gebhart/patrepeval huggingface dataset:
Regulation of Human Lung Fibroblast Collagen Production by Recombinant Interleukin‐1, Tumor Necrosis Factor, and Interferon‐γa (1990)

Several cytokines have been shown to modulate the synthesis of matrix molecules, but few reports have defined how the cytokines interact with one another in mediating these regulatory effects. To define the cytokine network regulating collagen production, we have studied the effects of interferon-gamma, interleukin-1, and tumor necrosis factor on collagen synthesis by cultured human lung fibroblasts. Confluent cells were treated with cytokines for 24 h in the absence of serum or in media containing 1% serum. In the absence of serum, IL-1 and TNF each dose-dependently stimulated types I and III collagen production, with a maximal 2-4-fold increase in collagen accumulation being observed. Cells treated with IL-1 and TNF in combination showed less stimulation than with either cytokine alone. IFN-gamma also diminished the stimulatory effects of both IL-1 and TNF. In contrast, in 1% serum IL-1 and TNF individually had relatively minor effects, while IFN-gamma inhibited collagen production. However, the combination of IL-1 and TNF inhibited collagen production. Generally, these effects were achieved through control of mRNA levels. These studies demonstrate the existence of a cytokine network regulating fibroblast collagen production and suggest that cytokine effects in vivo may vary depending upon the constellation of factors present in the tissue.
Polyoma middle T abrogates TPA requirement of murine melanocytes and induces malignant melanoma. (1988)

We have transfected the polyoma middle T oncogene into an immortal murine melanocyte cell line, Mel-ab. This highly pigmented line is phorbol ester (TPA) dependent for in vitro growth, suggesting activation and/or down regulation of Protein Kinase C (PKC) is essential for mitogenesis. Moreover, cells of this line do not form tumours when injected subcutaneously into immunocompetent or immunoincompetent mice. Here we show that PyMT alone is sufficient to produce TPA-independence and transformation to the tumourigenic state in transfected Mel-ab cells. Western blot analysis shows that middle T overcomes the TPA requirement by a mechanism independent of PKC down regulation though this does appear to occur when Mel-ab cells are grown continuously in TPA. These results suggest that PyMT is not exerting its transforming effect by PKC down regulation, but conceivably at some later stage of second messenger signalling, possibly through PyMT-c-src protein kinase activity.
Allosteric Dominance in Carbamoyl Phosphate Synthetase (1999)

A linked-function analysis of the allosteric responsiveness of carbamoyl phosphate synthetase (CPS) from E. coli was performed by following the ATP synthesis reaction at low carbamoyl phosphate concentration. All three allosteric ligands, ornithine, UMP, and IMP, act by modifying the affinity of CPS for the substrate MgADP. Individually ornithine strongly promotes, and UMP strongly antagonizes, the binding of MgADP. IMP causes only a slight inhibition at 25 degreesC. When both ornithine and UMP were varied, models which presume a mutually exclusive binding relationship between these ligands do not fit the data as well as does one which allows both ligands (and substrate) to bind simultaneously. The same result was obtained with ornithine and IMP. By contrast, the actions of UMP and IMP together must be explained with a competitive model, consistent with previous reports that UMP and IMP bind to the same site. When ornithine is bound to the enzyme, its activation dominates the effects when either UMP or IMP is also bound. The relationship of this observation to the structure of CPS is discussed.
Vagus nerve stimulation and cognition (2006)

Vagus nerve stimulation (VNS) has been developed as an add-on treatment for patients with refractory epilepsy. Based on the clinical observation of improved cognition in many epilepsy patients who received VNS, we reviewed the recent literature for evidence concerning the cognitive effects of this treatment. From most of these studies it seems that, with currently used stimulation parameters, the effects on memory are only of theoretical importance. However, some animal studies suggest positive effects on specific modalities of memory function. In studies in epilepsy patients, there is no evidence of adverse effects on cognition but clear-cut positive effects cannot be expected either. Preliminary results of VNS in the treatment of diseases associated with cognitive decline such as Alzheimer's disease seem promising but need to be further investigated.
A Mechanism for IL-10-Mediated Diabetes in the Nonobese Diabetic (NOD) Mouse: ICAM-1 Deficiency Blocks Accelerated Diabetes (2000)

Neonatal islet-specific expression of IL-10 in nonobese diabetic (NOD) mice accelerates the onset of diabetes, whereas systemic treatment of young NOD mice with IL-10 prevents diabetes. The mechanism for acceleration of diabetes in IL-10-NOD mice is not known. Here we show, by adoptive transfers, that prediabetic or diabetic NOD splenocytes upon encountering IL-10 in the pancreatic islets readily promoted diabetes. This outcome suggests that the compartment of exposure, not the timing, confers proinflammatory effects on this molecule. Moreover, injection of IL-10-deficient NOD splenocytes into transgenic IL-10-NOD.scid/scid mice elicited accelerated disease, demonstrating that pancreatic IL-10 but not endogenous IL-10 is sufficient for the acceleration of diabetes. Immunohistochemical analysis revealed hyperexpression of ICAM-1 on the vascular endothelium of IL-10-NOD mice. The finding suggests that IL-10 may promote diabetes via an ICAM-1-dependent pathway. We found that introduction of ICAM-1 deficiency into IL-10-NOD mice as well as into NOD mice prevented accelerated insulitis and diabetes. Failure to develop insulitis and diabetes was preceded by the absence of GAD65-specific T cell responses. The data suggest that ICAM-1 plays a role in the formation of the "immunological synapse", thereby affecting the generation and/or expansion of islet-specific T cells. In addition, ICAM-1 also played a role in the effector phase of autoimmune diabetes because adoptive transfer of diabetogenic BDC2.5 T cells failed to elicit clinical disease in ICAM-1-deficient IL-10-NOD and NOD mice. These findings provide evidence that pancreatic IL-10 is sufficient to drive pathogenic autoimmune responses and accelerates diabetes via an ICAM-1-dependent pathway.
Electronic Energy Levels of the Trivalent Lanthanide Aquo Ions. IV. Eu3+ (1968)

The free-ion energy level scheme of Eu3+ (aquo) to ∼40 000 cm−1 has been determined from the absorption spectrum of Eu3+ in dilute acid solution at 25°. Energy-level assignments were made on the basis of correlations between calculated and observed intensities. A least-squares fit of 26 J levels, including the effects of configuration interaction, gave an rms deviation of 40 cm−1. The parameter values were E1 = 5573.0, E2 = 26.708, E3 = 557.39, ζ4f = 1326.0, α = 25.336, β = − 580.25, and γ = 1155.7.
Identification of a nuclear localization signal, RRMKWKK, in the homeodomain transcription factor PDX‐1 (1999)

Pancreatic duodenal homeobox-containing transcription factor 1 (PDX-1) plays a crucial role in pancreas development and beta-cell gene regulation. Absence of PDX-1 leads to pancreas agenesis and its malfunction causes MODY4 diabetes mellitus. PDX-1 has been suggested to be involved in the glucose-dependent regulation of insulin gene transcription. Whereas DNA-binding and transactivation domains of PDX-1 are in the process of being characterized, protein sequences responsible for its nuclear translocation remain unknown. By combining site-directed mutagenesis of putative phosphorylation sites and nuclear localization signal (NLS) motifs with on-line monitoring of GFP-tagged PDX-1 translocation, we demonstrate that the NLS motif RRMKWKK is necessary and in conjunction with the integrity of the 'helix 3' domain of the PDX-1 homeodomain is sufficient for the nuclear import of PDX-1. Furthermore, we show that there is no glucose-dependent cytoplasmic-nuclear cycling of PDX-1.
Formation of a stable complex between the human immunodeficiency virus integrase protein and viral DNA (1994)

The integrase (IN) protein of the human immunodeficiency virus (HIV) mediates two distinct reactions: (i) specific removal of two nucleotides from the 3' ends of the viral DNA and (ii) integration of the viral DNA into target DNA. Although IN discriminates between specific (viral) DNA and nonspecific DNA in physical in vitro assays, a sequence-specific DNA-binding domain could not be identified in the protein. A nonspecific DNA-binding domain, however, was found at the C terminus of the protein. We examined the DNA-binding characteristics of HIV-1 IN, and found that a stable complex of IN and viral DNA is formed in the presence of Mn2+. The IN-viral DNA complex is resistant to challenge by an excess of competitor DNA. Stable binding of IN to the viral DNA requires that the protein contains an intact N-terminal domain and active site (in the central region of the protein), in addition to the C-terminal DNA-binding domain.
INTRA‐OPERATIVE ULTRASOUND FOR THE DETECTION OF HEPATIC METASTASES FROM COLORECTAL CANCER (1993)

The aim of this study was to compare the accuracy of intra-operative ultrasound (IOUS) with other imaging modalities and with surgical palpation in detecting liver metastases from colorectal cancer (CRC). Intra-operative ultrasound was performed in 100 patients undergoing surgery for CRC. All patients had pre-operative liver function tests, transcutaneous ultrasound and computerized tomography (CT) scan of the liver. The liver was palpated intra-operatively by a surgeon who was unaware of the pre-operative findings. The liver was then assessed by IOUS. Intra-operative ultrasound detected more patients with metastases than either CT scan, transcutaneous ultrasound or surgical palpation. It also detected a greater number of smaller metastases in these patients and allowed better anatomical definition compared with pre-operative investigations.
Identification of Autotoxic Compounds in Fibrous Roots of Rehmannia (Rehmannia glutinosa Libosch.) (2012)

Rehmannia is a medicinal plant in China. Autotoxicity has been reported to be one of the major problems hindering the consecutive monoculture of Rehmannia. However, potential autotoxins produced by the fibrous roots are less known. In this study, the autotoxicity of these fibrous roots was investigated. Four groups of autotoxic compounds from the aqueous extracts of the fibrous roots were isolated and characterized. The ethyl acetate extracts of these water-soluble compounds were further analyzed and separated into five fractions. Among them, the most autotoxic fraction (Fr 3) was subjected to GC/MS analysis, resulting in 32 identified compounds. Based on literature, nine compounds were selected for testing their autotoxic effects on radicle growth. Seven out of the nine compounds were phenolic, which significantly reduced radicle growth in a concentration-dependent manner. The other two were aliphatic compounds that showed a moderate inhibition effect at three concentrations. Concentration of these compounds in soil samples was determined by HPLC. Furthermore, the autotoxic compounds were also found in the top soil of the commercially cultivated Rehmannia fields. It appears that a close link exists between the autotoxic effects on the seedlings and the compounds extracted from fibrous roots of Rehmannia.
Effects of a lignin peroxidase-expressing recombinant, Streptomyces lividans TK23.1, on biogeochemical cycling and the numbers and activities of microorganisms in soil (1993)

A recombinant actinomycete, Streptomyces lividans TK23.1, expressing a pIJ702-encoded extracellular lignin peroxidase gene cloned from the chromosome of Streptomyces viridosporus T7A, was released into soil in flask- and microcosm-scale studies to determine its effects on humification and elemental cycling and on the numbers, types, and activities of microorganisms native to the soil. Strain TK23.1 had been shown previously to transiently increase the rate of organic carbon mineralization in soil via an effect that was recombinant specific and particularly significant in nonsterile soils already possessing an active microflora. The results of this study confirmed the previous findings and showed that additional effects were measurable upon release of the recombinant strain TK23.1 into unamended soil and into soil amended with lignocellulose. In addition to a transient enhancement of carbon mineralization, the recombinant affected soil pH, the rate of incorporation of carbon into soil humus fractions, nitrogen cycling, the relative populations of some microbial groups, and also certain soil enzyme activities. Whereas the survival or persistence in soil of the recombinant TK23.1 strain and that of its parent, TK23, were similar, the observed effects on microbial numbers, types, and activities were recombinant specific and did not occur when the parental strain was released into soil. All of the measured effects were transient, generally lasting for only a few days. While the effects were statistically significant, their ecological significance appears to be minimal. This is the first report showing that a recombinant actinomycete can affect the microbial ecology of soil in ways that can be readily monitored by using a battery of microbiological, enzymological, and chemical assays.
Thiophene-based covalent organic frameworks (2013)

We report the synthesis and characterization of covalent organic frameworks (COFs) incorporating thiophene-based building blocks. We show that these are amenable to reticular synthesis, and that bent ditopic monomers, such as 2,5-thiophenediboronic acid, are defect-prone building blocks that are susceptible to synthetic variations during COF synthesis. The synthesis and characterization of an unusual charge transfer complex between thieno[3,2-b]thiophene-2,5-diboronic acid and tetracyanoquinodimethane enabled by the unique COF architecture is also presented. Together, these results delineate important synthetic advances toward the implementation of COFs in electronic devices.
Program decision logic optimization using predication and control speculation (2001)

The mainstream arrival of predication, a means other than branching of selecting instructions for execution, has required compiler architects to reformulate fundamental analyses and transformations. Traditionally, the compiler has generated branches straightforwardly to implement control flow designed by the programmer and has then performed sophisticated "global" optimizations. to move and optimize code around them. In this model, the inherent tie between the control state of the program and the location of the single instruction pointer serialized run-time evaluation of control and limited the extent to which the compiler could optimize the control structure of the program (without extensive code replication). Predication provides a means of control independent of branches and instruction fetch location, freeing both compiler and architecture from these restrictions; effective compilation of predicated code, however requires sophisticated understanding of the program's control structure. This paper explores a representational technique which, through direct code analysis, maps the program's control component into a canonical database, a reduced ordered binary decision diagram (ROBDD), which fully enables the compiler to utilize and manipulate predication. This abstraction is then applied to optimize the program's control component, transforming it into a form more amenable to instruction level parallel (ILP) execution.
Postinfarction Treatment With an Adenoviral Vector Expressing Hepatocyte Growth Factor Relieves Chronic Left Ventricular Remodeling and Dysfunction in Mice (2003)

Postinfarction HGF gene therapy improved LV remodeling and dysfunction through hypertrophy of cardiomyocytes, infarct wall thickening, preservation of vessels, and antifibrosis. These findings imply a novel therapeutic approach against postinfarction heart failure.
Selection of Mutations in the Hepatitis B Virus Polymerase During Therapy of Transplant Recipients With Lamivudine (1996)

We describe mutations in the hepatitis B virus (HBV) polymerase gene in viruses which reactivated in two patients during therapy with -2'-deoxy-3'-thiacytidine, or lamivudine (3TC), and following orthotopic liver transplantation for chronic hepatitis B. Virus resistance to 3TC is associated with mutations which lead to amino acid substitutions in the highly conserved tyr-met-asp-asp (YMDD) motif, part of the active site of the polymerase, and which parallel those seen in resistant human immunodeficiency virus (HIV). Substitutions of valine and isoleucine for methionine were found in the two cases. The significance of single secondary mutations, which differ between viruses from the two patients, remains to be determined. Thus, viral resistance to lamivudine of hepatitis B virus mimics that of HIV and can occur in the setting of immunosuppression after liver transplantations.
Ultrafast Hydrogen-Bond Dynamics in the Infrared Spectroscopy of Water (2003)

We investigated rearrangements of the hydrogen-bond network in water by measuring fluctuations in the OH-stretching frequency of HOD in liquid D2O with femtosecond infrared spectroscopy. Using simulations of an atomistic model of water, we relate these frequency fluctuations to intermolecular dynamics. The model reveals that OH frequency shifts arise from changes in the molecular electric field that acts on the proton. At short times, vibrational dephasing reflects an underdamped oscillation of the hydrogen bond with a period of 170 femtoseconds. At longer times, vibrational correlations decay on a 1.2-picosecond time scale because of collective structural reorganizations.
Nitrogen-15 nuclear magnetic resonance studies on the tautomerism of 8-hydroxy-2'-deoxyguanosine, 8-hydroxyguanosine, and other C8-substituted guanine nucleosides (1990)

The favored tautomeric and ionic structures were examined for the oxidative DNA damage adduct 8-hydroxy-2'-deoxyguanosine and its RNA analogue 8-hydroxyguanosine by 15N NMR spectroscopy. In addition, 15N chemical shifts and coupling constants from 13 different guanine nucleosides, including a wide variety of C8 substitutions (OH, SH, Br, OCH2C6H5, OCH3, SCH3, and SO2CH3), have been analyzed with respect to their tautomeric structures. A -98.5-Hz proton-nitrogen coupling constant observed for the N7 resonance of 8-hydroxyguanosine in dimethyl sulfoxide was evidence for 8-keto substitution, which is contrary to the structure implied by the generally used nomenclature. The pH dependence of 15N NMR spectra of 8-hydroxyguanosine in aqueous solution showed downfield shifts of the N1 and N7 resonances that were greater than 50 ppm, which indicated the conversion from a neutral 6,8-diketo to a 6-enolate-8-keto (pKa1 = 8.6) and finally to a 6,8-dienolate structure (pKa2 = 11.7). There was no evidence of an 8-enol substituent in the absence of ionization. It is proposed that the syn conformation of these oxidized bases in duplex DNA and RNA can be further stabilized by abnormal hydrogen bonding or mispairing that involves N7-H. The combined data show that 15N NMR is a sensitive probe to examine tautomerism of the guanine ring system. The analysis indicates that the change from a single to a double bond for the C8 substituent, and the accompanying removal of the normal double bond between N7 and C8 on the imidazole ring system, has no detectable effect on the tautomerism at the N1-O6 site of the pyrimidine ring system for both the 8-keto and 8-thio substitutions. In addition, large differences in electronegativity of the C8 substituents do not alter the N1-O6 tautomerism.
Microbial biodiversity of the liquid fraction of rumen content from lactating cows (2014)

Host and dietary interactions with the rumen microbiome can affect the efficacy of supplements, and their effect on the composition of the bacterial population is still unknown. A 16S rRNA metagenomic approach and Next-Generation Sequencing (NGS) technology were used to investigate the bacterial microbiome composition in the liquid fraction of the rumen content collected via stomach tubing. To investigate biodiversity, samples were taken from three groups of four lactating dairy cows given a supplement of either 50 g of potato protein (Ctrl group), or 50 g of lyophilized Saccharomyces cerevisiae (LY group) or 50 g of dried S. cerevisiae (DY group) in a potato protein support. Rumen samples were collected after 15 days of dietary treatments and milk production was similar between the three groups. Taxonomic distribution analysis revealed a prevalence of the Firmicutes phylum in all cows (79.76%) and a significantly (P<0.05) higher presence of the genus Bacillus in the DY group. Volatile fatty-acid concentration was not significantly different between groups, possibly because of relatively high inter-animal variability or limited effect of the treatments or both, and the correlation analysis with bacterial taxa showed significant associations, in particular between many Firmicutes genera and butyrate. Limited differences were observed between dietary treatments, but the lack of microbiome data before yeast administration does not allow to draw firm conclusions on the effect of dietary treatments.
First Redo Heart Valve Replacement (1999)

Females and patients having an aortic valve replacement exhibit a longer interval to the first redo operation than do males and patients having mitral valve replacements, respectively. The time from the first replacement to the first redo operation significantly affects the size of the first redo valve.
Decreasing Incidence of Severe Diabetic Microangiopathy in Type 1 Diabetes (2003)

Our study demonstrates a decrease in the cumulative incidence of diabetic microangiopathy in type 1 diabetes over the past 35 years. Improved glycemic control, lower blood pressure (in part due to early aggressive antihypertensive treatment), and reduced prevalence of smoking rates were associated with the improved prognosis.
Migration of culture-expanded human mesenchymal stem cells through bone marrow endothelium is regulated by matrix metalloproteinase-2 and tissue inhibitor of metalloproteinase-3 (2007)

We show that MSC have the potential to migrate through bone marrow endothelium and that this process involves MMP-2. Moreover, the migration of MSC is significantly influenced by the level of culture confluence. Increased culture confluence impairs migration and is related to an upregulation of TIMP-3. The therapeutic use of MSC would benefit from a selection of culture conditions that allow optimal extravasation of these cells.
Phase reconstruction from reflectivity in uniform fiber Bragg gratings (1997)

We propose a method for phase, time-delay, and impulse-response reconstruction from spectral power reflectance or reflectivity and apply it to uniform fiber Bragg gratings. This method is based on causality conditions and uses Hilbert and Wiener-Lee transforms. Results show a good agreement between exact and reconstructed functions.