gebhart/patrepeval huggingface dataset:
ChemInform Abstract: Synthesis of Insect Antifeedants. (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.
High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression (2012)

Many eukaryotic genes possess multiple alternative promoters with distinct expression specificities. Therefore, comprehensively annotating promoters and deciphering their individual regulatory dynamics is critical for gene expression profiling applications and for our understanding of regulatory complexity. We introduce RAMPAGE, a novel promoter activity profiling approach that combines extremely specific 5'-complete cDNA sequencing with an integrated data analysis workflow, to address the limitations of current techniques. RAMPAGE features a streamlined protocol for fast and easy generation of highly multiplexed sequencing libraries, offers very high transcription start site specificity, generates accurate and reproducible promoter expression measurements, and yields extensive transcript connectivity information through paired-end cDNA sequencing. We used RAMPAGE in a genome-wide study of promoter activity throughout 36 stages of the life cycle of Drosophila melanogaster, and describe here a comprehensive data set that represents the first available developmental time-course of promoter usage. We found that >40% of developmentally expressed genes have at least two promoters and that alternative promoters generally implement distinct regulatory programs. Transposable elements, long proposed to play a central role in the evolution of their host genomes through their ability to regulate gene expression, contribute at least 1300 promoters shaping the developmental transcriptome of D. melanogaster. Hundreds of these promoters drive the expression of annotated genes, and transposons often impart their own expression specificity upon the genes they regulate. These observations provide support for the theory that transposons may drive regulatory innovation through the distribution of stereotyped cis-regulatory modules throughout their host genomes.
Proposal for the Effect of Chondrocyte Volume on the Mineralization Rate (2001)

Mineralization of the cartilage matrix in embryonic long bones and growth plates is preceded by hypertrophy of chondrocytes. We hypothesize that the swollen hypertrophic cells exert pressure on the matrix, and that this pressure plays a role in the cartilage mineralization process. For this study, we asked the following questions. First, does the ratio of cell volume to matrix volume (CV/MV) increase from the proliferation to the hypertrophic zone in embryonic long bones? Second, is there a correlation between cell-volume increase and the mineralization rate in embryonic and postnatal long bones? The CV/MV ratios in the proliferation and hypertrophic zones in embryonic mouse metatarsals at 17 days of gestational age were determined using morphometric analyses. Confocal laser scanning microscopy was used to determine chondrocyte volumes. Cell volumes in the proliferation and hypertrophic zones of embryonic mouse metatarsals at 17 days of gestational age were compared to the ones in the metatarsal growth plates of nine-day-old mice. The mineralization rate was determined using photographs at 24-hour intervals. The CV/MV increased significantly from the proliferation to the hypertrophic zone, from 1.30 ± 0.15 (mean ± standard deviation) to 1.80 ± 0.18. The relative increase in cell volume from the proliferation to the hypertrophic zone was 1.6 for embryonic cells, i.e. from 370 ± 101 mm3, and 2.8 for postnatal cells, i.e. from 280 ± 41 mm3 to 786 ± 1553 (p &lt; 0.05). The mineralization rate was 295 ± 47 mm/24 hours and 382 ± 149 mm/24 hours for embryonic and postnatal metatarsals, respectively (p &lt; 0.05). The finding that chondrocyte volume increase is accompanied by a higher mineralization rate supports the hypothesis that cell hypertrophy plays an important role during the mineralization process.
Action parsing and goal inference using self as simulator (2006)

The ability to understand a teammate's actions in terms of goals and other mental states is an important element of cooperative behavior. Simulation theory argues in favor of an embodied approach whereby humans reuse parts of their cognitive structure for not only generating behavior, but also for simulating the mental states responsible for generating that behavior in others. We present our simulation-theoretic approach and demonstrates its performance in a collaborative task scenario. The robot offers its human teammate assistance by either inferring the human's belief states to anticipate their informational needs, or inferring the human's goal states to physically help the human achieve those goals.
Timing of Formation of a Wassonite-bearing Chondrule (2014)

Wassonite, ideally stoichiometric TiS, is a titanium monosulfide recently discovered in the Yamato 691 EH3 enstatite chondrite. Wassonite grains were located within the mesostasis of a single barred olivine chondrule. Such chondrules likely formed in the solar nebula by melting of fine grained precursor dust. The reduced nature of enstatite chondrites, and the wassonite-bearing chondrule in particular, may suggest precursor materials included Ti-bearing troilite, metallic Fe-Ni, and possibly graphite. Under the reducing conditions present in enstatite chondrites S can partition more readily into silicate melt, leading to raised Ti content of the residual Fe-FeS melt. By the time sulfide crystallized from the melt, the Ti concentration was high enough to form small grains of pure TiS - wassonite. As a mineral not previously observed in nature wassonite and its host chondrule may provide additional constraints on physical and chemical conditions in the solar nebula at a specific time and location relevant to planetary formation. Enstatite chondrites and Earth share similar isotopic compositions of Cr, Ni, Ti, O and N. Understanding the formation conditions of enstatite chondrite chondrules may therefore have wider relevance for terrestrial planet accretion and other early inner solar system processes. Here we present preliminary results of an investigation of the Al-Mg systematics of the only known wassonite-bearing chondrule. The goal of this study is to determine whether this chondrule's formation was contemporaneous with other enstatite chondrite chondrules and to establish its place in the broader timeline of solar system events.
Diagnostic Accuracy of Screening Arterial Spin-Labeling MRI Using Hadamard Encoding for the Detection of Reduced CBF in Adult Patients with Ischemic Moyamoya Disease (2021)

ASL MR imaging using Hadamard-encoded multiple postlabeling delays may be applicable as a screening tool because it can detect reduced CBF on brain perfusion SPECT with 100% sensitivity and a 100% negative predictive value in adult patients with ischemic Moyamoya disease.
Communicatiestoornissen na een hersentrauma (2014)

Een hersenletsel kan hoofdzakelijk tot drie typen communicatiestoornissen leiden: afasie, dysartrie en apraxie. Deze drie typen communicatiestoornissen kunnen voorkomen ongeacht de aard van het letsel. Een afasie kan bijvoorbeeld het gevolg zijn van een cerebrovasculair accident (cva), maar kan ook optreden ten gevolge van een tumor, een degeneratieve aandoening, een infectie, intoxicatie of ten gevolge van een trauma. Toch worden naargelang de aard van de hersenaandoening ook meer specifieke beelden gezien. Eén groep patiënten die aldus als een aparte populatie kan worden beschouwd, zijn de hersentraumapatiënten.
The Effect of -Cyclodextrin Inclusion on the Morphology of[Ru(bpy)<sub>2</sub>Cl(BPEB)](PF<sub>6</sub>) Films by Scanning Force Microscopy (2005)

Molecular level organization has been a subject of great relevance in supramolecular chemistry and nanotechnology. Supramolecular chemists count on the ability of molecules to form several kinds of organization, allowing the development of nanoscaled devices. In this way, the scanning probe microscopy provides a great tool for characterization, manipulation and interfacing such devices [1]. Regarding the ruthenium complexes [Ru(bpy)2Cl(BPEB)](PF6) and {[Ru(bpy)2Cl]2(BPEB)}(PF6)2, where bpy = 2,2'-bipyridine, the presence of the BPEB (1,4-bis[4-pyridyl)ethenyl]benzene) ligand has an important role as a recognition site for van der Waals interactions (Figure 1). On the other hand, cyclodextrins are macrocyclic molecules bearing a hydrophobic cavity that can support several types of guest molecules [2-3]. In this work we are showing the influence of the recognition site of the BPEB ligand and the formation of an inclusion compound in the patterning structures of films deposited over mica substrates, by SFM microscopy.
A comparative analysis of methods for air-launching vehicles from earth to sub-orbit or orbit (2006)

A variety of air-launched sub-orbital and orbital vehicles are demonstrated and others have been proposed recently by different organizations. The purpose of this article is three-fold: (a) to identify benefits of air-launching vehicles for space missions; (b) to categorize airlaunched vehicles with respect to how they are integrated to their carrier vehicle; (c) to identify benefits and shortcomings of these methods. Our analysis study shows that air-launching provides mobility and deployment advantages over surface launching. It can also provide performance advantages over surface launching. However, many air-launch concepts proposed require advance technologies that are currently not available.
Application of MRI Post-processing in Presurgical Evaluation of Non-lesional Cingulate Epilepsy (2018)

<b>Background and Purpose:</b> Surgical management of patients with cingulate epilepsy (CE) is highly challenging, especially when the MRI is non-lesional. We aimed to use a voxel-based MRI post-processing technique, implemented in a morphometric analysis program (MAP), to facilitate detection of subtle epileptogenic lesions in CE, thereby improving surgical evaluation of patients with CE with non-lesional MRI by visual inspection. <b>Methods:</b> Included in this retrospective study were 9 patients with CE (6 with negative 3T MRI and 3 with subtly lesional 3T MRI) who underwent surgery and became seizure-free or had marked seizure improvement with at least 1-year follow-up. MRI post-processing was applied to pre-surgical T1-weighted volumetric sequence using MAP. The MAP finding was then coregistered and compared with other non-invasive imaging tests (FDG-PET, SPECT and MEG), intracranial EEG ictal onset, surgery location and histopathology. <b>Results:</b> Single MAP+ abnormalities were found in 6 patients, including 3 patients with negative MRI, and 3 patients with subtly lesional MRI. Out of these 6 MAP+ patients, 4 patients became seizure-free after complete resection of the MAP+ abnormalities; 2 patients didn't become seizure-free following laser ablation that only partially overlapped with the MAP+ abnormalities. All MAP+ foci were concordant with intracranial EEG ictal onset (when performed). The localization value of FDG-PET, SPECT and MEG was limited in this cohort. FCD was identified in all patients' surgical pathology except for two cases of laser ablation with no tissue available. <b>Conclusion:</b> MAP provided helpful information for identifying subtle epileptogenic abnormalities in patients with non-lesional cingulate epilepsy. MRI postprocessing should be considered to add to the presurgical evaluation test battery of non-lesional cingulate epilepsy.
Frequency-domain engineering of bright squeezed vacuum for continuous-variable quantum information (2023)

Multimode bright squeezed vacuum is a non-classical state of light hosting a macroscopic photon number while offering promising capacity for encoding quantum information in its spectral degree of freedom. Here, we employ an accurate model for parametric downconversion in the high-gain regime and use nonlinear holography to design quantum correlations of bright squeezed vacuum in the frequency domain. We propose the design of quantum correlations over two-dimensional lattice geometries that are all-optically controlled, paving the way toward continuous-variable cluster state generation on an ultrafast timescale. Specifically, we investigate the generation of a square cluster state in the frequency domain and calculate its covariance matrix and the quantum nullifier uncertainties, that exhibit squeezing below the vacuum noise level.
The influence of random indium alloy fluctuations in indium gallium nitride quantum wells on the device behavior (2014)

In this paper, we describe the influence of the intrinsic indium fluctuation in the InGaN quantum wells on the carrier transport, efficiency droop, and emission spectrum in GaN-based light emitting diodes (LEDs). Both real and randomly generated indium fluctuations were used in 3D simulations and compared to quantum wells with a uniform indium distribution. We found that without further hypothesis the simulations of electrical and optical properties in LEDs such as carrier transport, radiative and Auger recombination, and efficiency droop are greatly improved by considering natural nanoscale indium fluctuations.
BuGZ facilitates loading of spindle assembly checkpoint proteins to kinetochores in early mitosis (2020)

BuGZ is a kinetochore component that binds to and stabilizes Bub3, a key player in mitotic spindle assembly checkpoint signaling. Bub3 is required for kinetochore recruitment of Bub1 and BubR1, two proteins that have essential and distinct roles in the checkpoint. Both Bub1 and BubR1 localize to kinetochores through interactions with Bub3, which are mediated through conserved GLEBS domains in both Bub1 and BubR1. BuGZ also has a GLEBS domain, which is required for its kinetochore localization as well, presumably mediated through Bub3 binding. Although much is understood about the requirements for Bub1 and BubR1 interaction with Bub3 and kinetochores, much less is known regarding BuGZ's requirements. Here, we used a series of mutants to demonstrate that BuGZ kinetochore localization requires only its core GLEBS domain, which is distinct from the requirements for both Bub1 and BubR1. Furthermore, we found that the kinetics of Bub1, BubR1, and BuGZ loading to kinetochores differ, with BuGZ localizing prior to BubR1 and Bub1. To better understand how complexes containing Bub3 and its binding partners are loaded to kinetochores, we carried out size-exclusion chromatography and analyzed Bub3-containing complexes from cells under different spindle assembly checkpoint signaling conditions. We found that prior to kinetochore formation, Bub3 is complexed with BuGZ but not Bub1 or BubR1. Our results point to a model in which BuGZ stabilizes Bub3 and promotes Bub3 loading onto kinetochores in early mitosis, which, in turn, facilitates Bub1 and BubR1 kinetochore recruitment and spindle assembly checkpoint signaling.
Industrialization of Hot Wire Chemical Vapor Deposition for thin film applications (2015)

The consequences of implementing a Hot Wire Chemical Vapor Deposition (HWCVD) chamber into an existing in-line or roll-to-roll reactor are described. The hardware and operation of the HWCVD production reactor is compared to that of existing roll-to-roll reactors based on Plasma Enhanced Chemical Vapor Deposition. The most important consequences are the technical consequences and the economic consequences, which are both discussed. The technical consequences are adaptations needed to the hardware and to the processing sequences due to the different interaction of the HWCVD process with the substrate and already deposited layers. The economic consequences are the reduced investments in radio frequency (RF) supplies and RF components. This is partially offset by investments that have to be made in higher capacity pumping systems. The most mature applications of HWCVD are moisture barrier coatings for thin film flexible devices such as Organic Light Emitting Diodes and Organic Photovoltaics, and passivation layers for multicrystalline Si solar cells, high mobility field effect transistors, and silicon heterojunction cells (also known as heterojunction cells with intrinsic thin film layers). Another example is the use of Si in thin film photovoltaics. The cost perspective per unit of thin film photovoltaic product using HWCVD is estimated at 0.07 €/Wp for the Si thin film component.
Resolving Cache-Load Imbalance Bottleneck of Stochastic Shared-Cache Networks (2022)

This work proposes a two-layered coded caching scheme to resolve the cache-load imbalance bottleneck of the coded caching in a stochastic shared-cache network where the association between users and shared caches is random, i.e., for the scenario where each user can appear within the coverage area of &#x2013; and subsequently is assisted by &#x2013; a specific cache-enabled helper node based on a uniform probability distribution. To insightfully capture the effectiveness of our scheme in mitigating the adverse effect of randomness in shared-cache networks, we derive the exact scaling laws of the average delivery time. In the scenario of an error-free broadcast channel of bounded capacity per unit of time where the delivery involves K users and &#x039B; cache-enabled helper nodes, we show that empowering users with an additional layer of caching can significantly mitigate, and in certain memory regimes completely nullify the adverse effects of the cache-load imbalance bottleneck.
Mycobacterium abscessus MAB2560 induces maturation of dendritic cells via Toll-like receptor 4 and drives Th1 immune response (2014)

In this study, we showed that Mycobacterium abscessus MAB2560 induces the maturation of dendritic cells (DCs), which are representative antigen-presenting cells (APCs). M. abscessus MAB2560 stimulate the production of pro-inflammatory cytokines [interleukin (IL)-6, tumor necrosis factor (TNF)-α, IL-1β, and IL-12p70] and reduce the endocytic capacity and maturation of DCs. Using TLR4-/- DCs, we found that MAB2560 mediated DC maturation via Toll-like receptor 4 (TLR4). MAB2560 also activated the MAPK signaling pathway, which was essential for DC maturation. Furthermore, MAB2560- treated DCs induced the transformation of naïve T cells to polarized CD4+ and CD8+ T cells, which would be crucial for Th1 polarization of the immune response. Taken together, our results indicate that MAB2560 could potentially regulate the host immune response to M. abscessus and may have critical implications for the manipulation of DC functions for developing DC-based immunotherapy.
Low-level multimodal integration on Riemannian manifolds for automatic pedestrian detection (2012)

In Computer Vision, automated pedestrian detection is surely one of the hottest topics, with important applications in surveillance and security. To this end, information integration from different imaging modalities, such as thermal infrared and visible spectrum, can significantly improve the detection rate with respect to monomodal stategies. A common scheme consists of extracting two sets of features, from thermal and visible images of the same scene respectively, and stacking them together into a single feature set, ignoring possible and meaningful inter-media dependencies. Here we propose a fusion scheme which acts at the feature-level, taking standard pixel characteristics (such as first/second order spatial derivatives or Local Binary Pattern) and designing a composite descriptor that, at the same time, encodes the information coming from the separate modalities, as well as the cross-modal mutual relationships in the form of covariances. The descriptor, which lies on a Riemannian manifold, is projected onto a Euclidean tangent space and then fed into a Support Vector Machine classifier. Experiments performed on the OTCBVS dataset [1], and validated statistically, demonstrate that our method outperforms significantly the single modality policies as well as different fusion schemes at the pixel, feature and decision level.
Gaussian deconvolution method for identification of impairments in optical signal transmission (2004)

Feature Issue on Optical Performance Monitoring (OPM). Amplitude histograms that have simultaneously deterministic perturbations and Gaussian noise are analyzed by a Gaussian deconvolution method that allows us to identify the deterministic perturbations that are usually hidden by the noise. In addition, the strength of the Gaussian noise and the parameters of the deterministic perturbations can be evaluated qualitatively and quantitatively. Numerical examples for the evaluation of histograms with intersymbol interference and with deterministic jitter show the validity of the method.
Effect of glucocorticoids and interferon-gamma on the oxidative responses of monocytes from leprosy patients and normal donors. (1991)

Leprosy patients suffering from erythema nodosum leprosum are frequently treated with glucocorticosteroids. The role glucocorticosteroids and interferon-gamma (IFN-gamma) play in regulating the interaction of phagocytic cells with Mycobacterium leprae was examined. Monocytes from leprosy patients receiving prednisone therapy responded to lower concentrations of IFN-gamma in vitro with enhanced superoxide anion release when challenged with M. leprae or M. bovis BCG than did monocytes from healthy subjects and other leprosy patients. Although the number of patients was small and the population heterogeneous, the data suggested that prednisone could alter IFN-gamma efficacy and led to the examination of the effect of glucocorticosteroids on IFN-gamma activation of monocytes. IFN-gamma treatment following in vitro dexamethasone pretreatment of monocytes from healthy subjects resulted in a greater enhancement of superoxide anion generation than that observed with IFN-gamma treatment alone. These findings are important considerations in evaluating patient immune function because IFN-gamma is being used in a number of clinical trials with leprosy patients.
The Situation Awareness Framework for Explainable AI (SAFE-AI) and Human Factors Considerations for XAI Systems (2022)

Recent advances in artificial intelligence (AI) have drawn attention to the need for AI systems to be understandable to human users. The explainable AI (XAI) literature aims to enhance human understanding and human-AI team performance by providing users with necessary information about AI system behavior. Simultaneously, the human factors literature has long addressed important considerations that contribute to human performance, including how to determine human informational needs, human workload, and human trust in autonomous systems. Drawing from the human factors literature, we propose the Situation Awareness Framework for Explainable AI (SAFE-AI), a three-level framework for the development and evaluation of explanations about AI system behavior. Our proposed levels of XAI are based on the informational needs of human users, which can be determined using the levels of situation awareness (SA) framework from the human factors literature. Based on our levels of XAI framework, we also suggest a method for assessing the effectiveness of XAI systems. We further detail human workload considerations for determining the content and frequency of explanations as well as metrics that can be used to assess human workload. Finally, we discuss the importance of appropriately calibrating user trust in AI systems through explanations along with other trust-related considerations for XAI, and we detail metrics that can be used to evaluate user trust in these systems.