gebhart/patrepeval huggingface dataset:
Renal Bioengineering with Scaffolds Generated from Human Kidneys (2014)

In 2011, more than 4,700 patients died while on the waiting list for a kidney transplant. In this context, we believe that cell-scaffold technology has the potential to form a bridge between regenerative medicine and transplantation surgery. These methods, in theory, could provide a potentially inexhaustible source of transplantable organs. Unfortunately, current investigations are still in their very early stages and clinical translation is not immediately available in the short term. Thus, identifying the most important obstacles confronting cell-scaffold technology and focusing research efforts in this direction will be important for advancing the state of the art and meeting the clinical needs. We believe that cell-scaffold technology research and development would benefit greatly from a deeper understanding of the physiological mechanisms underlying the natural organogenesis, regeneration, and repair that characterize embryonic humans and simpler organisms. Furthermore, the importance of vascularization - the fundamental caveat of modern surgery - cannot be overstated, especially when discussing the implantation of de novo organs.
A Novel Graph-based Approach for Determining Molecular Similarity (2016)

In this paper, we tackle the problem of measuring similarity among graphs that represent real objects with noisy data. To account for noise, we relax the definition of similarity using the maximum weighted co-$k$-plex relaxation method, which allows dissimilarities among graphs up to a predetermined level. We then formulate the problem as a novel quadratic unconstrained binary optimization problem that can be solved by a quantum annealer. The context of our study is molecular similarity where the presence of noise might be due to regular errors in measuring molecular features. We develop a similarity measure and use it to predict the mutagenicity of a molecule. Our results indicate that the relaxed similarity measure, designed to accommodate the regular errors, yields a higher prediction accuracy than the measure that ignores the noise.
Latent light-assisted poling of LiNbO_3 (2009)

The observation of latent light-assisted poling (LAP) in lithium niobate single crystals is reported. More specifically, the nucleation field is reduced and remains reduced for an extended time period (up to several hours) after irradiation with ultrafast (approximately 150 fs) laser light at a wavelength of 400 nm. The maximum nucleation field reduction measured using latent-LAP (62%) was significantly higher in comparison with regular non-time-delayed LAP (41%) under identical irradiation conditions in undoped congruent lithium niobate crystals. No latent-LAP effect was observed in MgO-doped crystals for the experimental conditions used, despite the strong effect observed using regular LAP. The latent-LAP effect is attributed to the formation of a slowly decaying photo-induced space-charge distribution which assists local ferroelectric domain nucleation. The dynamics of latent-LAP are compared with the dynamics of photorefractive grating decay, recorded in lithium niobate crystals of different doping, confirming the space charge hypothesis.
Device (1997)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text P. Delfyett, "Device," in Ultrafast Electronics and Optoelectronics, M. Nuss and J. Bowers, eds., Vol. 13 of OSA Trends in Optics and Photonics Series (Optica Publishing Group, 1997), paper UC1. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
CUP-CAGE RECONSTRUCTION FOR MAJOR ACETABULAR DEFECTS: TEN-YEAR UPDATE OF FULL AND HALF CAGE CONSTRUCTS (2023)

Cup-cage constructs are one of several methods commonly used to treat severe acetabular bone loss during contemporary revision total hip arthroplasty. The purpose of this study was to provide a long-term results of the technique with emphasis on implant survivorship, radiographic results, and clinical outcomes for both full and half cup-cage reconstructions. We identified 57 patients treated with a cup-cage reconstruction for major acetabular bone loss between 2002–2012. All patients had Paprosky Type 2B through 3B bone loss, with 60% having an associated pelvic discontinuity. Thirty-one patients received a full cup-cage construct, and 26 a half cup-cage. Mean age at reconstruction was 66 years, 75% were female, and the mean BMI was 27 kg/m 2 . Mean follow-up was 10 years. The 10-year cumulative incidences of any revision were 14% and 12% for the full and half cup-cage construct groups, respectively. Of the 9 revisions, 3 were for dislocation, 2 for aseptic loosening and construct failure (both were pelvic discontinuities), 1 for adverse local tissue reaction, and 1 for infection with persistent pelvic discontinuity. The 10-year cumulative incidences of revision for aseptic loosening were 4.5% and 5% for the full and half cup-cage constructs, respectively. Of the unrevised cases, incomplete and non-progressive zone 3 radiolucent lines were observed in 10% of patients in each group. Three patients experienced partial motor and sensory sciatic nerve palsies (2 in the full and 1 in the half cup-cage group). Both the full and half cup-cage cohorts demonstrated significantly improved Harris hip scores. Full and half cup-cage reconstructions for major acetabular defects were successful at 10 years in regards to acetabular fixation without appreciable differences between the two techniques. However, zone 3 radiolucent lines were not uncommon in association with discontinuities, and dislocation continues to be a problem.
Apical Budding of a Recombinant Influenza A Virus Expressing a Hemagglutinin Protein with a Basolateral Localization Signal (2002)

Influenza virions bud preferentially from the apical plasma membrane of infected epithelial cells, by enveloping viral nucleocapsids located in the cytosol with its viral integral membrane proteins, i.e., hemagglutinin (HA), neuraminidase (NA), and M2 proteins, located at the plasma membrane. Because individually expressed HA, NA, and M2 proteins are targeted to the apical surface of the cell, guided by apical sorting signals in their transmembrane or cytoplasmic domains, it has been proposed that the polarized budding of influenza virions depends on the interaction of nucleocapsids and matrix proteins with the cytoplasmic domains of HA, NA, and/or M2 proteins. Since HA is the major protein component of the viral envelope, its polarized surface delivery may be a major force that drives polarized viral budding. We investigated this hypothesis by infecting MDCK cells with a transfectant influenza virus carrying a mutant form of HA (C560Y) with a basolateral sorting signal in its cytoplasmic domain. C560Y HA was expressed nonpolarly on the surface of infected MDCK cells. Interestingly, viral budding remained apical in C560Y virus-infected cells, and so did the location of NP and M1 proteins at late times of infection. These results are consistent with a model in which apical viral budding is a shared function of various viral components rather than a role of the major viral envelope glycoprotein HA.
The effects of atacticity, comonomer content, and configurational defects on the equilibrium melting temperature of monoclinic isotactic polypropylene (2001)

Abstract A series of isotactic polypropylenes were investigated to account for total defect content using xylene fractionation and carbon‐13 NMR experimental methods. The defects of interest were percent atactic content, copolymer content, and configurational defects. Experimental equilibrium melting temperatures were obtained for each material using the Gibbs‐Thomson equation and extrapolation to infinite crystal thickness or the Hoffman‐Weeks analysis. The experimental equilibrium melting temperature was then compared with the theoretical equilibrium melting temperature predicted by Flory's melting point depression model. Flory's model was found to fit the experimental data using an equilibrium melting temperature of 186°C when configurational defects are ignored. However, to account for all defects, the equilibrium melting temperature for 100% isotactic polypropylene must be increased from 186 to 192°C. © 2001 John Wiley &amp; Sons, Inc. J Appl Polym Sci 81: 229–236, 2001
Purification and characterization of a novel lignin peroxidase from white-rot fungusPhanerochaete sordidaYK-624 (2003)

We characterized kinetics and substrate oxidation of a novel lignin peroxidase (YK-LiP) isolated from white-rot fungus Phanerochaete sordida YK-624. YK-LiP enzyme was identified and purified to homogeneity by anion-exchange chromatography and gel permeation chromatography. The molecular mass of YK-LiP was approximately 50 kDa, and the absorption spectrum of YK-LiP was almost the same as that of the LiP (Pc-LiP) from Phanerochaete chrysosporium. Steady-state kinetics of veratryl alcohol oxidation by YK-LiP (unlike that by Pc-LiP) revealed a bi-reactant sequential mechanism, although reactivity of YK-LiP to various monomeric substituted aromatic compounds was similar to that of Pc-LiP. Degradation of dimeric lignin model compounds was more effective by YK-LiP than by Pc-LiP, and the oxidation rate of sinapyl alcohol oligomer by YK-LiP was much faster than that by Pc-LiP.
Learning and visualizing statistical relationships between protein distributions from microscopy images (2014)

Multichannel microscopy has emerged as a technique for imaging multiple targets (molecules, protein distributions, etc.) simultaneously. Discovering the relative changes in these targets (i.e. distribution of different proteins) is fundamental for understanding cell structure and function. We describe a new method for quantifying and visualizing relationships between multiple targets, from a set of segmented multichannel cells. The method is based on combining the canonical correlation analysis technique with a framework for analyzing images based on the concept of optimal mass transportation. We apply the method towards understanding chromatin distribution in cancer nuclei as a function of nuclear envelope shape. We also show that sub cellular distribution of mitochondria can be used to predict the sub cellular localization of actin fibers in yeast cells. Finally, we also describe the application of the method towards understanding relationships between nuclear and cellular shapes in 2D HeLa cells. We believe that the method could serve as a general tool for mining relationships between different sub cellular protein/molecule distributions as well as organelle shapes.
Regenerative medicine of cornea by cell sheet engineering using temperature-responsive culture surfaces (2013)

Recently, regenerative medicine has been focused on as next-generation definitive therapies for several diseases or injuries for which there are currently no effective treatments. These therapies have been rapidly developed through the effective fusion between different fields such as stem cell biology and biomaterials. So far, we have proposed “cell sheet engineering” through our core technology that simply applies alterations of the temperature which allows regulation of the attachment or detachment of living cells on the culture surfaces grafted with the temperature-responsive polymer “poly(N-isoproplyacrylamide)”. This technology enables us to construct bioengineered sheet-like tissues, termed “cell sheets”, without the need of using biodegradable scaffolds and protease treatments that are traditionally used. Therefore, our carrier-free cell sheets not only are independent of the issues observed in conventional methods, but also showed further advantages in the reconstruction of the corneal epithelium or endothelium (e.g. improvement of optical transparency and cell-cell interactions to host stroma in reconstructed tissues). Moreover, our approach does not have issues such as immune rejection or limited number of donors, due to the use of cell sheets derived from autologous limbal (in patients with unilateral disease) or oral mucosal epithelial cells (in patients with bilateral disorders). Indeed, we have successfully performed the clinical application for the reconstruction of ocular surfaces through the transplantation of our carrier-free corneal epithelial cell sheets, as evidenced by improved visual acuity as well as long-term maintenance of postoperative health conditions on ocular surfaces in all patients. We have also proposed a novel approach for the reconstruction of the corneal endothelium using corneal endothelial cell sheets by demonstrating its successful application. Thus, our cell sheet engineering technique provides a breakthrough in the field of regenerative medicine applied to the cornea.
A 130K-gate mainframe chip set (1987)

This presentation will cover a mainframe chip set using three VLSIs containing 542K transistors, employing a rapid turn-around standard cell design methodology. Employing 1.3μm buld processing and controlled by an 8-phase clocking system, the chip operates with a cycle time of less than 60ns and an average propagation delay of less than 0.9ns.
Major antigenic epitopes of bullous pemphigoid 230 kDa antigen map within the C-terminal end of the protein. Evidence using a 55 kDa recombinant protein (2006)

In order to obtain greater insight into the nature of B-cell epitopes in bullous pemphigoid (BP), we generated a BP recombinant protein of 55 kDa M(r) (rBP 55) from a cDNA sequence encoding for the carboxyterminal region of the 230 kDa BP antigen. Serum IgG from guinea-pigs immunized with rBP 55 stained the basement membrane zone of normal human skin and immunoprecipitated the rBP 55 protein, and also the 230 kDa BP antigen recovered from extracts of cultured keratinocytes, thus confirming that the rBP 55 amino acid sequence is present in native BP antigen. The reactivity of sera from 60 patients with BP was analysed using an immunoblot assay on epidermal protein extracts and on the rBP 55 protein. Forty of the 60 BP sera (66%) contained autoantibodies to the 230 kDa polypeptide in an epidermal extract, and 37 of these 40 sera (92%) recognized the rBP 55 protein. In contrast, no reactivity against rBP 55 was detected with 20 BP sera devoid of autoantibodies against the 230 kDa antigen. Likewise, sera from patients with autoimmune blistering skin disorders other than BP (epidermolysis bullosa acquisita or pemphigus vulgaris), and control sera, were unreactive to rBP 55. These results clearly demonstrate the immunogenicity and antigenicity of the C-terminal end of the 230 kDa BP antigen. They confirm that this 555 amino acid segment, corresponding to rBP 55, contains major epitopes which can bind BP patients' autoantibodies, and suggest that the rBP 55 protein could be useful for further characterization of these B-cell epitopes.
Distributed User Selection in Network MIMO Systems with Limited Feedback (2015)

We propose a distributed user selection strategy in a network MIMO setting with M base stations serving K users. Each base station is equipped with L antennas, where LM ≪ K. The conventional selection strategy is based on a well known technique called semi-orthogonal user selection when the zero-forcing beamforming (ZFBF) is adopted. Such technique, however, requires perfect channel state information at the transmitter (CSIT), which might not be available or need large feedback overhead. This paper proposes an alternative distributed user selection technique where each user sets a timer that is inversely proportional to his channel quality indicator (CQI), as a means to reduce the feedback overhead. The proposed strategy allows only the user with the highest CQI to respond with a feedback. Such technique, however, remains collision free only if the transmission time is shorter than the difference between the strongest user timer and the second strongest user timer. To overcome the situation of longer transmission times, the paper proposes another feedback strategy that is based on the theory of compressive sensing, where collision is allowed and all users encode their feedback information and send it back to the base-stations simultaneously. The paper shows that the problem can be formulated as a block sparse recovery problem which is agnostic on the transmission time, which makes it a good alternative to the timer approach when collision is dominant.
Application of decision support systems in scheduling/planning of manufacturing/service systems: a critical review (2016)

A review of decision support systems' (DSS) history, evolution, taxonomy, and application in the planning/scheduling of manufacturing/service systems is presented. Different research conducted is categorised based on the DSS type applied - as well as the domain of the subject - and their limitations are explored. The investigation in literature indicates that although a considerable theoretical and practical advancement has been achieved in DSSs, in most of the research the applicability of the DSSs proposed remains an open question. Additionally, the integration of DSSs - which is an important issue in terms of proposing a comprehensive solution for manufacturing/service systems - has not been addressed in most of the DSSs reviewed.
Complex Target Volume Delineation and Treatment Planning in Radiotherapy for Malignant Pleural Mesothelioma (MPM) (2020)

Introduction: Radiotherapy alone or combined with surgery and/or chemotherapy is being investigated in the treatment of malignant pleural mesothelioma (MPM). This study aimed to simulate a Volumetric Modulated Arc Therapy (VMAT) treatment of a patient with MPM. Materials and Methods: CT images from a patient with intact lungs were imported via DICOM into the Pinnacle3 treatment planning (TP) system (TPS) and used as a model for MPM to delineate organs at risk (OAR) and both clinical and planning target volumes (CTV and PTV) with a margin of 5 mm. Elekta Synergy with 6 MV photons and 80 leafs MLCi2 was employed. VMAT plans were generated using two coplanar arcs with gantry rotation angles of 178&deg - 182&deg, the collimator angles of each arc were set to 90&deg, Octavius® 4D 729 was employed for quality assurance while the calculated and measured doses were compared using VeriSoft. Results: A TP was achieved. The Gamma volume analysis with criteria of 3 mm distance to agreement and 3% dose difference yielded the gamma passing rate = 99.9%. The reference isodose was 42.75 Gy with the coverage constraints for the PTV D95 and V95 = 95.0% of 45 Gy. The remaining dosimetric parameters met the recommendations from the clinically acceptable guidelines for the radiotherapy of MPM. Conclusion: Using well-defined TV and VMAT, a consistent TP compared to similar ones from publications was achieved. We obtained a high agreement between the 3D dose reconstructed and the dose calculated.
Experimentally‐based constitutive relations for co‐current gas‐liquid flow in randomly packed beds (2016)

Experimental Observations on average pulse velocity and frequency in concurrent gas‐liquid (down) flow through randomly packed beds are used to extract constitutive relations for the gas‐liquid interaction and mean curvature terms that appear in a recently proposed volume‐averaged two‐fluid model for bubbly flow. The proposed closures lead to a reasonably quantitative prediction of the average pressure drop and liquid saturation under bubbly flow conditions and in the near pulse regime. In addition, the proposed closures provide realistic estimates for the location of the bubble‐to‐pulse transition in microgravity and in 1g down‐flow and predict the disappearance of the bubbly flow pattern at low liquid fluxes in 1g down‐flow. © 2016 American Institute of Chemical Engineers AIChE J , 63: 812–822, 2017
Color transfer between high-dynamic-range images (2015)

Color transfer methods alter the look of a source image with regards to a reference image. So far, the proposed color transfer methods have been limited to low-dynamic-range (LDR) images. Unlike LDR images, which are display-dependent, high-dynamic-range (HDR) images contain real physical values of the world luminance and are able to capture high luminance variations and finest details of real world scenes. Therefore, there exists a strong discrepancy between the two types of images. In this paper, we bridge the gap between the color transfer domain and the HDR imagery by introducing HDR extensions to LDR color transfer methods. We tackle the main issues of applying a color transfer between two HDR images. First, to address the nature of light and color distributions in the context of HDR imagery, we carry out modifications of traditional color spaces. Furthermore, we ensure high precision in the quantization of the dynamic range for histogram computations. As image clustering (based on light and colors) proved to be an important aspect of color transfer, we analyze it and adapt it to the HDR domain. Our framework has been applied to several state-of-the-art color transfer methods. Qualitative experiments have shown that results obtained with the proposed adaptation approach exhibit less artifacts and are visually more pleasing than results obtained when straightforwardly applying existing color transfer methods to HDR images.
TP53 suppression promotes erythropoiesis in del(5q) MDS, suggesting a targeted therapeutic strategy in lenalidomide-resistant patients (2013)

Stabilization of p53 in erythroid precursors in response to nucleosomal stress underlies the hypoplastic anemia in myelodysplastic syndromes (MDS) with chromosome 5q deletion [del(5q)]. We investigated whether cenersen, a clinically active 20-mer antisense oligonucleotide complementary to TP53 exon10, could suppress p53 expression and restore erythropoiesis in del(5q) MDS. Cenersen treatment of ribosomal protein S-14-deficient erythroblasts significantly reduced cellular p53 and p53-up-regulated modulator of apoptosis expression compared with controls, accompanied by a significant reduction in apoptosis and increased cell proliferation. In a two-stage erythroid differentiation assay, cenersen significantly suppressed nuclear p53 in bone marrow CD34+ cells isolated from patients with del(5q) MDS, whereas erythroid burst recovery increased proportionally to the magnitude of p53 suppression without evidence of del(5q) clonal suppression (r = -0.6; P = 0.005). To explore the effect of p53 suppression on erythropoiesis in vivo, dexamethasone, a glucocorticoid receptor-dependent p53 antagonist, was added to lenalidomide treatment in eight lower-risk, transfusion-dependent, del(5q) MDS patients with acquired drug resistance. Transfusion independence was restored in five patients accompanied by expansion of erythroid precursors and decreased cellular p53 expression. We conclude that targeted suppression of p53 could support effective erythropoiesis in lenalidomide-resistant del(5q) MDS.
Engineering of Osmium(II)‐Based Light Absorbers for Dye‐Sensitized Solar Cells (2012)

Panchromatic OsII sensitizers for dye-sensitized solar cells (DSCs) were prepared. A DSC based on TF-52 (see picture) showed promising performance characteristics: short-circuit photocurrent density JSC=23.3 mA cm−2, open-circuit photovoltage VOC=600 mV, fill factor (FF)=0.633, and power conversion efficiency η=8.85 % under AM 1.5G simulated one-sun irradiation. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Supplementary Data from Targeting BET Proteins BRD2 and BRD3 in Combination with PI3K-AKT Inhibition as a Therapeutic Strategy for Ovarian Clear Cell Carcinoma (2023)

&lt;p&gt;Supplementary Table 1. Arrayed RNAi Screen Data on Ovarian Clear Cell (OCI-C5x) and Serous (OCI-P5x)&lt;/p&gt;