gebhart/patrepeval huggingface dataset:
Characterization of the rat carbonic anhydrase II gene structure: sequence analysis of the 5′ flanking region and 3′ UTR (1997)

The rat carbonic anhydrase II gene was characterized and found to be approximately 15.5 kb in length and to contain 7 exons and 6 introns. All intron/exon junction and branch point sequences conform to consensus sequences, and the overall rat CA II genomic structure appears to be conserved upon comparison with mouse, human, and chicken CA II genes. The putative cis-acting elements within the analyzed 1014 bp 5' flanking region include: TATA box, 4 Sp1 binding sites, 2 AP2 sites and putative tissue-specific beta-globin-like repeat elements. A CpG island of approximately 800 bp was identified that begins about 600 bp upstream of exon 1 and extends about 200 bp into intron 1. In the 3' UTR, two polyadenylation signals (AATAAA) are present, the second of which is believed to be utilized. Northern blot analysis reveals that the 1.7 kb rat CA II mRNA is abundantly expressed in adult male brain and kidney, while negligible amounts are detected in heart and liver.
Sulforaphane and its glutathione conjugate but not sulforaphane nitrile induce UDP-glucuronosyl transferase (UGT1A1) and glutathione transferase (GSTA1) in cultured cells (2002)

Glucoraphanin in Brassica vegetables breaks down to either sulforaphane or sulforaphane nitrile depending on the conditions, and sulforaphane can be further conjugated with glutathione. Using a high-throughput microtitre plate assay and TaqMan real time quantitative RT-PCR to measure mRNA, we show that sulforaphane and its glutathione conjugate, but not the nitrile, increased significantly (P < 0.05) both UGT1A1 and GSTA1 mRNA levels in HepG2 and HT29 cells. These changes were accompanied by an increase in UGT1A1 protein, as assessed by immunoblotting, and a 2-8-fold increase in bilirubin glucuronidation. When treated together, the nitrile derivative did not affect sulforaphane induction. The induction of UGT1A1 and GSTA1 mRNA by sulforaphane was time and concentration dependent. The results show a functional induction of glucuronidation by sulforaphane but not sulforaphane nitrile, and show that the pathway of metabolism of glucosinolates in Brassica vegetables is important in determining the resulting biological and anticarcinogenic activities.
Environmental benefits of methanesulfonic acid (1999)

This paper reviews some chemical and physical characteristics of methanesulfonic acid and the short-chain alkanesulfonic acids in general. The aqueous solubility of metal methanesulfonates, the conductivity of aqueous methanesulfonic acid (MSA) solutions and the low toxicity of MSA all make MSA(aq) an ideal electrolyte for many electrochemical processes, especially those involving tin and lead. Aspects of aqueous process effluent treatment, acid recovery and metal alkanesulfonate salt preparation are also environmentally favorable. Emphasis in this paper is given to rationalizing the rapidly growing commercial preference for MSA(aq) as an electrochemical electrolyte, especially with respect to the substitution of MSA for HBF4 in the electroplating of Sn/Pb solder. Economic aspects of MSA are also considered.
Autologous Bone-Marrow Mononuclear Cell Implantation Improves Endothelium-Dependent Vasodilation in Patients With Limb Ischemia (2004)

These findings suggest that BM-MNC implantation augments endothelium-dependent vasodilation in patients with limb ischemia.
A prognostic index for ductal carcinoma in situ of the breast (1996)

DCIS patients with VNPI scores of 3 or 4 can be considered for treatment with excision only. Patients with intermediate scores (5, 6, or 7) show a 17% decrease in local recurrence rates with radiation therapy. Patients with VNPI scores of 8 or 9 exhibit extremely high local recurrence rates, regardless of irradiation, and should be considered for mastectomy.
A sEMG-based method for assessing the design of computer mice (2005)

Computer users who experience repetitive wrist movements and awkward hand positions are prone to developing upper extremity disorders. Manufacturers have designed various ergonomic mice in response to complaints of pain and discomfort related to computer mouse use. The objective of this work was to validate the use of surface electromyography (sEMG) in assessing the design of nonkeyboard input devices (computer mice). While holding the computer mouse in different grasp positions sEMG of the forearm and hand were recorded during a set of static tasks. The sEMG signal provided information regarding the level of muscle activity and the varied combinations of muscular effort needed to position the hand in a specified posture. A significant decrease in the level of sEMG activity was observed for the pronator muscles when subjects were tested using ergonomic computer mice. The sEMG-based method was validated to be sensitive to the impact of subtle differences in shape/design on the amplitude of the surface EMG data. We also proved a significant effect of hand size and grasp position on the level of muscle activity associated with different mice.
Elimination of viruses, bacteria and protozoan oocysts by slow sand filtration (2004)

The decimal elimination capacity (DEC) of slow sand filters (SSF) for viruses, bacteria and oocysts of Cryptosporidium has been assessed from full-scale data and pilot plant and laboratory experiments. DEC for viruses calculated from experimental data with MS2-bacteriophages in the pilot plant filters was 1.5-2 log10. E. coli and thermotolerant coliforms (Coli44) were removed at full-scale and in the pilot plant with 2-3 log10. At full-scale, Campylobacter bacteria removal was 1 log10 more than removal of Coli44, which indicated that Coli44 was a conservative surrogate for these pathogenic bacteria. Laboratory experiments with sand columns showed 2-3 and >5-6 log10 removal of spiked spores of sulphite-reducing clostridia (SSRC; C. perfringens) and oocysts of Cryptosporidium respectively. Consequently, SSRC was not a good surrogate to quantify oocyst removal by SSF. Removal of indigenous SSRC by full-scale filters was less efficient than observed in the laboratory columns, probably due to continuous loading of these filter beds with spores, accumulation and retarded transport. It remains to be investigated if this also applies to oocyst removal by SSF. The results additionally showed that the schmutzdecke and accumulation of (in)organic charged compounds in the sand increased the elimination of microorganisms. Removal of the schmutzdecke reduced DEC for bacteria by +/-2 log10, but did not affect removal of phages. This clearly indicated that, besides biological activity, both straining and adsorption were important removal mechanisms in the filter bed for microorganisms larger than viruses.
Nomenclature of organic chemistry : IUPAC recommendations and preferred names 2013 (2014)

General Principles, Rules, and Conventions Parent Hydrides Characteristic (Functional) and Substituent Groups Rules for Name Construction Selecting Preferred IUPAC Names and Constructing Names of Organic Compounds Applications to Specific Classes of Compounds Radicals, Ions, and Related Species Isotopically Modified Compounds Specification of Configuration and Conformation Parent Structures for Natural Products and Related Compounds References Appendix 1 Appendix 2 Appendix 3
A biodegradable bovine collagen membrane as a dermal template for human in vivo wound healing (2001)

A bovine collagen membrane was used as a template for dermal regeneration in human full thickness wounds. Healing was allowed for 7, 21, or 42 days. The formation of neodermis, basement membrane, and terminal differentiation were assessed histologically and immunohistochemically. The collagen template was neovascularised within 7 days, and from day 21 small vessels were detected throughout the transplanted area. The procollagen content decreased whereas the number of fibroblasts increased with time. Collagen type IV was not detected after 7 days but was deposited with time from the wound edges and inwards over the transplanted area. Re-epithelialisation was complete at day 7 and terminal differentiation was similar to normal human skin from day 21. We have shown the time course of dermal and epidermal healing with the aid of a ready-to-use biodegradable collagen membrane. This material may be used as a true dermal template-because of the evidence of dermal regeneration and, in addition, its availability and ease of handling.
Epidemiology and Mortality Risk of Vancomycin-Resistant Enterococcal Bloodstream Infections (1995)

Risk factors for vancomycin-resistant enterococcal (VRE) bloodstream infection (BSI) were studied at a tertiary-care hospital by comparing 46 patients with VRE-BSI with 46 randomly selected patients with vancomycin-susceptible enterococcal (VSE) BSI. Among patients with an enterococcal BSI, risk factors for mortality were determined. Independent risk factors for VRE-BSI were increasing APACHE II score (odds ratio [OR], 2.3/5-point increase; 95% confidence interval [CI], 1.4-3.9), receipt of vancomycin (OR, 11; 95% CI, 5.5-21), or diagnosis of hematologic malignancy (OR, 8.4; 95% CI, 3.9-18). After controlling for APACHE II score and gender, patients with VRE- versus VSE-BSI did not have a significantly elevated risk of mortality (OR, 3.3; 95% CI, 0.7-15). Five of 28 VRE blood isolates typed using pulsed-field gel electrophoresis had identical banding patterns. These data suggest that increasing severity of illness, underlying disease, and receipt of vancomycin are major risk factors for VRE-BSI.
Gecko‐Inspired Controllable Adhesive Structures Applied to Micromanipulation (2012)

Abstract Gecko‐inspired angled elastomer micropillars with flat or round tip endings are presented as compliant pick‐and‐place micromanipulators. The pillars are 35 μm in diameter, 90 μm tall, and angled at an inclination of 20°. By gently pressing the tip of a pillar to a part, the pillar adheres to it through intermolecular forces. Next, by retracting quickly, the part is picked from a given donor substrate. During transferring, the adhesion between the pillar and the part is high enough to withstand disturbances due to external forces or the weight of the part. During release of the part onto a receiver substrate, the contact area of the pillar to the part is drastically reduced by controlled vertical or shear displacement, which results in reduced adhesive forces. The maximum repeatable ratio of pick‐to‐release adhesive forces is measured as 39 to 1. It is found that a flat tip shape and shear displacement control provide a higher pick‐to‐release adhesion ratio than a round tip and vertical displacement control, respectively. A model of forces to serve as a framework for the operation of this micromanipulator is presented. Finally, demonstrations of pick‐and‐place manipulation of micrometer‐scale silicon microplatelets and a centimeter‐scale glass cover slip serve as proofs of the concept. The compliant polymer micropillars are safe for use with fragile parts, and, due to exploiting intermolecular forces, could be effective on most materials and in air, vacuum, and liquid environments.
NUCLEOCYTOPLASMIC TRANSPORT: The Soluble Phase (1998)

Active transport between the nucleus and cytoplasm involves primarily three classes of macromolecules: substrates, adaptors, and receptors. Some transport substrates bind directly to an import or an export receptor while others require one or more adaptors to mediate formation of a receptor-substrate complex. Once assembled, these transport complexes are transferred in one direction across the nuclear envelope through aqueous channels that are part of the nuclear pore complexes (NPCs). Dissociation of the transport complex must then take place, and both adaptors and receptors must be recycled through the NPC to allow another round of transport to occur. Directionality of either import or export therefore depends on association between a substrate and its receptor on one side of the nuclear envelope and dissociation on the other. The Ran GTPase is critical in generating this asymmetry. Regulation of nucleocytoplasmic transport generally involves specific inhibition of the formation of a transport complex; however, more global forms of regulation also occur.
Regional perspectives on World Development Report 1995 : involving workers in East Asia's growth (1996)

This report, a summary of the key messages of World Development Report 1995: Workers in an Integrating World, reviews East Asia's development from the perspective of labor and explores the new challenges faced by the region's governments and workers. It shows how good policies have been central to workers' gains in the past and discusses the implications of globalization, the problems faced by many workers, the complex requirements for better labor policy, and the special difficulties faced by transition economies. The report concludes that the future is potentially bright for East Asia's workers, but only if the new policy and institutional challenges are effectively met. The key areas for policy vary greatly by development stage. They include sound basic education and agricultural development strategies in Indochina, dealing with the special needs of China's state enterprise workers in the process of transition, modernizing labor policy in many economies, and managing the process of labor upgrading in a world of shifting comparative advantage in East Asia's newly industrializing economies. Special attention needs to be paid to the vulnerable. In all these areas the involvement of workers in the process of social and economic change is critical to the welfare of nations and to the lives of the workers and their families.
Involvement of a NF-kappa B-like transcription factor in the activation of the interleukin-6 gene by inflammatory lymphokines. (1990)

Interleukin-6 (IL-6) is one of the major mediators of inflammation, and its expression is inducible by the other inflammatory lymphokines, interleukin-1 (IL-1) and tumor necrosis factor alpha (TNF-alpha). We demonstrate that a common IL-6 promoter element, termed inflammatory lymphokine-responsive element (ILRE), is important for induction of IL-6 gene expression by IL-1 and TNF-alpha despite possible differences in the mechanisms of action of these lymphokines. Remarkably, the ILRE sequence, located between -73 to -63 relative to the mRNA cap site, is highly homologous to NF-kappa B transcription factor-binding motifs and binds an IL-1-TNF-alpha-inducible nuclear factor; the sequence specificities, binding characteristics, and subcellular localizations of this factor are indistinguishable from those of NF-kappa B. In addition, mutations of the ILRE sequence which impair the binding of this nuclear factor abolished the induction of IL-6 gene expression by IL-1 and TNF-alpha in vivo. These results indicate that a nuclear factor indistinguishable from NF-kappa B is involved in the transcriptional activation of the IL-6 gene by IL-1 and TNF-alpha.
Genetic Correction of Hereditary Disease (1989)

Several hereditary disorders may be potentially correctable by the introduction and incorporation of the normal gene into human tissues using a variety of systems. Although technical issues surrounding integration, stable expression and potential insertional mutagenesis to the treated cells has not yet been fully resolved, enough scientific progress has already been made to consider somatic cell gene therapy acceptable from both the scientific and ethical viewpoints. Tissue-specific stem cell and embryonic stem cell transplantation will allow therapy earlier in the developing embryo. As technical problems are eliminated, these procedures will become morally permissible, as they will allow the correction of devastating hereditary disease.
Guidelines for the Recording and Evaluation of Pharmaco-EEG Data in Man: The International Pharmaco-EEG Society (IPEG) (2012)

The International Pharmaco-EEG Society (IPEG) presents guidelines summarising the requirements for the recording and computerised evaluation of pharmaco-sleep data in man. Over the past years, technical and data-processing methods have advanced steadily, thus enhancing data quality and expanding the palette of sleep assessment tools that can be used to investigate the activity of drugs on the central nervous system (CNS), determine the time course of effects and pharmacodynamic properties of novel therapeutics, hence enabling the study of the pharmacokinetic/pharmacodynamic relationship, and evaluate the CNS penetration or toxicity of compounds. However, despite the presence of robust guidelines on the scoring of polysomnography -recordings, a review of the literature reveals inconsistent -aspects in the operating procedures from one study to another. While this fact does not invalidate results, the lack of standardisation constitutes a regrettable shortcoming, especially in the context of drug development programmes. The present guidelines are intended to assist investigators, who are using pharmaco-sleep measures in clinical research, in an effort to provide clear and concise recommendations and thereby to standardise methodology and facilitate comparability of data across laboratories.
Kinetic Investigation of Reaction Between Metallic Silver and Nitric Acid Solutions (2000)

In this study, the reaction kinetics between metallic silver and nitric acid solutions was investigated by taking into consideration the parameters of temperature, solid-to-liquid ratio, stirring speed, nitric acid concentration, particle size and addition of sodium nitrite. It was determined that the dissolution rate of the process increased with decreasing particle size and solid-to-liquid ratio, and increasing nitric acid concentration, reaction temperature and the amount of the sodium nitrite in the solution. In addition, it was observed that the stirring speed had more effect on the dissolution rate at low stirring speeds than at high stirring speeds. In the present study, the examination of shrinking core models of fluid-solid systems showed that the dissolution of metallic silver in the nitric acid solutions was controlled by the reaction on the surface. A semiempirical model, which represented well the process, was developed by statistical methods. The activation energy of the process was found to be 57.66 kJ mol–1.
Assessing combined methylation–sensitive high resolution melting and pyrosequencing for the analysis of heterogeneous DNA methylation (2011)

Heterogeneous DNA methylation leads to difficulties in accurate detection and quantification of methylation. Methylation-sensitive high resolution melting (MS-HRM) is unique among regularly used methods for DNA methylation analysis in that heterogeneous methylation can be readily identified, although not quantified, by inspection of the melting curves. Bisulfite pyrosequencing has been used to estimate the level of heterogeneous methylation by quantifying methylation levels present at individual CpG dinucleotides. Sequentially combining the two methodologies using MS-HRM to screen the amplification products prior to bisulfite pyrosequencing would be advantageous. This would not only replace the quality control step using agarose gel analysis prior to the pyrosequencing step but would also provide important qualitative information in its own right. We chose to analyze DAPK1 as it is an important tumor suppressor gene frequently heterogeneously methylated in a number of malignancies, including chronic lymphocytic leukemia (CLL). A region of the DAPK1 promoter was analyzed in ten CLL samples by MS-HRM. By using a biotinylated primer, bisulfite pyrosequencing could be used to directly analyze the samples. MS-HRM revealed the presence of various extents of heterogeneous DAPK1 methylation in all CLL samples. Further analysis of the biotinylated MS-HRM products by bisulfite pyrosequencing provided quantitative information for each CpG dinucleotide analyzed, and confirmed the presence of heterogeneous DNA methylation. Whereas each method could be used individually, MS-HRM and bisulfite pyrosequencing provided complementary information for the assessment of heterogeneous methylation.
Covalent immobilization of DNA onto glassy carbon electrodes (1992)

Abstract Denatured calf thymus deoxyribonucleic acid (DNA) and synthetic poly(dG)poly(dC) have been covalently immobilized onto oxidized glassy carbon electrode surfaces using the water‐soluble carbodiimide, 1‐(3‐dimethylaminopropyl)‐3‐ethylcarbodiimide. Immobilized DNA has been detected using the complex Co(bpy) (bpy = 2,2′ ‐bipyridine). This complex has a reversible one‐electron oxidation ( E o ′ = 0.33 V versus SHE), binds electrostatically in the minor groove of the DNA double helix, and preconcentrates at the surface of the DNA‐modified electrode prior to a voltammetric scan. Our cyclic voltammetric data indicate that larger Co(bpy) signals are observed at low ionic strength; this is consistent with the larger association constants obtained for the binding of Co(bpy) with calf thymus DNA at low ionic strength. While immobilizations were attempted for four species, poly(dA)poly(dT), native calf thymus DNA, denatured calf thymus DNA, and poly(dG)poly(dC), only the last two species could be successfully immobilized with the carbodiimide procedure; these results show that guanosine and/or cytosine bases will bind covalently to the o‐acylisourea on the glassy carbon surface.
Upregulation of a Silent Sodium Channel After Peripheral, but not Central, Nerve Injury in DRG Neurons (1999)

After transection of their axons within the sciatic nerve, DRG neurons become hyperexcitable. Recent studies have demonstrated the emergence of a rapidly repriming tetrodotoxin (TTX)-sensitive sodium current that may account for this hyperexcitability in axotomized small (<27 microm diam) DRG neurons, but its molecular basis has remained unexplained. It has been shown previously that sciatic nerve transection leads to an upregulation of sodium channel III transcripts, which normally are present at very low levels in DRG neurons, in adult rats. We show here that TTX-sensitive currents in small DRG neurons, after transection of their peripheral axonal projections, reprime more rapidly than those in control neurons throughout a voltage range of -140 to -60 mV, a finding that suggests that these currents are produced by a different sodium channel. After transection of the central axonal projections (dorsal rhizotomy) of these small DRG neurons, in contrast, the repriming kinetics of TTX-sensitive sodium currents remain similar to those of control (uninjured) neurons. We also demonstrate, with two distinct antibodies directed against different regions of the type III sodium channel, that small DRG neurons display increased brain type III immunostaining when studied 7-12 days after transection of their peripheral, but not central, projections. Type III sodium channel immunoreactivity is present within somata and neurites of peripherally axotomized, but not centrally axotomized, neurons studied after <24 h in vitro. Peripherally axotomized DRG neurons in situ also exhibit enhanced type III staining compared with control neurons, including an accumulation of type III sodium channels in the distal portion of the ligated and transected sciatic nerve, but these changes are not seen in centrally axotomized neurons. These observations are consistent with a contribution of type III sodium channels to the rapidly repriming sodium currents observed in peripherally axotomized DRG neurons and suggest that type III channels may at least partially account for the hyperexcitibility of these neurons after injury.