gebhart/patrepeval huggingface dataset:
Human Spot 14 Glucose and Thyroid Hormone Response: Characterization and Thyroid Hormone Response Element Identification (2003)

Spot 14 is a 17-kDa protein expressed in lipogenic tissues and is postulated to play a role in thyroid hormone stimulation of lipogenesis. To further our understanding of Spot 14 regulation in humans, our laboratory recently cloned the human Spot 14 gene. The gene is highly homologous to the rat Spot 14 ortholog and located on a chromosomal region implicated in human obesity. Because our understanding of Spot 14 transcriptional regulation is derived from rat promoter studies, we assessed the thyroid hormone responsivity of the human Spot 14 promoter. These studies revealed a significantly greater thyroid hormone response for the human promoter, compared with the rat. Deletional studies of the human Spot 14 promoter reveal a 774-bp region at approximately position -2700, which is both necessary and sufficient for the thyroid hormone response. EMSAs with subfragments from this region identify a 146-bp DNA fragment capable of binding a TRbeta1-retinoid X receptor heterodimer. Site-directed mutagenesis confirmed the identity of a candidate DR-4 thyroid hormone response element within this fragment that is similar, but not identical, to the two rat Spot 14 thyroid hormone response elements. We hypothesize that the difference in thyroid hormone response between the orthologous promoters may allow a selective advantage to each species based on their different nutritional and physiological niches.
Context-Dependent Bidirectional Regulation of the MutS Homolog 2 by Transforming Growth Factor β Contributes to Chemoresistance in Breast Cancer Cells (2010)

The TGF-β, a tumor suppressive cytokine in normal cells, is abused in cancer to promote the malignancy. In this study, we reported that TGF-β downregulated the mutS homolog 2 (MSH2), a central component of the DNA mismatch repair (MMR) system, in HER2-transformed MCF10A mammary epithelial cells and in breast cancer (BC) cells. This was mediated by a TGF-β-induced micro RNA (miRNA), miR-21, which targeted the 3' untranslated region of MSH2 mRNA and downregulated its expression. A negative correlation between the expression of TGF-β1 and MSH2 was also detected in primary breast tumors. In contrast, TGF-β upregulated MSH2 in nontransformed cells through Smad-mediated, p53-dependent promoter activation, which was absent in BC cells with impaired p53 function. Although this upregulating mechanism also existed in MCF10A/HER2 and p53-proficient BC cells, both basal and TGF-β-induced MSH2 promoter activities were significantly lower than those in MCF10A. Moreover, the basal and TGF-β-induced miR-21 levels were markedly higher in transformed cells, suggesting that the preset levels of miR-21 and MSH2 promoter activity, which is affected by the p53 status, determine the outputs of the bidirectional regulation of MSH2 by TGF-β in a certain cellular context. We further found that by downregulating MSH2, TGF-β contributed to resistance to DNA-damaging chemotherapy agents in cancer cells. Our results indicated a regulatory antagonism between promoter activation and miRNA-mediated posttranscriptional inhibition underlying a dual effect of TGF-β on the DNA repair machinery, which may influence the genomic stability in a context-dependent manner and contribute to chemoresistance in cancer.
In Z-DNA the sequence G-C-G-C is neither methylated by Hha I methyltransferase nor cleaved by Hha I restriction endonuclease. (1984)

Plasmids carrying 24- or 32-base-pair inserts of alternating (dG-dC) residues were used to analyze the level of methylation of the G-C-G-C sites by Hha I DNA methyltransferase and their cleavage by Hha I endonuclease in the B-DNA or Z-DNA conformation. In supercoiled plasmids in which the inserts formed Z-DNA, the extent of methylation at the insert G-C-G-C sites was dramatically lower than the level of methylation at the G-C-G-C sites located outside the insert in the same plasmid. Similarly, cleavage by Hha I endonuclease was sharply lowered when the insert was in the Z-DNA form. In the relaxed plasmid, all its G-C-G-C sites were methylated to the same extent and the unmethylated sites were readily cleaved. After treatment with the methylase, the supercoiled plasmid was linearized and then digested with Hha I restriction endonuclease. This exposed unmethylated G-C-G-C sites from the insert that had been protected against cleavage in the Z conformation. A chemical reaction was used to study the distribution of the unmethylated cytosine residues. No accumulation of unmethylated cytosine residues was found anywhere along the entire 32-base-pair insert, which is consistent with a cooperative B-Z transition.
Differential regulation of human fibroblast growth factor 1 transcripts provides a distinct mechanism of cell-specific growth factor expression. (1997)

Four variants of fibroblast growth factor 1 (FGF-1) mRNA, FGF-1.A, -1.B, -1.C, and -1.D, originate from four discrete promoters of the gene. Each promoter is coupled with its 5'-untranslated exon. These four promoters are separated by as much as 70 kbp in the FGF-1 locus. The present study indicates that expression of these transcripts in different cell types is regulated by distinct mechanisms. FGF-1.C mRNA requires de novo protein synthesis and de novo transcription for expression and processing, and this mRNA increases acutely in response to TGF-beta and serum stimulation. The serum-induced FGF-1.C correlates with a marked increase in protein level. In addition, FGF-1.C mRNA also increases significantly (more than 100-fold) in response to phorbol 12-myristate 13-acetate. FGF-1.D mRNA is uniquely superinduced by serum in the presence of cycloheximide and displays delayed early kinetics, suggesting that this mRNA does not require de novo protein synthesis for expression. In sharp contrast to the FGF-1.C and -1.D mRNAs, FGF-1.B mRNA levels do not increase in response to serum or phorbol 12-myristate 13-acetate and are in fact slightly down-regulated. Furthermore, FGF-1.B mRNA is stable and appears to have a long half-life (> 12 h). Thus, the unique cell-specific regulation of these FGF-1 transcripts and subsequent protein synthesis indicate that each transcript may have a distinct role in development, normal cellular processes, and, upon aberrant regulation, disease. In support of these conclusions, multiple FGF-1 transcripts in normal, fetal, and diseased tissues, containing mixed cell types, were detected. Our results suggest that FGF-1 transcripts FGF-1.C and -1.D arising from promoters 1C and 1D are specific and are potential markers for proliferation of certain cells, whereas transcripts FGF-1.A and -1.B arising from promoters 1A and 1B are specific for maintenance and survival of cells, particularly cardiac and neuronal cells. Together, these data provide evidence for a biological function for multiple promoter usage of a single gene. The discrete mechanisms for expression of the FGF-1 gene further underscore the biological significance of this growth factor.
Porosity-permeability relationships in interlayered limestone-dolostone reservoirs (2005)

Porosity and permeability data from five carbonate platform successions of different settings, ages, and burial depths are examined to identify overall similarities and differences in the reservoir quality of interlayered limestones and dolostones. Each succession consists mainly of limestone and dolostone, with subordinate proportions of intermediate, partly dolomitized compositions. In the three deeply buried platforms, the key features are that limestones have much lower average porosity than associated dolostones, and that limestones and dolostones show little difference in average permeability-for-given-porosity. In contrast, the shallowly buried platforms show little difference in average porosity between limestones and dolostones and also display higher average permeability-for-given-porosity in dolostones than limestones. These data suggest the following general guidelines for depositional and diagenetic controls on reservoir architecture in carbonates consisting of interlayered limestone and dolostone. (1) Reservoir compartmentalization by the formation of tight limestone barriers is largely a burial diagenetic process involving calcite cementation locally produced by chemical compaction. (2) Both the pattern of early dolomitization and the distribution of clay minerals (because they influence the localization of chemical compaction) are key factors that determine the distribution of tight limestone barriers separating flow units. Thus, the pattern of eventual burial compartmentalization follows a template that is hardwired into the stratigraphic architecture by depositional mineralogy and early diagenesis. (3) After burial (2–3 km; 1.2–1.8 mi), dolostones should not be expected to have higher permeability-for-given- porosity than associated limestones. These rules assume dolomitization to occur early relative to chemical compaction, which will commonly be the case because of combined hydrologic and mass-balance constraints. Dolomitization and concentration of clay appear linked to cycle and sequence architecture in the present examples and thus may have a useful degree of predictability, at least in terms of statistical parameters, such as net/gross and probability of flow-unit thickness distribution.
DNA-dependent protein kinase (Ku protein-p350 complex) assembles on double-stranded DNA. (1994)

The Ku protein is an autoantigen that consists of 70- and 80-kDa polypeptides. It associates with double-stranded DNA at free ends. In the present study, we examined the ability of anti-Ku antibodies to immunoprecipitate various structures from extracts of HeLa cells prepared at different salt concentrations. Under physiological conditions, these antibodies identified a complex containing the Ku protein and the 350-kDa component (p350) of DNA-dependent protein kinase (DNA-PK), which appeared to be closely associated on the DNA strand. In reconstitution experiments with cell extracts and biochemically purified components, the Ku protein-p350 complex formed only in the presence of double-stranded DNA. The reconstituted complex was catalytically active. Together with previous studies, these results indicate that the Ku protein interacts with DNA to create a binding site for p350 as the DNA-PK holoenzyme assembles.
PERMEABILITY OF BACTERIAL SPORES II (1961)

Gerhardt, Philipp (University of Michigan, Ann Arbor) and S. H. Black. Permeability of bacterial spores. II. Molecular variables affecting solute permeation. J. Bacteriol. 82:750-760. 1961.-More than 100 compounds were tested for their uptake by dormant spores of a bacillus. The extent of penetration was found to be dependent on at least three molecular properties: (i) The dissociation of electrolytes usually resulted in high or low uptake predictable from their charge. (ii) Lipid insolubility restricted permeation of small molecules. (iii) The molecular weight of unsubstituted glycol and sugar polymers exponentially limited penetration to eventual exclusion at mol wt above 160,000. The results were plotted as a generalized curve, calculations from which permitted an interpretation that the effective spore surface contains pores varying in diameter from 10 to 200 A.
Slow Eye Movements and Subjective Estimates of Sleepiness Predict EEG Power Changes During Sleep Deprivation (2007)

Results suggest that subjective and EEG changes associated with higher sleepiness are paralleled by an increase in slow eye movement activity, but this relationship exists almost exclusively with the eyes closed. Hence, its use in practical and operational contexts seems limited.
An angiotensin II receptor antagonist reduces myocardial damage in an animal model of myocarditis. (1994)

This study suggests that angiotensin II plays an important pathophysiological role in viral myocarditis. Treatment with TCV-116, an angiotensin II receptor antagonist, had a cardioprotective effect.
Peptide density targets and impedes triple negative breast cancer metastasis (2018)

The C-X-C chemokine receptor type 4 (CXCR4, CD184) pathway is a key regulator of cancer metastasis. Existing therapeutics that block CXCR4 signaling are dependent on single molecule-receptor interactions or silencing CXCR4 expression. CXCR4 localizes in lipid rafts and forms dimers therefore CXCR4 targeting and signaling may depend on ligand density. Herein, we report liposomes presenting a CXCR4 binding peptide (DV1) as a three-dimensional molecular array, ranging from 9k to 74k molecules μm<sup>-2</sup>, target triple negative breast cancer (TNBC). TNBC cells exhibit a maxima in binding and uptake of DV1-functionalized liposomes (L-DV1) in vitro at a specific density, which yields a significant reduction in cell migration. This density inhibits metastasis from a primary tumor for 27 days, resulting from peptide density dependent gene regulation. We show that complementing cell membrane receptor expression may be a strategy for targeting cells and regulating signaling.
Visual Feedback Guided Robotic Cherry Tomato Harvesting (1996)

Harvesting cherry tomatoes is more laborious than harvesting larger size tomatoes because of the high fruit density in every cluster. To save labor costs, robotic harvesting of cherry tomatoes has been studied in Japan. An effective vision algorithm, to detect positions of many small fruits, was developed for guidance of robotically harvested cherry tomatoes. A spectral reflectance in the visible region was identified and extracted to provide high contrast images for the fruit cluster identification. The 3-D position of each fruit cluster was determined using a binocular stereo vision technique. The robot harvested one fruit at a time and the position of the next target fruit was updated based on a newly acquired image and the latest manipulator position. The experimental results showed that this visual feedback control based harvesting method was effective, with a success rate of 70%.
Organic and Inorganic Blocking Layers for Solution‐Processed Colloidal PbSe Nanocrystal Infrared Photodetectors (2010)

Abstract A PbSe solution‐processed nanocrystal‐based infrared photodetector incorporating carrier blocking layers is demonstrated, and significant reduction of dark current is achieved. Detectivity values close to 10 12 Jones are achieved by using poly[(9,9′‐dioctylfluorenyl‐2,7‐diyl)‐ co ‐(4,4′‐( N ‐(4‐ sec ‐butyl))diphenylamine)] (TFB) and ZnO nanocrystals (NC) as the electron blocker and hole blocker, respectively. An improvement in lifetime is also observed in the devices with the ZnO NCs hole blocking layer.
The Thioredoxin Superfamily: Redundancy, Specificity, and Gray-Area Genomics (1999)

The views expressed in this feature do not necessarily represent the views of the journal or of ASM .

Issues of thiol-disulfide redox chemistry were nowhere in our consciousness when we began to study the export of Escherichia coli alkaline phosphatase from the cytoplasm. We chose this periplasmic
Epirubicin glucuronidation is catalyzed by human UDP-glucuronosyltransferase 2B7. (2001)

Epirubicin is one of the most active agents for breast cancer. The formation of epirubicin glucuronide by liver UDP-glucuronosyltransferase (UGT) is its main inactivating pathway. This study aimed to investigate epirubicin glucuronidation in human liver microsomes, to identify the specific UGT isoform for this reaction, and to correlate epirubicin glucuronidation with other UGT substrates. Microsomes from human livers were used. UGTs specifically expressed in cellular systems, as well as two UGT2B7 variants, were screened for epirubicin glucuronidation. Epirubicin, morphine, and SN-38 glucuronides were measured by high-pressure liquid chromatography. The mean +/- S.D. formation rate of epirubicin glucuronide in human liver microsomes (n = 47) was 138 +/- 37 pmol/min/mg (coefficient of variation, 24%). This phenotype was normally distributed. We screened commercially available UGT1A1, UGT1A3, UGT1A4, UGT1A6, UGT1A9, UGT2B7, and UGT2B15 for epirubicin glucuronidation. Only UGT2B7 converted epirubicin to its glucuronide. No differences in epirubicin glucuronidation were found in HK293 cells expressing the two UGT2B7 variants at position 268. Catalytic efficiency (V(max)/K(m)) of epirubicin glucuronidation was 1.4 microl/min/mg, a value higher than that observed for morphine, a substrate of UGT2B7. Formation of epirubicin glucuronide was significantly related to that of morphine-3-glucuronide (r = 0.76, p < 0.001) and morphine-6-glucuronide (r = 0.73, p < 0.001). No correlation was found with SN-38, a substrate of UGT1A1 (r = 0.04). UGT2B7 is the major human UGT catalyzing epirubicin glucuronidation, and UGT2B7 is the candidate gene for this phenotype. The reported tyrosine to histidine polymorphism in UGT2B7 does not alter the formation rate of epirubicin glucuronide, and undiscovered genetic polymorphisms in UGT2B7 might change the metabolic fate of this important anticancer agent.
Pain from distension of the pelvic colon by inflating a balloon in the irritable colon syndrome (1973)

The effects of inflating a balloon introduced through a sigmoidoscope to 35 cm in the pelvic colon have been observed and compared in 67 patients with the irritable colon syndrome and in 16 normal and constipated subjects acting as controls. Inflation to 60 ml caused pain in 6% of the controls at a mean diameter of 3.8 cm and in 55% of patients with the irritable colon syndrome (diameter 3.4 cm). An estimate of gut wall tension at this volume of inflation showed it to be normal in patients with the irritable colon syndrome; the incidence of pain in relation to wall tension was increased nearly tenfold in the irritable colon group. Inflation of the balloon to different volumes was normally painless to a maximum acceptable diameter which remained constant for each study under constant conditions; continued inflation eventually gave rise to pain without increasing the diameter. The pain was felt in the hypogastrium in 40%, in one or both iliac fossae in 31%, and in the rectum in 21%; the other 8% felt pain in the back or elsewhere and there were no significant differences between clinical groups. Exceptionally, in 6% of the controls, and in 52% of patients with the irritable colon syndrome, pain occurred at balloon diameters that could still be increased by 10% or more with further inflation. This was probably the outcome of a low threshold for visceral pain in the section of bowel in contact with the balloon. Colonic hyperalgesia of this kind, possibly a random occurrence, may be an important contributory factor in the aetiology of the irritable colon syndrome.
Low-Temperature Miscibility of Ethanol-Gasoline-Water Blends in Flex Fuel Applications (2009)

Abstract The miscibility of blends of gasoline and hydrous ethanol was investigated experimentally at −25°C and −2°C. Furthermore, the maximum water content was found for ethanol in flex fuel blends. The results strongly indicate that blends containing ethanol with a water content above that of the ethanol/water azeotrope (4.4% water by mass) can be used as Flex Fuel blends together with gasoline at ambient temperatures of −25°C and −2°C, without phase separation occurring. Additionally, it was shown that the ethanol purity requirement of ethanol-rich flex fuel blends falls with increasing ethanol content in the gasoline-rich flex fuel blend. Keywords: bioethanolbiofuelethanolflex fuelflex fuel vehiclegasoholgasolinehydrous ethanolmiscibilityphase separationternary phase diagram Acknowledgments The authors wish to thank the Danish Technological Institute (Aarhus), where the experimental work was conducted. Notes 1More recently, some miscibility tests of ethanol-gasoline-water have been reported, but only for low-level ethanol blends (< 15%) (CitationPeng et al., 1996; CitationFrench and Malone, 2005; CitationGramajo de Doz. et al., 2004). 2 http://www.shell.com/home/page/dk-da/produkt_og_sikkerhedsdatablade/app_products_0310_1510.html. 3The experimental data can be found in Appendix II: Experimental Data. 5Meaning of subscripts: FFBE is mass percentage relates to the ethanol-rich FFB; FFBG is mass percentage relates to the gasoline-rich FFB; PSP is mass percentage relates to the blend at the phase separation point.
Fabrication of Nanofiber Microarchitectures Localized within Hydrogel Microparticles and Their Application to Protein Delivery and Cell Encapsulation (2012)

Abstract A simple method to generate well‐defined microscopic architectures composed of electrospun nanofibers is reported and their potential application to biomedical fields are described. The photopatterning of polyethylene glycol (PEG) hydrogel on electrospun polycarprolactone (PCL) nanofibers leads to the formation of two different microdomains in nanofibrous mats: a bare nanofiber region and a hydrogel‐entrapped nanofiber region. The selective dissolution of bare nanofibers with an organic solvent that cannot penetrate the PEG hydrogel enables the localization of PCL nanofibers within the hydrogel microstructures, thus generating microarchitectured nanofibers. The resultant microarchitectures are easily detached from the substrate by the water‐induced swelling of the PEG hydrogel. Microparticles are ultimately obtained, the size and shape of which can be easily controlled with proper photomask designs. In proof of concept experiments, bovine serum albumin(BSA)‐loaded PCL nanofibers that are entrapped within the hydrogel microparticles are prepared and the sustained release of BSA from micropatterned nanofibers is successfully demonstrated, indicating the potential application of the proposed microarchitectured nanofibers to drug delivery systems. For another possible application, the capability of the nanofiber‐incorporated hydrogel to encapsulate mammalian cells is investigated and the incorporation of nanofibers within the PEG hydrogel promoted cell adhesion and spreading when compared with bare PEG hydrogel is confirmed.
[Effect of cyclic 3,5-adenosine monophosphate on the virulence of Salmonella typhimurium]. (1988)

To study the role of cAMP in the virulence of S. typhimurium, cAMP-producing plasmid pTG 4 was transferred to cAMP-deficient S. typhimurium mutant. The transfer of the plasmid enhanced the virulence of the microorganisms due to the increased destruction of macrophages and the intensified multiplication of salmonellae in the spleen of mice.
Treatment of Vancomycin-Resistant Enterococcal Infections in the Immunocompromised Host: Quinupristin-Dalfopristin in Combination with Minocycline (2001)

Between February 1994 and November 1998, 56 oncology patients infected with vancomycin-resistant enterococci (VRE) were treated with quinopristin-dalfopristin (Q-D) plus minocycline (MIN). Infections included bacteremia, urinary tract infection, pneumonia, and wound infection. The response rate was 68%, and the most frequent adverse event was arthralgia or myalgia (36%). Q-D-MIN is effective for VRE infection in cancer patients but is associated with a substantial frequency of arthralgia or myalgia.