gebhart/patrepeval huggingface dataset:
Fluorescent Acid-Fast Microscopy for Measuring Phagocytosis of <i>Mycobacterium avium</i> , <i>Mycobacterium intracellulare</i> , and <i>Mycobacterium scrofulaceum</i> by <i>Tetrahymena pyriformis</i> and Their Intracellular Growth (2001)

Fluorescent acid-fast microscopy (FAM) was used to enumerate intracellular Mycobacterium avium, Mycobacterium intracellulare, and Mycobacterium scrofulaceum in the ciliated phagocytic protozoan Tetrahymena pyriformis. There was a linear relationship between FAM and colony counts of M. avium cells both from cultures and within protozoa. The Ziehl-Neelsen acid-fast stain could not be used to enumerate intracellular mycobacteria because uninfected protozoa contained acid-fast, bacterium-like particles. Starved, 7-day-old cultures of T. pyriformis transferred into fresh medium readily phagocytized M. avium, M. intracellulare, and M. scrofulaceum. Phagocytosis was rapid and reached a maximum in 30 min. M. avium, M. intracellulare, and M. scrofulaceum grew within T. pyriformis, increasing by factors of 4- to 40-fold after 5 days at 30 degrees C. Intracellular M. avium numbers remained constant over a 25-day period of growth (by transfer) of T. pyriformis. Intracellular M. avium cells also survived protozoan encystment and germination. The growth and viability of T. pyriformis were not affected by mycobacterial infection. The results suggest that free-living phagocytic protozoa may be natural hosts and reservoirs for M. avium, M. intracellulare, and M. scrofulaceum.
Ga<sup>3+</sup>/Ln<sup>3+</sup> Metallacrowns: A Promising Family of Highly Luminescent Lanthanide Complexes That Covers Visible and Near-Infrared Domains (2016)

Luminescent lanthanide(III)-based molecular scaffolds hold great promises for materials science and for biological applications. Their fascinating photophysical properties enable spectral discrimination of emission bands that range from the visible to the near-infrared (NIR) regions. In addition, their strong resistance to photobleaching makes them suitable for long duration or repeated biological experiments using a broad range of sources of excitation including intense and focalized systems such as lasers (e.g., confocal microscopy). A main challenge in the creation of luminescent lanthanide(III) complexes lies in the design of a ligand framework that combines two main features: (i) it must include a chromophoric moiety that possesses a large molar absorptivity and is able to sensitize several different lanthanide(III) ions emitting in the visible and/or in the near-infrared, and (ii) it must protect the Ln(3+) cation by minimizing nonradiative deactivation pathways due to the presence of -OH, -NH and -CH vibrations. Herein, a new family of luminescent Ga(3+)/Ln(3+) metallacrown (MC) complexes is reported. The MCs with the general composition [LnGa4(shi)4(C6H5CO2)4(C5H5N) (CH3OH)] (Ln-1, Ln = Sm(3+)-Yb(3+)) were synthesized in a one pot reaction using salicylhydroxamic acid (H3shi) with Ga(3+) and Ln(3+) nitrates as reagents. The molecular structure of [DyGa4(shi)4(C6H5CO2)4(C5H5N) (CH3OH)] was obtained by X-ray analysis of single crystals and shows that the complex is formed as a [12-MCGa(III)shi-4] core with four benzoate molecules bridging the central Dy(3+) ion to the Ga(3+) ring metals. The powder X-ray diffraction analysis demonstrates that all other isolated complexes are isostructural. The extended analysis of the luminescence properties of these complexes, excited by the electronic states of the chromophoric ligands, showed the presence of characteristic, sharp f-f transitions that can be generated not only in the NIR (Sm, Dy, Ho, Er, Yb) but also in the visible (Sm, Eu, Tb, Dy, Tm). All Ln-1 complexes possess very high quantum yield values with respect to other literature compounds, indicating a good sensitization efficiency of the [12-MCGa(III)shi-4] scaffold. Especially, as of today, the Yb-1 complex exhibits the highest NIR quantum yield reported for a lanthanide(III) complex containing C-H bonds with a value of 5.88(2)% in the solid state. This work is a significant step forward toward versatile, easily prepared luminescent lanthanide(III) complexes suitable for a variety of applications including highly in demand biological imaging, especially in the NIR domain.
West Nile virus-induced cytoplasmic membrane structures provide partial protection against the interferon-induced antiviral MxA protein (2007)

The human MxA protein is a type I and III interferon (IFN)-induced protein with proven antiviral activity against RNA viruses. In this study, we investigated the effect of MxA expression on the replication of West Nile Virus strain Kunjin (WNV(KUN)). Pretreatment of A549 cells with IFN-alpha lead to increased expression of MxA, which contributed to inhibition of WNV(KUN) replication and secretion. However, in Vero cells stably expressing the MxA protein, WNV(KUN) replication, maturation and secretion was not inhibited. Biochemical and subcellular localization studies of WNV(KUN) proteins and MxA suggest that the MxA activity was not compromised by a flavivirus-encoded antagonist. Instead, we show that characteristic membranous structures induced during WNV(KUN) replication provide partial protection from MxA, possibly by 'hiding' WNV(KUN) replication components. This distinct compartmentalization of viral replication and components of the cellular antiviral response may be an evolutionary mechanism by which flaviviruses can hide from host surveillance.
Isolation, characterization and molecular cloning of cathepsin D from lizard ovary: Changes in enzyme activity and mRNA expression throughout ovarian cycle (1999)

During vitellogenesis, the oocytes of oviparous species accumulate in the cytoplasm a large amount of proteic nutrients synthetized in the liver. Once incorporated into the oocytes, these nutrients, especially represented by vitellogenin (VTG) and very low-density lipoprotein (VLDL), are cleaved into a characteristic set of polypeptides forming yolk platelets. We have studied the molecular mechanisms involved in yolk formation in a reptilian species Podarcis sicula, a lizard characterized by a seasonal reproductive cycle. Our results demonstrate the existence in the lizard ovary of an aspartic proteinase having a maximal activity at acidic pH and a molecular mass of 40 kDa. The full-length aspartic proteinase cDNA produced from total RNA by RT-PCR is 1,442 base pairs long and encodes a protein of 403 amino acids. A comparison of the proteic sequence with aspartic proteinases from various sources demonstrates that the lizard enzyme is a cathepsin D. Lizard ovarian cathepsin D activity is maximal in June, in coincidence with vitellogenesis and ovulation, and is especially abundant in vitellogenic follicles and in eggs. Ovarian cathepsin D activity can be enhanced during the resting period by treatment with FSH in vivo. Northern blot analysis shows that cathepsin D mRNA is exceedingly abundant during the reproductive period, and accumulates preferentially in previtellogenic oocytes. Mol. Reprod. Dev. 52:126–134, 1999. © 1999 Wiley-Liss, Inc.
Mixed-valent interactions in rigid dinuclear systems: electrochemical and spectroscopic studies of CrICr0 ions with controlled torsion of the biphenyl bridge (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMixed-valent interactions in rigid dinuclear systems: electrochemical and spectroscopic studies of CrICr0 ions with controlled torsion of the biphenyl bridgeD. T. Pierce and W. E. GeigerCite this: Inorg. Chem. 1994, 33, 2, 373–381Publication Date (Print):January 1, 1994Publication History Published online1 May 2002Published inissue 1 January 1994https://pubs.acs.org/doi/10.1021/ic00080a029https://doi.org/10.1021/ic00080a029research-articleACS PublicationsRequest reuse permissionsArticle Views128Altmetric-Citations59LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Identification of peptides that promote the rapid precipitation of germania nanoparticle networks via use of a peptide display libraryElectronic Supplementary Information (ESI) is available describing the biopanning, germania precipitation assay, and molybdenum blue assay procedures. See http://www.rsc.org/suppdata/cc/b4/b402480j/ (2004)

Peptides that promote the rapid, room-temperature precipitation of amorphous germania nanoparticle networks from solution have been identified via use of a combinatorial peptide display library.
Cost models for BaseBand Unit (BBU) hotelling: From local to cloud (2015)

In this work we model and compare three different strategies for BaseBand Unit (BBU) hotelling: BBU stacking, BBU pooling, and Cloud RAN. We propose the building-block models for every strategy and elaborate on a cost model in order to evaluate their benefits. We also propose shelf and rack design for the implementation of the presented models. The assessment includes cost comparisons and sensitivity analysis with respect to pooling and virtualization gains. We obtain that the best option in terms of cost savings is the cloud-based BBU hotel. However, we show that, under equal pooling gains, the benefits are mainly based on the implementation of the technology and the shelf/rack design.
Online optimization algorithms for multi-armed (2017)

Nowadays the online learning area is actively developing as a part of machine learning. In this regard, there arises the problem of choosing an algorithm that solves the optimization problem with regard to online data processing. Since currently one of the active areas of online learning is ranking, the comparison of several state of art online optimization algorithms for the multi-armed bandit problem in case of online ranking is presented.
High insulin-like growth factor 1 receptor (IGF1R) expression is associated with poor survival in surgically treated non-small cell lung cancer (NSCLC) patients (pts) (2007)

7550 Background: IGF1R represents a novel molecular target in NSCLC. We aimed to evaluate the association between IGF1R expression, clinical characteristics and survival in operable NSCLC pts. Methods: 184 consecutive surgically treated pts (median follow up of 32 months [range: 13–51 months]) were included in the study. There were 23% females, 55% pts with squamous cell carcinoma, 28% with adenocarcinoma, 3% with large cell carcinoma, 13% with mixed carcinoma and 1% with other types, 5% were never-smokers. Median age was 64 years (range: 37–85 years). Pathological stage I was diagnosed in 41%, stage II –22%, stage III –33% and stage IV –4% pts. Induction or adjuvant treatment was not routinely used. IGF1R was evaluated in tissue microarray by immunohistochemistry and scored by two observers according to H-score, taking into account proportion of cells with positive staining times staining intensity (scale 0–400). Results: IGF1R IHC expression was low in analyzed samples (median H-score 20, range: 0–223). Higher IGF1R score was observed in adenocarcinomas vs. squamous-cell carcinomas (p=0.02) and never-smokers vs. smokers (p=0.02). IGF1R score did not depend on stage (p=0.98) and sex (p=0.83). When analyzed as a continuous variable, IGF1R score tended to associate with worse survival in the entire cohort (p=0.10), and was significantly associated with inferior survival in patients with complete (R0) resections (p=0.04). When categorized with cut-off point of 50 (30% of patients positive), IGF1R expression was again associated with poor survival (p=0.05). This association was confined to pathological stage I (hazard ratio, HR=3.07; 95% confidence interval, CI=1.41–6.70, p=0.005) vs. all other stages (HR=1.03; 95% CI=0.63–1.70, p=0.90), and to patients with adenocarcinoma histology (HR=2.67; 95%CI=1.17–6.70, p=0.02 vs. all other histologies (HR=1.28; 95%CI=0.79–2.11, p=0.32). Conclusion: In this cohort of operable NSCLC pts, high IGF1R expression was associated with never-smoking history, adenocarcinoma histology, and poor survival, particularly in stage I disease and in patients with adenocarcinoma. These results support involvement of IGF pathway in the progression of early-stage NSCLC. No significant financial relationships to disclose.
The intrinsic electrophysiological properties of neurons derived from mouse embryonic stem cells overexpressing neurogenin-1 (2010)

A mouse embryonic stem (ES) cell line containing an inducible transgene for the proneural gene Neurog1 has been used to generate glutamatergic neurons at a high efficiency. The present study used in vitro electrophysiology to establish the timeline for acquiring a functional neuronal phenotype in Neurog1-induced cells exhibiting a neuronal morphology. TTX-sensitive action potentials could be evoked from over 80% of the cells after only 4.5 days in vitro (DIV). These cells uniformly showed rapidly adapting responses to current injection, firing one to three action potentials at the onset of the stimulus. In the absence of Neurog1, a limited number of ES cells adopted a neuronal morphology, but these cells displayed slow calcium depolarizations rather than sodium-based spikes. Voltage-gated Na(+), K(+), and Ca(2+) currents were present in nearly all induced cells as early as 4.5 DIV. The voltage-dependent properties of these currents changed little from 4 to 12 DIV with half-activation voltage varying by <10 mV for any current type throughout the culture period. This study demonstrates that forced expression of proneural genes can induce ES cells to quickly acquire a functional neuronal phenotype with mature electrophysiological properties. Transient overexpression of Neurog1 may be used in neural repair strategies that require the rapid induction of functional neurons from pluripotent stem cells.
P2‐185: FTLD‐U‐linked missense mutations in VCP/p97 alter localization of endogenous TDP‐43 and induce cell death (2008)

Frontotemporal dementia with inclusion body myopathy and Paget disease of bone (IBMPFD) is a rare, autosomal-dominant disorder caused by mutations in the valosin-containing protein (VCP) gene. The disease is characterized neuropathologically by frontal and temporal lobar atrophy, neuron loss and gliosis, and a pattern of ubiquitin-positive inclusions (FTLD-U) which is distinct from that seen in other sporadic and familial FTLD-U entities. The major component of the ubiquitinated inclusions of FTLD with VCP mutation is the TAR DNA-binding protein 43 (TDP-43) which becomes hyperphosphorylated, ubiquitinated, and cleaved to form C-terminal fragments; a minor component of the inclusions is valosin-containing protein. TDP-43 is a common pathologic substrate linking sporadic amyotrophic lateral sclerosis (SALS) and a variety of distinct patterns of FTLD-U pathology caused by different genetic alterations. Understanding the relationship between different gene defects and pathologic TDP-43 will facilitate the characterization of the mechanisms leading to neurodegeneration. Using cell culture models, we have investigated the role of wild-type and mutant VCP in intracellular trafficking, proteasomal function, and neurodegeneration. Protein-protein interactions were investigated using immunoprecipitation and in vitro binding assays. In neuroblastoma cell lines, mutations in the VCP gene alter trafficking of TDP-43, impair cell viability, increase markers of apoptosis, and decreases proteaosome activity. VCP mutation-induced neurodegeneration is mediated by several cellular mechanisms including impaired survival pathways; the contribution of each to pathogenesis remains to be determined.
Structural Studies of the System Na(saccharinate)⋅<i>n</i> H<sub>2</sub>O: A Model for Crystallization (2005)

Nicht weit vom Kristallkeim? Die komplexe Kristallstruktur von Natriumsaccharin-„Dihydrat“ könnte ein gutes Modell für die Keimbildung sein (siehe Bild). Die asymmetrische Einheit enthält 362 Atome und viel Wasser, und im Kristall liegen geordnete wie fehlgeordnete Bereiche vor. Verblüffend ist, dass die Kristallstruktur dieser in großen Mengen produzierten metastabilen Verbindung in den 125 Jahren seit ihrer Isolierung nicht bestimmt worden ist. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2005/z462967_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
From genetic to structural characterization of a new class of RNA-binding domain within the Sac Y/BglG family of antiterminator proteins (1997)

International audience
A Study on Structuration of the Housing Submarkets Considering Urban Space (2017)

The real estate market is formed by regional or local communities, each of local market is to look for regional differences even in the real estate market indicators such as price, supply and demand. In addition, due to the nature of the real estate market, real estate heterogeneous characteristics are differentiated according to the region, income, property type, such as layered demand, thus differentiating the real estate market is difficult to organize have individual characteristics. The territory of housing market has been limited to a certain spatial region segmentation is happening in this part of the market by the mismatch of supply and demand imbalance occurs due. Therefore, by analyzing the local region formed for housing markets and market conditions may be desirable to derive the policy options accordingly. This paper seeks to let the statistical data for administrative units of Busan and Daegu define housing market segments by multivariate analysis. First, factor analysis is used to extract a set of factors based on the statistical similarity. Second, factor scores are calculated and cluster analysis is used to determine the composition of housing submarkets. From this study, the housing market in Busan and Daegu is confirmed that working is divided into a huge market rather than the six housing submarkets, and through a variety of factors that affect the supply and demand sides of the housing market can look at the characteristics of the market. Through this, it is possible to structure a housing market that is formed in the metropolitan area, and it will be an effective policy data for developing a customized housing policy for sustainable urban development.
Morphological and Functional Characteristics of Three-Dimensional Engineered Bone-Ligament-Bone Constructs Following Implantation (2009)

The incidence of ligament injury has recently been estimated at 400,000/year. The preferred treatment is reconstruction using an allograft, but outcomes are limited by donor availability, biomechanical incompatibility, and immune rejection. The creation of an engineered ligament in vitro solely from patient bone marrow stromal cells (has the potential to greatly enhance outcomes in knee reconstructions. Our laboratory has developed a scaffoldless method to engineer three-dimensional (3D) ligament and bone constructs from rat bone marrow stem cells in vitro. Coculture of these two engineered constructs results in a 3D bone-ligament-bone (BLB) construct with viable entheses, which was successfully used for medial collateral ligament (MCL) replacement in a rat model. 1 month and 2 month implantations were applied to the engineered BLBs. Implantation of 3D BLBs in a MCL replacement application demonstrated that our in vitro engineered tissues grew and remodeled quickly in vivo to an advanced phenotype and partially restored function of the knee. The explanted 3D BLB ligament region stained positively for type I collagen and elastin and was well vascularized after 1 and 2 months in vivo. Tangent moduli of the ligament portion of the 3D BLB 1 month explants increased by a factor of 2.4 over in vitro controls, to a value equivalent to those observed in 14-day-old neonatal rat MCLs. The 3D BLB 1 month explants also exhibited a functionally graded response that closely matched native MCL inhomogeneity, indicating the constructs functionally adapted in vivo.
Concordance of human leukocyte antigen haplotype-sharing, CD4 decline and AIDS in hemophilic siblings (1995)

Objective: To assess the association between human leukocyte antigen (HLA) haplotypes and the incidence rates of CD4 decline to < 20% and to AIDS. Design: Retrospective cohort study of 95 HIV-1-infected hemophilic sibling pairs. Methods: HLA haplotype-sharing between siblings was assigned on the basis of serologic typing of HLA class I alleles and molecular typing of HLA class II alleles. Concordance of time to CD4 decline to < 20% and to AIDS within and between sibling pairs was assessed by analysis of variance models and calculations of intraclass correlation coefficients. The age-adjusted relative risks of these two endpoints for unique class II haplotypes were determined from proportional hazards models. Results: Sibling pairs sharing one or two haplotypes were significantly concordant in CD4 decline and AIDS status within 5 years of seroconversion. No concordance was found in pairs sharing zero haplotypes. At 6-10 years after seroconversion, significant concordance of these two endpoints was also observed in the pairs sharing one haplotype. The concordant results were not explained by the use of zidovudine within the pairs. Among the individuals in this cohort, the relative hazards for CD4 decline to < 20% and for AIDS were significantly elevated for one class II haplotype (DQB1*0501, DQA1*0101, DRB1*0101). In addition, the risk for AIDS was significantly increased for two other class II haplotypes (DQB1*0603, DQA1*0103, DRB1*1300, DRB3*0202 and DQB1*0301, DQA1*0501, DRB1*1400, DRB3*0202) and significantly decreased for one haplotype (DQB1*0302, DQA1*0301, DRB1*0401, DRB4*0101). Conclusions: These data demonstrate that HIV-1 disease progression is associated with the genes in the major histocompatibility complex that regulate the host's immune response.
An Accurate SER Estimation Method Based on Propagation Probability (2007)

In this paper, we present an accurate but very fast soft error rate (SER) estimation technique for digital circuits based on error propagation probability (EPP) computation. Experiments results and comparison of the results with the random simulation technique show that our proposed method is on average within 6% of the random simulation method and four to five orders of magnitude faster.
Electrical and thermal layout design considerations for integrated power electronics modules (2003)

A methodology was developed to optimize the 3D geometrical design layout of an active integrated power electronics module (IPEM) by considering both electrical and thermal performance. This paper is focused on the electrical analysis, including the parasitic extraction done by the Maxwell Q3D Extractor. A parametric study was conducted to determine the common model EMI noise of several different layouts. The final design layout was achieved after tradeoff between electrical and thermal performance.