gebhart/patrepeval huggingface dataset:
Fibroblast Growth Factor Receptor 3 Is Overexpressed in Urinary Tract Carcinomas and Modulates the Neoplastic Cell Growth (2005)

Abstract Purpose: Fibroblast growth factor receptor 3 (FGFR3) mutations have been associated with achondroplastic syndromes and urinary bladder carcinomas. Here we describe changes in FGFR3 mRNA and protein expression in transitional carcinomas and determine the effect of monoclonal antibodies against FGFR3 in RT-112 cell line proliferation. Experimental Design: We used microarray tools to evaluate FGFR3 mRNA expression in 22 urinary bladder carcinomas at different stages (noninvasive pTa, lamina propria invasive pT1, and muscular invasive pT2) and 7 nonneoplastic tissue controls. FGFR3 protein expression was evaluated by Western blotting in 15 different carcinomas and 3 nonneoplastic controls. Two hundred thirty-seven urinary bladder and renal pelvis carcinomas and 21 negative controls were tested on tissue microarrays by immunohistochemistry. The effect on cell proliferation in the RT-112 bladder cancer cell line of monoclonal antibodies against FGFR3 was also evaluated. Results: Overexpression of FGFR3 mRNA was found in pTa and pT1 stage carcinomas (fold change &amp;gt;8) and in pT2 carcinomas (fold change &amp;gt;4). Nonneoplastic urinary bladder samples do not express FGFR3 protein. However, 83% of pTa, 100% of pT1, and 50% of pT2 carcinomas expressed FGFR3 as determined by Western blotting. By immunohistochemistry, FGFR3 was positive in 71.4% of pTa, 72% of pT1, and 49.2% of pT2 cases as well as 61.5% of upper urinary tract carcinomas. Proliferation of the RT-112 cell line was inhibited with monoclonal antibodies against FGFR3. Conclusions: FGFR3 seems to play an important role in transitional cell carcinoma development. Our results suggest that FGFR3 antagonists could be developed as possible therapeutics for treatment of urinary tract carcinoma.
Multi-disciplinary characterizations of the Bedretto Lab – a unique underground geoscience research facility (2021)

Abstract. The increased interest in subsurface development (e.g., unconventional hydrocarbon, deep geothermal, waste disposal) and the associated (triggered or induced) seismicity calls for a better understanding of the hydro-seismo-mechanical coupling in fractured rock masses. Being able to bridge the knowledge gap between laboratory and reservoir scales, controllable meso-scale in situ experiments are deemed indispensable. In an effort to access and instrument rock masses of hectometer size, the Bedretto Underground Laboratory for Geosciences and Geoenergies (‘Bedretto Lab’) was established in 2018 in the existing Bedretto Tunnel (Ticino, Switzerland), with an average overburden of 1000 m. In this paper, we introduce the Bedretto Lab, its general setting and current status. Combined geological, geomechanical and geophysical methods were employed in a hectometer-scale rock mass explored by several boreholes to characterize the in situ conditions and internal structures of the rock volume. The rock volume features three distinct units, with the middle fault zone sandwiched by two relatively intact units. The middle fault zone unit appears to be a representative feature of the site, as similar structures repeat every several hundreds of meters along the tunnel. The lithological variations across the characterization boreholes manifest the complexity and heterogeneity of the rock volume, and are accompanied by compartmentalized hydrostructures and significant stress rotations. With this complexity, the characterized rock volume is considered characteristic of the heterogeneity that is typically encountered in subsurface exploration and development. The Bedretto Lab can adequately serve as a test-bed that allows for in-depth study of the hydro-seismo-mechanical response of fractured crystalline rock masses.
Optimization, Yield Studies and Morphology of WO3Nano-Wires Synthesized by Laser Pyrolysis in C2H2and O2Ambients—Validation of a New Growth Mechanism (2008)

Abstract Laser pyrolysis has been used to synthesize WO 3 nanostructures. Spherical nano-particles were obtained when acetylene was used to carry the precursor droplet, whereas thin films were obtained at high flow-rates of oxygen carrier gas. In both environments WO 3 nano-wires appear only after thermal annealing of the as-deposited powders and films. Samples produced under oxygen carrier gas in the laser pyrolysis system gave a higher yield of WO 3 nano-wires after annealing than the samples which were run under acetylene carrier gas. Alongside the targeted nano-wires, the acetylene-ran samples showed trace amounts of multi-walled carbon nano-tubes; such carbon nano-tubes are not seen in the oxygen-processed WO 3 nano-wires. The solid–vapour–solid (SVS) mechanism [B. Mwakikunga et al., J. Nanosci. Nanotechnol., 2008] was found to be the possible mechanism that explains the manner of growth of the nano-wires. This model, based on the theory from basic statistical mechanics has herein been validated by length-diameter data for the produced WO 3 nano-wires.
Printertainment (1999)

We explored a new type of user interface, interactive cover sheets: computer forms laid out on the banner pages of print jobs that people can mark on, scan back into a multifunction printer/scanner, and use as input to applications. Cover sheets are commonly strewn around printer rooms; with interactivity, they can let people see what others have to say, add their own comments, or play games, all while waiting for their print jobs. We designed three prototype applications and deployed them briefly in our research lab. We found that interactive cover sheets can be very appealing, that the sheets must be designed so that people can still identify these pages as cover sheets, and that the slow interaction cycle favors asynchronous applications.
Solid lipid nanoparticles as drug delivery systems (2005)

For a decade, trials have been made to utilize solid lipid nanoparticles (SLNs) as alternative drug delivery systems to colloidal drug delivery systems such as lipid emulsions, liposomes, and polymeric nanoparticles. Various lipid matrices, surfactants, and other excipients used in formulation, preparation methods, sterilization and lyophilization of SLNs are discussed in this article. Entrapment efficiency of drug carrier and its effect on physical parameters, drug release, and release mechanisms of various compositions are reviewed and discussed. Important points in characterization and stability of SLNs are outlined. Various in vitro studies carried out by different research groups are mentioned in addition to in vivo evaluation. Exploitation potential of SLNs to administer by various routes of administration are covered. Passive and active drug targeting using SLNs are presented.
Cladding-pumped ytterbium-doped helical-core fiber laser (2005)

Efficient single-mode operation of a cladding-pumped ytterbium-doped multimode helical-core fiber laser has been demonstrated. The laser yielded 60.4W of output at 1043nm in a beam with M2&lt;1.4 for 92.6W launched pump power from a diode-stack at 976nm. The corresponding slope efficiency was ~84%, which compares favourably with best slope efficiencies achievable with conventional straight-core Yb-doped double-clad fiber lasers. A theoretical model was also used in the design of the helical-core fiber and the theory fit with the experimental results well.
A modeling study of vacuum sorption characteristics of carbon dioxide on 4A zeolite molecular sieves (1987)

A model is presented to describe the isothermal adsorption of carbon dioxide (CO/sub 2/) and of nitrogen (N/sub 2/) on 4A zeolite molecular sieves under cryogenic conditions. The model is comprised of a fluid-phase mass balance representing the dynamics of gas in the bed and a one-dimensional diffusion equation representing adsorption in the solid. Cubic crystals of 4A zeolite are assumed to be spherical, and the concentration dependence of the diffusivity of the sorbate in both the gas and solid phases is considered. Numerical solution of the parabolic partial differential model equations is accomplished using orthogonal collocation in conjunction with an ordinary differential equation integrator suitable for stiff equations. 34 refs., 18 figs., 5 tabs.
Methods and systems for authenticating identity (2023)

Systems and methods are disclosed that provide for secure communications between a user device and an authentication system. The systems and methods create a dynamic identification for the device that is stored in both the device and authentication system.
Dashing: fast and accurate genomic distances with HyperLogLog (2019)

Dashing is a fast and accurate software tool for estimating similarities of genomes or sequencing datasets. It uses the HyperLogLog sketch together with cardinality estimation methods that are specialized for set unions and intersections. Dashing summarizes genomes more rapidly than previous MinHash-based methods while providing greater accuracy across a wide range of input sizes and sketch sizes. It can sketch and calculate pairwise distances for over 87K genomes in 6 minutes. Dashing is open source and available at https://github.com/dnbaker/dashing.
P0942HYPOXEMIA AND UREMIA INDUCE OXIDATIVE IMBALANCE IN ENDOTHELIAL CELLS (2020)

Abstract Background and Aims Intradialytic hypoxemia is associated with oxidative stress, endothelial dysfunction, inflammation, higher erythropoietin requirements, and higher all-cause hospitalization and mortality in hemodialysis (HD) patients (Meyring-Wosten, et al., 2016). The aim of the present study was to further expand our insights into the hypoxia-uremia axis by investigating the oxidative balance in endothelial cells (EC) under hypoxic and uremic conditions. Method Human umbilical EC were incubated with DMEM medium supplemented with 10% of fetal bovine serum (FBS; control) or with sera obtained from healthy subjects (S-CON) or HD patients (S-HD, 1:10), respectively, for 40 minutes, 4 hours, and 24 hours under normoxic (21% O2) or hypoxic (5% O2) conditions (Culture Chamber ProOx, Biospherix). EC were analyzed by flow cytometer (BD Accuri™ C6 Plus) to assess a) intracellular production of reactive oxygen species (ROS, DCFH-DA probe, Abcam); b) reduced glutathione (GSH) content (ThiolTracker Violet probe, Thermo Fisher Scientific). Results S-HD increased intracellular ROS production at all time points compared to S-CON. Moreover, ROS production was higher under hypoxic conditions. ROS production declined after 24 hours. S-HD induced slightly higher GSH content when compared to S-CON in normoxia (Table 1). Conclusion In our in vitro experiments, hypoxia and uremia jointly favor EC oxidative imbalance. This effect is particularly pronounced after 4 hours. Translational studies are warranted to explore the clinical relevance of our findings.
Local Sensitive Hashing (LSH) and Convolutional Neural Networks (CNNs) for Object Recognition (2018)

Having a large dataset of labeled samples is necessary for the supervised training of most convolutional neural network (CNN) models. Lacking sufficient data or labeled samples for training a CNN can be problematic. To address this issue, we present a new approach for unsupervised learning that all CNN models with an image data type will be able to deploy. We tested this approach for object recognition on two popular datasets (CIFAR-10, and STL-10), and compared the results with results from available methods [11,20]. The experimental results demonstrate that our approach is comparable with the other methods of unsupervised training.
Effect of a Single Apolipoprotein L1 Gene Nephropathy Variant on the Risk of Advanced Lupus Nephritis in Brazilians (2019)

Although initial kidney lesions and treatment responses were similar, a single <i>APOL1</i> RRA in nonwhite Brazilians with LN was associated with increased risk of advanced CKD and possibly more tubulointerstitial damage.
B lymphocyte activation: Entry into cell cycle is accompanied by decreased expression of IgD but not IgM (1983)

To gain insight into the function of cell surface IgM (sIgM) and IgD (sIgD), the expression of these markers on B lymphocytes was quantitated during activation and progression through the cell cycle. Specifically, analysis and correlation of changes in cell cycle state, sIgM and sIgD expression and cell size following exposure of murine B cells to mitogenic levels of lipopolysaccharide and dextran sulfate is reported. As assessed by flow cytometric acridine orange analysis, a large proportion of normal splenic B cells respond within 48 h of exposure to these mitogens by entry into the cell cycle. This response is accompanied by an increase in cell size as determined by flow cytometric "time of flight" measurement. Flow cytometric immunofluorescence analysis reveals a simultaneous alteration in sIg expression. Specifically, cells leaving G0 and transiting G1 increase in diameter from 5 microns to 6 microns and lose greater than 80% of sIgD while sIgM remains constant. Progression through the remainder of the cell cycle is accompanied by a further increase in mean cell diameter to approximately 12 microns while sIgM and sIgD levels remain at G1 levels. The abrupt loss of sIgD as cells transit G1 suggests that an active process mediates this decrease.
The Palomar Digital Sky Survey (DPOSS) (1998)

We describe DPOSS, a new digital survey of the northern sky, based on the POSS-II photographic sky atlas. The survey covers the entire sky north of delta = -3 deg in 3 bands, calibrated to the Gunn $gri$ system, reaching to equivalent limiting magnitude of B_lim ~ 22 mag. As a result of the state-of-the-art digitisation of the plates, detailed processing of the scans, and a very extensive CCD calibration program, the data quality exceedes that of the previous photographically-based efforts. The end product of the survey will be the Palomar-Norris Sky Catalog, anticipated to contain &gt; 50 million galaxies and &gt; 2 billion stars, down to the survey classification limit, ~ 1 mag above the flux detection limit. Numerous scientific projects utilising these data have been started, and we describe briefly some of them; they illustrate the scientific potential of the data, and serve as the scientific verification tests of the survey. Finally, we discuss some general issues posed by the advent of multi-terabyte data sets in astronomy.
Figure S6 from <i>BRCA2</i> Germline Mutations Identify Gastric Cancers Responsive to PARP Inhibitors (2023)

&lt;p&gt;MLH1 KO cells do not display MSI.&lt;/p&gt;
Combined Epigenetic Therapy with the Novel Histone Methyl Transferase EZH2 Inhibitor 3-Deazaneplanocin and Histone Deacetylase Inhibitor Panobinostat Exerts Synergistic Activity against Human Mantle Cell Lymphoma Cells (2008)

Abstract Lysine specific histone methylation and deacetylation and DNA hypermethylation are involved in the epigenetic silencing of tumor suppressor genes (TSG), e.g., p16 and JunB. The multi-protein complex PRC (polycomb repressive complex) 2 that contains the three core proteins EZH2, SUZ12 and EED, has intrinsic histone methyltransferase (HMTase) activity. This is mediated by the SET domain of EZH2, which induces tri-methylation (3Me) of lysine (K)-27 on histone H3, as well as promotes cell proliferation and aggressiveness of neoplastic cells. EZH2 is preferentially overexpressed in proliferating but not resting Mantle Cell Lymphoma (MCL) cells. In the present studies we demonstrate that treatment with the S-adenosylhomocysteine hydrolase inhibitor 3-Deazaneplanocin A (DZNep) dose-dependently (500 nM to 2.0 uM) depletes EZH2, SUZ12 and EED levels, as well as inhibits 3Me K27 on H3 while inducing K27 H3 acetylation. DZNep treatment also induces the levels of p21, p27, JunB and FBXO32, while depleting cyclin D1 and cyclin E levels in the cultured human MCL Jeko-1, MO2058 and Z138 cells and in primary patient-derived MCL cells. Treatment with DZNep induces PARP cleavage activity of the caspases and apoptosis in the cultured and primary MCL cells. DZNep promoted proteasomal degradation of EZH2 and SUZ12, since co-treatment with bortezpmib significantly restored EZH2 and SUZ12 levels in the MCL cells. We had previously reported that treatment with the pan-histone deacetylase (HDAC) inhibitor panobinostat (PS) (LBH589, Novartis Pharmaceutical Corp) depletes the levels of EZH2, SUZ12 and EED in cultured and primary AML cells (Mol Cancer Ther.2006; 5:3096). Within the PRC2 complex, EZH2 bound and recruited the DNA methyltransferases DNMT1, and treatment with PS also disrupted the interaction of EZH2 with DNMT1, attenuated DNMT1 levels and its binding to the EZH2-targeted gene promoters, e,g, JunB. Here, we also demonstrate that, PS treatment depletes DNMT1 levels and induces JunB levels in cultured MCL cells. As compared to treatment with either agent alone, co-treatment with DZNep and PS caused more depletion of EZH2 and SUZ12, but not of DNMT1, more induction of JunB, p21 and p27, as well as synergistically induced apoptosis of cultured MCL cells (combination indices &lt; 1.0). Taken together, these findings indicate that DZNep and PS mediated targeting of EZH2 and the PRC2 complex is an effective epigenetic therapy of MCL, which also results in undermining several molecular determinants of MCL cell proliferation and survival. Additionally, combined epigenetic therapy with DZNep and PS exerts synergistic in vitro activity against human MCL cells, suggesting that this combination may be a promising novel treatment for MCL.
Chemical properties which control selectivity and efficacy of aromatic N-oxide bioreductive drugs. (1996)

Pulse radiolysis was used to generate radicals from one electron reduction of 1,2,4-benzotriazine-1,4-dioxides (derivatives of tirapazamine), and of imidazo [1,2-a]quinoxaline-4-oxides (analogues of RB90740), which have selective toxicity towards hypoxic cells. Radicals from the mono N-oxides (from the latter compounds) react with oxygen approximately 10-40 times faster than does the tirapazamine radical. Radicals from the tirapazamine analogues studied react with oxygen up to approximately 10 times slower than tirapazamine radicals. The quinoxaline N-oxide radicals are involved in prototropic equilibria with pK(a) values (5.5 to 7.4) spanning that reported for tirapazamine (6.0). Generation of radicals radiolytically in the presence of H donors (formate, 2-propanol, deoxyribose) indicate a chain reaction ascribed to H abstraction by the drug radical. The protonated drug radical is much more reactive than the radical anion (H abstraction rate constant approximately equal to 10(2) - 10(3) dm3 mol-1 s-1). Chain termination is ascribed to drug radical-radical reactions, i.e. radical stability in anoxia, with rate constants 2k approximately equal to 1 x 10(7) to 2 x 10(8) dm3 mol-1 s-1 at pH approximately 7.4. Estimates of the reduction potentials of the drug-radical couples in water at pH 7 for two of the mono-N-oxides were in the range-0.7 to 0.8 V vs NHE at pH 7.
Easy fabrication of high quality nickel mold for deep polymer microfluidic channels (2016)

Mass fabrication of disposable microfluidic chips with hot embossing is a key technology for microfluidic chip based biosensors. In this work, we develop a new method of fabricating high quality and highly durable nickel molds for hot embossing polymer chips. The process involves the addition of a thick, patterned layer of negative photoresist AZ-125nxT to a 4'' silicon wafer, followed by nickel electroplating and delamination of the nickel mold. Our investigations found that compared to a pillar mask, a hole mask can minimize the diffraction effect in photolithography of a thick photoresist, reduce the adhesion of the AZ-125nxT to the photomask in photolithography, and facilitate clean development of the photoresist patterns. By optimizing the hot embossing and chip bonding parameters, microfluidic chips with deep channels are achieved.
Design and fabrication of hollow flexible terahertz waveguides (2010)

A low loss, hollow, flexible waveguide was designed and fabricated for the transmission of terahertz radiation. Polycarbonate and glass tubing was chosen as the base material of the waveguide. The inner surface of the dielectric tube was coated with silver using a wet chemistry method. The waveguides were fabricated in several diameters namely, 2.4 mm, 3.2 mm, 3.8 mm, and 4.6 mm. The attenuation coefficients for the waveguides were measured at a wavelength of 215 &mu;m using an optically pumped terahertz laser. The free space Gaussian mode from the terahertz laser source was coupled into the lowest loss TE<sub>11</sub> mode inside the waveguide. The mode profiles of the output beam from the waveguides were shown. A loss of 3.5 dB/m was measured for the silver coated dielectric tube of diameter 4.6 mm.
Enhancing the efficacy of engraftment of cord blood for hematopoietic cell transplantation (2016)

Clinical cord blood (CB) hematopoietic cell transplantation (HCT) has progressed well since the initial successful CB HCT that saved the life of a young boy with Fanconi anemia. The recipient is alive and well now 28 years out since that first transplant with CB cells from his HLA-matched sister. CB HCT has now been used to treat over 35,000 patients with various malignant and non-malignant disorders mainly using HLA-matched or partially HLA-disparate allogeneic CB cells. There are advantages and disadvantages to using CB for HCT compared to other sources of transplantable hematopoietic stem (HSC) and progenitor (HPC) cells. One disadvantage of the use of CB as a source of transplantable HSC and HPC is the limited number of these cells in a single CB collected, and slower time to neutrophil, platelet and immune cell recovery. This review describes current attempts to: increase the collection of HSC/HPC from CB, enhance the homing of the infused cells, ex-vivo expand numbers of collected HSC/HPC and increase production of the infused CB cells that reach the marrow. The ultimate goal is to manipulate efficiency and efficacy for safe and economical use of single unit CB HCT.
Competing influence of an in-plane electric field on the Stark shifts in a semiconductor quantum dot (2011)

We report on the fabrication of a side-gate structure which enables a purely lateral electric field to be applied onto a self-assembled quantum dot. The lateral field produces an unconventional “M’-shaped exciton energy shift—a blueshift followed by a redshift. The unconventional energy shift is reproduced by calculation. The calculation shows that only the positively charged exciton shows the unconventional shift. The origin is attributed to the field-induced hole-concentration in the bottom-corner of the dot, which strongly enhances the repulsive direct Coulomb interaction and reduces the exciton binding energy.
ChemInform Abstract: PHOTODIMERE VON 3‐METHYLCYCLOHEX‐2‐ENON (1970)

Abstract Belichtung von 3‐Methylcyclohex‐2‐enon (I) in wäßrigem Alkohol liefert die Dimeren (II) und (III).
Gut Hormones and Appetite Control: A Focus on PYY and GLP-1 as Therapeutic Targets in Obesity (2012)

The global obesity epidemic has resulted in significant morbidity and mortality. However, the medical treatment of obesity is limited. Gastric bypass is an effective surgical treatment but carries significant perioperative risks. The gut hormones, peptide tyrosine tyrosine (PYY) and glucagon-like peptide 1 (GLP-1), are elevated following gastric bypass and have been shown to reduce food intake. They may provide new therapeutic targets. This review article provides an overview of the central control of food intake and the role of PYY and GLP-1 in appetite control. Key translational animal and human studies are reviewed.