gebhart/patrepeval huggingface dataset:
Isolation and characterization of the bovine k‐casein gene (1988)

1. The bovine kappa-casein gene has been isolated as a series of overlapping lambda clones and shown to consist of five exons distributed over a total length of approximately 13 kb. Most of the mature protein-coding sequence is contained in a single large exon. 2. Approximately 65% of the gene has been sequenced together with portions of the 5'- and 3'-flanking sequences. The immediate 5'-flanking sequence contains several motifs which are characteristic of upstream regions including a TATA box, a CAAT box, a sequence similar to that recognized by transcription factor AP-1 and a purine-rich sequence resembling that found upstream in all other lactoprotein genes. Other possible regulatory sequences are found upstream of exon 4. 3. The organization of the kappa-casein gene, together with its upstream sequence, confirms previous conclusions that it is unrelated to the calcium-sensitive-casein gene family to which it is linked. Evidence is presented which supports a previous suggestion that kappa-casein and the fibrinogens are evolutionarily related. 4. Intron sequences contain several examples of the A family of the artiodactyl Alu-like repeated sequences, together with a single example of a C-family sequence. The remainders of the introns of the kappa-casein gene, compared with the repeat elements and exons, are A + T-rich. 5. Among the lambda clones isolated, representatives were found of the A and B genetic variants which can be distinguished by restriction-enzyme analysis. Several other examples of polymorphisms in the non-coding region were found.
Transformation of intestinal stem cells into gastric stem cells on loss of transcription factor Cdx2 (2014)

The endodermal lining of the adult gastro-intestinal tract harbours stem cells that are responsible for the day-to-day regeneration of the epithelium. Stem cells residing in the pyloric glands of the stomach and in the small intestinal crypts differ in their differentiation programme and in the gene repertoire that they express. Both types of stem cells have been shown to grow from single cells into 3D structures (organoids) in vitro. We show that single adult Lgr5-positive stem cells, isolated from small intestinal organoids, require Cdx2 to maintain their intestinal identity and are converted cell-autonomously into pyloric stem cells in the absence of this transcription factor. Clonal descendants of Cdx2(null) small intestinal stem cells enter the gastric differentiation program instead of producing intestinal derivatives. We show that the intestinal genetic programme is critically dependent on the single transcription factor encoding gene Cdx2.
Mass spectrometric analysis of tobacco-specific nitrosamine hemoglobin adducts in snuff dippers, smokers, and nonsmokers. (1990)

Hemoglobin adducts of the carcinogenic tobacco-specific nitrosamines 4-(methylnitrosamino)-1(3-pyridyl)-1-butanone and N'-nitrosonornicotine were quantified in blood samples collected from snuff dippers, smokers, and nonsmokers. Mild base treatment of hemoglobin adducted by 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone or N'-nitrosonornicotine releases 4-hydroxy-1-(3-pyridyl)-1-butanone (HPB). HPB was enriched by solvent partitioning and derivatized to its pentafluorobenzoate. After purification by high performance liquid chromatography, HPB-pentafluorobenzoate was analyzed by capillary column gas chromatography with detection by negative ion chemical ionization mass spectrometry and selected ion monitoring. [4,4-D2]HPB was used as internal standard. The detection limit for HPB-pentafluorobenzoate was approximately 100 amol/injection or 5 fmol/g hemoglobin. Mean adduct levels (fmol HPB/g hemoglobin) were 517 +/- 538 (SD) in snuff dippers, 79.6 +/- 189 in smokers, and 29.3 +/- 25.9 in nonsmokers. Adduct levels in snuff dippers and in a subgroup of smokers were higher than would have been predicted solely based on estimates of exposure to tobacco-specific nitrosamines. The results of this study provide the first measurements of tobacco-specific nitrosamine hemoglobin adducts in humans and suggest new approaches to understanding the metabolic activation of 4-(methyl-nitrosamino)-1-(3-pyridyl)-1-butanone and N'-nitrosonornicotine in humans.
Biological Dressings and Evaporative Water Loss from Burn Wounds (1980)

Increased evaporative water loss following thermal injury sometimes results in electrolyte abnormalities, negative nitrogen balance, and hypothermia. Because different biological dressings have been claimed effective in diminishing evaporative loss, a prospective study was designed to compare them. Cadaver allograft, porcine xenograft (sheet and meshed), and amnion were placed on 28 granulating wounds for twenty-four hours. Water loss was then measured with an Evaporimeter, revealing that in both full-thickness and partial thickness wounds, allograft was twice as effective as sheet porcine and five times as effective as meshed porcine or amnion. In the absence of available cadaver allografts, sheet porcine xenograft is a satisfactory substitute for use on granulating wounds to diminish evaporative water loss, while amnion and meshed porcine are less effective.
Establishment and characterization of a new human prostatic cancer cell line: DuCaP. (2001)

This cell line exhibits many phenotypic characteristics of clinical prostate carcinoma, including expression of PSA, PSMA, PAP and AR.
Inhibition of rat vascular smooth muscle proliferation in vitro and in vivo by bone morphogenetic protein-2. (1997)

Vascular proliferative disorders are characterized by the proliferation of vascular smooth muscle cells (SMCs) and excessive extracellular matrix synthesis. We found that bone morphogenetic protein-2 (BMP-2) inhibited serum-stimulated increases in DNA synthesis and cell number of cultured rat arterial SMCs in a fashion quite different from that in the case of transforming growth factor-beta1 (TGF-beta1). In addition, TGF-beta1 stimulated collagen synthesis in SMCs, whereas BMP-2 did not. In an in vivo rat carotid artery balloon injury model, the adenovirus-mediated transfer of the BMP-2 gene inhibited injury-induced intimal hyperplasia. These results indicate that BMP-2 has the ability to inhibit SMC proliferation without stimulating extracellular matrix synthesis, and suggest the possibility of therapeutic application of BMP-2 for the prevention of vascular proliferative disorders.
Short-step chemical synthesis of DNA by use of MMTrS group for protection of 5' hydroxyl group (2007)

4-methoxytrithylthio (MMTrS) group was applied for the appropriately protected four canonical nucleosides. We prepared the phosphoroamidite units by use of these nucleosides and developed the synthesis of oligodeoxynucleotides without any acidic treatment. Moreover, the new DNA synthesis protocol was applied to an automated DNA synthesizer for the synthesis of longer oligodeoxynucleotides.
Characterization of homologous DNA recombination activity in normal and immortal mammalian cells (1996)

Homologous DNA recombination levels were measured in normal and spontaneously immortalized murine and human fibroblasts, and in a number of primate and murine established fibroblast cell lines. Immortal cell lines and tumor-derived clones homologously recombined extrachromosomal plasmid substrates at frequencies approximately 100-fold higher than did normal cells. To further explore the mechanism responsible for this phenotype, homologous recombination frequency was measured using nuclear extracts derived from normal and immortalized murine and human fibroblasts. Extracts prepared from immortal cells catalyzed high levels of homologous recombination, whereas very little recombination activity was detected in extracts prepared from normal fibroblasts. Similarly, only extracts derived from immortal cells contained strand-transferase activity as measured by the recently described pairing-on-membrane assay. Mixing experiments indicated that a recombination enhancing factor or factors present in immortal cells, rather than a recombination inhibitor in normal cells, was responsible for the enhanced homologous recombination activity observed using extracts derived from the former.
Prevention of diabetes does not completely prevent insulin secretory defects in the ZDF rat (1995)

The rapid insulin secretory pulses that occur in the perfused rat pancreas can be entrained by an oscillatory glucose concentration in pancreata from nondiabetic rats but not from X diabetic Zucker diabetic fatty (ZDF) rats. To investigate whether this defect is present in prediabetic ZDF rats and whether treatment with either pioglitazone or acarbose can prevent or reverse this defect, 39 ZDF and 5 lean ZDF control rats were studied. The ZDF rats were divided into six groups depending on age, form of therapy used, and the time at which pioglitazone was started in relation to the onset of diabetes. The pancreas was isolated and perfused using a sine wave-shaped glucose concentration (mean 7 mM, period 10 min, amplitude 10%). The results, assessed by spectral analysis, revealed that in prediabetic animals and in controls, entrainment of pulsatile insulin secretion was normal. Initiation of pioglitazone therapy in ZDF rats at the time of weaning or before diabetes onset prevented hyperglycemia. However, entrainment was only partially retained. Thus, in these two groups, the spectral power at 10 min was greater than in untreated animals but lower than in prediabetic and control animals. Treatment with acarbose before or with pioglitazone after diabetes onset improved but did not normalize glucose levels, and it did not improve entrainment. The results demonstrate the presence of insulin secretory defects in 13-wk-old ZDF rats in which hyperglycemia was prevented.
Polymap: A Versatile Client-Side Image Map for the Web (1995)

Image mapping techniques have been used to improve the interactivity of graphics-based content on the World Wide Web (WWW). However, the current WWW image-mapping technique requires a very cumbersome setup: a client-server architecture with the server acting as a point-in-polygon decoding engine to the inert client. While the advantages of having the server participate in the client/WWW browser users' activities are controversial, the need to move the decoding task to the browser is apparent, especially when better interactivity is desired. We propose a mechanism (Polymapping) that stores the hotspot information in an otherwise unessential part of the image file---the comment field of existing common image formats. Since adding data in the comment field does not violate most image format standards, this mechanism provides Polymap-enabled WWW browsers the information needed to achieve client-side hotspot decoding while allowing nonenabled clients to remain dependent on the servers.
Fe-Based Catalysts for Oxygen Reduction in PEMFCs (2006)

Fe-based catalysts for the oxygen reduction reaction (ORR) in polymer electrolyte membrane fuel cells (PEMFCs) have been prepared with commercial and developmental carbon black powders containing initially between 0 and 0.8 atom % of nitrogen. The catalysts were obtained by adsorbing 0.2 wt % Fe from iron acetate on each carbon support, which is then pyrolyzed at 900°C for 1 h in a mixture. Under these conditions, N contents from 0 to 2.3 atom % are measured at the surface of the catalysts and increased N content leads to increased activity for the ORR. The N content correlates with the weight loss of the carbon support due to a reaction with during pyrolysis. It was found that reacts mainly with the disorganized carbon, leaving nitrogen at the surface of the support. The larger the amount of disorganized carbon in the pristine carbon black, the better the activity for ORR of the resulting catalyst. The most active non-noble catalyst was tested in fuel cells, where it was found that its specific activity (in A per of electrode) is still about two orders of magnitude below the target of a non-noble catalyst for automotive applications. However, such catalysts could already compete with Pt in, e.g., methanol fuel cells because they are ORR-selective.
Bioactivity and Pharmacological Actions of Carbon Monoxide-Releasing Molecules (2003)

Carbon monoxide (CO) is a resourceful gas as recent advances in the area of cell signaling are revealing an unexpected physiological role for CO in the cardiovascular, immune and nervous systems. Transition metal carbonyls have been lately discovered to function as CO-releasing molecules (CO-RMs) and elicit distinct pharmacological activities in biological systems. Studies currently ongoing in our laboratories are investigating both the chemical and bioactive features of a series of water-soluble CO-RMs and their specific utilization as vasoactive mediators, anti-inflammatory agents and inhibitors of cellular and tissue damage. The data presented in this review corroborate the notion that transition metal carbonyls could be used as carriers to deliver CO in mammals and highlight the bioactivity and potential therapeutic features of CO-RMs in the mitigation of cellular and organ dysfunction.
CCVT transient fundamentals (2012)

Potential transformers and coupling capacitor voltage transformers (CCVT's) have been used successfully for providing voltage to the inputs of meters and relays since the 1960's. At voltage levels above 138kV economics dictate that CCVT's be used to provide secondary voltages to relays. As we'll see later CCVT's consist of a capacitive voltage divider along with a step down transformer and other associated equipment. Placing capacitance in series and shunt to the natural inductance of the power system leads to resonant circuits and RC time constants that affect the faithful reproduction of the primary voltage on the output terminals of the CCVT. These transients weren't a problem for electromechanical relays, but with the advent of faster solid state relays and modern microprocessor relays CCVT transients became a problem that needed attention. This paper will discuss coupling capacitor voltage transformer design. What factors in the design influence the transient behavior of the CCVT. What factors in the power system contribute to the transient behavior of the CCVT. How CCVT transient behavior affects relay performance. Finally, how relay manufacturers take this transient behavior into account in relay design. A Capacitive Voltage Transformer (CVT) is a CCVT without carrier accessories. The paper will use these terms interchangeably. Even though there is a slight difference between the two, the portion of the device in that pertains to the transient response is the same.
The Role of Rapid Urine Myoglobin Test in Early Detection of Renal Involvement in Crushing Injury: Possible Implication in Disaster Medicine (2004)

To investigate the role of rapid urine test for myoglobin in early detection of renal involvement in crushing injury, we underwent a prospective investigation to study a urine rapid test specific for myoglobin in the specific population. Fifty-four consecutive patients presenting with crushing injury and a serum creatine kinase (CK) of >5000 IU/L from 1999 to 2001 have been enrolled as study population. Serum CK and its isoenzyme CK-MB, serum and urine myoglobin were also measured. A urine rapid myoglobin test was also performed as comparisons. All of the victims with crushing injury accepted standard medical and surgical treatment as indicated. The rate of renal involvement was about 56% (30 out of 54 patients). Urine myoglobin was present in 29 of these 30 victims (97%) with renal involvement and 2 of 24 patients (8%) without it by the rapid urine myoglobin test. The cut-off value of positive rapid urine myoglobin test was around 50 nmol/L by the ROC analysis with the sensitivity of 98% [95% CI 92-100%] and the specificity 86% [95% CI 80-92%]. In conclusion, the rapid urine myoglobin test can provide a rapid and reliable test for early detection of renal involvement in crushing injury.(Ann Disaster Med. 2004;2:80-85)
Optimal and suboptimal control of switching systems (2004)

An optimal control problem for a switching system is solved; no assumptions about the number of switches nor about the mode sequence are made. They are determined by the solution of the problem. The switching system is embedded into a larger family of systems and the optimization problem is formulated for the latter. It is shown that the set of trajectories of the switching system is dense in the set of trajectories of the embedded system. Sufficient and necessary conditions for optimally are formulated for the second optimization problem. If they exist, bang-bang type solutions of the embedded optimal control problem are solutions of the original problem. Otherwise, suboptimal solutions are obtained via the Chattering Lemma.
Brain Anatomical Structure Segmentation by Hybrid Discriminative/Generative Models (2008)

In this paper, a hybrid discriminative/generative model for brain anatomical structure segmentation is proposed. The learning aspect of the approach is emphasized. In the discriminative appearance models, various cues such as intensity and curvatures are combined to locally capture the complex appearances of different anatomical structures. A probabilistic boosting tree (PBT) framework is adopted to learn multiclass discriminative models that combine hundreds of features across different scales. On the generative model side, both global and local shape models are used to capture the shape information about each anatomical structure. The parameters to combine the discriminative appearance and generative shape models are also automatically learned. Thus, low-level and high-level information is learned and integrated in a hybrid model. Segmentations are obtained by minimizing an energy function associated with the proposed hybrid model. Finally, a grid-face structure is designed to explicitly represent the 3-D region topology. This representation handles an arbitrary number of regions and facilitates fast surface evolution. Our system was trained and tested on a set of 3-D magnetic resonance imaging (MRI) volumes and the results obtained are encouraging.
Highly water-soluble neutral near-infrared emissive BODIPY polymeric dyes (2011)

Three highly water-soluble near-infrared emissive polymeric BODIPY dyes (polymers A–C) were prepared by the palladium-catalyzed Suzuki polymerization of highly water-soluble 2,6-diiodo-3,5-distyryl-BODIPY dyes with 1,4-phenyldiboronic acid and 2,7-bis(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-9,9-di[1-[2-(2-methoxyethoxy)ethoxy]ethyl]fluorene, respectively. Partial replacement of fluorine subunits of BODIPY cores at 4,4-positions of polymer C with ethynyl subunits resulted in a highly water-soluble BODIPY polymeric dye (polymer D). Polymers A–D show solubility of at least 20 mg mL−1 in aqueous solution. For comparison purposes, polymers E and F were prepared by palladium-catalyzed Sonogashira polymerization of highly water-soluble 2,6-diiodo-3,5-distyryl-BODIPY dye with highly water-soluble 1,4-diethynylbenzene and 2,6-diethynyl BODIPY dye bearing branched oligo(ethylene glycol)methyl ether residues, respectively. Upon comparison, polymer E shows low solubility in aqueous solution (0.1 mg mL−1), whereas polymer F is almost insoluble in aqueous solution (less than 0.05 mg mL−1), but both are soluble in organic solvents such as chloroform, DMSO and DMF (at least 10 mg mL−1).
Sorption-Enhanced Hydrogen Production: A Review (2008)

In the sorption-enhanced hydrogen production process, hydrocarbon reforming, water gas shift, and CO2 separation reactions occur simultaneously in a single reaction step over a reforming catalyst mixed with a CO2 sorbent. Transferring CO2 as it is formed from the gas to the solid phase shifts the normal equilibrium restrictions and allows both the reforming and water gas shift reactions to approach completion. Depending on reaction conditions, the product (dry basis) may contain as much as 98% H2 and only ppmv levels of CO and CO2, thereby minimizing the final H2 purification step or even eliminating it for some applications. A number of CO2 sorbents have been studied including calcium-based oxides, K-promoted hydrotalcite, and mixed metal oxides of lithium and sodium. The sorbent is consumed during H2 production so that the process is intrinsically unsteady state. Process economics requires that the sorbent be regenerable and used in many reaction−regeneration cycles. Regeneration may occur via temperature swing, pressure swing, or a combination. Much of the current research is devoted to testing and improving sorbent multicycle durability. Both circulating fluid-bed reactors and dual fixed-bed reactors with alternating reaction−regeneration functions have been proposed to provide overall steady state H2 production.
Seven-bit reconfigurable optical true time delay line based on silicon integration (2014)

We design, fabricate, and characterize a 7-bit reconfigurable optical true time delay line consisting of Mach-Zehnder interferometer (MZI) switches on the silicon photonics platform. Variable optical attenuators (VOAs) are embedded to suppress the inter-symbol crosstalk caused by the finite extinction ratio of switches. The device can provide a maximum of 1.27 ns delay with a 10 ps resolution over a wide wavelength range. Eye diagram measurement of a 25 Gbps 2(51)-1 pseudo-random bit sequence (PRBS) signal reveals the power penalties only increase 0.17 dB and 0.77 dB after transmission through the shortest (reference) and the longest (1.27 ns delay) paths, respectively.
Separation of Metallic and Semiconducting Single‐Walled Carbon Nanotubes via Covalent Functionalization (2007)

Chemical functionalization can help separate semiconducting from metallic single-walled carbon nanotubes (SWNTs). Depending on their geometry, SWNTs can be either metallic or semiconducting (see image). They are so far the only known material to possess this unique property. For electronic applications it is of vital importance to separate the two materials. Recent advances in separation techniques, based on chemical functionalization, are described.
Localization of the cleavage site specificity determinant of Haemophilus influenzae immunoglobulin A1 protease genes (1990)

Immunoglobulin A1 (IgA1) proteases are produced by a number of different species of bacteria which cause infection at human mucosal surfaces. The sole substrate of these proteases is human IgA1. Cleavage is within the hinge region of IgA1, although there is variability in the exact peptide bond within the hinge region that is cut by a particular protease. The cleavage site of the Haemophilus influenzae type 1 protease is located four amino acids from the cleavage site of the type 2 enzyme. In this study, the region of the H. influenzae IgA1 protease gene (iga) that determines the cleavage site specificity was localized through the comparison of the type 1 and type 2 genes and the construction and analysis of type 1-type 2 hybrid genes. The hybrid genes were generated by in vivo and in vitro techniques which facilitated the selection and screening of randomly generated hybrids. The cleavage site determinant was found to be within a 370-base-pair region near the amino-terminal coding region, in one of two large areas of nonhomology between the two types of H. influenzae iga genes. DNA sequence analysis of the cleavage site determinant and surrounding regions did not reveal a simple mechanism whereby one enzyme type could be converted to the other type. Comparison of the type 2 gonococcal IgA1 protease gene to the two Haemophilus genes revealed a significant amount of homology around the cleavage site determinant, with the two type 2 genes showing greater homology.