gebhart/patrepeval huggingface dataset:
Plant-Derived Transfer DNAs (2005)

The transfer of DNA from Agrobacterium to plant cell nuclei is initiated by a cleavage reaction within the 25-bp right border of Ti plasmids. In an effort to develop all-native DNA transformation vectors, 50 putative right border alternatives were identified in both plant expressed sequence tags and genomic DNA. Efficacy tests in a tobacco (Nicotiana tabacum) model system demonstrated that 14 of these elements displayed at least 50% of the activity of conventional Agrobacterium transfer DNA borders. Four of the most effective plant-derived right border alternatives were found to be associated with intron-exon junctions. Additional elements were embedded within introns, exons, untranslated trailers, and intergenic DNA. Based on the identification of a single right border alternative in Arabidopsis and three in rice (Oryza sativa), the occurrence of this motif was estimated at a frequency of at least 0.8x10(-8). Modification of plasmid DNA sequences flanking the alternative borders demonstrated that both upstream and downstream sequences play an important role in initiating DNA transfer. Optimal DNA transfer required the elements to be preceded by pyrimidine residues interspaced by AC-rich trinucleotides. Alteration of this organization lowered transformation frequencies by 46% to 93%. Despite their weaker resemblance with left borders, right border alternatives also functioned effectively in terminating DNA transfer, if both associated with an upstream A[C/T]T[C/G]A[A/T]T[G/T][C/T][G/T][C/G]A[C/T][C/T][A/T] domain and tightly linked cytosine clusters at their junctions with downstream DNA. New insights in border region requirements were used to construct an all-native alfalfa (Medicago sativa) transfer DNA vector that can be used for the production of intragenic plants.
Enhanced electron injection in organic electroluminescence devices using an Al/LiF electrode (1997)

A bilayer is used as an electrode for organic electroluminescent devices. The bilayer consists of an ultrathin LiF layer adjacent to an electron-transporting layer and an aluminum outerlayer. Devices with the bilayer electrode showed enhanced electron injection and high electroluminescence efficiency as compared with a Mg0.9Ag0.1 cathode. Similar effects were observed when replacing MgO for LiF. The improvements are attributed to band bending of the organic layer in contact with the dielectrics.
Next Generation Post- combustion Capture: Combined CO2 and SO2 Removal (2013)

A major consideration for post-combustion CO2 capture is the adverse effect of the presence of SO2 on the absorption desorption process. The most common approach is to remove the SO2 from the flue gases in a flue gas desulfurization (FGD) unit prior the CO2 recovery process. This paper reports the experimental and modeling results of a new process for simultaneous removal of CO2 and SO2 for post-combustion applications. This process is named CASPER (CO2-capture And Sulphur Precipitation for Enhanced Removal), and is based on the precipitation of K2SO4 for sulphur removal. The selected CO2 absorbing solvent is an amino-acid, preferably a potassium amino-acid salt solution. The presence of potassium leads to the subsequent formation of K2SO4, which solubility in the CO2 loaded aqueous solvent solution changes depending on the applied conditions. The optimal crystallization conditions were first determined by characterization of K2SO4 solubility window and then evaluated in the lab-scale crystallization unit. In the next step the model system based on potassium beta-alanate solutions, also with addition of sulphate, were tested for CO2 absorption and desorption pressures by performing VLE (Vapor Liquid Equilibrium) measurements at 40°C and 120°C, respectively. Obtained values were included in preliminary technical assessment, which showed an energetic improvement of 0.7%-points for the CASPER model solvent system in comparison to the baseline 30wt% MEA case.
Antiproliferative effect of nonsteroidal antiinflammatory drugs against human colon cancer cells. (1994)

Several lines of evidence suggest that nonsteroidal antiinflammatory drugs may be effective in preventing colorectal cancer. These include animal experiments, case-control studies, and clinical experience with sulindac in promoting the regression of adenomatous colon polyps in adenomatous polyposis coli. We determined the antiproliferative activity of various nonsteroidal antiinflammatory drugs, including two sulindac derivatives, against human colon cancer cells in vitro. Ht-29, SW480, and DLD-1 cells were continuously incubated with serial drug dilutions for 6 days prior to fixation. Cell number was determined using the sulforhodamine B assay, and drug concentrations which inhibited cell growth by 50% were estimated for each agent by interpolation. All drugs exhibited antiproliferative activity against Ht-29 and DLD-1 cells, and most inhibited SW480 cells. For Ht-29 cells, the 50% inhibitory concentration varied from 55 microM for diclofenac to 2100 microM for 5-aminosalicylic acid, with three drug groups of high, intermediate, and low potency evident. Inhibition of cell growth by sulindac sulfide was reversible following drug removal. Nonsteroidal antiinflammatory drugs exert an antiproliferative effect against human colon cancer cells with a wide range of potencies. A cytostatic response was demonstrated with sulindac sulfide. These data further support the potential role of these agents for chemoprevention of colorectal neoplasia.
Epidermal Permeability Barrier Recovery Is Delayed in Vitiligo-Involved Sites (2010)

Barrier recovery following tape stripping of the SC is delayed in vitiligo. Therefore, improvement in epidermal permeability barrier function may be an important unrecognized factor to be considered in treating patients with vitiligo.
Medical Big Data: Neurological Diseases Diagnosis Through Medical Data Analysis (2016)

Diagnosis of neurological diseases is a growing concern and one of the most difficult challenges for modern medicine. According to the World Health Organisation's recent report, neurological disorders, such as epilepsy, Alzheimer's disease and stroke to headache, affect up to one billion people worldwide. An estimated 6.8 million people die every year as a result of neurological disorders. Current diagnosis technologies (e.g. magnetic resonance imaging, electroencephalogram) produce huge quantity data (in size and dimension) for detection, monitoring and treatment of neurological diseases. In general, analysis of those medical big data is performed manually by experts to identify and understand the abnormalities. It is really difficult task for a person to accumulate, manage, analyse and assimilate such large volumes of data by visual inspection. As a result, the experts have been demanding computerised diagnosis systems, called "computer-aided diagnosis (CAD)" that can automatically detect the neurological abnormalities using the medical big data. This system improves consistency of diagnosis and increases the success of treatment, save lives and reduce cost and time. Recently, there are some research works performed in the development of the CAD systems for management of medical big data for diagnosis assessment. This paper explores the challenges of medical big data handing B Siuly Siuly
Iron(II)-ethylenediaminetetraacetic acid catalyzed cleavage of RNA and DNA oligonucleotides: similar reactivity toward single- and double-stranded forms (1990)

Fe(II)-EDTA catalyzes the cleavage of nucleic acids with little or no base-sequence specificity. We have now studied the preference of this reagent in catalyzing the cleavage of single- versus double-stranded nucleic acid structures. Three RNA and two DNA molecules, each expected to contain both single- and double-stranded regions, were synthesized and their structures characterized by enzymatic digestion using secondary structure specific nucleases. Fe(II)-EDTA catalyzed nearly uniform strand scission along the entire length of each molecule; no correlation with secondary structure was observed. The homopolymer sequence dA30:dT30, embedded in a mixed-sequence context to promote exact register of the homopolymer tract, was cleaved to an extent similar to that of flanking sequences. The reactions were relatively insensitive to K+, Na+, and Mg2+ in the range 10-100 mM and were quenched by Tris-HCl buffer. We conclude that the Fe(II)-EDTA-catalyzed strand scission reaction does not discriminate between typical single- and double-stranded regions, which simplifies the interpretation of experiments in which the reaction is used to probe the tertiary structure of RNA molecules [Latham, J. A., & Cech, T. R. (1989) Science 245, 276-282].
The Ecarin Clotting Time, a Universal Method to Quantify Direct Thrombin Inhibitors (2003)

The ecarin clotting time (ECT) is a meizothrombin generation test that allows for precise quantification of direct thrombin inhibitors. The ECT has demonstrated its usefulness for more than 10 years in biochemical-pharmacological investigations as well as in clinical research and in the clinical routine. It has proved valuable especially as a drug-monitoring method in r-hirudin therapy. This test has been adjusted to clinical requirements by numerous modifications. Following the description of the biochemical background and the measuring principle of the ECT, this article gives a short survey of several modifications of the ECT for both preclinical and clinical use, e.g., for biochemical investigations, as a point-of-care method and for cardiac surgery. Advantages and disadvantages of these methods are discussed.
Identification of Hodgkin and Reed-Sternberg cell-specific genes by gene expression profiling (2003)

Hodgkin lymphoma (HL) is a malignancy of unknown pathogenesis. The malignant Hodgkin and Reed/Sternberg (HRS) cells derive from germinal center B cells (or rarely, T cells) but have a heterogeneous and largely uncharacterized phenotype. Using microarrays, we compared the gene expression profile of four HL cell lines with profiles of the main B cell subsets and B cell non-HLs to find out whether HRS cells, despite their described heterogeneity, show a distinct gene expression, to study their relationship to other normal and malignant B cells, and to identify genes aberrantly or overexpressed by HRS cells. The HL lines indeed clustered as a distinct entity, irrespective of their B or T cell derivation, and their gene expression was most similar to that of EBV-transformed B cells and cell lines derived from diffuse large cell lymphomas showing features of in vitro–activated B cells. Twenty-seven genes, most of which were previously unknown to be expressed by HRS cells, showed aberrant expression specifically in these cells, e.g., the transcription factors GATA-3, ABF1, EAR3, and Nrf3. For five genes, expression in primary HRS cells was confirmed. The newly identified HL-specific genes may play important roles in the pathogenesis of HL, potentially represent novel diagnostic markers, and can be considered for therapeutic targeting.
Cloning and sequence analysis of the meso-diaminopimelate decarboxylase gene from Bacillus methanolicus MGA3 and comparison to other decarboxylase genes (1993)

The lysA gene of Bacillus methanolicus MGA3 was cloned by complementation of an auxotrophic Escherichia coli lysA22 mutant with a genomic library of B. methanolicus MGA3 chromosomal DNA. Subcloning localized the B. methanolicus MGA3 lysA gene into a 2.3-kb SmaI-SstI fragment. Sequence analysis of the 2.3-kb fragment indicated an open reading frame encoding a protein of 48,223 Da, which was similar to the meso-diaminopimelate (DAP) decarboxylase amino acid sequences of Bacillus subtilis (62%) and Corynebacterium glutamicum (40%). Amino acid sequence analysis indicated several regions of conservation among bacterial DAP decarboxylases, eukaryotic ornithine decarboxylases, and arginine decarboxylases, suggesting a common structural arrangement for positioning of substrate and the cofactor pyridoxal 5'-phosphate. The B. methanolicus MGA3 DAP decarboxylase was shown to be a dimer (M(r) 86,000) with a subunit molecular mass of approximately 50,000 Da. This decarboxylase is inhibited by lysine (Ki = 0.93 mM) with a Km of 0.8 mM for DAP. The inhibition pattern suggests that the activity of this enzyme in lysine-overproducing strains of B. methanolicus MGA3 may limit lysine synthesis.
Estimation of 3D fractal dimension of real electrical tree patterns (2002)

In this study, we investigated methods of reconstructing higher-resolution three-dimensional (3D) patterns of real electrical tree patterns. We studied two kinds of reconstruction methods, and both methods were applied to the same specimen. One method is a mechanical preparation of serial cross sections and the other is a computerized tomography method using projections. Furthermore, to examine the fractal properties of reconstructed 3D tree patterns, the fractal dimension of their patterns was estimated by means of a box counting method. The results showed that both methods can reconstruct 3D electrical tree pattern accurately and the obtained patterns have fractal properties.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Importance of aliphatic side-chain structure at positions 2 and 3 of the insulin A chain in insulin-receptor interactions (1992)

In order to evaluate the cause of the greatly decreased receptor-binding potency of the naturally occurring mutant human insulin Insulin Wakayama ([LeuA3]insulin, 0.2% relative potency), we examined (by the semisynthesis of insulin analogues based on N alpha-PheB1,N epsilon-LysB29-bisacetyl-insulin) the importance of aliphatic side chain structure at positions A2 and A3 (Ile and Val, respectively) in directing the interaction of insulin with its receptor. Analogues bearing glycine, alanine, alpha-amino-n-butyric acid, norvaline, norleucine, valine, isoleucine, allo-isoleucine, threonine, tert-leucine, or leucine at positions A2 or A3 were assayed for their potencies in competing for the binding of 125I-labeled insulin to isolated canine hepatocytes, as were analogues bearing deletions from the A-chain amino terminus or the B-chain carboxyl terminus. Selected analogues were also analyzed by far-UV CD and absorption spectroscopy of Co2+ complexes. Our results identify that (a) Ile and Val serve well at position A2, whereas residues with other side chains (including those with straight chains, alternatively configured beta-branches, or a gamma-branch) exhibit relative receptor-binding potencies in the range 1-5%; (b) greater flexibility is allowed side-chain structure at position A3, with Ile, allo-Ile, alpha-amino-n-butyric acid, and tert-Leu exhibiting relative receptor-binding potencies in the range 11-36%; and (c) simultaneous replacements at positions A2 and A3, and deletions of the COOH-terminal domain of the insulin B chain in related analogues, yield cumulative effects. These findings are discussed with respect to a model for insulin-receptor interactions that involves a structure-orienting role for residue A2, the direct interaction of residue A3 with receptor, and multiple separately defined elements of structure and of conformational adjustment.
Hypoxic but not anoxic stabilization of HIF-1α requires mitochondrial reactive oxygen species (2002)

The molecular mechanisms by which cells detect hypoxia (1.5% O2), resulting in the stabilization of hypoxia-inducible factor 1alpha (HIF-1alpha) protein remain unclear. One model proposes that mitochondrial generation of reactive oxygen species is required to stabilize HIF-1alpha protein. Primary evidence for this model comes from the observation that cells treated with complex I inhibitors, such as rotenone, or cells that lack mitochondrial DNA (rho(0)-cells) fail to generate reactive oxygen species or stabilize HIF-1alpha protein in response to hypoxia. In the present study, we investigated the role of mitochondria in regulating HIF-1alpha protein stabilization under anoxia (0% O2). Wild-type A549 and HT1080 cells stabilized HIF-1alpha protein in response to hypoxia and anoxia. The rho(0)-A549 cells and rho(0)-HT1080 cells failed to accumulate HIF-1alpha protein in response to hypoxia. However, both rho(0)-A549 and rho(0)-HT1080 were able to stabilize HIF-1alpha protein levels in response to anoxia. Rotenone inhibited hypoxic, but not anoxic, stabilization of HIF-1alpha protein. These results indicate that a functional electron transport chain is required for hypoxic but not anoxic stabilization of HIF-1alpha protein.
Global Regulatory Impact of ClpP Protease ofStaphylococcus aureuson Regulons Involved in Virulence, Oxidative Stress Response, Autolysis, and DNA Repair (2006)

Staphylococcus aureus is an important pathogen, causing a wide range of infections including sepsis, wound infections, pneumonia, and catheter-related infections. In several pathogens ClpP proteases were identified by in vivo expression technologies to be important for virulence. Clp proteolytic complexes are responsible for adaptation to multiple stresses by degrading accumulated and misfolded proteins. In this report clpP, encoding the proteolytic subunit of the ATP-dependent Clp protease, was deleted, and gene expression of DeltaclpP was determined by global transcriptional analysis using DNA-microarray technology. The transcriptional profile reveals a strong regulatory impact of ClpP on the expression of genes encoding proteins that are involved in the pathogenicity of S. aureus and adaptation of the pathogen to several stresses. Expression of the agr system and agr-dependent extracellular virulence factors was diminished. Moreover, the loss of clpP leads to a complete transcriptional derepression of genes of the CtsR- and HrcA-controlled heat shock regulon and a partial derepression of genes involved in oxidative stress response, metal homeostasis, and SOS DNA repair controlled by PerR, Fur, MntR, and LexA. The levels of transcription of genes encoding proteins involved in adaptation to anaerobic conditions potentially regulated by an Fnr-like regulator were decreased. Furthermore, the expression of genes whose products are involved in autolysis was deregulated, leading to enhanced autolysis in the mutant. Our results indicate a strong impact of ClpP proteolytic activity on virulence, stress response, and physiology in S. aureus.
Omitting vitamin and trace mineral premixes from diets during late finishing (190 to 250 lb) did not reduce growth performance, carcass leanness, or muscle quality (1995)

Average daily gain; F/G; dressing percentage; tenth rib fat thickness; and depth, marbling, color, and firmness of the longissimus muscle were not influenced by omitting the vitamin and(or) trace mineral premixes from diets during late finishing (190 to 250 lb). Thus, our data suggest that the KSU vitamin and trace mineral premixes can be omitted during late finishing to reduce cost of gain without decreasing growth performance, carcass merit, or muscle quality.; Swine Day, Manhattan, KS, November 16, 1995
Digital PCR on a SlipChip (2010)

This paper describes a SlipChip to perform digital PCR in a very simple and inexpensive format. The fluidic path for introducing the sample combined with the PCR mixture was formed using elongated wells in the two plates of the SlipChip designed to overlap during sample loading. This fluidic path was broken up by simple slipping of the two plates that removed the overlap among wells and brought each well in contact with a reservoir preloaded with oil to generate 1280 reaction compartments (2.6 nL each) simultaneously. After thermal cycling, end-point fluorescence intensity was used to detect the presence of nucleic acid. Digital PCR on the SlipChip was tested quantitatively by using Staphylococcus aureus genomic DNA. As the concentration of the template DNA in the reaction mixture was diluted, the fraction of positive wells decreased as expected from the statistical analysis. No cross-contamination was observed during the experiments. At the extremes of the dynamic range of digital PCR the standard confidence interval determined using a normal approximation of the binomial distribution is not satisfactory. Therefore, statistical analysis based on the score method was used to establish these confidence intervals. The SlipChip provides a simple strategy to count nucleic acids by using PCR. It may find applications in research applications such as single cell analysis, prenatal diagnostics, and point-of-care diagnostics. SlipChip would become valuable for diagnostics, including applications in resource-limited areas after integration with isothermal nucleic acid amplification technologies and visual readout.
Bis C-Glycosylated Diphenylmethanes for Stable Glycoepitope Mimetics (1999)

Bis C-glycosylated diphenylmethanes, in which two sugar units protrude from a diphenylmethane scaffold by C-glycosylated bonds, were synthesized as versatile glycoepitope mimetics using C-glycosylated aryl tins and C-glycosylated benzyl bromides. The synthetic method was applied to the synthesis of a sLeX mimetic. Besides, triphenylphosphine oxide was found to be a crucial additive in the Stille coupling reaction.
TNF-□ Reduces the Activity of Ecto-5′-Nucleotidase in Human Endothelial Cells (2006)

Ecto-5’-nucleotidase is a membrane linked enzyme anchored by a phospholipase C (PLC) sensitive glycosyl phosphoinositol (GPI) linkage and is responsible for the generation of adenosine from AMP. Adenosine is involved in a number cardioprotective mechanisms1 . Recently, adenosine was found to attenuate the production of tumour necrosis factor-α (TNFα) through the stimulation of the A2a and A3 receptors 2. TNFα is a pro-inflammatory cytokine implicated in ischaemia-reperfusion injury, sepsis, chronic heart failure, viral myocarditis, and cardiac allograft rejection3. TNFα stimulates many independent signalling pathways, including activation of p38 mitogen activated protein kinase, Ras, NF-kB and phospholipases3 and thus may affect expression of membrane linked enzymes. In the present study, we investigated the effects of TNF-α on the activity of ecto5’ -nucleotidase and other adenosine metabolising enzymes
Acoustofluidics 2: Perturbation theory and ultrasound resonance modes (2011)

In the second part of the thematic tutorial series "Acoustofluidics--exploiting ultrasonic standing waves forces and acoustic streaming in microfluidic systems for cell and particle manipulation", we develop the perturbation theory of the acoustic field in fluids and apply the result in a study of acoustic resonance modes in microfluidic channels.
Changes of Structure and Species Composition of Degraded Plant Community along Disturbance Gradients of Different Intensities (2000)

Structure and species composition of degraded plant community, along a human-induced disturbance gradient in Dagou watershed of the upper reaches of the Minjiang River, were investigated. In general, attributes of woody-layer structure (density, height, basal area, species diversity and biomass) were negatively related with increasing disturbance. Herbaceous layer attributes (coverage, biomass, diversity, ecological dominance etc.) responded positively. This may be common response of various plant communities on disturbance except their density attribute. Although individual woody species exhibited a range of responses to disturbance, overall species compositional changes were not related directly to the intensity of disturbance. According to their response along the human-induced disturbance gradient, 47 species were classified into three behavioral species groups: 16 in the invasive, 6 in the sensitive and 25 in the tolerant. Some useful conclusions were drawn: (a) degraded endpoint of scrub community in Dagou watershed may be marquises in which dominant species are those shrubs in the invasive species response group; (b) plant community degraded as a major form of structural decline, its species compositional change have hysteresis effect, and community structure may be more sensitive indicator to disturbance than species composition. How to restore and rehabilitate the degraded community has also been discussed in the paper.