gebhart/patrepeval huggingface dataset:
Characterization and Modeling of the Remodeling Process that Occurs in Modular Tissue Engineered Constructs Assembled Within Microfluidic Perfusion Chambers (2011)

Using a modular approach, a vascularized tissue construct is created by embedding functional cells within submillimeter-sized collagen cylinders (modules) while the outside surfaces are seeded with endothelial cells (EC). The void spaces created by randomly packing modules into a container form EC-lined perfusion channels. Upon implantation, the tissues are remodeled by and integrated into the host and experience, to some degree, immune and inflammatory responses. This work utilized microfluidic techniques to study and model the tissue remodeling in vitro in the absence of the host response. When the construct’s tortuous perfusion channels were reproduced in poly(dimethylsiloxane) microfluidic devices and lined with EC, perfusion at higher flow rates reduced EC activation and maintained the desired quiescent EC phenotype. When applying these results to collagen constructs, higher flow rates were not achievable due to the weak mechanical properties of collagen. To increase the collagen’s mechanical strength, a semi-synthetic collagen/poloxamine-methacrylate hydrogel was examined but due to its heterogeneous surface composition, there was inadequate EC attachment and the material was deemed unsuitable for this application. Proceeding with lower flow rates, tissues assembled within microfluidic perfusion chambers from EC-seeded collagen modules showed that over the course of 24 hours, perfusion did not significantly increase activation but instead increased KLF2 expression, a transcription factor involved in the establishment of EC quiescence, and disrupted VE-cadherin bonds between adjacent EC. However, after 1 week of perfusion, the majority of EC were lost. To ameliorate this loss, mesenchymal stromal cells (MSC) were embedded within the modules in order to take advantage of their anti-apoptotic and immunomodulation effects. The MSC temporarily mitigated the loss of the EC but did not prevent it. They did, however, take on a phenotype similar to smooth muscle cells and migrated towards the EC. Perhaps this indicates that the combination of EC, MSC and perfusion drives the creation and assembly of pseudo vessels. Together, the microfluidic techniques used in this study to assemble and perfuse modular tissues revealed new insights into the remodeling process and exposed critical issues surrounding the adaptation of the EC to the combination of perfusion, remodeling and changing flow fields.
The evolutionary spintronic technologies and their usage in high performance computing (2015)

This paper gives a comprehensive summary of our study in using the spintronic technologies for the on-chip cache density improvement of high performance computing systems. We will start with the spin-transfer torque random access memory (STT-RAM) at the early of stage of commercialization and then extend it to the emerging racetrack memory that has been successfully demonstrated at device and small array level. In multi-level cell (MLC) STT-RAM cache, the cell design constrains, e.g., the switching current requirement and asymmetry in write operations, severely limit the density benefit. Moreover, the two-step read/write accesses and inflexible data mapping strategy may even result in system performance degradation. This paper will discuss our circuit and architecture combined solution. Advanced spintronic technology, i.e., racetrack memory, enables an extremely high storage density and offers a faster-than-Moores law scaling path. Unorthodox new memory hierarchies are necessary to minimize the impact of pseudo-sequential accesses of racetrack memory.
Refined Metallicity Indices for M Dwarfs Using the SLoWPoKES Catalog of Wide, Low-mass Binaries (2011)

We report the results from spectroscopic observations of 113 ultra-wide, low-mass binary systems, composed largely of M0--M3 dwarfs, from the SLoWPoKES catalog of common proper motion pairs identified in the Sloan Digital Sky Survey. Radial velocities of each binary member were used to confirm that they are co-moving and, consequently, to further validate the high fidelity of the SLoWPoKES catalog. Ten stars appear to be spectroscopic binaries based on broad or split spectral features, supporting previous findings that wide binaries are likely to be hierarchical systems. We measured the Hα equivalent width of the stars in our sample and found that components of 81% of the observed pairs has similar Hα levels. The difference in Hα equivalent width amongst components with similar masses was smaller than the range of Hα variability for individual objects. We confirm that the Lepine et al. ζ(CaH2+CaH3, TiO5) index traces iso-metallicity loci for most of our sample of M dwarfs. However, we find a small systematic bias in ζ, especially in the early-type M dwarfs. We use our sample to recalibrate the definition of ζ. While representing a small change in the definition, the new ζ is a significantly better predictor of iso-metallicity for the higher mass M dwarfs.
The basis of the placement approach: vocational evaluation (2017)

In choosing an appropriate placement model for a client with a traumatic brain injury (TBI), a practical first step is generally vocational evaluation or assessment. Without some type of uniform vocational goal-setting procedure, the choice of a placement approach or model can become left to chance. Several articles or chapters in the literature present an overview of the vocational evaluation process in traumatic brain injury rehabilitation. These include work by Fraser (1991)’ and Chan et al. (1991). 2 The current chapter reviews some of the core issues and describes categories of activity within the vocational evaluation process.
Homogeneous Isotropic Fluid Turbulence Simulated with the Lattice Vortex Tube Model (1992)

Fully developed turbulence is analised with the lattice model employing vortex tube representation which is introduced recently by the authors. Several characteric features observed in experiments and direct numeric integrations are reproduced. Not only Kolmogorov's inertial range is observed, but also several local probability distribution functions are obtained as well. Those of the local velocities are close to the Gaussian and exponential-like distributions appear in local vorticity, relative velocities and local velocity consisting of only higher wave number components. Coherent structure of vortex tubes is seen, too. Moreover required cpu-time and memory-size are very little comparing with the conventional pseudo-spectral method. keywords : fluid turbulence, vortex tube, lattice model, numerical technic.
Visualization-by-Sketching: An Artist's Interface for Creating Multivariate Time-Varying Data Visualizations (2015)

We present Visualization-by-Sketching, a direct-manipulation user interface for designing new data visualizations. The goals are twofold: First, make the process of creating real, animated, data-driven visualizations of complex information more accessible to artists, graphic designers, and other visual experts with traditional, non-technical training. Second, support and enhance the role of human creativity in visualization design, enabling visual experimentation and workflows similar to what is possible with traditional artistic media. The approach is to conceive of visualization design as a combination of processes that are already closely linked with visual creativity: sketching, digital painting, image editing, and reacting to exemplars. Rather than studying and tweaking low-level algorithms and their parameters, designers create new visualizations by painting directly on top of a digital data canvas, sketching data glyphs, and arranging and blending together multiple layers of animated 2D graphics. This requires new algorithms and techniques to interpret painterly user input relative to data "under" the canvas, balance artistic freedom with the need to produce accurate data visualizations, and interactively explore large (e.g., terabyte-sized) multivariate datasets. Results demonstrate a variety of multivariate data visualization techniques can be rapidly recreated using the interface. More importantly, results and feedback from artists support the potential for interfaces in this style to attract new, creative users to the challenging task of designing more effective data visualizations and to help these users stay "in the creative zone" as they work.
Gene expression profiling of peripheral blood leukocytes identifies potential novel biomarkers of chronic obstructive pulmonary disease in current and former smokers (2010)

These gene expression profiles represent potential biomarkers for COPD and may help increase mechanistic understanding of the disease.
SID-2 negatively regulates development likely independent of nutritional dsRNA uptake (2020)

RNA interference (RNAi) is a gene regulatory mechanism based on RNA-RNA interaction conserved through eukaryotes. Surprisingly, many animals can take-up human-made double stranded RNA (dsRNA) from the environment to initiate RNAi suggesting a mechanism for dsRNA-based information exchange between organisms and their environment. However, no naturally occurring example has been identified since the discovery of the phenomenon 22 years ago. Therefore it remains enigmatic why animals are able to take up dsRNA. Here, we explore other possible functions by performing phenotypic studies of dsRNA uptake deficient <i>sid-2</i> mutants in <i>Caenorhabditis elegans</i>. We find that SID-2 does not have a nutritional role in feeding experiments using genetic sensitized mutants. Furthermore, we use robot assisted imaging to show that <i>sid-2</i> mutants accelerate growth rate and, by maternal contribution, body length at hatching. Finally, we perform transcriptome and lipidome analysis showing that <i>sid-2</i> has no effect on energy storage lipids, but affects signalling lipids and the embryo transcriptome. Overall, these results suggest that <i>sid-2</i> has mild effects on development and is unlikely functioning in the nutritional uptake of dsRNA. These findings broaden our understanding of the biological role of SID-2 and motivate studies identifying the role of environmental dsRNA uptake.
A Diverse Repertoire of Exopolysaccharide Biosynthesis Gene Clusters in Lactobacillus Revealed by Comparative Analysis in 106 Sequenced Genomes (2019)

Production of exopolysaccharides (EPS) is one of the unique features of <i>Lactobacillus</i> genus. EPS not only have many physiological roles such as in stress tolerance, quorum sensing and biofilm formation, but also have numerous applications in the food and pharmaceutical industries. In this study, we identified and compared EPS biosynthesis gene clusters in 106 sequenced <i>Lactobacillus</i> genomes representing 27 species. Of the 146 identified clusters, only 41 showed the typical generic organization of genes as reported earlier. Hierarchical clustering showed highly varied nature of the clusters in terms of the gene composition; nonetheless, habitat-wise grouping was observed for the gene clusters from host-adapted and nomadic strains. Of the core genes required for EPS biosynthesis, <i>epsA</i>, <i>B</i>, <i>C</i>, <i>D</i> and <i>E</i> showed higher conservation, whereas <i>gt</i>, <i>wzx</i> and <i>wzy</i> showed high variability in terms of the number and composition of the protein families. Analysis of the distribution pattern of the protein families indicated a higher proportion of mutually exclusive families in clusters from host-adapted and nomadic strains, whereas those from the free-living group had very few unique families. Taken together, this analysis highlights high variability in the EPS gene clusters amongst <i>Lactobacillus</i> with some of their properties correlated to the habitats.
Eleven-Year Outcomes From an Integrated Residency Program to Train Research Psychiatrists (2013)

In 2000, to address the critical shortage of research psychiatrists, faculty in the Residency Training Program in General Adult Psychiatry at the University of California, San Francisco, School of Medicine developed and implemented a research resident training program (RRTP). In this article, the authors describe the program’s development process, including its organizational structure, eligibility criteria for residents, and core program elements, and they report 11 years of outcomes data. Notable RRTP components include research and career mentorship, individualized training plans, the integration of clinical and research experiences, protected research time, and research funding. From 2000 to 2011, the RRTP enrolled 48 residents. The authors’ primary outcome of interest in determining the success of the program was whether or not each RRTP resident entered a postdoctoral research fellowship after graduation. The authors found that more than 80% of graduates had matriculated to postdoctoral research fellowships, irrespective of their previous doctoral-level training in the basic or social sciences. The authors conclude that this flexible, individualized, and innovative training program for psychiatry residents was successful in facilitating the entry of participants into primary research careers, reasoning that it may serve as a model for other residency programs with similar goals. More widespread adoption of similar educational models may help to address the critical shortage of research psychiatrists.
Experimental Demonstration of DSP-Assisted Electrical Duobinary Optimization for High Speed PON 25+ Gbps Using 10 Gbps APD Receiver (2018)

We compare experimentally two variants of electrical duobinary using adaptive equalization for 25-40Gbps high-speed PON, showing the advantageous of designing an automatic digital signal processing receiver selecting the more appropriate adaptive equalization depending on available bandwidth and link dispersion.
Two-dimensional Magnetism in κ-(BEDT-TTF)2Cu[N(CN)2]Cl, a Spin-1/2 Heisenberg Antiferromagnet with Dzyaloshinskii–Moriya Interaction (2015)

The finite phase transition temperature, T-N, of quasi two-dimensional (2D) Heisenberg antiferromagnetic (AF) crystals results from in-plane anisotropy or coupling between layers. It is usually not known which is the determining factor when both are weak. We show by an electron spin resonance experiment that in the quasi 2D antiferromagnetic crystal,kappa-(BEDT-TTF)(2)Cu[N(CN)(2)] Cl, TN is determined by in-plane anisotropy while interlayer coupling plays a minor role. The compound has a large isotropic Heisenberg exchange interaction between sites with S = 1/2 spins. The Dzyaloshinskii-Moriya (DM) interaction is the main source of anisotropy, while in-plane anisotropy and the interlayer coupling are very weak. The external-field field-induced static and fluctuating AF magnetizations are independent in adjacent layers above the (zero-field) ordering temperature.
Human Non-Hodgkin's Lymphomas Overexpress a Wild-Type Form of p53 Which Is a Functional Transcriptional Activator of the Cyclin-Dependent Kinase Inhibitor p21 (1997)

A large fraction of non-Hodgkin's lymphomas (NHLs) accumulate a wild-type form of the p53 tumor suppressor protein at the nuclear level. In normal cells, p53 induction is associated with a temporary cell growth arrest at the G1-S boundary of the cell cycle. This activity of p53 as a G1 checkpoint molecule is strictly dependent on its ability to induce the transcription of the inhibitor of the cyclin dependent kinase, p21. To verify the functionality of the wild-type p53 protein accumulated in NHL cells, 70 cases were comparatively analyzed for p53 and p21 expression and status of the respective genes. Overexpression of the wt p53 protein was associated with the accumulation of p21, indicating that p53 is functional with respect to p21 induction in these tumors. The coaccumulation of p53 with Ki-67 antigen indicates that wt p53-positive cells and p21-positive cells, as well, are actively proliferative elements, supporting the notion that p53-induced, p21-mediated growth arrest is somehow overridden in NHL cells. No p21 mutation or particular allele variant was shown to correlate with p21 protein accumulation, thus excluding a role for p21 structural abnormalities. Taken together, our data suggest the existence in NHL of a peculiar mechanism of functional inactivation of the p53 G1 checkpoint pathway occurring downstream of the CDK inhibitor p21.
Shedding of dipeptidyl peptidase 4 is mediated by metalloproteases and up‐regulated by hypoxia in human adipocytes and smooth muscle cells (2014)

Dipeptidyl peptidase 4 is an important drug target for diabetes and a novel adipokine. However, it is unknown how soluble DPP4 (sDPP4) is cleaved from the cell membrane and released into the circulation. We show here that MMP1, MMP2 and MMP14 are involved in DPP4 shedding from human vascular smooth muscle cells (SMC) and MMP9 from adipocytes. Hypoxia increased DPP4 shedding from SMC which is associated with increased mRNA expression of MMP1. Our data suggest that constitutive as well as hypoxia-induced DPP4 shedding occurs due to a complex interplay between different MMPs in cell type-specific manner.
Design and experimental performance of a small centrifugal pump for liquid hydrogen (1960)

Radial-bladed centrifugal pumps for liquid hydrogen may be expected to utilize relatively large outlet-to inlet-diameter ratios and large numbers of splitter blades in order to avoid flow reversals along the blade surfaces.A 4-inch-diameter hydrogen pump was designed and experimentally investigated.tion adapted from a centrifugal-compressor design which, through an iterative procedure, resulted in passage and blade shapes, number and position of blades, and calculated velocities throughout the pump rotor passage.coefficient of 0.2, a pressure coefficient of 0.585, and an indicated hydraulic efficiency of about 0.65.for a small low-specific-speed pump rotor and is taken as an indication that the arbitrary area allowance made for desired velocity distributions is of the right order of magnitude and that reasonably good internal flow conditions were established.An unshrouded model of this pump rotor was also investigated.However, as might be expected when minimum allowable clearance is large compared to the height of the flow passage, a large reduction in performance was experienced compared with the shrouded-pump performance.The design utilized a stream-filament solu-A 4-inch-diameter shrouded pump rotor was operated at a flow This is a relatively good performance
The use of expanded microporous polytetrafluoroethylene for limb salvage: a preliminary report. (1976)

Initial laboratory and clinical evaluations of a new prosthetic material, expanded microporous polytetrafluoroethylene (PTFE), for small vessel replacement is promising and encourages further clinical trial. Frequently the autogenous saphenous vein is not available for bypass procedures, and alternative arterial substitutes have not proved reliable for replacement of small vessels. In this study, 15 patients with impending loss of limb and no available saphenous vein underwent revascularization of the lower extremity with expanded microporous PTFE grafts. Thirteen of 15 patients now demonstrate viable extremities with a resulting over-all early patency and limb salvage rate of 87 percent for this series. Follow-up ranges from one to 8 months. Seven patients had diabetes mellitus and eight had atherosclerotic heart disease. Nine grafts crossed the knee joint. In all patients arterial runoff was poor. Six patients had previous femoropopliteal bypasses, five with autogenous veins and one with Dacron velour. Two patients had multiple previous operations that failed, first with autogenous vein and later with fabric grafts. The current limb salvage and patency rate of 87 percent in high-risk patients suggests that expanded PTFE may be the prosthesis of choice when an autogenous vein is not available and possibly an equally good substitute when the venous autograft is available.
Detecting Cortical Surface Regions in Structural MR Data (2007)

We present a novel level-set method for evolving open surfaces embedded in three-dimensional volumes. We adapt the method for statistical detection and segmentation of cytoarchitectonic regions of the cortical ribbon (e.g., Brodmann areas). In addition, we incorporate an explicit interface appearance model which is oriented normal to the open surface, allowing one to model characteristics beyond voxel intensities and high gradients. We show that such models are well suited to detecting embedded cortical structures. Appearance models of the interface are used in two ways: firstly, to evolve an open surface in the normal direction for the purpose of detecting the location of the surface, and secondly, to evolve the boundary of the surface in a direction tangential to the surface in order to delineate the extent of a specific Brodmann area within the cortical ribbon. The utility of the method is demonstrated on a challenging ex-vivo structural MR dataset for detection of Brodmann area 17.
Supersonic Inlet-Torsional Cascade Flutter (1975)

Currently there is a dearth of fundamental dynamic aeroelastic cascade data with which to validate and/or indicate necessary refinements in mathematical models of such phenomena. This paper describes a unique supersonic inlet with a subsonic axial component, torsional flutter cascade experiment, wherein a computer controlled electromagnetic airfoil excitation system is used to simulate the fundamental time-dependent airfoil interaction, assure physical periodicity, and control the interblade phasing angle. Experimental data are presented which indicate the variation and significance of the cascade inlet Mach number, the stagger angle, and, in particular, the interblade phasing angle on the cascade dynamic torsional aeroelastic characteristics.
ChemInform Abstract: STRUCTURAL MODIFICATIONS OF ANGUIDIN AND ANTITUMOR ACTIVITIES OF ITS ANALOGS (1982)

Abstract Scirpentriol (I) reagiert mit Chloressigsäureanhydrid zu einem Gemisch der Verbindungen (II).
Conformational Behaviour of Comb‐Like Poly(4‐vinylpyridinium) Salts and their Complexes with Surfactants in Solution and on a Flat Surface (2007)

Abstract We synthesised P4VP bromides with octyl and dodecyl pendant groups; the bromide anions in these polymer salts were further substituted with dodecylsulfate or bis(2‐ethylhexylsuccinate) anions. Direct SFM visualisation of the original P4VP chains, of the macromolecular salts and of their complexes, showed that the attachment of the pendant groups and especially the complexation with the surfactants promotes stretching of the macromolecules while adsorbing on mica substrate. On the other hand, viscosimetry showed that in solution (chloroform) the comb‐like chains and their complexes with dodecylsulfate had more compact conformations than those of the original P4VP. The scaling exponents describing the correlation between the contour length and the end‐to‐end distance of the adsorbed macromolecules were found to be ca. 3/4, which is indicative of 2D self‐avoiding walk statistics. magnified image