gebhart/patrepeval huggingface dataset:
The BLyS family of ligands and receptors: an archetype for niche‐specific homeostatic regulation (2004)

Discovery and characterization of the tumor necrosis factor (TNF) family member B-lymphocyte stimulator (BLyS) has opened a novel chapter in the role of TNF family members in the homeostatic control of lymphocyte populations. BLyS and its sister cytokine APRIL (a proliferation-inducing ligand) act primarily as soluble trimers and serve to regulate the steady-state numbers of nearly all B-cell compartments. This homeostatic regulation is accomplished through the regulation of B-cell production rates, selection thresholds, and lifespan. Differential expression of the three BLyS receptors during differentiation and activation provides related yet distinct homeostatic niches for follicular, marginal zone, and memory B-cell subsets.
An RNA interference model of RPS19 deficiency in Diamond-Blackfan anemia recapitulates defective hematopoiesis and rescue by dexamethasone: identification of dexamethasone-responsive genes by microarray (2005)

Diamond-Blackfan anemia (DBA), a congenital erythroblastopenia, is a model disease for the study of erythroid differentiation but is poorly understood. RPS19 is the only gene yet to have been associated with DBA, but its relevance to erythroid differentiation is unclear. The molecular basis for the stimulation of erythropoiesis by glucocorticoids in patients with DBA has not been identified. We demonstrate that targeted degradation of the RPS19 transcript, through retroviral expression of short hairpin RNAs (shRNAs), blocks the proliferation and differentiation of erythroid progenitor cells in cultured human CD34(+) cells. Treatment of RPS19-deficient cells with dexamethasone restores erythroid differentiation to normal levels. We investigated the molecular basis of pharmacologic therapies for DBA using oligonucleotide microarrays to survey gene expression in CD34(+) cells treated with combinations of dexamethasone, erythropoietin, stem cell factor, and interleukin-3. Dexamethasone did not alter expression of RPS19 but activated a genetic program that includes a set of key hematopoietic regulatory genes. Genes specific to erythroid progenitor cells were up-regulated by dexamethasone, while genes specific to nonerythroid lineages were down-regulated. Deficiency of RPS19 therefore blocks proliferation of immature erythroid progenitor cells, and dexamethasone activates proliferation of the same cell population through mechanisms independent of RPS19.
Potential Repair of Rat Spinal Cord Injuries Using Stimulated Homologous Macrophages (1999)

The failure of the adult mammalian central nervous system (CNS) to regenerate after injury has long been viewed as a unique phenomenon resulting from the specific nature of this system. The finding that some CNS axons could be induced to regrow if provided with a permissive environment suggested that this failure is a result, at least in part, of the nature of the postinjury neuronal environment. It was further shown that the involvement of inflammatory cells, particularly macrophages, in postinjury processes in the CNS is limited. We have suggested that, to achieve recovery after injury, the adult mammalian CNS may require the assistance of the same postinjury factors as those involved in the recovery of spontaneously regenerating systems but that its accessibility to such assistance is restricted. Accordingly, we proposed that it might be possible to circumvent the restriction, allowing regeneration to occur. We showed that the implantation of autologous macrophages, which had been prestimulated by exposure to a regenerative (sciatic) nerve, into completely transected spinal cords of adult rats led to partial motor recovery. This treatment intervenes in the postinjury process by simulating in the axotomized CNS the events that occur naturally in spontaneously regenerating systems.
p62/SQSTM1 cooperates with Parkin for perinuclear clustering of depolarized mitochondria (2010)

PINK1 and Parkin were first identified as the causal genes responsible for familial forms of early-onset Parkinson's disease (PD), a prevalent neurodegenerative disorder. PINK1 encodes a mitochondrial serine/threonine protein kinase, whereas Parkin encodes an ubiquitin-protein ligase. PINK1 and Parkin cooperate to maintain mitochondrial integrity; however, the detailed molecular mechanism of how Parkin-catalyzed ubiquitylation results in mitochondrial integrity remains an enigma. In this study, we show that Parkin-catalyzed K63-linked polyubiquitylation of depolarized mitochondria resulted in ubiquitylated mitochondria being transported along microtubules to cluster in the perinuclear region, which was interfered by pathogenic mutations of Parkin. In addition, p62/SQSTM1 (hereafter referred to as p62) was recruited to depolarized mitochondria after Parkin-directed ubiquitylation. Intriguingly, deletion of p62 in mouse embryonic fibroblasts resulted in a gross loss of mitochondrial perinuclear clustering but did not hinder mitochondrial degradation. Thus, p62 is required for ubiquitylation-dependent clustering of damaged mitochondria, which resembles p62-mediated 'aggresome' formation of misfolded/unfolded proteins after ubiquitylation.
Should patients with cardiovascular disease take fish oil? (2008)

The scientific community and the public have been fascinated by epidemiologic data showing the beneficial effects that a diet rich in fish oils can have on cardiovascular disease. As a result, several clinical trials have been performed that have examined the effects of omega-3 polyunsaturated fatty
The SHARON-Anammox process for treatment of ammonium rich wastewater. (2001)

The treatment of ammonium rich wastewater, like sludge digester effluent, can be significantly improved when new biotechnological processes are introduced. In this paper, the combination of a partial nitrification process (SHARON) and anoxic ammonium oxidation (Anammox) process for the treatment of ammonia rich influents is evaluated. Herein the combined process has been studied with sludge recycle liquor from the WWTP Rotterdam-Dokhaven. The SHARON process was operated stably for more than 2 years in a 10ICSTR under continuous aeration with a HRT of 1 day. The ammonia in the sludge liquor was converted by 53% to nitrite only. During the test period no formation of nitrate was observed. The effluent of the SHARON process was ideally suited as influent for the Anammox reactor. The Anammox process was operated as a granular sludge SBR-process. More than 80% of the ammonia was converted into dinitrogen gas at a load of 1.2 kgN/m3 per day. Planctomycete-like bacteria dominated the mixed community of the Anammox reactor, and only a small percentage of the population consisted of aerobic ammonium-oxidizing bacteria. This showed that the ammonium-oxidizers in the effluent of the SHARON process did not accumulate in the SBR. The test period showed that the combined SHARON-Anammox system can work stably over long periods and the process is ready for full-scale implementation.
Microbial Fuel Cells for Sulfide Removal (2006)

Thus far, microbial fuel cells (MFCs) have been used to convert carbon-based substrates to electricity. However, sulfur compounds are ubiquitously present in organic waste and wastewater. In this study, a MFC with a hexacyanoferrate cathodic electrolyte was used to convert dissolved sulfide to elemental sulfur. Two types of MFCs were used, a square type closed to the air and a tubular type in which the cathode compartment was open to the air. The square-type MFCs demonstrated a potential-dependent conversion of sulfide to sulfur. In the tubular system, up to 514 mg sulfide L(-1) net anodic compartment (NAC) day(-1) (241 mg L(-1) day(-1) total anodic compartment, TAC) was removed. The sulfide oxidation in the anodic compartment resulted in electricity generation with power outputs up to 101 mW L(-1) NAC (47 W m(-3) TAC). Microbial fuel cells were coupled to an anaerobic upflow anaerobic sludge blanket reactor, providing total removals of up to 98% and 46% of the sulfide and acetate, respectively. The MFCs were capable of simultaneously removing sulfate via sulfide. This demonstrates that digester effluents can be polished by a MFC for both residual carbon and sulfur compounds. The recovery of electrons from sulfides implies a recovery of energy otherwise lost in the methane digester.
Molecular analysis of a GM2-activator deficiency in two patients with GM2-gangliosidosis AB variant. (1996)

Lysosomal degradation of ganglioside GM2 by beta-hexosaminidase A (hex A) requires the presence of the GM2 activator protein (GM2AP) as an essential cofactor. A deficiency of the GM2 activator causes the AB variant of GM2 gangliosidosis, a recessively inherited disorder characterized by excessive neuronal accumulation of GM2 and related glycolipids. Two novel mutations in the GM2 activator gene (GM2A) have been identified by the reverse-transcriptase-PCR method--a three-base deletion, AAG262-264, resulting in a deletion of Lys88, and a single-base deletion, A410, that causes a frameshift. The latter results in substitution of 33 amino acids and the loss of another 24 amino acid residues. Both patients are homoallelic for their respective mutations inherited from their parents, who are heteroallelic at the GM2A locus. Although the cultured fibroblasts of both patients produce normal levels of activator mRNA, they lack a lysosomal form of GM2AP. Pulse/chase labeling of cultured fibroblasts of the patients, in presence and absence of brefeldin A, indicates a premature degradation of both--mutant and truncated--GM2APs in the endoplasmic reticulum or Golgi. These results were supported by in vitro translation experiments and expression of the mutated proteins. When the mutated GM2APs were expressed in Escherichia coli, both mature GM2AP forms turned proved to exhibit only residual activities in an in vitro assay.
Data augmentation for machine learning redshifts applied to Sloan Digital Sky Survey galaxies (2015)

We present analyses of data augmentation for machine learning redshift estimation. Data augmentation makes a training sample more closely resemble a test sample, if the two base samples differ, in order to improve measured statistics of the test sample. We perform two sets of analyses by selecting 800 000 (1.7 million) Sloan Digital Sky Survey Data Release 8 (Data Release 10) galaxies with spectroscopic redshifts. We construct a base training set by imposing an artificial &lt;it&gt;r&lt;/it&gt;-band apparent magnitude cut to select only bright galaxies and then augment this base training set by using simulations and by applying the &lt;scp&gt;k-correct&lt;/scp&gt; package to artificially place training set galaxies at a higher redshift. We obtain redshift estimates for the remaining faint galaxy sample, which are not used during training. We find that data augmentation reduces the error on the recovered redshifts by 40 per cent in both sets of analyses, when compared to the difference in error between the ideal case and the non-augmented case. The outlier fraction is also reduced by at least 10 per cent and up to 80 per cent using data augmentation. We finally quantify how the recovered redshifts degrade as one probes to deeper magnitudes past the artificial magnitude limit of the bright training sample. We find that at all apparent magnitudes explored, the use of data augmentation with tree-based methods provide an estimate of the galaxy redshift with a low value of bias, although the error on the recovered redshifts increases as we probe to deeper magnitudes. These results have applications for surveys which have a spectroscopic training set which forms a biased sample of all photometric galaxies, for example if the spectroscopic detection magnitude limit is shallower than the photometric limit.
Tyrosine Kinase Inhibitors. 16. 6,5,6-Tricyclic Benzothieno[3,2-d]pyrimidines and Pyrimido[5,4-b]- and -[4,5-b]indoles as Potent Inhibitors of the Epidermal Growth Factor Receptor Tyrosine Kinase (1999)

Several elaborations of the fundamental anilinopyrimidine pharmacophore have been reported as potent and selective inhibitors of the epidermal growth factor receptor (EGFr) tyrosine kinase. This paper reports on a series of inhibitors whereby some 6,5-bicyclic heteroaromatic systems were fused through their C-2 and C-3 positions to this anilinopyrimidine pharmacophore. Although the resulting tricycles did not produce the enormous potency of some of the (5/6),6,6-bicyclic systems, the best of them had IC(50)s for the EGFr TK around 1 nM. Investigation of 4-position side chains in the indolopyrimidines confirmed that m-bromoaniline was an optimal substituent for potency. Investigation of substitution within the C-(benzo)ring of benzothienopyrimidines confirmed that introduction of an extra ring can change sharply the effects of substituents when compared to similar bicyclic nuclei, and only two substituents were found which even moderately enhanced inhibitory activity over the parent compound for this series.
Induction of antiestrogen resistance in human breast cancer cells by random insertional mutagenesis using defective retroviruses: identification of bcar-1, a common integration site. (1993)

Duration of response to antiestrogen therapy in metastatic breast cancer is limited due to the development of antiestrogen-resistant tumors. The mechanisms involved are not understood but could originate from (epi)genetic alterations within the tumor cells. We have applied in vitro random insertional mutagenesis with replication defective retroviruses to identify those genes playing a key role in development of antiestrogen resistance in human breast cancer cells. Eighty antiestrogen-resistant cell clones were isolated from 7 x 10(8) estrogen-dependent ZR-75-1 cells, mass-infected with defective retroviruses and subjected to 4-OH-tamoxifen selection. Integration site-specific DNA probes were made by inverse polymerase chain reaction techniques and used to search for common integration sites. Six cell clones were identified with retroviral genome integrations in the same orientation in a single locus, designated breast cancer antiestrogen resistance locus-1 (bcar-1). These bcar-1 cell clones had lost estrogen receptor expression and had become estrogen independent. Our results strongly suggest that alteration of the bcar-1 locus is responsible for development of antiestrogen resistance in human breast cancer cells in vitro. In addition, we have shown that in vitro insertional mutagenesis using defective retroviruses can be applied for gene tagging in human cells.
An enzymic method for the spectrophotometric determination of oxalic acid. (1976)

A simple method is described for the measurement of urinary oxalate. Oxalate decarboxylase is coupled with NAD+ requiring formate dehydrogenase and the result recorded spectrophotometrically. Accurate determination can be carried out either on urine or a citrate extract or urine. Using the citrate extract procedure, the urinary samples can be stored for at least 3 months without any effect on the oxalate content.
In Vivo Fluorescence Detection of Glucose Using a Single-Walled Carbon Nanotube Optical Sensor:  Design, Fluorophore Properties, Advantages, and Disadvantages (2005)

In this work, several aspects of in vivo glucose detection using a nanotube-based optical sensor are considered. The optical properties of commonly used organic and nanoparticle fluorescent probes are compared with respect to quantum yield, human tissue penetration, and photobleaching stability. The latter two factors are shown to dominate sensor viability and require a near-infrared nanoparticle fluorophore for practical device operation. The dynamics of a model optical sensor are compared to a flux-measuring electrochemical sensor of equal area using a mathematical simulation of a healthy patient ingesting three predefined meals per day. Both sensors demonstrate an approximately linear response to blood glucose levels. It is shown that the optical sensor, which transduces glucose concentration, not flux, directly is significantly more stable to membrane biofouling.
Cardiovascular and parasympathetic effects of dexmedetomidine in healthy subjects (2004)

We evaluated the cardiovascular effects of intravenously (i.v.) and buccally administered dexmedetomidine, a selective alpha2-adrenoceptor agonist. Six healthy male subjects were studied unmedicated and after 2 micro g/kg i.v. or buccal doses of dexmedetomidine, using repeated recordings of ECG and blood pressure. Cardiac parasympathetic activity was estimated by measurements of high-frequency (HF) heart rate variability. Intravenous, but not buccal, dexmedetomidine raised systolic blood pressure by 11 +/- 5 mmHg (mean +/- SEM) and diastolic by 16 +/- 3 mmHg (maxima at 10 min). Later on, both i.v., and buccal dexmedetomidine produced a very similar hypotensive effect: on average, >or=10 mmHg reductions in systolic and diastolic pressure at 3 h. Intravenous dosing was followed by a decline in heart rate (-11 +/- 2 beats/min) accompanied by a trend toward enhanced HF variability (maximal effect at 10 min), which probably reflected baroreflex-mediated parasympathetic efferent neuronal activation. Buccal dexmedetomidine increased significantly the HF variability (maximum at 45 min) without influencing heart rate. We conclude that dexmedetomidine, when administered by a method that avoids concentration peaks, e.g., buccal dosing, can be used to produce a prolonged augmentation of cardiac parasympathetic efferent neuronal activity.
DNA Damage and the Activation of the p53 Pathway Mediate Alterations in Metabolic and Secretory Functions of Adipocytes (2016)

Activation of the p53 pathway in adipose tissue contributes to insulin resistance associated with obesity. However, the mechanisms of p53 activation and the effect on adipocyte functions are still elusive. Here we found a higher level of DNA oxidation and a reduction in telomere length in adipose tissue of mice fed a high-fat diet and an increase in DNA damage and activation of the p53 pathway in adipocytes. Interestingly, hallmarks of chronic DNA damage are visible at the onset of obesity. Furthermore, injection of lean mice with doxorubicin, a DNA damage-inducing drug, increased the expression of chemokines in adipose tissue and promoted its infiltration by proinflammatory macrophages and neutrophils together with adipocyte insulin resistance. In vitro, DNA damage in adipocytes increased the expression of chemokines and triggered the production of chemotactic factors for macrophages and neutrophils. Insulin signaling and effect on glucose uptake and Glut4 translocation were decreased, and lipolysis was increased. These events were prevented by p53 inhibition, whereas its activation by nutlin-3 reproduced the DNA damage-induced adverse effects. This study reveals that DNA damage in obese adipocytes could trigger p53-dependent signals involved in alteration of adipocyte metabolism and secretory function leading to adipose tissue inflammation, adipocyte dysfunction, and insulin resistance.
Modulation of drug resistance in a daunorubicin resistant subline with oligonucleoside methylphosphonates. (1989)

Human K562 erythroleukemia cells were selected in sequential steps for resistance to daunorubicin (K562/III) and found to be cross-resistant to a number of drugs, including vincristine, dactinomycin, doxorubicin, etoposide, and teniposide. In this paper, we report that the K562/III subline showed amplification of an mdr1 gene and its 4.5 kb transcript. Our results also show that non-ionic oligonucleoside methylphosphonates, complementary to the initiation codon and 15 bases upstream of the mdr1 gene, can completely inhibit the synthesis of P-glycoprotein and partially increase the toxicity of daunorubicin.
Interaction of human plasma fibronectin with viral proteins of human immunodeficiency virus (1994)

Fibronectin (FN) is present in soluble and matrix forms in various body fluids and tissues, and has been shown to bind to several pathogens, including viruses. The interaction of FN with viral proteins of human immunodeficiency virus (HIV-1) was investigated by immunofluorescence technique using a cell line chronically infected with HIV-1 (H9-V). The results of this study showed that FN binds to HIV-1 infected cells. especially at FN concentration of 5 µg/ml. In addition, FN-pentapeptide has shown the ability to bind to HIV-1 infected cells. On the other hand, preincubation with antibodies against FN abolished the binding of FN to HIV-1 infected cells. Finally, FN has shown to bind to HIV-1 glycoproteins, including gp41 and pg120. In contrast, no binding to HIV-1 core proteins, including p15 and p24, was noted. We suggest that FN, in binding HIV-1 particles, may reduce viremia and thus may be involved in the clearance of viral proteins from the cells.
Immunisation of common marmosets with vaccinia virus expressing Epstein-Barr virus (EBV) gp340 and challenge with EBV (1996)

Epstein-Barr virus (EBV) is the cause of infectious mononucleosis and is associated with a variety of life-threatening diseases in humans. Therefore the development of an effective vaccine is an important objective. Many of the initial studies of vaccine efficacy analyse the ability of vaccine preparations to prevent the induction of lymphomas in cottontop tamarins by the B95-8 strain of EBV. We used a vaccinia virus recombinant expressing gp340, vMA1, tested previously in the cotton-top tamarin, to evaluate a common marmoset model in which the challenge virus, M81, resembles more closely the wild-type strains of EBV in the general population than does the standard B95-8 strain. We characterised the M81 strain of EBV with respect to the sequence of its gp340/220 gene and in regard to the presence of a region deleted in B95-8. Replication of the challenge virus in the group vaccinated with vMA1 was decreased when compared to control groups.
Approximate Material Properties in Isotropic Materials (1985)

Selection de materiaux utilises dans les transducteurs d'ultrasons et les systemes de mesure ultrasonore. Cette selection peut etre effectuee sur la base des proprietes telles que vitesse acoustique, impedance et attenuation mais egalement sur la propriete d'adherence a l'epoxyde, la linearite et la propriete d'absorption de l'eau. Table des materiaux qui ont ete mesures ou dont les proprietes ont ete obtenues a partir de references
Analysis of Gene Expression During Maturation of Immature Dendritic Cells Derived from Peripheral Blood Monocytes (2002)

Dendritic cells (DCs) are the most important antigen-presenting cells. Many recent studies have compared the function of immature DCs (iDCs) and mature DCs (mDCs), but there have been few reports of the molecular changes that occur in DCs during maturation. Here, we report on differential gene expression in iDCs generated from peripheral blood monocytes compared with mDCs. Gene expression was evaluated using the differential display method after activation of iDCs with a low concentration of lipopolysaccharide (LPS) to induce maturation. Proteasome subunit alpha type 3 (PSMA3), transcription factor EC (TFEC) isoform and BTK region clone 2f10-rpi were transiently upregulated. Tryptophanyl-tRNA synthetase and CD63 antigen were upregulated for at least 24 h. Neuronal apoptosis inhibitory protein (NAIP) and transforming growth factor-beta-induced 68 kDa protein were downregulated. This is the first report of NAIP expression in human DCs. By comparing the expression of NAIP with that of other members of the inhibitor of apoptosis protein (IAP) family and the Bcl-2 family, only NAIP was found to be strongly expressed in iDCs before stimulation by LPS. PSMA3 was also induced in the DCs stimulated with immune complex. These findings might contribute to our understanding of DC maturation and the effectiveness of DC-based vaccines.
Cardiac Hypertrophy Is Not a Required Compensatory Response to Short-Term Pressure Overload (2000)

In this experimental setting, calcineurin blockade with CsA prevented LV hypertrophy due to pressure overload. TAB mice treated with CsA maintain normal LV size and systolic function.