gebhart/patrepeval huggingface dataset:
Advanced Fiber Soliton Sources for Nonlinear Deep Tissue Imaging in Biophotonics (2013)

Optical imaging plays a major role in both basic biological research and clinical diagnostics, providing noninvasive or minimally invasive microscopic imaging capability to investigate biological tissues. Optical image acquisition through significant depths of biological tissues, however, presents a major challenge since tissue is extremely heterogeneous and the strong scattering of the various tissue components has restricted high-resolution optical imaging to superficial layers. Multiphoton microscopy (MPM) has significantly extended the penetration depth of high-resolution optical imaging, particularly for in vivo applications. Multiphoton imaging critically depends on ultrafast technologies, particularly pulsed excitation sources. In this paper, the basics of deep tissue MPM and its improvements utilizing soliton self-frequency shift (SSFS) are reviewed. Wavelength tunable, high-energy soliton generation through SSFS in large-mode-area (LMA) fibers and photonic crystal rods is presented. The application of these solitons to MPM enables noninvasive imaging in biological tissues with unprecedented depth. The main characteristics of the excitation source for deep tissue MPM, such as wavelength, pulse energy, and repetition rate, are discussed.
Further Understanding of the Chemistry of Manganese‐Induced Peroxide Decomposition (2003)

Abstract Manganese is the most effective catalyst for the hydrogen peroxide decomposition during peroxide bleaching used in the pulp and paper industry. We studied the chemistry involved in this project. The results showed that Mn 2+ and Mn 3+ are present during the course of the reaction. We followed the Mn 2+ and Mn 3+ concentrations during the course. It was found that a steady state of Mn 3+ concentration was attained until the hydrogen peroxide concentration was zero. At this time, the Mn 3+ concentration was maximum, then it decreased due to the disproportionation to form MnO 2 . Removal of O 2 from the system slowed down the rate of decomposition. The detailed reactions involved were discussed.
Molecular simulation on interfacial structure and gettering efficiency of direct silicon bonded (110)/(100) substrates (2010)

Direct silicon bonded (DSB) substrates with (110)/(100) hybrid orientation technology are attracting considerable attention as a promising technology for high performance bulk complementary metal-oxide semiconductor technology. We have investigated the structure and the gettering efficiency of the (110)/(100) interface parallelling each ⟨110⟩ direction (DSB interface) by molecular dynamics (MD) and first-principles calculation. In MD calculations, initial calculation cells of 15 atomic-configurations with coincidence-site lattices were prepared. It was found that (i) the calculated DSB interface was stable independent of the initial atomic-configurations and (ii) the interfacial structures were essentially the same among the calculated models. Moreover, the calculated interfacial structure corresponds to the reported TEM observation. The first-principles calculation showed that Si atoms in the DSB interface formed covalent bonding. The dangling bonds in Si (110) and (100) surfaces disappeared due to restructuring in the DSB interface. Furthermore, the DSB interface, which exists just below the device active region, was found to be an efficient gettering site for Al, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, and Hf atoms.
Metabolic profiling of plasma from pigs fed high rye fibre or high cellulosic fibre diets using a liquid chromatography-mass spectrometry (LC-MS) approach (2010)

To unravel how whole-grain consumption reduces the risk of developing cardiovascular diseases studies on specific plasma metabolites have been performed. However, traditional approaches focused on specific biomarkers often fail to detect or oversee metabolic changes due to the complexity of the metabolic response. Using a 1H NMR-based metabonomic approach previous studies have shown that consumption of whole-grain diets produces metabolic changes in both rats and pigs. Betaine was identified as one of the components being increased after consumption of whole grain diets. The aim of the present study was to investigate the metabolic profiles of pigs fed a high rye fibre diet (HRF) or a high cellulosic fibre diet (HCF) using a LC-MS based approach in order to confirm the changes in the betaine level shown in previous studies and possibly reveal further changes in the metabolic profile as MS techniques are more sensitive than NMR. A total of 17 hypercholesterolemic pigs were fed HRF (n=9) or HCF (n=8) for 9-10 weeks. Both diets were enriched with fat and cholesterol and had similar dietary fibre content. Fasting plasma samples were taken 2 days before the dietary intervention and after 8 and 12 day on the experimental diets, while postprandial samples were taken at the end of the experiment. Protein precipitation was performed with methanol. The precipitated samples are resuspended in 0.1% formic acid in H2O and injected into a reversed-phased C18 column and detection was performed with a quadropole time-of-flight mass spectrometer. Data were analysed using principal components analysis (PCA) that allows a visualisation of the similarities/dissimilarities of the data with respect to their biochemical composition. Betaine was identified as a one of the metabolites involved in the overall biochemical effect of a high rye fibre diet. Several other metabolites, discriminating the dietary treatment groups were found and await further identification.
ChemInform Abstract: Simple Methods for the Preparation of Cryptands (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Politics: A Study of Control Behavior. By Neil A. McDonald. New Brunswick, NJ: Rutgers University Press. 1965. Pp. xii, 264. $7.50. (1966)

An abstract is not available for this content so a preview has been provided. Please use the Get access link above for information on how to access this content.
Peptide directed transmembrane transport and nuclear localization of Ru(ii) polypyridyl complexes in mammalian cells (2013)

The targeted delivery of luminescent Ru(II) polypyridyl complexes to the nucleus of live mammalian cells by a Nuclear Localisation Signal (NLS) peptide; NF-κB is demonstrated.
Functions of Polymeric Additives in Thermally Induced Phase Separation Process of Poly(Vinylidene Difluoride) (2020)

Poly(vinylidene difluoride) (PVDF) is the main stream material for water treatment membrane. Thermally induced phase separation (TIPS) is frequently used as a manufacturing technology to produce a porous membrane. In phase separation technology, polymeric additives can be added to control the pore structure of the porous membranes. In this study, in order to clarify the functions of the polymeric additives such as Poly(ethylene glycol) (PEG) and Poly(vinyl pyrrolidone) (PVP) in the PVDF TIPS process, phase diagrams were prepared on TIPS process. In addition, cast films were prepared using dopes whose phase diagrams were prepared, and their surface structures were observed by SEM analysis. As a result, we clarified the mechanisms for controlling the pore structures of PVDF by selection of polymeric additives.
Small Refinements to the DAM Can Have Big Consequences for Data-Structure Design (2019)

Storage devices have complex performance profiles, including costs to initiate IOs (e.g., seek times in hard drives), parallelism and bank conflicts (in SSDs), costs to transfer data, and firmware-internal operations. The Disk-Access Machine (DAM) model simplifies reality by assuming that storage devices transfer data in blocks of size B and that all transfers have unit cost. Despite its simplifications, the DAM model is reasonably accurate. In fact, if B is set to the half-bandwidth point, where the latency and bandwidth of the hardware are equal, the DAM approximates the IO cost on any hardware to within a factor of 2. Furthermore, the DAM explains the popularity of B-trees in the 70s and the current popularity of B-trees and log-structured merge trees. But it fails to explain why some B-trees use small nodes, whereas all B-trees use large nodes. In a DAM, all IOs, and hence all nodes, are the same size. In this paper, we show that the affine and PDAM models, which are small refinements of the DAM model, yield a surprisingly large improvement in predictability without sacrificing ease of use. We present benchmarks on a large collection of storage devices showing that the affine and PDAM models give good approximations of the performance characteristics of hard drives and SSDs, respectively. We show that the affine model explains node-size choices in B-trees and B+-trees. Furthermore, the models predict that the B-tree is highly sensitive to variations in the node size whereas B-trees are much less sensitive. These predictions are born out empirically. Finally, we show that in both the affine and PDAM models, it pays to organize data structures to exploit varying IO size. In the affine model, B-trees can be optimized so that all operations are simultaneously optimal, even up to lower order terms. In the PDAM model, B-trees (or B+-trees) can be organized so that both sequential and concurrent workloads are handled efficiently. We conclude that the DAM model is useful as a first cut when designing or analyzing an algorithm or data structure but the affine and PDAM models enable the algorithm designer to optimize parameter choices and fill in design details.
Empirical State Determination of Entangled Two-Level Systems and its Relation to Information Theory (1999)

Theoretical methods for empirical state determination of entangled two-level systems are analyzed in relation to information theory. We show that hidden variable theories would lead to a Shannon index of correlation between the entangled subsystems which is larger that that predicted by quantum mechanics. Canonical representations which have maximal correlations are treated by the use of Schmidt decomposition of the entangled states, including especially the Bohm singlet state and the GHZ entangled states. We show that quantum mechanics does not violate locality, but does violate realism.
Supplementary Figures 1 through 7 and Supplementary Table 1 from Glioblastoma Eradication Following Immune Checkpoint Blockade in an Orthotopic, Immunocompetent Model (2023)

&lt;p&gt;Supplemental Figure 1. Bioluminescence plots of individual animals following treatment with immune checkpoint blocking mAbs. Supplemental Figure 2. Immune cell infiltrates within intracranial GL261-luc2 tumor following treatment with isotype control IgG or combination therapy with CTLA-4 plus PD-1 mAb therapy. Supplemental Figure 3: Treatment antibody and detection antibody for PD-1 do not share same the epitope. Supplemental Figure 4. Representative immunohistochemistry results of intratumoral CD3+, CD4+ and CD8+ T cell infiltrates following immune checkpoint therapy with mAbs against CTLA-4, PD-1 and both CTLA-4 and PD-1. Supplemental Figure 5. Immune cell infiltration within the draining cervical lymph node (cLN) of GL261-luc2 tumor-bearing mice following treatment with isotype control IgG or combination therapy with mAbs against CTLA-4 plus PD-1. Supplemental Figure 6. Comparisons of chemokine expression levels in sera of mice treated with checkpoint blockade. Supplemental Figure 7: Expression of checkpoint ligands and receptors on GL261-Luc cells in vitro. Supplementary Table 1. Arrangement of chemokines on the Mouse Chemokine Antibody Array.&lt;/p&gt;
SVM-based intrusion detection system for wireless ad hoc networks (2003)

Wireless ad hoc networks present more security problems than the conventional wired and wireless networks. Intrusion detection, as a complementary mechanism to the regular intrusion prevention approaches, is needed to secure the wireless ad hoc networks. In this paper we focus on the network layer security issues and propose a practical support vector machine (SVM) based intrusion detection system. The effectiveness of our proposed approach has been verified by extensive simulation results.
Candidate Architecture for MIMO LTE-Advanced Receivers with Multiple Channels Capabilities and Reduced Complexity and Cost (2009)

International audience
RAD-TGTs: Measurement of cellular tensions via flow cytometry and DNA sequencing enabled by force-dependent rupture and delivery of DNA tension probes (2022)

Abstract Mechanical force is a key driver of cellular processes and is dysregulated in many diseases. Measuring cellular tensions to elucidate mechanotransduction pathways typically involves high-resolution but low throughput imaging of surfaces and arduous experimental preparation of materials. We present here Rupture and Deliver DNA-duplex based molecular tension sensors-RAD-TGTs. RAD-TGTs consist of immobilized DNA duplexes conjugated to a ligand and indicator (fluorophore, barcode etc) which rupture in a force-dependent manner when cells are bound. Readout of rupture is performed in cells of interest using high throughput methods such as flow cytometry and leveraging covalent DNA-protein linking HUH-tags simplifies the preparation of the tension sensor to allow use of “off-the-shelf” oligos. We demonstrate that rupture and delivery is decreased by inhibitors of cytoskeletal dynamics and knockout of mechanosensing proteins. We also show that rupture and delivery correlates with ligand affinity. Excitingly, we demonstrate that rupture and delivery of barcoded DNA-duplexes can be quantified using DNA sequencing, propelling cellular force measurements into the -omics era.
Nanoscopic measurements of surface recombination velocity and diffusion length in a semiconductor quantum well (2002)

We use a near-field microscopic technique to probe photoluminescence from the edge area of a quantum well. Near the edge, surface recombination gives rise to a gradual variation of the photoluminescence signal on a micrometer length scale. The overall shape in this transition region depends strongly on the excitation intensity. From solving two dimensional diffusion equations, we deduce the surface recombination velocity and the diffusion length. It is shown that the surface recombination velocity decreases with increasing intensity due to the saturation of nonradiative defect states.
Conversion of fish processing wastewater into fish feed ingredients through submerged cultivation of Aspergillus oryzae (2020)

Abstract Fish processing towards production of fillet gives rise to wastewater streams that are ultimately directed to biogas production and/or wastewater treatment. However, these wastewater streams are rich in minerals, fat, and proteins that can be converted to protein-rich feed ingredients through submerged cultivation of edible filamentous fungi. In this study, the origin of wastewater stream, initial pH, cultivation time, and extent of washing during sieving, were found to influence the amount of recovered material from the wastewater streams and its protein content, following cultivation with Aspergillus oryzae . Through cultivation of the filamentous fungus in sludge, 330 kg of material per ton of COD were recovered by sieving, corresponding to 121 kg protein per ton of COD, while through its cultivation in salt brine, 210 kg of material were recovered per ton of COD, corresponding to 128 kg protein per ton of COD. Removal ranges of 12–43%, 39–92%, and 32–66% for COD, total solids, and nitrogen, respectively, were obtained after A. oryzae growth and harvesting in the wastewater streams. Therefore, the present study shows the versatility that the integration of fungal cultivation provides to fish processing industries, and should be complemented by economic, environmental, and feeding studies, in order to reveal the most promising valorization strategy. Graphic abstract
Characterisation of Asphaltenes and Modelling of Flocculation – State of the Art (2006)

This document describes a state of the art concerning the flocculation of asphaltenes with two major sections: characterisation of asphaltenes in various environments and modelling of flocculation. This review starts with the characterisation of asphaltenes as such, then their characterisation in synthetic solvents or crudes. Emphasis is placed on molar mass determination and diffraction techniques. The impact of adding a good/poor solvent is also discussed. The second part of this review is dedicated to modelling. We first examine the various models in the literature before describing the Szewczyk and Béhar (1999) model and its integration in a reservoir simulator. The models available still require experimental data which is difficult to collect and further research is needed to improve this situation.
Automated interpretation of subcellular location patterns (2005)

Fluorescence microscopy is widely used to analyze the distribution of proteins within cells. As currently practiced, the assignment of a protein to a particular organelle is done by visual inspection of images or comparison between the distribution of the unknown protein and markers with known location patterns. In order to use fluorescence microscopy for large scale or proteome-wide analysis of protein location, improved approaches that are more automated, objective, and sensitive are needed. Our group has therefore developed automated systems that can recognize the major subcellular location patterns in images of single cultured cells, and has shown that these systems are more sensitive than visual inspection. The foundations of these systems are sets of numerical features that describe the essential characteristics of a subcellular pattern without being overly sensitive to the size, shape and orientation of that cell within the field of view. These features can be used to measure the similarity between protein patterns and therefore for the first time to group proteins in an objective manner based on their high-resolution patterns.
Cellular functions and pathways affected by PCGEM1, a prostate-specific gene associated with African-American prostate cancer patients (2004)

Proc Amer Assoc Cancer Res, Volume 45, 2004

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PCGEM1 is a novel class of prostate specific, androgen regulated gene that lacks protein-coding capacity, and may function as a non-coding RNA riboregulator. Evaluation of PCGEM1 expression in laser microdissected paired normal and tumor cells of 90 prostate cancer (CaP) patients revealed significantly elevated PCGEM1 expression levels in CaP cells of African- American patients (p=0.0002), suggesting potential roles for PCGEM1 in CaP biology. The objective of this study was to determine the cell biologic functions of PCGEM1 . LNCaP cells overexpressing PCGEM1 exhibited a marked growth advantage compared to vector control both in cell proliferation and in colony formation assays. Stably transfected LNCaP cells overexpressing PCGEM1 were used to assess biochemical mechanisms underlying its cell growth promoting effects. The effect of PCGEM1 overexpression in LNCaP cells on the phosphorylation state of key proteins involved in cellular pathways related to cell cycle, cell proliferation, and apoptosis was assayed. Protein lysates from exponentially growing cells were subjected to Western blotting and assayed using a panel of 36 phospho-specific antibodies. In LNCaP cells overexpressing PCGEM1 , a significant increase in phosphorylation of three out of 36 proteins, Rb(Ser807/811), GSK3beta(Ser9), and p38MAPK(Thr180/Tyr182) was detected. The phosphorylation of specific sites on these key signaling proteins induce specific downstream events currently under investigation in our laboratory. We conclude that overexpression of PCGEM1 promotes cell proliferation/colony formation of LNCaP cells and the underlying mechanisms may involve at least three different major pathways: the Rb, GSK3beta and p38MAPK pathways. These novel observations warrant future studies aimed at PCGEM1 functions, and its potential as therapeutic/biomarker target of CaP development especially in African-American patients.
Corn Stover Harvest, Tillage, and Cover Crop Effects on Soil Health Indicators (2018)

Core Ideas In no‐till continuous corn, cover crops increased potentially mineralizable N. Particulate organic matter C responded to tillage and residue removal at 0 to 5 cm. Stover removal for 5 yr negatively affected 2 of 12 measured soil properties. Monitoring soil health indicators (SHI) will help ensure that corn ( Zea mays L.) stover harvest is sustainable. This study examines SHI changes after 5 yr of growing continuous corn with either chisel plow or no‐tillage practices and harvesting 0, ∼35, or ∼60% of the stover. Two no‐tillage treatments with a cereal rye ( Secale cereale L.) cover crop and stover harvest rates of ∼35 or ∼60% were evaluated. All eight treatments were replicated four times in a randomized complete block design at an 11‐ha site in Boone County, IA. Soil samples were collected following grain and stover harvest from 0‐ to 5‐ and 5‐ to 15‐cm depth increments. Particulate organic matter C (POM‐C) decreased when stover was removed or the soil was chisel plowed. No‐till with 0% stover removal had 10 mg g –1 POM‐C in the 0‐ to 5‐cm soil layer, which was 1.9‐fold higher than in other treatments. Potentially mineralizable N (PMN) was greater under cover crop treatments. Average PMN values were 56.9 and 45.5 µg g –1 PMN for no‐till with cereal rye at 0‐ to 5‐ and 5‐ to 15‐cm depths, respectively, compared with 17.5 and ‐3.7 µg g –1 PMN for the same no‐till treatments without cereal rye. Other soil properties did not respond to increasing levels of stover removal. At this location and at the studied removal rates, 5 yr of harvesting corn stover did not decrease soil health, but POM‐C data suggest that changes may be occurring. Long‐term monitoring should continue to assess corn stover harvest sustainability.
Forest leaf area density profiles from the quantitative fusion of radar and hyperspectral data (2002)

The leaf area density (LAD) of a forest is an important indicator of forest biomass and is therefore pertinent to monitoring carbon sequestration and change. Quantitative physical models were used to estimate forest LAD from radar and hyperspectral airborne remote sensing observations. A parameter‐estimation technique based on physical models minimizes the need for in situ observations and thereby facilitates global remote sensing of forest structure. Using data from the NASA Airborne Synthetic Aperture Radar (AIRSAR) and the NASA Airborne Visible and Infrared Imaging Spectrometer (AVIRIS) over three forest plots in Central Oregon, parameters were estimated separately from the radar and hyperspectral data and then combined to form LAD. Gaussian relative LAD profiles were estimated from multialtitude interferometric and polarimetric AIRSAR data. Leaf area indices (LAI) were estimated from AVIRIS data and used to normalize the relative density profiles to produce LAD as a function of height. LAD was also determined from field measurements of geometric tree properties and LAI. LADs in the three forest plots were in the 0.02–0.18 m 2 m −3 range, with LAIs in the range 0.8–2.4 m 2 m −2 . The agreement between the remotely sensed and field‐measured LAD was typically 0.02 m 2 m −3 but occasionally as high as 0.06 m 2 m −3 , which was within a 1–2 standard error range. More complex models for the remotely sensed relative density, along with more diverse radar observation strategies, will improve LAD accuracy in the future. LAD estimation will also improve when radar, hyperspectral, and other relevant remote sensing data sets are combined in a single parameter‐estimation process, as opposed to the separate estimations performed in this first LAD demonstration.