gebhart/patrepeval huggingface dataset:
Predicting deformation mechanisms in architected metamaterials using GNN (2022)

The present paradigm in design and modelling of lattice architected mechanical metamaterials is mostly limited to traditional numerical methods like finite element analysis. Recently, the use of machine learning and artificial intelligence techniques have become popular and here we extend these ideas to architected metamaterials. We show that truss based lattices have a natural resemblance to computational graphs which serve as an input for the rapidly emerging field of graph neural networks (GNNs). A dataset comprising thousands of such extremely complex lattices is trained using a GNN to predict the underlying dominant deformation mechanism viz. stretching and bending. The trained GNN achieves &gt; 90% accuracy on a previously unseen complex lattice dataset. Such graph-based learning of metamaterials has the capability to predict a range of properties, from elastic moduli to fracture toughness and promises AI driven discovery of emergent metamaterials possessing superlative properties.
Protein adsorption and platelet adhesion onto ion-containing polyurethanes (2007)

Protein adsorption and platelet adhesion properties of polyurethane biomaterials are important considerations for blood-contacting applications. Although the presence of ionic groups on the surface of biomaterials is believed to influence their blood response, their exact role is not known. The objective of this work was to study the protein adsorption and platelet adhesion properties of ion-containing polyurethane biomaterials. Thus, we prepared polyurethanes that contained ions either on the soft segment or hard segment and investigated their in vitro protein adsorption and platelet adhesion. The presence of ions increased the amount of adsorbed proteins and adhered platelets on the synthesized polyurethanes. Whereas albumin and lysozyme adsorption were independent of the location of the ions (soft vs. hard segments), fibrinogen adsorption was strongly dependent on the location of the ions. Platelet adhesion, on the other hand, was found to be less dependent on the location of the ions within the polyurethane structure. This is the first evidence to unequivocally demonstrate the exact role of ions on protein adsorption and platelet adhesion. Taken together, our study suggests that in the absence of known biocompatible chains such as polyethyleneoxide, ion-containing polyurethanes do not demonstrate improved blood compatibility. Therefore, we conclude that ion incorporation into polyurethanes may not be a viable approach to design polyurethane biomaterials for blood-contacting applications.
A prototype system for static and dynamic program understanding (2002)

A tool called PUNDIT (Program Understanding Investigation Tool) is described. It is a prototype intended to serve as a vehicle for exploring and testing ideas in the area of program understanding; it combines static analysis information with information collected at runtime. The architecture of PUNDIT is described, together with its two main components (the C source analyzer and a graphical user interface). Several of the views provided by the tool are explained, including a high-level structure chart, a dynamic call graph, a control flow graph animated during program execution, a type definition window, and others. By integrating static and dynamic information, the tool provides a more comprehensive understanding of a program as the first step to reengineering or maintaining the application that can be obtained by static analysis alone.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Topology of Euglena Chloroplast Protein Precursors within Endoplasmic Reticulum to Golgi to Chloroplast Transport Vesicles (1999)

Euglena chloroplast protein precursors are transported as integral membrane proteins from the endoplasmic reticulum (ER) to the Golgi apparatus prior to chloroplast localization. All Euglena chloroplast protein precursors have functionally similar bipartite presequences composed of an N-terminal signal peptide domain and a stromal targeting domain containing a hydrophobic region approximately 60 amino acids from the predicted signal peptidase cleavage site. Asparagine-linked glycosylation reporters and presequence deletion constructs of the precursor to the Euglena light-harvesting chlorophyll a/b-binding protein of photosystem II (pLHCPII) were used to identify presequence regions translocated into the ER lumen and stop transfer membrane anchor domains. An asparagine-linked glycosylation site present at amino acid 148 of pLHCPII near the N terminus of mature LHCPII was not glycosylated in vitro by canine microsomes while an asparagine-linked glycosylation site inserted at amino acid 40 was. The asparagine at amino acid 148 was glycosylated upon deletion of amino acids 46-146, which contain the stromal targeting domain, indicating that the hydrophobic region within this domain functions as a stop transfer membrane anchor sequence. Protease protection assays indicated that for all constructs, mature LHCPII was not translocated across the microsomal membrane. Taken together with the structural similarity of all Euglena presequences, these results demonstrate that chloroplast precursors are anchored within ER and Golgi transport vesicles by the stromal targeting domain hydrophobic region oriented with the presequence N terminus formed by signal peptidase cleavage in the vesicle lumen and the mature protein in the cytoplasm.
Diffusive and Drift Halide Perovskite Memristive Barristors as Nociceptive and Synaptic Emulators for Neuromorphic Computing (2021)

Abstract With the current research impetus on neuromorphic computing hardware, realizing efficient drift and diffusive memristors are considered critical milestones for the implementation of readout layers, selectors, and frameworks in deep learning and reservoir computing networks. Current demonstrations are predominantly limited to oxide insulators with a soft breakdown behavior. While organic ionotronic electrochemical materials offer an attractive alternative, their implementations thus far have been limited to features exploiting ionic drift a.k.a. drift memristor technology. Development of diffusive memristors with organic electrochemical materials is still at an early stage, and modulation of their switching dynamics remains unexplored. Here, halide perovskite (HP) memristive barristors (diodes with variable Schottky barriers) portraying tunable diffusive dynamics and ionic drift are proposed and experimentally demonstrated. An ion permissive poly(3,4‐ethylenedioxythiophene):polystyrene sulfonate interface that promotes diffusive kinetics and an ion source nickel oxide (NiO x ) interface that supports drift kinetics are identified to design diffusive and drift memristors, respectively, with methylammonuim lead bromide (CH 3 NH 3 PbBr 3 ) as the switching matrix. In line with the recent interest on developing artificial afferent nerves as information channels bridging sensors and artificial neural networks, these HP memristive barristors are fashioned as nociceptive and synaptic emulators for neuromorphic sensory signal computing.
Reactive oxygen species (ROS) generation as an underlying mechanism of inorganic phosphate (Pi)-induced mineralization of osteogenic cells (2020)

Reactive Oxygen Species (ROS) are a natural byproduct of oxygen metabolism. At physiological levels, ROS regulate multiple cellular processes like proliferation, migration, and differentiation. Increased levels of ROS are associated with pathological conditions, such as inflammation and vascular calcification, where they elicit cytotoxic effects. These contrasting outcomes of ROS have also been reported in osteogenic precursor cells. However, the role of ROS in committed osteogenic cells has not been investigated. Cytotoxic and physiologic effects have also been demonstrated for extracellular phosphate (P<sub>i</sub>). Specifically, in committed osteogenic cells P<sub>i</sub> stimulates their major function (mineralization), however in osteogenic precursors and endothelial cells P<sub>i</sub> cytotoxicity has been reported. Interestingly, P<sub>i</sub> cytotoxic effects have been associated with ROS production in the pathological vascular mineralization. In this study, we investigated a molecular mechanistic link between elevated P<sub>i</sub> and ROS production in the context of the mineralization function of committed osteogenic cells. Using committed osteogenic cells, 17IIA11 odontoblast-like cell and MLO-A5 osteoblast cell lines, we have unveil that P<sub>i</sub> enhances intracellular ROS production. Furthermore, using a combination of mineralization assays and gene expression analyses, we determined that P<sub>i</sub>-induced intracellular ROS supports the physiological mineralization process. In contrast, the exogenous ROS, provided in a form of H<sub>2</sub>O<sub>2</sub>, was detrimental for osteogenic cells. By comparing molecular signaling cascades induced by extracellular ROS and P<sub>i</sub>, we identified differences in signaling routes that determine physiologic versus toxic effect of ROS on osteogenic cells. Specifically, while both extracellular and P<sub>i</sub>-induced intracellular ROS utilize Erk1/2 signaling mediator, only extracellular ROS induces stress-activated mitogen-activated protein kinases P38 and JNK that are associated with cell death. In summary, our results uncovered a physiological role of ROS in the P<sub>i</sub>-induced mineralization through the molecular pathway that is distinct from ROS-induced cytotoxic effects.
Bidirectional Relaying via Network Coding: Design Algoriithm and Performance Evaluation (2013)

International audience
Inactivation of parvovirus B19 during STIM‐4 vapor heat treatment of three coagulation factor concentrates (2008)

The newly demonstrated effective inactivation of B19V by vapor heating, in contrast to the earlier used animal parvoviruses, results in significant B19V safety margins for STIM-4-treated coagulation factor concentrates.
Lay Bystanders' Perspectives on What Facilitates Cardiopulmonary Resuscitation and Use of Automated External Defibrillators in Real Cardiac Arrests (2017)

Several factors other than previous hands-on CPR training facilitate lay bystander instigation of CPR and AED use. The recognition and modification of these factors may increase lay bystander CPR rates and patient survival following an out-of-hospital cardiac arrest.
Reduction of Fuel Consumption on Hybrid Marine Power Plants by Strategic Loading With Energy Storage Devices (2016)

Recent advances in energy storage devices (ESDs) technology have enabled new guidance strategies for power generation and distribution on hybrid marine power plants, supported by new class regulations. In this paper, a new model to calculate the fuel saving and emission reduction potential is derived based on the ESD maximum charge/discharge rate, engine efficiency, and specific fuel oil consumption (SFOC) curve. Several cases were analyzed with generator disconnection and also without it. Spline approximation for the discrete fuel oil consumption curve is used for numerical solution and later optimized using the Karush–Kuhn–Tucker method. A second approach is proposed, using linear interpolation, reducing the optimization process computational time. It is shown that fuel savings can be increased and emissions reduced by charging and discharging the energy storage device. This is denoted as strategic loading according to the proposed model. The cases with highest potential for fuel saving are shown to be cases where generators are disconnected.
P4–252: Novel compounds active in the prevention of amyloid–beta accumulation, ROS production, and related neurotoxicity (2006)

Alzheimer's disease (AD) is a progressive neurodegenerative disease characterized by the accumulation of Aβ peptides which elicit oxidative stress and neuronal apoptosis. To identify genes abnormally spliced in brain from AD patients, to pinpoint unprecedented pathways and essential targets which impact APP processing, Aβ and ROS production and related neurotoxicity, to characterize small molecules as potential drugs for the treatment of AD. ExonHit Therapeutics has used its proprietary technology DATAS™. (1) Alternative splicing of the small GTP–binding protein Rac1 led to the expression of a constitutively active, ROS producing, variant in AD brain. ExonHit Therapeutics has developed several series of compounds acting as specific Rac1 inhibitors. EHT1864 series prevent ROS generation and Aβ production in vitro, acting at the level of the γ–secretase without affecting Notch processing. In vivo, EHT1864, the prototypic member of these series, efficiently crosses the BBB and exhibits a good bioavailability and tolerability in rodents, and significantly reduces Aβ levels in guinea pigs. Therefore, Aβ generation by γ–secretase is under the control of Rac1 in vivo (J Biol Chem. 2005 280(45):37516). EHT1864 series represent good candidates for inhibiting Aβ formation and ROS production in the AD brain. (2) The epsilon subunit of the GABAA receptor and several actors of the cAMP cascade were identified as specifically altered at the level of alternative splicing in AD. EHT0202, a specific regulator of epsilon subunit–containing GABAA receptors and a PDE–4 inhibitor, was selected as a potential drug for AD. EHT0202 has shown in vitro and in vivo (oral administration) neuroprotective properties against excitotoxic and oxidative stresses. EHT0202 reduces Aβ toxicity and redirects APP processing towards the non amyloidogenic pathway, potentially reducing Aβ production and plaques formation. In cognition models using old rats, EHT0202 improves attention, learning capabilities and cognitive behavior. In phase I trials (single / repeated dose), EHT0202 is well tolerated with no sedative or adverse memory effects. EHT0202 is a promising drug for Aβ–related neurodegenerative disorders with cognitive impairment. These data confirm the power of ExonHit Therapeutics' DATAS™ technology to rapidly identify pharmacologically relevant targets in complex diseases such as AD.
Treating Respiratory Viral Diseases with Chemically Modified, Second Generation Intranasal siRNAs (2008)

Chemically synthesized short interfering RNA (siRNA) of pre-determined sequence has ushered a new era in the application of RNA interference (RNAi) against viral genes. We have paid particular attention to respiratory viruses that wreak heavy morbidity and mortality worldwide. The clinically significant ones include respiratory syncytial virus (RSV), parainfluenza virus (PIV) and influenza virus. As the infection by these viruses is clinically restricted to the respiratory tissues, mainly the lungs, the logical route for the application of the siRNA was also the same, i.e., via the nasal route. Following the initial success of intranasal siRNA against RSV, second-generation siRNAs were made against the viral polymerase large subunit (L) that were chemically modified and screened for improved stability, activity and pharmacokinetics. 2'-O-methyl (2'-O-Me) and 2'-deoxy-2'-fluoro (2'-F) substitutions in the ribose ring were incorporated in different positions of the sense and antisense strands and the resultant siRNAs were tested with various transfection reagents intranasally against RSV. Based on these results, we propose the following consensus for designing intranasal antiviral siRNAs: (i) modified 19-27 nt long double-stranded siRNAs are functional in the lung, (ii) excessive 2'-OMe and 2'-F modifications in either or both strands of these siRNAs reduce efficacy, and (iii) limited modifications in the sense strand are beneficial, although their precise efficacy may be position-dependent.
Obesity and the Liver (2004)

Within the past decade, the growing epidemic of obesity has taken center stage as a clinical, scientific, and public health issue. More than 30% of adults in the United States have obesity, defined as a body mass index (BMI) of at least 30 kg/m2 (∼30 or more pounds overweight). This is double the rate of obesity as recently as thirty years ago. Obesity in children is growing even faster-3-fold in the past generation-suggesting that this epidemic will not abate in the foreseeable future.
Thermally assisted delayed fluorescence (TADF): fluorescence delayed is fluorescence denied (2020)

Thermally assisted delayed fluorescence (TADF) allows for efficient collection of both singlet and triplet excitons with both emitting through the singlet channel. TADF opens the door to photo- and electroluminescence efficiencies close to 100%.
Albumin causes increased myosin light chain kinase expression in astrocytes via p38 mitogen-activated protein kinase (2011)

Myosin light chain kinase (MLCK) plays an important role in the reorganization of the cytoskeleton, leading to disruption of vascular barrier integrity in multiple organs, including the blood-brain barrier (BBB), after traumatic brain injury (TBI). MLCK has been linked to transforming growth factor (TGF) and rho kinase signaling pathways, but the mechanisms regulating MLCK expression following TBI are not well understood. Albumin leaks into the brain parenchyma following TBI, activates glia, and has been linked to TGF-β receptor signaling. We investigated the role of albumin in the increase of MLCK in astrocytes and the signaling pathways involved in this increase. After midline closed-skull TBI in mice, there was a significant increase in MLCK-immunoreactive (IR) cells and albumin extravasation, which was prevented by treatment with the MLCK inhibitor ML-7. Using immunohistochemical methods, we identified the MLCK-IR cells as astrocytes. In primary astrocytes, exposure to albumin increased both isoforms of MLCK, 130 and 210. Inhibition of the TGF-β receptor partially prevented the albumin-induced increase in both isoforms, which was not prevented by inhibition of smad3. Inhibition of p38 MAPK, but not ERK, JNK, or rho kinase, also prevented this increase. These results are further evidence of a role of MLCK in the mechanisms of BBB compromise following TBI and identify astrocytes as a cell type, in addition to endothelium in the BBB, that expresses MLCK. These findings implicate albumin, acting through p38 MAPK, in a novel mechanism by which activation of MLCK following TBI may lead to compromise of the BBB.
Low-Profile Vertical Polarized Slotted Antenna for On-Road RFID-Enabled Intelligent Parking (2019)

A low-profile vertical polarized antenna is presented for radio frequency identification (RFID)-enabled intelligent parking system applications. In order to reduce the crosstalk between antennas and false detection of vehicles in the parking zone, a bidirectional antenna with low vertical obstacle is required by industry. To that end, a low-profile cavity-excited magnetic dipole-based antenna with vertical polarization is designed. Two vertical sides of the antenna are kept open for the easy access of the reader and powering components. In order to increase the polarization purity along the intended sides, a rectangular truncated ground plane is proved to be beneficial compared to a typical square shaped one. The overall structure of the on-road antenna over the ground plane is around 0.2 × 0.55 × 0.06 λ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> (λ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> is the free space wavelength of the center frequency). The design process and operating principle of the antenna are described in detail along with the effects of different parameters. The antenna is prototyped and measured. The antenna attains high reflection coefficient of -20 dB over 912-930 GHz covering the intended Australian ultrahigh-frequency (UHF) RFID band. The antenna demonstrates bidirectional radiation patterns having a maximum gain of 5 dBi over the required band with -20 dBi cross-polarization level. On-road measurements of the prototype show that the 3 dB beamwidth extends to ±90° elevation angles, which provides high read range while the tags embedded in the vehicle's license plate are in low elevation. The antenna has a rugged structure to sustain more than 10 years in regular road and traffic conditions. By meeting all the requirements, it has been proved to be an effective part of the on-road RFID-enabled intelligent parking system.
Rethinking childhood ependymoma: a retrospective, multi-center analysis reveals poor long-term overall survival (2017)

Ependymoma is the third most common brain tumor in children, but there is a paucity of large studies with more than 10 years of follow-up examining the long-term survival and recurrence patterns of this disease. We conducted a retrospective chart review of 103 pediatric patients with WHO Grades II/III intracranial ependymoma, who were treated at Dana-Farber/Boston Children's Cancer and Blood Disorders Center and Chicago's Ann & Robert H. Lurie Children's Hospital between 1985 and 2008, and an additional 360 ependymoma patients identified from the Surveillance Epidemiology and End Results (SEER) database. For the institutional cohort, we evaluated clinical and histopathological prognostic factors of overall survival (OS) and progression-free survival (PFS) using the log-rank test, and univariate and multivariate Cox proportional-hazards models. Overall survival rates were compared to those of the SEER cohort. Median follow-up time was 11 years. Ten-year OS and PFS were 50 ± 5% and 29 ± 5%, respectively. Findings were validated in the independent SEER cohort, with 10-year OS rates of 52 ± 3%. GTR and grade II pathology were associated with significantly improved OS. However, GTR was not curative for all children. Ten-year OS for patients treated with a GTR was 61 ± 7% and PFS was 36 ± 6%. Pathological examination confirmed most recurrent tumors to be ependymoma, and 74% occurred at the primary tumor site. Current treatment paradigms are not sufficient to provide long-term cure for children with ependymoma. Our findings highlight the urgent need to develop novel treatment approaches for this devastating disease.
Tinea capitis: ringworm of the scalp (2007)

The guideline tinea capitis, as passed by three German medical societies, is presented in the present study.
Confocal Laser Scanning Microscopic Observation of Polymer-Stabilized Blue Phase I (2007)

The structure of the polymer-stabilized blue phase I with a cubic structure of the order of optical wavelength was observed by the confocal laser scanning microscope. The spacing of a striped pattern observed in the (110) plane of the polymer-stabilized blue phase I was a couple of hundred nm, which agreed to the interval of the ordered double twisted cylinders estimated based on a well-known model of blue phase I with O8 symmetry.
Automated patient-ventilator interaction analysis during neurally adjusted non-invasive ventilation and pressure support ventilation in chronic obstructive pulmonary disease (2014)

In COPD patients, non-invasive NAVA improves patient-ventilator interaction compared to PSV, delivered either by a dedicated or ICU ventilator. The automated analysis of patient-ventilator interaction allowed for an objective detection of patient-ventilator interaction during NIV. In addition, we found that progressive mismatch between neural effort and pneumatic timing is associated with wasted efforts.