gebhart/patrepeval huggingface dataset:
Transfer of long-chain fluorescent fatty acids between small and large unilamellar vesicles (1993)

Transfer of 12-(9-anthroyloxy)stearic acid (12AS) was measured between small unilamellar vesicles (SUV) and between large unilamellar vesicles (LUV), over a temperature range of 5-50 degrees C. The results of this study clearly establish the biexponential nature of the time dependence of the transfer in a variety of vesicle types and confirm our previous results using egg phosphatidylcholine (EPC) SUV at 25 degrees C (Storch & Kleinfeld, 1986). In our previous study we developed a kinetic model of the transfer process and concluded that the observed time dependence of the transfer of long-chain 12-(9-anthroyloxy) fatty acids (AOFA) was due to transbilayer flip-flop that was much slower than the rate at which the fatty acids (FA) move from the vesicle and into the surrounding aqueous phase (the off step). In the present study, experimental and theoretical advances have allowed us to examine, in detail, predictions of the kinetic model that critically depend upon the slow rate of flip-flop. The current results verify these predictions and demonstrate that slow AOFA flip-flop is rate limiting in at least three different vesicle systems and at all temperatures studied. Moreover, both flip-flop and the off rate constants were almost an order of magnitude smaller in EPC-LUV than in EPC-SUV. Flip-flop was found to be asymmetric (the rate constant for transfer from the inner to outer hemileaflet of the bilayer is approximately twice that from the outer to inner hemileaflet) in SUV but virtually symmetric in LUV. The temperature dependence of transfer was used to determine the thermodynamic activation potentials for the flip-flop and off rate constants.(ABSTRACT TRUNCATED AT 250 WORDS)
Recurrent chromosomal gains and heterogeneous driver mutations characterise papillary renal cancer evolution (2015)

Papillary renal cell carcinoma (pRCC) is an important subtype of kidney cancer with a problematic pathological classification and highly variable clinical behaviour. Here we sequence the genomes or exomes of 31 pRCCs, and in four tumours, multi-region sequencing is undertaken. We identify BAP1, SETD2, ARID2 and Nrf2 pathway genes (KEAP1, NHE2L2 and CUL3) as probable drivers, together with at least eight other possible drivers. However, only ~10% of tumours harbour detectable pathogenic changes in any one driver gene, and where present, the mutations are often predicted to be present within cancer sub-clones. We specifically detect parallel evolution of multiple SETD2 mutations within different sub-regions of the same tumour. By contrast, large copy number gains of chromosomes 7, 12, 16 and 17 are usually early, monoclonal changes in pRCC evolution. The predominance of large copy number variants as the major drivers for pRCC highlights an unusual mode of tumorigenesis that may challenge precision medicine approaches.
A multiplex implantable microdevice assay identifies synergistic combinations of cancer immunotherapies and conventional drugs (2022)

Systematically identifying synergistic combinations of targeted agents and immunotherapies for cancer treatments remains difficult. In this study, we integrated high-throughput and high-content techniques-an implantable microdevice to administer multiple drugs into different sites in tumors at nanodoses and multiplexed imaging of tumor microenvironmental states-to investigate the tumor cell and immunological response signatures to different treatment regimens. Using a mouse model of breast cancer, we identified effective combinations from among numerous agents within days. In vivo studies in three immunocompetent mammary carcinoma models demonstrated that the predicted combinations synergistically increased therapeutic efficacy. We identified at least five promising treatment strategies, of which the panobinostat, venetoclax and anti-CD40 triple therapy was the most effective in inducing complete tumor remission across models. Successful drug combinations increased spatial association of cancer stem cells with dendritic cells during immunogenic cell death, suggesting this as an important mechanism of action in long-term breast cancer control.
Using a single RGB frame for real time 3D hand pose estimation in the\n wild (2017)

We present a method for the real-time estimation of the full 3D pose of one\nor more human hands using a single commodity RGB camera. Recent work in the\narea has displayed impressive progress using RGBD input. However, since the\nintroduction of RGBD sensors, there has been little progress for the case of\nmonocular color input. We capitalize on the latest advancements of deep\nlearning, combining them with the power of generative hand pose estimation\ntechniques to achieve real-time monocular 3D hand pose estimation in\nunrestricted scenarios. More specifically, given an RGB image and the relevant\ncamera calibration information, we employ a state-of-the-art detector to\nlocalize hands. Given a crop of a hand in the image, we run the pretrained\nnetwork of OpenPose for hands to estimate the 2D location of hand joints.\nFinally, non-linear least-squares minimization fits a 3D model of the hand to\nthe estimated 2D joint positions, recovering the 3D hand pose. Extensive\nexperimental results provide comparison to the state of the art as well as\nqualitative assessment of the method in the wild.\n
A Network Analysis to Compare Biomarker Profiles in Patients with and without Diabetes Mellitus in Acute Heart Failure (2017)

Patients with AHF and diabetes, compared with those without diabetes, have distinct biomarker profiles. Network analysis suggests that cardiac remodelling, inflammation, and fibrosis are closely associated with each other in patients with diabetes. Furthermore, potassium levels may be sensitive to changes in renal function as reflected by the strong renal-potassium-glucose correlation. These findings were not seen among patients without diabetes and may suggest distinct pathophysiological processes among AHF patients with diabetes.
Introduction to Interactive Boundary Layer Theory (2002)

One of the major achievements in fluid mechanics in the last quarter of the twentieth century has been the development of an asymptotic description of perturbations to boundary layers known generally as 'triple deck theory'. These developments have had a major impact on our understanding of laminar fluid flow, particularly laminar separation. It is also true that the theory rests on three quarters of a century of development of boundary layer theory which involves analysis, experimentation and computation. All these parts go together, and to understand the triple deck it is necessary to understand which problems the triple deck resolves and which computational techniques have been applied. This book presents a unified account of the development of laminar boundary layer theory as a historical study together with a description of the application of the ideas of triple deck theory to flow past a plate, to separation from a cylinder and to flow in channels. The book is intended to provide a graduate level teaching resource as well as a mathematically oriented account for a general reader in applied mathematics, engineering, physics or scientific computation.
Evolution-Strategies-Driven Optimization on Secure and Reconfigurable Interconnection PUF Networks (2021)

Physical Unclonable Functions (PUFs) are known for their unclonability and light-weight design. However, several known issues with state-of-the-art PUF designs exist including vulnerability against machine learning attacks, low output randomness, and low reliability. To address these problems, we present a reconfigurable interconnected PUF network (IPN) design that significantly strengthens the security and unclonability of strong PUFs. While the IPN structure itself significantly increases the system complexity and nonlinearity, the reconfiguration mechanism remaps the input–output mapping before an attacker could collect sufficient challenge-response pairs (CRPs). We also propose using an evolution strategies (ES) algorithm to efficiently search for a network configuration that is capable of producing random and stable responses. The experimental results show that applying state-of-the-art machine learning attacks result in less than 53.19% accuracy for single-bit output prediction on a reconfigurable IPN with random configurations. We also show that, when applying configurations explored by our proposed ES method instead of random configurations, the output randomness is significantly improved by 220.8% and output stability by at least 22.62% in different variations of IPN.
Honeycomb like templates prepared from balsa wood (2015)

In the current study, we have used sodium chlorite and sodium hydroxide as extraction solutions, to remove lignin and hemicelluloses from the Balsa (Ochroma Lagopus) wood tissues, without damaging ...
Determination of a HLA II Promiscuous Peptide Cocktail as Potential Vaccine Against EBV Latency II Malignancies (2007)

The Epstein-Barr virus (EBV) is associated with several malignant diseases, which can be distinguished by their patterns of viral latent gene expression. The latency II program is limited to the expression of the nonimmunodominant antigens EBNA1, LMP1 and LMP2 and is seen in EBV-positive Hodgkin disease, nasopharyngeal carcinomas, and peripheral T/NK-cell lymphomas. CD4 T cells may play a crucial role in controlling these EBV latency II malignancies. In this study, we used the prediction software TEPITOPE to predict promiscuous major histocompatibility complex class II epitopes derived from the latency II antigens EBNA1, LMP1, and LMP2. The predicted peptides were then submitted to peptide-binding assays on HLA II purified molecules, which allowed the selection of 6 peptides (EBNA1: 3; LMP1: 1; and LMP2: 2) with a highly promiscuous capability of binding. This peptide cocktail was immunogenic in a model of HLA-DR1 transgenic mice, leading to a specific cellular and humoral TH1 response. The peptides were also recognized by human CD4 T cells from individuals expressing various HLA II genotypes. This promiscuous peptide cocktail could be immunogenic in the majority of the population and may be used as a peptide-based vaccine in EBV latency II malignancies.
Identification and characterization of a high-affinity interaction between v-Crk and tyrosine-phosphorylated paxillin in CT10-transformed fibroblasts. (1993)

The genome of avian sarcoma virus CT10 encodes a fusion protein in which viral Gag sequences are fused to cellular Crk sequences containing primarily Src homology 2 (SH2) and Src homology 3 (SH3) domains. Transformation of chicken embryo fibroblasts (CEF) with the Gag-Crk fusion protein results in the elevation of tyrosine phosphorylation on specific cellular proteins with molecular weights of 130,000, 110,000, and 70,000 (p130, p110, and p70, respectively), an event which has been correlated with cell transformation. In this study, we have identified the 70-kDa tyrosine-phosphorylated protein in CT10-transformed CEF (CT10-CEF) as paxillin, a cytoskeletal protein suggested to be important for organizing the focal adhesion. Tyrosine-phosphorylated paxillin was found to be complexed with v-Crk in vivo as evident from coimmunoprecipitation studies. Moreover, a bacterially expressed recombinant glutathione S-transferase (GST)-CrkSH2 fragment bound paxillin in vitro with a subnanomolar affinity, suggesting that the SH2 domain of v-Crk is sufficient for binding. Mapping of the sequence specificity of a GST-CrkSH2 fusion protein with a partially degenerate phosphopeptide library determined a motif consisting of pYDXP, and in competitive coprecipitation studies, an acetylated A(p)YDAPA hexapeptide was able to quantitatively inhibit the binding of GST-CrkSH2 to paxillin and p130, suggesting that it meets the minimal structural requirements necessary for the interaction of CrkSH2 with physiological targets. To investigate the mechanism by which v-Crk elevates the tyrosine phosphorylation of paxillin in vivo, we have treated normal CEF and CT10-CEF with sodium vanadate to inhibit protein tyrosine phosphatase activity. These data suggest that paxillin is involved in a highly dynamic kinase-phosphatase interplay in normal CEF and that v-Crk binding may interrupt this balance to increase the steady-state level of tyrosine phosphorylation. By contrast, the 130-kDa protein was not tyrosine phosphorylated upon vanadate treatment of normal CEF and only weakly affected in the CT10-CEF, suggesting that a different mechanism may be involved in its phosphorylation.
Resting State Functional Connectivity in Children: A New Paradigm. (2018)

Resting state functional connectivity (rsFC) can provide awindow into the neural architecture of functional networks inthe brain. Functional networks measured both during task andduring “resting” (task-absent) state are correlated withcognitive function, and much development of these networksoccurs between infancy and adulthood. However, rsFC studyin young children has been sparse, mainly due to a paucity ofchild-appropriate neural measures and behavioral paradigms.We present a new paradigm to measure rsFC in children,utilizing functional near-infrared spectroscopy (fNIRS) andFreeplay, a behavioral setup designed to approximate restingstate in children. Results suggest this paradigm is practicaland has good construct validity and test-retest reliability.
Scene-Graph Augmented Data-Driven Risk Assessment of Autonomous Vehicle Decisions (2020)

Despite impressive advancements in Autonomous Driving Systems (ADS), navigation in complex road conditions remains a challenging problem. There is considerable evidence that evaluating the subjective risk level of various decisions can improve ADS' safety in both normal and complex driving scenarios. However, existing deep learning-based methods often fail to model the relationships between traffic participants and can suffer when faced with complex real-world scenarios. Besides, these methods lack transferability and explainability. To address these limitations, we propose a novel data-driven approach that uses scene-graphs as intermediate representations. Our approach includes a Multi-Relation Graph Convolution Network, a Long-Short Term Memory Network, and attention layers for modeling the subjective risk of driving maneuvers. To train our model, we formulate this task as a supervised scene classification problem. We consider a typical use case to demonstrate our model's capabilities: lane changes. We show that our approach achieves a higher classification accuracy than the state-of-the-art approach on both large (96.4% vs. 91.2%) and small (91.8% vs. 71.2%) synthesized datasets, also illustrating that our approach can learn effectively even from smaller datasets. We also show that our model trained on a synthesized dataset achieves an average accuracy of 87.8% when tested on a real-world dataset compared to the 70.3% accuracy achieved by the state-of-the-art model trained on the same synthesized dataset, showing that our approach can more effectively transfer knowledge. Finally, we demonstrate that the use of spatial and temporal attention layers improves our model's performance by 2.7% and 0.7% respectively, and increases its explainability.
10,200 km 22/spl times/2/spl times/10 Gbit/s RZ-DQPSK dense WDM transmission without inline dispersion compensation through optical phase conjugation (2005)

Using optical phase conjugation with a polarization independent periodically-poled lithium-niobate subsystem, we demonstrate dense WDM 2/spl times/10 Gbit/s RZ-DQPSK transmission over 10,200 km of SSMF with a record accumulated dispersion exceeding 80,000 ps/nm.
Growth behavior of self-formed barrier at Cu–Mn∕SiO2 interface at 250–450°C (2007)

A diffusion barrier layer was self-formed at the interface between Cu–Mn alloy and tetraethylorthosilicate oxide layers at 250–450°C. No interdiffusion occurred across the self-formed barrier layer during annealing at these temperatures up to 100h. The growth of the barrier layer obeyed a logarithmic law and depended on manganese concentration. The barrier thickness could be controlled in the range of 2–8nm.
Characterization of micro-RNA Profile in the Blood of Patients with Marfan's Syndrome (2017)

The altered abundance level of different miRNAs in whole blood of MFS patients lays the ground to the development of novel diagnostic approaches with altered miRNAs levels associated with MFS with manifestations associated with cardiovascular diseases.
ChemInform Abstract: Palladium‐Catalyzed Coupling of 2‐Bromonaphthoquinones with Stannanes: A Concise Synthesis of Antibiotics WS 5995 A and C and Related Compounds. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Template-nonlithographic nanopatterning for site control growth of InGaN nanodots (2006)

A site-control nucleation and growth approach for dense InGaN nanodots has been demonstrated on the surface of GaN using a nonlithographic nanopatterning technique by metal organic chemical vapor deposition. Shallow nanopore arrays with a depth of ∼15nm are created by inductively coupled plasma etching in the GaN surface using anodic aluminum oxide films as etch masks. The nanopores are found to be the preferential sites for the InGaN nanodot formation. Uniform InGaN nanodot arrays with a density as high as 1010∕cm2 as defined by the nanopores in GaN were observed on the surface. A strong photoluminescence (PL) emission peak near 2.8eV is observed from the InGaN nanodots. The temperature dependence of PL shows the enhanced carrier localization with higher activation energy in the InGaN nanodots when compared to the InGaN thin layer grown simultaneously on the nonpatterned GaN surface.
Optical fibre diameter variations and their effect on backscatter loss measurements (1981)

Diameter variations in optical fibres are shown to affect back-scatter loss measurements by a mechanism which primarily involves attenuation of the backward travelling light. A simple model which predicts anticorrelated loss features when measured from opposite ends of the fibre is verified experimentally.
Building Selectivity for NO Sensing in a NOx Mixture with Sonochemically Prepared CuO Structures (2015)

Several technologies are available for decreasing nitrogen oxide (NOx) emissions from combustion sources, including selective catalytic reduction methods. In this process, ammonia reacts with nitric oxide (NO) and nitrogen dioxide (NO2). As the stoichiometry of the two reactions is different, electrochemical sensor systems that can distinguish between NO and NO2 in a mixture of these two gases are of interest. Since NO and NO2 can be brought to equilibrium, depending on the temperature and the surfaces that they are in contact with, the detection of NO and NO2 independently is a difficult problem and has not been solved to date. In this study, we explore a high surface area sonochemically prepared CuO as the resistive sensing medium. CuO is a poor catalyst for NOx equilibration, and requires temperatures of 500 C to bring about equilibration. Thus, at 300 C, NO and NO2 retain their levels after interaction with CuO surface. In addition, NO adsorbs more strongly on the CuO over NO2. Using these two concepts, we can detect NO with minimal interference from NO2, if the latter gas concentration does not exceed 20% in a NOx mixture over a range of 100–800 ppm. Since this range constitutes most of the range of total NOx concentrations in diesel and other lean burn engines, this sensor should find application in selective detection of NO in this combustion application. A limitation of this sensor is the interference with CO, but with combustion in excess air, this problem should be alleviated.
Optical Components for Remote Chemical Sensors based on IR Absorption Spectroscopy. (2013)

Infrared absorption spectroscopy provides very high sensitivity and specificity. Report on infrared fibers including chalcogenide photonic crystal fibers and progress on a novel Anti-Reflection Surface Structure (ARSS) technique for reducing surface reflection will be presented.
Chimpanzee and pig-tailed macaque iPSCs: Improved culture and generation of primate cross-species embryos (2022)

As our closest living relatives, non-human primates uniquely enable explorations of human health, disease, development, and evolution. Considerable effort has thus been devoted to generating induced pluripotent stem cells (iPSCs) from multiple non-human primate species. Here, we establish improved culture methods for chimpanzee (Pan troglodytes) and pig-tailed macaque (Macaca nemestrina) iPSCs. Such iPSCs spontaneously differentiate in conventional culture conditions, but can be readily propagated by inhibiting endogenous WNT signaling. As a unique functional test of these iPSCs, we injected them into the pre-implantation embryos of another non-human species, rhesus macaques (Macaca mulatta). Ectopic expression of gene BCL2 enhances the survival and proliferation of chimpanzee and pig-tailed macaque iPSCs within the pre-implantation embryo, although the identity and long-term contribution of the transplanted cells warrants further investigation. In summary, we disclose transcriptomic and proteomic data, cell lines, and cell culture resources that may be broadly enabling for non-human primate iPSCs research.
Square Tetrapalladium Sheet Sandwich Complexes: Cyclononatetraenyl as a Versatile Face-Capping Ligand (2009)

An unusual square tetrapalladium sheet sandwich complex, [Pd(4)(mu(4)-C(9)H(9))(mu(4)-C(8)H(8))][B(Ar(f))(4)] has been isolated and structurally characterized. X-ray structure analysis showed that the square palladium sheet is flanked by the nine-membered cyclononatetraenyl and eight-membered cyclooctatetraene ligands to form a square metal sheet molecular sandwich structure. The coordinative unsaturation of the complex was revealed by phosphine titration experiments.
Long-term outcomes of patients with light chain amyloidosis (AL) after renal transplantation with or without stem cell transplantation (2011)

KTx can be successfully performed in AL patients in complete hematologic response and meet the usual KTx selection criteria. Outcomes appear similar whether hematologic response was achieved with ASCT or by nonmyeloablative therapy.
VEGFR-1/Flt-1 inhibition increases angiogenesis and improves muscle function in a mouse model of Duchenne muscular dystrophy (2021)

Duchenne muscular dystrophy is characterized by structural degeneration of muscle, which is exacerbated by localized functional ischemia due to loss of nitric oxide synthase-induced vasodilation. Treatment strategies aimed at increasing vascular perfusion have been proposed. Toward this end, we have developed monoclonal antibodies (mAbs) that bind to the vascular endothelial growth factor (VEGF) receptor VEGFR-1 (Flt-1) and its soluble splice variant isoform (sFlt-1) leading to increased levels of free VEGF and proangiogenic signaling. The lead chimeric mAb, 21B3, had high affinity and specificity for both human and mouse sFlt-1 and inhibited VEGF binding to sFlt-1 in a competitive manner. Proof-of-concept studies in the <i>mdx</i> mouse model of Duchenne muscular dystrophy showed that intravenous administration of 21B3 led to elevated VEGF levels, increased vascularization and blood flow to muscles, and decreased fibrosis after 6-12 weeks of treatment. Greater muscle strength was also observed after 4 weeks of treatment. A humanized form of the mAb, 27H6, was engineered and demonstrated a comparable pharmacologic effect. Overall, administration of anti-Flt-1 mAbs in <i>mdx</i> mice inhibited the VEGF:Flt-1 interaction, promoted angiogenesis, and improved muscle function. These studies suggest a potential therapeutic benefit of Flt-1 inhibition for patients with Duchenne muscular dystrophy.