gebhart/patrepeval huggingface dataset:
Prognostic MicroRNA Panel for HCV-Associated HCC: Integrating Computational Biology and Clinical Validation (2022)

Early detection of hepatocellular carcinoma (HCC) will reduce morbidity and mortality rates of this widely spread disease. Dysregulation in microRNA (miRNA) expression is associated with HCC progression. The objective is to identify a panel of differentially expressed miRNAs (DE-miRNAs) to enhance HCC early prediction in hepatitis C virus (HCV) infected patients. Candidate miRNAs were selected using a bioinformatic analysis of microarray and RNA-sequencing datasets, resulting in nine DE-miRNAs (miR-142, miR-150, miR-183, miR-199a, miR-215, miR-217, miR-224, miR-424, and miR-3607). Their expressions were validated in the serum of 44 healthy individuals, 62 non-cirrhotic HCV patients, 67 cirrhotic-HCV, and 72 HCV-associated-HCC patients using real-time PCR (qPCR). There was a significant increase in serum concentrations of the nine-candidate miRNAs in HCC and HCV patients relative to healthy individuals. MiR-424, miR-199a, miR-142, and miR-224 expressions were significantly altered in HCC compared to non-cirrhotic patients. A panel of five miRNAs improved sensitivity and specificity of HCC detection to 100% and 95.12% relative to healthy controls. Distinguishing HCC from HCV-treated patients was achieved by 70.8% sensitivity and 61.9% specificity using the combined panel, compared to alpha-fetoprotein (51.4% sensitivity and 60.67% specificity). These preliminary data show that the novel miRNAs panel (miR-150, miR-199a, miR-224, miR-424, and miR-3607) could serve as a potential non-invasive biomarker for HCC early prediction in chronic HCV patients. Further prospective studies on a larger cohort of patients should be conducted to assess the potential prognostic ability of the miRNAs panel.
Engineering of Electrodes and Operating Conditions for Pure-Water-Fed Anion Exchange Membrane Water Electrolyzers (2022)

Many industrial processes such as petroleum refining, ammonia production, and metal refining have hydrogen gas as a feedstock. Hydrogen gas can be produced via fossil fuel reforming, photo-electrochemical conversion, thermochemical water decomposition, as well as water electrolysis. Among the various water electrolysis technologies, anion exchange membrane water electrolyzers (AEMWEs) possess possible qualities that will allow for them to out-compete incumbent alkaline electrolyzers and proton exchange membrane electrolyzers PEMWEs). AEMWEs have to possibility to combine platinum group metal–free (PGM-free) catalysts, low-cost cell components and operation at high pressure. It is also desirable for AEMWEs to be operated with a pure water feed, high performance and long life – all of which has been elusive thus far. In this presentation, we will demonstrate device engineering pathways to achieve high performance with pure-water-fed AEMWEs. This was accomplished by optimizing the type and amount of electrocatalyst on both anode and cathode alongside the flow conditions and operating temperature. The optimized pure-water-fed AEMWEs have been successfully operated at steady-state at a voltage below 1.90 V at 1.0 Acm -2 at 80 °C. Differences will be highlighted between DI water and electrolyte-fed systems. The importance of pre-treatment to ensure pure DI-water operation will also be discussed. This work emphasizes the importance of engineering electrodes and operating conditions to reach the highest performance of pure-water-fed AEMWEs, which is expected to allow these devices to out-compete existing water electrolysis technologies.
Amyloid, Presenilins, and Alzheimer’s Disease (2003)

The regulated intramembrane proteolysis of the amyloid precursor protein (APP) that results in the generation of a toxic 40 to 42 amino acid fragment, Abeta, and a C-terminal intracellular fragment stands central in the pathogenesis of Alzheimer's disease. The fibrillar Abeta peptide is extracellularly deposited in plaques in the amygdala, the hippocampus, and the neocortex of affected individuals. The APP intracellular fragment binds to transcription factors and is translocated to the nucleus, where it influences transcription. Regulated intramembrane proteolysis of APP is dependent on the activity of a multimeric protein complex of which the essential components are presenilin, nicastrin, PEN-2, and APH-1. Further research into this emerging field of presenilin-dependent APP proteolysis within the plane of the membrane might reveal the necessity of an additional transport step-bringing substrate and enzyme together-before APP can actually be processed.
Depth Estimation Using an Infrared Dot Projector and an Infrared Color Stereo Camera (2016)

This paper proposes a method of estimating depth from two kinds of stereo images: color stereo images and infrared stereo images. An infrared dot pattern is projected on a scene by a projector so that infrared cameras can capture the scene textured by the dots and the depth can be estimated even where the surface is not textured. The cost volumes are calculated for the infrared and color stereo images for each frame and are extended in the time direction to define a spatiotemporal cost volume (st-cost volume). We also extend the cost volume filter in the time direction by modifying the cross-based local multipoint filter (CLMF) and applying it to the st-cost volumes in order to restrain flicker on the time-varying depth maps. To get a reliable cost volume, the infrared and color st-cost volumes are integrated into a single cost volume by selecting the cost of either the infrared or the color st-cost volumes according to the size of the adaptive kernel used for the CLMF. Then, a graphcut is executed on the cost volume in order to estimate the disparity robustly even when the baselines of the stereo cameras are set wide enough to ensure spatially high resolution in the depth direction and the shapes of blocks are deformed by the affine transformation. A 2D graphcut is executed on each scan line to reduce the processing time and memory consumption. We experimented with the proposed method using infrared color stereo data sets of scenes in the real world and evaluated its effectiveness by comparing it with other recent stereo matching methods and depth cameras.
Initial Relaxation of Spatially Evolving Turbulent Channel Flow with Blowing and Suction (2001)

A direct numerical simulation is performed to examine the initial relaxation of spatially evolving turbulent channel flow subjected to uniform wall blowing and suction. Just beyond the entrance section, a uniform blowing is applied at the lower wall and a uniform suction at the upper. The relaxation processes of the mean velocity, turbulence intensities, Reynolds shear stresses, and vorticity fluctuations after the sudden wall blowing and suction are scrutinized. The effect of wall blowing and suction on the location and strength of the streamwise vortices is significant. The relaxation associated with suction is much slower than that with blowing. The initial relaxation is evaluated in terms of the turbulent kinetic energy transport. Blowing enhances the intercomponent energy transfer between the Reynolds stresses, whereas suction suppresses it.
Tunable nonlinear liquid-crystal photonic crystals (2003)

Summary form only given. Nematic liquid crystals (NLC) possess very broadband (400 nm to 20 /spl mu/m) birefringence and transparency, and extraordinarily large optical nonlinearity. In this paper, we report a novel approach of directly writing permanent (but electrically switchable) 2-D holographic gratings on pure liquid crystalline structures fabricated with well established alignment surfaces. Our theoretical analysis shows that such structures exhibit tunable bandgap, and will also enable super-prism beam steering effects.
Production of β-glucosidase and diauxic usage of sugar mixtures byCandida molischiana (1996)

The fermentation of cellobiose is a rare trait among yeasts. Of the 308 yeast species that utilize cellobiose aerobically, only 12 species ferment it, and only 2 species, Candida molischiana and Candida wickerhamii, also ferment cellodextrins. Candida molischiana produced beta-glucosidase activity on all carbon sources tested, except glucose, mannose, and fructose. When these sugars were added to cultures growing on cellobiose, the synthesis of beta-glucosidase ceased. However, the total amount of enzyme activity remained constant, indicating that the C. molischiana beta-glucosidase is catabolite repressed and not catabolite inactivated. When grown in medium initially containing glucose plus xylose, cellobiose, maltose, mannitol, or glucitol, C. molischiana preferentially utilized glucose and produced little beta-glucosidase activity until glucose was nearly depleted from the medium. When grown in medium containing cellobiose plus either fructose or mannose, the yeast preferentially utilized the monosaccharides and produced little beta-glucosidase activity. Candida molischiana produced beta-glucosidase and co-utilized cellobiose and xylose, maltose, or trehalose. Glucose and fructose, mannose, or trehalose were co-utilized; however, no beta-glucosidase activity was detected. Thus, the order of substrate preference groups appeared to be (glucose, trehalose, fructose, mannose) > (cellobiose, maltose, xylose) > (mannitol, glucitol).
Crimean-Congo hemorrhagic fever virus replication imposes hyper-lipidation of MAP1LC3 in epithelial cells (2020)

Crimean-Congo hemorrhagic fever virus (CCHFV) is a virus that causes severe liver dysfunctions and hemorrhagic fever, with high mortality rate. Here, we show that CCHFV infection caused a massive lipidation of LC3 in hepatocytes. This lipidation was not dependent on <i>ATG5, ATG7</i> or <i>BECN1</i>, and no signs for recruitment of the alternative ATG12-ATG3 pathway for lipidation was found. Both virus replication and protein synthesis were required for the lipidation of LC3. Despite an augmented transcription of <i>SQSTM1</i>, the amount of proteins did not show a massive and sustained increase in infected cells, indicating that degradation of SQSTM1 by macroautophagy/autophagy was still occurring. The genetic alteration of autophagy did not influence the production of CCHFV particles demonstrating that autophagy was not required for CCHFV replication. Thus, the results indicate that CCHFV multiplication imposes an overtly elevated level of LC3 mobilization that involves a possibly novel type of non-canonical lipidation. <b>Abbreviations:</b> BECN1: Beclin 1; CCHF: Crimean-Congo hemorrhagic fever; CCHFV: Crimean-Congo hemorrhagic fever virus; CHX: cycloheximide; ER: endoplasmic reticulum; GFP: green fluorescent protein; GP: glycoproteins; MAP1LC3: microtubule associated protein 1 light chain 3; MOI: multiplicity of infection; n.i.: non-infected; NP: nucleoprotein; p.i.: post-infection; SQSTM1: sequestosome 1.
Ligand Effects on Rates and Regioselectivities of Rh(I)-Catalyzed (5 + 2) Cycloadditions: A Computational Study of Cyclooctadiene and Dinaphthocyclooctatetraene as Ligands (2012)

The first theoretical study on the effects of ligands on the mechanism, reactivities, and regioselectivities of Rh(I)-catalyzed (5 + 2) cycloadditions of vinylcyclopropanes (VCPs) and alkynes has been performed using density functional theory (DFT) calculations. Highly efficient and selective intermolecular (5 + 2) cycloadditions of VCPs and alkynes have been achieved recently using two novel rhodium catalysts, [Rh(dnCOT)](+)SbF(6)(-) and [Rh(COD)](+)SbF(6)(-), which provide superior reactivities and regioselectivities relative to that of the previously reported [Rh(CO)(2)Cl](2) catalyst. Computationally, the high reactivities of the dnCOT and COD ligands are attributed to the steric repulsions that destabilize the Rh-product complex, the catalyst resting state in the catalytic cycle. The regioselectivities of reactions with various alkynes and different Rh catalysts are investigated, and a predictive model is provided that describes substrate-substrate and ligand-substrate steric repulsions, electronic effects, and noncovalent π/π and C-H/π interactions. In the reactions with dnCOT or COD ligands, the first new C-C bond is formed proximal to the bulky substituent on the alkyne to avoid ligand-substrate steric repulsions. This regioselectivity is reversed either by employing the smaller [Rh(CO)(2)Cl](2) catalyst to diminish the ligand-substrate repulsions or by using aryl alkynes, for which the ligand-substrate interactions become stabilizing due to π/π and C-H/π dispersion interactions. Electron-withdrawing groups on the alkyne prefer to be proximal to the first new C-C bond to maximize metal-substrate back-bonding interactions. These steric, electronic, and dispersion effects can all be utilized in designing new ligands to provide regiochemical control over product formation with high selectivities. The computational studies reveal the potential of employing the dnCOT family of ligands to achieve unique regiochemical control due to the steric influences and dispersion interactions associated with the rigid aryl substituents on the ligand.
Electrical Wavelength Switching of Thermal Emitters Based on Quantum Wells and Photonic Crystals (2016)

We demonstrate electrical high-speed wavelength switching of narrowband thermal emission on a single chip by using intersubband transitions in multiple quantum wells and optical resonances of photonic crystals.
D'Amico Risk Stratification Correlates With Degree of Suspicion of Prostate Cancer on Multiparametric Magnetic Resonance Imaging (2011)

Our data support the notion that using multiparametric magnetic resonance prostate imaging one may assess the degree of risk associated with magnetic resonance visible lesions in the prostate.
ChemInform Abstract: Rapid and Practical Synthesis of D‐myo‐Inositol 1,4,5‐Trisphosphate. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
MECP2e1 isoform mutation affects the form and function of neurons derived from Rett syndrome patient iPS cells (2015)

MECP2 mutations cause the X-linked neurodevelopmental disorder Rett Syndrome (RTT) by consistently altering the protein encoded by the MECP2e1 alternative transcript. While mutations that simultaneously affect both MECP2e1 and MECP2e2 isoforms have been widely studied, the consequence of MECP2e1 deficiency on human neurons remains unknown. Here we report the first isoform-specific patient induced pluripotent stem cell (iPSC) model of RTT. RTTe1 patient iPS cell-derived neurons retain an inactive X-chromosome and express only the mutant allele. Single-cell mRNA analysis demonstrated they have a molecular signature of cortical neurons. Mutant neurons exhibited a decrease in soma size, reduced dendritic complexity and decreased cell capacitance, consistent with impaired neuronal maturation. The soma size phenotype was rescued cell-autonomously by MECP2e1 transduction in a level-dependent manner but not by MECP2e2 gene transfer. Importantly, MECP2e1 mutant neurons showed a dysfunction in action potential generation, voltage-gated Na(+) currents, and miniature excitatory synaptic current frequency and amplitude. We conclude that MECP2e1 mutation affects soma size, information encoding properties and synaptic connectivity in human neurons that are defective in RTT.
Stem cells in prostate cancer: Resolving the castrate-resistant conundrum and implications for hormonal therapy (2006)

Androgen deprivation therapy (ADT) is initial systemic therapy for advanced prostate cancer and is used as an adjuvant to local therapy for high-risk disease, but responses in advanced disease are transient. Prostate cancer stem cells are a small fraction of tumor cells that give rise to malignant cells. Initial or acquired stem cell resistance to castration must therefore underlie castrate-resistant prostate cancer. We sought to review the evidence on cancer stem cells and androgen deprivation therapy to determine if prostate cancer stem cell resistance occurs from the outset, or if it is an acquired resistance. Prostate cancer stem cells do not express androgen receptor (AR) and hence should not be directly responsive to androgen deprivation therapy. However, castrate-resistant tumors that are derived from stem cells, have molecular changes such as amplification of the androgen receptor gene, or other genetic changes resulting in gain-of-function changes in AR, implying an acquired resistance to androgen deprivation. The origins of castrate-resistant tumors, with mechanisms such as androgen receptor gene amplification from androgen receptor negative prostate cancer stem cells, is an apparent conundrum. Insight into how this occurs may lead to new treatments that overcome or delay castrate-resistance. Herein, we review the evidence on cancer stem cells, the benefits of ADT, the biological basis of response to ADT, and mechanisms of castrate-resistance. We also explore the apparent conundrum of why AR-negative prostate cancer stem cells can give rise to castrate-resistant prostate cancer. We propose possible explanations that may resolve this conundrum and discuss implications for hormonal therapy.
Overall Survival in Malignant Glioma Is Significantly Prolonged by Neurosurgical Delivery of Etoposide and Temozolomide from a Thermo-Responsive Biodegradable Paste (2019)

The significant survival benefit of intracavity chemotherapy demonstrates clinical applicability of PLGA/PEG paste-mediated delivery of temozolomide and etoposide adjuvant to radiotherapy. PLGA/PEG paste offers a future platform for combination delivery of molecular targeted compounds.
HIP Resolution and Rendezvous Mechanisms (2004)

Abstract — The Host Identity Protocol (HIP) decouples the name and locator roles that IP addresses serve in the current Internet architecture. This document discusses resolution mechanisms that map domain names into host identities and IP addresses and their effects of the overall HIP architecture, with a focus on rendezvous between nodes. It argues that HIP will benefit from removing its current dependencies on the presence of a deployed DNS infrastructure, resulting in a simpler, more modular system. Although such a system will require a new HIP resolution service to translate host identities into IP addresses, HIP will at the same time not require a dedicated rendezvous infrastructure anymore. Rendezvous servers become an optional component of the overall system that optimizes HIP performance in extreme situations, e.g., for highly mobile nodes, or enables advanced capabilities, such as location privacy. I.
ChemInform Abstract: KATALYTISCHE REAKTIONEN VON AMINEN MIT OLEFINEN (1973)

Abstract Unter dem katalytischen Einfluß von Lithiumdimethylamid oder Alkyllithium reagiert Tetramethyläthylendiamin (I) mit Äthylen (IIa) bzw. Propen (IIb) im Autoklaven bei 150°C in 24 Stdn. zu Dimethylvinylamin (III) und Dimethyl= äthylamin (IVa) bzw. Dimethylisopropylamin (IVb).
On Model Selection for Scalable Time Series Forecasting in Transport Networks (2021)

The transport literature is dense regarding short-term traffic predictions, up to the scale of 1 hour, yet less dense for long-term traffic predictions. The transport literature is also sparse when it comes to city-scale traffic predictions, mainly because of low data availability. In this work, we report an effort to investigate whether deep learning models can be useful for the long-term large-scale traffic prediction task, while focusing on the scalability of the models. We investigate a city-scale traffic dataset with 14 weeks of speed observations collected every 15 minutes over 1098 segments in the hypercenter of Los Angeles, California. We look at a variety of state-of-the-art machine learning and deep learning predictors for link-based predictions, and investigate how such predictors can scale up to larger areas with clustering, and graph convolutional approaches. We discuss that modelling temporal and spatial features into deep learning predictors can be helpful for long-term predictions, while simpler, not deep learning-based predictors, achieve very satisfactory performance for link-based and short-term forecasting. The trade-off is discussed not only in terms of prediction accuracy vs prediction horizon but also in terms of training time and model sizing.
Peptide Functionalized Gold Nanorods for the Sensitive Detection of a Cardiac Biomarker Using Plasmonic Paper Devices (2015)

The sensitivity of localized surface plasmon resonance (LSPR) of metal nanostructures to adsorbates lends itself to a powerful class of label-free biosensors. Optical properties of plasmonic nanostructures are dependent on the geometrical features and the local dielectric environment. The exponential decay of the sensitivity from the surface of the plasmonic nanotransducer calls for the careful consideration in its design with particular attention to the size of the recognition and analyte layers. In this study, we demonstrate that short peptides as biorecognition elements (BRE) compared to larger antibodies as target capture agents offer several advantages. Using a bioplasmonic paper device (BPD), we demonstrate the selective and sensitive detection of the cardiac biomarker troponin I (cTnI). The smaller sized peptide provides higher sensitivity and a lower detection limit using a BPD. Furthermore, the excellent shelf-life and thermal stability of peptide-based LSPR sensors, which precludes the need for special storage conditions, makes it ideal for use in resource-limited settings.
Fluconazole for Refractory Oropharyngeal Candidiasis in AIDS Patients (1995)

Oropharyngeal candidiasis is a major lesion in HIV-infected patients. Effective antifungal therapy is required to prevent weight loss, nutritional compromise, and systemic infection. The response to oral fluconazole in patients refractory to prior topical or systemic antifungal therapy was evaluated. A case of oropharyngeal candidiasis in a patient with advanced AIDS that was refractory to topical clotrimazole and oral itraconazole, but responded to oral fluconazole therapy, is reported. Oral fluconazole should be considered the primary treatment for oropharyngeal candidiasis in the HIV-infected population with AIDS status.
Pressureless Sintering and Mechanical and Biological Properties of Fluor‐hydroxyapatite Composites with Zirconia (2003)

Fluor‐hydroxyapatite (FHA) fabricated by a reaction between fluorapatite (FA) and hydroxyapatite (HA) was mixed with ZrO 2 to produce FHA–ZrO 2 composites. When the relative amount of FA to HA increased, the decomposition of the composite was decreased gradually because of the formation of thermally stable FHA solid solutions. With such suppression of decomposition, the FHA–ZrO 2 composites retained fully densified bodies. As a result, significant enhancements in mechanical properties, such as hardness, flexural strength, and fracture toughness, were achieved as the relative amount of FA to HA increased. The highest values in strength and toughness were 220 MPa and 2.5 MPa·m 1/2 , respectively, with FHA–40 vol% ZrO 2 composites. In vitro proliferation of osteoblast‐like cells (MG63) on the composites showed behavior similar to that observed on pure HA and FHA. Alkaline phosphatase (ALP) activity of the growing cells (HOS) on the composites was slightly down‐regulated compared with that on pure HA and FHA at prolonged periods.