractures in Horizontal Completions (2011)

Abstract The opening of a propped transverse fracture in horizontal wells causes a reorientation of stresses in its neighborhood, which in turn affects the direction of propagation of subsequent fractures. This phenomenon, often referred to as stress shadowing, can negatively impact the efficiency of each frac stage. By mapping the angle of stress reorientation and the horizontal deviatoric stress in multi-fractured horizontal wells, we offer some insight on the completion designs that will (a) minimize induced fracture spacing without compromising the efficiency of each frac stage and (b) effectively stimulate natural fractures in the vicinity of the created fracture. The rapid development of shale gas in North America can be tied to the combination of horizontal drilling and multi-stage fracturing. The spacing between fractures and perforation clusters as well as the ability to stimulate the fractures naturally present in the rock are thought to be major factors in the success of horizontal completions in shale gas reservoirs. The understanding and quantification of the mechanical stress interference generated during the stimulation of horizontal wells is crucial to improving reservoir drainage in shale gas reservoirs Transverse fractures initiated from a horizontal well may deviate toward or away from the previous fracture depending on the mechanical properties of the reservoir rock, fracture spacing, and the orientation of the previous fracture. Using a numerical model allowing non-transverse fractures (those that deviate from the orthogonal path), we show that some induced fractures propagate into previously stimulated areas during the consecutive fracturing of a Barnett shale well, thus decreasing the reservoir drainage efficiency of the frac treatment. The observed net pressure trend matches field observations during fracturing and microseismic measurements. The alternate sequencing of transverse fractures as well as multi-lateral completions were recognized to be effective ways to enhance natural fracture stimulation, by allowing fracture stages to experience a smaller stress contrast during propagation. More importantly, it is shown that net fracturing pressure data measured in the field can be used to detect mechanical interference between multiple transverse fractures and optimize fracture spacing for a specific well.
Diversity has stronger top‐down than bottom‐up effects on decomposition (2009)

The flow of energy and nutrients between trophic levels is affected by both the trophic structure of food webs and the diversity of species within trophic levels. However, the combined effects of trophic structure and diversity on trophic transfer remain largely unknown. Here we ask whether changes in consumer diversity have the same effect as changes in resource diversity on rates of resource consumption. We address this question by focusing on consumer-resource dynamics for the ecologically important process of decomposition. This study compares the top-down effect of consumer (detritivore) diversity on the consumption of dead organic matter (decomposition) with the bottom-up effect of resource (detrital) diversity, based on a compilation of 90 observations reported in 28 studies. We did not detect effects of either detrital or consumer diversity on measures of detrital standing stock, and effects on consumer standing stock were equivocal. However, our meta-analysis indicates that reductions in detritivore diversity result in significant reductions in the rate of decomposition. Detrital diversity has both positive and negative effects on decomposition, with no overall trend. This difference between top-down and bottom-up effects of diversity is robust to different effect size metrics and could not be explained by differences in experimental systems or designs between detritivore and detrital manipulations. Our finding that resource diversity has no net effect on consumption in "brown" (detritus-consumer) food webs contrasts with previous findings from "green" (plant-herbivore) food webs and suggests that effects of plant diversity on consumption may fundamentally change after plant death.
High‐temperature stability of YSZ and MSZ ceramic materials in CaF 2 –MgF 2 –MgO molten salt system (2017)

Abstract The high‐temperature stability of YSZ and MSZ specimens was investigated in CaF 2 –MgF 2 –MgO molten salt at 1200°C. YSZ was mostly composed of m‐ZrO 2 and a small part of YF 3 in the early stages. The formation of YF 3 was attributed to the chemical reaction between Y 2 O 3 and MgF 2 , which can lead to the leaching of Y 2 O 3 from YSZ . With an increase in exposure time, the degraded surface was coarser, and considerable amount of cracks, pores, and spallations were formed. Furthermore, no Y 2 O 3 was found up to 120 μm of the YSZ bulk in the early stages. MSZ was composed of t‐ZrO 2 after 24 hours. However, the volume fraction of m‐ZrO 2 was 72% after 72 hours, and CaZrO 3 was formed by the chemical reaction between CaO and ZrO 2 after 168 hours. In addition, the volume fraction of m‐ZrO 2 was 60% in 2.5 wt% MgO and 49% in 10 wt% MgO. In 5 wt% MgO, CaZrO 3 was formed. We demonstrate that the high‐temperature stability of MSZ was better than that of YSZ , and that 10 wt% MgO was much more stable than the other concentrations of MgO.
A split‐body, randomized, blinded study to evaluate the efficacy of a topical spray composed of essential oils and essential fatty acids from plant extracts with antimicrobial properties (2016)

These results demonstrate that use of a topical spray which contains plant-derived essential oils and fatty acids, and compounds with antimicrobial properties (Manuka oil and N-acetyl cysteine) may help to speed resolution of pyoderma and may allow for shorter antimicrobial treatment time.
Simple and Low-Cost Technique for Carbon Nanotube Synthesis (2020)

Currently, the methods that use microwaves to promote the growth of carbon nanotubes (CNT) employ waveguides in their configuration. We describe a method for synthesizing CNT based on the use of a microwave plasma at atmospheric pressure, and maintained by a resonant cavity. The replacement of waveguides by the resonant cavity results in deposition areas greater than 15 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , and is therefore not limited by the equipment configuration, since plasma is formed in almost the entire length of the quartz tube. As a result, confirmed by Raman spectroscopy and scanning and transmission electron microscopy, good quality carbon nanotubes were obtained, with an ID/IG ratio less than one unit in addition to the possibility of tuning the nanostructure diameter through process conditions.
News Classification using Neural Networks (2016)

Classification of data in data mining is used to determine the category to which data belongs. Classification is required in order to search and manage data in databases. In this era of information, news are accessible very easily as news are available through online sources. This becomes a necessity to classify such data as news articles pose a great influence on various sections of our lives. This paper presents a system for the classification of news articles based on artificial neural networks and have compared the results with the previously used techniques for classification.
A stability condition for the Hartree–Fock solution of the infinite one-dimensional system (1989)

A simplified stability condition for the Hartree–Fock (HF) solution giving the self-consistent field crystal orbitals (SCF-CO) of the infinite one-dimensional system is derived. Since the present formulation, particularly for the systems having nearly or entirely degenerated highest occupied and the lowest unoccupied COs, contains only two physical parameters, that is, the density of states and the Coulomb repulsion integrals both at the Fermi level, it is tractable to examine the stability of the HF solutions of such polymers as well as the ordinary molecular systems. An example of its application to metallic trans-type polyacetylene is also shown.
Effect of nitrogen fixing bacteria on plant growth and yield of Brassica juncea. (2010)

Brassica juncea (L.) Czern & Coss. is one of the major oilseed crops cultivated in India and around the world. The aim of this study was to evaluate the efficiency of Azotobacter , Azospirillum and their combination on plant growth and yield parameters of Brassica juncea cv. Varuna. A pot experiment was conducted in the net house of Department of Botany, G.F. (P.G.) College, Shahjahanpur (U.P.) to study the effect of two bacterial inoculations Azotobater , Azospirillun and their combination on growth and yield of Brassica juncea . Azotobacter and Azospirillum were applied separately and combination of both the bacteria in half doses. Application of both the bacteria recorded higher plant growth and yield in Brassica juncea . Azospirillum inoculation resulted in higher growth and yield parameters in comparison to Azotobacter inoculation. However, the combination of half dose of both the bacteria proved best in improving plant growth and yield in comparison to individual inoculation. Key words: Brassica juncea , Nitrogen fixing bacteria Irfan Khan et al. Effect of Nitrogen Fixing Bacteria on Plant Growth and Yield of Brassica juncea . J Phytol 2/9 (2010) 25-27.
Elevated Chemokine Responses Are Maintained in Lungs after Clearance of Viral Infection (2002)

We observed two patterns of chemokine expression in the lungs of mice infected with murine gammaherpesvirus 68: peaks of chemokine expression correlated with or occurred after the peak of viral gene expression. Chemokine expression remained elevated through 29 days postinfection.
Kinetics of eotaxin expression and its relationship to eosinophil accumulation and activation in bronchial biopsies and bronchoalveolar lavage (BAL) of asthmatic patients after allergen inhalation (1998)

We investigated the kinetics of allergen-induced eotaxin expression and its relationship to eosinophil accumulation and activation in the airways of patients with allergic asthma. Twenty-four patients with allergic asthma and late asthmatic responses to allergen inhalation were randomly allocated into three groups of eight patients each, who received bronchoscopy with bronchial biopsies and BAL at 2, 4 and 24 h, respectively, after the inhalation of the diluent and the allergen. The expression of eotaxin mRNA and protein and eotaxin release were evaluated by in situ hybridization, immunohistochemistry, immunocytochemistry, and radioimmunoassay. Increased transcription from the eotaxin gene preceded the appearance of the late asthmatic response and the influx of activated eosinophils in bronchial tissue and BAL fluid (BALF). This was followed by increased cell expression of eotaxin protein (P<0.001) and increased eotaxin release (P<0.001), which correlated with the numbers of total and activated eosinophils and the level of airflow obstruction at 4 h after allergen exposure (P<0.05 for all correlations). At 24 h after allergen inhalation, enhanced eotaxin expression declined without a similar reduction in the numbers of eosinophils in bronchial biopsies and when there was a further increase in the number of these cells in BALF (P<0.05). These results indicate that eotaxin contributes to the early phase of allergen-induced recruitment of activated eosinophils into the airways of patients with allergic asthma and that other factors are implicated in the persistence of eosinophil infiltration.
Human skin chymotrypsin-like proteinase chymase. Subcellular localization to mast cell granules and interaction with heparin and other glycosaminoglycans. (1987)

The subcellular localization of human skin chymase to mast cell granules was established by immunoelectron microscopy, and binding of chymase to the area of the dermo-epidermal junction, a basement membrane, was demonstrated immunocytochemically in cryosections incubated with purified proteinase prior to immunolabeling. Because heparin and heparan sulfate proteoglycans are major constituents of mast cell granules and basement membranes, respectively, the ability of chymase to bind to glycosaminoglycans (GAG) was investigated. Among a variety of GAGs, only binding of chymase to heparin and heparan sulfate appears physiologically significant. Binding was ionic strength-dependent, involved amino groups on the proteinase, and correlated with increasing GAG sulfate content, indicating a predominantly electrostatic association. Interaction with heparin was observed in solutions containing up to 0.5 M NaCl, and interaction with heparan sulfate was observed in solutions containing up to 0.3 M NaCl. Binding of heparin did not detectably affect catalysis of peptide substrates, but may reduce accessibility of proteinase to protein substrates. Measurements among a series of serine class proteinases indicated that heparin binding was a more common property of mast cell proteinases than proteinases stored in other secretory granules. Binding of chymase to heparin is likely to have a storage as well as a structural role within the mast cell granule, whereas binding of chymase to heparan sulfate may have physiological significance after degranulation.
Tailormade Polysaccharides with Defined Branching Patterns: Enzymatic Polymerization of Arabinoxylan Oligosaccharides (2018)

The heterogeneous nature of non-cellulosic polysaccharides, such as arabinoxylan, makes it difficult to correlate molecular structure with macroscopic properties. To study the impact of specific structural features of the polysaccharides on crystallinity or affinity to other cell wall components, collections of polysaccharides with defined repeating units are required. Herein, a chemoenzymatic approach to artificial arabinoxylan polysaccharides with systematically altered branching patterns is described. The polysaccharides were obtained by glycosynthase-catalyzed polymerization of glycosyl fluorides derived from arabinoxylan oligosaccharides. X-ray diffraction and adsorption experiments on cellulosic surfaces revealed that the physicochemical properties of the synthetic polysaccharides strongly depend on the specific nature of their substitution patterns. The artificial polysaccharides allow structure-property relationship studies that are not accessible by other means.
Structure of a LOV protein in apo-state and implications for construction of LOV-based optical tools (2017)

Unique features of Light-Oxygen-Voltage (LOV) proteins like relatively small size (~12-19 kDa), inherent modularity, highly-tunable photocycle and oxygen-independent fluorescence have lately been exploited for the generation of optical tools. Structures of LOV domains reported so far contain a flavin chromophore per protein molecule. Here we report two new findings on the short LOV protein W619_1-LOV from Pseudomonas putida. First, the apo-state crystal structure of W619_1-LOV at 2.5 Å resolution reveals conformational rearrangements in the secondary structure elements lining the chromophore pocket including elongation of the Fα helix, shortening of the Eα-Fα loop and partial unfolding of the Eα helix. Second, the apo W619_1-LOV protein binds both natural and structurally modified flavin chromophores. Remarkably different photophysical and photochemical properties of W619_1-LOV bound to 7-methyl-8-chloro-riboflavin (8-Cl-RF) and lumichrome imply application of these variants as novel optical tools as they offer advantages such as no adduct state formation, and a broader choice of wavelengths for in vitro studies.
A Randomized Trial of Intensive Insulin Therapy in Newly Diagnosed Insulin-Dependent Diabetes Mellitus (1989)

A period of early, intensive insulin treatment is thought to improve subsequent beta-cell function in insulin-dependent diabetes mellitus (IDDM). To study this hypothesis, we randomly assigned adolescents with newly diagnosed IDDM to receive either conventional treatment (n = 14) (NPH insulin, 1 U per kilogram of body weight per day, in two divided doses) or an experimental treatment (n = 12) (a two-week hospitalization with maintenance of blood glucose levels between 3.3 and 4.4 mmol per liter by continuous insulin infusion delivered by an external artificial pancreas [Biostator]). During the two-week intervention, the experimental-therapy group received four times more insulin than the conventionally treated group, and their endogenous insulin secretion was more completely suppressed, as evidenced by a urinary C-peptide excretion rate one seventh that of the conventionally treated group. After the first two weeks, both groups were treated similarly and received similar amounts of insulin. At one year, the mean (+/- SEM) plasma level of C peptide was significantly higher after mixed-meal stimulation in the experimental-therapy group than in the conventionally treated group (0.51 +/- 0.07 vs. 0.27 +/- 0.06; P less than 0.01). The experimental-therapy group also had better metabolic control, as evidenced by lower glycohemoglobin values (7.2 +/- 0.7 vs. 10.8 +/- 1.2 percent; P less than 0.01). We conclude that suppression of endogenous insulin by intensive, continuous insulin treatment during the first two weeks after the diagnosis of IDDM may improve beta-cell function during the subsequent year.
Pulmonary hypertension (2015)

Pulmonary hypertension is a haemodynamic and pathophysiological condition defined as an increase in the mean pulmonary arterial pressure of ≥25 mmHg at rest, as assessed by right heart catheterization. In fact, while transthoracic echocardiography may provide clues on the presence of pulmonary hypertension, the haemodynamic evaluation offers a more precise and comprehensive assessment. Pulmonary hypertension is heterogeneous from a pathophysiological point of view, and the diversity is reflected in the haemodynamic definitions. The different haemodynamic forms of pulmonary hypertension can be found in multiple clinical conditions which have been classified into six main groups and at least twenty-six subgroups. Each main clinical group shows specific pathological changes in the lung distal arteries, capillaries, and small veins. If we combine the haemodynamic and clinical heterogeneity, we understand the complexity of an accurate diagnosis in the individual patient which is crucial for the prognostic assessment and treatment strategy. In addition, the concomitant presence of different haemodynamic and clinical mechanisms cannot be excluded in individual cases (e.g. in patients with congestive heart failure and associated lung diseases). The presence of pulmonary hypertension, as defined above, is always an ominous prognostic sign, even if the severity may differ according to the haemodynamic changes and underlying clinical condition. The therapeutic approach also is markedly different, according to the clinical group, and symptomatic and haemodynamic severity. For these reasons, the four more frequent clinical groups are discussed individually, while the classifications are described in the Introduction section.
Digital phase detection for high-precision surface acoustic wave sensor systems (2006)

We are developing a highly sensitive surface acoustic wave (SAW) sensor system for biomedical and industrial applications. One of the key components of such a system is the signal read-out unit based on digital phase detection, which is needed to quantitatively determine tiny mass change on the sensor. To find a method that produces the highest precision, we have compared several digital phase detection methods (fast-Fourier transform, zero-crossing and sine-wave fitting) and found the zero-crossing method to be the most promising one. Using this method, a phase detection limit of 0.03/spl deg/ has been achieved on an AlN/sapphire SAW sensor operating at 255.05 MHz. And the minimum phase detection limit of our system could reach 0.01/spl deg/ at the same frequency.