gebhart/patrepeval huggingface dataset:
Evidence of a splitting of the Mn-O distance and of a large lattice disorder in the charge-ordered phase ofLiMn2O4obtained by EXAFS (2003)

We measured the extended x-ray-absorption fine-structure (EXAFS) spectrum of ${\mathrm{LiMn}}_{2}{\mathrm{O}}_{4}$ below room temperature in the charge-ordered phase and for comparison at room temperature in the cubic phase. By means of a standard fit procedure we verified that, as reported by neutron-scattering experiments, also at the local level there are two different Mn-O distances below room temperature, which correspond to the surroundings of well-defined ${\mathrm{Mn}}^{3+}$ and ${\mathrm{Mn}}^{4+}$ ions. This result is different from the ones obtained from previous EXAFS measurements and confirms the physical picture of the phase transition caused by the ordering of charges in contrast to a cooperative Jahn-Teller phenomenon. Moreover a large lattice disorder in the charge-ordered state, which determines a significant static contribution to the EXAFS Debye-Waller factor, has been found. This last result can be considered as the EXAFS spectral mark of charge-order transitions, even in those materials in which there is no clear evidence of the splitting of bond lengths.
Author response: Early immune markers of clinical, virological, and immunological outcomes in patients with COVID-19: a multi-omics study (2022)

Immune markers measured at the early stage of COVID-19 infection are associated with various clinical outcomes and can be used to predict disease progression, T cell memory, viral shedding, and the antibody response of the COVID-19 patients.
Detection, Characterization, and Abundance of Engineered Nanoparticles in Complex Waters by Hyperspectral Imagery with Enhanced Darkfield Microscopy (2012)

We introduce a novel methodology based on hyperspectral imagery with enhanced Darkfield microscopy for detection, characterization, and analysis of engineered nanoparticles in both ultrapure water and in complex waters, such as simulated-wetland ecosystem water and wastewater. Hyperspectral imagery analysis of 12 different nanoparticle sample types, scattering the obliquely incident visible and near-infrared light (VNIR: 400-1000 nm) in an enhanced Darkfield background, showed that the sample information in terms of the spatial distribution as well as spectral characteristics unique to each nanoparticle types, at a sensitivity of single nanoparticle (size ≥10 nm) can be obtained. Hyperspectral imagery and Raman spectral analyses of the silver nanoparticles (AgNPs) revealed that the apparent hydrodynamic size of the particle increased while the primary size remained unchanged in the presence of coatings, which is further confirmed by dynamic light scattering measurements. Similar in size, AgNPs with different coatings exhibited similar spectral color (or peak position) but a red-shift in the peak positions by same amount relative to Bare AgNPs was observed. In conclusion, hyperspectral imagery with enhanced Darkfield microscopy can be a promising tool for detection and characterization of engineered nanoparticles in environmental systems, facilitating studies on fate and transformation of these particles in various types of water samples.
Massive SVM Parallelization Using Hardware Accelerators (2011)

Support Vector Machines (SVMs) are some of the most widely used classification and regression algorithms for data analysis, pattern recognition, or cognitive tasks. Yet learning problems that can be solved by SVMs are limited in size because of high computational cost and excessive storage requirements. Many variations of the original SVM algorithm were introduced that scale better to large problems. They change the SVM framework quite drastically, such as apply optimizations other than the maximum margin, or introduce different error metrics for the cost function. Such algorithms may work for some applications, but they do not have the robustness and universality that make SVMs so popular.
Fenton-Like Reaction Catalyzed by the Rare Earth Inner Transition Metal Cerium (2008)

Cerium (Ce) is a rare earth metal that is not known to have any biological role. Cerium oxide materials of several sizes and shapes have been developed in recent years as a scaffold for catalysts. Indeed even cerium oxide nanoparticles themselves have displayed catalytic activities and antioxidant properties in tissue culture and animal models. Because of ceria's ability to cycle between the +3 and +4 states at oxygen vacancy sites, we investigated whether cerium metal would catalyze a Fenton-like reaction with hydrogen peroxide. Indeed, cerium chloride did exhibit radical production in the presence of hydrogen peroxide, as assessed by relaxation of supercoiled plasmid DNA. Radical production in this reaction was also followed by production of radical cation of 2,2'-azinobis-(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS). Radical scavengers and spin traps were capable of competing with ABTS for radicals produced in this cerium dependent Fenton-like reaction. Electron paramagnetic resonance experiments reveal both hydroxyl radical and superoxide anion in a reaction containing cerium and hydrogen peroxide. Based on these results we propose that cerium is capable of redox-cycling with peroxide to generate damaging oxygen radicals.
Connective Tissue Growth Factor Promotes Efficient Generation of Human Induced Pluripotent Stem Cell-Derived Choroidal Endothelium (2017)

Age-related macular degeneration (AMD) is a leading cause of irreversible blindness in the Western world. Although, the majority of stem cell research to date has focused on production of retinal pigment epithelial (RPE) and photoreceptor cells for the purpose of evaluating disease pathophysiology and cell replacement, there is strong evidence that the choroidal endothelial cells (CECs) that form the choriocapillaris vessels are the first to be lost in this disease. As such, to accurately evaluate disease pathophysiology and develop an effective treatment, production of patient-specific, stem cell-derived CECs will be required. In this study, we report for the first time a stepwise differentiation protocol suitable for generating human iPSC-derived CEC-like cells. RNA-seq analysis of the monkey CEC line, RF/6A, combined with two statistical screens allowed us to develop media comprised of various protein combinations. In both screens, connective tissue growth factor (CTGF) was identified as the key component required for driving CEC development. A second factor tumor necrosis factor (TNF)-related weak inducer of apoptosis receptor was also found to promote iPSC to CEC differentiation by inducing endogenous CTGF secretion. CTGF-driven iPSC-derived CEC-like cells formed capillary tube-like vascular networks, and expressed the EC-specific markers CD31, ICAM1, PLVAP, vWF, and the CEC-restricted marker CA4. In combination with RPE and photoreceptor cells, patient-specific iPSC derived CEC-like cells will enable scientists to accurately evaluate AMD pathophysiology and develop effective cell replacement therapies. Stem Cells Translational Medicine 2017;6:1533-1546.
Potential role for insulin and cycloheximide in regulating the intrinsic activity of glucose transporters in isolated rat adipocytes. (1993)

We examined the hypothesis that insulin stimulation of cellular glucose transport may involve a protein synthesis-dependent regulation of glucose transporter (GTer) activity independent of GTer translocation to the cell surface. Rat adipocytes were isolated, incubated with or without 10 micrograms/ml (36 microM) cycloheximide (CHX) for 60 min, and then with or without 7 nM insulin for 30 min. Glucose transport rates were assessed in intact cells, and both glucose transport rates and GTer levels were assessed in subcellular fractions of membrane vesicles before and after reconstitution into artificial liposomes. GTer functional and intrinsic activities were calculated as the ratio between these transport rates and GTer levels in native and reconstituted membranes, respectively. Insulin increased functional activity by 340% in native plasma membrane (PM) vesicles and intrinsic activity by 60% in reconstituted membranes (from 54 +/- 4 to 86 +/- 4 molecules transported per GTer/sec, P < 0.02). CHX preincubation of cells did not interfere with the insulin effect to stimulate glucose transport rate in either intact cells or in native PMs; it did, however, reduce PM GTer levels by 27-30%, but not affecting those in the intracellular pool. However, CHX additively increased the insulin-stimulated intrinsic activity of PM GTers by 67%. Relative reconstitution efficiencies, assessed by immunoblotting both native and reconstituted membranes against specific antibodies, were similar for GLUT 1 and GLUT 4. Although insulin did not alter this efficiency, CHX slightly decreased it for GLUT 4. Our data suggest that insulin stimulation of glucose transport may involve, as part of its mechanism, modulation of the GTer intrinsic activity. We further hypothesize that CHX effects on increasing this activity state of GTer may involve as yet unknown protein synthesis-dependent regulator(s).
Diamond-turned optics aid alignment and assembly of a dual-field infrared imaging missile tracker (1998)

Diamond-turning as a manufacturing method for infrared optics opens new possibilities for solving packaging problems. Optical surfaces and mechanical mounting features may be related to one another to reduce design complexity, tolerance accumulation, and cost.
Controlled generation and use of CO in flow (2016)

A tube-in-tube flow reactor allows the generation and immediate use of CO, without the need for CO cylinders.
Data from Hepatitis C Virus Proteins Modulate MicroRNA Expression and Chemosensitivity in Malignant Hepatocytes (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Hepatocellular cancer (HCC) is highly resistant to chemotherapy and is associated with poor prognosis. Chronic hepatitis C virus (HCV) infection is a major cause of HCC. However, the effect of viral proteins in mediating chemosensitivity in tumor cells is unknown. We postulated that HCV viral proteins could modulate therapeutic responses by altering host cell microRNA (miRNA) expression.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; HepG2 malignant hepatocytes were stably transfected with full-length HCV genome (Hep-394) or an empty vector (Hep-SWX). MiRNA profiling was done by using a custom microarray, and the expression of selected miRNAs was validated by real-time PCR. Protein expression was assessed by Western blotting, whereas caspase activation was assessed by a luminometric assay.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; The IC&lt;sub&gt;50&lt;/sub&gt; to sorafenib was lower in Hep-394 compared with Hep-SWX control cells. Alterations in miRNA expression occurred with 10 miRNAs downregulated &gt;2-fold and 23 miRNAs upregulated &gt;2-fold in Hep-394 cells compared with controls. Of these, miR-193b was overexpressed by 5-fold in Hep-394 cells. miR-193b was predicted to target Mcl-1, an antiapoptotic protein that can modulate the response to sorafenib. The expression of Mcl-1 was decreased, and basal caspase-3/7 activity and poly ADP ribose polymerase cleavage were increased in Hep-394 cells compared with controls. Moreover, transfection with precursors to miR-193b decreased both Mcl-1 expression and the IC&lt;sub&gt;50&lt;/sub&gt; to sorafenib.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions&lt;/b&gt;: Cellular expression of full-length HCV increases sensitivity to sorafenib by the miRNA-dependent modulation of Mcl-1 and apoptosis. Modulation of miRNA responses may be a useful strategy to enhance response to chemotherapy in HCC. Clin Cancer Res; 16(3); 957–66&lt;/p&gt;&lt;/div&gt;
Design of Antennas for UHF RFID Tags (2012)

This paper is mainly dedicated to the design of radio-frequency identification (RFID) tags, particularly the antennas that allow the tag to be fed, communicate, and exchange data with the reader. Good performance tags require optimized antenna that take into account numerous constraints as well as the environment of the application under consideration. Both conventional tags and robust tags are discussed. This paper also discusses how to transform a tag into an RFID sensor.
Nanoparticle‐based detection of cancer‐associated RNA (2014)

Hassan Azzazy is an author of patent applications describing the use of nanoparticles for detection of disease biomarkers. He is the co-founder and chief scientist of D-Kimia, an L.L.C., which develops nanodiagnostic assays.
Anti-invasive effects of decitabine, a DNA methyltransferase inhibitor, through tightening of tight junctions and inhibition of matrix metalloproteinase activities in AGS human gastric carcinoma cells (2012)

The DNA methyltransferase inhibitor decitabine, 5-Aza-2'-deoxycytidine, possesses anti-metabolic and anticancer activities in various cancer cells. However, the biochemical mechanisms underlying decitabine-induced inhibition of invasiveness and metastasis have not been thoroughly studied. In this study, we investigated the effect of decitabine on the correlation between tightening of tight junctions (TJs) and anti-invasive activity in AGS human gastric cancer cells. Our data indicated that the inhibitory effects of decitabine on cell motility and invasiveness were associated with increased tightness of the TJ, which was demonstrated by an increase in transepithelial electrical resistance (TER). Immunoblotting results indicated that decitabine repressed the levels of the claudin proteins, major components of TJs that play a key role in the control and selectivity of paracellular transport. Furthermore, matrix metalloproteinase (MMP)-2 and -9 activity in the AGS cells was dose-dependently inhibited by treatment with decitabine, and this was correlated with a decrease in mRNA and protein expression. In addition, these effects were related to inactivation of the phosphoinositide 3-kinase (PI3K)/Akt pathway in AGS cells. In conclusion, this study suggests that TJs and MMPs are critical targets of decitabine-induced inhibition of invasiveness in AGS human gastric cancer cells.
Supplementary Figure S1 from Thyroid Cancers Exhibit Oncogene-Enhanced Macropinocytosis that Is Restrained by IGF1R and Promote Albumin–Drug Conjugate Response (2023)

&lt;p&gt;Albumin uptake is dependent on macropinocytosis in ATC&lt;/p&gt;
Convergent Synthesis of N-Linked Glycopeptides on a Solid Support (1998)

Solid-supported synthesis can be conducted to produce a variety of glycopeptides in good overall yields. The carbohydrates are formed by the glycal assembly method. The polymer-bound construct terminates in a glycal. The terminal double bond can be functionalized to provide a C2−N-acetyl glucosamine linkage with an amino group in the anomeric position. The latter can be coupled, in a convergent manner, to the γ-carboxyl group of an aspartyl residue on a preformed peptide. Iodosulfonamidation of the polymer-bound glucal to the N-acetyl glucosamine using anthracenesulfonamide was crucial for the success of the solid-phase synthesis. This general method was employed in the formation of a variety of glycopeptides.
Development of a Planar Waveguide Microarray for the Monitoring and Early Detection of Five Harmful Algal Toxins in Water and Cultures (2014)

A novel multiplex microarray has been developed for the detection of five groups of harmful algal and cyanobacterial toxins found in marine, brackish, and freshwater environments including domoic acid (DA), okadaic acid (OA, and analogues), saxitoxin (STX, and analogues), cylindrospermopsin (CYN) and microcystins (MC, and analogues). The sensitivity and specificity were determined and feasibility to be used as a screening tool investigated. Results for algal/cyanobacterial cultures (n = 12) and seawater samples (n = 33) were compared to conventional analytical methods, such as high performance liquid chromatography (HPLC) and liquid chromatography tandem mass spectrometry (LC-MS/MS). Detection limits for the 15 min assay were 0.37, 0.44, 0.05, 0.08, and 0.40 ng/mL for DA, OA, STX, CYN, and MC, respectively. The correlation of data obtained from the microarray compared to conventional analysis for the 12 cultures was r(2) = 0.83. Analysis of seawater samples showed that 82, 82, 70, 82, and 12% of samples were positive (>IC20) compared to 67, 55, 36, 0, and 0% for DA, OA, STX, CYN, and MC, respectively, for conventional analytical methods. The discrepancies in results can be attributed to the enhanced sensitivity and cross-reactivity profiles of the antibodies in the MBio microarray. The feasibility of the microarray as a rapid, easy to use, and highly sensitive screening tool has been illustrated for the five-plex detection of biotoxins. The research demonstrates an early warning screening assay to support national monitoring agencies by providing a faster and more accurate means of identifying and quantifying harmful toxins in water samples.
Progress in fabrication of waveguide spatial light modulators via femtosecond laser micromachining (2017)

We have previously introduced a femtosecond laser micromachining-based scheme for the fabrication of anisotropic waveguides in lithium niobate for use in a guided-wave acousto-optic spatial light modulator. This spatial light modulation scheme is extensible to off-plane waveguide holography via the integration of a Bragg reflection grating. In this paper, we present femtosecond laser-based direct-write approaches for the fabrication of (1) waveguide in-coupling gratings and (2) volume Bragg reflection gratings via permanent refractive index changes within the lithium niobate substrate. In combination with metal surface-acoustic-wave transducers, these direct-write approaches allow for complete fabrication of a functional spatial light modulator via femtosecond laser direct writing.
Impact of Bilateral Open and Closed-angle Glaucoma on Glaucoma-specific Functioning in Asians (2011)

Bilateral glaucoma is worse than the mild form in any eye and is significantly associated with poor glaucoma-specific functioning in this Singaporean Chinese sample. These data emphasize the need for strategies to identify patients early and prevent deterioration beyond the mild form of the condition.
Developmentally Regulated Post-translational Modification of Nucleoplasmin Controls Histone Sequestration and Deposition (2015)

Nucleoplasmin (Npm) is an abundant histone chaperone in vertebrate oocytes and embryos. During embryogenesis, regulation of Npm histone binding is critical for its function in storing and releasing maternal histones to establish and maintain the zygotic epigenome. Here, we demonstrate that Xenopus laevis Npm post-translational modifications (PTMs) specific to the oocyte and egg promote either histone deposition or sequestration, respectively. Mass spectrometry and Npm phosphomimetic mutations used in chromatin assembly assays identified hyperphosphorylation on the N-terminal tail as a critical regulator for sequestration. C-terminal tail phosphorylation and PRMT5-catalyzed arginine methylation enhance nucleosome assembly by promoting histone interaction with the second acidic tract of Npm. Electron microscopy reconstructions of Npm and TTLL4 activity toward the C-terminal tail demonstrate that oocyte- and egg-specific PTMs cause Npm conformational changes. Our results reveal that PTMs regulate Npm chaperoning activity by modulating Npm conformation and Npm-histone interaction, leading to histone sequestration in the egg.
Heminasal Proboscis, A Rare Craniofacial Cleft (2013)

Craniofacial clefts are extremely rare congenital anomalies, the importance of which lies in their great range of variety of anatomic forms and their complex management. Proboscis is one of the rare cases of this kind in which half of the nose is separated from the face and it is only pedicled on the right or left medial canthal regions by a nose-like, rudimentary tubular structure. This article reports the case of a 3-month-old infant with left-sided proboscis. Left lower eyelid coloboma was also present. The proboscis was treated with local flaps at the age of 3 months, and at the age of 10 months the coloboma was managed.
Large-Scale Visible and Infrared Optical Phased Arrays in Silicon Nitride (2017)

Large-scale optical phased arrays at 635nm and 1550nm wavelengths are demonstrated with aperture sizes up to 4 × 4mm2. A diffraction limited spot with a record 0.021°×0.021° divergence and output powers as high as 400mW are shown.
Photodynamic therapy in a pleural cavity using monte carlo simulations with 2D/3D Graphical Visualization (2022)

Cancer therapy using Photodynamic Therapy (PDT) has been investigated for some time [1,2] and now it is a growing area of interest in clinical trials [3]. Monte Carlo (MC) simulations were used for early laboratory studies [4,5] for analysis in PDT. Various improvements in the MC method have advanced the field in recent years.
Estimation of Glycerides and Free Fatty Acid in Oils Extracted From Various Seeds from the Indian Region by NMR Spectroscopy (2011)

Abstract The present study is focused on the quantification of glycerides and free fatty acid in oils extracted from various seeds for biodiesel production from Indian territory. A new method based on 1 H‐ and 13 C‐NMR spectroscopic techniques was developed in order to estimate triglycerides (TG), diglycerides, monoglycerides, free fatty acids (FFA) and various other components such as para‐substituted phenols, silylated methyl esters, aromatic acids, naphthalenes, etc. Iodine values of the extracted oils were estimated using the developed 1 H‐NMR spectroscopic method, which was correlated with the TG content present in the sample. Results by the NMR method were validated by the blend preparation, fatty acid composition determined by the GC and from the iodine value of the samples. The developed method is direct, rapid and no sample treatment is required. The results from these comprehensive studies indicated that NMR spectroscopic technique is useful for the quantification of extracted oils and can be used effectively for the development and monitoring of biodiesel production and determining the fuel quality.
12.3: A New Low‐Power TFT‐LCD Driver for Portable Devices (2000)

Abstract In this paper, we describe a new low‐power data‐line driver for TFT‐LCDs for portable devices. The driver contains newly‐developed output buffers with low static current in place of operational amplifiers in a conventional driver. The new driver test‐IC achieves about 85 % reduction in static current dissipation with a high output‐voltage‐resolution and a wide dynamic‐output‐range.
Ion-Current Measurement in Small Two-Stroke SI Engines (2008)

&lt;div class="htmlview paragraph"&gt;The cyclic changes of the cylinder pressure are mainly influenced by the primary inflammation phase, which in turn depends on the local air/fuel ratio and the residual-gas fraction at the spark plug. The ion-current measurement technique is based on the conductivity of the mixture during the internal combustion. It is therefore possible to use the signal for combustion diagnostics when using the spark plug as a sensor.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;This article demonstrates the potential of ion sensing at the spark plug and in the combustion chamber to detect sources of interference which prevent an optimal combustion process. Comparing the ion signals of consecutive combustion cycles delivers explanations of phenomena that could not yet be sufficiently characterized by cylinder-pressure indication. The results allow new fundamental approaches to the optimization of the combustion process.&lt;/div&gt;