gebhart/patrepeval huggingface dataset:
Synthesis of α-Monobrominated Pyrrole Derivatives (1995)

Abstract Surprisingly stable N-t-BOC-2-bromo-4-hexyl-pyrrole is prepared from N-t-BOC-2-trimethylstannyl-4-hexyl-pyrrole using N-bromosuccinimide as reagent. The bromo-stannyl exchange reaction is performed quantitatively in THF at -70[ddot]C under inert atmosphere. Similarly, N-t-BOC-2-bromopyrrole and N-benzenesulfonyl-2-bromopyrrole have been synthesized from N-t-BOC-2-trimethylstannylpyrrole and N-benzenesulfonyl-2-trimethylstannylpyrrole, respectively.
Toll interacting protein protects bronchial epithelial cells from bleomycin‐induced apoptosis (2020)

Idiopathic pulmonary fibrosis (IPF) is characterized by altered epithelial cell phenotypes, which are associated with myofibroblast accumulation in the lung. Atypical alveolar epithelial cells in IPF express molecular markers of airway epithelium. Polymorphisms within and around Toll interacting protein (TOLLIP) are associated with the susceptibility to IPF and mortality. However, the functional role of TOLLIP in IPF is unknown. Using lung tissues from IPF and control subjects, we showed that expression of TOLLIP gene in the lung parenchyma is globally lower in IPF compared to controls. Lung cells expressing significant levels of TOLLIP include macrophages, alveolar type II, and basal cells. TOLLIP protein expression is lower in the parenchyma of IPF lungs but is expressed in the atypical epithelial cells of the distal fibrotic regions. Using overexpression and silencing approaches, we demonstrate that TOLLIP protects cells from bleomycin-induced apoptosis using primary bronchial epithelial cells and BEAS-2B cells. The protective effects are mediated by reducing mitochondrial reactive oxygen species (ROS) levels and upregulating autophagy. Therefore, global downregulation of the TOLLIP gene in IPF lungs may predispose injured lung epithelial cells to apoptosis and to the development of IPF.
Machine learning based classification of mitochondrial morphologies from fluorescence microscopy images of Toxoplasma gondii cysts (2023)

The mitochondrion is intimately linked to energy and overall metabolism and therefore the morphology of mitochondrion can be very informative for inferring the metabolic state of cells. In this study we report an approach for automatic classification of mitochondrial morphologies using supervised machine learning to efficiently classify them from a large number of cells at a time. Fluorescence microscopy images of the chronic encysted form of parasite Toxoplasma gondii were used for this development. Manually classifying these morphologies from the hundreds of parasites within typical tissue cysts is tedious and error prone. In addition, because of inherent biological heterogeneity in morphologies, there can be variability and lack of reproducibility in manual classification. We used image segmentation to detect mitochondrial shapes and used features extracted from them in a multivariate logistic regression model to classify the detected shapes into five morphological classes: Blobs, Tadpoles, Lasso/Donuts, Arcs, and Other. The detected shapes from a subset of images were first used to obtain consensus classification among expert users to obtain a labeled set. The model was trained using the labeled set from five cysts and its performance was tested on the mitochondrial morphologies from ten other cysts that were not used in training. Results showed that the model had an average overall accuracy of 87%. There was high degree of confidence in the classification of Blobs and Arcs (average F scores 0.91 and 0.73) which constituted the majority of morphologies (85%). Although the current development used microscopy images from tissue cysts of Toxoplasma gondii, the approach is adaptable with minor adjustments and can be used to automatically classify morphologies of organelles from a variety of cells.
Nanoindentation study of polydimethylsiloxane elastic modulus usingBerkovich and flat punch tips (2014)

ABSTRACT This article explores polydimethylsiloxane (PDMS) mechanical properties, and presents nanoindentation experiments with Berkovich and flat punch indenters. In the Berkovich tip quasi‐static nanoindentation test, there are pull‐in and pull‐off events observed during the initial tip contact, and when withdrawing from the surface, respectively. The pull‐in interaction needs to be accounted for to properly determine the initial contact point, and thus the accurate contact area. Once accounted for the pull‐in event, the Berkovich and flat punch tips quasi‐static nanoindentation tests give comparable results of about 1.5 MPa for the PDMS elastic modulus (5 : 1 elastomer base to the curing agent ratio). However, PDMS unloading stiffness is higher than the loading stiffness, and dynamic PDMS testing yields higher elastic modulus of about 3.6 MPa. While these results are comparable with the large strain macroscopic compression test results, the difference underscores the complexity of elastomer mechanical characterization and illustrates the discrepancies typical of the reported values. This article describes nanoindentation methods and critical aspects of interpreting results to assess PDMS mechanical properties. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015 , 132 , 41384.
Abstract 13268: Differential Thrombin Generation by Newer Anti-Xa and Anti-IIa Drugs in Prothrombin Complex: Relevance to Endogenous Modulation of Thrombogenesis (2011)

Several anti-Xa agents (apixaban, otamixaban, rivaroxaban and edoxaban) and anti-IIa agents (dabigatran and melagatran) have been developed for clinical use. These agents are strong inhibitors of f...
Potential clinical uses of neuroactive steroids. (2000)

Neuroactive steroids rapidly modulate gamma-aminobutyric acid (GABA) and glutamate receptors. GABA-enhancing steroids have potential clinical utility as anesthetics, hypnotics, anticonvulsants and anxiolytics. Furthermore, GABAergic neurosteroids may participate in regulating mood and the effects of alcohol on the nervous system, suggesting a potential role in major psychiatric disorders. Neuroactive steroids that alter the function of glutamate receptors could be useful for treating neurodegenerative disorders, and as cognitive enhancers. Recent progress in developing water-soluble steroids and steroids with enhanced oral efficacy foster optimism that certain neuroactive steroids will be developed for clinical use.
Influence of Flexibility and Dimensions of Nanocelluloses on the Flow Properties of Their Aqueous Dispersions (2015)

We report that the intrinsic viscosity [η] of nanocellulose dispersions can be solely expressed as a function of the aspect ratio p of the nanocellulose. Both short rod-like nanocrystalline and long spaghetti-like nanofibrillated celluloses were prepared as dispersions in water. The influence of the flexibility and dimensions of the nanocelluloses on the flow properties of their dispersions was investigated by experimental and theoretical approaches using seven nanocellulose samples with different widths (2.6-14.4 nm) and aspect ratios (23-376). As the aspect ratio of a nanocellulose increases, it becomes more flexible, and its dispersion has higher viscosity. Irrespective of the flexibility and dimensions of these nanocelluloses, the relationship between [η] and p was ρ[η] = 0.15 × p(1.9), where ρ is the density of the nanocellulose.
NP-06: a novel anti-human immunodeficiency virus polypeptide produced by a Streptomyces species (1995)

From an extract of a Streptomyces culture, we identified and purified a novel compound, NP-06, which is active against human immunodeficiency virus (HIV) in vitro. Analyses indicate that NP-06 is a hydrophobic 21-mer oligopeptide, N terminally cyclized through the side chain of Asp-9, containing two intramolecular cystine linkages with a molecular weight of 2,163.4. The 50% inhibitory concentrations were 2.8 and 1.3 microM when NP-06 was tested for in vitro anti-HIV-1 activity in ATH8 cells and phytohemagglutinin-activated peripheral blood mononuclear cells, respectively, NP-06 appears to block the early stage of HIV-1 infection, most likely at the stage of virus-cell fusion.
BIOLOGICAL AND BIOCHEMICAL EFFECTS OF RETAINED POLYHALOGENATED HYDROCARBONS (1991)

The polyhalogenated aromatic hydrocarbons (PHHs), consisting of the chlorinated and brominated biphenyls, dibenzo-p-dioxins and dibenzofurans, are important environmental contaminants affecting both wildlife and humans. Although the biological effects due to acute or chronic exposure to these compounds have been extensively investigated with animal models, relatively little is known concerning the long-term ramifications of such exposure due to the persistent body burdens of some PHH congeners. This review examines the persistent effects of these contaminants for two biological end points: tumor formation and induction of cytochrome P-450-associated mixed function oxygenases in target tissues. Literature and data are presented that indicate that retained PHH congeners continue for many months to exert biological effects that contribute to tumor development in rodent livers and lungs. Effects of specific congeners, retention profiles of these congeners in target tissues and the long-term induction of cytochrome P-450 IA1-associated enzyme activity are all consistent with activation of the Ah receptor's being an integral part of the tumor promotion response.
Synthesis, Characterization, and Aqueous Solution Behavior of Electrolyte- and pH-Responsive Carboxybetaine-Containing Cyclocopolymers (2003)

A novel pH- and salt-responsive carboxybetaine monomer, 4-(N,N-diallyl-N-methylammonio)butanoate (2), was prepared and cyclocopolymerized with the cationic monomer N,N-diallyl-N,N-dimethylammonium chloride (3) in 0.5 M NaCl aqueous solution (pH = 7.0) using 2-hydroxy-1-[4-(hydroxyethoxy)phenyl]-2-methyl-1-propanone (Irgacure 2959) as the free-radical photoinitiator. The molar feed ratio of 2:3 was varied from 100:0 to 0:100 with the total monomer concentration held constant at 2.5 M. Cyclopolymerization to five-membered ring structures common to diallylammonium salts was confirmed by 13C NMR spectroscopy. Reactivity ratio studies indicate that 2 and 3 copolymerize in a nearly ideal fashion (r1 = 0.86, r2 = 0.99). Weight-average molecular weights and second virial coefficients vary from (6.0 to 12.8) × 104 g mol-1 and (1.62 to 5.36) × 10-4 mL mol g-2, respectively. Dilute solution viscosity behavior depends on copolymer composition, ionic strength, and pH. Copolymers with a large excess charge exhibit typical polyelectrolyte behavior, while those with balanced charge exhibit “anti-polyelectrolyte” behavior reported for zwitterionic (co)polymers. The polymers studied here are closely analogous cyclocopolymers we prevoiusly reported containing sulfobetaine mer units.25 Unlike solutions of sulfobetaine-containing polymers, soltuions of poly(2-co-3) remain soluble at very low ionic strength even up to 100% incorporation of 2. Additionally, while the sulfobetaine systems are insensitive to pH, solutions of poly(2-co-3) exhibit a pH-dependent viscosity. All the copolymers have an apparent pKa of ∼3.6. Copolymers with 2 incorporations of 28 mol % and above have viscosity responsiveness between pH values of 2.5 and 4.5. The maximum pH response was achieved for solutions of poly(2-co-3) containing 37 and 56 mol % of the carboxybetaine monomer 2.
Clonal cytopenia of undetermined significance (CCUS) with dysplasia is enriched for MDS‐type molecular findings compared to CCUS without dysplasia (2021)

CCUS-D patients exhibit a molecular (but not clinical) profile more similar to MDS patients than CCUS-ND, suggesting CCUS-D may represent a more immediate precursor to MDS and may warrant closer clinical follow-up.
Modeling Lambertian Surfaces Under Unknown Distant Illumination Using Hemispherical Harmonics (2011)

A surface reflectance function represents the process of turning irradiance signals into outgoing radiance. Irradiance signals can be represented using low-order basis functions due to their low-frequency nature. Spherical harmonics (SH) have been used to provide such basis. However the incident light at any surface point is defined on the upper hemisphere, full spherical representation is not needed. We propose the use of hemispherical harmonics (HSH) to model images of convex Lambertian objects under distant illumination. We formulate and prove the addition theorem for HSH in order to provide an analytical expression of the reflectance function in the HSH domain. We prove that the Lambertian kernel has a more compact harmonic expansion in the HSH domain when compared to its SH counterpart. We present the approximation of the illumination cone in the HSH domain where the non-negative lighting constraint is forced. Our experiments illustrate that the 1st order HSH outperforms 1st and 2nd order SH in the process of image reconstruction as the number of light sources grows. In addition, we provide empirical justification of the nonnecessity of enforcing the non-negativity constraint in the HSH domain, allowing us to use unconstrained least squares which is faster than the constrained one, while maintaining the same quality of the reconstructed images.
Direct carrier modulation for wireless digital communications using an improved microwave-photonic vector modulator (MPVM) approach (2003)

This paper presents a demonstration of direct carrier modulation via the use of an improved microwave/photonic vector modulator (MPVM). This modulation approach is suitable for direct digital modulation of microwave and millimeter-wave signals and allows for tuning of the carrier frequency over wide bandwidths and dynamic reconfiguration of the modulation format. An all-optical control approach is used to achieve faster data rates and better carrier tunability than previously reported work in this area. Specifically, experimental results showing direct QPSK and 16 QAM modulation of carrier frequencies between 1.0 and 2.0 GHz with data rates to 8 Mbs are presented.
Selection of optimum waste treatment for the polar environment. Final report. Phase 1 report (1989)

Stretchable conductive nanocomposites fabricated by integrating metallic nanomaterials with elastomers have become a vital component of human-friendly electronics, such as wearable and implantable devices, due to their unconventional electrical and mechanical characteristics. Understanding the detailed material design and fabrication strategies to improve the conductivity and stretchability of the nanocomposites is therefore important. This Review discusses the recent technological advances toward high performance stretchable metallic nanocomposites. First, the effect of the filler material design on the conductivity is briefly discussed, followed by various nanocomposite fabrication techniques to achieve high conductivity. Methods for maintaining the initial conductivity over a long period of time are also summarized. Then, strategies on controlled percolation of nanomaterials are highlighted, followed by a discussion regarding the effects of the morphology of the nanocomposite and postfabricated 3D structures on achieving high stretchability. Finally, representative examples of applications of such nanocomposites in biointegrated electronics are provided. A brief outlook concludes this Review.
A CMOS High-Power Broadband 260-GHz Radiator Array for Spectroscopy (2013)

A high-power broadband 260-GHz radiation source using 65-nm bulk CMOS technology is reported. The source is an array of eight harmonic oscillators with mutual coupling through four 130-GHz quadrature oscillators. Based on a novel self-feeding structure, the harmonic oscillator simultaneously achieves the optimum conditions for the fundamental oscillation and the 2nd-harmonic generation. The signals at 260 GHz radiate through eight on-chip slot antennas, and are in-phase combined inside a hemispheric silicon lens attached at the backside of the chip. Similar to the laser pulse-driven photoconductive emitter in many THz spectrometers, the radiation of this source can also be modulated by narrow pulses generated on chip, which achieves broad radiation bandwidth. Without modulation, the chip achieves a measured continuous-wave radiated power of 1.1 mW, and an EIRP of 15.7 dBm. Under modulation, the measured bandwidth of the source is 24.7 GHz. This radiator array consumes 0.8-W DC power from a 1.2-V supply.
Bites of Venomous Snakes (2002)

At least 2000 persons are bitten by venomous snakes in the United States each year. This article reviews the diagnosis and management of bites from venomous snakes encountered in North America, but the same principles apply to management of snakebites elsewhere in the world. The review summarizes the complications of envenomation and explains the current recommendations for the use of antivenoms. It explains how to distinguish venomous from nonvenomous snakes.
A data-flow graph generation algorithm for a coarse-grained reconfigurable processor (2009)

In this paper, we present a C-to-DFG generation algorithm for coarse-grained reconfigurable processor in multimedia application field. The algorithm exploits the operation parallelism available in the sequential code; maximizes parallelism by loop unrolling and scalar replacement. Loop unrolling increases the size of basic block and fully exposes the intrinsic data parallelism. Scalar replacement eliminates memory access instructions from the basic block under the prerequisite condition of keeping data dependency. For mapping kernels, the three parts of DFGs are corresponding to the three sub-components of reconfigurable unit. The experiments evaluating the degrees of parallelism on DFGs suggest 5.2x to 120.4x speedups on four kernels from common multimedia algorithms. <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup>
Comparative analysis of floc characteristics and microbial communities in anoxic and aerobic suspended growth processes (2022)

A fully anoxic suspended growth process is an appealing alternative to conventional activated sludge (AS) due to considerable aeration reduction and improved carbon processing efficiency for biological nutrient removal (BNR). With development of the hybrid membrane aerated biofilm reactor (MABR) technology, implementation of a fully anoxic suspended growth community in BNR facilities became practical. To better understand potential limitations with the elimination of aeration, we carried out microscopic examination and 16S rRNA gene-based microbial community profiling to determine how an anoxic suspended growth would differ from the conventional aerobic process in floc characteristics, microbial diversity, microbial temporal dynamics, and community assembly pattern. Fewer filamentous populations were found in the anoxic mixed liquor, suggesting easily sheared flocs. The anoxic microbial community had distinct composition and structure, but its diversity and temporal dynamics were similar to the conventional aerobic community. A variety of well-studied functional guilds were also identified in the anoxic community. The anoxic microbial community assembly was more stochastic than the conventional aerobic community, but deterministic assembly was still significant with a large core microbiome adapted to the anoxic condition. PRACTITIONER POINTS: Flocs developed under the anoxic conditions had less filamentous backbones, implying reduced flocculation capacity and easily sheared flocs. Knowledge about the ecophysiology of Thauera, Thiothrix, and Trichococcus can help achieve good properties of the anoxic flocs. A diverse microbial community sustainably adapted to the fully anoxic condition, containing a variety of filaments, denitrifiers, and PAOs. The anoxic microbial community displayed a similar degree of diversity and temporal dynamics compared to the aerobic counterpart. The anoxic community's assembly was more stochastic, so it may be less subject to changes in environmental variables.
GPU Accelerated ACF Detector (2018)

The field of pedestrian detection has come a long way in recent decades. In terms of accuracy, the current state-of-the-art is hands down reached by Deep Learning methods. However in terms of running speed this is not always the case, traditional methods are often still faster than their Deep Learning counterparts. This is especially true on embedded hardware, embedded platforms are often used in applications that require realtime performance while at same the time having to make do with a limited amount of resources. In this paper we present a GPU implementation of the ACF pedestrian detector and compare it to current Deep Learning approaches (YOLO) on both a desktop GPU as well as the Jetson TX2 embedded GPU platform.
A link between the expression of the stem cell marker HMGA2, grading, and the fusion CRTC1‐MAML2 in mucoepidermoid carcinoma (2009)

Recently, the concept of cancer stem cells and their expression of embryonic stem cell markers has gained considerable experimental support. In this study, we examined the expression of one such marker, the high-mobility group AT-hook 2 gene (HMGA2) mRNA, in 53 formalin-fixed, paraffin-embedded mucoepidermoid carcinomas (MEC) and four normal parotid tissues using quantitative real-time RT-PCR (qPCR). MECs are often characterized by the fusion gene CRTC1-MAML2, the detection of which is an important tool for the diagnosis and prognosis of MEC. For detection of the CRTC1-MAML2 fusion transcript, we performed RT-PCR. The mean expression level of HMGA2 was higher in fusion negative (302.8 +/- 124.4; n = 14) than in positive tumors (67.3 +/- 13.1; n = 39). Furthermore, the fusion-negative tumors were often high-grade tumors and the HMGA2 expression level rose with the tumor grade (low: 43.7 +/- 11.0, intermediate: 126.2 +/- 28.3, and high: 271.2 +/- 126.5). A significant difference was found in the HMGA2 expression levels between the different grading groups (one-way ANOVA, P = 0.04) and among the fusion-negative and -positive tumors (t-test, P = 0.05), indicating that the expression level of HMGA2 was closely linked to grading, the presence/absence of the CRTC1-MAML2 fusion, and the tumor behavior of MECs. These findings offer further evidence for the theory that the MEC group comprises two subgroups: one group with the CRTC1-MAML2 fusion, which is a group with a moderate aggressiveness and prognosis, and the other group lacking that fusion corresponding to an increased stemness, and thus, higher aggressiveness and worse prognosis.