gebhart/patrepeval huggingface dataset:
Promoter-Specific Roles for Liver X Receptor/Corepressor Complexes in the Regulation of ABCA1 and SREBP1 Gene Expression (2003)

Liver X receptors (LXRs) regulate the expression of genes involved in cholesterol and fatty acid homeostasis, including the genes for ATP-binding cassette transporter A1 (ABCA1) and sterol response element binding protein 1 (SREBP1). Loss of LXR leads to derepression of the ABCA1 gene in macrophages and the intestine, while the SREBP1c gene remains transcriptionally silent. Here we report that high-density-lipoprotein (HDL) cholesterol levels are increased in LXR-deficient mice, suggesting that derepression of ABCA1 and possibly other LXR target genes in selected tissues is sufficient to result in enhanced HDL biogenesis at the whole-body level. We provide several independent lines of evidence indicating that the repressive actions of LXRs are dependent on interactions with the nuclear receptor corepressor (NCoR) and the silencing mediator of retinoic acid and thyroid hormone receptors (SMRT). While dissociation of NCoR and SMRT results in derepression of the ABCA1 gene in macrophages, it is not sufficient for derepression of the SREBP1c gene. These findings reveal differential requirements for corepressors in the regulation of genes involved in cholesterol and fatty acid homeostasis and raise the possibility that these interactions may be exploited to develop synthetic ligands that selectively modulate LXR actions in vivo.
3R and 4R tau isoforms in paired helical filaments in Alzheimer’s disease (2013)

presence of 4r tau in AD pathologies may be underestimated when rD4 is used. However, anti-4r (available from Cosmo Bio Co., Ltd.) raised against rD4 peptide with N279D substitution stained both wild-type and deamidated 4r tau, and strongly stained rD3+/rD4-tangles and smearing tau fragments in sarkosyl-insoluble fraction of AD brain
A Quantitative Analysis of Sutural Contributions to Variability in Back Vertex Distance and Transmittance in Rabbit Lenses as a Function of Development, Growth, and Age (2002)

Lens sutures significantly influence average BVD throughout development and growth, and variability in BVD throughout aging. In addition, even though the rabbit lenses appeared transparent throughout growth and aging, unequal length and area of anterior vs. posterior suture branches and planes respectively, as well as a greater degree of age-related posterior lens compaction, were factors contributing to increased scatter.
Molecular Cloning and Characterization of Glucanase Inhibitor Proteins (2002)

A characteristic plant response to microbial attack is the production of endo-beta-1,3-glucanases, which are thought to play an important role in plant defense, either directly, through the degradation of beta-1,3/1,6-glucans in the pathogen cell wall, or indirectly, by releasing oligosaccharide elicitors that induce additional plant defenses. We report the sequencing and characterization of a class of proteins, termed glucanase inhibitor proteins (GIPs), that are secreted by the oomycete Phytophthora sojae, a pathogen of soybean, and that specifically inhibit the endoglucanase activity of their plant host. GIPs are homologous with the trypsin class of Ser proteases but are proteolytically nonfunctional because one or more residues of the essential catalytic triad is absent. However, specific structural features are conserved that are characteristic of protein-protein interactions, suggesting a mechanism of action that has not been described previously in plant pathogen studies. We also report the identification of two soybean endoglucanases: EGaseA, which acts as a high-affinity ligand for GIP1; and EGaseB, with which GIP1 does not show any association. In vitro, GIP1 inhibits the EGaseA-mediated release of elicitor-active glucan oligosaccharides from P. sojae cell walls. Furthermore, GIPs and soybean endoglucanases interact in vivo during pathogenesis in soybean roots. GIPs represent a novel counterdefensive weapon used by plant pathogens to suppress a plant defense response and potentially function as important pathogenicity determinants.
Reversal of Type 1 Hepatorenal Syndrome With the Administration of Midodrine and Octreotide (1999)

The aim of the study was to verify the effects of the administration of an inhibitor of the release of endogenous vasodilators together with a vasoconstrictor agent in patients with hepatorenal syndrome (HRS). This new medical perspective was compared with a traditional medical approach for HRS, such as the infusion of nonpressor doses of dopamine to produce renal vasodilation. Thirteen patients with type 1 HRS were enrolled in the study. Five of them were treated with the oral administration of midodrine and the parenteral administration of octreotide. In addition, the patients received 50 to 100 mL of 20% human albumin solution daily for 20 days. Midodrine and octreotide were dosed to obtain a stable increase of at least 15 mm Hg of mean arterial pressure. Eight patients were treated with the intravenous administration of nonpressor doses of dopamine (2-4 micrograms/kg/min) and the same daily amount of albumin. After 20 days of treatment with midodrine and octreotide, an impressive improvement in renal plasma flow (RPF), glomerular filtration rate, and urinary sodium excretion was observed in patients. This was accompanied by a significant reduction in plasma renin activity, plasma vasopressin, and plasma glucagon. No side effects were observed. Three patients were discharged from the hospital. One of them successfully underwent liver transplantation. One of the two remaining patients is still alive after 472 days with a preserved renal function, and the other died from terminal liver failure after 76 days. One of the two patients who were not discharged from the hospital successfully underwent liver transplantation, and the other died from pneumonia after 29 days. Seven out of eight patients who were treated with dopamine experienced a progressive deterioration in renal function and died during the first 12 days. Only one patient recovered renal function and underwent liver transplantation. In conclusion, the long-term administration of midodrine and octreotide seems to be an effective and safe treatment of type 1 HRS in patients with cirrhosis.
Management of Colorectal Cancer (1997)

Focusing on recent developments in the understanding and treatment of colorectal cancer, this detailed reference covers all aspects of the disease, with contributions from a strong international team of authors.
Comparative Assessment of Methods for Estimating Tumor Volume and Standardized Uptake Value in 18F-FDG PET (2010)

The method used to estimate tumor volume and SUV greatly affects the reliability of the estimates. The T(bgd) and Fit methods yielded low errors in volume estimates in a broad range of situations. The PVE-corrected SUV based on T(bgd) and Fit were more accurate and reproducible than SUV(max).
Low‐dose methotrexate compared with auranofin in adult rheumatoid arthritis (1990)

Weekly treatment with low-dose oral methotrexate (MTX) was compared with daily auranofin (AUR) treatment in a 36-week double-blind, randomized, multicenter study of 281 patients with active, adult-onset rheumatoid arthritis. Both treatment groups showed significant improvement by the usual measures of clinical efficacy. The response with MTX occurred earlier and was consistently greater than that with AUR. An intent-to-treat analysis showed significantly greater improvement (P less than 0.01) with MTX for painful and swollen joint counts and physician and patient global assessments of disease activity. Adverse reactions were reported more frequently in the AUR group, and more AUR-treated patients were withdrawn from the study because of toxicity. MTX was thus more effective and better tolerated than AUR in this study.
Photochemical production of double-strand breaks in cellular DNA (1995)

In a recent publication we described a novel route for the introduction of DNA double-strand breaks (DSBs) into cellular DNA. This involved the labelling of cellular DNA with bromodeoxyuridine (BrdU) and exposure to UVA light in the presence of Hoechst dye No. 33258. Here, we report an extension of that work to the use of iododeoxyuridine (IdU); cells substituted with known levels of IdU were subjected to a similar photolysis treatment and analyzed for strand breaks by elution assays. Results indicate that both single-strand breaks (SSBs) and DSBs depend linearly on the level of IdU substitution and fluence of UVA light. The yields of SSBs and DSBs were found to be 3.5 x 10(-5) and 9.5 x 10(-7)/IdU moiety/kJm-2, respectively. These results indicate that approximately 15-fold less SSBs and 5-fold less DSBs are produced per IdU than per BrdU moiety.
Pumping gases by a silicon micro pump with dynamic passive valves (2002)

Pumping gases by a membrane pump requires a strong compression ratio inside the pump chamber. This demand is fulfilled by an optimized micro pump with dynamic passive valves, working at the resonance frequency. The experimental results for the zero-load pump rate and the maximum pump pressure are 7.5 ml/min and 2.8 kPa, respectively. The pump's behaviour is described by a mathematical model. The calculated values coincide with the experimental data quite well.
Functional mapping in the human brain using high magnetic fields (1999)

An avidly pursued new dimension in magnetic resonance imaging (MRI) research is the acquisition of physiological and biochemical information non-invasively using the nuclear spins of the water molecules in the human body. In this trial, a recent and unique accomplishment was the introduction of the ability to map human brain function non-invasively. Today, functional images with subcentimetre resolution of the entire human brain can be generated in single subjects and in data acquisition times of several minutes using 1.5 tesla (T) MRI scanners that are often used in hospitals for clinical purposes. However, there have been accomplishments beyond this type of imaging using significantly higher magnetic fields such as 4 T. Efforts for developing high magnetic field human brain imaging and functional mapping using MRI (fMRI) were undertaken at about the same time. It has been demonstrated that high magnetic fields result in improved contrast and, more importantly, in elevated sensitivity to capillary level changes coupled to neuronal activity in the blood oxygenation level dependent (BOLD) contrast mechanism used in fMRI. These advantages have been used to generate, for example, high resolution functional maps of ocular dominance columns, retinotopy within the small lateral geniculate nucleus, true single-trial fMRI and early negative signal changes in the temporal evolution of the BOLD signal. So far these have not been duplicated or have been observed as significantly weaker effects at much lower field strengths. Some of these high-field advantages and accomplishments are reviewed in this paper.
Characterization of Arabidopsis decapping proteins AtDCP1 and AtDCP2, which are essential for post‐embryonic development (2007)

Although decapping is an important process in eukaryotic mRNA turnover, little is known about this process in plants. Here, we identified Arabidopsis thaliana decapping proteins AtDCP1 and AtDCP2 and showed that (I) AtDCP2 is an active decapping enzyme, (II) AtDCP1 interacts with itself, (III) AtDCP1 and AtDCP2 are localized to cytoplasmic foci (putative Arabidopsis processing body), and (IV) AtDCP1 and AtDCP2 are essential for post-embryonic development. Our findings provide new insights into the role of decapping-dependent mRNA turnover.
New Synthesis of Isoquinoline Derivatives by Reactions of 2-(2-Methoxyethenyl)benzonitriles with Organolithiums and Lithium Dialkylamides (2004)

Abstract A simple and efficient synthesis of 1-alkyl(or aryl)isoquinoline and isoquinolin-1-amine derivatives based on intramolecular cyclization of 2-(2-methoxyethenyl)benzonitriles initiated by the addition of alkyl(or aryl)lithiums and lithium dialkylamides to the nitrile carbons, respectively, is described.
Comparison of the proteolytic susceptibilities of homologous L‐amino acid, D‐amino acid, and N‐substituted glycine peptide and peptoid oligomers (1995)

Abstract A series of homologous L‐amino acid, D‐amino acid, and both parallel and anti‐parallel (retro) sequence N‐substituted glycine peptide and peptoid oligomers were prepared and incubated with a series of enzymes representative of the major classes of proteases. Each respective L‐amino acid containing peptide sequence was readily cleaved by the appropriate enzyme, namely Ac‐L‐ala‐L‐leu‐L‐phe‐L‐ala‐L‐leu‐L‐arg‐NH 2 by chymotrypsin, Ac‐L‐ala‐L‐ala‐L‐ala‐L‐leu‐L‐phe‐L‐arg‐NH 2 by elastase, Ac‐L‐ala‐L‐phe‐L‐glu‐L‐leu‐L‐ala‐L‐ala‐NH 2 by papain, Z‐L‐ala‐L‐his‐L‐phe‐L‐phe‐L‐arg‐L‐leu‐NH 2 by pepsin, Ac‐L‐phe‐L‐ala‐L‐arg‐L‐ala‐L‐arg‐L‐asp‐NH 2 by trypsin, and Ac‐L‐ala‐L‐tyr‐Lala‐L‐phe‐OH for carboxypeptidase A. In contrast, equivalent D‐amino acid containing and N‐substituted glycine containing oligomers were cleaved minimally or not at all by the respective enzymes. The N‐substituted glycine peptoids represent a new class of combinatorial diversity for lead discovery with improved pharmaceutical characteristics relative to L‐amino acid containing peptides. © 1995 Wiley‐Liss, Inc.
Antigenic specificities of human CD4+ T-cell clones recovered from recurrent genital herpes simplex virus type 2 lesions (1994)

Lesions resulting from recurrent genital herpes simplex virus (HSV) infection are characterized by infiltration of CD4+ lymphocytes. We have investigated the antigenic specificity of 47 HSV-specific CD4+ T-cell clones recovered from the HSV-2 buttock and thigh lesions of five patients. Clones with proliferative responses to recombinant truncated glycoprotein B (gB) or gD of HSV-2 or purified natural gC of HSV-2 comprised a minority of the total number of HSV-specific clones isolated from lesions. The gC2- and gD2-specific CD4+ clones had cytotoxic activity. The approximate locations of the HSV-2 genes encoding HSV-2 type-specific CD4+ antigens have been determined by using HSV-1 x HSV-2 intertypic recombinant virus and include the approximate map regions 0.30 to 0.46, 0.59 to 0.67, 0.67 to 0.73, and 0.82 to 1.0 units. The antigenic specificity of an HLA DQ2-restricted, HSV-2 type-specific T-cell clone was mapped to amino acids 425 to 444 of VP16 of HSV-2 by sequential use of an intertypic recombinant virus containing VP16 of HSV-2 in an HSV-1 background, recombinant VP16 fusion proteins, and synthetic peptides. Each of the remaining four patients also yielded at least one type-specific T-cell clone reactive with an HSV-2 epitope mapping to approximately 0.67 to 0.73 map units. The antigenic specificities of lesion-derived CD4+ T-cell clones are quite diverse and include at least 10 epitopes. Human T-cell clones reactive with gC and VP16 are reported here for the first time.
Ion‐Current Rectification in Nanopores and Nanotubes with Broken Symmetry (2006)

Abstract This article focuses on ion transport through nanoporous systems with special emphasis on rectification phenomena. The effect of ion‐current rectification is observed as asymmetric current–voltage ( I–V ) curves, with the current recorded for one voltage polarity higher than the current recorded for the same absolute value of voltage of opposite polarity. This diode‐like I–V curve indicates that there is a preferential direction for ion flow. Experimental evidence that ion‐current rectification is inherent to asymmetric, e.g., tapered, nanoporous systems with excess surface charge is provided and discussed. The fabrication and operation of asymmetric polymer nanopores, gold nanotubes, glass nanocapillaries, and silicon nanopores are presented. The possibility of tuning the direction and extent of rectification is discussed in detail. Theoretical models that have been developed to explain the ion‐current rectification effect are also presented.
Metabolic and cardiorespiratory responses to “the lactate clamp” (2002)

To evaluate the hypothesis that precursor supply limits gluconeogenesis (GNG) during exercise, we examined training-induced changes in glucose kinetics [rates of appearance (R(a)) and disappearance (R(d))], oxidation (R(ox)), and recycling (R(r)) with an exogenous lactate infusion to 3.5-4.0 mM during rest and to pretraining 65% peak O(2) consumption (VO(2 peak)) levels during exercise. Control and clamped trials (LC) were performed at rest pre- (P(R)R, P(R)R-LC) and posttraining (P(O)R, P(O)R-LC) and during exercise pre- (P(R)E(X)) and posttraining at absolute (P(O)A(B), P(O)A(B)-LC) and relative (P(O)R(L), P(O)R(L)-LC) intensities. Glucose R(r) was not different in any rest or exercise condition. Glucose R(a) did not differ as a result of LC. Glucose R(ox) was significantly decreased with LC at P(O)R (0.38 +/- 0.03 vs. 0.56 +/- 0.04 mg. kg(-1). min(-1)) and P(O)A(B) (3.82 +/- 0.51 vs. 5.0 +/- 0.62 mg. kg(-1). min(-1)). Percent glucose R(d) oxidized decreased with all LC except P(O)R(L)-LC (P(R)R, 32%; P(R)R-LC, 22%; P(O)R, 27%; P(O)R-LC, 20%; P(O)A(B), 95%; P(O)A(B)-LC, 77%), which resulted in a significant increase in oxidation from alternative carbohydrate (CHO) sources at rest and P(O)A(B). We conclude that 1) increased arterial [lactate] did not increase glucose R(r) measured during rest or exercise after training, 2) glucose disposal or production did not change with increased precursor supply, and 3) infusion of exogenous CHO in the form of lactate resulted in the decrease of glucose R(ox).
High frequency nonlinear B-scan imaging of microbubble contrast agents (2005)

It has been shown that nonlinear scattering can be stimulated from microbubble contrast agents at high-transmit frequencies (14-32 MHz). This work was extended to demonstrate the feasibility of nonlinear contrast imaging through modifications of existing ultrasound biomicroscopy linear B-scan imaging instrumentation. In this study, we describe the development and evaluation of prototype coherent flow imaging instrumentation for nonlinear microbubble imaging using transmit frequencies from 10 to 50 MHz. Phantom validation experiments were conducted to demonstrate color and power flow imaging using nonlinear 10 MHz (subharmonic) scattering induced by a 20 MHz transmit frequency. In vivo flow imaging of a rabbit ear microvessel was successfully performed. This work indicates the feasibility of performing flow imaging at high frequencies using nonlinear scattering from microbubbles.
Using coupling measurement for impact analysis in object-oriented systems (1999)

Many coupling measures have been proposed in the context of object oriented (OO) systems. In addition, due to the numerous dependencies present in OO systems, several studies have highlighted the complexity of using dependency analysis to perform impact analysis. An alternative is to investigate the construction of probabilistic decision models based on coupling measurement to support impact analysis. In addition to providing an ordering of classes where ripple effects are more likely, such an approach is simple and can be automated. In our investigation, we perform a thorough analysis on a commercial C++ system where change data has been collected over several years. We identify the coupling dimensions that seem to be significantly related to ripple effects and use these dimensions to rank classes according to their probability of containing ripple effects. We then assess the expected effectiveness of such decision models.
Exposure to Environmental Tobacco Smoke and Cognitive Abilities among U.S. Children and Adolescents (2004)

We used the Third National Health and Nutrition Examination Survey (NHANES III), conducted from 1988 to 1994, to investigate the relationship between environmental tobacco smoke (ETS) exposure and cognitive abilities among U.S. children and adolescents 6-16 years of age. Serum cotinine was used as a biomarker of ETS exposure. Children were included in the sample if their serum cotinine levels were less than or equal to 15 ng/mL, a level consistent with ETS exposure, and if they denied using any tobacco products in the previous 5 days. Cognitive and academic abilities were assessed using the reading and math subtests of the Wide Range Achievement Test-Revised and the block design and digit span subtests of the Wechsler Intelligence Scale for Children-III. Analyses were conducted using SUDAAN software. Of the 5,365 6- to 16-year-olds included in NHANES III, 4,399 (82%) were included in this analysis. The geometric mean serum cotinine level was 0.23 ng/mL (range, 0.035-15 ng/mL); 80% of subjects had levels < 1 ng/mL. After adjustment for sex, race, region, poverty, parent education and marital status, ferritin, and blood lead concentration, there was a significant inverse relationship between serum cotinine and scores on reading (beta = -2.69, p = 0.001), math (beta = -1.93, p = 0.01), and block design (beta = -0.55, p < 0.001) but not digit span (beta = -0.08, p = 0.52). The estimated ETS-associated decrement in cognitive test scores was greater at lower cotinine levels. A log-linear analysis was selected as the best fit to characterize the increased slope in cognitive deficits at lower levels of exposure. These data, which indicate an inverse association between ETS exposure and cognitive deficits among children even at extremely low levels of exposure, support policy to further restrict children's exposure.
Direct Iterative Closest Point for real-time visual odometry (2011)

In RGB-D sensor based visual odometry the goal is to estimate a sequence of camera movements using image and/or range measurements. Direct methods solve the problem by minimizing intensity error. In this work a depth map obtained from a RGB-D sensor is considered as a new measurement which is combined with a direct photometric cost function. The minimization of the bi-objective cost function produces 3D camera motion parameters which registers two 3D surfaces within a same coordinate system. The given formulation does not require any predetermined temporal correspondencies nor feature extraction when having a sufficient frame rate. It is shown how incorporating the depth measurement robustifies the cost function in case of insufficient texture information and non-Lambertian surfaces. Finally the method is demonstrated in the Planetary Robotics Vision Ground Processing (PRoVisG) competition where visual odometry and 3D reconstruction results are solved for a stereo image sequence captured using a Mars rover.
Lymph-Borne Chemokines and Other Low Molecular Weight Molecules Reach High Endothelial Venules via Specialized Conduits While a Functional Barrier Limits Access to the Lymphocyte Microenvironments in Lymph Node Cortex (2000)

Lymph-borne, soluble factors (e.g., chemokines and others) influence lymphocyte recirculation and endothelial phenotype at high endothelial venules (HEVs) in lymph node cortex. Yet the route lymph-borne soluble molecules travel from the subcapsular sinus to the HEVs is unclear. Therefore, we injected subcutaneously into mice and rats a wide variety of fluorophore-labeled, soluble molecules and examined their distribution in the draining lymph nodes. Rather than percolating throughout the draining lymph node, all molecules, including microbial lipopolysaccharide, were very visible in the subcapsular and medullary sinuses but were largely excluded from the cortical lymphocyte microenvironments. Exclusion prevailed even during the acute lymph node enlargement accompanying viral infection. However, low molecular mass (MW) molecules, including chemokines, did gain entry into the cortex, but in a very defined manner. Low MW, fluorophore-labeled molecules highlighted the subcapsular sinus, the reticular fibers, and the abluminal and luminal surfaces of the associated HEVs. These low MW molecules were in the fibers of the reticular network, a meshwork of collagen fibers ensheathed by fibroblastic reticular cells that connects the subcapsular sinus floor and the HEVs by intertwining with their basement membranes. Thus, low MW, lymph-borne molecules, including chemokines, traveled rapidly from the subcapsular sinus to the HEVs using the reticular network as a conduit.