gebhart/patrepeval huggingface dataset:
Protein expression of TTF1 and cMYC define distinct molecular subgroups of small cell lung cancer with unique vulnerabilities to aurora kinase inhibition, DLL3 targeting, and other targeted therapies (2017)

// Robert J. Cardnell 1 , Lerong Li 2 , Triparna Sen 1 , Rasha Bara 1 , Pan Tong 2 , Junya Fujimoto 3 , Abbie S. Ireland 4 , Matthew R. Guthrie 4 , Sheila Bheddah 5 , Upasana Banerjee 1 , Nene N. Kalu 1 , You-Hong Fan 1 , Scott J. Dylla 5 , Faye M. Johnson 1,6 , Ignacio I. Wistuba 3 , Trudy G. Oliver 4 , John V. Heymach 1 , Bonnie S. Glisson 1 , Jing Wang 2,4,* and Lauren A. Byers 1,6,* 1 Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA 2 Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA 3 Department of Molecular Translational Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA 4 Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, UT, USA 5 AbbVie StemCentrx, LLC, San Franciso, CA, USA 6 The University of Texas Graduate School of Biomedical Sciences, Houston, TX, USA * Co-senior authors Correspondence to: Lauren A. Byers, email: // Keywords : Alisertib, DLL3, rovalpituzumab tesirine, SCLC, TTF1 Received : July 04, 2017 Accepted : August 14, 2017 Published : September 01, 2017 Abstract Small cell lung cancer (SCLC) is a recalcitrant cancer for which no new treatments have been approved in over 30 years. While molecular subtyping now guides treatment selection for patients with non-small cell lung cancer and other cancers, SCLC is still treated as a single disease entity. Using model-based clustering, we found two major proteomic subtypes of SCLC characterized by either high thyroid transcription factor-1 (TTF1)/low cMYC protein expression or high cMYC/low TTF1. Applying “drug target constellation” (DTECT) mapping, we further show that protein levels of TTF1 and cMYC predict response to targeted therapies including aurora kinase, Bcl2, and HSP90 inhibitors. Levels of TTF1 and DLL3 were also highly correlated in preclinical models and patient tumors. TTF1 (used in the diagnosis lung cancer) could therefore be used as a surrogate of DLL3 expression to identify patients who may respond to the DLL3 antibody-drug conjugate rovalpituzumab tesirine. These findings suggest that TTF1, cMYC or other protein markers identified here could be used to identify subgroups of SCLC patients who may respond preferentially to several emerging targeted therapies.
CelE, a Multidomain Cellulase from <i>Clostridium cellulolyticum</i> : a Key Enzyme in the Cellulosome? (2000)

CelE, one of the three major proteins of the cellulosome of Clostridium cellulolyticum, was characterized. The amino acid sequence of the protein deduced from celE DNA sequence led us to the supposition that CelE is a three-domain protein. Recombinant CelE and a truncated form deleted of the putative cellulose binding domain (CBD) were obtained. Deletion of the CBD induces a total loss of activity. Exhibiting rather low levels of activity on soluble, amorphous, and crystalline celluloses, CelE is more active on p-nitrophenyl-cellobiose than the other cellulases from this organism characterized to date. The main product of its action on Avicel is cellobiose (more than 90% of the soluble sugars released), and its attack on carboxymethyl cellulose is accompanied by a relatively small decrease in viscosity. All of these features suggest that CelE is a cellobiohydrolase which has retained a certain capacity for random attack mode. We measured saccharification of Avicel and bacterial microcrystalline cellulose by associations of CelE with four other cellulases from C. cellulolyticum and found that CelE acts synergistically with all tested enzymes. The positive influence of CelE activity on the activities of other cellulosomal enzymes may explain its relative abundance in the cellulosome.
Suspended optical fiber-to-waveguide mode size converter for Silicon photonics (2010)

In this paper, an efficient and novel optical fiber-to-waveguide mode size converter for Si Photonics devices with sub-micron waveguides is developed on the SOI platform. This optical converter is composed of a suspended SiO(2) waveguide and overlapped Si nano-tapers located in the center of suspended SiO(2) waveguide. Laterally connected SiO(2) beams provide structural support for the suspended SiO(2) waveguide. The optical input signal from the optical fiber is launched into the suspended SiO(2) waveguide, and then coupled into the Si nano-taper. The measured coupling loss using a lensed fiber with 5 microm spot diameter is 1.7 ~2.0 dB/facet for TE mode and 2.0 ~2.4 dB/facet for TM mode in the wavelength range of 1520 ~1600 nm. When a cleaved fiber with 9.2microm spot diameter is used, the coupling losses for both TE and TM modes are less than 4.0 dB/facet at 1550 nm. For the case of lensed fiber, the alignment tolerances for both TE and TM modes are about +/- 1.7 microm for 1 dB excess loss in both X and Y axes. The alignment tolerances for both modes of TE and TM are relaxed, exceeding +/- 2.5 microm for 1 dB excess loss in both X and Y axes when a cleaved fiber is used.
Biocatalysis for the application of CO<sub>2</sub> as a chemical feedstock (2015)

Biocatalysts, capable of efficiently transforming CO2 into other more reduced forms of carbon, offer sustainable alternatives to current oxidative technologies that rely on diminishing natural fossil-fuel deposits. Enzymes that catalyse CO2 fixation steps in carbon assimilation pathways are promising catalysts for the sustainable transformation of this safe and renewable feedstock into central metabolites. These may be further converted into a wide range of fuels and commodity chemicals, through the multitude of known enzymatic reactions. The required reducing equivalents for the net carbon reductions may be drawn from solar energy, electricity or chemical oxidation, and delivered in vitro or through cellular mechanisms, while enzyme catalysis lowers the activation barriers of the CO2 transformations to make them more energy efficient. The development of technologies that treat CO2-transforming enzymes and other cellular components as modules that may be assembled into synthetic reaction circuits will facilitate the use of CO2 as a renewable chemical feedstock, greatly enabling a sustainable carbon bio-economy.
Isolated-Word Confusion Metrics and the PGPfone Alphabet (1996)

Although the confusion of individual phonemes and features have been studied and analyzed since (Miller and Nicely, 1955), there has been little work done on extending this to a predictive theory of word-level confusions. The PGPfone alphabet is a good touchstone problem for developing such word-level confusion metrics. This paper presents some difficulties incurred, along with their proposed solutions, in the extension of phonetic confusion results to a theoretical whole-word phonetic distance metric. The proposed solutions have been used, in conjunction with a set of selection filters, in a genetic algorithm to automatically generate appropriate word lists for a radio alphabet. This work illustrates some principles and pitfalls that should be addressed in any numeric theory of isolated word perception.
Detection of encrypted streams for egress monitoring (2007)

Leakage of confidential information from an organization's networks has become a big threat to its information security. Egress monitoring and filtering have thus become popular for detecting such security breaches. Egress monitoring tools scan outgoing packets for keywords or their combinations present in the confidential documents. These content filtering techniques however fail when the data is encrypted. The solution proposed in this thesis is simple yet an effective approach to prevent information leakage when the data is encrypted. We assume that a policy is in place which disallows encrypted content from specific hosts, ports and applications and wish to detect any violations to this policy. This work aims at analyzing encrypted and unencrypted traffic flows across a gateway and detecting unauthorized encrypted traffic flows. The work discusses a low level approach to detect encryption, based on entropy calculation and packet analysis. The technique is based on the fact that encrypted data consists of a random distribution of symbols whose entropy is expected to be quite high as compared to an unencrypted file. Techniques to differentiate between encrypted and high entropy compressed traffic are also discussed. This thesis implements and compares statistical methods for a fast online detection of encrypted traffic from all the other unencrypted traffic flowing across a network.
Prevalence of Abnormal Lipid Profiles and the Relationship With the Development of Microalbuminuria in Adolescents With Type 1 Diabetes (2009)

In this longitudinal study of adolescents with type 1 diabetes, sustained lipid abnormalities were related to age, duration, BMI, and A1C. Furthermore, ACR was related to both total cholesterol and non-HDL cholesterol, indicating a potential role in the pathogenesis of diabetic nephropathy.
[Cloning of drug resistance-related gene fragments differentially expressed on lung adenocarcinoma cell line A549 and its DDP-resistant counterpart A549DDP]. (2001)

Four differentially expressed gene fragments between lung adenocarcinoma cell line and its cisplatin-resistant counterpart were identified by mRNA differential display technique. It remains to be studied whether the newly identified gene fragments and those showing sequence homology to ICE and MM45srRNA are indeed positively or negatively related to drug resistance.
Use of spectral decomposition technique for mapping geologic features of ‘Reigh’ field, Onshore Niger Delta (2021)

Spectral Decomposition Technique based on Short-Window Discrete Fourier Transform (SWDFT) was applied to threedimensional (3D) seismic data obtained from ‘Reigh’ field, onshore Niger Delta with a view to enhancing stratigraphic interpretation for geological features which are beyond seismic resolution. Two sands units from the study area were studied to produce spectrally decomposedsurfaces. The result of the study revealed thin bed layer at the centre of the field on sand unit ‘A’. Sand-filled meandering channel wasdetected and highlighted in the northern part of sand unit ‘B’ based on Red-Green-Blue frequency modulation of spectral decomposition. The study has enhanced geologic understanding of the field by improving thin bed resolution, highlighting geologic features and displaying bed thickness variation of studied sand units in the study area. Keywords: geologic features, Niger Delta, seismic data, spectral decomposition
Statins to improve cardiovascular outcomes in treated HIV infection (2015)

Statins are likely to improve cardiovascular outcomes for patients with HIV, but results of the first outcome study are not expected until 2020. In the meantime, clinicians should individualize statin prescriptions, and should consider using more potent statins (rosuvastatin, atorvastatin, and pitavastatin) when possible.
A monoclonal anti-IgE antibody against an epitope (amino acids 367-376) in the CH3 domain inhibits IgE binding to the low affinity IgE receptor (CD23). (1988)

We have produced three different mAb specific for human IgE-Fc. Their binding pattern to either heat-denatured IgE or a family of overlapping IgE-derived recombinant peptides and their ability to affect interaction of IgE with its low affinity receptor Fc epsilon R2/CD23 demonstrate that they recognize distinct epitopes on the IgE molecule. All three mAb were able to induce basophil degranulation as measured by the induction of histamine release. mAb 173 recognizes a thermolabile epitope in the CH4 domain. It does not affect the binding of IgE to Fc epsilon R2/CD23. mAb 272 recognizes a thermostable epitope that maps to a sequence of 36 amino acids (AA) spanning part of the CH2 and CH3 domain and it does not affect the binding of IgE to Fc epsilon R2/CD23. mAb 27 recognizes a thermolabile epitope located on a 10 AA stretch (AA 367-376) in the CH3 domain. This area contains one N-linked oligosaccharide (Asn-371), but the antibody is not directed against carbohydrate because it binds to Escherichia coli-derived IgE peptides. mAb 27 inhibits the binding of IgE to Fc epsilon R2/CD23 but is still capable of reacting with IgE already bound to Fc epsilon R2/CD23. These data suggest that upon binding to Fc epsilon R2/CD23, the IgE molecule engages one of two equivalent-binding sites close to the glycosylated area of the CH3 domain.
Lipid nanoparticle-mediated codelivery of Cas9 mRNA and single-guide RNA achieves liver-specific in vivo genome editing of<i>Angptl3</i> (2021)

Loss-of-function mutations in Angiopoietin-like 3 (<i>Angptl3</i>) are associated with lowered blood lipid levels, making <i>Angptl3</i> an attractive therapeutic target for the treatment of human lipoprotein metabolism disorders. In this study, we developed a lipid nanoparticle delivery platform carrying Cas9 messenger RNA (mRNA) and guide RNA for CRISPR-Cas9-based genome editing of <i>Angptl3</i> in vivo. This system mediated specific and efficient <i>Angptl3</i> gene knockdown in the liver of wild-type C57BL/6 mice, resulting in profound reductions in serum ANGPTL3 protein, low density lipoprotein cholesterol, and triglyceride levels. Our delivery platform is significantly more efficient than the FDA-approved MC-3 LNP, the current gold standard. No evidence of off-target mutagenesis was detected at any of the nine top-predicted sites, and no evidence of toxicity was detected in the liver. Importantly, the therapeutic effect of genome editing was stable for at least 100 d after a single dose administration. This study highlights the potential of LNP-mediated delivery as a specific, effective, and safe platform for Cas9-based therapeutics.
Antibacterial activities of antineoplastic agents (1985)

Fourteen antineoplastic agents were examined for in vitro antibacterial activity against 101 aerobic and anaerobic bacterial isolates representing indigenous human microflora and selected opportunistic pathogens. Only 5-fluorouracil, mitomycin, and etoposide demonstrated inhibitory effects at achievable plasma concentrations, while the remaining drugs lacked appreciable antibacterial activities.
Stereocomplex formation between enantiomeric poly(lactic acid). VIII. Complex fibers spun from mixed solution of poly(<scp>D</scp>‐lactic acid) and poly(<scp>L</scp>‐lactic acid) (1994)

Abstract To obtain poly(lactic acid) (PLA) complex fibers, spinning was performed by wet and dry methods from 5–10 g/dL chloroform solutions of poly(D‐lactic acid) (PDLA) and poly(L‐lactic), both with a viscosity‐average molecular weight of 3 × 10 5 . The dope was extruded from a monohole nozzle into coagulation baths from ethanol and chloroform for wet spinning and into a drying column kept at 60°C for dry spinning. Scanning electron microscopic observation of the as‐spun fibers showed that the surface of the wet‐spun fiber had large basins with diameters of 50–100 μm and many pores with diameters from sub μm to 10 μm, whereas the surface of dry‐spun fiber had a microporous structure with the pore diameter of 1–3 μm. The tensile strength of the wet‐spun complex fiber was very low and could not be drawn at high temperatures, in contrast to the dry‐spun fiber. The tensile strength of dry‐spun complex fiber increased upon hot drawing and showed the tensile strength of 94 kg/mm 2 by drawing at 160°C to the draw ratio of 13. Differential scanning calorimetry revealed that the complex fibers contained both the stereocomplex crystallites (racemic crystallites) and the crystallites of the single polymers, PDLA and PLLA, regardless of the spinning methods. The ratio of the racemic crystallites to the single‐polymer crystallites increased with the draw ratio of the complex fiber. © 1994 John Wiley & Sons, Inc.
Visualization of lymphatic vessels by Prox1-promoter directed GFP reporter in a bacterial artificial chromosome-based transgenic mouse (2010)

Although the blood vessel-specific fluorescent transgenic mouse has been an excellent tool to study vasculogenesis and angiogenesis, a lymphatic-specific fluorescent mouse model has not been established to date. Here we report a transgenic animal model that expresses the green fluorescent protein under the promoter of Prox1, a master control gene in lymphatic development. Generated using an approximately 200-kb-long bacterial artificial chromosome harboring the entire Prox1 gene, this Prox1-green fluorescent protein mouse was found to faithfully recapitulate the expression pattern of the Prox1 gene in lymphatic endothelial cells and other Prox1-expressing organs, and enabled us to conveniently visualize detailed structure and morphology of lymphatic vessels and networks throughout development. Our data demonstrate that this novel transgenic mouse can be extremely useful for detection, imaging, and isolation of lymphatic vessels and monitoring wound-associated lymphangiogenesis. Together, this Prox1-green fluorescent protein transgenic mouse will be a great tool for the lymphatic research.
Increased resolution in neutral atom microscopy (2012)

The neutral atom microscope uses a beam of thermal noncharged atoms or molecules to probe an atomic surface with very low interaction energies (<70 meV). Continued optimization of the 'pinhole' neutral atom microscope has improved resolution to 0.35 μm. Recent images are presented demonstrating resolution and the contrast mechanisms identified so far. The future potential for sub-100 nm resolution is discussed.
On the scaling of the slip velocity in turbulent flows over superhydrophobic surfaces (2016)

Superhydrophobic surfaces can significantly reduce hydrodynamic skin drag by accommodating large slip velocity near the surface due to entrapment of air bubbles within their micro-scale roughness elements. While there are many Stokes flow solutions for flows near superhydrophobic surfaces that describe the relation between effective slip length and surface geometry, such relations are not fully known in the turbulent flow limit. In this work, we present a phenomenological model for the kinematics of flow near a superhydrophobic surface with periodic post-patterns at high Reynolds numbers. The model predicts an inverse square root scaling with solid fraction, and a cube root scaling of the slip length with pattern size, which is different from the reported scaling in the Stokes flow limit. A mixed model is then proposed that recovers both Stokes flow solution and the presented scaling, respectively, in the small and large texture size limits. This model is validated using direct numerical simulations of turbulent flows over superhydrophobic posts over a wide range of texture sizes from L+ ≈ 6 to 310 and solid fractions from ϕs = 1/9 to 1/64. Our report also embarks on the extension of friction laws of turbulent wall-bounded flows to superhydrophobic surfaces. To this end, we present a review of a simplified model for the mean velocity profile, which we call the shifted-turbulent boundary layer model, and address two previous shortcomings regarding the closure and accuracy of this model. Furthermore, we address the process of homogenization of the texture effect to an effective slip length by investigating correlations between slip velocity and shear over pattern-averaged data for streamwise and spanwise directions. For L+ of up to O(10), shear stress and slip velocity are perfectly correlated and well described by a homogenized slip length consistent with Stokes flow solutions. In contrast, in the limit of large L+, the pattern-averaged shear stress and slip velocity become uncorrelated and thus the homogenized boundary condition is unable to capture the bulk behavior of the patterned surface.
A hybrid electrochemical device based on a synergetic inner combination of Li ion battery and Li ion capacitor for energy storage (2017)

Li ion battery (LIB) and electrochemical capacitor (EC) are considered as the most widely used energy storage systems (ESSs) because they can produce a high energy density or a high power density, but it is a huge challenge to achieve both the demands of a high energy density as well as a high power density on their own. A new hybrid Li ion capacitor (HyLIC), which combines the advantages of LIB and Li ion capacitor (LIC), is proposed. This device can successfully realize a potential match between LIB and LIC and can avoid the excessive depletion of electrolyte during the charge process. The galvanostatic charge-discharge cycling tests reveal that at low current, the HyLIC exhibits a high energy density, while at high current, it demonstrates a high power density. Ragone plot confirms that this device can make a synergetic balance between energy and power and achieve a highest energy density in the power density range of 80 to 300 W kg<sup>-1</sup>. The cycle life test proves that HyLIC exhibits a good cycle life and an excellent coulombic efficiency. The present study shows that HyLIC, which is capable of achieving a high energy density, a long cycle life and an excellent power density, has the potential to achieve the winning combination of a high energy and power density.
Inhibiting poly ADP-ribosylation increases fatty acid oxidation and protects against fatty liver disease (2016)

Non-alcoholic fatty liver disease (NAFLD) is now considered to be the most common liver disease in the Western world and has no approved pharmacological therapy. PARP inhibitors given as a treatment in two different mouse models of NAFLD confer a protection against its development. PARP inhibitors may therefore represent a novel and practical pharmacological approach for treating NAFLD.
<title>Occurrence of ferromagnetic shape memory alloys</title> (2000)

This article presents an overview of the necessary conditions for the formation of Shape Memory Alloys (SMAs) and how these must overlap with the occurrence of ferromagnetism so that FerroMagnetic Shape Memory Alloys (MSMAs) may be formed. The electronic, elastic and geometric conditions permit an understanding of the occurrence of Cu and Fe based SMAs as well as NiMnGa Heusler MSMAs except that the naively determined critical electron concentration for the latter, 7.3, disagrees with the values of 1.5 and 8.6 accepted for the Hume-Rothery Phases and certain Fe- based systems.
Reversible Tumorigenesis Induced by Deficiency of Vasodilator-Stimulated Phosphoprotein (1999)

Random homozygous knockout (RHKO) is an antisense RNA strategy capable of identifying genes whose homozygous functional inactivation yields a selectable phenotype in cells growing in culture. Using this approach, we isolated NIH 3T3 fibroblast clones that showed the ability to form colonies on 0.5% agar and tumors in nude mice. The gene inactivated in one of these clones was found to encode VASP (vasodilator-stimulated phosphoprotein), a previously identified protein that binds to components of the cadherin-catenin junctional complex and has been implicated in cell-cell interactions, the formation of actin filaments, and the transmission of signals at the cytoskeleton-membrane interface. Fibroblasts made deficient in VASP by RHKO showed loss of contact inhibition, and consequently, continued cell division past confluence. Restoration of VASP function by reversal of RHKO yielded cells that had lost the neoplastic capabilities acquired during RHKO. Overproduction of VASP mRNA in the sense or antisense orientation from expression constructs introduced by transfection into naive NIH 3T3 fibroblasts also resulted in neoplastic transformation, implying that normal cell growth may require the maintenance of VASP expression within a narrow range. Our results implicate VASP in tumorigenesis and/or cancer progression.