gebhart/patrepeval huggingface dataset:
Meso-Scale Modeling of Polysaccharides in Plant Cell Walls: An Application to Translation of CBMs on the Cellulose Surface (2010)

A coarse-grained model and force field for simulating cellulose Iβ surface (1,0,0) was derived, in which each β-d-glucose unit is represented by three beads. The coarse-grained model can reproduce a stable cellulose (1,0,0) surface with an excellent agreement with an all-atom model. When used to study the interaction of the family 1 carbohydrate-binding module (CBM1) with this cellulose surface model, the CBM “opens” as in earlier atomistic simulations. This cellulose Iβ surface model produces simulations in which the CBM translates along a broken cellodextrin chain. This processive motion of the exoglucanase cellobiohydrolase I has long been suggested by experimental studies, but has never before been observed in computer simulations.
Diagnosis and treatment of dementia: 4. Approach to management of mild to moderate dementia (2008)

Much has been learned about the care of patients with mild to moderate dementia and the support of their primary caregivers. There is a pressing need for the development, and dissemination, of collaborative systems of care.
444. One-Time Gene Therapy to Prevent Peanut-Induced Anaphylaxis (2015)

Peanut allergy is a major public health problem that accounts for the majority of fatal food-induced anaphylactic reactions. There are no curative or preventative therapies. Therapy with omalizumab, a human anti-IgE monoclonal antibody, is transiently effective, but it must be administered parenterally, has a short half-life and is costly, thus it is challenging to use as a preventative for peanut allergy. To circumvent this challenge, we hypothesized that a one-time administration of an adeno-associated virus (AAV) gene transfer vector expressing the genetic sequence of omalizumab would provide persistent high circulating levels of anti-IgE sufficient to protect against repeated peanut exposure in the peanut allergic host. To assess this hypothesis, we created a humanized murine model of peanut allergy by reconstituting NOD-scid IL2rgnull mice with 3 x107 blood mononuclear cells (PBMC) derived from peanut allergic individuals or non-allergic controls and treating the mice with a non-human primate serotype rh.10 AAV expressing omalizumab (AAVrh.10anti-IgE) or control vector. Administration of a single dose (1×1011 gc) of AAVrh.10anti-IgE resulted in persistent high levels of anti-IgE in both wild type and humanized mouse models, with anti-IgE levels > 400 mg/ml at 6 wk and remained at similar levels to the last time point evaluated at 24 wk in wild type mice and levels above 220 mg/ml were achieved in NSG mice at wk 8. No anti-IgE was detected in serum from mice that received a non-relevant control vector or PBS alone. The humanized NOD-scid IL2rgnull mice were sensitized intraperitoneally with crude peanut extract (CPE) weekly for 4 wk and then challenged with CPE via oral gavage. Total serum human IgG, IgE and peanut-specific IgE were measured weekly. After challenge, allergic phenotype was assessed using an anaphylaxis score, histamine levels, rectal temperature and behavior. All NSG mice were successfully reconstituted with mononuclear cells as measured by persistent levels of human IgG. Mice treated with AAVrh.10anti-IgE had elevated total and peanut-specific IgE from day 28 onwards with total IgE lower in the AAVrh.10anti-IgE treated mice. Strikingly, after peanut challenge, AAVrh.10anti-IgE treated mice displayed a less severe allergic phenotype compared to those that received the control vector as defined by decreased histamine release, a lower anaphylaxis score, no drop in rectal temperature and suppressed ambulation. These results demonstrate that a single treatment with AAVrh.10anti-IgE provides long term protection from peanut allergen challenge in the peanut sensitized population, representing a paradigm shift in current therapeutic approaches.
Electromagnetic scattering from complex targets located in a four-layer medium model of a densely forested environment (2007)

In this paper, a simple four-layer configuration has been developed from the physical point of view for modeling a densely forested environment in the VHF/UHF band. In the model, the first layer, i.e. the uppermost layer, is air, where the incident and scattered fields are considered, while the canopies of the trees are modeled as a homogeneous medium in the second layer. The third layer is again air where the conducting and non-metallic objects are located. The fourth layer is a semi-infinite half space. Based on this, a MoM model has been developed for analysis of electromagnetic scattering from complex targets located in the third layer of the four-layer configuration.
Plasmonic Nanoassemblies: Tentacles Beat Satellites for Boosting Broadband NIR Plasmon Coupling Providing a Novel Candidate for SERS and Photothermal Therapy (2020)

Optical theranostic applications demand near-infrared (NIR) localized surface plasmon resonance (LSPR) and maximized electric field at nanosurfaces and nanojunctions, aiding diagnosis via Raman or optoacoustic imaging, and photothermal-based therapies. To this end, multiple permutations and combinations of plasmonic nanostructures and molecular "glues" or linkers are employed to obtain nanoassemblies, such as nanobranches and core-satellite morphologies. An advanced nanoassembly morphology comprising multiple linear tentacles anchored onto a spherical core is reported here. Importantly, this core-multi-tentacle-nanoassembly (CMT) benefits from numerous plasmonic interactions between multiple 5 nm gold nanoparticles (NPs) forming each tentacle as well as tentacle to core (15 nm) coupling. This results in an intense LSPR across the "biological optical window" of 650-1100 nm. It is shown that the combined interactions are responsible for the broadband LSPR and the intense electric field, otherwise not achievable with core-satellite morphologies. Further the sub 80 nm CMTs boosted NIR-surface-enhanced Raman scattering (SERS), with detection of SERS labels at 47 × 10<sup>-9</sup> m, as well as lower toxicity to noncancerous cell lines (human fibroblast Wi38) than observed for cancerous cell lines (human breast cancer MCF7), presents itself as an attractive candidate for use as biomedical theranostics agents.
Physical constrains and functional plasticity of cellulases: Linear scaling relationships for a heterogeneous enzyme reaction (2020)

Abstract Enzyme reactions, both in Nature and technical applications, commonly occur at the interface of immiscible phases. Nevertheless, stringent descriptions of interfacial enzyme catalysis remain sparse, and this is partly due to a shortage of coherent experimental data to guide and assess such work. We have produced and kinetically characterized 83 cellulases, which revealed a conspicuous linear free energy relationship (LFER) between the strength of substrate binding and the activation barrier. This common scaling occurred despite the investigated enzymes were structurally and mechanistically diverse. We suggest that the scaling reflects basic physical restrictions of the hydrolytic process and that evolutionary selection have condensed cellulase phenotypes near the line. One consequence of the LFER is that the activity of a cellulase can be estimated from substrate binding strength, irrespectively of structural and mechanistic details, and this appears promising for in silico selection and design within this industrially important group of enzymes. On a more general note, the LFER may identify a link to inorganic heterogeneous catalysis, and hence open for the implementation of approaches from this field within interfacial enzymology.
Dynamics of Tar Mat Formation Due to Asphaltenes Accumulation Under Gas Charge in Reservoirs (2015)

Abstract Tar mats in reservoirs can cause severe issues in oil production such as preventing aquifer pressure support and water sweep. Therefore, it's important to understand the fluid geodynamics that occur in geologic time that give rise to heavy oil gradients and to tar mats. A common event in reservoirs especially in deepwater is a late gas charge into an oil-filled reservoir. In this case, the gas can quickly migrate to the top of the reservoir through fault planes without mixing (except locally) with the existing reservoir fluid. This newly charge gas can then diffuse down into the oil column thereby significantly altering solution gas and dissolved asphaltene content and their gradients. In particular, an increase in solution gas causes a reduction of asphaltene solubility. This process can result in significant variations in asphaltene concentration throughout the column. Moreover, a density inversion can be created due to the combined effects of methane diffusion and diffusion and expulsion of asphaltenes. This results in convective flow of asphaltene-rich fluids which can yield large asphaltene concentrations and tar mats at the base of the oil column. In addition, rapid gas charge can overwhelm the ability of asphaltenes to migrate thereby leading to upstructure tar deposition. Both scenarios can be associated with Flow Assurance concerns over part or all of the field. In this paper, we discuss case studies that exhibit such potentially problematic fluid columns. Simulated cases are also modeled to provide guidance for understanding the fluid geodynamics. The ability to model density inversion and asphaltenes gravity currents is seen to help significantly in understanding of reservoir fluids dynamics.
On scheduling atomic and composite continuous media objects (2002)

In multiuser multimedia information systems (e.g., movie-on-demand, digital-editing), scheduling the retrievals of continuous media objects becomes a challenging task. This is because of both intra and inter lobject time dependencies. Intraobject time dependency refers to the real-time display requirement of a continuous media object. Interobject time dependency is the temporal relationships defined among multiple continuous media objects. In order to compose tailored multimedia presentations, a user might define complex time dependencies among multiple continuous media objects with various lengths and display bandwidths. Scheduling the retrieval tasks corresponding to the components of such a presentation in order to respect both inter and intra task time dependencies is the focus of this study. To tackle this task scheduling problem (CRS), we start with a simpler scheduling problem (ARS) where there is no inter task time dependency (e.g., movie-on-demand). Next, we investigate an augmented version of ARS (termed ARS/sup +/) where requests reserve displays in advance (e.g., reservation-based movie-on-demand). Finally, we extend our techniques proposed for ARS and ARS/sup +/ to address the CRS problem. We also provide formal definition of these scheduling problems and proof of their NP-hardness.
A MoTe2-based light-emitting diode and photodetector for silicon photonic integrated circuits. (2017)

One of the current challenges in photonics is developing high-speed, power-efficient, chip-integrated optical communications devices to address the interconnects bottleneck in high-speed computing systems. Silicon photonics has emerged as a leading architecture, in part because of the promise that many components, such as waveguides, couplers, interferometers and modulators, could be directly integrated on silicon-based processors. However, light sources and photodetectors present ongoing challenges. Common approaches for light sources include one or few off-chip or wafer-bonded lasers based on III-V materials, but recent system architecture studies show advantages for the use of many directly modulated light sources positioned at the transmitter location. The most advanced photodetectors in the silicon photonic process are based on germanium, but this requires additional germanium growth, which increases the system cost. The emerging two-dimensional transition-metal dichalcogenides (TMDs) offer a path for optical interconnect components that can be integrated with silicon photonics and complementary metal-oxide-semiconductors (CMOS) processing by back-end-of-the-line steps. Here, we demonstrate a silicon waveguide-integrated light source and photodetector based on a p-n junction of bilayer MoTe<sub>2</sub>, a TMD semiconductor with an infrared bandgap. This state-of-the-art fabrication technology provides new opportunities for integrated optoelectronic systems.
Ion track reconstruction in 3D using alumina-based fluorescent nuclear track detectors (2013)

Fluorescent nuclear track detectors (FNTDs) based on Al2O3: C, Mg single crystal combined with confocal microscopy provide 3D information on ion tracks with a resolution only limited by light diffraction. FNTDs are also ideal substrates to be coated with cells to engineer cell-fluorescent ion track hybrid detectors (Cell-Fit-HD). This radiobiological tool enables a novel platform linking cell responses to physical dose deposition on a sub-cellular level in proton and heavy ion therapies. To achieve spatial correlation between single ion hits in the cell coating and its biological response the ion traversals have to be reconstructed in 3D using the depth information gained by the FNTD read-out. FNTDs were coated with a confluent human lung adenocarcinoma epithelial (A549) cell layer. Carbon ion irradiation of the hybrid detector was performed perpendicular and angular to the detector surface. In situ imaging of the fluorescently labeled cell layer and the FNTD was performed in a sequential read-out. Making use of the trajectory information provided by the FNTD the accuracy of 3D track reconstruction of single particles traversing the hybrid detector was studied. The accuracy is strongly influenced by the irradiation angle and therefore by complexity of the FNTD signal. Perpendicular irradiation results in highest accuracy with error of smaller than 0.10°. The ability of FNTD technology to provide accurate 3D ion track reconstruction makes it a powerful tool for radiobiological investigations in clinical ion beams, either being used as a substrate to be coated with living tissue or being implanted in vivo.
Recovery Analysis for Plug-and-Play Priors using the Restricted\n Eigenvalue Condition (2021)

The plug-and-play priors (PnP) and regularization by denoising (RED) methods\nhave become widely used for solving inverse problems by leveraging pre-trained\ndeep denoisers as image priors. While the empirical imaging performance and the\ntheoretical convergence properties of these algorithms have been widely\ninvestigated, their recovery properties have not previously been theoretically\nanalyzed. We address this gap by showing how to establish theoretical recovery\nguarantees for PnP/RED by assuming that the solution of these methods lies near\nthe fixed-points of a deep neural network. We also present numerical results\ncomparing the recovery performance of PnP/RED in compressive sensing against\nthat of recent compressive sensing algorithms based on generative models. Our\nnumerical results suggest that PnP with a pre-trained artifact removal network\nprovides significantly better results compared to the existing state-of-the-art\nmethods.\n
Effectiveness of peer detailing in a diarrhea program in Nigeria (2017)

Diarrhea causes more than 500,000 deaths of children younger than 5 years, globally, each year. A combination of oral rehydration salts (ORS) and zinc is regarded as the most effective treatment to prevent diarrhea-related deaths among children. We study the effectiveness of a program in Nigeria aimed at increasing usage of ORS and zinc. Peer detailers (educators) reinforce the benefits of the treatment to patent and proprietary medicine vendors (PPMVs), a main source of healthcare in the country. Two aspects of program effectiveness are analyzed: 1) PPMV knowledge that this combination is the most effective treatment and 2) PPMV inventory of ORS and zinc. Hypothesis tests reveal that the percentage of PPMVs with knowledge of the most effective treatment increases significantly in most of the tested Nigerian states after peer detailing. Surprisingly, no significant patterns were detected regarding the percentage of PPMVs with inventory of ORS and zinc. Logistic regression results suggest that PPMVs that were detailed have significantly higher odds ratios for both knowledge and inventory. We discuss our findings regarding the overall effectiveness of the program and the limitations of the study, as well as suggestions for future activities to support information dissemination.
A multi-gigahertz, Josephson flash A/D converter with a pipelined encoder using large-dynamic-range current-latch comparators (1991)

The design of a multigigahertz 4-b A/D converter with a pipelined encoder is presented. A wideband and large dynamic range comparator serves as basic building block for both the quantizer and the encoder, which simplifies the design. The design of the comparator and the building of the quantizer and the encoder with the comparator circuits are discussed. Simulation and initial test results are presented, and the possibility of adapting the design to high-T/sub c/ circuit is discussed.
Analysis and correction of bias induced by phase stepping jitter in grating-based X-ray phase-contrast imaging (2018)

Grating-based X-ray phase-contrast (gbPC) is an X-ray phase-contrast imaging method involving optical gratings that typically employs the Talbot self-imaging effect. X-ray phase contrast is known to provide significant benefits for biomedical imaging. To investigate these benefits for gbPC, a high-sensitivity gbPC micro-CT setup for small biological samples has been constructed. A gbPC projection measurement simultaneously retrieves the transmittance, differential-phase and dark-field modalities of a sample. Phase stepping, the most common gbPC acquisition technique, involves several acquisitions at different lateral positions of one of the gratings. The three modalities can then be retrieved by least-squares- or FFT-based methods. Unfortunately, increasing differential-phase sensitivity also leads to an increased magnitude of artifacts introduced during retrieval of the modalities from the phase-stepping data, which limits image quality. Most importantly, processing of phase-stepping data with incorrect stepping positions (i.e., spatial sampling jitter) can introduce artifacts to the modalities. Using data from the high-sensitivity gbPC setup, as well as simulations, we show that an artifact is introduced by the jitter which is correlated with the phase of the stepping curve. We present a theoretical explanation for this correlation by introducing small deviations to an equidistant sampling of a stepping curve and approximating the effect on the calculation of the three gbPC modalities with a first-order Taylor approximation. Finally, we present an algorithm for the detection and removal of these artifacts that exploits these correlations. We show that this algorithm is able to eliminate these artifacts without degrading true image information.
Intravascular parasympathetic cardiac nerve stimulation prevents ventricular arrhythmias during acute myocardial ischemia (2005)

The IPS suppressed ventricular arrhythmias during acute ischemia mainly through its bradycardiac effect.
Pigment Analysis Using Techniques from the Field of Materials Science – a Contribution to the Restoration of the “Frankfurt Kitchen” (2021)

Abstract For the chemical and structural analysis of paint pigments from a historic “Frankfurt Kitchen”, a correlative approach was employed, using optical microscopy, scanning electron microscopy and energy dispersive X-ray spectroscopy complemented by X-ray phase analysis. This paper will demonstrate how metallographic techniques can be used for issues beyond our traditional area of activity.
Visual support for analyzing network traffic and intrusion detection events using TreeMap and graph representations (2009)

Network security depends heavily on automated Intrusion Detection Systems (IDS) to sense malicious activity. Unfortunately, IDS often deliver both too much raw information, and an incomplete local picture, impeding accurate assessment of emerging threats. We propose a system to support analysis of IDS logs, that visually pivots large sets of Net-Flows. In particular, two visual representations of the flow data are compared: a TreeMap visualization of local network hosts, which are linked through hierarchical edge bundles with the external hosts, and a graph representation using a force-directed layout to visualize the structure of the host communication patterns. Three case studies demonstrate the capabilities of our tool to 1) analyze service usage in a managed network, 2) detect a distributed attack, and 3) investigate hosts in our network that communicate with suspect external IPs.
Trimming of Athermal Silicon Resonators (2012)

Thin photosensitive layer of As2S3 sandwiched in between a-Si core and negative thermo-optic polymer over-cladding enables trimming of athermal rings. Exposure to visible light can shift their resonances by 195GHz at trimming rates around 1GHz/min.
Image analysis-derived metrics of histomorphological complexity predicts prognosis and treatment response in stage II-III colon cancer (2016)

The complexity of tumor histomorphology reflects underlying tumor biology impacting on natural course and response to treatment. This study presents a method of computer-aided analysis of tissue sections, relying on multifractal (MF) analyses, of cytokeratin-stained tumor sections which quantitatively evaluates of the morphological complexity of the tumor-stroma interface. This approach was applied to colon cancer collection, from an adjuvant treatment randomized study. Metrics obtained with the method acted as independent markers for natural course of the disease, and for benefit of adjuvant treatment. Comparative analyses demonstrated that MF metrics out-performed standard histomorphological features such as tumor grade, budding and configuration of invasive front. Notably, the MF analyses-derived "α<sub>max</sub>" -metric constitutes the first response-predictive biomarker in stage II-III colon cancer showing significant interactions with treatment in analyses using a randomized trial-derived study population. Based on these results the method appears as an attractive and easy-to-implement tool for biomarker identification.
Techniques to encode and compress fault dictionaries (2003)

Dictionary encoding schemes have not addressed the cost of reconstructing the dictionary during fault location. We show that by modifying a previously proposed dictionary encoding scheme only small portions of the information need be reconstructed during fault location. This provides a mechanism to reduce the number of secondary accesses during fault location. For pass-fail dictionaries, we present a simplified encoding scheme that reduces both the secondary storage requirement as well as the number of secondary accesses. A novel dictionary structure, known as hybrid dictionaries, which retains the full resolution with respect to modeled faults is presented. Heuristics to compute such dictionaries, its usefulness and how such dictionaries can be encoded for quick information retrieval are discussed.