gebhart/patrepeval huggingface dataset:
Oxygen and carbon dioxide kinetic challenges for thermophilic mineral bioleaching processes (2004)

Agitated bacterial tank bioleaching reactors are currently sparged with air to satisfy both oxygen and CO(2) requirements of microbial cells. Under high-sulphide loading conditions, as is the case with high-grade metal sulphide concentrates, the microbial and chemical demand for oxygen is significantly increased during the bioleaching process. Sparging with enriched oxygen gas may offer an alternative process option to increased agitation and sparged aeration, to overcome the mass transfer difficulties at elevated temperatures where thermophilic Archaea, rather than Bacteria, are used. In the case of air sparging, the DO (dissolved oxygen) concentration in tank reactors could not be increased to a point where it would become inhibitory due to the limited oxygen content of air (20.9% O(2)). The use of enriched oxygen in such reactors at large scale does, however, pose its own set of process risks. The first aim of this investigation was, therefore, to determine the effects of various DO concentrations, in both the limiting and inhibitory ranges, on the microbial activity of Sulfolobus sp. U40813, a typical thermophilic mineral-leaching archaeon. Secondly, the effect of CO(2) concentration on the rate of ferrous iron oxidation was investigated. Both the oxygen and CO(2) kinetics were examined in controlled batch cultures at 78 degrees C, using ferrous sulphate and potassium tetrathionate as energy sources. The optimal DO concentration for iron oxidation was found to be between 1.5 and 4.1 mg.l(-1). The use of elevated DO concentrations (above 4.1 mg.l(-1)) inhibited the ferrous oxidation rates. The optimal gas CO(2) concentration for ferrous iron oxidation was found to be in the range 7-17% (v/v). The iron oxidation rates were, however, severely limited at CO(2) concentrations less than 7%, indicating that the CO(2) supply was limiting in this range and inhibited the microbial growth rate.
Diastereoselective Chloroallylboration of α-Chiral Aldehydes (1998)

Double asymmetric reaction of chiral (Z)-(γ-chloroallyl)borane, 2, with α-chiral aldehydes (3−7) provide a new practical method for the generation of 2,3-syn-3,4-anti and 2,3-syn-3,4-syn chiral vinylchlorohydrins (8−17) and vinyl epoxides (18−27). Both enantiomers of 2 exhibited excellent diatereoselectivity (≥90 de) for matched cases. The mismatched cases yielded moderate to good diastereoselectivity.
The influence of molar mass of oligosaccharides on their ability to disperse iron hydroxide (III). (1994)

The ability of oligosaccharides to disperse iron hydroxide (III) was investigated. It was found that products of electrochemical oxidation of oligosaccharides (aldonic acid) exhibit higher dispergation activity them the corresponding oligosaccharides.
Fabrication of tapered, strain-gradent chirped fibreBragg gratings (1995)

Chirped fibre Bragg gratings have been fabricated using a novel process in which the outer diameter of the fibre is tapered with a computer-controlled acid etching process. The strain gradient formed along the grating when the fibre is held under tension produces a varying shift in the Bragg spacing, resulting in a tunable, chirped grating.
Characterization of isolated in Taiwan by immunofluorescence and restriction fragment length polymorphism analyses (1997)

A total of 10 strains of Orientia tsutsugamushi were isolated from field rodents and chiggers in Taiwan, and characterized by immunofluorescence analysis with monoclonal antibodies and by restriction fragment length polymorphism analysis of the 56-kilodalton (kDa) protein gene. The isolates were divided into two groups consisting of 1 and 9 strains which showed some relation to Gilliam and Karp type strains, respectively. However, all these isolates possessed characteristics distinct not only from those of known prototype strains including Gilliam and Karp but also from all isolates from Japan. These findings suggest the existence of a large number of immunotypic and genotypic variants among the strains of O. tsutsugamushi, and the distribution of distinguishable strains in each area to which this species is endemic.
Alcoholic hepatitis: Diagnosis and prognosis (2013)

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Dimerization of a selectin and its ligand stabilizes cell rolling and enhances tether strength in shear flow (2001)

Selectins mediate rolling of leukocytes by rapid formation and dissociation of selectin-ligand bonds, which are assumed to require high mechanical strength to prevent premature dissociation by the forces applied in shear flow. This assumption is based largely on the observation that increasing wall shear stress increases only modestly the dissociation of transient leukocyte tethers on very low selectin densities. P-selectin binds to the N-terminal region of P-selectin glycoprotein ligand-1 (PSGL-1), a mucin on leukocytes. Both PSGL-1 and P-selectin are extended homodimers. We perfused transfected cells expressing wild-type dimeric PSGL-1 or a chimeric monomeric form of PSGL-1 on immobilized dimeric or monomeric forms of P-selectin. Cells expressing dimeric or monomeric PSGL-1 tethered to P-selectin at equivalent rates. However, cells expressing dimeric PSGL-1 established more stable rolling adhesions, which were more shear resistant and exhibited less fluctuation in rolling velocities. On low densities of dimeric P-selectin, increasing wall shear stress more rapidly increased transient tether dissociation of cells expressing monomeric PSGL-1 than dimeric PSGL-1. Tether dissociation on low densities of monomeric P-selectin was even more shear sensitive. We conclude that dimerization of both PSGL-1 and P-selectin stabilizes tethering and rolling, probably by increasing rebinding within a bond cluster. Because transient tethers may have more than one bond, the mechanical strength of selectin-ligand bonds is likely to be lower than initially estimated. Tether strength may rely more on bond clusters to distribute applied force.
Correlation of vascular endothelial growth factor messenger RNA expression with peritumoral vasogenic cerebral edema in meningiomas (1996)

Intracranial meningiomas are often complicated by peritumoral vasogenic cerebral edema, which appears to result from increased microvascular permeability and extravasation of proteinaceous and plasma fluid into the adjacent peritumoral space. The source of such edema has long been mysterious. The contents of this paper support the concept that vascular endothelial growth factor (VEGF) production plays a significant role in edema formation. Vascular endothelial growth factor messenger RNA expression has been found in a wide range of intracranial neoplasms, including malignant gliomas, metastatic melanomas, meningiomas, and other benign tumors. Several studies have confirmed the importance of VEGF in tumorigenesis, neovascularization, and edema production. This study tests the hypothesis that the presence of peritumoral edema in meningiomas is positively correlated with increased expression of VEGF mRNA. To investigate this hypothesis, 31 meningioma specimens were subjected to Northern blot analysis, hybridization with a complementary DNA VEGF probe, and laser densitometry to determine the relative levels of VEGF mRNA expression. Magnetic resonance imaging was then used in a double-blind fashion to correlate the neuropathological tissue samples with the presence of preoperative peritumoral edema. Of 31 patients studied, 14 exhibited no edema and 17 exhibited some level of peritumoral fluid accumulation. There was a marked increase in VEGF expression in patients with edema (p = 0.0004, Wilcoxon-Mann-Whitney rank-sum test). Meningiomas with peritumoral edema exhibited 3.4 times the level of VEGF mRNA as those without edema. These data demonstrate a strong link between VEGF mRNA expression and peritumoral edema and indicate that VEGF expression is an important factor in the etiology of edema around meningiomas.
Light-Evoked Responses of the Mouse Retinal Pigment Epithelium (2004)

In response to light, the retinal pigment epithelium (RPE) generates a series of slow potentials that can be recorded as the c-wave, fast oscillation (FO), and light peak (LP) of the electroretinogram (ERG). As these potentials can be related to specific cellular events, they provide information about RPE function and how that may be altered by disease or experimental manipulation. In the present study we describe a noninvasive means for recording the light-evoked responses of the mouse RPE and use this to define the stimulus-response properties of the major components in three inbred strains of mice (BALBc/ByJ, C57BL/6J, and 129/SvJ) and two mouse mutants that reduce activity in the rod pathway. All of the major ERG components generated by the RPE are readily measured in the mouse. In albino strains (BALBc/ByJ and 129/SvJ) the intensity-response functions for the c-wave, FO, and LP are shifted toward lower intensities in comparison to those for C57BL/6J mice. Each of these components was markedly reduced in mice lacking transducin in which rod phototransduction is interrupted, indicating that they reflect primarily rod photoreceptor activity. All components were observed in no b-wave (nob) mutant mice, indicating that inner retinal activity does not make a major contribution to these potentials. Further studies of mutant mice will allow us to define the functional consequences of gene manipulation on RPE function and to evaluate specific hypotheses regarding the generation of ERG components.
Absorber and emitter for solar thermo-photovoltaic systems to achieve efficiency exceeding the Shockley-Queisser limit (2009)

We present theoretical considerations as well as detailed numerical design of absorber and emitter for Solar Thermophotovoltaics (STPV) applications. The absorber, consisting of an array of tungsten pyramids, was designed to provide near-unity absorptivity over all solar wavelengths for a wide angular range, enabling it to absorb light effectively from solar sources regardless of concentration. The emitter, a tungsten slab with Si/SiO(2) multilayer stack, provides a sharp emissivity peak at the solar cell band-gap while suppressing emission at lower frequencies. We show that, under a suitable light concentration condition, and with a reasonable area ratio between the emitter and absorber, a STPV system employing such absorber-emitter pair and a single-junction solar cell can attain efficiency that exceeds the Shockley-Queisser limit.
Novel biologically based therapies for myeloma. (2001)

Recent advances in our understanding of the molecular regulation of myeloma cells suggest novel strategies for treating multiple myeloma. Some myeloma cells express a 69 kD variant of Ku86, a heterodimer subunit that is essential for double-stranded DNA break repair. Presence of the variant impairs DNA repair; therefore normal Ku86 in myeloma cells confers resistance to therapy and may represent a therapeutic target. The upregulation of NF-kappaB-dependent interleukin-6 (IL-6) transcription and secretion that occurs following adhesion of myeloma cells to bone marrow stromal cells (BMSCs) may serve as a potential therapeutic target, as IL-6 is a growth and survival factor for myeloma cells. Accordingly, proteasome inhibitors inhibit activation of NF-kappaB and induce apoptosis of myeloma cells; they also inhibit the NF-kappaB-dependent up-regulation of IL-6 in BMSCs and related paracrine growth of adherent tumor cells. Therapeutic strategies may also target the mitogen-activated protein kinase (MAPK) pathway that is thought to mediate the IL-6-induced proliferation of myeloma cells. Vascular endothelial growth factor (VEGF) is also upregulated by adhesion of myeloma cells to BMSCs and may serve as a growth and/or survival factor for myeloma cells; preliminary studies suggest that VEGF receptor inhibitors may block proliferation of tumor cells. Thalidomide was recently used successfully to treat myeloma in patients whose disease was refractory to conventional treatment. An enhanced understanding of the mechanisms of action of thalidomide may result in the development of analogues with enhanced potency and fewer side effects. The potential mechanisms of action of thalidomide are reviewed, including antiangiogenic effects; direct effects of thalidomide on the growth and survival of myeloma cells and BMSCs; modulation of adhesive interactions; and regulation of secretion and bioactivity of cytokines. Immune-based strategies for treating multiple myeloma are also reviewed. Therapeutic obstacles include excessive toxicity after allografting, contaminating tumor cells in autografts, and the persistence of minimal residual disease (MRD) after high-dose therapy followed by allogenic or autologous stem cell transplantation. Allografting can be performed safely in myeloma, donor lymphocyte infusions (DLI) may effectively treat relapsed myeloma post allografting; and use of CD4+ T cell-enriched DLI may reduce the risk of graft-versus-host disease. Treatment with autografting is frequently compromised by MRD in the autograft and in the patient post myeloablative therapy. Adenoviral purging prior to autotransplantation and in vivo and ex vivo stimulation of autoimmune cells are discussed as potential approaches to address these problems.
Problems in land use classification and mapping (1972)

Abstract: The accuracy and use/illness of land use maps is primarily dependent upon map scale and the availability and reliability of basic data. This paper presents a technique devised to make the maximum possible use of available agricultural statistics for the meaningful delineation of land use boundaries at small scales.
Retinoic acid-induced expression of tissue transglutaminase in human promyelocytic leukemia (HL-60) cells. (1985)

Addition of retinoic acid to human promyelocytic leukemia cells results in a dramatic increase in cellular transglutaminase activity. This increase is due to the induction of a specific intracellular transglutaminase, tissue transglutaminase. Retinoic acid-induced expression of tissue transglutaminase is potentiated by analogues of cyclic AMP. The induction of the enzyme can be detected within 6 h of the addition of the retinoid to the cell and results in increases of the enzyme of at least 50-fold. The induction of HL-60 transglutaminase is a specific response of the cells to retinoic acid and is not seen with other agents that induce HL-60 differentiation. We believe that the induction of tissue transglutaminase is a useful index of the early events in retinoid-regulated gene expression in both normal and transformed cells.
The effect of recombinant human insulin‐like growth factor‐I treatment on growth hormone secretion in two subjects with growth hormone insensitivity (Laron syndrome) (1993)

GH secretion is suppressed by exogenous IGF-I therapy in GH insensitive subjects. The failure to maintain high serum IGF-I levels overnight, presumably due to a persisting defect in serum IGFBP-3 levels, was associated with an early return of GH secretion. These findings may have implications for the dose and regimen of IGF-I therapy in subjects with growth hormone insensitivity.
Learning to Refine Object Contours with a Top-Down Fully Convolutional Encoder-Decoder Network (2017)

We develop a novel deep contour detection algorithm with a top-down fully convolutional encoder-decoder network. Our proposed method, named TD-CEDN, solves two important issues in this low-level vision problem: (1) learning multi-scale and multi-level features; and (2) applying an effective top-down refined approach in the networks. TD-CEDN performs the pixel-wise prediction by means of leveraging features at all layers of the net. Unlike skip connections and previous encoder-decoder methods, we first learn a coarse feature map after the encoder stage in a feedforward pass, and then refine this feature map in a top-down strategy during the decoder stage utilizing features at successively lower layers. Therefore, the deconvolutional process is conducted stepwise, which is guided by Deeply-Supervision Net providing the integrated direct supervision. The above proposed technologies lead to a more precise and clearer prediction. Our proposed algorithm achieved the state-of-the-art on the BSDS500 dataset (ODS F-score of 0.788), the PASCAL VOC2012 dataset (ODS F-score of 0.588), and and the NYU Depth dataset (ODS F-score of 0.735).
Effects of Strontium on Calcium Metabolism in Rats. II. Strontium Prevents the Increased Rate of Bone Turnover in Ovariectomized Rats. (1995)

The effects of stable strontium were investigated in ovariectomized (OVX) rats by calcium balance and calcium kinetic studies, histomorphometric analysis and measurements of calcium levels in bone. After 10 days of pair-feeding with a control diet, 71-day-old female Wistar rats were either sham-operated (Sham group) or ovariectomized. The OVX rats were divided into two subgroups: those that were treated with strontium (OVX+Sr group, strontium intake; 87.5 mumol/day/rat) and those that were not (OVX group). Both groups were pair-fed their respective control or strontium diets for 2 weeks. Calcein and tetracycline were injected every 2 weeks from 1 week before ovariectomy to calculate the rate of bone formation in the diaphyseal femora cortex (% BFFC). In the OVX group, urinary calcium and % BFFC decreased, while bone resorption, bone formation and femora length increased at the end of the experiment, as compared with those in the Sham group. No such changes were observed in rats in the OVX+Sr group. The calcium balance, calcium levels in bone and trabecular bone volume in the metaphysis did not change in any of the three groups. These results suggest that strontium may be able to prevent the changes in bone turnover induced by estrogen deficiency.
Detection of Nucleosomal Substructures using Solid-State Nanopores (2012)

Histone proteins assemble onto DNA into nucleosomes that control the structure and function of eukaryotic chromatin. More specifically, the structural integrity of nucleosomes regulates gene expression rates and serves as an important early marker for cell apoptosis. Nucleosomal (sub)structures are however hard to detect and characterize. Here, we show that solid-state nanopores are well suited for fast and label-free detection of nucleosomes and its histone subcomplexes. (Nucleo-)protein complexes are individually driven through the nanopore by an applied electric field, which results in characteristic conductance blockades that provide quantitative information on the molecular size of the translocating complex. We observe a systematic dependence of the conductance blockade and translocation time on the molecular weight of the nucleosomal substructures. This allows discriminating and characterizing these protein and DNA-protein complexes at the single-complex level. Finally, we demonstrate the ability to distinguish nucleosomes and dinucleosomes as a first step toward using the nanopore platform to study chromatin arrays.
Protein folds and families: sequence and structure alignments (1999)

Dali and HSSP are derived databases organizing protein space in the structurally known regions. We use an automatic structure alignment program (Dali) for the classification of all known 3D structures based on all-against-all comparison of 3D structures in the Protein Data Bank. The HSSP database associates 1D sequences with known 3D structures using a position-weighted dynamic programming method for sequence profile alignment (MaxHom). As a result, the HSSP database not only provides aligned sequence families, but also implies secondary and tertiary structures covering 36% of all sequences in Swiss-Prot. The structure classification by Dali and the sequence families in HSSP can be browsed jointly from a web interface providing a rich network of links between neighbours in fold space, between domains and proteins, and between structures and sequences. In particular, this results in a database of explicit multiple alignments of protein families in the twilight zone of sequence similarity. The organization of protein structures and families provides a map of the currently known regions of the protein universe that is useful for the analysis of folding principles, for the evolutionary unification of protein families and for maximizing the information return from experimental structure determination. The databases are available from http://www.embl-ebi.ac.uk/dali/
Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes (2010)

Noncoding RNAs are important components of regulatory networks controlling the epigenetic state of chromatin. We analyzed the role of pRNA (promoter-associated RNA), a noncoding RNA that is complementary to the rDNA promoter, in mediating de novo CpG methylation of rRNA genes (rDNA). We show that pRNA interacts with the target site of the transcription factor TTF-I, forming a DNA:RNA triplex that is specifically recognized by the DNA methyltransferase DNMT3b. The results reveal a compelling new mechanism of RNA-dependent DNA methylation, suggesting that recruitment of DNMT3b by DNA:RNA triplexes may be a common and generally used pathway in epigenetic regulation.
A tileable switch module architecture for homogeneous 3D FPGAs (2009)

3D technology is an attractive solution for reducing wirelength in a field programmable gate array (FPGA). However, trough silicon vias (TSV) are limited in number. In this paper, we propose a tilable switch module architecture based on the 3D disjoint switch module for 3D FPGAs. Experimental results over 20 MCNC benchmarks show 62% reduction in the number of TSVs on average and small improvements in horizontal channel width and delay compared to the original 3D disjoint SM.
Localized Intracoronary Gamma-Radiation Therapy to Inhibit the Recurrence of Restenosis after Stenting (2001)

Intracoronary irradiation with iridium-192 resulted in lower rates of clinical and angiographic restenosis, although it was also associated with a higher rate of late thrombosis, resulting in an increased risk of myocardial infarction. If the problem of late thrombosis within the stent can be overcome, intracoronary irradiation with iridium-192 may become a useful approach to the treatment of in-stent restenosis.
N-Acetylcysteine-Mediated Antioxidation Prevents Hyperglycemia-Induced Apoptosis and Collagen Synthesis in Rat Mesangial Cells (2008)

It is concluded that NAC prevents HG-induced mesangial apoptosis and fibrogenesis pathways by the reduction of oxidative stress.
Identification of Mammalian microRNA Host Genes and Transcription Units (2004)

To derive a global perspective on the transcription of microRNAs (miRNAs) in mammals, we annotated the genomic position and context of this class of noncoding RNAs (ncRNAs) in the human and mouse genomes. Of the 232 known mammalian miRNAs, we found that 161 overlap with 123 defined transcription units (TUs). We identified miRNAs within introns of 90 protein-coding genes with a broad spectrum of molecular functions, and in both introns and exons of 66 mRNA-like noncoding RNAs (mlncRNAs). In addition, novel families of miRNAs based on host gene identity were identified. The transcription patterns of all miRNA host genes were curated from a variety of sources illustrating spatial, temporal, and physiological regulation of miRNA expression. These findings strongly suggest that miRNAs are transcribed in parallel with their host transcripts, and that the two different transcription classes of miRNAs ('exonic' and 'intronic') identified here may require slightly different mechanisms of biogenesis.