gebhart/patrepeval huggingface dataset:
Specific genetic analysis of microscopic tissue after selective ultraviolet radiation fractionation and the polymerase chain reaction. (1992)

A method using selective ultraviolet radiation fractionation followed by polymerase chain reaction (PCR) can analyze specific cell subsets present on a microscope section. Direct ultraviolet radiation of fixed and stained tissue sections prevents subsequent amplification by PCR. An "umbrella" or dot placed physically over small numbers of pure cell populations selected by microscopic examination protects these cells from the ultraviolet inactivation. The DNA in these protected cells can be specifically amplified while no signal is derived from the unprotected surrounding cells. Specific amplification was demonstrated by detecting human papillomavirus sequences only if infected cells were protected. Similarly, loss of heterozygosity at the p53 locus was documented by selective dotting of normal or tumor cells. The method allows the specific and sensitive molecular genetic analysis of small numbers of cells histologically identified and selected under the microscope.
Microstructure of highly strained BiFeO3 thin films: Transmission electron microscopy and electron-energy loss spectroscopy studies (2014)

Microstructure and electronic structure of highly strained bismuth ferrite (BiFeO3) thin films grown on lanthanum aluminate substrates are studied using high-resolution transmission and scanning transmission electron microscopies and electron energy loss spectroscopy (EELS). Monoclinic and tetragonal phases were observed in films grown at different temperatures, and a mix of both phases was detected in a film grown at intermediate temperature. In this film, a smooth transition of the microstructure was found between the monoclinic and the tetragonal phases. A considerable increase in the c-axis parameters was observed in both phases compared with the rhombohedral bulk phase. The off-center displacement of iron (Fe) ions was increased in the monoclinic phase as compared with the tetragonal phase. EEL spectra show different electronic structures in the monoclinic and the tetragonal phases. These experimental observations are well consistent with the results of theoretical first-principle calculations performed.
Abstract PR09: A systematic approach to create patient-derived models of rare tumors (2020)

Abstract Precision cancer medicine is based on the ability to predict the dependencies of a given tumor from its molecular makeup. Despite successes in multiple common cancers, such prediction remains challenging for the majority of rare and understudied tumors, given the absence of laboratory model systems in which to discover and/or validate therapeutic hypotheses. Here, we describe our efforts to address this challenge systematically with the ultimate goal of making it possible to learn how to predict ex vivo growth requirements for cancer samples based on technical, clinical, and genomic properties of the starting tumor material. Over the last 5 years, we have processed nearly 2,000 tumor biospecimens and created over 375 genomically confirmed patient-derived cell lines, organoids, and neurosphere cultures, with &amp;gt;10% of these representing rare cancers. To make this possible, we have implemented three key workflows including (1) direct-to-patient sample sourcing, (2) a tissue cryopreservation and genomic credentialing system to ensure quality prior to model creation, and (3) a systematic empirical approach to screening rich media and variations on organoid technologies ex vivo (HYBRID). We have begun performing genome-wide CRISPR viability screens in these cultures as part of our larger activities to generate a systematic laboratory-based functional map of cancer dependencies (a “Cancer Dependency Map”). The novel organoid, spheroid, and cell line models created as part of this effort are being made publicly available to the scientific community. Looking ahead, as the barriers to culturing rare tumors are overcome, we expect that preclinical functional genomics data will be useful for difficult-to-treat tumors without existing molecularly guided standard-of-care regimens. This abstract is also being presented as Poster A06. Citation Format: Yuen-Yi Tseng, Paula Keskula, Rebecca Deasy, Andrew Hong, Priya Chatterji, Francisca Vazquez, Adam Bass, Barbara Van Hare, David Sandak, Keith Ligon, Jesse Boehm. A systematic approach to create patient-derived models of rare tumors [abstract]. In: Proceedings of the AACR Special Conference on the Evolving Landscape of Cancer Modeling; 2020 Mar 2-5; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2020;80(11 Suppl):Abstract nr PR09.
Multidetector CT for Visualization of Coronary Stents (2006)

Whereas the clinical diagnosis of in-stent thrombosis is straightforward, that of in-stent restenosis remains a problem, because although many patients experience chest pain after coronary stent placement, that symptom is secondary to ischemia in only a few. The use of a noninvasive technique to identify such patients for early invasive intervention versus more conservative management is thus highly desirable. Multidetector computed tomography (CT) performed with 16-section scanners recently emerged as such a technique and has overtaken modalities such as electron-beam CT and magnetic resonance imaging as an alternative to conventional angiography for the assessment of in-stent restenosis. The improved hardware design of the current 64-section CT scanners allows even better delineation of stent struts and lumen. The more reliable criterion of direct lumen visualization thus may be substituted for the presence of distal runoff, which lacks specificity for a determination of in-stent patency because of the possibility of collateral pathways. However, the capability to accurately visualize the in-stent lumen depends partly on knowledge of the causes of artifacts and how they can be compensated for with postprocessing and proper image display settings. In addition, an understanding of the major stent placement techniques used in the treatment of lesions at arterial bifurcations is helpful.
Transcriptional silencing induced by Arabidopsis T-DNA mutants is associated with 35S promoter siRNAs and requires genes involved in siRNA-mediated chromatin silencing (2010)

The utility of many T-DNA insertion mutant lines of Arabidopsis is compromised by their propensity to trigger transcriptional silencing of transgenes expressed from the CaMV 35S promoter. To try to circumvent this problem, we characterized the genetic requirements for maintenance of 35S promoter homology-dependent transcriptional gene silencing induced by the dcl3-1 (SALK_005512) T-DNA insertion mutant line. Surprisingly, even though DCL3 and RDR2 are known components of the siRNA-dependent transcriptional gene silencing pathway, transcriptional gene silencing of a 35S promoter-driven GUS hairpin transgene did occur in plants homozygous for the dcl3-1 T-DNA insertion and was unaffected by loss of function of RDR2. However, the transcriptional gene silencing was alleviated in dcl2 dcl3 dcl4 triple mutant plants and also by mutations in AGO4, NRPD2, HEN1 and MOM1. Thus, some T-DNA insertion mutant lines induce 35S promoter homology-dependent transcriptional silencing that requires neither DCL3 nor RDR2, but involves other genes known to function in siRNA-dependent transcriptional silencing. Consistent with these results, we detected 35S promoter siRNAs in dcl3-1 SALK line plants, suggesting that the 35S promoter homology-dependent silencing induced by some T-DNA insertion mutant lines is siRNA-mediated.
DECIDUOUS: decentralized source identification for network-based intrusions (2003)

DECIDUOUS is a security management framework for identifying the sources of network-based intrusions. The first key concept in DECIDUOUS is dynamic security associations, which efficiently and collectively provide location information for attack sources. DECIDUOUS is built on top of the IETF's IPSEC/ISAKMP infrastructure, and it does not introduce any new network protocol for source identification in a single administrative domain. It defines a collaborative protocol for inter-domain attack source identification. The second key concept in DECIDUOUS is the management information integration of the intrusion detection system (IDS) and attack source identification system (ASIS) across different protocol layers. For example, in DECIDUOUS, it is possible for a network-layer security control protocol (e.g., IPSEC) to collaborate with an application-layer intrusion detection system module (e.g., IDS for the SNMP engine). In this paper, we present the motivations, design, and prototype implementation of the DECIDUOUS framework.
Reducing motion sickness - A comparison of autogenic-feedback training and an alternative cognitive task (1982)

Eighteen men were randomly assigned to three groups matched for susceptibility to Coriolis motion sickness. All subjects were given six Coriolis Sickness Susceptibility Index (CSSI) tests separated by 5-d intervals. Treatment Group I subjects were taught to control their own autonomic responses before the third, fourth, and fifth CSSI tests (6 h total training). Group II subjects were given 'sham' training in an alternative cognitive task under conditions otherwise identical to those of Group I. Group III subjects received no treatment. Results showed that Group I subjects could withstand the stress of Coriolis acceleration significantly longer after training. Neither of the other two groups changed significantly.
Augmentation of catecholamine release elicited by an Eugenia punicifolia extract in chromaffin cells (2011)

Plant extracts of Eugenia punicifolia (Kunth) DC., Myrtaceae, are used in Amazon region of Brazil to treat diarrhea and stomach disturbances, and as hypoglycemic medicine. We have recently shown that an aqueous extract of E. punicifolia augmented cholinergic neurotransmission in a rat phrenic nerve-diaphragm preparation. In this study, we investigated the effects of an E. punicifolia dichloromethane extract (EPEX) in a neuronal model of cholinergic neurotransmission, the bovine adrenal chromaffin cell. EPEX augmented the release of catecholamine triggered by acetylcholine (ACh) pulses but did not enhance ACh-evoked inward currents, which were inhibited by 30%. Since EPEX did not cause a blockade of acetylcholinesterase or butyrylcholinesterase, it seems that EPEX is not directly activating the cholinergic system. EPEX also augmented K+-elicited secretion without enhancing the whole-cell inward calcium current. This novel and potent effect of EPEX in enhancing exocytosis might help to identify the active component responsible for augmenting exocytosis. When elucidated, the molecular structure of this active principle could serve as a template to synthesise novel compounds to regulate the exocytotic release of neurotransmitters.
Semantic Image Based Geolocation Given a Map (2016)

The problem visual place recognition is commonly used strategy for localization. Most successful appearance based methods typically rely on a large database of views endowed with local or global image descriptors and strive to retrieve the views of the same location. The quality of the results is often affected by the density of the reference views and the robustness of the image representation with respect to viewpoint variations, clutter and seasonal changes. In this work we present an approach for geo-locating a novel view and determining camera location and orientation using a map and a sparse set of geo-tagged reference views. We propose a novel technique for detection and identification of building facades from geo-tagged reference view using the map and geometry of the building facades. We compute the likelihood of camera location and orientation of the query images using the detected landmark (building) identities from reference views, 2D map of the environment, and geometry of building facades. We evaluate our approach for building identification and geo-localization on a new challenging outdoors urban dataset exhibiting large variations in appearance and viewpoint.
erythro-2-Morpholino-1,2-diphenylethanol (2002)

The title compound, C18H21NO2, consists of two aromatic rings and a morpholine ring attached to an ethanol moiety. The mol­ecule is non-planar. There is an intramolecular O—H⋯N hydrogen bond.
POWER CONSUMPTION IN UNBAFFLED TANKS: SUB AND SUPER-CRITICAL REGIMES (2013)

Unbaffled stirred tanks are increasingly recognized as a viable alternative to common baffled tanks for a range of processes (e.g. crystallization, food and pharmaceutical processes, etc) where the presence of baffles is undesirable for some reason. Also, in the case of bioreactors for animal cell cultivation, where cell damage is mainly related to bubbles bursts at the air –liquid interface, unbaffled tanks have been shown to be able to provide sufficient mass transfer through the free surface vortex. As a consequence bubble formation and subsequent bursting is conveniently avoided (Scargiali et al., 2012). The same feature clearly makes unbaffled vessels potentially advantageous for any foaming gas-liquid system, provided that process rates, and relevant gas consumption needs, are compatible with the relatively small gas transfer rates achievable. Notwithstanding the increasing industrial interest towards unbaffled tanks, available experimental information on unbaffled tanks behavior is still scant, even for basic quantities such as mechanical power drawn. In this work the influence of Reynolds and Froude numbers on power consumption characteristics of unbaffled stirred tanks operating both in sub-critical conditions (the free surface vortex has not yet reached the impeller) and in super-critical conditions (the free surface vortex has reached the impeller and a gas phase is ingested and dispersed inside the reactor) is presented. Experimental results show that in the former case Power Number dependence on Reynolds and Froude numbers is consistent with previous results by Rushton et al. (1950). At rotational speeds higher than Ncrit (super-critical regime) air entrapment and dispersion inside the reactor occurs while a steep reduction on power number is observed. A novel correlation for power number prediction as a function of Reynolds and Froude number is finally proposed.
Atomic engineering of high-density isolated Co atoms on graphene with proximal-atom controlled reaction selectivity (2018)

Controllable synthesis of single atom catalysts (SACs) with high loading remains challenging due to the aggregation tendency of metal atoms as the surface coverage increases. Here we report the synthesis of graphene supported cobalt SACs (Co<sub>1</sub>/G) with a tuneable high loading by atomic layer deposition. Ozone treatment of the graphene support not only eliminates the undesirable ligands of the pre-deposited metal precursors, but also regenerates active sites for the precise tuning of the density of Co atoms. The Co<sub>1</sub>/G SACs also demonstrate exceptional activity and high selectivity for the hydrogenation of nitroarenes to produce azoxy aromatic compounds, attributable to the formation of a coordinatively unsaturated and positively charged catalytically active center (Co-O-C) arising from the proximal-atom induced partial depletion of the 3d Co orbitals. Our findings pave the way for the precise engineering of the metal loading in a variety of SACs for superior catalytic activities.
Simultaneous localization and mapping using multiple view feature descriptors (2005)

We propose a vision-based SLAM algorithm incorporating feature descriptors derived from multiple views of a scene, incorporating illumination and viewpoint variations. These descriptors are extracted from video and then applied to the challenging task of wide baseline matching across significant viewpoint changes. The system incorporates a single camera on a mobile robot in an extended Kalman filter framework to develop a 3D map of the environment and determine egomotion. At the same time, the feature descriptors are generated from the video sequence, which can be used to localize the robot when it returns to a mapped location. The kidnapped robot problem is addressed by matching descriptors without any estimate of position, then determining the epipolar geometry with respect to a known position in the map.
Technique of synovial biopsy of metacarpophalangeal joints using the needle arthroscope (2002)

We demonstrate the technique, advantages, and disadvantages of metacarpophalangeal joint examination with needle arthroscope. We evaluated our experience from biopsies of 10 metacarpophalangeal joints of eight rheumatoid women aged 41-45 years. The procedures were performed using a 1-mm needle arthroscope. The synovium biopsy was taken with a microforceps. The procedure was performed under local anesthesia. The tight tension of the joint and traction of the finger is necessary for good visualization, but despite this visibility can be difficult. Needle biopsy is a useful method for the early diagnosis of rheumatoid arthritis.
AF-TRUST, Air Force Team for Research in Ubiquitous Secure Technology (2010)

Abstract : AF-TRUST was established to address Air Force challenges associated with the Global Information Grid (GIG) and Network Centric Enterprise Systems (NCES). The AF-TRUST team (Berkeley, Cornell, Vanderbilt) focused on top Air Force research priorities and advanced the state-of-the-art in cyber-assurance to address key trust- and Quality of Service (QoS)-related properties simultaneously throughout the lifecycles of large-scale Air Force systems. This was done via a novel combination of analytical and experimental techniques with research and development activities focused in three areas: (1) Scalable, Real-Time, and Fault-Tolerant Quality of Service (QoS), (2) Very Large-Scale Information Assurance and Security Policy Management, and (3) Scalable and Secure Discovery, Information Architecture, and Mediation.
Identification of the Caprine Keratin-Associated Protein 20-2 (KAP20-2) Gene and Its Effect on Cashmere Traits (2017)

The gene encoding the high glycine/tyrosine keratin-associated protein 20-2 (KAP20-2) gene has been described in humans, but has not been identified in any livestock species. A search for similar sequences in the caprine genome using the human KAP20-2 gene (<i>KRTAP20-2</i>) revealed a homologous sequence on chromosome 1. Three different banding patterns representing distinct sequences (<i>A</i>-<i>C</i>) in Longdong cashmere goats were identified using polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP) analysis. These sequences shared high sequence similarity with the human and mouse <i>KRTAP20-2</i> sequences, suggesting that <i>A</i>-<i>C</i> are caprine variants of the human and mouse genes. Four single nucleotide polymorphisms (SNPs) were identified, and three of them were non-synonymous. <i>KRTAP20-2</i> was found to be expressed in secondary hair follicles, but not in heart, liver, lung, kidney, spleen, or <i>longissimus dorsi</i> muscle. The presence of <i>A</i> was associated with increased cashmere fibre weight, while the presence of <i>B</i> was associated with a decrease in cashmere fibre weight and curly fibre length. Goats with genotype <i>AA</i> had a higher cashmere fibre weight and a higher curly fibre length than those with genotypes <i>AB</i> or <i>BB</i>. These results indicate that caprine <i>KRTAP20-2</i> variation may have value as a genetic marker for improving cashmere fibre weight.
Synthesis of purine‐like ring systems derived from 1,2,6‐thiadiazine 1,1‐dioxide (1976)

Abstract 7‐Amino‐1 H ,4 H ‐imidazo[2,3‐ c ][1,2,6]thiadiazine 5,5‐dioxide was prepared by a multi‐step reaction sequence form 3,5‐diamino‐4 H ‐1,2,6‐thiadiazine 1,1‐dioxide. 7‐Amino‐4 H ‐furazano‐[3,4‐ c ][1,2,6]thiadiazine 5,5‐dioxide was obtained by lead tetraacetate oxidation of 3,5‐diamino‐4‐hydroxyimino‐4 H ‐1,2,6‐thiadiazine 1,1‐dioxide.
β-D-Xylanases of Bacillus circulans WL-12 (1982)

Bacillus circulans WL-12 secretes two endo-β-D-xylanases (A and B, respectively) (EC 3.2.1.8.) and one β-D-xylosidase (EC 3.2.1.37) when cultured in liquid media with xylan as the sole carbon source. Xylanases A and B have been partially characterized with respect to their main physicochemical parameters and β-D-xylosidase to a lesser extent on account of its low stability. Both endo-β-D-xylanase A and β-D-xylosidase were adsorbed on DEAE-Biogel A, had similar molecular weights (approximately 85 000), and had optimum pH values of 5.5–7, but exhibited different isoelectric points (4.5 for β-D-xylanase A and 4.7 for β-D-xylosidase) and different mobilities in polyacrylamide gel electrophoresis. The apparent Michaelis constant for β-D-xylanase A was 8 mg∙mL −1 and the hydrolysis products produced were xylose, xylobiose, xylotriose, and xylotetraose.The second endo-β-D-xylanase (β-D-xylanase B) bound to CM-Biogel A and exhibited a molecular weight of approximately 15 000 and an optimum pH value in the range of 5.5–7. The isoelectric point was 9.1 and the apparent Michaelis constant was 4 mg∙mL −1 . The hydrolysis products produced by this enzyme were xylobiose, xylotriose, and xylotetraose, but never xylose. In polyacrylamide gel electrophoresis at pH 8 the enzyme moved towards the negative electrode.
[Preface for special issue on industrial bioprocess technique front (2015)]. (2015)

Industrial bioprocess is one of the most important research fields supports the promoting of biological manufacturing industry in China, and guarantees the implementation of bioscience and biotechnology research results into the industrial applications. For improving the interconnection between academic researchers and industrial stuffs and pushing research achievement into industrial implementation, bioprocess modelling and control committee of Chinese Society for Microbiology organized two tandem conferences separately in 2012 and 2014 on the topic of "Industrial bioprocess technology", focusing mainly technique front of industrial bioprocess. A special session on industrial technique applications was hold to stimulate cooperation. The conference received many good submissions from academic and industrial sectors. This special issue is based on selected excellent papers from the submissions, together with free submissions. The special issue consists of reviews and original papers, mainly involving the aspects closely related to the bio-industrial sectors including, i) high yield strain constructing and high throughput screening; ii) optimization and modification of industrial enzymes, and iii) bioprocess modelling and high efficient scale-up method.
Effect of Sustained-Release PDGF and TGF-β on Cyclophosphamide-Induced Impaired Wound Healing (2009)

Sustained-release delivery of TGF-beta and PDGF in combination, but not separately, by a subcutaneously implanted drug delivery system significantly improves cyclophosphamide-induced impaired wound healing in rats.