gebhart/patrepeval huggingface dataset:
ergm.graphlets: A Package for ERG Modeling Based on Graphlet Statistics (2014)

Exponential-family random graph models (ERGMs) are probabilistic network models that are parametrized by sufficient statistics based on structural (i.e., graph-theoretic) properties. The ergm package for the R statistical computing system is a collection of tools for the analysis of network data within an ERGM framework. Many different network properties can be employed as sufficient statistics for ERGMs by using the model terms defined in the ergm package; this functionality can be expanded by the creation of packages that code for additional network statistics. Here, our focus is on the addition of statistics based on graphlets. Graphlets are small, connected, and non-isomorphic induced subgraphs that describe the topological structure of a network. We introduce an R package called ergm.graphlets that enables the use of graphlet properties of a network within the ergm package of R. The ergm.graphlets package provides a complete list of model terms that allows to incorporate statistics of any 2-, 3-, 4- and 5-node graphlet into ERGMs. The new model terms of ergm.graphlets package enable both ERG modelling of global structural properties and investigation of relationships between nodal attributes (i.e., covariates) and local topologies around nodes.
Evacetrapib is a novel, potent, and selective inhibitor of cholesteryl ester transfer protein that elevates HDL cholesterol without inducing aldosterone or increasing blood pressure (2011)

Cholesteryl ester transfer protein (CETP) catalyses the exchange of cholesteryl ester and triglyceride between HDL and apoB containing lipoprotein particles. The role of CETP in modulating plasma HDL cholesterol levels in humans is well established and there have been significant efforts to develop CETP inhibitors to increase HDL cholesterol for the treatment of coronary artery disease. These efforts, however, have been hampered by the fact that most CETP inhibitors either have low potency or have undesirable side effects. In this study, we describe a novel benzazepine compound evacetrapib (LY2484595), which is a potent and selective inhibitor of CETP both in vitro and in vivo. Evacetrapib inhibited human recombinant CETP protein (5.5 nM IC(50)) and CETP activity in human plasma (36 nM IC(50)) in vitro. In double transgenic mice expressing human CETP and apoAI, evacetrapib exhibited an ex vivo CETP inhibition ED(50) of less than 5 mg/kg at 8 h post oral dose and significantly elevated HDL cholesterol. Importantly, no blood pressure elevation was observed in rats dosed with evacetrapib at high exposure multiples compared with the positive control, torcetrapib. In addition, in a human adrenal cortical carcinoma cell line (H295R cells), evacetrapib did not induce aldosterone or cortisol biosynthesis whereas torcetrapib dramatically induced aldosterone and cortisol biosynthesis. Our data indicate that evacetrapib is a potent and selective CETP inhibitor without torcetrapib-like off-target liabilities. Evacetrapib is currently in phase II clinical development.
Analysis of on-road remote sensing as a tool for automobile emissions control. Final report (1990)

The goal of the project was to demonstrate the ability of remote sensing to determine, and potentially lead to control of mobile source emissions in the Chicago metropolitan area. A remote sensor for on-road carbon monoxide motor vehicle emissions was used in conjunction with a video freeze-frame system which allows the instantaneous carbon monoxide emissions measurements obtained from passing vehicles to be superimposed on a picture of the vehicle and its license plate. The license plates can then be recorded and identified through state records and the emissions linked to that vehicle. The remote sensor for on-road carbon monoxide (CO) emissions has been developed at the University of Denver. The results have been verified by comparison to on-road and to on-dynamometer vehicle emissions readings.
Analysis of the constituents of the volatile oil from the Leaf of Lindera Glauca(Sieb.et Zucc.)BL.from Zhejiang (2011)

OBJECTIVE To analyze the chemical constituents of the volatile oil from the leaves of Lindera Glauca(Sieb.et Zucc.) BL.from Zhejiang.METHODS The volatile oil was extracted by steam distillation,analyzed by Gas Chromatography-Mass Spectrometry and elucidated based on the standard mass spectral data.The relative content of each composition was calculated by area normalization method.RESULTS Twenty-one kinds of essential components were identified from the volatile oil.CONCLUSION Of the volatile oil,the major constituents were.alpha.-Cadinol,Caryophyllene oxide,.tau.-Muurolol,1,6,10-Dodecatrien-3-ol,3,7,11-trimethyl-,(S-(Z))-,1-Naphthalenol,1,2,3,4,4a,7,8,8a-octahydro-1,6-dimethyl-4-(1-methylethyl)-,(1R-(1.alpha.,4.beta.,4a.beta.,8a.beta.))-,Alloaromadendrene oxide-(1),n-Hexadecanoic acid,Santalol,2,6,10-Dodecatrien-1-ol,3,7,11-trimethyl-,(E,E)-,which were 50.07% of the whole volatile oil.
Query-Adaptive Fusion for Multimodal Search Search systems need to have the flexibility to adapt to each query so a search strategy that is likely to provide the most useful retrieval results can be employed. (2008)

We conduct a broad survey of query-adaptive search strategies in a variety of application domains, where the internal retrieval mechanisms used for search are adapted in response to the anticipated needs for each individual query experienced by the system. While these query-adaptive ap- proaches can range from meta-search over text collections to multimodal search over video databases, we propose that all such systems can be framed and discussed in the context of a single,unifiedframework.Inourpaper,wekeepaneyetowards the domain of video search, where search cues are available from a rich set of modalities, including textual speech transcripts, low-level visual features, and high-level semantic concept detectors. The relative efficacy of each of the modal- ities is highly variant between many types of queries. We observe that the state of the art in query-adaptive retrieval frameworks for video collections is highly dependent upon the definition of classes of queries, which are groups of queries that share similar optimal search strategies, while many applica- tions in text and web retrieval have included many advanced strategies, such as direct prediction of search method perfor- mance and inclusion of contextual cues from the searcher. We conclude that such advanced strategies previously developed for text retrieval have a broad range of possible applications in future research in multimodal video search.
Complement Activation in Circulation and Central Nervous System after Rituximab (Anti-CD20) Treatment of B-Cell Lymphoma (2001)

Rituximab (IDEC-C2B8, Mabthera, Rituxan), a chimeric monoclonal antibody against the B-cell specific CD20-antigen, has been demonstrated to be effective in the treatment of non-Hodgkin's B-cell lymphoma (B-NHL). Previous in vitro studies have shown that direct complement-dependent cytotoxicity (CDC), ADCC and apoptosis are important in the rituximab-induced killing of lymphoma cells. It is, however, unknown whether rituximab penetrates the blood-brain barrier. Therefore, we studied rituximab levels and complement (C) activation in blood and cerebrospinal fluid (CSF) following intravenous rituximab therapy in a patient with relapsing non-Hodgkin's lymphoma with central nervous system (CNS) involvement. Longitudinal samples from blood and CSF were taken at 13 time-points during the treatment period. The results show that the C cascade becomes activated in blood during the first mAb infusion (C3a-desArg concentration rose from 55 to 138 microg/ml during the first 2 hours). After the first infusion the proportions of lymphocytes positive for the CD19- and CD20-antigens in the peripheral blood were reduced from 41% and 35%, respectively, to a level of 2% (for both). In CSF the rituximab concentration increased after successive infusions, but remained below 0.55 microg/ml (compared to a Cmax of 400 microg/ml in peripheral blood). Although a minor and delayed C activation response was seen in the CSF the treatment did not clear CD20-positive cells away from the CNS. Thus, it appears that an intact blood-brain barrier restricts the entry of rituximab into the CNS. Possible options to circumvent this would be dose escalation or intrathecal rituximab treatment.
Controlled release and stealthy circulation of polymersomes (2003)

The biocompatibility and controlled release profiles of polymersome were investigated. These hyperstable self-assembled block copolymers were injected into rats to elucidate in vivo circulation lifetimes, t-half. For these synthetic vesicles, t-half is 20-30 hours, which is comparable to stealth liposomes. Clearance appears to be primarily mediated by opsonization in spite of the heavily PEGylated brush arising from the hydrophilic fractions of all these block copolymers. Nonetheless, the t-half of these polymersomes compares well with any stealth liposome system. Therefore, novel controlled release polymersomes were prepared by blending the hydrolysable block copolymer poly (ethyleneoaide)-poly(lactic acid) (PEO-PLA) with the diblock copolymer poly(ethyleneoaide)-poly(butadiene) (PEO-PBD). The average time, t-release, for encapsulant release in vitro is obtained from exponential decays in the intact vesicle population and ranges from tens of hours to days or longer. Release kinetics showed minimal difference in plasma at 37/spl deg/C and the rate depends linearly on the mean molar ratio of PEO-PLA incorporated into the vesicle membrane. We propose a mechanism of membrane poration wherein partially hydrolyzed PLA chains congregate and achieve the desired spontaneous membrane curvature by forming a pore and rupturing the membrane, synonymous with detergent-mediated poration, release, and degradation. Emerging studies probe the encapsulant release dynamics in vivo of systems with t-release = t-half.
Mechanisms of Myocardial Ischemia in Hypertrophic Cardiomyopathy (2016)

Coronary flow in patients with HCM is deranged. Distally, compressive deformation of intramyocardial blood vessels during systole results in an abnormally large backward compression wave, whereas proximally, severe left ventricular outflow tract obstruction is associated with an additional deceleration wave. Perfusion abnormalities in HCM are not simply a consequence of supply/demand mismatch or remodeling of the intramyocardial blood vessels; they represent a dynamic interaction with the mechanics of myocardial ischemia that may be amenable to treatment.
Optical waveguide combiners for AR headsets: features and limitations (2019)

This paper is a review of the main waveguide combiner architectures that have been implemented in industry and academia to produce Augmented Reality (AR) and Optical See-Through (OST) Mixed Reality (MR) Head Mounted Displays (HMDs). We review their features and limitations and show product examples. We review also the design constrains and the main optical simulation techniques used to model and predict the overall performances of such optical waveguide combiners.
Fast IR imaging with sub-wavelength resolution using a transient near-field probe (1998)

We present a method for the remote generation of a transient near-field probe using conventional IR microscopy optics. Photo-induced reflectivity generated by picosecond pulses of visible light incident on the surface of a semiconductor substrate is used to create transient mirrors with dimensions determined by the spot size of the visible light. The IR light scattered by such sub-wavelength-size mirror is collected after propagating through the sample. As the sample is located on the semiconductor substrate, no near-field distance control is required, and the image can be taken at the speed of typical laser scanning microscope. And since the near-field probe is generated remotely – using light – the sample to be imaged can be covered by, or encased in, a transparent liquid or solid. The resolution of such an IR microscope is determined by the dimensions of the transient mirror, i.e., by the spot size of the visible light and its penetration depth into the substrate. To prevent resolution degradation due to diffusion of the photo-excited carriers in the substrate, the probe (IR) pulse duration should not exceed a few tens of picoseconds.
Imaging through scattering medium from multiple speckle images using microlens array (2004)

We propose and experimentally demonstrate a new method of seeing objects hidden in a scattering medium from multiple speckle images. The objects hidden between two biological tissues (chicken breast) are reconstructed from many speckled images formed by a microlens array. Each microlens from the array projects a small different speckle image of the hidden object onto a CCD camera. The entire set of noisy images from the array are digitally processed to obtain the desired image of the hidden objects. Following the first proposed method, a different algorithm implemented on the same optical system has been developed. This modified algorithm, based on the point-source reference method improves the resolution of the previous method. Laboratory experiments with two kinds of objects are presented.
Nanometrology of Biomass for Bioenergy: The Role of Atomic Force Microscopy and Spectroscopy in Plant Cell Characterization (2018)

Ethanol production using extracted cellulose from plant cell walls (PCW) is a very promising 4 approach to biofuel production. However, efficient throughput has been hindered by the pheno5 menon of recalcitrance, leading to high costs for the lignocellulosic conversion. To overcome 6 recalcitrance, it is necessary to understand the chemical and structural properties of the plant 7 biological materials, which have evolved to generate the strong and cohesive features observed 8 in plants. Therefore, tools and methods that allow the investigation of how the different molecular 9 components of PCW are organized and distributed and how this impacts the mechanical proper10 ties of the plants are needed but challenging due to the molecular and morphological complexity 11 of PCW. Atomic force microscopy (AFM), capitalizing on the interfacial nanomechanical forces, 12 encompasses a suite of measurement modalities for nondestructive material characterization. 13 Here, we present a review focused on the utilization of AFM for imaging and determination of 14 physical properties of plant-based specimens. The presented review encompasses the AFM 15 derived techniques for topography imaging (AM-AFM), mechanical properties (QFM), and sur16 face/subsurface (MSAFM, HPFM) chemical composition imaging. In particular, the motivation and 17 utility of force microscopy of plant cell walls from the early fundamental investigations to achieve 18 a better understanding of the cell wall architecture, to the recent studies for the sake of advancing 19 the biofuel research are discussed. An example of delignification protocol is described and the 20 changes in morphology, chemical composition and mechanical properties and their correlation at 21 the nanometer scale along the process are illustrated.
Enhanced fermentation systems with continuous removal of inhibitory products (1994)

A variety of advanced bioreactors are being developed to improve production of fuels, solvents, organic acids, and other fermentation products. A major limitation of microbial fermentations is the dilute aqueous product streams that result, largely due to inhibition of the microbes by the desired products. If these inhibitory products can be removed during the ongoing fermentation, the overall rates, yields, and net product formation may be increased. Simultaneous fermentation and separation have been tested with different separation techniques, such as adsorption, liquid extraction, pervaporation, membrane separations, distillation, and others. These separations can occur directly in situ within the fermentor or indirectly using a sidestream separator with recycle of the unused substrate. These approaches are briefly reviewed. At Oak Ridge National Laboratory (ORNL), we have investigated two modified immobilized-cell fluidized-bed bioreactors (FBRs) to remove the inhibitory product directly from the continuous fermentation. One involves the separation by adsorption of tactic acid, and the other uses liquid solvent extraction for the production of butanol. Keywords: extractive fermentation, in situ separation, adsorption, tactic acid, butanol.
<title>All-optical clock recovery using injection mode-locked laser diodes</title> (1997)

Semiconductor laser diodes may play an important role in synchronous optical networks as sources of optical modelocked pulse trains with robust timing stability. In this paper, it is demonstrated how injection modelocked semiconductor lasers can be used in all-optical clock recovery systems. Experimental measurement of clock recovery dynamics shows that these devices offer robust clock recovery with low injected data power (less than 6 uW), large repetition rate locking bandwidth (2.9 X 10<SUP>-3</SUP> fractional bandwidth), and small timing jitter (less than 93 fs). Clocking from an injected data stream at 1/50th the clocking repetition rate is demonstrated.
3.2 PARVALBUMIN INTERNEURON IMPAIRMENT INDUCED BY OXIDATIVE STRESS AS A COMMON PATHOLOGICAL MECHANISM IN ANIMAL MODELS OF SCHIZOPHRENIA (2018)

Parvalbumin inhibitory interneurons (PVIs) are crucial for maintaining proper excitatory/inhibitory balance and high-frequency neuronal synchronization. Their activity supports critical developmental trajectories, sensory and cognitive processing, and social behavior. Despite heterogeneity in the etiology across schizophrenia and autism spectrum disorder, PVI circuits are altered in these psychiatric disorders. Identifying mechanism(s) underlying PVI deficits is essential to establish treatments targeting in particular cognition. Based on our previous publications and new data, we propose oxidative stress as a common pathological mechanism leading to PVI impairment in schizophrenia and some forms of autism. Using immunohistochemistry technique and confocal imaging analysis, we assessed the relationship between oxidative stress (as revealed by 8-oxo-DG immunolabeling) and PVI and their perineuronal net (PNN) in twelve established animal models relevant to autism (i.e., the fmr1 KO and CNV 15q13.3) and schizophrenia (CNV: 22q11, 15q13.3, 1q21, serine racemase (SR) KO, GRIN2A KO, Gclm KO) with or without additional insult (e.g., environmental: Gclm KO + GBR12909, GRIN2A KO + GBR12909, neonatal ventral hippocampal lesion (NVHL), methylazoxymethanol acetate developmental rodent model (MAM) and poly:IC). When PVI deficits in the anterior cingulate cortex were found in these animal models carrying genetic and/or environmental risks relevant to diverse etiological aspects of these disorders, oxidative stress was always present. Specifically, oxidative stress was negatively correlated with the integrity of PVIs and the extracellular perineuronal net enwrapping these interneurons. Oxidative stress may result from dysregulation of systems typically affected in schizophrenia, including glutamatergic, dopaminergic, immune, and antioxidant signaling. As convergent endpoint, redox dysregulation has successfully been targeted to protect PVIs with antioxidants/redox regulators across several animal models (e.g., Gclm KO, NVHL rats, GRIN2A KO and SR KO mice). D-serine, an allosteric modulator of brain NMDA receptor also protected PVIs and PNN against oxidative stress in SR KO mice. In view of the fact that the established pathophysiological processes dopamine excess, immune dysregulation and NMDA receptor hypofunction could all induce oxidative stress and are potentiated by additional oxidative insults, this mechanism could be central to damage of the highly metabolically active PVIs and the PNN surrounding them. Antioxidant systems are therefore potential therapeutic targets, assuming that redox regulators could be applied early, during environmental impacts, long before the clinical emergence of the disease.
Serum Leptin in Children and Young Adults with Inflammatory Bowel Disease (1998)

The determinants of serum leptin were the same in young patients with inflammatory bowel disease as in normal populations, indicating that alterations in leptin levels are unlikely to mediate the anorexia and growth failure associated with this disease.
Incidence and predictors of cardiogenic shock following surgical or transcatheter tricuspid valve intervention (2022)

In patients undergoing TV intervention for TR, surgery versus TTVI and elevated CVP are associated with advanced postprocedural CS. Patients developing advanced CS are at increased risk of in-hospital mortality.
Low-Noise and High-Power GaAlAs Laser Diodes with a New Real Refractive Index Guided Structure (1995)

We demonstrate for the first time a real refractive index guided GaAlAs laser structure that has both very low-noise characteristics at a low output power (reading mode) and a stable fundamental transverse mode up to a high power level (writing mode) sufficient for optical read-write systems. The low-noise characteristics are realized by self-sustained pulsation which is induced by large saturable absorbers outside a stripe, and the high power is achieved by using a thin active layer which confines the optical flux very loosely. In order to optimize the device parameters, numerical simulation of the structure is proposed with consideration of interaction between optical field and carrier diffusion under gain nonlinearity and carrier diffusion taken into account. The calculated results are verified experimentally. The lasers showed relative intensity noise level less than -135 dB/Hz under 0-20% optical feedback and output power higher than 60 mW.
Generation of 100 µj femtosecond pulses in high-gain Yb-fiber CPA systems (2000)

53 dB gain has been achieved in a single Yb-fiber amplification stage providing 220 fs and 100 µJ pulses with average powers of up to 5.5 W when seeded with 0.5 nJ pulses from a femtosecond Raman-shifted and frequency-doubled Er-fiber laser.
Phytochrome-induced SIG2 expression contributes to photoregulation of phytochrome signalling and photomorphogenesis in Arabidopsis thaliana (2013)

Chloroplast-localized sigma factor (SIG) proteins promote specificity of the plastid-encoded RNA polymerase. SIG2 function appears to be necessary for light-grown Arabidopsis thaliana plants. Specific photoreceptors or light-dependent factors that impact the light-induced accumulation of SIG2 have not been reported. A molecular link between phytochromes and nuclear-encoded SIG2, which impacts photomorphogenesis specifically under red (R) and far-red (FR) light, is described here. Both phyA and phyB promote SIG2 transcript accumulation. Disruption of SIG2 results in R- and FR-specific defects in the inhibition of hypocotyl elongation and cotyledon expansion, although no impairments in these responses are detected for sig2 mutants under blue (B) or white (W) light. SIG2 also impacts root elongation under W and R, and the R-dependent expression of PIF4, encoding a phytochrome-interacting factor, and HY2, which encodes a phytochrome chromophore biosynthetic enzyme. Whereas SIG2 apparently impacts the accumulation of the phytochromobilin (PΦB) phytochrome chromophore, sig2 mutants differ significantly from PΦB mutants, primarily due to wavelength-specific defects in photomorphogenesis and disruption of a distinct subset of phytochrome-dependent responses. The molecular link between phytochromes and SIG2 is likely to be an important part of the co-ordination of gene expression to maintain stoichiometry between the nuclear-encoded phytochrome apoprotein and plastid-derived PΦB, which combine to form photoactive phytochromes, and/or light-dependent SIG2 accumulation is involved in an inductive light signalling pathway co-ordinating components between nucleus and plastids.