gebhart/patrepeval huggingface dataset:
Expression of CDK8 and CDK8-interacting Genes as Potential Biomarkers in Breast Cancer (2015)

CDK8 and its paralog CDK19, in complex with CCNC, MED12 and MED13, are transcriptional regulators that mediate several carcinogenic pathways and the chemotherapy-induced tumor-supporting paracrine network. Following up on our previous observation that CDK8, CDK19 and CCNC RNA expression is associated with shorter relapse-free survival (RFS) in breast cancer, we now found by immunohistochemical analysis that CDK8/19 protein is overexpressed in invasive ductal carcinomas relative to non-malignant mammary tissues. Meta-analysis of transcriptomic data revealed that higher CDK8 expression is associated with shorter RFS in all molecular subtypes of breast cancer. These correlations were much stronger in patients who underwent systemic adjuvant therapy, suggesting that CDK8 impacts the failure of systemic therapy. The same associations were found for CDK19, CCNC and MED13. In contrast, MED12 showed the opposite association with a longer RFS. The expression levels of CDK8 in breast cancer samples were directly correlated with the expression of MYC, as well as CDK19, CCNC and MED13 but inversely correlated with MED12. CDK8, CDK19 and CCNC expression was strongly increased and MED12 expression was decreased in tumors with mutant p53. Gene amplification is the most frequent type of genetic alterations of CDK8, CDK19, CCNC and MED13 in breast cancers (9.7% of which have amplified MED13), whereas point mutations are more common in MED12. These results suggest that the expression of CDK8 and its interactive genes has a profound impact on the response to adjuvant therapy in breast cancer in accordance with the role of CDK8 in chemotherapy-induced tumor-supporting paracrine activities.
Elevated Serum Carboxymethyl-Lysine, an Advanced Glycation End Product, Predicts Severe Walking Disability in Older Women: The Women's Health and Aging Study I (2012)

Advanced glycation end products (AGEs) have been implicated in the pathogenesis of sarcopenia. Our aim was to characterize the relationship between serum carboxymethyl-lysine (CML), a major circulating AGE, and incident severe walking disability (inability to walk or walking speed <0.4 m/sec) over 30 months of followup in 394 moderately to severely disabled women, ≥65 years, living in the community in Baltimore, Maryland (the Women's Health and Aging Study I). During followup, 154 (26.4%) women developed severe walking disability, and 23 women died. Women in the highest quartile of serum CML had increased risk of developing of severe walking disability in a multivariate Cox proportional hazards model, adjusting for age and other potential confounders. Women with elevated serum CML are at an increased risk of developing severe walking disability. AGEs are a potentially modifiable risk factor. Further work is needed to establish a causal relationship between AGEs and walking disability.
Specific antibodies to PAS IV, a glycoprotein of bovine milk-fat-globule membrane, bind to a similar protein in cardiac endothelial cells and epithelial cells of lung bronchioles (1985)

We recently described the tissue distribution of PAS IV (periodic acid/Schiff-positive Band IV), a hydrophobic glycoprotein isolated from bovine milk-fat-globule membrane [Greenwalt & Mather (1985) J. Cell Biol. 100, 397-408]. By using immunofluorescence techniques, PAS IV was detected in mammary epithelial cells, the bronchiolar epithelium of lung, and the capillary endothelium of several tissues, including heart, salivary gland, pancreas, spleen and intestine. In the present paper we describe the specificity of the antibodies used for these studies. Two monoclonal antibodies, E-1 and E-3, were shown by solid-phase immunoassay and immunoaffinity chromatography to be specific for PAS IV (of Mr 76000) in milk-fat-globule membrane and recognize a glycoprotein of slightly higher Mr (85000) in heart. Affinity-purified rabbit antibodies to PAS IV were also shown to recognize components of Mr 76000 and 85000 in fat-globule membrane and heart respectively, by using immunoblotting procedures after sodium dodecyl sulphate/polyacrylamide-gel electrophoresis. Additionally, an immunoreactive protein in lung of Mr 85000 was detected. Despite these differences in molecular size, the fat-globule membrane and heart forms of PAS IV were shown to be very similar by peptide-mapping techniques. The possible significance of the expression of similar forms of PAS IV in both epithelial and capillary endothelial cells is briefly discussed.
Structure and function of human tissue‐type plasminogen activator (t‐PA) (1986)

Full-length tissue-type plasminogen activator (t-PA) cDNA served to construct deletion mutants within the N-terminal "heavy" (H)-chain of the t-PA molecule. The H-chain cDNA consists of an array of structural domains homologous to domains present on other plasma proteins ("finger," "epidermal growth factor," "kringles"). These structural domains have been located on an exon or a set of exons. The endpoints of the deletions nearly coincide with exon-intron junctions of the chromosomal t-PA gene. Recombinant t-PA deletion mutant proteins were obtained after transient expression in mouse Ltk- cells, transfected with SV40-pBR322-derived t-PA cDNA plasmids. It is demonstrated that the serine protease moiety of t-PA and its substrate specificity for plasminogen is entirely contained within the C-terminal "light" (L)-chain of the protein. The presence of cDNA, encoding the t-PA signal peptide preceding the remaining portion of t-PA, suffices to achieve secretion of (mutant) t-PA into the medium. The stimulatory effect of fibrin on the plasminogen activator activity of t-PA was shown to be mediated by the kringle K2 domain and, to a lesser extent, by the finger domain. The other domains on the H-chain, kringle K1, and the epidermal growth-factor-like domain, do not contribute to this property of t-PA. These findings correlate well with the fibrin-binding properties of the rt-PA deletion-mutant proteins, indicating that stimulation of the activity is based on aligning of the substrate plasminogen and its enzyme t-PA on the fibrin matrix. The primary target for endothelial plasminogen activator inhibitor (PAI) is located within the L-chain of t-PA. Deleting specific segments of t-PA H-chain cDNA and subsequent transient expression in mouse Ltk- cells of t-PA deletion-mutant proteins did not affect the formation of a stable complex between mutant t-PA and PAI.
Type II Transforming Growth Factor-β Receptor Recycling Is Dependent upon the Clathrin Adaptor Protein Dab2 (2010)

Transforming growth factor (TGF)-β family proteins form heteromeric complexes with transmembrane serine/threonine kinases referred to as type I and type II receptors. Ligand binding initiates a signaling cascade that generates a variety of cell type-specific phenotypes. Whereas numerous studies have investigated the regulatory activities controlling TGF-β signaling, there is relatively little information addressing the endocytic and trafficking itinerary of TGF-β receptor subunits. In the current study we have investigated the role of the clathrin-associated sorting protein Disabled-2 (Dab2) in TGF-β receptor endocytosis. Although small interfering RNA-mediated Dab2 knockdown had no affect on the internalization of various clathrin-dependent (i.e., TGF-β, low-density lipoprotein, or transferrin) or -independent (i.e., LacCer) cargo, TGF-β receptor recycling was abrogated. Loss of Dab2 resulted in enlarged early endosomal antigen 1-positive endosomes, reflecting the inability of cargo to traffic from the early endosome to the endosomal recycling compartment and, as documented previously, diminished Smad2 phosphorylation. The results support a model whereby Dab2 acts as a multifunctional adaptor in mesenchymal cells required for TGF-β receptor recycling as well as Smad2 phosphorylation.
The angiotensin converting enzyme inhibitor perindopril improves survival after experimental myocardial infarction in pigs. (1992)

In this randomized, blinded study the effect of the angiotensin converting enzyme inhibitor perindopril on electrical stability after myocardial infarction in pigs was compared to placebo. The left anterior descending artery was occluded for 45 min. Perindoprilat (0.06 mg/kg, n = 12) or saline (n = 12) was injected 15 min before reperfusion. Treatment was continued till day 13 with perindopril (12 mg, once daily) or placebo. At day 14 an electrophysiologic study was performed. The release of creatine phosphokinase did not differ significantly. During the subsequent days, seven of 12 placebo-treated pigs died (six within 24 h), whereas two of the 12 perindopril-treated pigs died (one within 24 h; p less than 0.04). Sustained ventricular tachycardia was inducible in one of five placebo-treated pigs versus three of 10 perindopril-treated survivors (NS). Late potentials had developed in one placebo-treated pig but not in pigs that received perindopril. Characteristics of infarct border zone heterogeneity (percentages of a reference electrode in viable myocardium) such as a dispersion of current thresholds (127 +/- 96 vs. 238 +/- 463% in perindopril-treated pigs, NS) and refractoriness (9.8 +/- 8.4 vs. 11.9 +/- 6.0% in perindopril-treated pigs, NS) were comparable. This treatment with perindopril significantly improved survival while electrical stability was comparable between survivors. The latter indicates that a comparable electrical stability 2 weeks after myocardial infarction is obtained in perindopril-treated pigs at a significantly higher survival rate.
Effects of virus infection and light environment on population dynamics of Eupatorium makinoi (Asteraceae) (2001)

We studied the effects of virus infection on dynamics of three Eupatorium makinoi populations in contrasting light environments, Gora-dani (a shaded population) and Minou 1 and Minou 2 (open-site populations). Censuses of the plants were taken for 8 yr in Gora-dani and 4 yr in Minou 1 and Minou 2. After the epidemics of virus infection, most plants were virus infected at both sites. The number of plants and the proportion of flowering individuals decreased rapidly and simultaneously in the shaded population in Gora-dani. By contrast, in the open-site populations of Minou, the proportion of flowering plants decreased first, and then the number of plants decreased gradually. Growth analysis of the plants in the Gora-dani population revealed that stem growth was significantly suppressed by infection and that flowering and survivorship of the infected plants decreased with reducing plant height. Since light availability affected plant growth and thereby flowering and survivorship, the differences in population dynamics between the two field sites could be caused by the differences in light environments. Although populations in open sites may persist for considerable periods after virus epidemics, the individual local populations of E. makinoi would eventually become extinct irrespective of light environments.
Flow-Through Comb Electroporation Device for Delivery of Macromolecules (2012)

We present a microfluidic electroporation device with a comb electrode layout fabricated in polydimethylsiloxane (PMDS) and glass. Characterization experiments with HeLa cells and fluorescent dextran show efficient delivery (~95%) with low toxicity (cell viability ~85%) as well as rapid pore closure after electroporation. The activity of delivered molecules is also verified by silencing RNA (siRNA) studies that demonstrate gene knockdown in GFP expressing cells. This simple, scalable approach to microfluidic, flow-through electroporation could facilitate the integration of electroporation modules within cell analysis devices that perform multiple operations.
Comparative in vivo studies with paclitaxel and liposome-encapsulated paclitaxel. (1998)

Our study was designed to evaluate the pharmacokinetics, tissue distribution, toxicity and therapeutic efficacy of liposome-encapsulated paclitaxel (LET) in comparison to conventional paclitaxel. In normal mice, LET was much less toxic than the conventional drug. A dose of 32.5 mg/kg of conventional paclitaxel administered i.v. on three consecutive days produced 100% mortality by day three, while liposomal paclitaxel exhibited no mortality. The control group which received Diluent 12 (Chremophor EL and ethanol; 1:1 v/v), a vehicle used in conventional paclitaxel, 30% mortality was observed at this dosage level. In murine ascitic L1210 leukemia model, liposomal paclitaxel and conventional paclitaxel showed comparable antitumor activity. The pharmacokinetics of conventional paclitaxel and LET was studied in mice at dose levels of 5 mg/kg and 20 mg/kg. After intravenous administration of conventional paclitaxel at a dose of 5 mg/kg, the area under the plasma-concentration-time curve (AUC) was 2-fold lower and, the elimination half-life was 2-times shorter compared to LET. At a dose of 20 mg/kg, the terminal half-lives were comparable, however, conventional paclitaxel displayed non-linear pharmacokinetics with disproportionate increase in AUC. At the two dose levels studied, LET demonstrated linear kinetics. Tissue distribution of paclitaxel after administration of LET showed levels 10-fold higher in spleen and 3.5-fold higher in liver as compared to conventional paclitaxel. The significant decrease in toxicity shown by LET, coupled with an increase in plasma AUC and half-life indicates that LET may be a viable alternative to the therapeutic use of the conventional preparation of paclitaxel.
Reprogramming a maize plant: transcriptional and metabolic changes induced by the fungal biotroph Ustilago maydis (2008)

The fungal pathogen Ustilago maydis establishes a biotrophic relationship with its host plant maize (Zea mays). Hallmarks of the disease are large plant tumours in which fungal proliferation occurs. Previous studies suggested that classical defence pathways are not activated. Confocal microscopy, global expression profiling and metabolic profiling now shows that U. maydis is recognized early and triggers defence responses. Many of these early response genes are downregulated at later time points, whereas several genes associated with suppression of cell death are induced. The interplay between fungus and host involves changes in hormone signalling, induction of antioxidant and secondary metabolism, as well as the prevention of source leaf establishment. Our data provide novel insights into the complexity of a biotrophic interaction.
Nevis Synchrocyclotron Conversion Program-RF System (1971)

The <B> for the revised Nevis Synchrocylotron magnet will increase from 18 kG at the center to 20 kG at 80 in. radius. This gives 27.48 MHz at injection, and 19.23 MHz for extraction (550 MeV, 76 in. radius). The resonator will be tuned so that f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">min</sub> = f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">extraction</sub> including a slow RF turnoff where df/dt ≈ 0 for adiabatic energy damping. The peak dee voltage ≥ 30 kV with the maximum near injection. The repetition rate will be 300 Hz with <50% RF duty factor. The single dee and dee stem structure will be ~ 150 in. wide and 163 in. long. One of the three pairs of sector-iron shims is to be incorporated into the dee and the assembly supported on cooled alumina structural insulators. The resonator frequency is varied by two rotating capacitors located at the end of the dee stem, which is split outside the magnet circle. Excitation of the resonator will be provided by a grounded-grid, triode oscillator having the anode and cathode coupled to the resonator via coupling loops and transmission lines of proper length and impedance. A series tube modulator will permit the slow linear RF turnoff needed for adiabatic energy damping of the phase oscillations before extraction.
Fabrication of Thermally Actuated Micromirror Using CMOS Compatible Surface MEMs Process with XeF2 Release Etch (2008)

Thermally actuated micromirrors were fabricated to demonstrate a CMOS compatible surface micromachined MEMs process that was developed. A key step in the process was the used of a XeF2 etch to release the structures. A design was created that varied key factors including mirror pad size and number of anchors. For the smallest pads attached by a single anchor, the length and width was varied. The release etch was found to require a sacrificial layer of greater than one micron for fest lateral undercutting. Mirrors with the longest and narrowest necks were found to display the greatest deflection.
Synthesis of analogues of 5-aminoimidazole ribonucleotides and their effects as inhibitors and substrates of the enzymes, phosphoribosylaminoimidazole carboxylase and phosphoribosylaminoimidazolesuccinocarboxamide synthetase involved in the biosynthesis of purine nucleotides de novo (1976)

α- and β-D-Arabinofuranosyl, α- and β-D-xylofuranosyl nucleotide analogues and the 2-bromo derivatives of 5-amino-1-β-D-ribofuranosylimidazole 4-carboxylic acid 5′-phosphate (CAIR), a central intermediate in the de novo biosynthetic pathway to purine nucleotides, and its α-anomer have been synthesised by sequences of reactions from 2,3,5-tri-O-benzoyl-D-arabinofuranosyl azide, 3,5-O-isopropylidene-D-xylofuranosylamine or ethyl 5-amino-1-α- and β-D-ribofuranosyl-imidazole 4-carboxylates, respectively; the β- but not the α- forms are shown to have inhibitory activity on the enzyme duet AIR-carboxylase and SAICAR-kinosynthetase whilst the arabinose and xylose analogues of CAIR were also converted by a mixture of pathway enzymes through at least two steps into the arabinose and xylose analogues of 5-amino-1-β-D-ribofuranosylimidazole 4-carboxamide 5′-phosphate (AICAR), respectively.
Photoacid generating polymers based on sulfonyloxymaleimides and application as single‐component resists (1996)

Three sulfonyloxymaleimides (RsOMI), N-(tosyloxy)maleimide (TsOMI), N-(methane-sulfonyloxy)maleimide (MsOMI), and N-(trifluoromethanesulfonyloxy)maleimide (TfOMI), have been synthesized and used to make novel photoacid generating polymers. The sulfonyloxymaleimides easily copolymerized with styrene derivatives to give high molecular weight polymers having an alternating structure of both monomer units. Terpolymers based on RsOMI and p-(tert-butyloxycarbonyloxy)styrene (t-BOCSt) were prepared for enhancing resist properties such as adhesion to substrates, solubility in aqueous alkaline solutions, or transparency in the deep-UV region. The RsOMI copolymers were found to produce corresponding sulfonic acids (RsOH), TsOH, MsOH, and TfOH, by deep-UV irradiation in the film state. Thus, the polymers having both the RsOMI and t-BOCSt units show the capability of a single-component, chemically amplified resist system in the deep-UV region without addition of any photoacid generator. Positive- and negative-tone images were obtained by exposure of the polymer films to deep-UV and post-exposure bake followed by development with organic solvents or aqueous alkaline solutions. © 1996 John Wiley & Sons, Inc.
Continuous Delivery of Neutralizing Antibodies Elevate CCL2 Levels in Mice Bearing MCF10CA1d Breast Tumor Xenografts (2017)

Chemokines are small soluble molecules that play critical roles in wound healing, infection, and cancer progression. In particular, overexpression of the C-C motif chemokine ligand 2 (CCL2) in multiple cancer types correlates with poor patient prognosis. Animal studies have shown that CCL2 signals to macrophages and breast cancer cells to promote tumor growth, invasion, and metastasis, indicating that CCL2 is a promising therapeutic target. However, the effectiveness of human-specific neutralizing antibodies has not been fully evaluated. Furthermore, controversies remain on the use of neutralizing antibodies to target CCL2 and could be due to mode of drug delivery. Here, we investigated the effects of continuous delivery of human CCL2-neutralizing antibodies on breast cancer progression. Nude mice bearing MCF10CA1d breast tumor xenografts were implanted with osmotic pumps containing control IgG or anti-CCL2 and analyzed for CCL2 levels and tumor progression over 4 weeks. Despite inhibiting CCL2-induced migration in vitro, CCL2-neutralizing antibodies did not significantly affect tumor growth, invasion, macrophage recruitment, or tumor angiogenesis. CCL2 antibodies did not affect murine CCL2 levels but significantly increased human CCL2 levels in circulating blood and tumor interstitial fluid. CCL2-neutralizing antibodies reduced CCL2 levels in cultured cells short term at high concentrations. Enzyme-linked immunosorbent assay analysis of CCL2 in cultured fibroblasts and breast cancer cells revealed that the neutralizing antibodies sequestered CCL2 in the media. CCL2 levels were restored once the antibodies were removed. These studies reveal limitations in CCL2-neutralizing antibodies as a therapeutic agent, with important implications for translating CCL2 targeting to the clinic.
A new 2-regression model for the Actical accelerometer (2007)

For most activities examined the new 2-regression model predicted METs more accurately than currently available equations for the Actical accelerometer.
Insulin Secretagogues (2002)

Existing oral insulin secretagogues, sulphonylureas, are associated with hyperinsulinaemia, risk of hypoglycaemia and weight gain. Furthermore, they are not able to offer durable glycaemic control in patents with type 2 diabetes and are associated with progressive decline of beta-cell function. New insulin secretagogues offer an exciting opportunity. Repaglinide, the first prandial glucose regulator, now has convincing data that, compared to sulphonylurea use, it has a lower risk of hypoglycaemia. When used in a flexible dosing regime in a large cohort of patients, it is associated with better glycaemic control, a reduction in HbA1c, weight loss and improved quality of life compared to sulphonylureas. Early data shows the possibility of an effective combination with night time isophane insulin with significant falls in HbA1c and lower doses of insulin required. Nateglinide is an amino acid derivative. It again acts directly on the pancreatic beta-cell. Because of its very short duration of action, and the fact that it appears to secrete insulin in a glucose-dependent manner, it appears to secrete insulin in the closest way to that seen in a person without diabetes. Early data, both in monotherapy and in combination with metformin, show that it is an effective agent in terms of lowering HbA1c, has a low risk of hypoglycaemia and potentially less risk of significant weight gain. These characteristics mean that it may be the ideal agent to be used very early in the disease process, or even in subjects with impaired glucose tolerance, in whom early-phase insulin response is already lost. However these concepts, at the present time, are unproven.