gebhart/patrepeval huggingface dataset:
Oxidized LDL Receptor 1 (OLR1) as a Possible Link between Obesity, Dyslipidemia and Cancer (2011)

Recent studies have linked expression of lectin-like ox-LDL receptor 1 (OLR1) to tumorigenesis. We analyzed microarray data from Olr1 knockout (KO) and wild type (WT) mice for genes involved in cellular transformation and evaluated effects of OLR1 over-expression in normal mammary epithelial cells (MCF10A) and breast cancer cells (HCC1143) in terms of gene expression, migration, adhesion and transendothelial migration. Twenty-six out of 238 genes were inhibited in tissues of OLR1 KO mice; the vast majority of OLR1 sensitive genes contained NF-κB binding sites in their promoters. Further studies revealed broad inhibition of NF-kB target genes outside of the transformation-associated gene pool, with enrichment themes of defense response, immune response, apoptosis, proliferation, and wound healing. Transcriptome of Olr1 KO mice also revealed inhibition of de novo lipogenesis, rate-limiting enzymes fatty acid synthase (Fasn), stearoyl-CoA desaturase (Scd1) and ELOVL family member 6 (Elovl6), as well as lipolytic phospholipase A2 group IVB (Pla2g4b). In studies comparing MCF10A and HCC1143, the latter displayed 60% higher OLR1 expression. Forced over-expression of OLR1 resulted in upregulation of NF-κB (p65) and its target pro-oncogenes involved in inhibition of apoptosis (BCL2, BCL2A1, TNFAIP3) and regulation of cell cycle (CCND2) in both cell lines. Basal expression of FASN, SCD1 and PLA2G4B, as well as lipogenesis transcription factors PPARA, SREBF2 and CREM, was higher in HCC1143 cells. Over-expression of OLR1 in HCC1143 cells also enhanced cell migration, without affecting their adherence to TNFα-activated endothelium or transendothelial migration. On the other hand, OLR1 neutralizing antibody inhibited both adhesion and transmigration of untreated HCC1143 cells. We conclude that OLR1 may act as an oncogene by activation of NF-kB target genes responsible for proliferation, migration and inhibition of apoptosis and de novo lipogenesis genes.
Automated In-Tube Solid-Phase Microextraction Coupled to High-Performance Liquid Chromatography (1997)

Recently, solid-phase microextraction (SPME) was successfully coupled to high-performance liquid chromatography. However, the efficiency of this analytical method, in terms of manpower, still suffers from its manual operation technique. Furthermore, the selectivity obtained for the analysis of very polar compounds is still poor because of a limited selection of commercially available fiber coatings that can withstand the aggressive HPLC conditions (solvents). This paper describes the first approach to developing an automated SPME-HPLC system. A mixture of polar thermally labile analytes, phenylurea pesticides, was selected for microextraction directly from an aqueous sample. A piece of a ordinary capillary GC column with its coating (Omegawax 250) was used for the absorption of analytes from the aqueous sample (in-tube solid-phase microextraction). A needle hosts the capillary when it is pierced through the septum of the vial containing the spiked aqueous sample. The aqueous samples were stored in 2 mL vials on the tray of a commercial autosampler. A sample of 25 μL was aspirated and dispensed several times from the sample into the capillary using a syringe. After the extraction the absorbed analytes were released from the coating by aspiring methanol into the column and then dispensing the methanol into the HPLC injector loop. The absorption−time profiles, the amounts absorbed by different coatings, linearity, and precision were studied under different sampling conditions using spiked aqueous samples. SPME selectivity for polar compounds, which represent an important compound class for water analysis, can be improved by using more polar column coatings such as Carbowax instead of poly(dimethylsiloxane)-coated columns. Compared to the manual version this automated SPME-HPLC system could increase productivity and reproducibility. Furthermore, the desorption step is quantitative; i.e., no carryover could be detected. This entire method for automated SPME sample preparation is simple and controlled by a commercial autosampler from LC Packings which was modified to operate in-tube SPME. The automated SPME-HPLC device obtains RSD for all investigated compounds below 6%. A simple mathematical model was used to calculate the concentrations vs length profiles in the column for any time. The model was in good agreement with experimental data which was obtained for benzene as a model compound. Thus, the main parameters affecting the partitioning process were determined and the amount absorbed by the coating could be predicted.
A model for the potential contribution of HLA-DR-restricted macrophage activation to the pathogenesis of rheumatoid arthritis: Comment on the article by Cantwell et al (1998)

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<title>Effects of polymer matrix on electro-optic properties of liquid crystals mixed with polymer</title> (1996)

The presence of hysteresis in transmittance-voltage characteristics of liquid crystal mixed with polymer (LCMP) has been the main cause for the residual image of LCMP display devices. This hysteresis is regarded to originate in the interaction between liquid crystal material and matrix polymer. The molecular motion of the matrix polymer of LCMP is varied systematically by changing the monomer and photo-initiator content. The hysteresis of LCMP decreases as the elastic modulus of matrix polymer decreases. It has been found quite effective to lower the elastic modulus of matrix polymer in reducing the hysteresis of LCMP.
Applying database support for large scale data driven science in distributed environments (2004)

There is a rapidly growing set of applications, referred to as data driven applications, in which analysis of large amounts of data drives the next steps taken by the scientist, e.g., running new simulations, doing additional measurements, extending the analysis to larger data collections. Critical steps in data analysis are to extract the data of interest from large and potentially distributed datasets and to move it from storage clusters to compute clusters for processing. We have developed a middleware framework, called GridDB-Lite, that is designed to efficiently support these two steps. We describe the application of GridDB-Lite in large scale oil reservoir simulation studies and experimentally evaluate several optimizations that can be employed in the GridDB-Lite runtime system.
Fuel Effects on Oxidation Catalysts and Catalyst-Equipped Vehicles (1973)

&lt;div class="htmlview paragraph"&gt;The effects of lead and sulfur in gasoline on the activity of two platinum oxidation catalysts have been studied using engine dynamometer units. Under the steady-state conditions used, no poisoning due to sulfur was observed. Prolonged operations with lead up to 0.07 g/gal reduced the hydrocarbon (HC) conversion activity of the catalysts in proportion to time and lead concentration, but did not affect carbon monoxide (CO) conversions. The overall extent of lead poisoning was relatively minor, however. Catalysts exposed to the equivalent of 25,000 miles' operation with a fuel containing 0.07 g of lead/gal still met the original 1975 federal emissions standards of 3.4 g/mile of CO and 0.41 g/mile of HC when tested on an experimental vehicle. Exposure of platinum catalysts to exhaust from 20 gal of fuel containing 0.5 g of lead/gal caused an immediate drop in catalyst activity, but this loss was rapidly recovered when operations continued with a lead-free fuel. Thus, short-term contamination of catalyst-equipped cars with lead may not be the serious problem it was formerly thought to be.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Several 1973 model vehicles have been converted by the addition of experimental oxidation catalyst systems and used to determine the effects of fuel gravity and volatility on emissions and performance. To the extent tested, these catalyst-equipped cars gave driveability and fuel economy at least as good as that demonstrated by the corresponding 1973 vehicles. At an ambient temperature of 70°F, using the 1975 federal test procedure (FTP), fuel volatility and gravity did not significantly affect HC and CO emissions for these systems.&lt;/div&gt;
In vivo protective anti‐HIV immune responses in non‐human primates through DNA immunization (1996)

An effective immune response involves the specific recognition of and elimination of an infectious organism at multiple levels. In this context DNA immunization can present functional antigenic proteins to the host for recognition by all arms of the immune system, yet provides the opportunity to delete any genes of the infectious organism which code for antigens or pieces of antigens that may have deleterious effects. Our group has developed the use of nucleic acid immunization as a possible method of vaccination against Human immunodeficiency virus type 1 (HIV-1) [1,2,3,10,11,12]. Sera from non-human primates immunized with DNA vectors that express the envelope proteins from HIV-1 contain antibodies specific to the HIV-1 envelope. These sera also neutralize HIV-1 infection in vitro and inhibit cell to cell infection in tissue culture. Analysis of cellular responses is equally encouraging. T cell proliferation as well as cytotoxic T cell lysis of relevant env expressing target cells were observed. In addition, evidence that DNA vaccines are capable of inducing a protective response against live virus was demonstrated using a chimeric SIV/HIV (SHIV) challenge in vaccinated cynomologous macaques. We found that nucleic acid vaccination induced protection from challenge in one out of four immunized cynomolgus macaques and viral load was lower in the vaccinated group of animals versus the control group of animals. These data encouraged us to analyze this vaccination technique in chimpanzees, the most closely related animal species to man. We observed the induction of both cellular and humoral immune responses with a DNA vaccine in chimpanzees. These studies demonstrate the utility of this technology to induce relevant immune responses in primates which may ultimately lead to effective vaccines.
Prehospital Intubations and Mortality: A Level 1 Trauma Center Perspective (2009)

This prospective study showed a 31% incidence of failed PHI in a large metropolitan trauma center. We found no difference in mortality between patients who were properly intubated and those who were not, supporting the use of bag-valve-mask as an adequate method of airway management for critically ill trauma patients in whom intubation cannot be achieved promptly in the prehospital setting.
Is FOXP3 a bona fide marker for human regulatory T cells? (2008)

FOXP3 is a specific marker for naturally occurring regulatory T cells (nTreg). FOXP3 expression is correlated with development and function of nTreg. Recent evidence suggests that, upon activation, human effector T (Teff) cells and type 1 regulatory T (Tr1) cells can express FOXP3, albeit transiently. While the role of transient FOXP3 expression in Teff cells is poorly understood, it is becoming clear that it does not correlate with suppressor function. Furthermore, FOXP3-independent mechanisms, mediated by IL-10, contribute to the induction and suppressor functions of Tr1 cells.
Apparent digestibility of protein and amino acids in broiler chickens fed a corn-soybean diet supplemented with microbial phytase (1997)

The effect of microbial phytase supplementation on CP and amino acid (AA) digestibility was investigated in a 28-d trial using 360 sexed, day-old broiler chickens fed corn-soybean meal diets. The experimental design was a completely randomized one with a 3 x 2 factorial arrangement of treatments. The variables included P and Ca levels and phytase: P and Ca levels were: normal P-normal Ca [0.45% available P (Pa), 1.0% Ca], low P-normal Ca (0.35% Pa, 1.0% Ca), and low P-low Ca (0.35 Pa and 0.6% Ca); and phytase at 0 and 600 U/kg diet. Phytase supplementation increased body weight gain (P < 0.014) and feed intake (P < 0.004) at 19 d in male chickens; in females, phytase increased (P < 0.012) only body weight gain at 19 d. The low P-normal Ca diet reduced (P < 0.05) feed intake and body weight gain in both sexes at 7, 14, and 19 d, compared to the normal P-normal Ca diet; the reduction of Ca in the low P diet prevented the above depression, resulting in body weight gain and feed intake to a level comparable to that of the normal P-normal Ca diet. Microbial phytase supplementation had no effect (P < 0.065) on the apparent ileal digestibility (AID) of CP or any AA except Met and Phe in male broiler chickens. In females, adding phytase increased the AID of all AA except Lys, Met, Phe, and Pro. The low P-normal Ca diet reduced (P < 0.05) the AID of Phe, Asp, and Ser in male chickens and reduced the AID of all the AA except Met and Pro in females compared to the normal P-normal Ca diet. The reduction of Ca in the low P diet prevented the depression of the AID of the AA caused by the low P-normal Ca diet, resulting in AID of AA having a level comparable to that of the normal P-normal Ca diet in both sexes. Phytase supplementation did not have any effect (P > 0.05) on apparent "fecal" digestibility (AFD) of CP or any of the AA in male chickens; however, in female chickens it increased the AFD of Thr, Asp, Glu, and Ser. In summary, phytase supplementation increased growth performance in both sexes; increased AID and AFD of most of the AA, particularly in female chickens. The optimum growth performance and AA digestibilities were obtained with the lowest input of resources, in the low P-low Ca diet supplemented with microbial phytase.
Tissue-engineered intervertebral discs produce new matrix, maintain disc height, and restore biomechanical function to the rodent spine (2011)

Lower back and neck pain are leading physical conditions for which patients see their doctors in the United States. The organ commonly implicated in this condition is the intervertebral disc (IVD), which frequently herniates, ruptures, or tears, often causing pain and limiting spinal mobility. To date, approaches for replacement of diseased IVD have been confined to purely mechanical devices designed to either eliminate or enable flexibility of the diseased motion segment. Here we present the evaluation of a living, tissue-engineered IVD composed of a gelatinous nucleus pulposus surrounded by an aligned collagenous annulus fibrosus in the caudal spine of athymic rats for up to 6 mo. When implanted into the rat caudal spine, tissue-engineered IVD maintained disc space height, produced de novo extracellular matrix, and integrated into the spine, yielding an intact motion segment with dynamic mechanical properties similar to that of native IVD. These studies demonstrate the feasibility of engineering a functional spinal motion segment and represent a critical step in developing biological therapies for degenerative disc disease.
Cell responses to BMP‐2 and IGF‐I released with different time‐dependent profiles (2004)

During wound healing, growth factors are expressed in time-dependent amounts. Constant delivery of biomolecules, however, is often used to influence cell and tissue behavior. In the present studies, a crosslinked gelatin-coating system was used to deliver bone morphogenetic protein 2 (BMP-2) or insulin-like growth factor (IGF-I) to three types of mesenchymal cells with three temporally varying release profiles. The "early" delivery profile released most of the growth factor within the first 2 days. The "pseudo-zero-order" profile approximated constant rate of delivery for about 5 days. The "late" delivery profile released most of the growth factor after about 5 days. Early delivery of IGF-I had the greatest effect on mitogenesis of SaOS-2 human osteosarcoma cells with a secondary effect noted nearly 5 days after delivery was completed. Late delivery of BMP-2 resulted in greatest alkaline phosphatase (AP) activity in mouse pluripotent C3H10T1/2 cells. Rat bone marrow stromal cells (BMCs) responded to all delivery profiles of BMP-2, with the duration of elevated AP activity increasing as the amount of BMP-2 delivered increased. In addition to an early increase in AP activity, late release also stimulated BMCs over a longer portion of the culture period. BMCs responded similarly to SaOS-2 cells when seeded on early IGF-I delivery coatings, increasing AP activity after delivery had ended. Overall, these studies further show the importance of delivery profile, specifically the characteristics of time and concentration, on cell and tissue responses.
Antibacterial effects of a bioactive glass paste on oral microorganisms (1998)

Bioactive glasses contain oxides of calcium, sodium, phosphorus, and silicon in a proportion that provides the material with surface activity and concomitantly with the property of forming a strong bond with bone. Bioactive glasses have been tested as bone substitutes in different clinical situations. In an aqueous environment, Ca2+, Na+, PO4(3-) , and Si4+ are released from the glass, resulting in a rise in pH and in osmotic pressure in its vicinity. Since these are factors that potentially influence the viability of oral microorganisms at the dentogingival margin, we studied the effects of bioactive glass S53P4 on the oral microorganisms Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Actinomyces naeslundii, Streptococcus mutans, and Streptococcus sanguis. This was done by incubating each microbe in a suspension, in the presence of bioactive glass S53P4 in powder form. A. naeslundii was found to lose its viability within 10 min under the experimental conditions. A. actinomycetemcomitans, P. gingivalis, and S. mutans lost their viability within 60 min. Also for S. sanguis a significant loss of viability was seen within 60 min, but it was the only microbe that had any viable cells left after 60 min. Thus, in aqueous solutions the powdered bioactive glass S53P4 appears to have a broad antimicrobial effect on microorganisms of both supra- and subgingival plaque. Consequently, it could be useful as an ingredient in tooth-care products that may have beneficial effects on oral health both from a cariologic and a periodontal point of view.
Mortality, course of disease and prognosis of patients with ankylosing spondylitis. (2003)

Patients with ankylosing spondylitis (AS) have about a 50% increased risk of mortality on the basis of the limited amount of data available. There is some evidence that the progression of disease is strongest in the first 10 years of disease but it is also clear that the disease keeps on being active for further decades. The overall burden of disease is similar to rheumatoid arthritis but the overall disease duration of AS is longer. Prognostic factors have also not been studied extensively in AS but it seems clear that early hip involvement indicates a worse outcome. The same is true for early limitation of spinal mobility, laboratory evidence of ongoing disease activity (ESR, hypergammaglobulinemia), peripheral arthritis and dactylitis. The significance of organ involvement for the prognosis, especially in the kidney in the form of amyloidosis, and in the heart and lungs, is less clear. Radiation therapy of the spine, which had been performed quite extensively in former decades, has been associated with a mean radiation dose of about double that of atomic bomb survivors and an increased risk of leukemia and mortality. This therapy has been largely abandoned nowadays. Elder rheumatologists report however that the clinical improvement of irradiated patients has been partly impressive.
NMR Solution Structure of an Oligonucleotide Hairpin with a 2‘F-ANA/RNA Stem:  Implications for RNase H Specificity toward DNA/RNA Hybrid Duplexes (2001)

The first structure of a 2'-deoxy-2'-fluoro-D-arabinose nucleic acid (2'F-ANA)/RNA duplex is presented. We report the structural characterization by NMR spectroscopy of a small hybrid hairpin, r(GGAC)d(TTCG)2'F-a(GTCC), containing a 2'F-ANA/RNA stem and a four-residue DNA loop. Complete (1)H, (13)C, (19)F, and (31)P resonance assignments, scalar coupling constants, and NOE constraints were obtained from homonuclear and heteronuclear 2D spectra. In the chimeric duplex, the RNA strand adopts a classic A-form structure having C3' endo sugar puckers. The 2'F-ANA strand is neither A-form nor B-form and contains O4' endo sugar puckers. This contrasts strongly with the dynamic sugar conformations previously observed in the DNA strands of DNA/RNA hybrid duplexes. Structural parameters for the duplex, such as minor groove width, x-displacement, and inclination, were intermediate between those of A-form and B-form duplexes and similar to those of DNA/RNA duplexes. These results rationalize the enhanced stability of 2'F-ANA/RNA duplexes and their ability to elicit RNase H activity. The results are relevant for the design of new antisense drugs based on sugar-modified nucleic acids.
Effect of LDD structure and channel poly-Si thinning on a gate-all-around TFT (GAT) for SRAM's (1999)

A lightly doped drain (LDD) structure was used in a gate-all-around TFT (GAT). This suppresses the leakage current much more than the LDD used in a single-gate TFT (SGT), and the current level of the GAT with the LDD is almost the same as that of the single-gate TFT (SGT) with the LDD keeping the GAT's advantage of a high on-current. This is because the LDD effectively relaxes the electric field at the drain edge and reduces the effect of the electric field from the surrounded gate of the GAT. Furthermore, the GAT can suppress individual performance variations. The suppression mechanism of the individual performance variation in a GAT was investigated using a poly-Si TFT simulator. The thinner the channel poly-Si, the smaller the individual performance variation of the TFT. The GAT is more effective in decreasing the individual performance variation for thin channels than the SGT because the GAT can achieve the full depletion of the channel poly-Si with a channel thickness twice as large as the SGT. The GAT is eminently suitable for use in high-density, low-voltage operations, and low-power SRAM's.
Monoclonal endothelial cell proliferation is present in primary but not secondary pulmonary hypertension. (1998)

The etiology and pathogenesis of the vascular lesions characterizing primary pulmonary hypertension (PPH), an often fatal pulmonary vascular disease, are largely unknown. Plexiform lesions composed of proliferating endothelial cells occur in between 20 and 80% of the cases of this irreversible pulmonary vascular disease. Recently, technology to assess monoclonality has allowed the distinction between cellular proliferation present in neoplasms from that in reactive nonneoplastic tissue. To determine whether the endothelial cell proliferation in plexiform lesions in PPH is monoclonal or polyclonal, we assessed the methylation pattern of the human androgen receptor gene by PCR (HUMARA) in proliferated endothelial cells in plexiform lesions from female PPH patients (n = 4) compared with secondary pulmonary hypertension (PH) patients (n = 4). In PPH, 17 of 22 lesions (77%) were monoclonal. However, in secondary PH, all 19 lesions examined were polyclonal. Smooth muscle cell hyperplasia in pulmonary vessels (n = 11) in PPH and secondary PH was polyclonal in all but one of the examined vessels. The monoclonal expansion of endothelial cells provides the first marker that allows the distinction between primary and secondary PH. Our data of a frequent monoclonal endothelial cell proliferation in PPH suggests that a somatic genetic alteration similar to that present in neoplastic processes may be responsible for the pathogenesis of PPH.