gebhart/patrepeval huggingface dataset:
Primed mesenchymal stem cells package exosomes with metabolites associated with immunomodulation (2019)

Mesenchymal stem cell (MSC) based therapies are currently being evaluated as a putative therapeutic in numerous human clinical trials. Recent reports have established that exosomes mediate much of the therapeutic properties of MSCs. Exosomes are nanovesicles which mediate intercellular communication, transmitting signals between cells which regulate a diverse range of biological processes. MSC-derived exosomes are packaged with numerous types of proteins and RNAs, however, their metabolomic and lipidomic profiles to date have not been well characterized. We previously reported that MSCs, in response to priming culture conditions that mimic the in vivo microenvironmental niche, substantially modulate cellular signaling and significantly increase the secretion of exosomes. Here we report that MSCs exposed to such priming conditions undergo glycolytic reprogramming, which homogenizes MSCs' metabolomic profile. In addition, we establish that exosomes derive from primed MSCs are packaged with numerous metabolites that have been directly associated with immunomodulation, including M2 macrophage polarization and regulatory T lymphocyte induction.
Highly Efficient Solar Steam Generators Based on Multicore@Shell Nanostructured Aerogels of Carbon and Silica as the Light Absorber−Heat Insulator (2021)

Herein, highly efficient, low‐cost, and lightweight solar steam generation systems are fabricated using engineered carbon and silica‐based porous nanostructures with 3D networks as light absorber and heat insulator, respectively. In this regard, systems with three different designs are considered to localize the heat efficiently through harvesting more photons and reducing heat losses. The fabricated systems are multilayered structures including polymeric foam and felt as the substrate and water‐carrier medium, respectively. Highly porous nanostructured particles of carbon aerogel (CA) as an absorber, silica aerogel (SiA) as a superinsulator, and multicore@shell aerogel of CA and SiA (CA core−SiA shell) as both absorber and insulator are synthesized. The used architectures are double layered (substrate covered by CA), triple layered (substrate covered by a layer of CA and a layer of SiA), and multicore@shell (substrate covered by CA−SiA multicore@shell aerogel). Using the double‐layered system, an efficiency of 83% corresponding to 1.2 kg m −2 h −1 water evaporation rate is achieved, which is enhanced to 90% in the triple‐layered system, where the SiA superinsulator is added. Remarkably, when the multicore@shell absorber−insulator is used, the efficiency increments of 27% and 16% are achieved compared with the double‐layered and triple‐layered ones with the same amount of absorber, respectively.
<i>De Novo</i> Assembly and Phasing of Dikaryotic Genomes from Two Isolates of <i>Puccinia coronata</i> f. sp. <i>avenae</i> , the Causal Agent of Oat Crown Rust (2018)

Oat crown rust, caused by the fungus <i>Pucinnia coronata</i> f. sp. <i>avenae</i>, is a devastating disease that impacts worldwide oat production. For much of its life cycle, <i>P. coronata</i> f. sp. <i>avenae</i> is dikaryotic, with two separate haploid nuclei that may vary in virulence genotype, highlighting the importance of understanding haplotype diversity in this species. We generated highly contiguous <i>de novo</i> genome assemblies of two <i>P. coronata</i> f. sp. <i>avenae</i> isolates, 12SD80 and 12NC29, from long-read sequences. In total, we assembled 603 primary contigs for 12SD80, for a total assembly length of 99.16 Mbp, and 777 primary contigs for 12NC29, for a total length of 105.25 Mbp; approximately 52% of each genome was assembled into alternate haplotypes. This revealed structural variation between haplotypes in each isolate equivalent to more than 2% of the genome size, in addition to about 260,000 and 380,000 heterozygous single-nucleotide polymorphisms in 12SD80 and 12NC29, respectively. Transcript-based annotation identified 26,796 and 28,801 coding sequences for isolates 12SD80 and 12NC29, respectively, including about 7,000 allele pairs in haplotype-phased regions. Furthermore, expression profiling revealed clusters of coexpressed secreted effector candidates, and the majority of orthologous effectors between isolates showed conservation of expression patterns. However, a small subset of orthologs showed divergence in expression, which may contribute to differences in virulence between 12SD80 and 12NC29. This study provides the first haplotype-phased reference genome for a dikaryotic rust fungus as a foundation for future studies into virulence mechanisms in <i>P. coronata</i> f. sp. <i>avenae</i><b>IMPORTANCE</b> Disease management strategies for oat crown rust are challenged by the rapid evolution of <i>Puccinia coronata</i> f. sp. <i>avenae</i>, which renders resistance genes in oat varieties ineffective. Despite the economic importance of understanding <i>P. coronata</i> f. sp. <i>avenae</i>, resources to study the molecular mechanisms underpinning pathogenicity and the emergence of new virulence traits are lacking. Such limitations are partly due to the obligate biotrophic lifestyle of <i>P. coronata</i> f. sp. <i>avenae</i> as well as the dikaryotic nature of the genome, features that are also shared with other important rust pathogens. This study reports the first release of a haplotype-phased genome assembly for a dikaryotic fungal species and demonstrates the amenability of using emerging technologies to investigate genetic diversity in populations of <i>P. coronata</i> f. sp. <i>avenae</i>.
Enforcing Integrity in Multimedia Surveillance (2005)

In this paper, we propose a secure distribution model for multimedia Surveillance data, where different locations of the monitored facilities may have different security requirements. We propose a multilevel security framework, wherein the surveillance data streams are classified according to the sensitivity of the location of the surveillance devices, and users (guards) have corresponding security clearances. Guards monitor live multimedia feeds emanating from surveillance devices placed throughout the facility. Our position is that during normal mode of operation, guards are allowed to access only those multimedia streams for which they have the proper authorizations. However, in an emergency, guards may receive pre-computed emergency instructions and/or cover stories. We show how to compose multilevel secure SMIL documents, compute views for each security classification, enforce integrity, confidentiality and access control, and deliver the secure views to handheld devices while
Identification and characterization of a recombinant metallothionein protein from a marine alga, Fucus vesiculosus (1999)

A cDNA library was constructed from macroalgae adapted to prolonged elevated environmental copper levels. To investigate the possible existence of a metallothionein (MT) gene, the library was screened with degenerate probes designed using plant MT cysteine-rich motifs. A gene was identified (1229 bp) with a putative open reading frame (204 bp) encoding a 67-amino-acid protein exhibiting several characteristic features of MT proteins, including 16 cysteine residues (24%) and only one aromatic residue. Although the protein sequence showed high identity with plant and invertebrate MTs, it contained a unique ‘linker ’ region (14 amino acid residues) between the two putative metal-binding domains which contained no cysteine residues. This extended linker is larger than the tripeptide found in archetypal vertebrate MTs, but does not conform either with the 40-amino-acid linkers commonly found in plant MT sequences. An S-peptide Fucus MT fusion protein expressed in Escherichia coli exhibited a relative molecular mass of ∼ 14 kDa. The recombinant fusion bound seven Cd ions, of which 50% were dissociated at pH 4.1. Under anaerobic conditions, the Cd ions were displaced by Cu(I), which associated with the protein at a ratio of 13:1. Laboratory exposure of F. vesiculosus to elevated copper resulted in induction of the MT gene. Thus this paper describes, for the first time, an MT gene identified from macroalgae which is induced by copper exposure and whose encoded protein product binds cadmium and copper.
Impact of Fuel Composition on Blow Off and Flashback in Swirl Stabilized Lean Premixed Combustion (2013)

Co firing of natural gas with renewable fuels such as hydrogen can reduce greenhouse gas emissions, and meet other sustainability considerations. At the same time, adding hydrogen to natural gas alters combustion properties, such as burning speeds, heating values, flammability limits, and chemical characteristics. It is important to identify how combustion stability relates to fuel mixture composition in industrial gas turbines and burners and correlate such behavior to fuel properties or operating conditions. Ultimately, it is desired to predict and prevent operability issues when designing a fuel flexible gas turbine combustor. Fuel interchangeability is used to describe the ability of a substitute fuel composition to replace a baseline fuel without significantly altering performance and operation. Any substitute fuel, while maintaining the same heating load as the baseline fuel, must also provide stable combustion with low pollutant emissions. Interchangeability indices try to predict the impact of fuel composition on lean blowoff and flashback. Correlations for operability limits have been reported, though results are more consistent for blowoff compared to flashback. Yet, even for blowoff, some disagreement regarding fuel composition effects are evident. In the present work, promising correlations and parameters for lean blow off and flashback in a swirl stabilized lean premixed combustor are evaluated. Measurements are conducted for fuel compositions ranging from pure natural gas to pure hydrogen under different levels of preheat and air flow rates. The results are used to evaluate the ability of existing approaches to predict blowoff and flashback. The results show that, while a Damköhler number approach for blowoff is promising, important considerations are required in applying the method. For flashback, the quench constant parameter suggested for combustion induced vortex breakdown was applied and found to have limited success for predicting flashback in the present configuration.
Faculty Opinions recommendation of Contribution of protein fractionation to depth of analysis of the serum and plasma proteomes. (2007)

In-depth analysis of the serum and plasma proteomes by mass spectrometry is challenged by the vast dynamic range of protein abundance and substantial complexity. There is merit in reducing complexity through fractionation to facilitate mass spectrometry analysis of low-abundance proteins. However, fractionation reduces throughput and has the potential of diluting individual proteins or inducing their loss. Here, we have investigated the contribution of extensive fractionation of intact proteins to depth of analysis. Pooled serum depleted of abundant proteins was fractionated by an orthogonal two-dimensional system consisting of anion-exchange and reversed-phase chromatography. The resulting protein fractions were aliquotted; one aliquot was analyzed by shotgun LC-MS/MS, and another was further resolved into protein bands in a third dimension using SDS-PAGE. Individual gel bands were excised and subjected to in situ digestion and mass spectrometry. We demonstrate that increased fractionation results in increased depth of analysis based on total number of proteins identified in serum and based on representation in individual fractions of specific proteins identified in gel bands following a third-dimension SDS gel analysis. An intact protein analysis system (IPAS) based on a two-dimensional plasma fractionation schema was implemented that resulted in identification of 1662 proteins with high confidence with representation of protein isoforms that differed in their chromatographic mobility. Further increase in depth of analysis was accomplished by repeat analysis of aliquots from the same set of two-dimensional fractions resulting in overall identification of 2254 proteins. We conclude that substantial depth of analysis of proteins from milliliter quantities of serum or plasma and detection of isoforms are achieved with depletion of abundant proteins followed by two-dimensional protein fractionation and MS analysis of individual fractions. PMID: 17696519
Supplemental Figure S7 from Akt Inhibition Enhances Expansion of Potent Tumor-Specific Lymphocytes with Memory Cell Characteristics (2023)

&lt;p&gt;Supplemental Figure S7. Pharmacologic inhibition of Akt modulates global metabolic profile and key lipid metabolites of antigen-experienced murine CD8+ T cells.&lt;/p&gt;
Retroviruses in human leukemia (1983)

After decades of work, a retrovirus of true human origin has been isolated first from a U.S. adult case of T-cell lymphoma and then from cases from various regions of the world. This virus, named HTLV-I, is strongly associated with a malignant leukemia-lymphoma of mature T-cells. This disease was first clinically characterized in Japan but subsequently found to cluster in the Caribbean region, areas of the U.S. and in other countries. This retrovirus-associated malignancy has an adult onset and usually a rapidly fatal course. Lymphadenopathy, hepatosplenomegaly, cutaneous infiltration and hypercalcemia are found. HTLV-I has been characterized in detail and shown to be an exogenous retrovirus. HTLV-I infection is detected in normal populations and is endemic in restricted areas of Japan, the Caribbean, South America, and the U.S. Cases of ATL tend to cluster in these areas. Future studies will focus on learning (1) how HTLV-I is transmitted from individual to individual; (2) the nature of the mechanism by which HTLV-I transforms T-cells; (3) whether we can use probes from HTLV-I to detect other (related) retroviruses in other human neoplasms.
In vivo adherence and colonization of Vibrio cholerae strains that differ in hemagglutinating activity and motility (1987)

A scanning electron microscopic study was carried out to compare the in vivo pathogenicity of two strains of Vibrio cholerae in an adult rabbit ligated-gut test model. V. cholerae C5 (serotype Ogawa, biotype El Tor), a motile strain possessing hemagglutinating activity in vitro, and C21 (serotype Ogawa, classical biotype), a nonmotile strain possessing no hemagglutinating activity, were tested. Tissue samples from small intestinal loops were examined 3, 6, 9, and 12 h postinoculation. Contradictory to most published data, neither hemagglutinating activity nor motility appeared to be essential prerequisites for the pathogenesis of cholera in the experimental animal model used: nonmotile hemagglutinin-negative strain C21 adhered to and colonized the small intestine at least to the same extent as did motile hemagglutinin-positive strain C5. Maximum colonization was seen at 9 h postinoculation for both strains. C5 and C21 vibrios caused comparable damage to the villi of the small intestine. The villous epithelium showed only mild changes during the first 9 h postinoculation. However, after 12 h the epithelium was seriously damaged concomitant with a decrease in the number of vibrios. Many villi showed partial or total denudation, owing to repelled epithelium, leaving a bare basal lamina with only some to moderate numbers of vibrios attached. Since similar changes were induced by pure cholera enterotoxin, these changes were likely the result of excessive fluid accumulation. From this study it is concluded that, at least in the animal model used, factors other than hemagglutinating activity and motility may also play a role in the association of V. cholerae with the small intestinal surface.
151 Apparent diet digestibility and morphometric measurements of ruminal papillae of water buffaloes finished in feedlot (2017)

The objective of this study was to evaluate the relationship between parameters of apparent diet digestibility and morphometric measurements of ruminal papillae of water buffaloes (Bubalus bubalis) finished in feedlot. Sixty-five non-castrated males (BW and mean age of 314 ± 117 kg and 390 ± 58 d, respectively) were used. The animals were allocated in collective pens and received a diet based on corn silage (30%), milled grain (53.19%), cotton meal (12.99%), urea (0.76%), calcitic lime (0.75%), and mineral salt (2.24%). Diets were offered in an automatic feeder system (Intergado®, MG, Brazil) with ad libitum access. Animal DMI and ADG were recorded. In order to estimate the apparent digestibility of nutrients (DM, CP, NDF, ADF, TDN, and OM), fecal collection was used to calculate fecal excretion from the internal indigestible neutral detergent fiber marker (iNDF). A fragment (1 cm2, approximately) of each rumen from cranial sac (atrium ruminis) was collected for the study of macroscopic morphological variables, such as number of papillae (NOP; n/cm2 of rumen wall); papillae surface area (PSA; mm2); papillae width (W); papillae length (L); absorptive surface area (ASA; cm2/cm2 of rumen wall) calculated as follows: [1 + (NOP × PSA) − (NOP × 0.002)]; and proportion of the papillae on absorptive surface (PPAS; %) calculated as follows: [(NOP × PSA/ASA) × 100]. Data were obtained from captures and analysis of the images by software (Image J, National Institutes of Health, Bethesda, MD, USA). Subsequently, data were analyzed with PROC CORR (SAS, Inst. Inc., Cary, NC). There were associations among the nutrient digestibilities (P < 0.05) with ASA, PPAS, and W, except to W and DigCP (P > 0.05). Relationships were observed (P < 0.05) among papillae length, ADG, and DMI. The relationship between papillary morphometric characteristics and nutrient digestibility illustrates the efficiency of water buffaloes in the utilization of the feed. Supported by FAPESP #2014/05473-7 and #2016/01109-4. *P < 0.05, **P < 0.10 *P < 0.05, **P < 0.10
Synthesis and anticonvulsant activity of some new 4-aryl-4-imidazoline-2-one derivatives. (1992)

In this study, some new 4-aryl-4-imidazoline-2-one derivatives have been prepared by the reaction of potassium cyanate with some aminoethanone hydrochlorides. The structure of these compounds have been confirmed by UV, IR, 1H-NMR and elementary analysis. Their anticonvulsant activities were determined by maximal electroshock (MES) and subcutaneous metrazol (ScMet) tests according to the ADD (Antiepileptic Drug Development) programme Phase I. Neurotoxicity of the compounds was evaluated by rotarod test. While 2 of the compounds showed protection against ScMet induced seizures at 30 and 300 mg/kg dose levels, 3 of the compounds showed neurotoxicity.
STAC-A2 on Intel Architecture: From Scalar Code to Heterogeneous Application (2014)

STAC-A2 is compute and memory intensive industry benchmark in the field of market risk analysis. The benchmark specifications were created by the Securities Technology Analysis Center (aka STAC®) and are based on inputs collected from the leading trading companies, universities, and high performance computing vendors. The specifications describe the models which represent realistic market risk analysis workloads.In this paper we discuss the development steps that lead to competitive performance of the STAC-A2 benchmark executed on systems consisting of Intel® Xeon® processor(s) and an Intel® Xeon Phi coprocessor. We show the importance of utilization of all parallel resources available on Intel architectures to achieve maximum performance. We demonstrate that the offload extension supported by Intel® Composer XE minimizes the efforts required to create accelerated applications by using only C/C++ language.With Intel's latest implementation of the STAC-A2 benchmark we were able to achieve a significant (800%) performance gain by using a heterogeneous approach running on two Intel Xeon E5-2699 v3 processors and a single Intel® Xeon Phi 7120A card, compared to earlier version running on only two Intel Xeon E5-2697 v2 processors. This implementation outperforms Nvidia's implementation based on an Intel Xeon processor based server with two NVIDIA* K20Xm cards.
A machine learning approach to modeling and identification of automotive three-way catalytic converters (2000)

The working of three-way catalytic converters (TWCs) is based on chemical reactions whose rates are nonlinear functions of temperature and reactant concentrations all along the device. The choice of suitable expressions and the tuning of their parameters is particularly difficult in dynamic conditions. In this paper, we introduce a hybrid modeling technique which allows one to preserve the most important features of an accurate, distributed parameter TWC model, while it circumvents both the structural and the parameter uncertainties of "classical" reaction kinetics models, and saves the computational time; in particular, we compute the rates within the TWC dynamic model by a neural network which becomes a static nonlinear component of a larger dynamic system. A purposely designed genetic algorithm, in conjunction with a fast ad hoc partial differential equation integration procedure, allows one to train the neural network, embedded in the whole model structure, using currently available measurement data and without computing gradient information.
Standardization of the functional syndesmosis widening by dynamic U.S examination (2013)

Normal values for the syndesmosis clear space on ultrasound examination were determined as 3.78mm in neutral, 3.64mm in internal rotation and 4.08mm in external rotation. The clear space was shown to decrease with age both as an absolute measure and when rotational stresses are applied. Females tend to have a larger clear space and a greater functional widening.These findings provide a useful reference for radiologists and sports physicians when performing ultrasound assessment of ankle syndesmotic injuries and we encourage use of this modality.
A Specialized Unit for Adolescent Oncology Patients. Is It Worth It? (1984)

No AccessJournal of Urology1 May 1984A Specialized Unit for Adolescent Oncology Patients. Is It Worth It? C.K. Tebbi and B.G. Koren C.K. TebbiC.K. Tebbi More articles by this author and B.G. KorenB.G. Koren More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(17)50767-3AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "A Specialized Unit for Adolescent Oncology Patients. Is It Worth It?." The Journal of Urology, 131(5), p. 1023 © 1984 by The American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 131Issue 5May 1984Page: 1023 Advertisement Copyright & Permissions© 1984 by The American Urological Association Education and Research, Inc.MetricsAuthor Information C.K. Tebbi More articles by this author B.G. Koren More articles by this author Expand All Advertisement PDF downloadLoading ...