gebhart/patrepeval huggingface dataset:
DNA‐Assisted Self‐Assembly of Pyrene Foldamers (2009)

The self-organization of oligopyrene foldamers is described. Bi- and tri-segmental oligomers composed of nucleotides and non-nucleosidic, achiral pyrene monomers form double-stranded helical structures, as shown by absorbance, fluorescence, and CD spectroscopy. The mixed nature of alternating aromatic and phosphate groups ensures water solubility which, in turn, favors folding of the aromatic units. Pyrene molecules also assemble though interstrand stacking interactions. Structural organization of the pyrene units is an intrinsic property of the oligoaryl part and takes place independently from the sequence of the attached DNA. Chirality transfer from DNA to the pyrene segment leads to formation of a double helix, in which neighboring pyrene units are, in the present case, twisted in a right-handed manner. Pyrene helicity is most pronounced in a bi-segmental chimera, in which a DNA stem is present only at one end of the pyrene section.
Detection of Schistosoma mansoni and Schistosoma haematobium DNA by Loop-Mediated Isothermal Amplification: Identification of Infected Snails from Early Prepatency (2010)

Monitoring post-control transmission of schistosomes by examining humans becomes less effective as infection rates among humans decrease. Molecular monitoring of prepatent schistosome infection in snails by the polymerase chain reaction (PCR) has been used for studying human-to-snail transmission, and snail prepatent infection rates were found to correspond to infection prevalence and average intensity in human populations contacting the sites studied. We have now developed loop-mediated isothermal amplification (LAMP) assays for identifying Schistosoma mansoni and S. haematobium to facilitate large-scale evaluation of post-intervention transmission potential. LAMP primers were designed based on the Sm1-7 and DraI repeated sequences of the corresponding schistosomes, and amplification by LAMP of these 121-basepair highly abundant sequences provided a detection sensitivity of 0.1 fg of genomic DNA. When these LAMP assays were applied for examining infected laboratory snails, it was possible to identify infection from the first day after exposure to miracidia. The potential advantages of these assays are discussed.
Prediction of Survival Among Patients Receiving Transarterial Chemoembolization for Hepatocellular Carcinoma: A Response‐Based Approach (2019)

A TACE-specific and extensively validated model based on routinely available clinical features and response after first TACE permitted patient-level prognostication.
C@PA: Computer-Aided Pattern Analysis to Predict Multitarget ABC Transporter Inhibitors (2021)

Based on literature reports of the last two decades, a computer-aided pattern analysis (C@PA) was implemented for the discovery of novel multitarget ABCB1 (P-gp), ABCC1 (MRP1), and ABCG2 (BCRP) inhibitors. C@PA included basic scaffold identification, substructure search and statistical distribution, as well as novel scaffold extraction to screen a large virtual compound library. Over 45,000 putative and novel broad-spectrum ABC transporter inhibitors were identified, from which 23 were purchased for biological evaluation. Our investigations revealed five novel lead molecules as triple ABCB1, ABCC1, and ABCG2 inhibitors. C@PA is the very first successful computational approach for the discovery of promiscuous ABC transporter inhibitors.
Phenamil, an amiloride analogue, inhibits differentiation of Friend murine erythroleukemic cells (1988)

Amiloride has been reported to inhibit Friend murine erythroleukemic (MEL) cell commitment to differentiate by inhibiting the MEL cell plasma membrane Na+-Ca2+ antiporter (R. L. Smith, I. G. Macara, R. Levenson, D. Housman, and L. Cantley. J. Biol. Chem. 257: 773-780, 1982). We therefore screened a series of amiloride analogues to determine whether a more potent and specific inhibitor of MEL cell differentiation could be found. In our experiments, as in those of Lubin (J. Cell. Physiol. 124: 539-544, 1985), amiloride itself did not inhibit MEL cell differentiation. However, we did find that the amiloride analogue phenamil reversibly inhibits dimethyl sulfoxide (DMSO)-induced MEL cell commitment to differentiate with a K1/2 of 2.5-5.0 microM (in plasma clot assay). At an extracellular concentration of 15 microM, phenamil inhibits commitment to differentiate by approximately 90% in the plasma clot assay while having a minimal effect on growth. Phenamil is not metabolized but is rapidly taken up by MEL cells. Phenamil was most effective as an inhibitor when present during the first 12 h of DMSO treatment, indicating that phenamil affects the early commitment process rather than later steps involved in hemoglobin synthesis. Phenamil does not, however, inhibit the early differentiation-induced decrease in [Na+]i and the concomitant drop in the Na+-K+ pump rate. A specific binding site for phenamil is suggested because some analogues in which the phenamil structure is slightly modified are unable to inhibit differentiation.
[Participation of apoptosis in renal amyloidosis]. (1998)

Renal amyloidosis shows symptoms of renal dysfunction due to the deposition of amyloid protein in the kidney. Recently, it was reported that apoptosis plays an important role in the pathogenesis of type-2 diabetes mellitus and Alzheimer's disease of which amyloid deposition is seen in the tissue. We investigated whether or not apoptosis and related factors are observed in renal amyloidosis. In situ nick end labeling (TUNEL) was performed in seven autopsied renal tissues with primary and secondary amyloidosis and 10 autopsied renal tissues without renal disease as the control. The number of TUNEL-positive cells was significantly increased in both the glomeruli and tubulus of the kidney with amyloidosis than in the control. Electron microscopic analysis was performed on one biopsied renal tissue with amyloidosis and six biopsied renal tissues with minor abnormalities as the control. Typical apoptotic cells were observed only in the former. Bax product, an inducer of apoptosis, and Bcl-2 protein, an inhibitor of apoptosis, were examined immunohistochemically in the seven autopsied renal tissues with amyloidosis and 10 autopsied control tissues. Bax was overexpressed in the tubulus and glomeruli of subjects with renal amyloidosis, compared to the normal controls. However, Bcl-2 protein was not detected in the glomeruli in any of the subjects examined. These results indicate that apoptotic cells are increased in number in renal amyloidosis and Bax overexpression may play an important role in this increase.
Stress-induced leakage current and trap generation in HfO2 thin films (2012)

International audience
ChemInform Abstract: Synthesis of Glaziovianin A: A Potent Antitumor Isoflavone. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Ross Operation for Bicuspid Aortic Valve Disease in Adults: is it a Valid Surgical Option? (2002)

Pre-existing larger diameters of the aortic and pulmonary annuli in the aortic insufficiency group combined with the significantly increased left ventricular end-diastolic diameters, may predispose these patients to significant dilatation of the unsupported aortic sinuses after a Ross operation. This dilatation does not, however, lead to increase in the autograft valve insufficiency at short-term follow-up if the aortic annulus and the distal ascending aorta are tailored to the size of the pulmonary autograft. Ross operation, employing freestanding aortic root replacement technique, may therefore be recommended in adult patients with bicuspid aortic valve disease with excellent short-term results.
Single-neuron models linking electrophysiology, morphology and transcriptomics across cortical cell types (2020)

Abstract Identifying the cell types constituting brain circuits is a fundamental question in neuroscience and motivates the generation of taxonomies based on electrophysiological, morphological and molecular single cell properties. Establishing the correspondence across data modalities and understanding the underlying principles has proven challenging. Bio-realistic computational models offer the ability to probe cause-and-effect and have historically been used to explore phenomena at the single-neuron level. Here we introduce a computational optimization workflow used for the generation and evaluation of more than 130 million single neuron models with active conductances. These models were based on 230 in vitro electrophysiological experiments followed by morphological reconstruction from the mouse visual cortex. We show that distinct ion channel conductance vectors exist that distinguish between major cortical classes with passive and h-channel conductances emerging as particularly important for classification. Next, using models of genetically defined classes, we show that differences in specific conductances predicted from the models reflect differences in gene expression in excitatory and inhibitory cell types as experimentally validated by single-cell RNA-sequencing. The differences in these conductances, in turn, explain many of the electrophysiological differences observed between cell types. Finally, we show the robustness of the herein generated single-cell models as representations and realizations of specific cell types in face of biological variability and optimization complexity. Our computational effort generated models that reconcile major single-cell data modalities that define cell types allowing for causal relationships to be examined. Highlights Generation and evaluation of more than 130 million single-cell models with active conductances along the reconstructed morphology faithfully recapitulate the electrophysiology of 230 in vitro experiments. Optimized ion channel conductances along the cellular morphology (‘all-active’) are characteristic of model complexity and offer enhanced biophysical realism. Ion channel conductance vectors of all-active models classify transcriptomically defined cell-types. Cell type differences in ion channel conductances predicted by the models correlate with experimentally measured single-cell gene expression differences in inhibitory (Pvalb, Sst, Htr3a) and excitatory (Nr5a1, Rbp4) classes. A set of ion channel conductances identified by comparing between cell type model populations explain electrophysiology differences between these types in simulations and brain slice experiments. All-active models recapitulate multimodal properties of excitatory and inhibitory cell types offering a systematic and causal way of linking differences between them.
Requirements Engineering for Large and Very Large Scale Systems Part I ‐ Processes and Tooling (2010)

Abstract Requirements engineering processes in the large are very different from those on small to medium size systems. Most texts on requirements engineering, for example tend to describe small or medium scale systems (up to about 5K requirements), or if the systems are large, describe the processes associated with product development and product lines. Industrial projects, however, start at 20K requirements and up. The creation of scalable processes that will support a large infrastructure project of the kind we are reading about in the headlines today (e.g. “shovel ready”) can be a daunting prospect. This tutorial will present some of the challenges associated with the requirements engineering of such large and very large projects, and describe how to setup processes and tooling to support such projects. This is part one of a two part tutorial. The morning session describes how to set up processes and tooling for very large industrial projects, typically dealing with 50 thousand or more requirements. The afternoon session describes the unique nature of requirements engineering processes for contract based projects. Either session may be taken independently, but the attendee will get the most out of the tutorial by attending both sessions.
Fabrication and evaluation of hybrid silica/polymer optical fibre sensors for large strain measurement (2009)

Silica-based optical fibre sensors are widely used in structural health monitoring systems for strain and deflection measurement. One drawback of silica-based optical fibre sensors is their low strain toughness. In general, silica-based optical fibre sensors can only reliably measure strains up to 2%. Recently, polymer optical fibre sensors have been investigated for large strain measurement. Because of their high optical losses, the length of the polymer optical fibres is limited to 100 m. In this paper, we present a novel economical technique to fabricate hybrid silica/polymer optical fibre sensors that are capable of measuring large strain. First, stress analysis of a surface-mounted optical fibre sensor is performed to understand the effect of mechanical properties on the load distribution between the optical fibre and the host structure. Next, the procedure for fabricating a tapered polymer sensing element between two silica optical fibres is explained. The experimental set-up and the components used in the fabrication process are described in detail. Test results of the fabricated silica/polymer optical fibre strain sensor are presented.
In Situ Hierarchical Strain Transfer From the Articular Cartilage Surface to the Chondrocyte Nucleus (2012)

Osteoarthritis (OA) is a disabling disease, commonly thought of as the “wear and tear” of articular cartilage, afflicting 27 million Americans [1]. Multiple (e.g. biomechanical and biochemical) factors [2] contribute to maintenance of healthy joints through chondrocyte and extracellular matrix interactions. Interestingly, volumetric contractions of nuclei exhibit a zonal dependence [3], suggesting that nuclear mechanics may play a key role in the maintenance of healthy tissue by mechanically-mediated pathways.
Molecular tracing of the emergence, adaptation, and transmission of hospital-associated methicillin-resistant Staphylococcus aureus (2012)

Hospital-associated infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are a global health burden dominated by a small number of bacterial clones. The pandemic EMRSA-16 clone (ST36-II) has been widespread in UK hospitals for 20 y, but its evolutionary origin and the molecular basis for its hospital association are unclear. We carried out a Bayesian phylogenetic reconstruction on the basis of the genome sequences of 87 S. aureus isolates including 60 EMRSA-16 and 27 additional clonal complex 30 (CC30) isolates, collected from patients in three continents over a 53-y period. The three major pandemic clones to originate from the CC30 lineage, including phage type 80/81, Southwest Pacific, and EMRSA-16, shared a most recent common ancestor that existed over 100 y ago, whereas the hospital-associated EMRSA-16 clone is estimated to have emerged about 35 y ago. Our CC30 genome-wide analysis revealed striking molecular correlates of hospital- or community-associated pandemics represented by mobile genetic elements and nonsynonymous mutations affecting antibiotic resistance and virulence. Importantly, phylogeographic analysis indicates that EMRSA-16 spread within the United Kingdom by transmission from hospitals in large population centers in London and Glasgow to regional health-care settings, implicating patient referrals as an important cause of nationwide transmission. Taken together, the high-resolution phylogenomic approach used resulted in a unique understanding of the emergence and transmission of a major MRSA clone and provided molecular correlates of its hospital adaptation. Similar approaches for hospital-associated clones of other bacterial pathogens may inform appropriate measures for controlling their intra- and interhospital spread.
Suppression of Plant Defenses by a Myzus persicae (Green Peach Aphid) Salivary Effector Protein (2014)

The complex interactions between aphids and their host plant are species-specific and involve multiple layers of recognition and defense. Aphid salivary proteins, which are released into the plant during phloem feeding, are a likely mediator of these interactions. In an approach to identify aphid effectors that facilitate feeding from host plants, eleven Myzus persicae (green peach aphid) salivary proteins and the GroEL protein of Buchnera aphidicola, a bacterial endosymbiont of this aphid species, were expressed transiently in Nicotiana tabacum (tobacco). Whereas two salivary proteins increased aphid reproduction, expression of three other aphid proteins and GroEL significantly decreased aphid reproduction on N. tabacum. These effects were recapitulated in stable transgenic Arabidopsis thaliana plants. Further experiments with A. thaliana expressing Mp55, a salivary protein that increased aphid reproduction, showed lower accumulation of 4-methoxyindol-3-ylmethylglucosinolate, callose and hydrogen peroxide in response to aphid feeding. Mp55-expressing plants also were more attractive for aphids in choice assays. Silencing Mp55 gene expression in M. persicae using RNA interference approaches reduced aphid reproduction on N. tabacum, A. thaliana, and N. benthamiana. Together, these results demonstrate a role for Mp55, a protein with as-yet-unknown molecular function, in the interaction of M. persicae with its host plants.
Rethinking large-scale Economic Modeling for Efficiency: Optimizations for GPU and Xeon Phi Clusters (2018)

We propose a massively parallelized and optimized framework to solve high-dimensional dynamic stochastic economic models on modern GPU-and KNL-based clusters. First, we introduce a novel approach for adaptive sparse grid index compression alongside a surplus matrix reordering, which significantly reduces the global memory throughput of the compute kernels and maps randomly accessed data onto cache or fast shared memory. Second, we fully vectorize the compute kernels for AVX, AVX2 and AVX512 CPUs, respectively. Third, we develop a hybrid cluster oriented work-preempting scheduler based on TBB, which evenly distributes the time iteration workload onto available CPU cores and accelerators. Numerical experiments on Cray XC40 KNL "Grand Tave" and on Cray XC50 "Piz Daint" systems at the Swiss National Supercomputer Centre (CSCS) show that our framework scales nicely to at least 4,096 compute nodes, resulting in an overall speedup of more than four orders of magnitude compared to a single, optimized CPU thread. As an economic application, we compute global solutions to an annually calibrated stochastic public finance model with sixteen discrete, stochastic states with unprecedented performance.
Depth controlled symmetric function fanin tree restructure (2013)

A symmetric-function fanin tree (SFFT) is a fanout-free cone of logic that computes a symmetric function such as AND, OR and XOR. These trees are usually created during logic synthesis, when there is no knowledge of the tree gate locations. Because of this, large SFFTs present a challenge to placement algorithms. The consequence is that the tree placements are generally far from optimal, leading to wiring congestion, excess buffering, and timing problems. [10] proposed a fanin-tree restructure algorithm to reduce the SFFT wirelength. However, [10] was based on Steiner trees and might cause serious timing problems due to the high Steiner tree depth. In this paper, we extend the SFFT tree identification algorithm to allow both positive and negative tree inputs. Contrary to the Steiner-tree based approach, we propose a new tree restructure flow to build SFFTs from bottom to top level by level at the physical design stage. The tree restructure algorithm is in a transaction mode so that only improved trees are accepted, and the new tree won't cause any placement legal issue. A new partitioning algorithm is proposed to serve for gate creation. In addition, various optimization techniques are developed to reduce tree wirelength On tested designs, the total tree wirelength is reduced by 31% with similar tree gates and tree depths.
Pro Android Augmented Reality (2012)

Augmented reality (AR) offers a live direct or indirect view of a physical, real-world environment, where the elements and surroundings are augmented by computer-generated sensory input such as graphi
Secure satellite communication using multi-photon tolerant quantum communication protocol (2015)

This paper proposes and analyzes the potential of a multi-photon tolerant quantum communication protocol to secure satellite communication. For securing satellite communication, quantum cryptography is the only known unconditionally secure method. A number of recent experiments have shown feasibility of satellite-aided global quantum key distribution (QKD) using different methods such as: Use of entangled photon pairs, decoy state methods, and entanglement swapping. The use of single photon in these methods restricts the distance and speed over which quantum cryptography can be applied. Contemporary quantum cryptography protocols like the BB84 and its variants suffer from the limitation of reaching the distances of only Low Earth Orbit (LEO) at the data rates of few kilobits per second. This makes it impossible to develop a general satellite-based secure global communication network using the existing protocols. The method proposed in this paper allows secure communication at the heights of the Medium Earth Orbit (MEO) and Geosynchronous Earth Orbit (GEO) satellites. The benefits of the proposed method are two-fold: First it enables the realization of a secure global communication network based on satellites and second it provides unconditional security for satellite networks at GEO heights. The multi-photon approach discussed in this paper ameliorates the distance and speed issues associated with quantum cryptography through the use of contemporary laser communication (lasercom) devices. This approach can be seen as a step ahead towards global quantum communication.
Microstructure and properties of high chromium cast irons: effect of heat treatments and alloying additions (2009)

Different combinations of critical and subcritical heat treatments variously modify the initial as cast microstructure of high chromium white cast irons leading to secondary carbide precipitation of different extent and nature. Destabilisation (critical heat treatment) of austenite at 970°C for 2·5 h followed by annealing (subcritical heat treatment) at 600°C for 13 h results in massive precipitation of M23C6 carbide particles along with spheroidised M7C3. The reversed order of heat treatments leads to extensive precipitation of M7C3 secondary carbide particles. Mo has a favouring effect on the hardness of the microstructures containing pearlite by limiting pearlite formation. The gradual increase in the alloying additions, C and Cr, increases the hardness of the materials at the different treatment states by inducing carbide precipitation. The increase in the Si content leads to the opposite effect by favouring pearlite formation.