gebhart/patrepeval huggingface dataset:
Comparison of template registration methods for multi-site meta-analysis of brain morphometry (2016)

Neuroimaging consortia such as ENIGMA can significantly improve power to discover factors that affect the human brain by pooling statistical inferences across cohorts to draw generalized conclusions from populations around the world. Voxelwise analyses such as tensor-based morphometry also allow an unbiased search for effects throughout the brain. Even so, such consortium-based analyses are limited by a lack of high-powered methods to harmonize voxelwise information across study populations and scanners. While the simplest approach may be to map all images to a single standard space, the benefits of cohort-specific templates have long been established. Here we studied methods to pool voxel-wise data across sites using templates customized for each cohort but providing a meaningful common space across all studies for voxelwise comparisons. As non-linear 3D MRI registrations represent mappings between images at millimeter resolution, we need to consider the reliability of these mappings. To evaluate these mappings, we calculated test-retest statistics on the volumetric maps of expansion and contraction. Further, we created study-specific brain templates for ten T1-weighted MRI datasets, and a common space from four study-specific templates. We evaluated the efficacy of using a two-step registration framework versus a single standard space. We found that the two-step framework more reliably mapped subjects to a common space.
Synthesis and Evaluation of the Luciferase‐Oligodeoxynucleotide for the Sequence‐Selective Detection of Nucleic Acids (2008)

A new method for the synthesis of ODN-luciferase conjugate was investigated as a signal-amplifying sensor of the target nucleic acids. The conjugation of the luciferase was successfully achieved between the cysteine residue and the 2-amino-6-vinylpurine nucleoside of the ODN probe without significant inactivation of luciferase. The ODN-luciferase conjugate modified with PEG retained the luciferase activity and selectivity during the hybridization with the target ODN.
Improved understanding of peripheral T-cell lymphomas. (2010)

Peripheral T-cell lymphomas (PTCLs) are rare and heterogeneous non-Hodgkin lymphomas that have been separated by clinical presentation, histology, immunohistochemistry markers, infectious agents, and genetic abnormalities. They may have extranodal dissemination and are often aggressive, especially when they express cytotoxic markers. The international T-cell Non-Hodgkin Lymphoma Study Group collaboration has highlighted differences in the frequency of these entities in different geographic areas.[1,2] For example, HTLV-1+ adult T-cell lymphomas are found in Japan and nasal NK/T-cell lymphoma occurs predominantly in Asian countries. The most common PTCLs are unique and not able to be classified by a specific marker or tumor antigen, and are known as peripheral T-cell lymphomas, not otherwise specified (PTCL-NOS).
Comparison between software volumetric breast density estimates in breast tomosynthesis and digital mammography images in a large public screening cohort (2018)

• There was a high correlation between continuous volumetric breast density in DM and BT. • There was substantial agreement between software breast density categories (four groups) in DM and BT; with clinically warranted binary software breast density categories, the agreement increased markedly. • There was moderate agreement between radiologists' BI-RADS scores and software breast density categories in DM and BT.
Integrated appraisal of water quality for Qiangwei River based on neural network (2009)

基于BP神经网络的改进算法,提出了以Matlab7.0为平台的算法程序的人工神经网络水质评价模型.参照 (GB 3838-2002),确定了神经网络学习和训练的样本以及模型的相应参数,并以流经连云港市蔷薇河的六个断面的水质数据为样本,进行水质综合评价分析.
Repression and inactivation of α-amylase in Thermomonospora species during growth on cellobiose (1997)

Thermophilic actinomycetes establish themselves as numerically dominant bacterial populations in selected high temperature environments by virtue of their exoenzymic ability to degrade the complex polysaccharides in thermogenic plant biomass. When <i>Thermomonospora curvata and Thermomonospora fusca</i> were grown on a mixture of cellulose and starch in mineral salts minimal medium, α-amylase was repressed via inhibition of maltose uptake by cellobiose. Addition of cellobiose to exponential phase cells growing on maltose or maltotriose triggered rapid degradation of extant amylase in the culture fluid of wild-type cells, but not in a protease-deficient mutant of <i>T. fusca.</i> A serine protease purified from <i>T. fusca</i> caused inactivation of the amylase in culture fluid of the mutant when added at a concentration approximating to that of the wild-type strain. The chelating agent, EDTA, accelerated inactivation by the protease, while the presence of calcium or amylase reaction products protected the amylase. Therefore, during growth in an environment containing multiple polysaccharides, these thermophiles control the levels of their extracellular depolymerizing enzymes via both inducer exclusion and proteolytic inactivation.
Expanded expression of Sonic Hedgehog inAstyanaxcavefish:multiple consequences on forebrain development and evolution (2007)

Ventral midline Sonic Hedgehog (Shh) signalling is crucial for growth and patterning of the embryonic forebrain. Here, we report how enhanced Shh midline signalling affects the evolution of telencephalic and diencephalic neuronal patterning in the blind cavefish Astyanax mexicanus, a teleost fish closely related to zebrafish. A comparison between cave- and surface-dwelling forms of Astyanax shows that cavefish display larger Shh expression in all anterior midline domains throughout development. This does not affect global forebrain regional patterning, but has several important consequences on specific regions and neuronal populations. First, we show expanded Nkx2.1a expression and higher levels of cell proliferation in the cavefish basal diencephalon and hypothalamus. Second, we uncover an Nkx2.1b-Lhx6-GABA-positive migratory pathway from the subpallium to the olfactory bulb, which is increased in size in cavefish. Finally, we observe heterochrony and enlarged Lhx7 expression in the cavefish basal forebrain. These specific increases in olfactory and hypothalamic forebrain components are Shh-dependent and therefore place the telencephalic midline organisers in a crucial position to modulate forebrain evolution through developmental events, and to generate diversity in forebrain neuronal patterning.
Limiting Flexibility in Multiplication over GF(2m): A Design Methodology (2006)

Multiplication over the field GF(2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sup> ) is computationally expensive, not least because the operation involves modulo reduction. It is typical to fix the field and field representation to improve performance, but some applications need to operate over multiple fields. This work investigates the cost of this flexibility with application to elliptic curve cryptography (ECC), both analytically and empirically through FPGA implementation. A design methodology is presented for limiting the flexibility to a number of prescribed fields with the representation fixed for each, and the methodology is applied to the design of a bit-serial multiplier over GF(2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sup> ). FPGA implementation results are given; and it is shown that the practical advantage of the proposed approach is considerable in terms of speed versus area trade-off. In fact, only a 12.3% area overhead was incurred by the flexible implementation compared to the fixed field implementation, while still achieving the same speed performance
Subcontracting Microwork (2017)

Mainstream crowdwork platforms treat microtasks as indivisible units; however, in this article, we propose that there is value in re-examining this assumption. We argue that crowdwork platforms can improve their value proposition for all stakeholders by supporting subcontracting within microtasks. After describing the value proposition of subcontracting, we then define three models for microtask subcontracting: real-time assistance, task management, and task improvement, and reflect on potential use cases and implementation considerations associated with each. Finally, we describe the outcome of two tasks on Mechanical Turk meant to simulate aspects of subcontracting. We reflect on the implications of these findings for the design of future crowd work platforms that effectively harness the potential of subcontracting workflows.
Optimization and Performance Evaluation of Single-Mode SOI Waveguides for Ultra-Broadband C-to-S Wavelength Conversion (2023)

In order to keep up with expected growth in data traffic, using multiple bands beyond the C band is an appealing solution as it can partly reuse deployed optical fibers. One way of handling multi-band data generation and reception is by using all-optical wavelength converters (AOWCs) to translate to or from the C band, where commercial equipment is easily available. In this work, we therefore designed and realized an AOWC targeting C-to-S band conversion. To respect the requirements of commercial applications, we aimed for a low-complexity high-bandwidth implementation with reasonably low power consumption, tolerance for typical process variations and potential for further integration. Thus we implemented the AOWC as a strip waveguide in a Silicon-on-insulator (SOI) technology. An optimization of the conversion bandwidth was conducted during design and initial characterizations confirmed a conversion efficiency of −32.8 dB and a high bandwidth of about 35 nm with grating couplers and likely beyond 50 nm for edge couplers. Using the fabricated converters, we were able to demonstrate a marginal 0.3 dB optical signal-to-noise ratio (OSNR) penalty for a back-to-back (b2b) transmission of a single-channel single-polarization 32 GBd quadrature-phase-shift keying (QPSK) signal converted from C to S band. Additionally, this converted signal was successfully transmitted over 100 km of standard single-mode fiber (SSMF). Finally, crosstalk issues arising in multi-channel conversion were investigated.
Kinetics of intercalation of fluorescent probes in magnesium–aluminium layered double hydroxide within a multiscale reaction–diffusion framework (2016)

We report the synthesis of magnesium-aluminium layered double hydroxide (LDH) using a reaction-diffusion framework (RDF) that exploits the multiscale coupling of molecular diffusion with chemical reactions, nucleation and growth of crystals. In an RDF, the hydroxide anions are allowed to diffuse into an organic gel matrix containing the salt mixture needed for the precipitation of the LDH. The chemical structure and composition of the synthesized magnesium-aluminium LDHs are determined using powder X-ray diffraction (PXRD), thermo-gravimetric analysis, differential scanning calorimetry, solid-state nuclear magnetic resonance (SSNMR), Fourier transform infrared and energy dispersive X-ray spectroscopy. This novel technique also allows the investigation of the mechanism of intercalation of some fluorescent probes, such as the neutral three-dimensional rhodamine B (RhB) and the negatively charged two-dimensional 8-hydroxypyrene-1,3,6-trisulfonic acid (HPTS), using in situ steady-state fluorescence spectroscopy. The incorporation of these organic dyes inside the interlayer region of the LDH is confirmed via fluorescence microscopy, solid-state lifetime, SSNMR and PXRD. The activation energies of intercalation of the corresponding molecules (RhB and HPTS) are computed and exhibit dependence on the geometry of the involved probe (two or three dimensions), the charge of the fluorescent molecule (anionic, cationic or neutral) and the cationic ratio of the corresponding LDH.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.
Fatty acid synthetase activity in the liver and adipose tissue of rats fed with various carbohydrates (1972)

1. The inclusion of sucrose in the diet of rats led to an increase in hepatic fatty acid synthetase activity compared with that of rats fed with starch as the sole carbohydrate. The higher activity occurred within 18h of the introduction of sucrose and persisted with fluctuations for the 30 days of the experiment. Reversal of the diets in some rats after 21 days led to changes in the enzyme activity to values appropriate to the second diet. The plasma triglyceride concentration followed a similar pattern. 2. A comparison of the effects of diets with starch, glucose, maltose, sucrose or fructose showed that fructose gave the highest values of triglyceride content and of fatty acid synthetase activity in liver, but the lowest values of the synthetase activity in adipose tissue and the lowest values of plasma insulin concentration. These effects may perhaps be attributed to the low insulin response to fructose and to the high affinity of the liver for this sugar. 3. When the diet contained fructose or sucrose there was a correlation between hepatic synthetase activity and plasma triglyceride concentration. Neither of these, however, was related to plasma insulin concentration. On the other hand, there was a correlation between plasma insulin concentration and fatty acid synthetase activity in adipose tissue. 4. When rats were starved and then re-fed the differences in enzyme activities induced by fructose or glucose were minimized. This, together with the varying degree of difference during the course of the experiments, may explain why other workers, using the starvation-re-feeding technique and making measurements on one day only, have failed to observe differences in the activities of lipogenic enzymes in animals fed with either fructose or glucose.
Genetic analysis of blood molecular phenotypes reveals regulatory networks affecting complex traits: a DIRECT study (2021)

Abstract Genetic variants identified by genome-wide association studies can contribute to disease risk by altering the production and abundance of mRNA, proteins and other molecules. However, the interplay between molecular intermediaries that define the pathway from genetic variation to disease is not well understood. Here, we evaluated the shared genetic regulation of mRNA molecules, proteins and metabolites derived from whole blood from 3,029 human donors. We find abundant allelic heterogeneity, where multiple variants regulate a particular molecular phenotype, and pleiotropy, where a single variant was associated with multiple molecular phenotypes over multiple genomic regions. We find varying proportions of shared genetic regulation across phenotypes, highest between expression and proteins (66.6%). We were able to recapitulate a substantial proportion of gene expression genetic regulation in a diverse set of 44 tissues, with a median of 88% shared associations for blood expression and 22.3% for plasma proteins. Finally, the genetic and molecular associations were represented in networks including 2,828 known GWAS variants. One sub-network shows the trans relationship between rs149007767 and RTEN , and identifies GRB10 and IKZF1 as candidates mediating genes. Our work provides a roadmap to understanding molecular networks and deriving the underlying mechanism of action of GWAS variants across different molecular phenotypes.
Critical steps in degradation of chloroaromatics by rhodococci IV. Detailed kinetics of substrate removal and product formation by resting pre‐adapted cells (1989)

Abstract In kinetic experiments it was demonstrated that turnover of various monochloroaromatic non‐growth substrates (i.e. 2‐chloroaniline, 3‐chloroaniline, 3‐chlorophenol, 4‐chlorophenol, 3‐chlorobenzoic acid) by resting pre‐adapted cells of Rhodococcus sp. An 117 or An 213 typically results in the accumulation of cis ‐4‐carboxymethylene‐but‐2‐en‐4‐olide as the principle dead‐end product while cometabolic 2‐chloroaniline turnover by resting aniline‐grown cells of Rhodococcus rubropertinctus IMET 7481 yielded nearly stoichiometric amounts of 2‐chloro‐ cis,cis ‐muconic acid. Evidence is presented that the observed cometabolic effect of glucose on turnover of the respective monochloroaromatics is primarily associated with their initial oxygenative conversion into chlorocatechols. Based on the described experimental data, it was concluded that the failure of rhodococci to bring about total degradation of chloroaromatics through chlorocatechols is mainly due to the absence in these organisms of a modified ortho ‐cleavage pathway (i.e. maleylacetatepathway).
VP16-Dependent Association of Chromatin-Modifying Coactivators and Underrepresentation of Histones at Immediate-Early Gene Promoters during Herpes Simplex Virus Infection (2004)

During infection by herpes simplex virus type 1 (HSV-1), the virion protein VP16 activates the transcription of viral immediate-early (IE) genes. Genetic and biochemical assays have shown that the potent transcriptional activation domain of VP16 can associate with general transcription factors and with chromatin-modifying coactivator proteins of several types. The latter interactions are particularly intriguing because previous reports indicate that HSV-1 DNA does not become nucleosomal during lytic infection. In the present work, chemical cross-linking and immunoprecipitation assays were used to probe the presence of activators, general transcription factors, and chromatin-modifying coactivators at IE gene promoters during infection of HeLa cells by wild-type HSV-1 and by RP5, a viral strain lacking the VP16 transcriptional activation domain. The presence of VP16 and Oct-1 at IE promoters did not depend on the activation domain. In contrast, association of RNA polymerase II, TATA-binding protein, histone acetyltransferases (p300 and CBP), and ATP-dependent remodeling proteins (BRG1 and hBRM) with IE gene promoters was observed in wild-type infections but was absent or reduced in cells infected by RP5. In contrast to the previous evidence for nonnucleosomal HSV-1 DNA, histone H3 was found associated with viral DNA at early times of infection. Interestingly, histone H3 was underrepresented on IE promoters in a manner dependent on the VP16 activation domain. Thus, the VP16 activation domain is responsible for recruiting general transcription factors and coactivators to IE promoters and also for dramatically reducing the association of histones with those promoters.
Effective Terahertz Wave Parametric Generation Depending on the Pump Pulse Width Using a LiNbO3 Crystal (2017)

Injection-seeded terahertz (THz)-wave parametric generation pumped by subnanosecond pulses was demonstrated as an exploration of the effective pump pulse width. In experiments, pump sources with different pump widths of 35-850 ps were used. The relationship between the undesirable effect of stimulated Brillouin scattering (SBS) and the THz-wave output in LiNbO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> was analyzed. The transient effect on SBS was not actualized around the acoustic phonon lifetime of LiNbO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> . Pump widths below 420 ps were found to provide THz-wave generation with an energy conversion efficiency of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-4</sup> . With a pump width of 700 ps, which is around five phonon lifetimes, the conversion efficiency was decreased about one order of magnitude from that of the pump width of 420 ps. Additionally, the peak power of the THz-wave output was maintained at about 15 kW with an actual range of 10-20 kW below 200 ps. A continuous change in the THz-wave pulse energy was obtained for six-fold energy scaling from 100 to 600 nJ.
Stress-Induced Anomalous Growth in Lateral Solid-Phase Epitaxy of Ge-Incorporated Si Films (1995)

Lateral solid-phase epitaxy (LSPE) characteristics of Ge-incorporated amorphous Si films which are deposited on SiO 2 /Si (100) structures with [010] seed openings are investigated. It has been found in P-doped amorphous Si films that the LSPE growth rate at 600° C is enhanced about sixfold by incorporation of 0.5 at.% Ge atoms, and that the maximum growth length is about 21 µ m. It has also been found that the growth in the film with 1 at.% Ge atoms stops for a few hours upon annealing at temperatures lower than 600° C at a length of about 2 µ m from the seed edge and it proceeds again as annealing time is extended. To clarify the origin of the anomalous growth rate, the residual stress in the films has been measured using microprobe Raman spectrometry, and it is concluded that the origin of the enhanced growth is the residual stress in the films. Finally, it is suggested that the Ge-incorporated stress effect may be explained by the critical thickness theory in pseudomorphic growth of Si 1- x Ge x films on Si substrates.
Electrochemical Corrosion Behavior of Carbon Steel with and without High Residual Elements (2020)

Abstract Residual elements (RE) in carbon steel, not specifically included in the specified steel, appear to influence the corrosion rate under certain conditions, especially in services involving hydrofluoric acid (HF). The relative proportions of RE, specifically %C, %Ni, %Cu, and %Cr in carbon steel base and weld metals used in refineries, especially in alkylation processes with HF as the catalyst, significantly impact corrosion behavior. Studies described in the literature show corrosion damage with high RE (Cu + Ni + Cr &amp;gt;0.20) components as compared to low RE (Cu + Ni + Cr &amp;lt;0.20) components. In this study, electrochemical corrosion testing was performed on a 3-inch pipe elbow section with high REs that had developed a through-wall leak in service. Test results were compared to those obtained on a similar pipe elbow section with lower REs. The samples were exposed to 50% HF at room temperature and at 65°C. Linear polarization resistance (LPR) corrosion rates were measured at both temperatures. Potentiodynamic (PD) polarization scans were performed on samples of low and high RE steel exposed to 50% HF at room temperature. Test results indicated that LPR corrosion rates were higher for the high RE carbon steel samples than for low RE carbon steel samples at both temperatures. PD scans showed that the critical current densities were higher for high RE steel than for low RE steel.
Real-Time Approximate Subsurface Scattering on Graphics Hardware (2007)

This paper presents an image-space approximation technique for real-time subsurface scattering. We first create transmitted irradiance samples on shadow maps and then estimate single scattering efficiently using a method similar to shadow mapping, with adaptive deterministic sampling. We incorporate this single-scattering with a recently proposed technique for multiple scattering. We demonstrate that our technique produces high-quality images of animated scenes. We archived hundreds of frames per second on graphics hardware without lengthy preprocessing.