gebhart/patrepeval huggingface dataset:
Structure-Based Design of Melanocortin 4 Receptor Ligands Based on the SHU-9119-hMC4R Cocrystal Structure (2020)

The melanocortin receptors (MC1R-MC5R) belong to class A G-protein-coupled receptors (GPCRs) and are known to have receptor-specific roles in normal and diseased states. Selectivity for MC4R is of particular interest due to its involvement in various metabolic disorders, including obesity, feeding regulation, and sexual dysfunctions. To further improve the potency and selectivity of MC4R (ant)agonist peptide ligands, we designed and synthesized a series of cyclic peptides based on the recent crystal structure of MC4R in complex with the well-characterized antagonist <b>SHU-9119</b> (Ac-Nle<sup>4</sup>-c[Asp<sup>5</sup>-His<sup>6</sup>-DNal(2')<sup>7</sup>-Arg<sup>8</sup>-Trp<sup>9</sup>-Lys<sup>10</sup>]-NH<sub>2</sub>). These analogues were pharmacologically characterized <i>in vitro</i>, giving key insights into exploiting binding site subpockets to deliver more selective ligands. More specifically, the side chains of the Nle<sup>4</sup>, DNal(2')<sup>7</sup>, and Trp<sup>9</sup> residues in <b>SHU-9119</b>, as well as the amide linkage between the Asp<sup>5</sup> and Lys<sup>10</sup> side chains, were found to represent structural features engaging a hMC4R/hMC3R selectivity switch.
Fabrication of Long Scale Aluminum Foam by Transfer Heat Foaming of Precursor (2007)

In this paper, a new attempt of transfer heat foaming was examined on the precursor method to fabricate long scale aluminum foams. In this new method, the induction coil heater was moved along the longitudinal direction of a rod precursor to foam a part of the precursor continuously. Long scale aluminum precursor was successfully foamed by the transfer heat foaming in which heating coil was moved along the precursor to control the temperature of heated part constantly.
Improved Target-oriented Linear Full Waveform Inversion (2010)

Traditionally, seismic inversion takes place in the (time) migrated CMP-offset domain. In this paper, we present an alternative target-oriented, linear full waveform inversion scheme. We use a data-driven redatuming step towards a target event to optimally correct for overburden propagation effects. By assuming the target layers to be approximately parallel, a local inversion process per depth point in the linear Radon domain is carried out, allowing an accurate comparison with forward modeled events in the ray parameter domain. Per local inversion process, we apply more advanced inversion tools, including multiplicative regularization and detailed kinematics estimation, to improve upon conventional inversion techniques. This inversion strategy is demonstrated on field data from the Arabian Gulf.
Magnetic field-electric circuit coupled method for brush DC motor simulations (2012)

Micro-hybrid or “stop-start” developments for automotive applications are continuously growing due to recent European regulations on emissions and pollution. A reinforced starter is able to ensure this new function in addition to the classical cold start. Such devices must be optimized, especially their process of commutation in order to minimize commutator and brush wears and keep the device running during the whole life of the vehicle. The starter performances are computed with the help of a FE model, coupled with circuit equation. Brush/segment contact resistance introduced in the circuit model has been measured and computed. An electrical arc model has also been developed and used in the model. Losses in sliding contact, and also during arcing contact, and other internal variable can thus be determined.
Development of friction stir spot welding using rotating tool without probe and its application to low-carbon steel plates (2009)

A friction stir spot welding process, in which a rotating tool without a probe was employed, was applied to a lap joint of low carbon steel plates with 0.5 mm thickness. In this process, the rotating tool of 3.6 mm diameter, rotating at 18,000 rpm, was plunged into the upper plate at a rate of 0.2 mm/s, and then kept at a maximum plunged depth of 0.05–0.25 mm for 0–1 s (dwell time). In the weld obtained by this process, a hole due to the impression of the plunged tool probe was not formed, although a slight depression by the tool plunging remained. At tool plunge depths of 0.05 mm or less, it was impossible to weld the plates. At tool plunge depths from 0.1 to 0.14 mm, joints were fractured at the interface in tensile test, and the failure load increased with tool plunge depth. At tool plunge depths from 0.16 to 0.22 mm, joints were fractured at an almost constant load along the periphery of the depression, leaving a part of the upper plate on the bottom plate surface. The maximum tensile failure load of 1.8 kN was obtained at a plunge depth of 0.2 mm. Based on the observation of the weld microstructure and measurement of the thermal cycle at various spots in the weld, controlling factors of the joint strength are discussed.
Development of Decellularized Cornea by Organic Acid Treatment for Corneal Regeneration (2018)

This study successfully developed decellularized corneal scaffolds that were prepared by organic acid, which safely exist in animal tissues and plants. The results showed the highly efficient removal of cell debris from porcine corneas, and excellent preservation of optical properties, extracellular matrix (ECM) architecture, and biomolecules. In addition, decellularized corneal scaffolds revealed excellent biocompatibility and recellularization potential <i>in vitro</i>. In an animal model, the transplanted corneas were completely epithelialized, clear, showed no signs of immune response, and effectively supported stromal keratocytes growth. Hence, this could be a promising scaffold material for corneal tissue engineering applications.
Building Multicast Controller for Carrier-grade IPTV Service over Ethernet Passive Optical Network (2007)

Ethernet passive optical network (EPON) is an emerging high-speed access network technology that can provide an ideal transmission platform for high- bandwidth applications such as IPTV (internet protocol television). To deploy the carrier-grade IPTV service, especially HDTV (high definition TV), it is very essential to construct a controllable multicast architecture for IPTV service over EPON. In this paper, we present a multicast control solution over EPON system to satisfy the demand of the service management and control from the service providers. Furthermore, we successfully develop a multicast controller to perform the multicast control function including managing the eligibility of the subscribers and controlling the delivery of the multicast channels. The evaluation results demonstrate that the multicast controller can not only provide high processing performance but also improve the operation and management ability for the service providers greatly.
Generation and detection of terahertz radiation by non-resonant nonlinear process in GaAs using 1.56 μm fiber laser pulses (2006)

We demonstrate the generation and detection of a terahertz wave by non-resonant electro-optical processes with femtosecond 1.56 /spl mu/m laser pulses. Using a 0.5 mm-thick [110]-oriented GaAs wafer for optical rectification and electro-optical modulation, we achieve spectral sensitivity up to 3 THz. For high net efficiency of nonlinear process, it is important to evaluate the phase matching condition in electro-optical crystals.
A genetic linkage studyoffacioscapulohumeral (Landouzy-Dejerine) disease with24 polymorphic DNA probes (1989)

SUMMARY FromanalysisofDNApolymorphismsin a panelof455subjectsfrom25familieswithfacioscapulohumeral(Landouzy-Dejerine) disease, we havefound no evidenceforclose linkageofthe disease at 24 different genetic loci, including one from a candidate chromosomal region.Added to previous data, our results provide direction for future collaborative linkage studies. Facioscapulohumeral (Landouzy-Dejerine) disease(FSHD),with a prevalenceestimated at 5/100 0o0,1 2 is arguably one of the more common inheritedneuromusculardisorders. Clinical onset is usually inchildhood with facial weakness, but first sympto- maticpresentationwith shoulder girdle weaknessisoften delayed until the teens, early adulthood, or later.3 Progressionofweakness occurs, especially in the proximal muscles ofthe upper limbs, but often alsoinvolvestruncal,peroneal,and/or more proximallower limb muscles, so that up to 20% of FSHDheterozygotes require a wheelchair by middle age.4 ThequestionofwhetherLandouzy-Dejerine disease Received for publication 9 March 1989.Accepted for publication 31 March 1989.
A PSF width independent of aberrations in spatially incoherent interferometry (Conference Presentation) (2017)

Optical imaging usually suffers from aberrations that are induced by various structures when imaging biological samples. Usually aberrations degrade the imaging system performances by broadening the point spread function (PSF). Unexpectedly we show that in spatially incoherent interferometry like full-filed optical coherence tomography (FFOCT), the system PSF width is almost insensitive to aberrations. Instead of considering the PSF of a classical imaging system such as a microscope, we specifically pay attention to the system PSF of interferometric imaging systems for which an undistorted wavefront from a reference beam interferes with the distorted wavefront of the object beam. By comparing the cases of scanning OCT with spatially coherent illumination, wide-field OCT with spatially coherent illumination and FFOCT with spatially incoherent illumination, we found that in FFOCT with spatially incoherent illumination the system PSF width is almost independent of the aberrations and only its amplitude varies. This is demonstrated by theoretical analysis as well as numerical calculations for different aberrations, and confirmed by experiments with a FFOCT system. It is the first time to the best of our knowledge that such specific merit of incoherent illumination in FFOCT has been demonstrated. Based on this, the signal level is used as metric in our adaptive optics FFOCT system for retinal imaging. Only the main aberrations (defocus and astigmatism) that are dominating in eye are corrected to improve the signal to noise ratio and the high order aberrations are skipped. This would increase the correction speed thus reducing the imaging time.
The development of a robust, autonomous sensor network platform for environmental monitoring. (2003)

This paper describes an approach to the approaches being explored for a Sensor Network platform being developed for the DTI/NextWave technologies programme. The approach being adopted is to develop the system as a community of devices which use self-organising techniques to provide key functions. The devices are, largely, based on commodity technologies, thus providing a low cost basis. We give an outline of th eapproach and project and illustrate the techniques being developed with specific functions for: control, management, data retrieval and data quality control. The target application is off shore sea shelf monitoring; but the techniques being developed may be applied to a range of problems.
Synthesis, chirality-dependent conformational and biological properties of siRNAs containing 5′-(R)- and 5′-(S)-C-methyl-guanosine (2020)

Various chemical modifications have been identified that enhance potency of small interfering RNAs (siRNAs) and that reduce off-target effects, immune stimulation, and toxicities of metabolites of these therapeutic agents. We previously described 5'-C-methyl pyrimidine nucleotides also modified at the 2' position of the sugar. Here, we describe the synthesis of 2'-position unmodified 5'-(R)- and 5'-(S)-C-methyl guanosine and evaluation of these nucleotides in the context of siRNA. The (R) isomer provided protection from 5' exonuclease and the (S) isomer provided protection from 3' exonuclease in the context of a terminally modified oligonucleotide. siRNA potency was maintained when these modifications were incorporated at the tested positions of sense and antisense strands. Moreover, the corresponding 5' triphosphates were not substrates for mitochondrial DNA polymerase. Models generated based on crystal structures of 5' and 3' exonuclease oligonucleotide complexes with 5'-(R)- and 5'-(S)-C-methyl substituents attached to the 5'- and 3'-terminal nucleotides, respectively, provided insight into the origins of the observed protections. Structural properties of 5'-(R)-C-methyl guanosine incorporated into an RNA octamer were analysed by X-ray crystallography, and the structure explains the loss in duplex thermal stability for the (R) isomer compared with the (S) isomer. Finally, the effect of 5'-C-methylation on endoribonuclease activity has been explained.
PECAM-Independent Thioglycollate Peritonitis Is Associated With a Locus on Murine Chromosome 2 (2009)

These data potentiate further study of the diapedesis machinery, as well as potential identification of new components of this machinery. As such, this study is an important step to better understanding the processes of inflammation.
Studies of molecular alignments of monolayers deposited by a chemical adsorption technique (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudies of molecular alignments of monolayers deposited by a chemical adsorption techniqueKazufumi Ogawa, N. Mino, K. Nakajima, Y. Azuma, and T. OhmuraCite this: Langmuir 1991, 7, 7, 1473–1477Publication Date (Print):July 1, 1991Publication History Published online1 May 2002Published inissue 1 July 1991https://doi.org/10.1021/la00055a031Request reuse permissionsArticle Views141Altmetric-Citations15LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (577 KB) Get e-Alertsclose Get e-Alerts
TRAIT2D: a Software for Quantitative Analysis of Single Particle Diffusion Data (2021)

Single particle tracking (SPT) is one of the most widely used tools in optical microscopy to evaluate particle mobility in a variety of situations, including cellular and model membrane dynamics. Recent technological developments, such as Interferometric Scattering microscopy, have allowed recording of long, uninterrupted single particle trajectories at kilohertz framerates. The resulting data, where particles are continuously detected and do not displace much between observations, thereby do not require complex linking algorithms. Moreover, while these measurements offer more details into the short-term diffusion behaviour of the tracked particles, they are also subject to the influence of localisation uncertainties, which are often underestimated by conventional analysis pipelines. we thus developed a Python library, under the name of TRAIT2D (Tracking Analysis Toolbox - 2D version), in order to track particle diffusion at high sampling rates, and analyse the resulting trajectories with an innovative approach. The data analysis pipeline introduced is more localisation-uncertainty aware, and also selects the most appropriate diffusion model for the data provided on a statistical basis. A trajectory simulation platform also allows the user to handily generate trajectories and even synthetic time-lapses to test alternative tracking algorithms and data analysis approaches. A high degree of customisation for the analysis pipeline, for example with the introduction of different diffusion modes, is possible from the source code. Finally, the presence of graphical user interfaces lowers the access barrier for users with little to no programming experience.
Prevalence of Antibodies to Human Immunodeficiency Virus and to Human T Cell Leukemia Virus Type I in Transfused Sickle Cell Disease Patients (1990)

The prevalence of the human immunodeficiency virus (HIV) antibody and the human T cell leukemia virus type I (HTLV-I) antibody was examined in 116 adults with sickle cell disease. Eighty-eight of them had received a mean of 18.6 transfusions of red blood cells between 1978 and 1985, and none was positive for the HIV antibody. Of 116 patients, 9 (7.8%) tested positive for HTLV-I antibodies. HTLV-I-positive patients were similar to those without HTLV-I antibody with respect to age, number of transfusions, and proportion of patients with greater than 40 transfusions. However, 3 of the 9 HTLV-I-positive patients came from West Africa or from the Caribbean, whereas this proportion was much lower (7/107) in the HTLV-I-negative group (x2, 7.564; P less than .01). Our analysis suggests that the risk of HIV infection in transfused sickle cell disease patients is low. Although HTLV-I antibodies in these patients may not be related to blood transfusions, it seems prudent to screen blood donors for HTLV-I infection.
VE-cadherin regulates EphA2 in aggressive melanoma cells through a novel signaling pathway: Implications for vasculogenic mimicry (2006)

The formation of matrix-rich, vasculogenic-like networks, termed vasculogenic mimicry (VM), is a unique process characteristic of highly aggressive melanoma cells found to express genes previously thought to be exclusively associated with endothelial and epithelial cells. This study contributes new observations demonstrating that VE-cadherin can regulate the expression of EphA2 at the cell membrane by mediating its ability to become phosphorylated through interactions with its membrane bound ligand, ephrin-A1. VE-cadherin and EphA2 were also found to be colocalized in cell-cell adhesion junctions, both in vitro and in vivo. Immunoprecipitation studies revealed that EphA2 and VE-cadherin could interact, directly and/or indirectly, during VM. Furthermore, there was no change in the colocalization of EphA2 and VE-cadherin at cell-cell adhesion sites when EphA2 was phosphorylated on tyrosine residues. Although transient knockout of EphA2 expression did not alter VE-cadherin localization, transient knockout of VE-cadherin expression resulted in the reorganization of EphA2 on the cells' surface, an accumulation of EphA2 in the cytoplasm, and subsequent dephosphorylation of EphA2. Collectively, these results suggest that VE-cadherin and EphA2 act in a coordinated manner as a key regulatory element in the process of melanoma VM and illuminate a novel signaling pathway that could be potentially exploited for therapeutic intervention.
Size matters: Effect of granule size of the bone graft substitute (Herafill®) on bone healing using Masquelet's induced membrane in a critical size defect model in the rat's femur (2019)

The Masquelet technique for the treatment of large bone defects is a two-stage procedure based on an induced membrane. The size of a scaffold is reported to be a critical factor for bone healing response. We therefore aimed to investigate the influence of the granule size of a bone graft substitute on bone marrow derived mononuclear cells (BMC) supported bone healing in combination with the induced membrane. We compared three different sizes of Herafill® granules (Heraeus Medical GmbH, Wehrheim) with or without BMC in vivo in a rat femoral critical size defect. A 10 mm defect was made in 126 rats and a membrane induced by a PMMA-spacer. After 3 weeks, the spacer was taken out and membrane filled with different granule sizes. After 8 weeks femurs were taken for radiological, biomechanical, histological, and immunohistochemical analysis. Further, whole blood of the rat was incubated with granules and expression of 29 peptide mediators was assessed. Smallest granules showed significantly improved bone healing compared to larger granules, which however did not lead to an increased biomechanical stability in the defect zone. Small granules lead to an increased accumulation of macrophages in situ which could be assigned to the inflammatory subtype M1 by majority. Increased release of chemotactic respectively proangiogenic active factors in vitro compared to syngenic bone and beta-TCP was observed. Granule size of the bone graft substitute Herafill® has significant impact on bone healing of a critical size defect in combination with Masquelet's technique in terms of bone formation and inflammatory potential.
IC‐P‐144: Assessment of structural differences in normal aging and Alzheimer's disease: Quantitative and qualitative differences using subjects from the Alzheimer's Disease Neuroimaging Initiative (ADNI) (2009)

It has been suggested that the changes encountered in AD are largely an amplification of lesser but similar changes constituting “cognitive aging”. New automated techniques and large sample sizes allow for a more precise examination of between group morphological differences. We propose to examine whether AD and “normal aging” are only quantitatively different with respect to their cortical thickness and white and gray matter density “signature”, or differ in fundamental ways between the two groups. T1 volumes (196 elderly controls, 160 age-matched AD subjects; age range 57-91, mean = 76) were acquired from the ADNI database, and processed at the Montreal Neurological Institute by a fully automated analysis pipeline. The resultant tissue classification volumes were used in the voxel-based morphometry (VBM) analysis; cortical surfaces were used to extract cortical thickness values. Statistical analysis consisted regressing cortical thickness or tissue density, onto age and diagnostic group. Regression of cortical thickness onto diagnostic group, demonstrated significant widespread cortical thinning in the AD group in all lobes, with relative sparing of sensory and motor areas. The largest absolute losses were seen bilaterally in middle temporal gyri, insulae, and along with the left supramarginal gyrus (> ¼ mm loss), and in the medial temporal cortex bilaterally (> ½ mm loss). Normal elderly subjects showed additional age-related thinning in primary sensory and motor areas, including primary visual and auditory cortices. The VBM analyses found that differences within the medial temporal structures were primarily quantitative in nature, with both groups showing significant bilateral hippocampal atrophy, in addition to a significant white matter loss in three regions: periventricular, callosal, and adjacent to the hippocampus. AD-related morphological changes are both quantitatively and qualitatively different from normal aging. Tissue loss within frontal and temporal association cortex, in addition to that observed within and adjacent to the hippocampus, reflects an exacerbation of normal age-related changes. Conversely, tissue loss within the insulae is only seen in AD, whereas significant thinning within the primary sensory and motor cortices is reflective of normal aging.
Robust semiconductor overlay metrology with non-uniform illumination beams using digital holographic microscopy (2023)

Precise, accurate, and fast characterization of overlay between two layers of semiconductors during chip fabrication is an important monitoring and feedback step. Overlay, which is to be measured within the accuracy of a nanometer, is susceptible to many small imperfections in the measurement system. A digital holographic microscope measures the complex field of overlay targets using simple optics followed by computational algorithms for overlay metrology. We improved the precision of overlay measurement by correcting the inhomogeneities and asymmetries caused by the illumination spots, presenting a robust method resulting from simple calibration steps.