gebhart/patrepeval huggingface dataset:
Blocking α 4 β 7 integrin binding to SIV does not improve virologic control (2019)

A study in nonhuman primates reported that infusions of an antibody against α<sub>4</sub>β<sub>7</sub> integrin, in combination with antiretroviral therapy, showed consistent, durable control of simian immunodeficiency virus (SIV) in rhesus macaques. The antibody used has pleiotropic effects, so we set out to gain insight into the underlying mechanism by comparing this treatment to treatment with non-neutralizing monoclonal antibodies against the SIV envelope glycoprotein that only block α<sub>4</sub>β<sub>7</sub> binding to SIV Env but have no other host-directed effects. Similar to the initial study, we used an attenuated strain of SIV containing a stop codon in <i>nef.</i> The study used 30 macaques that all began antiretroviral therapy and then were divided into five groups to receive different antibody treatments. Unlike the published report, we found no sustained virologic control by these treatments in vivo.
Observation and modelling of homogenous nucleation in Ge2Sb2Te5 mushroom cells during SET operation (2023)

The crystallization mode during the SET operation in the nanoscale GST-based mushroom cell has been studied. The nucleation process detected in TEM has been quantified by modelling.
Interactions between endothetial cells and leukocytes (1986)

We present evidence that specific receptors are utilized by neutrophils to control their interaction with endothelial cells at sites of acute inflammation and that these receptors are related if not identical to lymphocyte "homing receptors" for lymphoid tissue high endothelium. We speculate that such receptors play a fundamental but not exclusive role in controlling the extravasation and tissue localization of all bone marrow-derived nucleated cells. In addition, we emphasize the active role of endothelial cells in the process of lymphocyte migration and leukocyte extravasation. By the expression of as yet unidentified organ-specific determinants for lymphocyte recognition, endothelial cells control the exit of particular lymphocyte subsets into mucosal versus nonmucosal sites, thus helping to determine the unique features of mucosal versus nonmucosal immune responses. Furthermore, we argue that endothelial cells are exquisitely responsive to local immune reactivity and present evidence that specific lymphokines, including gamma-interferon, play an important role in inducing postcapillary venules to express differentiated features required for the support of lymphocyte traffic into lymphoid organs and into sites of chronic inflammation. Leukocytes, endothelial cells, and probably other tissue cell classes appear to interact at multiple levels by a variety of mechanisms to regulate the local extravasation of immune effector cells.
REDUCTION OF INTRAOCULAR PRESSURE AND GLAUCOMA PROGRESSION (2003)

Heijl, A; Leske, M C; Bengtsson, B; Hyman, L; Hussein, M for the Early Manifest Glaucoma Trial Group Author Information
Supplementary Experimental Methods from Real-time Genomic Characterization of Advanced Pancreatic Cancer to Enable Precision Medicine (2023)

&lt;p&gt;Supplementary Experimental Methods&lt;/p&gt;
Hydrocyclones as cell retention device for CHO perfusion processes in single‐use bioreactors (2020)

Abstract In this study, a hydrocyclone (HC) especially designed for mammalian cell separation was applied for the separation of Chinese hamster ovary cells. The effect of key features on the separation efficiency, such as type of pumphead in the peristaltic feed pump, use of an auxiliary pump to control the perfusate flow rate, and tubing size in the recirculation loop were evaluated in batch separation tests. Based on these preliminary batch tests, the HC was then integrated to 50‐L disposable bioreactor bags. Three perfusion runs were performed, including one where perfusion was started from a low‐viability late fed‐batch culture, and viability was restored. The successive runs allowed optimization of the HC‐bag configuration, and cultivations with 20–25 days duration at cell concentrations up to 50 × 10 6 cells/ml were performed. Separation efficiencies up to 96% were achieved at pressure drops up to 2.5 bar, with no issues of product retention. To our knowledge, this is the first report in literature of high cell densities obtained with a HC integrated to a disposable perfusion bioreactor.
Interaction of Burkholderia pseudomallei and Burkholderia thailandensis with human monocyte-derived dendritic cells (2012)

Burkholderia pseudomallei is the causative agent of melioidosis, a disease endemic in areas of South-East Asia and northern Australia, and is classed as a category B select agent by the Centers for Disease Control and Prevention (CDC). Factors that determine whether host infection is achieved or if disease is chronic or acute are unknown but the type of host immune response that is mounted is important. B. pseudomallei can replicate within macrophages, causing them to multinucleate. In light of the common lineage of macrophages with dendritic cells (DCs), and the role played by DCs in orchestration of the immune response, we investigated the interactions of a variety of B. pseudomallei and B. thailandensis strains with DCs. This study demonstrates that, in the majority of cases, infection of human monocyte-derived dendritic cells is dramatically decreased or cleared by 12 h post-infection, showing a lack of ability to replicate and survive within DCs. Additionally we have shown that B. pseudomallei activates DCs, as measured by cytokine secretion, and live bacteria are not required for activation.
Plasmonic resonances in nanostructured transparent conducting oxide films (2012)

Transparent conducting oxides (TCO) are emerging as possible alternative constituent materials to replace noble metals such as silver and gold for low-loss plasmonic and metamaterial (MMs) applications in the near infrared (NIR) regime. The optical characteristics of TCOs have been studied to evaluate the functionalities and potential of these materials as metal substitutes in plasmonic and MM devices, even apart from their usual use as electrode materials. However, patterning TCOs at the nanoscale, which is necessary for plasmonic and MM devices, is not well-studied. This paper investigates nanopatterning processes for TCOs, especially the lift-off technique with electron-beam lithography, and the realization of plasmonic nanostructures with TCOs. By employing the developed nanopatterning process, we fabricate 2D-periodic arrays of TCO nanodisks and characterize the material's plasmonic properties to evaluate the performance of TCOs as metal substitutes. Light-induced collective oscillations of the free electrons in the TCOs (bulk plasmons) and localized surface plasmon resonances are observed in the wavelength range from 1.6 to 2.1 micron. Well-defined resonance peaks are observed, which can be dramatically tuned by varying the amount of dopant and by thermally annealing the TCO nanodisks in nitrogen gas ambient while maintaining the low-loss properties.
Biosynthesis of Monomers for Plastics from Renewable Oils (2012)

Omega-hydroxyfatty acids are excellent monomers for synthesizing a unique family of polyethylene-like biobased plastics. However, ω-hydroxyfatty acids are difficult and expensive to prepare by traditional organic synthesis, precluding their use in commodity materials. Here we report the engineering of a strain of the diploid yeast Candida tropicalis to produce commercially viable yields of ω-hydroxyfatty acids. To develop the strain we identified and eliminated 16 genes encoding 6 cytochrome P450s, 4 fatty alcohol oxidases and 6 alcohol dehydrogenases from the C. tropicalis genome. We also show that fatty acids with different chain lengths and degrees of unsaturation can be more efficiently oxidized by expressing different P450s within this strain background. Biocatalysis using engineered Candida tropicalis is thus a potentially attractive biocatalytic platform for producing commodity chemicals from renewable resources.
Supplementary Method SM1 from Intraductal Transplantation Models of Human Pancreatic Ductal Adenocarcinoma Reveal Progressive Transition of Molecular Subtypes (2023)

&lt;p&gt;Method Used to Define the Thresholds for Fast- and Slow-Progressing IGO-Derived Tumors&lt;/p&gt;
Transcriptomic Analysis of Hepatitis B Infected Liver for Prediction of Hepatocellular Carcinoma Risk (2022)

Abstract Hepatocellular cancer (HCC) is a leading cause of cancer related mortality worldwide and chronic hepatitis B virus infection (CHB) has been a major risk factor for HCC development. Pathogenesis of HBV related HCC has been a major focus revealing the interplay of a multitude of intracellular signaling pathways, yet the precise mechanisms and their implementations to clinical practice remains to be elucidated. This study utilizes publicly available transcriptomic data from livers of CHB patients in order to identify a population with a higher-risk of malignant transformation. We thus identified a novel list of genes which can generate clear transcriptomic sub-groups among HBV infected livers. The GSEA of one of the groups, which we named “PCI-U”, showed increased expression of cell cycle related genes and enrichment of liver cancer gene-sets in GSEA analysis, in addition an increased level of M1 macrophages, T cell infiltration and inflammation. We suggest that patients with a PCI-U signature be followed closely, as we predict such patients might have a higher chance of malignant transformation.
Effect of 802.11 Adaptive Exponential Backoffs on the Fluidity of Downlink Flows in Mesh Networks (2008)

Efficient multi-hop traffic management is a need for successful Wireless Mesh Networks (WMNs) deployment. Using an analogy with fluid mechanism, we classify a flow as laminar if the packets flow smoothly from the Wired Access Point (WAP) over the mesh network, and as turbulent otherwise. We identify
Graph Convolutional Networks with EigenPooling (2019)

Graph neural networks, which generalize deep neural network models to graph structured data, have attracted increasing attention in recent years. They usually learn node representations by transforming, propagating and aggregating node features and have been proven to improve the performance of many graph related tasks such as node classification and link prediction. To apply graph neural networks for the graph classification task, approaches to generate the \textit{graph representation} from node representations are demanded. A common way is to globally combine the node representations. However, rich structural information is overlooked. Thus a hierarchical pooling procedure is desired to preserve the graph structure during the graph representation learning. There are some recent works on hierarchically learning graph representation analogous to the pooling step in conventional convolutional neural (CNN) networks. However, the local structural information is still largely neglected during the pooling process. In this paper, we introduce a pooling operator $\pooling$ based on graph Fourier transform, which can utilize the node features and local structures during the pooling process. We then design pooling layers based on the pooling operator, which are further combined with traditional GCN convolutional layers to form a graph neural network framework $\m$ for graph classification. Theoretical analysis is provided to understand $\pooling$ from both local and global perspectives. Experimental results of the graph classification task on $6$ commonly used benchmarks demonstrate the effectiveness of the proposed framework.
Contribution of Lipids, Phenolic Acids and Protein Rich Components to Emulsifying Properties of Corn Fibre gum and Acacia Gum (2011)

Corn fibre (CF), the most abundant low-valued co-product of the corn wet-milling process, contains a high percentage of a valuable arabinoxylan (AX), which, once isolated from the cell wall and purified, is also called corn fibre gum (CFG). The fibrous co-products from corn are prepared either by wet-milling or dry-milling. Corn fibre produced by the corn-wet milling industry is also called white fibre and it contains fibre fractions from the kernel's pericarp and endosperm. The fibres from pericarp and endosperm are also called “coarse” and “fine” fibres, respectively.
Target‐Specific Chitosan‐Based Nanoparticle Systems for Nucleic Acid Delivery (2012)

This chapter contains sections titled: Introduction Chitosan-Based Nanoparticle Delivery Systems Illustrative Examples of DNAVaccine Delivery Illustrative Examples of Nucleic Acid Delivery Systems for Cancer Therapy Illustrative Examples of Nucleic Acid Delivery Systems for Anti-Inflammatory Therapy Conclusions and Future Perspectives References
<title>Time-recursive computation and real-time parallel architectures, with application on the Modulated Lapped Transform</title> (1993)

In this paper, we establish an architectural framework for parallel time-recursive computation. We consider a class of linear operators that consists of the discrete time, time invariant, compactly supported, but otherwise arbitrary kernel functions. We specify the properties of the linear operators that can be implemented efficiently in a time-recursive way. Based on these properties, we develop a routine that produces a time-recursive architectural implementation for a given operator. This routine is instructive for the design of a CAD tool that will facilitate the architecture derivation. Using this background, we design an architecture for the Modulated Lapped Transform (commonly called Modified Discrete Cosine Transform), which has linear cost in operator counts.
Polymers at Interfaces Edited by G. J. Fleer, M. A. Cohen Stuart, and J. M. H. M. Scheutjens (Wageningen Agricultural University, The Netherlands) and T. Cosgrove and B. Vincent (University of Bristol, United Kingdom). Chapman & Hall: London. 1993. xviii + 502 pp. $112.50. ISBN 0-412-58160-4. (1996)

ADVERTISEMENT RETURN TO ISSUEPREVBook ReviewNEXTPolymers at Interfaces Edited by G. J. Fleer, M. A. Cohen Stuart, and J. M. H. M. Scheutjens (Wageningen Agricultural University, The Netherlands) and T. Cosgrove and B. Vincent (University of Bristol, United Kingdom). Chapman & Hall: London. 1993. xviii + 502 pp. $112.50. ISBN 0-412-58160-4.Harry J. PloehnView Author Information University of South CarolinaCite this: J. Am. Chem. Soc. 1996, 118, 1, 297–298Publication Date (Web):January 10, 1996Publication History Published online10 January 1996Published inissue 1 January 1996https://doi.org/10.1021/ja945120jCopyright © 1996 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views582Altmetric-Citations-LEARN 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 Read OnlinePDF (53 KB) Get e-AlertsSUBJECTS:Adsorption,Interfaces,Layers,Polymer solutions,Polymers Get e-Alerts
<title>Lens measurement in fundamental units of length and power</title> (1992)

A lens configuration called the limiting lens has been studied which describes the highest power, shortest focal length system for a given cylindrical volume. We consider here the classification and study of lenses which are constrained to fit into small packages in terms of how close the configurations come to the limiting lens.
Identification of a cell surface 105 kd protein (Aic-2 antigen) which binds interleukin-3 (1990)

A mouse interleukin-3 (IL-3)-binding molecule that is an essential constituent of the mouse IL-3 receptor complex was identified as a cell surface protein of Mr 105 kd. A rat monoclonal antibody, anti-Aic-2 IgM, recognized and immunoprecipitated a cell surface 105 kd protein (Aic-2 antigen). The antigen (Aic-2) and IL-3 receptor were co-down-regulated upon incubation of IL-3-dependent mouse IC2 cells with either anti-Aic-2 IgM or IL-3 at 37 degrees C, whereas anti-Aic-2 did not inhibit the binding of IL-3 to IC2 cells at 15 degrees C. The Aic-2 antigen and IL-3 receptor were co-distributed on various cell lines and cell types. IL-3 was shown to bind specifically to the Aic-2 antigen (Mr 105 kd) in the immunoprecipitated complex with anti-Aic-2. Chemically cross-linking of IL-3 to surface molecules of IC2 cells produced three types of complexes with Mr 95, 140, and 200-340 kd in SDS-PAGE, and pre-incubation with anti-Aic-2 IgM at 37 degrees C reduced the intensity of the three bands to the same degree. Moreover, anti-Aic-2 immunoprecipitated these three IL-3-cross-linked complexes, whereas the same monoclonal antibody recognized a single 105 kd molecule. Anti-Aic-2 IgM enhanced IL-3-dependent growth of IC2 cells though it did not promote proliferation of IC2 cells.
Hubbard Model Physics in Transition Metal Dichalcogenide Moiré Bands (2018)

Flexible long period moiré superlattices form in two-dimensional van der Waals crystals containing layers that differ slightly in lattice constant or orientation. In this Letter we show theoretically that isolated flat moiré bands described by generalized triangular lattice Hubbard models are present in twisted transition metal dichalcogenide heterobilayers. The hopping and interaction strength parameters of the Hubbard model can be tuned by varying the twist angle and the three-dimensional dielectric environment. When the flat moiré bands are partially filled, candidate many-body ground states at some special filling factors include spin-liquid states, quantum anomalous Hall insulators, and chiral d-wave superconductors.
Study of High-Ge-Content Si0.16Ge0.84Gate Stack by Low Pressure Oxidation (2018)

In this study, we employed low-pressure oxidation (LPO) to achieve a high-quality dielectric gate stack on high-Ge-content (HGC) Si0.16Ge0.84. According to X-ray photoelectron spectroscopy depth-profiling results, lowering the oxidation pressure can drive out-diffusion of Si atoms from the HGC SiGe surface, resulting in the suppression of GeOx formation. A nearly GeOx-free interfacial layer detected at an O2 pressure of 0.01 torr at 600°C was used. Consequently, the formation of stable SiOx resulted in the improvement of Dit and gate leakage current, which in accumulation (VFB−1V) was also considerably reduced with an equivalent oxide thickness of 1.5 nm. Finally, by applying the LPO process and optimized process conditions, the interface trap density (Dit) was reduced to 2 × 1012 eV−1cm−2.
Control of grain-boundary tunneling barriers in polycrystalline silicon (2002)

The effect of oxidation and annealing on the electrical properties of grain boundaries (GBs) in heavily doped polycrystalline silicon is characterized using bulk films and 30-nm-wide nanowires. Oxidation at 650–750 °C selectively oxidizes the GBs. Subsequent annealing at 1000 °C increases the associated potential barrier height and resistance. These observations can be explained by structural changes in the Si–O network at the GBs and the competition between surface oxygen diffusion and oxidation from the GBs in the crystalline grains. A combination of oxidation and annealing may provide a method that can better control the GB potential barriers.
Motion Estimation for Self-Driving Cars with a Generalized Camera (2013)

In this paper, we present a visual ego-motion estimation algorithm for a self-driving car equipped with a close-to-market multi-camera system. By modeling the multi-camera system as a generalized camera and applying the non-holonomic motion constraint of a car, we show that this leads to a novel 2-point minimal solution for the generalized essential matrix where the full relative motion including metric scale can be obtained. We provide the analytical solutions for the general case with at least one inter-camera correspondence and a special case with only intra-camera correspondences. We show that up to a maximum of 6 solutions exist for both cases. We identify the existence of degeneracy when the car undergoes straight motion in the special case with only intra-camera correspondences where the scale becomes unobservable and provide a practical alternative solution. Our formulation can be efficiently implemented within RANSAC for robust estimation. We verify the validity of our assumptions on the motion model by comparing our results on a large real-world dataset collected by a car equipped with 4 cameras with minimal overlapping field-of-views against the GPS/INS ground truth.
Prevention of Nitroprusside-Induced Cyanide Toxicity with Hydroxocobalamin (1978)

To investigate hydroxocobalamin's role in preventing cyanide intoxication from sodium nitroprusside, we studied two groups of patients. One group received nitroprusside alone, and the other received nitroprusside and hydroxocobalamin. Red-cell and plasma cyanide levels were 83.44 +/- 23.12 and 3.51 +/- 1.01 microgram per 100 ml after nitroprusside alone and were 33.18 +/- 17.29 and 2.18 +/- 0.65 microgram per 100 ml after nitroprusside plus hydroxocobalamin. Acidosis developed in patients with red-cell cyanide levels higher than 75 microgram per 100 ml. When hydroxocobalamin infusion was stopped before sodium nitroprusside infusion was discontinued, blood cyanide levels and base deficit increased in a manner similar to that in the untreated group. The dose of nitroprusside used in each group did not differ statistically. These data show that hydroxocobalamin prevents cyanide transfer from red cells and plasma to tissue after nitroprusside metabolism, and thereby prevents cyanide toxicity from large intravenous doses of the drug.
Starting at the Front End: Processes for New Renewables as Feedstocks of the Future (2006)

The need for additional "new renewables" and the potential contribution of molecular plant genetics to the breeding of new industrial crops producing such novel plant ingredients are being discussed. Efforts to add new chemical candidates derived from existing plant-based feedstocks have so far met with limited success. It therefore seems necessary not only to invest in new derivatization technologies utilizing existing plant-based raw materials, but also to genetically engineer crops capable of producing new renewables. Such renewables should be inexpensive, convertible into bulk derivatives and chemical intermediates, and the conversion processes, or at least their early generations, should be compatible with the established infrastructure of the chemical industry. Icon Genetics AG is developing 'switchable amplification' production platforms which overcome the problems of limited yield and biotoxicity of recombinant proteins and enzymes made in plants. These expression processes, magnICON and rublCON Seed, are also a promising way for metabolic engineering of new compounds in vegetative plant biomass or in seed. Both systems allow for separation of growth/biomass formation and plant propagation, on one side, and product formation, on the other. Ingredient synthesis can therefore, at least theoretically, reach its biological maximum. Host plant species can be chosen from among non-food crops that have a necessary pool of biochemical precursors for overproduction of the compound of interest.