gebhart/patrepeval huggingface dataset:
In silico study of intrinsic dynamics of full-length apo-ACE2 and RBD-ACE2 complex (2021)

The key step for SARS-CoV-2 to infect human cells is the membrane fusion triggered by the binding of the viral extracellular Spike protein to the human extracellular receptor, the angiotensin-converting enzyme 2 (ACE2). Although the Cryo-electron microscopy (Cryo-EM) uncovered the static atomic details of ACE2 homodimers, there is still a lack of research on the kinetic and thermodynamic properties of these full-length structures. This information is helpful to understand and interpret the role of ACE2 in the cell entry of SARS-CoV-2. In order to obtain this information, we performed microsecond-scale conventional and accelerated molecular dynamics (MD) simulations of full-length all-atomic systems of the RBD-ACE2 complex, the normal and torsional conformations of the apo-ACE2 homodimer. The comparative analysis of these systems showed that there were differences in their allosteric signal pathways and motion trends. These results may be helpful to further explore the cell entry mechanism of SARS-CoV-2. Moreover, the binding free energy and hydrogen bond distribution analysis of RBD-ACE2 binding interface provided the binding motifs that may be critical to allosteric signal transmission and RBD binding. These multi-conformational binding motifs can be used as targets or templates for the inhibitor design of the cell entry of SARS-CoV-2.
The Power and Energy Storage Systems Toolbox -- PSTess v.1.0 (2021)

The Power and Energy Storage Systems Toolbox (PSTess) is a MATLAB-based computing package for dynamic simulation and analysis of utility-scale battery storage systems. This codebase is a fork of the Power Systems Toolbox Version 3.0, developed at Rensselaer Polytechnic Institute (RPI) and Cherry Tree Scientific Software. While PSTess shares a common lineage with PST, it is a substantially different application. As the name implies, the main distinguishing characteristic of PSTess is its ability to model inverter-based energy storage systems (ESS). The model that enables this is called ess.m, and it serves the dual role of representing ESS operational constraints and the generator/converter interface. With PSTess, the generator/converter interface is modeled as a controllable current source with the ability to modulate both active and reactive current. The model ess.m permits four-quadrant modulation, which allows it to represent a wide variety of inverter-based resources beyond energy storage when paired with an appropriate supplemental control model. Examples include utility-scale photovoltaic (PV) power plants, type 4 wind plants, and static synchronous compensators (STATCOM). This capability is especially useful for modeling hybrid plants that combine energy storage with renewable resources. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology &amp; Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525. SAND2021-8322 O
Effect of unfocused extracorporeal shockwave therapy on bone mineral content of twelve distal forearms of postmenopausal women: a clinical pilot study (2019)

Unfocused extracorporeal shockwave therapy is a safe treatment, but no increase in bone mass on the forearm was found at 0.3 mJ/mm<sup>2</sup> energy flux density. In this study, we were not able to demonstrate that a single treatment with unfocused shockwave therapy in unselected patients had any effect in terms of bone mineral density (BMD) or bone mineral content (BMC). A power analysis indicated that 174 patients per group are required to show an effect size of 0.3 with a power of 80%.
Remote phosphor LED modules for general illumination: toward 200 lm/W general lighting LED light sources (2008)

Phosphor converted white LEDs are becoming more and more attractive for general lighting applications because of the steadily increasing luminous efficacy numbers reported by LED-suppliers. Despite these high numbers, a further significant improvement step can be made when a low-to-medium brightness (&lt;500 kCd/m<sup>2</sup>) source is acceptable. The wall plug efficiency of a blue LED is generally better than that of a conventional white LED made from the same die. To take full advantage of this, we have developed medium-brightness LED-modules (~150 kCd/m<sup>2</sup>) for general lighting in which the phosphor is applied remote from the blue LEDs. By direct comparison with modules in which conventional high power white LEDs with almost identical dies are applied, we have shown that on system level the remote phosphor modules can have up to 50% better efficacy. Using a downlight module as a carrier, we have shown that in the relevant color temperature range of 2700 to 4000K a high CRI (&gt;80) can be obtained in combination with a high luminous efficacy, while the optical efficiency of the module can be over 85%. A module efficacy of over 100 lm/W at 4000K with CRI 80 seems to be within reach, with a long-term expectation of over 180 lm/W. The remote phosphor LED modules deliver well homogenized white light with a Lambertian radiation profile. They are ideal for general illumination, as they combine glare reduction with high system efficacy and enable high optical efficiencies of the luminaries. The RP modules enable forward compatibility by well defined interfaces and optical properties that are decoupled from the actual performance, form factor and number of LEDs in the module. The Philips Fortimo downlight system is based on this remote phosphor concept, featuring forward compatibility and a total system efficacy (including driver) of over 60 lm/W under operating conditions using currently available Luxeon Rebel emitters.
Primary diffuse leptomeningeal oligodendroglioma (1995)

The authors describe a case of a diffuse primary leptomeningeal oligodendroglioma in a 17-year-old girl who presented with raised intracranial pressure and hydrocephalus. She underwent imaging studies and a left frontotemporal craniotomy that revealed a cystic oligodendroglioma in the suprasellar cistern and spread of neoplastic cells to the spinal leptomeninges. The tumor showed little response to maximum radiotherapy and chemotherapy, and the patient died from complications of high-dose chemotherapy 2 years after diagnosis. Postmortem examination of the brain and spinal cord revealed diffuse meningeal infiltration by neoplastic cells and no evidence of an intraparenchymal origin. Glial heterotopias were noted at several sites along the brain base, adding circumstantial support to the theory that leptomeningeal gliomas are derived from ectopic glial tissue in the subarachnoid space.
Nuclear translocation of the SRF co‐activator MAL in cortical neurons: role of RhoA signalling (2005)

Although it is well established that RhoA signaling pathways play key roles in regulating neuronal morphology, their involvement in other aspects of neuronal function has received little attention. Recent studies have elucidated a novel intracellular signaling pathway used by RhoA to elicit activation of serum response factor (SRF)-mediated transcription. In this pathway, activation of RhoA triggers nuclear translocation of the SRF co-activator, megakaryocytic acute leukemia (MAL). In assessing whether RhoA regulates transcription in neurons via this pathway, we have found that a constitutively active form of Tech (transcript-enriched in cortex and hippocampus), a RhoA guanine nucleotide exchange factor (GEF) that is expressed in forebrain neurons, stimulates SRF reporter activity in extracts of primary cortical cultures and induces nuclear translocation of MAL in cortical neurons. Both of these responses appear to be mediated by Tech's activation of RhoA as they are not mimicked by a mutant Tech construct lacking RhoA GEF activity and are blocked by C3 transferase, a selective inhibitor of RhoA. Furthermore, Tech-induced increases in SRF activity are suppressed by a dominant negative MAL construct. These findings demonstrate that RhoA signaling pathways are able to regulate transcription in neurons by triggering translocation of the SRF co-activator MAL.
Oral Delivery of Biologics via the Intestine (2020)

Biologics are currently one of the most promising avenues for therapeutic interventions in conditions such as metabolic disease, ageing and inflammatory disorders, and for chronic ailments, oral delivery of such medicines has for years been recognised as an important goal. Despite decades of intensive research, oral delivery of biologics is only just starting to prove feasible. There has been much talk about the barriers to uptake of biologics, and indeed, one function of the intestine is to prevent, in one way or another, passage of unwanted materials across the gut, and yet, grams of biological agents both large and small pass across the intestinal cell wall every day. This review first describes the functioning of the gut under normal circumstances, then identifies the principle biological mechanisms which have been harnessed successfully, to date, to achieve oral uptake, outlining the pros and cons of each approach. Examples with different biologics are given, and information on result of the latest clinical trials is provided, where available.
Dynamic Redeployment to Counter Congestion or Starvation in Vehicle Sharing Systems. (2015)

Extensive usage of private vehicles has led to increased traffic congestion, carbon emissions, and usage of non-renewable resources. These concerns have led to the wide adoption of vehicle sharing (ex: bike sharing, car sharing) systems in many cities of the world. In vehicle-sharing systems, base stations (ex: docking stations for bikes) are strategically placed throughout a city and each of the base stations contain a pre-determined num-ber of vehicles at the beginning of each day. Due to the stochastic and individualistic movement of customers, there is typically either congestion (more than required) or starvation (fewer than required) of vehicles at cer-tain base stations. As demonstrated in our experimental results, this happens often and can cause a significant loss in demand. We propose to dynamically redeploy idle vehicles using carriers so as to minimize lost de-mand or alternatively maximize revenue for the vehicle sharing company. To that end, we contribute an opti-mization formulation to jointly address the redeploy-ment (of vehicles) and routing (of carriers) problems and provide two approaches that rely on decomposabil-ity and abstraction of problem domains to reduce the computation time significantly. Finally, we demonstrate the utility of our approaches on two real world data sets of bike-sharing companies. 1
Acid interleave coatings inhibit float-glass weathering, corrosion (2005)

An initial study has been conducted to determine whether the handling and relative performance of boric and citric acids offer sufficient advantage over presently used adipic acid.
A study on automatic wear debris recognition by using particle feature extraction (1998)

Wear debris morphology is closely related to the wear mode and mechanism occured. Image recognition of wear debris is, therefore, a powerful tool in wear monitoring. But it has usually required expert's experience and the results could be too subjective. Development of automatic tools for wear debris recognition is needed to solve this problem. In this work, an algorithm for automatic wear debris recognition was suggested and implemented by PC base software. The presented method defined a characteristic 3-dimensional feature space where typical types of wear debris were separately located by the knowledge-based system and compared the similarity of object wear debris concerned. The 3-dimensional feature space was obtained from multiple feature vectors by using a multi-dimensional scaling technique. The results showed that the presented automatic wear debris recognition was satisfactory in many cases application.
[Visual disorders induced by therapeutic levels of digoxin]. (2000)

We must remember that ocular toxicity may occur with therapeutic blood level of the medication and not only when the intoxication appears.
Clinical Response to a Lapatinib-Based Therapy for a Li-Fraumeni Syndrome Patient with a Novel HER2 V659E Mutation (2013)

The precise knowledge of the genomic alterations present in tumors is critical to selecting the optimal treatment for each patient. Here, we report the molecular characterization and clinical response to a lapatinib-based therapy for the tumors of a Li-Fraumeni patient showing prevalence of HER2 and EGFR genomic alterations.
Rapid and Accurate Validated Potentiometric Method for Bispyribac Herbicide Assessment in Rice and Agricultural Wastewater (2020)

A new validated method based on potentiometric transduction for bispyribac herbicide assessment in commercial formulations, rice and wastewater samples is fabricated and characterized. Sensors are based in terms of their fabrication on tridodecyl methyl ammonium chloride (TDMAC) as recognition material. TDMAC was plasticized in a poly (vinyl chloride) (PVC) matrix to prepare the membrane. Under static modes of operation, the sensors revealed a Nernstian anionic slope of −63.6 ± 0.7 mV/decade within a linear range of 9.1 × 10−6–1.0 × 10−2 in 50 mM phosphate buffer solution (PBS), pH7. The detection limit was 6.0 × 10−6 M. The sensor was successfully introduced in a flow-stream system revealing a Nernstian response of −53.8 ± 1.3 mV/decade over a linear range of 2 × 10−4–1.0 × 10−2 M and lower detection limit of 5.6 × 10⁻⁵ M. The sampling rate was calculated to be (~42 sample/h). Validation of the assay method is presented in detail including accuracy, trueness, bias, between-day variability and within-day variability, and good performance characteristics of the method are obtained. The presented method was successfully introduced to bispyribac determination in different complex matrices such as commercial bispyribac sodium known as (Nominee-kz, 3% soluble liquid (SL)), rice samples and agricultural wastewater samples. The samples were analyzed successfully under both static and hydrodynamic modes of operation. The results obtained were in a good agreement with those obtained by the liquid chromatographic method.
Efficient Rendering of Highly Detailed Volumetric Scenes with Giga Voxels (2010)

A CNN consists of a number of identical cells, which are arranged in a twodimensional structure and are only connected to neighboring cells, where each cell has input, current, and next states. Distant cells are inﬂuenced by the others through data propagation between neighboring cells. With the CNN approach, diﬀerent applications, such as visual processing and optimization, are achieved using the same algorithm with a diﬀerent set of parameters. Although the local connectivity of the cells is well suited for implementation on a GPU, there are two additional issues that we have to address: ﬁrst, the computational model of GPU is based on four-channel data, but the CNN data is conventionally organized in a one-channel format; second, the data transfer rate between the GPU and main memory is much slower than the transfer rate between the CPU and main memory.
Filtering System Metrics for Minimal Correlation-Based Self-Monitoring (2009)

Self-adaptive and self-organizing systems must be self-monitoring. Recent research has shown that self-monitoring can be enabled by using correlations between monitoring variables (metrics). However, computer systems often make a very large number of metrics available for collection. Collecting them all not only reduces system performance, but also creates other overheads related to communication, storage, and processing. In order to control the overhead, it is necessary to limit collection to a subset of the available metrics. Manual selection of metrics requires a good understanding of system internals, which can be difficult given the size and complexity of modern computer systems. In this paper, assuming no knowledge of metric semantics or importance and no advance availability of fault data, we investigate automated methods for selecting a subset of available metrics in the context of correlation-based monitoring. Our goal is to collect fewer metrics while maintaining the ability to detect errors. We propose several metric selection methods that require no information beside correlations. We compare these methods on the basis of fault coverage. We show that our minimum spanning tree-based selection performs best, detecting on average 66% of faults detectable by full monitoring (i.e., using all considered metrics) with only 30% of the metrics.
Genetic Predisposition, Nongenetic Risk Factors, and Coronary Infarct (2008)

Genetic predisposition may interact with hypertension and, perhaps, also with the level of non-HDL cholesterol, in the causation of CHD. Genetic predisposition and the other studied exposures seem to have converging effects. Thus, the GPS may identify individuals who could realize disproportional benefits by controlling their hypertension and, possibly, their non-HDL cholesterol level.
Figure S2 from Regulation of OATP1B1 Function by Tyrosine Kinase–mediated Phosphorylation (2023)

&lt;p&gt;Percent of total tyrosine-phosphorylated spectral counts for all OATP1B1 tyrosine residues after exposure to DMSO (vehicle) or nilotinib (10 μM). Three concentrated OATP1B1 protein extracts were purified by immunoprecipitation and analyzed by LC-MS analysis, per treatment group. *denotes P &lt; 0.05 vs vehicle or wild-type and all values represent mean {plus minus} SEM. Data is represented by 3 independent experiments.&lt;/p&gt;
Effect of Hesperidin on Barrier Function and Reactive Oxygen Species Production in an Oral Epithelial Cell Model, and on Secretion of Macrophage-Derived Inflammatory Mediators during Porphyromonas gingivalis Infection (2023)

<i>Porphyromonas gingivalis</i> is a periodontopathogenic bacterium that can adhere to and colonize periodontal tissues, leading to an inflammatory process, and, consequently, tissue destruction. New therapies using flavonoids, such as hesperidin, are being studied, and their promising properties have been highlighted. The aim of this study was to evaluate the effect of hesperidin on the epithelial barrier function, reactive oxygen species (ROS) production, and on the inflammatory response caused by <i>P. gingivalis</i> in in vitro models. The integrity of the epithelial tight junctions challenged by <i>P. gingivalis</i> was determined by monitoring the transepithelial electrical resistance (TER). <i>P. gingivalis</i> adherence to a gingival keratinocyte monolayer and a basement membrane model were evaluated by a fluorescence assay. A fluorometric assay was used to determine the ROS production in gingival keratinocytes. The level of pro-inflammatory cytokines and matrix metalloproteinases (MMPs) secretion was evaluated by ELISA; to assess NF-κB activation, the U937-3xjB-LUC monocyte cell line transfected with a luciferase reporter gene was used. Hesperidin protected against gingival epithelial barrier dysfunction caused by <i>P. gingivalis</i> and reduced the adherence of <i>P. gingivalis</i> to the basement membrane model. Hesperidin dose-dependently inhibited <i>P. gingivalis</i>-mediated ROS production by oral epithelial cells as well as the secretion of IL-1β, TNF-α, IL-8, MMP-2, and MMP-9 by macrophages challenged with <i>P. gingivalis</i>. Additionally, it was able to attenuate NF-κB activation in macrophages stimulated with <i>P. gingivalis</i>. These findings suggest that hesperidin has a protective effect on the epithelial barrier function, in addition to reducing ROS production and attenuating the inflammatory response associated with periodontal disease.
The Feasibility of Short-term Dry Eye Animal Model Using Concanavalin A (2007)

Purpose: To evaluate the possibility of short-term dry eye model in rabbits by injection of concanavalin A (conA) to the lacrimal and haderian gland of rabbits. Methods: We injected conA (10 mg/ml, 0.05 ml) to the lacrimal and haderian gland of rabbits twice to induce inflammation of lacrimal gland and compared with saline-injected control by lacrimal gland biopsy with H&E staining for identification of inflammation. The ratio of lacrimal secretion was evaluated by Schirmer test (preinjection vs. postinjection of conA) for 10 days and the number of goblet cells was counted in 10 consecutive high power field using impression cytology with PAS staining. The corneal & conjunctival apoptotic cell deaths were investigated with TUNEL staining 10 days after injection. Results: Infiltration of inflammatory cells and destructed normal architecture of lacrimal gland was found only in conA injected group till 10 days. The Schirmer test showed marked reduction (0.56±0.26) by 5days after injection compared with control group (1.07±0.35) (p=0.02) and its significant difference was maintained till 10days. The number of goblet cell was 9.70±5.03/×200HPF, which was statistically significant decreased compared to control (47.50±17.13/×200HPF) at 10 days (p=0.00). Apoptotic cells were increased in injected eye (26.20±4.27) compared with those in control (16.60±2.70). Conclusions: Injection of conA to lacrimal glands in rabbit shows decrease of lacrimal secretion and similar cytological changes of the cornea and conjunctiva in human dry eye patients. It suggests its possible feasibility of short-term dry eye animal model for the 10 days.
High performance of diamond p+-i-n+ junction diode fabricated using heavily doped p+ and n+ layers (2009)

A good ideality factor and rectification ratio were obtained in a p+-i-n+ diamond diode with p+ and n+ doping levels of ∼1020 cm−3, where the hopping conduction mechanism dominates in the bulk p+ and n+ layers. The diode characteristics show a rectification ratio of 108 at ±10 V and an ideality factor of n=1.32. This diode showed ruggedness with a large current density of over 15 000 A/cm2 at +35 V. These results indicate the possibility of large-current devices.
A state-space method for language modeling (2004)

A new state-space method for language modeling is presented. The complexity of the model is controlled by choosing the dimension of the state instead of the smoothing and back-off methods common in n-gram modeling. The model complexity also controls the generalization ability of the model, allowing the model to handle similar words in a similar manner. We compare the state-space model to a traditional n-gram model in a task of letter prediction. In this proof-of-concept experiment, the state-space model gives similar results as the n-gram model with sparse training data, but performs clearly worse with dense training data. While the initial results are encouraging, the training algorithm should be made more effective, so that it can fully exploit the model structure and scale up to larger token sets, such as words.