gebhart/patrepeval huggingface dataset:
Identification for building surface material based on hyperspectral remote sensing (2011)

In contrast with traditional remote sensing, hyperspectral remote sensing has the characteristics of high spectral resolution, combination of graph and spectrum, and large quantity of imaging bands. It has been used in many fields. According to the research results of other scholars, building surface has become a thermal active surface which has an important effect for forming city three-dimensional climate. In the 863 research project of relieving and analyzing of city heat island, based on summarizing now available spectrum identification methods, we selected frequently-used spectral angle match (SAM) identification method for the research, then we realized a program of identifying building surface material with IDL, and we did a simulation experiment for the program by using an AVIRIS image. Finally, we got a good result. It is proved that identifying building surface material based on hyperspectral remote sensing is feasible. So it makes a solid basis for further research.
Microfluidic separation of live and dead yeast cells using reservoir-based dielectrophoresis (2012)

Separating live and dead cells is critical to the diagnosis of early stage diseases and to the efficacy test of drug screening, etc. This work demonstrates a novel microfluidic approach to dielectrophoretic separation of yeast cells by viability. It exploits the cell dielectrophoresis that is induced by the inherent electric field gradient at the reservoir-microchannel junction to selectively trap dead yeast cells and continuously separate them from live ones right inside the reservoir. This approach is therefore termed reservoir-based dielectrophoresis (rDEP). It has unique advantages as compared to existing dielectrophoretic approaches such as the occupation of zero channel space and the elimination of any mechanical or electrical parts inside microchannels. Such an rDEP cell sorter can be readily integrated with other components into lab-on-a-chip devices for applications to biomedical diagnostics and therapeutics.
Statistical Mechanics: Theory and Molecular Simulation (2023)

Abstract Complex problems that cross traditional disciplinary lines between physics, chemistry, biology, and materials science can be studied at an unprecedented level of detail using increasingly sophisticated theoretical methodology and high-speed computing platforms. The tools of statistical mechanics provide the bridge between the atomistic descriptions of these complex systems and the macroscopic observables accessible to experimental investigations and predictable in computer simulations. The aim of this book is to prepare burgeoning users and developers to become active researchers in the theoretical and computational molecular sciences by uniting, in one monograph, the theoretical underpinnings of equilibrium and time-dependent classical and quantum statistical mechanics with modern computational techniques used to put these concepts into practice to address real-world applications. The book contains detailed reviews of classical and quantum mechanics and in-depth discussions of the most commonly used statistical ensembles side by side with modern computational methods such as molecular dynamics, Monte Carlo, advanced configurational and trajectory sampling approaches, free-energy based rare-event sampling approaches, Feynman path integral techniques, linear response theory and time correlation functions, stochastic methods, critical phenomena, and an introduction to machine learning and its uses in statistical mechanics. Readers of this book will be provided, in a pedagogical manner, with a firm foundation in both the theory and practical implementation of statistical mechanical concepts, thus allowing them to approach application technology with an understanding of the underlying algorithms and to become, themselves, creators of new and powerful approaches for solving challenging research problems.
Microbial communities related to biodegradation of dispersed <scp>M</scp> acondo oil at low seawater temperature with Norwegian coastal seawater (2015)

The Deepwater Horizon (DWH) accident in 2010 created a deepwater plume of small oil droplets from a deepwater well in the Mississippi Canyon lease block 252 ('Macondo oil'). A novel laboratory system was used in the current study to investigate biodegradation of Macondo oil dispersions (10 μm or 30 μm median droplet sizes) at low oil concentrations (2 mg l(-1)) in coastal Norwegian seawater at a temperature of 4-5°C. Whole metagenome analyses showed that oil biodegradation was associated with the successive increased abundances of Gammaproteobacteria, while Alphaproteobacteria (Pelagibacter) became dominant at the end of the experiment. Colwellia and Oceanospirillales were related to n-alkane biodegradation, while particularly Cycloclasticus and Marinobacter were associated with degradation of aromatic hydrocarbons (HCs). The larger oil droplet dispersions resulted in delayed sequential changes of Oceanospirillales and Cycloclasticus, related with slower degradation of alkanes and aromatic HCs. The bacterial successions associated with oil biodegradation showed both similarities and differences when compared with the results from DWH field samples and laboratory studies performed with deepwater from the Gulf of Mexico.
3D Point Cloud Denoising via Deep Neural Network based Local Surface Estimation (2019)

We present a neural-network-based architecture for 3D point cloud denoising called neural projection denoising (NPD). In our previous work, we proposed a two-stage denoising algorithm, which first estimates reference planes and follows by projecting noisy points to estimated reference planes. Since the estimated reference planes are inevitably noisy, multi-projection is applied to stabilize the denoising performance. NPD algorithm uses a neural network to estimate reference planes for points in noisy point clouds. With more accurate estimations of reference planes, we are able to achieve better denoising performances with only one-time projection. To the best of our knowledge, NPD is the first work to denoise 3D point clouds with deep learning techniques. To conduct the experiments, we sample 40000 point clouds from the 3D data in ShapeNet to train a network and sample 350 point clouds from the 3D data in ModelNet10 to test. Experimental results show that our algorithm can estimate normal vectors of points in noisy point clouds. Comparing to five competitive methods, the proposed algorithm achieves better denoising performance and produces much smaller variances.
Utilizing DART Mass Spectrometry to Pinpoint Halogenated Metabolites from a Marine Invertebrate-Derived Fungus (2011)

Prenylated indole alkaloids are a diverse group of fungal secondary metabolites and represent an important biosynthetic class. In this study we have identified new halogenated prenyl-indole alkaloids from an invertebrate-derived Malbranchea graminicola strain. Using direct analysis in real time (DART) mass spectrometry, these compounds were initially detected from hyphae of the fungus grown on agar plates, without the need for any organic extraction. Subsequently, the metabolites were isolated from liquid culture in artificial seawater. The structures of two novel chlorinated metabolites, named (-)-spiromalbramide and (+)-isomalbrancheamide B, provide additional insights into the assembly of the malbrancheamide compound family. Remarkably, two new brominated analogues, (+)-malbrancheamide C and (+)-isomalbrancheamide C, were produced by enriching the growth medium with bromine salts.
Studies on the Extracellular Polysaccharides (EPS) Produced <i>in vitro</i> by <i>Pseudomonas phaseolicola</i> (1987)

Abstract Native EPS produced by Pseudomonas syringae pv. phaseolicola in vitro was separated by ion exchange chromatography on DEAE fractogel into three different polysaccharide fractions. A neutral polysaccharide eluting with the void volume yielded only fructose upon hydrolysis and exhibited an IR spectrum similar to authentic levan. At about 300 mM KCl a mannuronan eluted. Comparison with authentic alginate by IR spectroscopy, elution behaviour during DEAE‐fractogel column chromatography, and monomer composition (mannuronic acid and traces of guluronic acid) confirmed the identity of this fraction as a bacterial alginate. It contained about 56 mol% acetyl groups. A third polysaccharide eluted at about 160 mM KCl. Its monomeric composition (rhamnose, fucose, glucose, and amino sugars), elution behaviour upon DEAE‐fractogel column chromatography, and TLC patterns, closely resembled the sugar moiety of lipopolysaccharides (LPS) from, Pseudomonas syringae pv. phaseolicola. The protein component of crude EPS represented a fourth macromolecular fraction. It was not covalently linked to any of the polysaccharides since it could be removed from the EPS by phenol extraction.
Interactive User Intent Modeling (2016)

In information retrieval systems, users often have difficulties in forming precise queries to express their information need. One approach to express information need is to explore the information space by providing relevance feedback to recommended items. This feedback is then used to model user search intent. Studies have shown how retrieval performance could be improved by allowing users to give feedback to multiple items such as keywords and documents instead of keywords only. In this thesis, I extend an existing user model which uses document-level and keyword-level feedback to include session-level feedback, and study the usefulness of this extension. By conducting simulation studies in various settings, I investigate the effect of session-level feedback. Based on these simulation results, I conclude that additional session-feedback helps in finding relevant documents by improving F1-score. Results show that more the additional session-feedback, more the improvement in F1-score. However, trade-off of session-feedback instead of document and keyword feedback results in drop in document F1-score, therefore indicating that session-feedback is less informative than document and keyword feedback.
Biochemical Evidence That Small Proline-rich Proteins and Trichohyalin Function in Epithelia by Modulation of the Biomechanical Properties of Their Cornified Cell Envelopes (1998)

The cornified cell envelope (CE) is a specialized structure involved in barrier function in stratified squamous epithelia, and is assembled by transglutaminase cross-linking of several proteins. Murine forestomach epithelium undergoes particularly rigorous mechanical trauma, and these CEs contain the highest known content of small proline-rich proteins (SPRs). Sequencing analyses of these CEs revealed that SPRs function as cross-bridgers by joining other proteins by use of multiple adjacent glutamines and lysines on only the amino and carboxyl termini and in functionally non-polar ways. Forestomach CEs also use trichohyalin as a novel cross-bridging protein. We performed mathematical modeling of amino acid compositions of the CEs of mouse and human epidermis of different body sites. Although the sum of loricrin + SPRs was conserved, the amount of SPRs varied in relation to the presumed physical requirements of the tissues. Our data suggest that SPRs could serve as modifiers of a composite CE material composed of mostly loricrin; we propose that increasing amounts of cross-bridging SPRs modify the structure of the CE, just as cross-linking proteins strengthen other types of tissues. In this way, different epithelia may use varying amounts of the cross-bridging SPRs to alter the biomechanical properties of the tissue in accordance with specific physical requirements and functions.
Theoretical Parameters to Characterize Antioxidants. Part 1. The case of vitamin E and analogs (1997)

Abstract The objectives of ibis work were ( a ) to evaluate parameters obtained by quantum‐mechanical calculations as predictors of antioxidant activities, and ( b ) to obtain information on the molecular mechanism(s) underlying the antioxidant effects of vitamin E and analogs. To this effect, we selected a large series of tocopherol analogs for which some experimental antioxidant activities were available in the literature ( i. e. , peak of oxidation potential, E p , and rate constant of the reaction with a free radical log k s ). AM1 Semi‐empirical calculations were performed, the results of which were validated by ab initio calculations on a subset of compounds. The quantum chemical descriptors considered here (HOMO, Δ H ox and Δ H abs ) were fairly well correlated with the experimental antioxidant activities ( E p and k s ). Moreover, these theoretical parameters were intercorrelated, suggesting that vitamin E analogs may act by a dual mechanism of single‐electron transfer (SET) and direct H‐atom abstraction.
Local RNA Translation at the Synapse and in Disease: Figure 1. (2011)

Local regulation of protein synthesis in neurons has emerged as a leading research focus because of its importance in synaptic plasticity and neurological diseases. The complexity of neuronal subcellular domains and their distance from the soma demand local spatial and temporal control of protein synthesis. Synthesis of many synaptic proteins, such as GluR and PSD-95, is under local control. mRNA binding proteins (RBPs), such as FMRP, function as key regulators of local RNA translation, and the mTORC1 pathway acts as a primary signaling cascade for regulation of these proteins. Much of the regulation occurs through structures termed RNA granules, which are based on reversible aggregation of the RBPs, some of which have aggregation prone domains with sequence features similar to yeast prion proteins. Mutations in many of these RBPs are associated with neurological diseases, including FMRP in fragile X syndrome; TDP-43, FUS (fused in sarcoma), angiogenin, and ataxin-2 in amyotrophic lateral sclerosis; ataxin-2 in spinocerebellar ataxia; and SMN (survival of motor neuron protein) in spinal muscular atrophy.
Perpendicular Magnetic Recording Integration and Robust Design (2007)

We have investigated the effects of stray magnetic field upon a perpendicular magnetic recording (PMR) system, which consists of a single pole type head and a double-layered perpendicular medium. We found that fields in the plane of the disk could cause serious erasure. External magnetic flux concentrates around the edges of a return pole and can cause very large fields to appear in the medium. In addition, the writing operation significantly enhances this erasure. We called this kind of erasure "corner erasure." Experimental 2.5-inch hard disk drives (HDDs) were used to study the combined effect of the external field and write field. We checked SER degradation after applying an in-plane field of 0.8 kA/m (10 Oe). With no write-current applied, there is no degradation. However, as little as 0.8 kA/m (10 Oe) applied during writing causes severe degradation equivalent to that produced by a 4.0 kA/m (50 Oe) field applied when the head is reading on-track. It is concluded that the realization of PMR in commercial HDD would require new transducer designs to solve these problems. We devised a new return pole design which has a stepped-back wing to improve the robustness against in-plane stray fields. The alternative design greatly reduces the concentration of magnetic flux at the edges of return pole. Consequently, the stepped wing structure achieves about twice the robustness of the conventional rectangular return pole. A method was developed to allow external field sensitivity to be carefully checked. The method allows the degraded areas of data to be associated with the exact feature on the head that caused the problem
A device for preparative elution electrophoresis using a polyacrylamide gel slab (1986)

Abstract A compact device, capable of being clipped onto the end of a 3 mm thick analytical polyacrylamide slab gel, has been developed for the collection of resolved protein zones as they elute from the end of the gel. Its unique feature is that eluted proteins were collected between two polyacrylamide‐embedded paper membranes and removed either by continuous or intermittent buffer elution. Because of this direct coupling to large gels identical to those used for analytical electrophoresis, protein zones were obtained with high resolution. The method was applicable to non‐denaturing cathodic and anodic electrophoresis, as well as sodium dodecyl sulfate electrophoresis. Medium‐scale quantities (up to 10 mg/cm 2 cross‐sectional area) of protein were fractionated in as little as 4 h with high recoveries.
Selective Conjugate Addition of Organolithium Reagents to γ,δ-Unsaturated β-Oxo Esters Derived from Glyceraldehyde Acetonide (1992)

Organolithium reagents react in an unusually selective conjugate manner with γ,δ-unsaturated β-oxo esters derived from glyceraldehyde acetonide. Thus, ester 6a gave ethyl 6,7-isopropylidenedioxy-5-(1-methylethenyl)-3-oxoheptanoate (5a) in 82% yield.
Learning to Generalize from Sparse and Underspecified Rewards (2019)

We consider the problem of learning from sparse and underspecified rewards, where an agent receives a complex input, such as a natural language instruction, and needs to generate a complex response, such as an action sequence, while only receiving binary success-failure feedback. Such success-failure rewards are often underspecified: they do not distinguish between purposeful and accidental success. Generalization from underspecified rewards hinges on discounting spurious trajectories that attain accidental success, while learning from sparse feedback requires effective exploration. We address exploration by using a mode covering direction of KL divergence to collect a diverse set of successful trajectories, followed by a mode seeking KL divergence to train a robust policy. We propose Meta Reward Learning (MeRL) to construct an auxiliary reward function that provides more refined feedback for learning. The parameters of the auxiliary reward function are optimized with respect to the validation performance of a trained policy. The MeRL approach outperforms our alternative reward learning technique based on Bayesian Optimization, and achieves the state-of-the-art on weakly-supervised semantic parsing. It improves previous work by 1.2% and 2.4% on WikiTableQuestions and WikiSQL datasets respectively.
Grating lobe suppression in an array antenna with element spacing greater than a half wavelength (2010)

The element allocation is formulated to suppress grating lobes in an array antenna with element spacing greater than a half wave-length. The number of the driven elements should be constant between lines of elements in order to eliminate larger periodicities than the element spacing. By this design, the sub-array shape can be kept identical. It is also easy to cope with linear polarizations. An array antenna with 192 elements was simulated and compared with the case of alternate allocations of driven and parasitic elements. It was shown that grating lobes are significantly suppressed by this design. Accordingly, the theoretical consideration has been confirmed.
DynPolAC: Dynamic Policy-Based Access Control for IoT Systems (2018)

In the near future, Internet-of-Things (IoT) systems will be comprised of autonomous, highly interactive and moving objects that require frequent handshakes to exchange information in time intervals of seconds. Examples of such systems are drones and self-driving cars. In these scenarios, data integrity, confidentiality, and privacy protection are of critical importance. Further, updates need to be processed quickly and with low overheads due to the systems' resource-constrained nature. This paper proposes Dynamic Policy-based Access Control (DynPolAC) as a model for protecting information in such systems. We construct a new access control policy language that satisfies the properties of highly dynamic IoT environments. Our access control engine is comprised of a rule parser and a checker to process policies and update them at run-time with minimum service disruption. DynPolAC achieves more than 7x performance improvements when compared to previously proposed methods for authorization on resource-constrained IoT platforms, and achieves more than 3x faster response times overall.
Semicrystalline polymers with high dielectric constant, melting temperature, and charge-discharge efficiency (2012)

The dielectric properties of semicrystalline poly(tetrafluoroethylene-hexafluoropropylene-vinylidene fluoride) (THV) terpolymers with different compositions are investigated in a broad temperature range and under high voltage for potential applications in high energy density film capacitors with high thermal stability. It was found that the capacitor charge-discharge efficiency under high voltage (>;200 MV/m) and the melting temperature can be significantly improved by increasing the tetrafluoroethylene (TFE) content. Melting temperature above 220°C can be achieved in THV terpolymers with high TFE content. Although the THV terpolymers have lower dielectric constant than polyvinylidene fluoride (PVDF), their high melting temperature, low leakage current, and high charge-discharge efficiency represent significant advantages for capacitors operated under high charge-discharge repetition rate and at high ambient temperatures.
X-Ray Fluorescence Computed Tomography With Polycapillary Focusing (2014)

Liposomal iodine nanoparticles (LINPs) have a long half-life and provide an excellent intravascular contrast. The nanoparticles can be functionalized as molecular probes for biological targets to facilitate numerous preclinical studies for translation toward diagnosis and therapy of various human diseases. Iodine has a K-edge at 33 keV due to the photoelectric absorption of photons, which emit X-ray fluorescence at 28 keV with a fluorescence yield of 0.88. Detections of the characteristic X-rays can be used for the imaging of iodine concentration distribution in an object. In this paper, we propose an X-ray fluorescence computed tomography method for reconstruction of a LINPs distribution over a region of interest (ROI) in a small animal. X-rays are focused onto a submillimeter focal spot utilizing a polycapillary lens, generating a pair of X-ray cones in the animal. This focused beam irradiates LINPs, the most strongly at the focal spot. Then, the focal spot can be scanned over an ROI in the object to produce X-ray fluorescence signals. From measured fluorescence data, a reliable image reconstruction can be achieved with a high spatial resolution. Numerical simulation studies are performed to demonstrate the superior imaging performance of this methodology.
H<scp>UMAN</scp> N<scp>EURODEGENERATIVE</scp> D<scp>ISEASE</scp> M<scp>ODELING</scp> U<scp>SING</scp> <i>D<scp>ROSOPHILA</scp></i> (2003)

A number of approaches have been taken to recreate and to study the role of genes associated with human neurodegenerative diseases in the model organism Drosophila. These studies encompass the polyglutamine diseases, Parkinson's disease, Alzheimer's disease, and tau-associated pathologies. The findings highlight Drosophila as an important model system in which to study the fundamental pathways influenced by these genes and have led to new insights into aspects of pathogenesis and modifier mechanisms.