gebhart/patrepeval huggingface dataset:
Quantitative CT Color Mapping of the Arterial Enhancement Fraction of the Liver to Detect Hepatocellular Carcinoma (2009)

Quantitative color mapping of the AEF can increase the sensitivity and diagnostic performance of multiphasic multidetector CT for detecting HCC. Supplementamaterial:http://radiology.rsnajnls.org/cgi/content/full/250/2/425/DC1http://radiology.rsnajnls.org/cgi/content/full/250/2/425/DC2http://radiology.rsnajnls.org/cgi/content/full/250/2/425/DC3
Hydrocolloids (2004)

Cereals & Grains Association is a nonprofit organization dedicated to advancing the knowledge and understanding of cereal grain science through research leadership, education, superior technical service, and advocacy.
Safe Constraint Queries (2000)

We extend some of the classical characterization theorems of relational database theory---particularly those related to query safety---to the context where database elements come with fixed interpreted structure and where formulae over elements of that structure can be used in queries. We show that the addition of common interpreted functions, such as real addition and multiplication, to the relational calculus preserves important characterization theorems of the relational calculus and also preserves certain combinatorial properties of queries. Our main result of the first kind is that there is a syntactic characterization of the collection of safe queries over the relational calculus supplemented by a wide class of interpreted functions---a class that includes addition, multiplication, and exponentiation---and that this characterization gives us an interpreted analog of the concept of range-restricted query from the uninterpreted setting. Furthermore, our range-restricted queries are particularly intuitive for the relational calculus with real arithmetic and give a natural syntax for safe queries in the presence of polynomial functions. We use these characterizations to show that safety is decidable for Boolean combinations of conjunctive queries for a large class of interpreted structures. We show a dichotomy theorem that sets a polynomial bound on the growth of the output of a query that might refer to addition, multiplication, and exponentiation. We apply the above results for finite databases to get results on constraint databases representing potentially infinite objects. We start by getting syntactic characterizations of the queries on constraint databases that preserve geometric conditions in the constraint data model. We consider classes of convex polytopes, polyhedra, and compact semilinear sets, the latter corresponding to many spatial applications. We show how to give an effective syntax to safe queries and prove that for conjunctive queries the preservation properties are decidable.
<title>Analysis of defocused image data for 3D shape recovery using a regularization technique</title> (1997)

The reconstruction of three-dimensional (3D) information from defocused image data is formulated as an inverse-problem that is solved through a regularization technique. The technique is based on modeling the sensing of defocused images in a camera system using a three-dimensional (3D) point spread function (PSF). Many images are acquired at different levels of defocus. The difference (mean-square error) between this acquired image data and the estimated image data corresponding to an initial solution for 3D shape is minimized. The initial solution for 3D shape is obtained from a focus and defocus analysis approach. A regularization approach that uses a smoothness constraint is proposed to improve this initial solution iteratively. The performance of this approach is compared with two other approaches: (1) gradient descent based on planar surface patch approximation, and (2) a local error minimization based on a limited search. We exploit some constraints such as the positivity of image brightness unique to this problem in the optimization procedure. Our experiments show that the regularization approach performs better than the other two and that high accuracy is attainable with relatively moderate computation. Experimental results are demonstrated for geometric optics model of 3D PSF on simulated image data.
Targeting Heat Shock Response to Sensitize Cancer Cells to Proteasome and Hsp90 Inhibitors (2006)

Novel classes of anticancer drugs, including proteasome inhibitors and Hsp90 inhibitors, potently induce heat shock proteins (Hsps). Because Hsps show antiapoptotic activities, we suggested that suppression of such induction may sensitize cancer cells to these drugs. Here, we knocked out the major heat shock transcription factor HSF-1 in several cancer cell lines using small interfering RNA and showed that such cells, which can no longer induce Hsps in response to proteasome and Hsp90 inhibitors, become more sensitive to these drugs. Furthermore, we developed a high-throughput screen for small molecules that inhibit induction of Hsps. The first step was a cell-based screen for inhibitors of Hsps-mediated luciferase refolding followed by a counterscreen for toxicity. The second step was a direct testing for inhibition of Hsp induction by immunoblotting with anti-Hsp72 antibody. After screening of 20,000 compounds from several diversity libraries, we focused on a compound we called NZ28, which potently inhibited induction of Hsps by heat shock, proteasome, and Hsp90 inhibitors in a variety of cell lines, and showed no significant toxicity. After testing of a set of analogues of NZ28, we identified a structural element that was critical for the activity. We also identified another inhibitor of the Hsp induction that was practically nontoxic. This compound, which we called emunin, strongly sensitized myeloma cells to proteasome and Hsp90 inhibitors and prostate carcinoma cells to proteasome inhibitors. This work indicates that targeting the heat shock response may facilitate use of proteasome and Hsp90 inhibitors for cancer treatment.
Effect of polymer molecular weight on adsorption and suspension rheology (2016)

The adsorption of poly(acrylic acid) [PAA] on the surface of commercial ball clay was studied. The adsorption isotherm of PAAs with different molecular weights was determined at pH 6 and 9. The results showed that the amount of PAA adsorbed on clay was independent of molecular weight. Also, the adsorption amount was decreased with increased pH. However, the overall adsorption amount was lower than the range predicted by a model based upon the mineralogy of kaolinite. A kinetic study of PAA adsorption presented plausible displacement of initially adsorbed PAA. PAA adsorption on clay particles decreased the viscosity of suspensions. Clay suspensions showed the minimum viscosity with a sufficient coverage of particles with PAA necessary for stable suspensions. Optimum chain length of PAA was revealed for effective dispersion.
Energy and mass distributions of impact ejecta blankets on the moon and Mercury (1978)

The distribution of the mass and energy of the ejecta from the impact of gabbroic anorthosite objects at 7 .5, 15, and 30 km/sec. on a half-space of similar material is described for planetary objects having the mass and radius of the moon and Mercury. For impact flows for which the peak stresses have decayed to a few kilobars, both the resulting mass and total energy distribution per unit area, S, decrease with radius, R, more slowly than the - 3 power of the radius, and the formula of the form: /n_(10)S = A + B /n_(10)R + C(/n^(10)R)^2 always displays a negative sign for the constant, C. The value of C is more negative for ejecta distributions on Mercury versus the moon. A newly recognized feature of the ejecta cloud is the near constancy with range of the ratio of internal energy to kinetic energy of ~1.1 to ~3 for material launched within a few shock transit times of the meteorite, whereas at times corresponding to many shock transit times in the meteorite this ratio exceeds ~10 when R ≥ l0^4 cm. Calculated "stratigraphic" sections indicate characteristics such that&#13;\nsuch units might be recognized in Apollo drill core on the basis of shock metamorphic zoning. The initial fast ejecta which arrives at great distances from the impact zone is lightly shocked, and largely represents target material which was near or at the free surface. Where resolved, this layer is overlain by a 5 to 10 times thicker, more heavily shocked ejecta layer. The latter is again overlain by a layer of lightly shocked material. The latter thickens rapidly toward the crater.
Ramucirumab and irinotecan in patients with previously treated gastroesophageal adenocarcinoma: Final analysis of a phase II trial. (2022)

284 Background: Ramucirumab, a humanized monoclonal antibody targeting VEGFR2, is used for treatment of metastatic gastroesophageal adenocarcinoma after disease progression on first-line chemotherapy. Superior survival outcome is expected when combined with paclitaxel. However, many patients suffer from chemotherapy-induced peripheral neuropathy after oxaliplatin-containing first-line treatment and are unable to tolerate paclitaxel. Irinotecan has shown survival benefit as a single agent or in combination with other agents for treating gastroesophageal cancer, but has not been evaluated with ramucirumab. We hypothesized that the combination regimen of irinotecan and ramucirumab administered as second-line treatment for advanced gastroesophageal adenocarcinoma will be better tolerated than ramucirumab and paclitaxel with similar clinical efficacy. Methods: The primary objective of this multi-institutional, single-arm phase 2 clinical trial is to determine the progression-free survival (PFS) after disease progression on up to one line of cytotoxic chemotherapy. Secondary objectives include objective response rate, overall survival, time to progression, and clinical benefit; and to evaluate toxicity and tolerability. Patient-derived xenograft and organoid models generated in a subgroup of patients. Investigation of blood-based angiome profiling and cell-free DNA are planned. Patients received 8 mg/kg ramucirumab with 180 mg/m 2 irinotecan IV every 14 days. A sample of 40 achieves 85.7% power at a one-sided significance level of 5% to detect a median PFS of 4 months compared to historic control of 2.5 months assuming the accrual time of 12 months and additional follow-up of 12 months and using a one-sample log rank test. NCT03141034. Results: Forty patients were enrolled from four institutions from December 2017 through May 2021. All patients received platinum-based chemotherapy prior to enrollment, 8 patients had HER2 positive disease, and 6 patients had received an immune checkpoint inhibitor. As of September 2021, median follow up time was 7.7 months. Median PFS was 4.6 months (95% CI 2.7 – 5.4). Of 31 patients evaluable for response, 9 patients (29%) had objective responses (1 complete response, 8 partial responses) and 5 patients (16%) had stable disease greater than 6 months. Diarrhea, nausea, vomiting, and neutropenia were common adverse events; no G3/4 neuropathy was reported. Patient-derived organoid and xenograft models were generated from 9 patient samples, treated in vitro to correlate with each patient’s disease response. Conclusions: Ramucirumab and irinotecan appears to be effective and well-tolerated in patients with previously treated gastroesophageal adenocarcinoma. This regimen is now part of standard guidelines and could be a preferred option for patients after disease progression on first-line chemotherapy. Clinical trial information: NCT03141034.
Simultaneous Nitrification-Denitrification to Meet Low Effluent Nitrogen Limits: Modeling, Performance and Reliability (2010)

Simultaneous Nitrification-Denitrification to Meet Low Effluent Nitrogen Limits: Modeling, Performance and ReliabilitySimultaneous nitrification-denitrification (SND) has been referred to as a biological process for nitrogen removal where nitrification and denitrification occur concurrently in the same aerobic reactor. SND facilities, investigated in this study, have been shown to remove 80 to 96 percent nitrogen without additional carbon and alkalinity. Carbon availability and bulk dissolved oxygen (DO)...Author(s)Jose JimenezDerya DursunPeter DoldJohn BratbyJürg KellerDenny ParkerSourceProceedings of the Water Environment FederationSubjectSession 40: Nitrogen Removal TechnologiesDocument typeConference PaperPublisherWater Environment FederationPrint publication date Jan, 2010ISSN1938-6478SICI1938-6478(20100101)2010:15L.2404;1-DOI10.2175/193864710798158968Volume / Issue2010 / 15Content sourceWEFTECFirst / last page(s)2404 - 2421Copyright2010Word count197Subject keywordsnutrient removalnitrogen removalsimultaneous nitrification-denitrificationprocess simulation
Probabilistic model by Bayesian network for the prediction of antibody glycosylation in perfusion and fed‐batch cell cultures (2021)

Glycosylation is a critical quality attribute of therapeutic monoclonal antibodies (mAbs). The glycan pattern can have a large impact on the immunological functions, serum half-life and stability. The medium components and cultivation parameters are known to potentially influence the glycosylation profile. Mathematical modelling provides a strategy for rational design and control of the upstream bioprocess. However, the kinetic models usually contain a very large number of unknown parameters, which limit their practical applications. In this article, we consider the metabolic network of N-linked glycosylation as a Bayesian network (BN) and calculate the fluxes of the glycosylation process as joint probability using the culture parameters as inputs. The modelling approach is validated with data of different Chinese hamster ovary cell cultures in pseudo perfusion, perfusion, and fed batch cultures, all showing very good predictive capacities. In cases where a large number of cultivation parameters is available, it is shown here that principal components analysis can efficiently be employed for a dimension reduction of the inputs compared to Pearson correlation analysis and feature importance by decision tree. The present study demonstrates that BN model can be a powerful tool in upstream process and medium development for glycoprotein productions.
Graphene On Au-Coated SiO$_{x}$ Substrate: Its Core-Level Photoelectron Microspectroscopy Study (2012)

The core-level electronic structures of the exfoliated graphene sheets on a Au-coated SiOx substrate have been studied by synchrotron radiation photoelectron spectroscopy (SR-PES) on a micron-scale. The graphene was firstly demonstrated its visibility on the Au-coated SiOx substrate by micro-optical characterization, and then conducted into SR-PES study. Because of the elimination of charging effect, precise C 1s core-level characterization clearly shows graphitic and contaminated carbon states of graphene. Different levels of Au-coating-induced p-type doping on single- and double-layer graphene sheets were also examined in the C 1s core-level shift. The Au-coated SiOx substrate can be treated as a simple but high-throughput platform for in situ studying graphene under further hybridization by PES.
Study on Thermal Conductivity of Scale Deposits in Supercritical Pressure Boilers (1980)

本報告は超臨界圧ボイラ水壁管における内面スケールの熱伝導率を半円周加熱面を用いた超臨界圧水の管内強制対流条件下で測定したものである.スケール熱伝導率の算出は管外面熱流束およびスケールの円周方向厚さ分布を考慮した管壁温度分布解析に基づいた.その結果,従来明確にされていなかった超臨界圧ボイラ水壁管のスケール熱伝導率を流体圧力280ata,流体温度200～400℃の範囲で明らかにした.
Nonlinear Refractory Plasmonics with TiN Nanoantennas (2016)

TiN is a novel refractory plasmonic material which can sustain high temperatures and exhibits large optical nonlinearities. We present for the first time second harmonic spectroscopy of TiN nanoantenna arrays resonant at about 1000 nm.
Herpesviruses in the Activated Phosphatidylinositol-3-Kinase-δ Syndrome (2018)

The phosphatidylinositol-3-kinase (PI3K)/Akt pathway is important for multiple stages of herpesvirus replication including virus entry, replication, latency, and reactivation. Recently, patients with gain-of-function mutations in the p110δ-catalytic subunit of PI3K or in the p85-regulatory subunit of PI3K have been reported. These patients have constitutively active PI3K with hyperactivation of Akt. They present with lymphoproliferation and often have infections, particularly recurrent respiratory infections and/or severe virus infections. The most frequent virus infections are due to Epstein-Barr virus (EBV) and cytomegalovirus (CMV); patients often present with persistent EBV and/or CMV viremia, EBV lymphoproliferative disease, or CMV lymphadenitis. No patients have been reported with CMV pneumonia, colitis, or retinitis. Other herpesvirus infections have included herpes simplex pneumonia, recurrent zoster, and varicella after vaccination with the varicella vaccine. Additional viral infections have included adenovirus viremia, severe warts, and extensive Molluscum contagiosum virus infection. The increased susceptibility to virus infections in these patients is likely due to a reduced number of long-lived memory CD8 T cells and an increased number of terminally differentiated effector CD8 T cells.
The measurement of the piston velocity of a hydraulic actuator (1989)

The use of three types of transducers to measure the velocity of the piston shaft of a hydraulic actuator is investigated. The types of transducers are linear magnetic scale, magnetostrictive, and optical rotary encoder. Different methods of calculating the piston velocity from the position information are proposed, and the results of the test measurement are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Digital microfabrication of user‐defined 3D microstructures in cell‐laden hydrogels (2013)

Complex 3D interfacial arrangements of cells are found in several in vivo biosystems such as blood vasculature, renal glomeruli, and intestinal villi. Current tissue engineering techniques fail to develop suitable 3D microenvironments to evaluate the concurrent effects of complex topography and cell encapsulation. There is a need to develop new fabrication approaches that control cell density and distribution within complex 3D features. In this work, we present a dynamic projection printing process that allows rapid construction of complex 3D structures using custom-defined computer-aided-design (CAD) files. Gelatin-methacrylate (GelMA) constructs featuring user-defined spiral, pyramid, flower, and dome micro-geometries were fabricated with and without encapsulated cells. Encapsulated cells demonstrate good cell viability across all geometries both on the scaffold surface and internal to the structures. Cells respond to geometric cues individually as well as collectively throughout the larger-scale patterns. Time-lapse observations also reveal the dynamic nature of mechanical interactions between cells and micro-geometry. When compared to conventional cell-seeding, cell encapsulation within complex 3D patterned scaffolds provides long-term control over proliferation, cell morphology, and geometric guidance. Overall, this biofabrication technique offers a flexible platform to evaluate cell interactions with complex 3D micro-features, with the ability to scale-up towards high-throughput screening platforms.
"Move the couch where?" : developing an augmented reality multimodal interface (2006)

This paper describes an augmented reality (AR) multimodal interface that uses speech and paddle gestures for interaction. The application allows users to intuitively arrange virtual furniture in a virtual room using a combination of speech and gestures from a real paddle. Unlike other multimodal AR applications, the multimodal fusion is based on the combination of time-based and semantic techniques to disambiguate a users speech and gesture input. We describe our AR multimodal interface architecture and discuss how the multimodal inputs are semantically integrated into a single interpretation by considering the input time stamps, the object properties, and the user context.
128 A New Method to Evaluate the Biomechanical Properties of Skin in a Porcine Model (2008)

Aims: A method to test the axial and transverse tensile properties of skin was developed in order to improve our understanding of the mechanical behavior of skin, and how it changes with the scarring response. This experimental technique was used to investigate the bidirectional mechanics of skin in the juvenile Yorkshire pig model. Methods: Skin samples were taken upon sacrifice, and all subcutaneous tissue was carefully removed via dissection. Dumbbell-shaped specimens were obtained from the skin using a custom designed stainless steel punch, to provide consistent geometry, and to avoid stress concentrations that can result from specimen gripping. Samples were taken in the axial (cranial-caudal) and transverse (dorsal-ventral) directions. Specimens were secured in an INSTRON universal test machine with serrated soft tissue grips, elongated to a desired preload, subjected to a 10% elongation and held for a 4-min isometric period. They were then returned to the original length and failed in tension at constant velocity. Results: This method of sample preparation indicated high repeatability in specimen geometry, showing standard deviations of 2% and 3% in gauge length and width, respectively (N = 12). Furthermore, no slippage was observed at the skin/grip interface, and all failures occurred within the specimen gauge length. Conclusions: This technique shows great promise for evaluating the viscoelastic and failure properties of skin, scar tissue, and pathologic scarring. Combining this biomechanical method with our parallel studies in molecular biology and biochemistry can likely produce correlations between constituent material organization and the mechanical properties of the tissue, as well as provide valuable information for the design of bioengineered tissue constructs. Acknowledgments: Alberta Ingenuity Fund, CIHR, and NSERC
Thioredoxin‐related protein of 14 kDa as a modulator of redox signalling pathways (2018)

Thioredoxin-related protein of 14 kDa (TRP14; also named TXNDC17 for thioredoxin domain-containing protein 17) is a highly conserved and ubiquitously expressed oxidoreductase. It is expressed in parallel with thioredoxin 1 (Trx1, TXN; TXN1), an efficient substrate for the mammalian cytosolic selenoprotein thioredoxin reductase 1 (TrxR1; TXNRD1). However, TRP14, in sharp contrast to Trx1, cannot support the activities of ribonucleotide reductase, peroxiredoxins or methionine sulfoxide reductases, thus is unable to directly support cell proliferation or antioxidant defence through these pathways. However, TRP14 has been shown to efficiently reduce l-cystine, which thereby indirectly supports glutathione synthesis. TRP14 can also suppress NF-κB signalling, is functionally linked to STAT3 signalling, and can directly reactivate oxidized protein-tyrosine phosphatase PTP1B. Furthermore, TRP14 can efficiently reduce persulfidated or nitrosylated cysteine residues in many proteins, thereby having the capacity to modulate signalling through hydrogen sulfide or NO. Additional bioinformatics analyses and observations suggest further roles for TRP14; therefore, further studies of its functions are warranted. Collectively, the results available suggest that TRP14 is a member of the thioredoxin system dedicated to the control of cellular redox signalling pathways. LINKED ARTICLES: This article is part of a themed section on Chemical Biology of Reactive Sulfur Species. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v176.4/issuetoc.