gebhart/patrepeval huggingface dataset:
Transfer of the Core Region Genes of the Yersinia enterocolitica WA-C Serotype O:8 High-Pathogenicity Island to Y. enterocolitica MRS40, a Strain with Low Levels of Pathogenicity, Confers a Yersiniabactin Biosynthesis Phenotype and Enhanced Mouse Virulence (2002)

The high-pathogenicity island (HPI) of yersiniae encodes an iron uptake system represented by its siderophore yersiniabactin (Ybt). The HPI is present in yersiniae with high levels of pathogenicity--i.e., Yersinia pestis, Y. pseudotuberculosis, and Y. enterocolitica biogroup (BG) 1B--but absent in Y. enterocolitica strains with low (BG 2 to 5) and no (BG 1A) levels of pathogenicity and has been shown to be an important virulence factor. Comparison of the HPI in Y. enterocolitica (Yen-HPI) and that in Y. pestis and Y. pseudotuberculosis revealed that, in contrast to genes of the variable region, genes of the core region (genes irp9 to fyuA) are highly homologous. In the present work the Yen-HPI core genes were rescued from the chromosome of Y. enterocolitica WA-C (BG 1B, serotype O:8) using the FRT-FLP recombinase system. Transfer of the resulting plasmid pCP1 into the siderophore-deficient strain Y. enterocolitica NF-O (BG 1A) led to no halo on siderophore indicator chrome azurol S (CAS) agar. Transfer of pCP1 into the Y. enterocolitica strain MRS40 (serotype O:9, BG 2; phenotype, CAS negative) led to a CAS halo larger than that of parental strain WA-C, indicating high Ybt production. pCP1 was highly unstable in iron-deficient medium, and no enhanced mouse virulence conferred by MRS40 carrying pCP1 could be detected. To overcome the problem of instability, pCP1 was integrated into the chromosome of MRS40, leading to the formation of a CAS halo comparable to that seen with WA-C and correspondingly to increased mouse virulence. Thus, the core genes of Yen-HPI are sufficient to confer a positive CAS phenotype and mouse virulence to Y. enterocolitica MRS40, BG 2, but are insufficient to confer this phenotype to Y. enterocolitica NF-O, BG 1A.
The affinity of different MBD proteins for a specific methylated locus depends on their intrinsic binding properties (2003)

The methyl-CpG binding domain (MBD) family of proteins was defined based on sequence similarity in their DNA binding domains. In light of their high degree of conservation, it is of inherent interest to determine the genomic distribution of these proteins, and their associated co-repressor complexes. One potential determinant of specificity resides in differences in the intrinsic DNA binding properties of the various MBD proteins. In this report, we use a capillary electrophoretic mobility shift assay (CEMSA) with laser-induced fluorescence (LIF) and neutral capillaries to calculate MBD-DNA binding affinities. MBD proteins were assayed on pairs of methylated and unmethylated duplex oligos corresponding to the promoter regions of the BRCA1, MLH1, GSTP1 and p16(INK4a) genes, and binding affinities for each case were calculated by Scatchard analyses. With the exception of mammalian MBD3 and Xenopus MBD3 LF, all the MBD proteins showed higher affinity for methylated DNA (in the nanomolar range) than for unmethylated DNA (in the micromolar range). Significant differences between MBD proteins in the affinity for methylated DNA were observed, ranging within two orders of magnitude. By mutational analysis of MBD3 and using CEMSA, we demonstrate the critical role of specific residues within the MBD in conferring selectivity for methylated DNA. Interestingly, the binding affinity of specific MBD proteins for methylated DNA fragments from naturally occurring sequences are affected by local methyl-CpG spacing.
Cladding pumped Ytterbium-doped fiber laser with holey inner and outer cladding (2001)

We have fabricated an ytterbium doped all-glass double-clad large mode area holey fiber. A highly efficient cladding pumped single transverse mode holey fiber laser has been demonstrated, allowing continuous-wave output powers in excess of 1W with efficiencies of more than 80%. Furthermore both Q-switched and mode-locked operation of the laser have been demonstrated.
Precomputed local radiance transfer for real-time lighting design (2005)

This paper introduces a new method for real-time relighting of scenes illuminated by local light sources. We extend previous work on precomputed radiance transfer for distant lighting to local lighting by introducing the concept of unstructured light clouds. The unstructured light cloud enables a compact representation of local lights in the model and real-time rendering of complex models with full global illumination due to local light sources. We use simplification of lights, and clustered PCA to obtain a compressed representation. When storing only the indirect component of the illumination, we are able to get high quality with only 8-16 lighting coefficients per vertex. Our results demonstrate real-time rendering of scenes with moving lights, dynamic cameras, glossy materials and global illumination.
Cell-based sensor microelectrode array characterized by imaging x-ray photoelectron spectroscopy, scanning electron microscopy, impedance measurements, and extracellular recordings (1998)

We are developing a cell-based biosensor consisting of a planar microelectrode array that allows detection of extracellular potentials and their modulation in the presence of toxins or other active agents. To improve cell–electrode coupling, the microelectrodes were electroplated with platinum black. We report on the use of imaging x-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), impedance measurements, and extracellular recordings to assess the effectiveness of this procedure. SEM provided highly detailed images of the shape and structure of well-formed deposits of thickness on the order of 1 μm or more. Because of its inherent high surface sensitivity, imaging XPS could reveal the presence of platinum deposits that were too thin to be detected by SEM. For typical, well-plated microelectrodes, impedance measurements showed reductions in the electrical resistance at 100 Hz from roughly 60 MΩ or more 1 MΩ. The overall electronic coupling of biopotentials to the microelectrodes was demonstrated by recordings obtained from beating rat myocytes and from rat spinal cord cells.
Accumulation of Homolanthionine and Activation of a Novel Pathway for Isoleucine Biosynthesis in Corynebacterium glutamicumMcbR Deletion Strains (2005)

In the present work, the metabolic consequences of the deletion of the methionine and cysteine biosynthesis repressor protein (McbR) in Corynebacterium glutamicum, which releases almost all enzymes of methionine biosynthesis and sulfate assimilation from transcriptional regulation (D. A. Rey, A. Pühler, and J. Kalinowski, J. Biotechnol. 103:51-65, 2003), were studied. C. glutamicum ATCC 13032 DeltamcbR showed no overproduction of methionine. Metabolome analysis revealed drastic accumulation of a single metabolite, which was not present in the wild type. It was identified by isotopic labeling studies and gas chromatography/mass spectrometry as L-homolanthionine {S-[(3S)-3-amino-3-carboxypropyl]-L-homocysteine}. The accumulation of homolanthionine to an intracellular concentration of 130 mM in the DeltamcbR strain was accompanied by an elevated intracellular homocysteine level. It was shown that cystathionine-gamma-synthase (MetB) produced homolanthionine as a side reaction. MetB showed higher substrate affinity for cysteine (Km = 260 microM) than for homocysteine (Km = 540 microM). The cell is able to cleave homolanthionine at low rates via cystathionine-beta-lyase (MetC). This cleavage opens a novel threonine-independent pathway for isoleucine biosynthesis via 2-oxobutanoate formed by MetC. In fact, the deletion mutant exhibited an increased intracellular isoleucine level. Metabolic flux analysis of C. glutamicum DeltamcbR revealed that only 24% of the O-acetylhomoserine at the entry of the methionine pathway is utilized for methionine biosynthesis; the dominating fraction is either stored as homolanthionine or redirected towards the formation of isoleucine. Deletion of metB completely prevents homolanthionine accumulation, which is regarded as an important step in the development of C. glutamicum strains for biotechnological methionine production.
GSK-3β negatively regulates skeletal myotube hypertrophy (2002)

To determine whether changes in glycogen synthase kinase-3beta (GSK-3beta) phosphorylation contribute to muscle hypertrophy, we delineated the effects of GSK-3beta activity on C(2)C(12) myotube size. We also examined possible insulin-like growth factor I (IGF-I) signaling of NFAT (nuclear factors of activated T cells)-inducible gene activity and possible modulation of NFAT activation by GSK-3beta. Application of IGF-I (250 ng/ml) or LiCl (10 mM) alone (i.e., both inhibit GSK-3beta activity) increased the area of C(2)C(12) myotubes by 80 and 85%, respectively. The application of IGF-I (250 ng/ml) elevated GSK-3beta phosphorylation and reduced GSK-3beta kinase activity by approximately 800% and approximately 25%, respectively. LY-294002 (100 microM) and wortmannin (150 microM), specific inhibitors of phosphatidylinositol 3'-kinase, attenuated IGF-I-induced GSK-3beta phosphorylation by 67 and 92%, respectively. IGF-I suppressed the kinase activity of GSK-3beta. IGF-I (250 ng/ml), but not LiCl (10 mM), induced an increase in NFAT-activated luciferase reporter activity. Cotransfection of a constitutively active GSK-3beta (cGSK-3beta) inhibited the induction by IGF-I of NFAT-inducible reporter activity. LiCl, which inhibits GSK-3beta, removed the block by cGSK-3beta on IGF-I-inducible NFAT-responsive reporter gene activity. These data suggest that the IGF-I-induced increase in skeletal myotube size is signaled, in part, through the inhibition of GSK-3beta.
Determining the Accuracy of an Eye Tracking System for Laser Refractive Surgery (2000)

implementation of this eye tracker would lead to improved alignment between the laser and eye during laser refractive surgery.
PCSK9 : un nouveau gène impliqué dans l’hypercholestérolémie familiale (2004)

RPE65 cause Leber’s congenital amaurosis. Nat Genet 1997 ; 17 : 139-41. 7. Gu SM, Thompson DA, Srikumari CR, et al. Mutations in RPE65 cause autosomal recessive childhoodonset severe retinal dystrophy. Nat Genet 1997; 17 : 194-7. 8. Thompson DA, Li Y, McHenry CL, et al. Mutations in the gene encoding lecithin retinol acyltransferase are associated with early-onset severe retinal dystrophy. Nat Genet 2001 ; 28 : 123-4. 9. Kuska V, Imanishi Y, Batten M, et al. Retinoid cycle in the vertebrate retina : experimental approaches and mechanisms of isomerization. Vision Res 2003; 43 : 2959-81. 10. Stockton DW, Lewis RA, Abboud EB, et al. A novel locus for Leber congenital amaurosis on chromosome 14q24. Hum Genet 1998 ; 103 : 328-33.
Identification of Cleaved Oligosaccharides by Matrix-Assisted Laser Desorptiotdonization (2003)

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) was introduced by Karas and Hillenkamp in 1988 (1) for the ionization of proteins and peptides, but was soon shown to be capable of ionizing many other types of biomolecules, such as oligosaccharides (2), glycolipids (3), and nucleotides (4). The technique involves cocrystallization of the sample with a UV-absorbing matrix and bombarding the mixture with a beam of laser radiation, usually in the UV range. Radiation of 337 nm from a nitrogen laser is most commonly used, although the frequency-quadrupled output at 266 nm from a Nd:YAG laser is sometimes used. The functions of the matrix are to absorb the laser energy, to dilute the sample to inhibit cluster formation, and to produce ions, most probably through reaction of the sample with active photochemical degradation products. The most common matrices are currently sinapinic acid (3,5-dimethoxy-4-hydroxycinnamic acid) (5), which is most often used for proteins, α-cyano-4-hydroxycinnamic acid (6) used for smaller peptides and glycolipids, and 2,5-dihydroxybenzoic acid (2,5-DHB, also known as gentisic acid) (7), which produces signals from a wide range of compounds.
Lentiviral Vectors: Regulated Gene Expression (2000)

Lentiviral vectors can deliver and express genes in a wide variety of dividing and nondividing cells. These include terminally differentiated neurons, myotubes, hepatocytes, and hematopoietic stem cells. We now describe the generation of lentiviral vectors in which the expression of the transgene can be regulated. We have developed an inducible lentiviral vector system that contains the entire tetracycline (Tet)-regulated system developed by H. Bujard and colleagues. The novel vector expresses the GFP reporter gene and the tetracycline transactivator under the control of the tetracycline-inducible promoter and the human CMV promoter, respectively. In vitro transduction of human 293 cells resulted in a very low basal expression of GFP in the presence of the effector substance doxycyline. Withdrawal of doxycyline induced a more than 500-fold increase in transgene expression. Switching transgene expression "off and on" did not change either the kinetics or the magnitude of induction. Maximal suppression of GFP mRNA transcription was achieved within 24 h of addition of the drug; however, due to the slow turnover rate of GFP, green fluorescent cells could be detected up to 10 days following doxycyline treatment. Following transduction of rat brain with recombinant lentiviruses, doxycyline-regulated GFP expression could be observed in terminally differentiated neurons. Specifically, by adding or withdrawing doxycyline from the rats' drinking water, induction and suppression of GFP expression could be regulated in vivo. These studies show that an inducible lentiviral vector can deliver and regulate transgene expression in vivo. We believe that regulated gene expression is an essential tool for successful gene therapy approaches.
Phased-Array Intracardiac Echocardiography Monitoring During Pulmonary Vein Isolation in Patients With Atrial Fibrillation (2003)

Intracardiac echocardiography improves the outcome of cooled-tip PVI. Power adjustment guided by direct visualization of microbubble formation reduces the risk of PV stenosis and improves long-term cure.
Cerebral Functional, Metabolic, and Hemodynamic Effects of Etomidate in Dogs (1985)

The effects of a continuous infusion of etomidate on cerebral function, metabolism, and hemodynamics and on the systemic circulation were examined in six dogs. The infusion rate of etomidate was progressively increased at 20-min intervals from 0.02 to 0.4 mg X kg-1 X min-1 for 2 h. Cerebral oxygen consumption (CMRO2) decreased until there was cessation of neuronal function as reflected by the onset of an isoelectric EEG. This occurred during an infusion of 0.3 mg X kg-1 X min-1 etomidate when the animals had received a total of 10.7 mg X kg-1 over 91 min. At this time the CMRO2 was 2.6 ml X min-1 X 100 g-1, 48% of control. Thereafter, despite continued administration of etomidate to a total dose of 21.4 mg X kg-1, CMRO2 did not decrease further. Cerebral blood flow (CBF) decreased in association with a marked increase in cerebrovascular resistance but was independent of changes in CMRO2. CBF decreased precipitously from 145 +/- 23 to 72 +/- 6 ml X min-1 X 100 g-1 during the lowest infusion rate of 0.02 mg X kg-1 X min-1 etomidate and stabilized at 34-36 ml X min-1 X 100 g-1 during an infusion rate of 0.1 mg X kg-1 X min-1. CBF remained at this level despite the continued administration of etomidate and a further decrease in CMRO2. Etomidate produced physiologically minor but statistically significant changes in the systemic hemodynamic variables. Assays of cerebral metabolites taken at the end of the infusion revealed a normal energy state and a very mild but significant increase in cerebral lactate to 1.49 mumol X g-1. We conclude that etomidate is a potent, direct cerebral vasoconstrictor that appears to be independent of its effect on CMRO2 and that the cerebral metabolic effects of etomidate are secondary to its effect on neuronal function, with little if any direct or toxic effects on metabolic pathways.
Differential protein composition of bovine whey: A comparison of whey from healthy animals and from those with clinical mastitis (2004)

During clinical mastitis in dairy cows, the quantity of milk produced decreases and the composition of the milk is altered. As the severity of inflammation associated with the disease increases, the chemical composition of milk approaches that of blood as a consequence of increased permeability of the blood mammary barrier, or de novo intramammary synthesis, as has been suggested for mammary associated serum amyloid A3. A better understanding of these events may provide new approaches for the diagnosis and treatment of mastitis. The objective of this study was to document the changes in the protein composition of milk during clinical mastitis using a proteomic approach, with the objective of identifying new diagnostic markers of mastitis. Whey from dairy cows with clinical mastitis was compared to whey from healthy animals by two-dimensional gel electrophoresis (2-DE) with colloidal Coomassie staining and matrix-assisted desorption/ionization mass spectrometry. Increases in the concentrations of proteins of blood serum origin, including serotransferrin and albumin, were identified in mastitic whey compared to normal whey, while concentrations of the major whey proteins alpha-lactalbumin and beta-lactoglobulin were reduced in mastitic whey. Mass spectrometry subsequently confirmed the location of albumin, alpha-lactalbumin and beta-lactoglobulin on the 2-DE gels at M(r)/pI of 69 294/5.8, 14 200/4.5 and 19 883/4.9 respectively.
Drug Discovery and Natural Products: End of an Era or an Endless Frontier? (2009)

Historically, the majority of new drugs have been generated from natural products (secondary metabolites) and from compounds derived from natural products. During the past 15 years, pharmaceutical industry research into natural products has declined, in part because of an emphasis on high-throughput screening of synthetic libraries. Currently there is substantial decline in new drug approvals and impending loss of patent protection for important medicines. However, untapped biological resources, "smart screening" methods, robotic separation with structural analysis, metabolic engineering, and synthetic biology offer exciting technologies for new natural product drug discovery. Advances in rapid genetic sequencing, coupled with manipulation of biosynthetic pathways, may provide a vast resource for the future discovery of pharmaceutical agents.
Molecular Properties, Biology, and Clinical Implications of TT Virus, a Recently Identified Widespread Infectious Agent of Humans (2001)

TT virus (TTV) was first described in 1997 by representational difference analysis of sera from non-A to non-G posttransfusion hepatitis patients and hence intensively investigated as a possible addition to the list of hepatitis-inducing viruses. The TTV genome is a covalently closed single-stranded DNA of approximately 3.8 kb with a number of characteristics typical of animal circoviruses, especially the chicken anemia virus. TTV is genetically highly heterogeneous, which has led investigators to group isolates into numerous genotypes and subtypes and has limited the sensitivity of many PCR assays used for virus detection. The most remarkable feature of TTV is the extraordinarily high prevalence of chronic viremia in apparently healthy people, up to nearly 100% in some countries. The original hypothesis that it might be an important cause of cryptogenic hepatitis has not been borne out, although the possibility that it may produce liver damage under specific circumstances has not been excluded. The virus has not yet been etiologically linked to any other human disease. Thus, TTV should be considered an orphan virus.
Evaluation of clinical meaningfulness of estrogen plus progesterone oral capsule (TX-001HR) on moderate to severe vasomotor symptoms (2018)

TX-001HR provided clinically meaningful improvements (as measured by 2 different methods), in addition to statistically significant reductions, in menopausal VMS frequency. TX-001HR may provide a new option, as a single oral capsule of estradiol and progesterone (identical to the hormones naturally occurring in women) for the treatment of moderate to severe VMS in menopausal women with a uterus.
Constitutive Nuclear Factor-κB Activity Is Required for Central Neuron Survival (2002)

The function of nuclear factor (NF)-kappaB within the developing and mature CNS is controversial. We have generated transgenic mice to reveal NF-kappaB transcriptional activity in vivo. As expected, constitutive NF-kappaB activity was observed within immune organs, and tumor necrosis factor-inducible NF-kappaB activity was present in mesenchymal cells. Intriguingly, NF-kappaB activity was also prominent in the CNS throughout development, especially within neocortex, olfactory bulbs, amygdala, and hippocampus. NF-kappaB in the CNS was restricted to neurons and blocked by overexpression of dominant-negative NF-kappaB-inducible kinase or the IkappaBalphaM super repressor. Blocking endogenous neuronal NF-kappaB activity in cortical neurons using recombinant adenovirus induced neuronal death, whereas induction of NF-kappaB activity increased levels of anti-apoptotic proteins and was strongly neuroprotective. Together, these data demonstrate a physiological role for NF-kappaB in maintaining survival of central neurons.
Recursive partitioning for tumor classification with gene expression microarray data (2001)

Precise classification of tumors is critically important for cancer diagnosis and treatment. It is also a scientifically challenging task. Recently, efforts have been made to use gene expression profiles to improve the precision of classification, with limited success. Using a published data set for purposes of comparison, we introduce a methodology based on classification trees and demonstrate that it is significantly more accurate for discriminating among distinct colon cancer tissues than other statistical approaches used heretofore. In addition, competing classification trees are displayed, which suggest that different genes may coregulate colon cancers.
Blue Fluorescent 4a-Aza-4b-boraphenanthrenes (2007)

[structure: see text]. Phenanthrene analogues with internalized B-N moieties were found to afford blue light emission with good quantum efficiencies, whereas the isomeric species with peripheral B-N moieties displayed only UV emission behavior, like the all-carbon framework.