gebhart/patrepeval huggingface dataset:
NMR solution structures of actin depolymerizing factor homology domains (2009)

Actin is one of the most conserved proteins in nature. Its assembly and disassembly are regulated by many proteins, including the family of actin-depolymerizing factor homology (ADF-H) domains. ADF-H domains can be divided into five classes: ADF/cofilin, glia maturation factor (GMF), coactosin, twinfilin, and Abp1/drebrin. The best-characterized class is ADF/cofilin. The other four classes have drawn much less attention and very few structures have been reported. This study presents the solution NMR structure of the ADF-H domain of human HIP-55-drebrin-like protein, the first published structure of a drebrin-like domain (mammalian), and the first published structure of GMF beta (mouse). We also determined the structures of mouse GMF gamma, the mouse coactosin-like domain and the C-terminal ADF-H domain of mouse twinfilin 1. Although the overall fold of the five domains is similar, some significant differences provide valuable insights into filamentous actin (F-actin) and globular actin (G-actin) binding, including the identification of binding residues on the long central helix. This long helix is stabilized by three or four residues. Notably, the F-actin binding sites of mouse GMF beta and GMF gamma contain two additional beta-strands not seen in other ADF-H structures. The G-actin binding site of the ADF-H domain of human HIP-55-drebrin-like protein is absent and distorted in mouse GMF beta and GMF gamma.
Scaling of high-k dielectrics towards sub-1nm EOT (2004)

High-k dielectric layers are deposited using ALD or MOCVD. Most of the work focused on Hf-based high-k dielectrics, either as pure HfO/sub 2/, as silicate or mixed with Al/sub 2/O/sub 3/. In some cases nitrogen is added to improve the high-temperature stability. Various surface preparation methods and deposition conditions are tested. Compatibility of the high-k stacks with poly-Si and metal electrodes is investigated. Significant improvements in yield and thermal stability are obtained by optimized modifications of the high-k stack. Scaling of the equivalent oxide thickness (EOT) is accomplished by implementing novel ideas in interface engineering and high-k materials processing. High-k stacks are tested in transistor structures with small gate lengths. The origin of the electrical instabilities and the observed drive current degradation of high-k transistors as compared to the SiO/sub 2/ reference transistors are studied in detail.
Dislocation Conversion in 4H-SiC Crystals Grown by Metastable Solvent Epitaxy (2013)

Dislocation conversion in 4H-SiC single crystals grown by metastable solvent epitaxy (MSE) was investigated using synchrotron X-ray topography, repeated polishing and molten KOH etching, and transmission electron microscopy (TEM). The conversion of basal plane dislocations to threading edge dislocations occurred not only near the interface between the MSE layer and the substrate, but also throughout the MSE layer. At the initial stage of MSE growth, all threading screw dislocations (TSDs) were converted into Frank-type basal plane stacking faults (Frank SFs). High resolution TEM observation revealed that the four extra SiC planes generated by this conversion were inserted among adjacent basal planes. These results suggest that the driving force for the conversion of TSDs is significantly larger for MSE growth than for growth by conventional chemical vapor deposition. A g·b analysis of the Frank partial dislocations (PDs) associated with the Frank SFs revealed that the total sum of the Burgers vectors of the four Frank PDs had two different values of b = c and b = c + a, and that approximately 50% of TSDs in the substrate had a Burgers vector component parallel to the a-axis.
Retzius‐sparing robot‐assisted laparoscopic radical prostatectomy: combining the best of retropubic and perineal approaches (2014)

The present results suggest that Retzius-sparing RALP, although technically more demanding, was as feasible and effective as conventional RALP, and also led to a shorter operating time and faster recovery of early continence. Retzius-sparing RALP was also reproducible and achievable in all cases.
XANES IN (TMTSeF)2Re04: POLARISATION DEPENDENCE OF THE Se K EDGE (1983)

We have measured XANES (X-ray Absorption Near Edge Spectra) near the Re Li (i=l,II,III) edges in (TMTTF)2Re04 and (TMTSeF) 2Re04 and the Se K edge in the latter compound. An important dependence of the XANES at the Se K edge on the polarisation of the incident beam with respect to the crystal axes was observed, whose interpretation can give information on the symmetry of the unoccupied conduction band states. The positions of the Re L edges were compared with those in several inorganic compounds containing Re in various oxidation states, and were found to be, within experimental error, the same as those in KRe04, suggesting the molecular environment in the organic materials affects little the chemical state of the perrhenate anion.
A Novel Generalized Nonlinear Dispersion Equation for Five-Layer Waveguides with Kerr-like Nonlinearity (1996)

A new method is proposed for the analysis of optical properties of stationary transverse electirc (TE) nonlinear waves in the five-layer waveguide which consists of a linear guiding layer with two nonlinear bounding layers sandwiched between a semi-infinite clad and a substrate. By using the relation of the interface electric fields, we obtain the generalized form of nonlinear dispersion equations as an analytic and flexible form. In order to verify the dispersion equation, we apply the dispersion equation to the analysis of the symmetric five-layer waveguide. The nonlinear dispersion curves for several thicknesses of the nonlinear thin film is also presented.
[Adherence to antipsychotic medication in schizophrenia patients]. (2002)

Antipsychotic agents are the mainstay of treatment for schizophrenia. However, almost 50% of schizophrenia patients exhibit non-compliance with antipsychotic drug therapy. This in turn may account for high relapse rate, reduced quality of life and increased burden on society. Identification of factors that may mediate adherence to treatment is therefore a primary clinical challenge. This paper reviews the literature regarding medication adherence among schizophrenia patients, with an emphasis on four groups of mediating factors: illness-related, patient-related, treatment-related and environmental-related factors. In addition, we describe a modified health-belief model that may facilitate better understanding of empirical findings. Therapeutic interventions to encourage better treatment compliance are discussed.
Improved Linewidth Tolerant Carrier Phase Recovery Based on Polar MAP Metric Estimate (2017)

A new metric that analytically approximates the maximum a posteriori (MAP) solution is presented. Used with a decision-directed carrier phase estimation algorithm, the linewidth tolerance exceeds the limits achieved when using the conventional Euclidean distance.
Extensive structure–activity studies of lactam derivatives of MT‐II and SHU‐9119: their activity and selectivity at human melanocortin receptors 3, 4, and 5 (2003)

The melanocortin system is involved in the regulation of several diverse physiologic pathways. Recently we have demonstrated that replacing His6 by Pro6 in the well-known antagonist SHU-9119 resulted in a potent agonist at the hMC5R (EC50 = 0.072 nm) with full antagonist activity at the hMC3R and the hMC4R. We have designed, synthesized, and pharmacologically characterized a series of peptide analogs of MT-II and SHU-9119 at the human melanocortin receptors MC3R, MC4R and MC5R. All these peptides were modified at position 6 with a Pro instead of a His residue. In this study, we have identified new scaffolds which are antagonists at the hMC4R and hMC3R. Additionally, we have discovered a new selective agonist at the hMC4R, Ac-Nle-c[Asp-Pro-D-Phe-Arg-Trp-Lys]-Pro-Val-NH2 (6, PG-931) which will be useful in further biologic investigations of the hMC4R. PG-931 was about 100-fold more selective for the hMC4R vs. the hMC3R (IC50 = 0.58 and 55 nm, respectively). Some of these new analogs have exceptional biologic potencies at the hMC5R and will be useful in further efforts to differentiate the substructural features responsible for selectivity at the hMC3R, hMC4R, and hMC5R.
Human Antibody Domains and Fragments Targeting Neutrophil Elastase as Candidate Therapeutics for Cancer and Inflammation-Related Diseases (2021)

Neutrophil elastase (NE) is a serine protease released during neutrophil maturation. High levels of NE are related to lung tissue damage and poor prognosis in cancer; thus, NE is a potential target for therapeutic immunotherapy for multiple lung diseases and cancers. Here, we isolate and characterize two high-affinity, specific, and noncompetitive anti-NE antibodies Fab 1C10 and V<sub>H</sub> 1D1.43 from two large phage-displayed human Fab and V<sub>H</sub> libraries. After fusion with human IgG1 Fc, both of them (V<sub>H</sub>-Fc 1D1.43 and IgG1 1C10) inhibit NE enzymatic activity with V<sub>H</sub>-Fc 1D1.43 showing comparable inhibitory effects to that of the small molecule NE inhibitor SPCK and IgG1 1C10 exhibiting even higher (2.6-fold) activity than SPCK. Their epitopes, as mapped by peptide arrays combined with structural modeling, indicate different mechanisms for blocking NE activity. Both V<sub>H</sub>-Fc and IgG1 antibodies block NE uptake by cancer cells and fibroblast differentiation. V<sub>H</sub>-Fc 1D1.43 and IgG1 1C10 are promising for the antibody-based immunotherapy of cancer and inflammatory diseases.
Photoreflectance spectroscopic technique: a new model for estimation of plasma-induced defect density in Si substrate (2002)

In recent years, reactive ion etching (RIE) has been widely used in ULSI process technology. However, the Si surface exposure to plasmas during RIE causes the generation of defects or damage in the Si substrate due to the energetic ion bombardment and etching species penetration. This plasma-induced damage strongly affects ULSI device performance and reliability. Si substrate damage induced by CHF/sub 3/-CF/sub 4/-Ar plasma processing has been characterized by photoreflectance (PR) spectroscopy. Moreover, the damage induced by Ar plasma has been characterized in-situ in the processing chamber. Both of the PR signal intensities decrease with the plasma treatment. The decrease in PR signal intensity is attributed to the decrease in modulation due to the introduction of the charged defects that changes the space charge density of the depletion layer. We propose a new model for the estimation of the defect density induced by plasma exposure. Using this model based on PR spectroscopy, the defect density can be quantitatively calculated.
High-Accuracy Thermal Analysis Methodology for Semiconductor Junction Temperatures by Considering Line Patterns of Three-Dimensional Modules (2009)

A novel computational fluid dynamics analysis method of predicting semiconductor junction temperatures precisely without modeling printed circuit board (PCB) line patterns was developed. First, PCBs are divided into multiple regions. The effective anisotropic thermal conductivity of each region is then assigned as follows. All the regions are divided into smaller subregions whose size is below the pattern width. The thermal conductivity of each subregion is defined by the property of the material at the center of the subregion. Next, a thermal circuit network composed of all the subregions is generated, and finally the anisotropic thermal conductivities of each region are computed by solving this thermal network matrix. When boards are divided into multiple regions, there is a convergence region size under which the analytical results show no further change. In this paper, the relationship between the size of the divided regions and the accuracy of the analytical results was investigated. It was confirmed that the calculated semiconductor junction temperatures were precisely coincident with the experimental results when the size of the regions was less than 20 times the line pattern width.
Alumina waveguides for full-spectrum integrated photonics (2017)

We demonstrate fully confined waveguides in the ultraviolet spectrum, and present amorphous aluminum oxide as a viable waveguide platform for broad-spectrum integrated photonics with transmission from the infrared to the ultraviolet. Fabrication of aluminum oxide photonic structures and experimental results are discussed.
A first digitally-controlled oscillator in a deep-submicron CMOS process for multi-GHz wireless applications (2003)

A novel digitally-controlled oscillator (DCO) architecture for multi-GHz RF applications is proposed and demonstrated. It deliberately avoids any use of an analog tuning voltage control line. Fine frequency resolution is achieved through high-speed dithering. This enables use of fully-digital frequency synthesizers in the most advanced deep-submicron digital CMOS processes which allow almost no analog extensions. It promotes cost-effective integration with the digital back-end on to a single silicon die. The demonstrator test chip has been fabricated in a digital 0.13 /spl mu/m CMOS process together with a DSP. The DCO core consumes 2.3 mA from a 1.5 V supply and has a very large tuning range of 500 MHz. The phase noise is -112 dBc/Hz at 500 kHz offset.
A peptide derived from the intercellular adhesion molecule-2 regulates the avidity of the leukocyte integrins CD11b/CD18 and CD11c/CD18. (1995)

beta 2 integrin (CD11a,b,c/CD18)-mediated cell adhesion is required for many leukocyte functions. Under normal circumstances, the integrins are nonadhesive, and become adhesive for their cell surface ligands, the intercellular adhesion molecules (ICAMs), or soluble ligands such as fibrinogen and iC3b, when leukocytes are activated. Recently, we defined a peptide derived from ICAM-2, which specifically binds to purified CD11a/CD18. Furthermore, this peptide strongly induces T cell aggregation mainly mediated by CD11a/CD18-ICAM-1 interaction, and natural killer cell cytotoxicity. In the present study, we show that the same ICAM-2 peptide also avidly binds to purified CD11b/CD18, but not to CD11c/CD18. This binding can be blocked by the CD11b antibody OKM10. The peptide strongly stimulates CD11b/CD18-ICAM-1-mediated cell aggregations of the monocytic cell lines THP-1 and U937. The aggregations are energy and divalent cation-dependent. The ICAM-2 peptide also induces CD11b/CD18 and CD11c/CD18-mediated binding of THP-1 cells to fibrinogen and iC3b coated on plastic. These findings indicate that in addition to induction of CD11a/CD18-mediated cell adhesion, the ICAM-2 peptide may also serve as a "trigger" for high avidity ligand binding of other beta 2 integrins.
Molecular Players Involved in TGF‐β1 induced CTGF/CCN2 expression in Primary Rat Osteoblasts: SBE, TRE and SRC/ERK (2007)

Connective tissue growth factor (CTGF/CCN2) regulates osteoblast differentiation and cell function. In osteoblasts, CTGF is induced by TGF-β1 where it acts as a mediator of some TGF-β1 induced biological functions. Two proximal promoter motifs, the TGF-β response element (TRE) and the SMAD binding element (SBE), were shown to mediate the induction of CTGF by TGF-β1 in a cell type specific fashion. To investigate if these motifs functioned in osteoblasts, we utilized CTGF promoter deletion and mutant constructs. We demonstrated the requirement of both motifs for induction of CTGF activity by TGF-β1 in osteoblasts. Electro-mobility assays using probes containing the TRE, SBE or both showed TGF-β1 inducible complexes that can be ablated by mutation of the motif, confirming their role in CTGF expression by TGF-β1. Smads and MAP kinases (JNK, p38 and ERK) are key mediators of TGF-β1 signaling and are activated in osteoblasts by TGF-β1. Only expression of dominant-negative (DN) ERK showed significant inhibition of TGF-β1 induced CTGF activity. Since the tyrosine kinase, SRC, is upstream of ERK signaling, we assessed its role in TGF-β1 induction of CTGF. Osteoblasts that were treated with the SRC kinase inhibitor, PP2 (10μM), or the kinase-dead SRC showed a decrease in TGF-β1 induced CTGF activity. In conclusion, CTGF induction by TGF-β1 in osteoblasts requires both the TRE and SBE motifs and the SRC/ERK signaling cascade.
Investigation of a MMP-2 Activity-Dependent Anchoring Probe for Nuclear Imaging of Cancer (2014)

The results indicate the possible usefulness of our MDAP strategy for tumor imaging.
Repeatability of ventilation and perfusion assessment by functional MRI in children with CF (2018)

<b>Background:</b> Chronic lung diseases such as cystic fibrosis (CF) can be monitored by imaging techniques. Pulmonary magnetic resonance imaging (MRI) techniques such as matrix pencil (MP) decomposition allow for the evaluation of regional impairment of the fractional ventilation (RFV) and relative perfusion (RQ). However, the repeatability of MP-MRI outcomes in children with CF is unknown. We examined the short-term variability of ventilation and perfusion impairment from MP-MRI. <b>Method:</b> Twenty-two CF and 12 healthy school-aged children, median (IQR) age 14.4 (10.4 to 17.1) and 12.0 (8.4 to 15.4) years, respectively, underwent MRI on two occasions 24 hours apart. The intra-class-coefficient (ICC), percentage change, and Bland-Altman limits of agreement of each outcome were evaluated to assess reproducibility. <b>Results:</b> In total, 68 measurements from MP-MRI were performed. The ICC between two visits for RFV and RQ ranged between 0.60 and 0.87 in individuals with CF and healthy controls. In CF, the percentage of change (95%CI) between the visits was 0.02 (-3.3 to3.4) for RFV and -1.10 (-4.6 to 2.4) for RQ. The upper and lower limits of agreement between both visits were -4.3 and 3.9 for RFV and -4.4 and 3.7 for RQ. <b>Conclusions:</b> In addition to easy application without breathing maneuvers or contrast agent, the good short-term repeatability make this a promising method for early detection of CF lung disease.
Two-step K^+–Na^+ and Ag^+–Na^+ ion-exchanged glass waveguides for C-band applications (2002)

A two-step K(+)-Na+ and Ag(+)-Na+ ion-exchange technique is introduced to fabricate single-mode channel waveguides in BK7 glass for the telecom-wavelength region. The dependencies of insertion loss, polarization-dependent loss (PDL), end bending loss of curved waveguides on channel width, diffusion time, and annealing time are investigated. Results show that postannealing is a required process for improving waveguide properties and an optimal annealing time exists. Although relatively narrow mask openings are used in most one-step ion-exchange processes, a wider channel width, to as wide as 10 microm, is preferred for this two-step method. The minimum coupling loss to/from single-mode fiber and the propagation loss is found to be 0.4 dB and 0.3 dB/cm, respectively. For 5-cm-long waveguides the PDL is less than 0.1 dB. For the S-bend structure the cosine curve exhibit apparently a lower bending loss than the double-arc curve.
Facile and low-cost synthesis of pure hematite (α-Fe2O3) nanoparticles from naturally occurring laterites and their superior adsorption capability towards acid-dyes (2019)

Hematite nanoparticles have a broad range of outstanding applications such as in wastewater treatment, electrolytic studies, and photoelectrochemical and superparamagnetic applications. Therefore, the development of facile and novel methods to synthesize hematite nanoparticles using low-cost raw materials is an important and timely requirement. In this study, we have developed a facile economical route to synthesize hematite nanoparticles, directly from the naturally occurring material laterite. Laterite is a rock that is rich in Fe and Al with extensive distribution in large mineable quantities in many countries around the world, though not yet utilized for major industrial applications. In this method, ferric ions in the laterite were leached out using acid and the solution obtained was hydrolyzed with slow-release hydroxyl ions which were acquired by aqueous decomposition of urea. The resulted precursor was calcined to obtain hematite nanoparticles. Characterization data shows that the final product is comprised of spherical hematite nanoparticles with a narrow particle size <i>vs.</i> frequency distribution with an average particle diameter of 35 nm. The synthesized product has a purity of over 98%. Furthermore, the synthesized nanoparticles show an excellent adsorption percentage as high as 70%, even when the initial dye concentration in water is 5000 ppm and the amount of material is minimal, towards acid dyes which are excessively used in textile based industries. Such acid dyes are a threat to the environment when they are released into water bodies by industries in massive quantities. Therefore synthesized hematite nanoparticles are ideal to treat dye wastewater in industrial effluents because such nanoparticles are low cost and economical, and the synthesis procedure is rather facile and effective.
[iPS cells for the generation of cartilage and for regenerative medicine and disease modeling of cartilage diseases]. (2016)

The development of induced pluripotent stem cells(iPSCs)has enabled the acquisition of patient-specific chondrocytes by converting somatic cells, such as dermal fibroblasts or blood cells, from patients to iPSCs and then differentiating them toward chondrocytes. We can further generate cartilage tissue from iPSC-derived chondrocytes. Studies on iPSC-derived chondrocytes/cartilage for the regeneration of articular cartilage injury are ongoing. These studies will in the future use autologous iPSCs and allogenic iPSCs from an iPSC stock prepared from donor cells. Drug discovery research for related diseases such as skeletal dysplasia is also being conducted.
Auranofin, an inhibitor of thioredoxin reductase, induces apoptosis in hepatocellular carcinoma Hep3B cells by generation of reactive oxygen species (2017)

Mammalian thioredoxin reductase (TrxR) plays a vital role in restoring cellular redox balance disrupted by reactive oxygen species (ROS) generation and oxidative damage. Here, we evaluated whether auranofin, a selective inhibitor of TrxR, could serve as a potential anti-cancer agent through its selective targeting of TrxR activity in Hep3B hepatocellular carcinoma cells. Auranofin treatment reduced the TrxR activity of these cells and induced apoptosis, which were accompanied by up-regulation of death receptors (DRs) and activation of caspases, as well as promotion of proteolytic degradation of poly(ADP-ribose)-polymerase. Treatment with a pan-caspase inhibitor reversed the auranofin-induced apoptosis and growth suppression, indicating that auranofin may induce apoptosis through a caspase-dependent mechanism involving both the intrinsic and extrinsic apoptotic pathways. Auranofin also significantly altered mitochondrial function, promoting mitochondrial membrane permeabilization and cytochrome c release by regulating Bcl-2 family proteins; these events were accompanied by an accumulation of ROS. Inhibition of ROS generation with the ROS quencher significantly attenuated the inactivation of TrxR in auranofin-treated cells and almost completely suppressed the auranofin-induced up-regulation of DRs and activation of caspases, thereby preventing auranofin-induced apoptosis and loss of cell viability. Taken together, these findings indicate that auranofin inhibition of TrxR activity in Hep3B cells activates ROS- and caspase-dependent apoptotic signaling pathways and triggers cancer cell death.