Miracle-dz/UniFAR-FTUs huggingface dataset:
Obesity, hormone therapy, estrogen metabolism and risk of postmenopausal breast cancer

Hormone therapy (HT) and body mass index (BMI) have been associated with postmenopausal breast cancer. Because estrogen metabolism may affect breast cancer risk and can be altered by weight and HT, it might play a role in the HT–BMI–breast cancer associations. We undertook a nested case‐control study within the Observational Study of the Women's Health Initiative. Baseline levels of 2‐ and 16α‐hydroxy estrone (2‐OHE1 and 16α‐OHE1) were measured in 200 women who developed breast cancer during follow‐up and 200 healthy controls matched to cases by ethnicity, enrollment date, clinic site, type of HT and years since menopause. Wilcoxon nonparametric tests were used to compare estrogen metabolite levels between cases and controls. Conditional logistic regression was used to assess the relationship between BMI, estrogen metabolites and breast cancer risk. 16α‐OHE1 levels were modestly but significantly higher in HT users among cases (median 356 pg/ml vs. 315 pg/ml) and controls (354 pg/ml vs. 298 pg/ml). 2‐OHE1 levels were substantially and significantly higher in HT users among cases (369 pg/ml vs. 125 pg/ml) and controls (347 pg/ml vs. 134 pg/ml). For non‐HT users only, greater BMI and higher 16α‐OHE1 levels were individually and jointly associated with increased breast cancer risk (OR for women with high BMI and high 16α‐OHE1 compared to those with low BMI and low 16α‐OHE1 = 3.51, 95% CI = 1.34–9.16). No associations between BMI, estrogen metabolism and breast cancer risk were found for HT users. Estrogen metabolism differs according to both BMI and HT use, potentially explaining the interaction between BMI and HT in relation to breast cancer risk. © 2005 Wiley‐Liss, Inc.
Dose-Response Curves in Chemical Carcinogenesis

Extrapolation from studies of chemical carcinogenicity in rodents, at high doses, to humans, at the typically low doses to which we are exposed, has been one of the most controversial issues in toxicology. Many chemical carcinogenesis experiments currently are evaluated on a linear scale for dose. Log dose has been the standard for decades in pharmacology and toxicology for noncancer toxicities and there is no reason to think that it should not apply to chemical carcinogenesis. Furthermore, log dose is consistent with fundamental principles of chemistry. Direct comparisons of linear and logarithmic scales for dose illustrate the deceptive nature of linear plots for dose; low doses, which is where our interest lies in comparing human exposures, are compressed beyond evaluation by a linear scale. Unequivocal thresholds for carcinogenicity are shown when the dose-response curves for animal studies done at high doses are evaluated on a log scale for dose. This observation now raises the issue of the relevance to human exposures of these high-dose experiments in animals. Studies analyzed by this log dose to linear response procedure demonstrate that the thresholds from animal experiments can be used to calculate safety factors for human exposure and that humans are more resistant than animals to carcinogenesis from chemicals.
Infection of Ciliated Cells by Human Parainfluenza Virus Type 3 in an In Vitro Model of Human Airway Epithelium

ABSTRACT We constructed a human recombinant parainfluenza virus type 3 (rPIV3) that expresses enhanced green fluorescent protein (GFP) and used this virus, rgPIV3, to characterize PIV3 infection of an established in vitro model of human pseudostratified mucociliary airway epithelium (HAE). The apical surface of HAE was highly susceptible to rgPIV3 infection, whereas only occasional cells were infected when virus was applied to the basolateral surface. Infection involved exclusively ciliated epithelial cells. There was little evidence of virus-mediated cytopathology and no spread of the virus beyond the ciliated cell types. Infection of ciliated cells by rgPIV3 was sensitive to a neuraminidase specific for α2-6-linked sialic acid residues, but not to a neuraminidase that cleaves α2-3- and α2-8-linked sialic acid residues. This provided evidence that rgPIV3 utilizes α2-6-linked sialic acid residues for initiating infection, a specificity also described for human influenza viruses. The PIV3 fusion (F) glycoprotein was trafficked exclusively to the apical surface of ciliated cells, which also was the site of release of progeny virus. F glycoprotein localized predominately to the membranes of the cilial shafts, suggesting that progeny viruses may bud from cilia per se. The polarized trafficking of F glycoprotein to the apical surface also likely restricts its interaction with neighboring cells and could account for the observed lack of cell-cell fusion. HAE derived from cystic fibrosis patients was not more susceptible to rgPIV3 infection but did exhibit limited spread of virus due to impaired movement of lumenal secretions due to compromised function of the cilia.
Prolonged Atrium Electromechanical Interval Is Associated with Stroke in Patients with Atrial Fibrillation After Catheter Ablation

Electromechanical Interval and Strokes After Ablations of AF. Introduction: Atrial fibrillation (AF) is associated with increased risk of embolic stroke. Catheter ablation of AF provides an effective therapy for patients with symptomatic and drug‐refractory AF. The aim of this study was to evaluate whether the atrial electromechanical interval is useful in identifying patients at risk of stroke after successful catheter ablation.
CFD and PIV analysis of hemodynamics in a growing intracranial aneurysm

Hemodynamics is thought to be a fundamental factor in the formation, progression, and rupture of cerebral aneurysms. Understanding these mechanisms is important to improve their rupture risk assessment and treatment. In this study, we analyze the blood flow field in a growing cerebral aneurysm using experimental particle image velocimetry (PIV) and computational fluid dynamics (CFD) techniques. Patient‐specific models were constructed from longitudinal 3D computed tomography angiography images acquired at 1‐y intervals. Physical silicone models were constructed from the computed tomography angiography images using rapid prototyping techniques, and pulsatile flow fields were measured with PIV. Corresponding CFD models were created and run under matching flow conditions. Both flow fields were aligned, interpolated, and compared qualitatively by inspection and quantitatively by defining similarity measures between the PIV and CFD vector fields. Results showed that both flow fields were in good agreement. Specifically, both techniques provided consistent representations of the main intra‐aneurysmal flow structures and their change during the geometric evolution of the aneurysm. Despite differences observed mainly in the near wall region, and the inherent limitations of each technique, the information derived is consistent and can be used to study the role of hemodynamics in the natural history of intracranial aneurysms. Copyright © 2011 John Wiley & Sons, Ltd.
Six-Year Experience With Endoscopic Thyroidectomy

Background: Though minimally invasive video-assisted thyroidectomy (MIVAT) offers many advantages over traditional thyroid surgery, its adoption in North America has been limited. This study analyzes the largest series of MIVAT in North America to explore its safety. Methods: A prospectively maintained database of all patients undergoing thyroid surgery by a single surgeon from 2003 to 2011 at an academic tertiary care medical center was evaluated. Demographic information, surgical and pathologic data, and postoperative outcomes were analyzed. Results: Beginning in 2005, a total of 260 MIVATs were performed during the study period. Outpatient surgery was accomplished in 234 MIVATs (90%). MIVAT patients were predominantly young (46.8 ± 14.8 years vs 52.4 ± 14.6 years for conventional thyroidectomy) and female (88.5% vs 75.5% for conventional thyroidectomy). There were no cases of permanent hypoparathyroidism or permanent recurrent laryngeal nerve dysfunction. Observed complications included transient recurrent laryngeal nerve dysfunction (n = 10; 3.8%), cellulitis (n = 1; 0.4%), and temporary hypocalcemia (n = 6; 2.3%). The overall complication rate for MIVAT (6.5%) was lower than the overall complication rate in conventional thyroidectomy (18.5%, P < .0001). Conclusion: MIVAT can be performed safely with a low complication profile in a high-volume practice. The safety of MIVAT represented by this experience supports broader adoption across surgical practices.
Economic burden of healthcare-associated infection in US acute care hospitals: societal perspective

Abstract Background: Assessing the costs of healthcare-associated infection (HAI) is challenging. Methodological issues abound. Previous estimates have been derived in diverse ways from varied perspectives in different settings with dissimilar data. Results can be confusing. Full societal costs, which are more inclusive than commonly reported direct hospital costs, have never been fully measured or reported. Objective: To update, combine, and expand previous cost estimates to determine the annual societal burden of illness (direct medical, non-medical, and indirect costs) arising from HAIs in US acute-care hospitals. Methods: The research approach encompassed literature and internet searches; reference identification, selection, and review; then data abstraction, compilation, and analyses to estimate full societal costs. Previously published systemic reviews, surveillance reports, and individual clinical studies, along with newly computed component costs, all contributed to final estimates. Results: HAIs in US acute-care hospitals lead to direct and indirect costs totaling $96–$147 billion annually. These results are subject to the same limitations as previous studies from which contributing data were derived. Conclusion: The enormous clinical and economic burden of infection places HAIs high on the list of devastating and costly illnesses, such as cancer, heart attack, stroke, and diabetes, thereby mandating further research and greater efforts to contain a pressing healthcare problem.
Comparative Analysis of Murine Dendritic Cells Derived from Spleen and Bone Marrow

In order to improve upon preclinical tumor vaccine strategies that employ dendritic cells (DC), we now have compared short-term cultures of spleen- and GMCSF/IL-4-stimulated bone marrow (BM) to determine if differences exist in phenotype and function of murine DC derived from primary and secondary hematolymphoid organs. Although cultures of BM contained a lower percentage of DC compared to spleen, their capacity to stimulate a primary allogeneic mixed leukocyte reaction (MLR) and to uptake fluorescent dextran was substantially greater. In addition, the overall yields of DC per animal was at least twofold greater from BM compared to spleen. Cultures of BM harvested at day 3, 6, or 9 stimulated comparable levels of primary allo-MLR on a per-cell basis. However, there was a consistent loss (at least twofold) of all cells occurring beyond day 6 as compared with cell yields from earlier time points. Importantly, we also improved on methods to rapidly obtain highly enriched DC (>90%) from BM, which has obviated the reported prior need for complex antibody and complement treatments to remove contaminating mature T and B lymphocytes, la-bearing cells, and granulocytes before DC generation. In contrast, although similar purity of DC with similar phenotype and function could be obtained from the spleen, substantial loss in yield occurred, suggesting a further difference in DC between the two tissue sources. The overall yield of DC derived from spleen and BM cultures could be substantially increased by in vivo pretreatment of the donor animals with recombinant Flt3-L. Collectively, these studies demonstrate that notable differences exist in DC preparations derived from spleen vs. BM and that BM provides the preferred source of DC that can be rapidly enriched to high purity for use in further vaccine development.
A hybrid differential evolution algorithm for open-order coil allocation problem in the steel industry

Open-order coils are defined as the coils which have not been yet assigned to any orders and are stored in the coil storage as surplus inventory. Open-order coil allocation problem is to allocate open-order coils to unfulfilled customer orders in order to reduce surplus inventory and improve the material utilization. We formulate the problem as an integer programming model considering specifications of coils and requirements of orders. Since the problem is NP-hard, an improved differential evolution algorithm (called HDE) is proposed to achieve the near optimal solutions for the problem. In the algorithm, mod mutation operators and a fitness-based mechanism are adopted to perform the global exploration. In addition, variable neighborhood search is embedded to further enhance the local exploitation. Computational experiments based on different scale instances are carried out to verify the effectiveness of the proposed model and algorithm.
Phylogenetics of the Chamaesyce clade (Euphorbia, Euphorbiaceae): reticulate evolution and long-distance dispersal in a prominent C4 lineage.

UNLABELLED PREMISE OF THE STUDY The Chamaesyce clade of Euphorbia is the largest lineage of C(4) plants among the eudicots, with 350 species including both narrow endemics and cosmopolitan weeds. We sampled this group worldwide to address questions about subclade relationships, the origin of C(4) photosynthesis, the evolution of weeds, and the role of hybridization and long-distance dispersal in the diversification of the group. • METHODS Two nuclear (ITS and exon 9 of EMB2765) and three chloroplast markers (matK, rpl16, and trnL-F) were sequenced for 138 ingroup and six outgroup species. Exon 9 of EMB2765 was cloned in accessions with >1% superimposed peaks. • KEY RESULTS The Chamaesyce clade is monophyletic and consists of three major subclades [1(2,3)]: (1) the Acuta clade, containing three North American species with C(3) photosynthesis and C(3)-C(4) intermediates; (2) the Peplis clade, mostly North American and entirely C(4); and (3) the Hypericifolia clade, all C(4), with both New World and Old World groups. Incongruence between chloroplast and ITS phylogenies and divergent cloned copies of EMB2765 exon 9 suggest extensive hybridization, especially in the Hawaiian Islands radiation. • CONCLUSIONS The Chamaesyce clade originated in warm, arid areas of North America, where it evolved C(4) photosynthesis. From there, it diversified globally with extensive reticulate evolution and frequent long-distance dispersals. Although many species are weedy, there are numerous local adaptations to specific substrates and regional or island radiations, which have contributed to the great diversity of this group.
Evidence of Differences between the Communities of Arbuscular Mycorrhizal Fungi Colonizing Galls and Roots of Prunus persica Infected by the Root-Knot Nematode Meloidogyne incognita

ABSTRACT Arbuscular mycorrhizal fungi (AMF) play important roles as plant protection agents, reducing or suppressing nematode colonization. However, it has never been investigated whether the galls produced in roots by nematode infection are colonized by AMF. This study tested whether galls produced by Meloidogyne incognita infection in Prunus persica roots are colonized by AMF. We also determined the changes in AMF composition and biodiversity mediated by infection with this root-knot nematode. DNA from galls and roots of plants infected by M. incognita and from roots of noninfected plants was extracted, amplified, cloned, and sequenced using AMF-specific primers. Phylogenetic analysis using the small-subunit (SSU) ribosomal DNA (rDNA) data set revealed 22 different AMF sequence types (17 Glomus sequence types, 3 Paraglomus sequence types, 1 Scutellospora sequence type, and 1 Acaulospora sequence type). The highest AMF diversity was found in uninfected roots, followed by infected roots and galls. This study indicates that the galls produced in P. persica roots due to infection with M. incognita were colonized extensively by a community of AMF, belonging to the families Paraglomeraceae and Glomeraceae, that was different from the community detected in roots. Although the function of the AMF in the galls is still unknown, we hypothesize that they act as protection agents against opportunistic pathogens.
TransKingdom RNA interference: a bacterial approach to challenges in RNAi therapy and delivery

Abstract Since its discovery in 1998 RNA interference (RNAi), a potent and highly selective gene silencing mechanism, has revolutionized the field of biological science. The ability of RNAi to specifically down-regulate the expression of any cellular protein has had a profound impact on the study of gene function in vitro. This property of RNAi also holds great promise for in vivo functional genomics and interventions against a wide spectrum of diseases, especially those with “undruggable” therapeutic targets. Despite the enormous potential of RNAi for medicine, development of in vivo applications has met with significant problems, particularly in terms of delivery. For effective gene silencing to occur, silencing RNA must reach the cytoplasm of the target cell. Consequently, various strategies using chemically modified siRNA, liposomes, nanoparticles and viral vectors are being developed to deliver silencing RNA. These approaches, however, can be expensive and in many cases they lack target cell specificity or clinical compatibility. Recently, we have shown that RNAi can be activated in vitro and in vivo by non-pathogenic bacteria engineered to manufacture
Glutamate transporter EAAT2 expression is up‐regulated in reactive astrocytes in human periventricular leukomalacia

The major neuropathological correlate of cerebral palsy in premature infants is periventricular leukomalacia (PVL), a disorder of the immature cerebral white matter. Cerebral ischemia leading to excitotoxicity is thought to be important in the pathogenesis of this disorder, implying a critical role for glutamate transporters, the major determinants of extracellular glutamate concentration. Previously, we found that EAAT2 expression is limited primarily to premyelinating oligodendrocytes early in development and is rarely observed in astrocytes until >40 weeks. In this study, we analyzed the expression of EAAT2 in cerebral white matter from PVL and control cases. Western blot analysis suggested an up‐regulation of EAAT2 in PVL compared with control cases. Single‐ and double‐label immunocytochemistry showed a significantly higher percentage of EAAT2‐immunopositive astrocytes in PVL (51.8% ± 5.6%) compared with control white matter (21.4% ± 5.6%; P = 0.004). Macrophages in the necrotic foci in PVL also expressed EAAT2. Premyelinating oligodendrocytes in both PVL and control cases expressed EAAT2, without qualitative difference in expression. The previously unrecognized up‐regulation of EAAT2 in reactive astrocytes and its presence in macrophages in PVL reported here may reflect a response to either hypoxic‐ischemic injury or inflammation. J. Comp. Neurol. 508:238–248, 2008. © 2008 Wiley‐Liss, Inc.
Peut-on définir des aires culturelles au Paléolithique inférieur ? : originalité des premières industries lithiques en Europe centrale dans le cadre du peuplement de l’Europe

Les modeles de diffusion de l’Homme hors d’Afrique considerent que les premiers groupes humains ont peuples l’Europe selon deux vagues correspondant chacune a une culture technique differente. Les premiers peuplements, qui remonte au million d’annee et se caracterisent par des productions d’eclats, associee a des outils sur galet. La deuxieme vague serait porteuse de l’Acheuleen, puisque les premieres industries comprenant des bifaces en Europe sont datees a 0,6 millions d’annee. Mais les donnees presentes en Europe centrale ont bien du mal a entrer dans ce cadre theorique. Pourtant sur le chemin des premiers peuplements hors d’Afrique, cette region n’a pas livre les donnees archeologiques auxquelles ont aurait pu s’attendre. Les premiers indices d’occupation humaines anterieures a 0,5 Ma sont rarissimes, les bifaces sont absents durant toute la duree du paleolithique inferieur et les industries presentes sont originales. L’Europe centrale est-elle une aire culturelle specifique au Paleolithique inferieur ? Ou est-ce nos propre outils methodologiques qui doivent etre interroges pour repondre a cet apparent paradoxe ? C’est a travers l’etude de l’industrie lithique de quatre sites que nous avons tente de repondre a ces questions. Le deux premiers assemblage (Korolevo VI en Ukraine et Karlich-Seeufer en Allemagne) sont dates aux environs de 0,5 Ma et ont livre une industrie basee sur la production d’eclats varies. Les deux autres collections (Vertesszolos en Hongrie et Bilzingsleben en Allemagne) se caracterisent au contraire par une industrie basee sur la confection de petits supports selectionnes. Les resultats de l’etude des premieres industries en Europe centrale, nous invite donc a reconsiderer la question du peuplement de l’Europe et a s’interroger sur les criteres pris en compte dans la definition des entites culturelles et des systemes techniques au Paleolithique inferieur.
AC Drive Observability Analysis

AC induction motors and permanent magnet synchronous drives became very popular for motion control applications due to their simple and reliable construction. Sensorless drive control is required in many applications to reduce drive production costs. While many approaches to magnetic flux, rotor speed, or other quantities needed to control electrical machine were proposed, conditions under which these quantities can be estimated are not often sufficiently investigated. In this paper, induction machine and permanent-magnet-synchronous-machine drive state observability analysis is presented, together with conditions allowing reliable rotor speed and position estimation. A method based on the nonlinear dynamical system state observability theory is proposed, resulting in a unified approach to the ac drive observability analysis.
Data-driven iterative learning control for I/O constrained LTI systems

In this paper, a novel data-driven iterative learning control (ILC) scheme is proposed for a class of constrained linear time-invariant (LTI) discrete-time systems with unknown system matrix. First, we only use the input and output information from previous iterations to estimate system Markov matrix obtained by the lifted technique. Second, three types of constraints, which include input constraint, system output constraint and the constraint of change rate of control input between two iteration index, are transferred into a linear constraint inequality in a unified manner. And then, by using the constructed objective function together with the linear constraint inequality, a quadratic programming (QP) problem can be formulated. The ILC control law in numerical manner can be obtained by solving the QP problem. The proposed control scheme is data-driven and does not need any model information. An illustrative example is provided to demonstrate the effectiveness of the proposed data-driven ILC strategy.