Miracle-dz/UniFAR-FTUs huggingface dataset:
Postexposure Protection of Guinea Pigs against a Lethal Ebola Virus Challenge Is Conferred by RNA Interference

Abstract BackgroundEbola virus (EBOV) infection causes a frequently fatal hemorrhagic fever (HF) that is refractory to treatment with currently available antiviral therapeutics. RNA interference represents a powerful, naturally occurring biological strategy for the inhibition of gene expression and has demonstrated utility in the inhibition of viral replication. Here, we describe the development of a potential therapy for EBOV infection that is based on small interfering RNAs (siRNAs) MethodsFour siRNAs targeting the polymerase (L) gene of the Zaire species of EBOV (ZEBOV) were either complexed with polyethylenimine (PEI) or formulated in stable nucleic acid–lipid particles (SNALPs). Guinea pigs were treated with these siRNAs either before or after lethal ZEBOV challenge ResultsTreatment of guinea pigs with a pool of the L gene–specific siRNAs delivered by PEI polyplexes reduced plasma viremia levels and partially protected the animals from death when administered shortly before the ZEBOV challenge. Evaluation of the same pool of siRNAs delivered using SNALPs proved that this system was more efficacious, as it completely protected guinea pigs against viremia and death when administered shortly after the ZEBOV challenge. Additional experiments showed that 1 of the 4 siRNAs alone could completely protect guinea pigs from a lethal ZEBOV challenge ConclusionsFurther development of this technology has the potential to yield effective treatments for EBOV HF as well as for diseases caused by other agents that are considered to be biological threats
Synthesis and Properties of MQ Copolymers: Current State of Knowledge

In this review, we discuss currently available studies on the synthesis and properties of MQ copolymers. The data on methods of producing hydrolytic and heterofunctional polycondensation of functional organosilanes as well as the obtaining MQ copolymers based on silicic acids and nature silicates are considered. The ratio of M and Q monomers and the production method determine the structure of MQ copolymers and, accordingly, their physicochemical characteristics. It is shown that the most successful synthetic approach is a polycondensation of organoalkoxysilanes in the medium of anhydrous acetic acid, which reduces the differences in reactivity of M and Q monomers and leads to obtaining a product with uniform composition in all fractions, with full absence of residual alkoxy-groups. The current concept of MQ copolymers is that of organo-inorganic hybrid systems with nanosized crosslinked inorganic regions limited by triorganosilyl groups and containing residual hydroxyl groups. The systems can be considered as a peculiar molecular composites consisting of separate parts that play the role of a polymer matrix, a plasticizer, and a nanosized filler.
Lung scintigraphy in the diagnosis of pulmonary embolism: current methods and interpretation criteria in clinical practice

Abstract Background. In current clinical practice lung scintigraphy is mainly used to exclude pulmonary embolism (PE). Modified diagnostic criteria for planar lung scintigraphy are considered, as newer scitigraphic methods, especially single photon emission computed tomography (SPECT) are becoming more popular. Patients and methods. Data of 98 outpatients who underwent planar ventilation/perfusion (V/Q) scintigraphy and 49 outpatients who underwent V/Q SPECT from the emergency department (ED) were retrospectively collected. Planar V/Q images were interpreted according to 0.5 segment mismatch criteria and revised PIOPED II criteria and perfusion scans according to PISA-PED criteria. V/Q SPECT images were interpreted according to the criteria suggested in EANM guidelines. Final diagnosis of PE was based on the clinical decision of an attending physician and evaluation of a 12 months follow-up period. Results. Using 0.5 segment mismatch criteria and revised PIOPED II, planar V/Q scans were diagnostic in 93% and 84% of cases, respectively. Among the diagnostic planar scans readings specificity for 0.5 segment mismatch criteria was 98%, and 99% for revised PIOPED II criteria. V/Q SPECT showed a sensitivity of 100% and a specificity of 98%, without any non-diagnostic cases. In patients with low pretest probability for PE, planar V/Q scans assessed by 0.5 segment mismatch criteria were diagnostic in 92%, and in 85% using revised PIOPED II criteria, while perfusion scintigraphy without ventilation scans was diagnostic in 80%. Conclusions. Lung scintigraphy yielded diagnostically definitive results and is reliable in ruling out PE in patients from ED. V/Q SPECT has excellent specificity and sensitivity without any non-diagnostic results. Percentage of nondiagnostic results in planar lung scintigraphy is considerably smaller when 0.5 segment mismatch criteria instead of revised PIOPED II criteria are used. Diagnostic value of perfusion scintigraphy according to PISA-PED criteria is inferior to combined V/Q scintigraphy; the difference is evident especially in patients with low pretest probability for PE.
Comparison of linear–stochastic and nonlinear–deterministic algorithms in the analysis of 15-minute clinical ECGs to predict risk of arrhythmic death

Objective: Comparative algorithmic evaluation of heartbeat series in low-to-high risk cardiac patients for the prospective prediction of risk of arrhythmic death (AD). Background: Heartbeat variation reflects cardiac autonomic function and risk of AD. Indices based on linear stochastic models are independent risk factors for AD in post-myocardial infarction (post-MI) cohorts. Indices based on nonlinear deterministic models have superior predictability in retrospective data. Methods: Patients were enrolled (N = 397) in three emergency departments upon presenting with chest pain and were determined to be at low-to-high risk of acute MI (>7%). Brief ECGs were recorded (15 min) and R-R intervals assessed by three nonlinear algorithms (PD2i, DFA, and ApEn) and four conventional linear-stochastic measures (SDNN, MNN, 1/f-Slope, LF/HF). Out-of-hospital AD was determined by modified Hinkle–Thaler criteria. Results: All-cause mortality at one-year follow-up was 10.3%, with 7.7% adjudicated to be AD. The sensitivity and relative risk for predicting AD was highest at all time-points for the nonlinear PD2i algorithm (p ≤0.001). The sensitivity at 30 days was 100%, specificity 58%, and relative risk >100 (p ≤0.001); sensitivity at 360 days was 95%, specificity 58%, and relative risk >11.4 (p ≤0.001). Conclusions: Heartbeat analysis by the time-dependent nonlinear PD2i algorithm is comparatively the superior test.
Post-transplant complications Pulmonary function abnormalities after allogeneic marrow transplantation: a systematic review and assessment of an existing predictive instrument

Summary: Pulmonary function testing (PFT) is used to characterize non-infectious pulmonary complications after allogeneic BMT. Identifying high-risk patients could facilitate preventive or early therapeutic measures. The objectives of the study were first, to review available data on PFT changes after BMT and second, to validate a previously published predictive index for PFT obstruction in patients transplanted at one center. For the systematic review, frequency, severity and time course of PFT changes after BMT and for the validation study, retrospective cohort comparing predicted with observed PFT, and calculation of indices of predictive accuracy were summarized. The validation study involved 434 patients from Princess Margaret Hospital, Toronto, Canada, who received their first BMT between 1980 and 1997, survived for at least 6 months and had adequate PFT follow-up. The systematic review included 20 studies. After BMT, decreased diffusion and total lung capacity were common and partially reversible. Obstruction was less common. The validation study of a previously published index, performed in 434 patients, found a sensitivity and specificity of 48% and 68% for identifying patients who develop obstruction. We concluded that PFT changes after BMT are common. A published predictive index is not sufficiently accurate to identify high-risk patients for potential preventive or early therapeutic strategies.
Role of Surface Redistribution in Sintering by Grain Boundary Transport

Abstract When a compact of particles densities- by grain boundary diffusion of matter from the boundaries between the particles, the matter entering the neck must redistribute itself over the neck surface. It is normally assumed that this redistribution is rapid, and that the rate of boundary diffusion limits the overall rate of densification. Under certain circumstances, however, the redistribution can be rate-limiting. An approximate model is developed for this coupled process, and the circumstances under which it is important are discussed.
Secretory Phospholipases A2 in Durum Wheat (Triticum durum Desf.): Gene Expression, Enzymatic Activity, and Relation to Drought Stress Adaptation

Phospholipases A2 (PLA2s) are known to mediate signaling cascades during plant growth and development, as well as biotic and abiotic stress responses. In this context, the present study provides extensive characterization of specific PLA2s in durum wheat, and assesses their involvement in durum wheat response to drought stress. In durum wheat leaves, four full-length expressed sequences encoding putative PLA2s were isolated and characterized as belonging to the class of secretory PLA2s (sPLA2s): TdsPLA2I, TdsPLA2II, TdsPLA2III and TdsPLA2IV. PLA2 activity was also detected, the characteristics of which resemble those of previously characterized plant sPLA2s: strong preference for phospholipids; requirement for millimolar Ca2+ concentrations; optimal activity at basic pH; heat stability; and inhibition by the reducing agent dithiothreitol. With drought stress imposed at both the vegetative and reproductive stages, accumulation of TdsPLA2I and TdsPLA2III transcripts, and to a lesser extent of TdsPLA2IV transcript, paralleled increased PLA2 activity; both transcript levels and enzymatic activity decreased as a consequence of stress recovery. Consistently, free fatty acid analysis of drought-stressed leaves revealed increased linoleate, linolenate and palmitate contents, which were reversed by plant re-watering. Overall, these findings strongly suggest that there are inducible sPLA2 isoforms in durum wheat that have roles in orchestrating the plant response to drought stress.
Multi-layered bird beaks: a finite-element approach towards the role of keratin in stress dissipation

Bird beaks are layered structures, which contain a bony core and an outer keratin layer. The elastic moduli of this bone and keratin were obtained in a previous study. However, the mechanical role and interaction of both materials in stress dissipation during seed crushing remain unknown. In this paper, a multi-layered finite-element (FE) model of the Java finch's upper beak (Padda oryzivora) is established. Validation measurements are conducted using in vivo bite forces and by comparing the displacements with those obtained by digital speckle pattern interferometry. Next, the Young modulus of bone and keratin in this FE model was optimized in order to obtain the smallest peak von Mises stress in the upper beak. To do so, we created a surrogate model, which also allows us to study the impact of changing material properties of both tissues on the peak stresses. The theoretically best values for both moduli in the Java finch are retrieved and correspond well with previous experimentally obtained values, suggesting that material properties are tuned to the mechanical demands imposed during seed crushing.
Characterization and Subcellular Targeting of GCaMP-Type Genetically-Encoded Calcium Indicators

Genetically-encoded calcium indicators (GECIs) hold the promise of monitoring [Ca2+] in selected populations of neurons and in specific cellular compartments. Relating GECI fluorescence to neuronal activity requires quantitative characterization. We have characterized a promising new genetically-encoded calcium indicator—GCaMP2—in mammalian pyramidal neurons. Fluorescence changes in response to single action potentials (17±10% ΔF/F [mean±SD]) could be detected in some, but not all, neurons. Trains of high-frequency action potentials yielded robust responses (302±50% for trains of 40 action potentials at 83 Hz). Responses were similar in acute brain slices from in utero electroporated mice, indicating that long-term expression did not interfere with GCaMP2 function. Membrane-targeted versions of GCaMP2 did not yield larger signals than their non-targeted counterparts. We further targeted GCaMP2 to dendritic spines to monitor Ca2+ accumulations evoked by activation of synaptic NMDA receptors. We observed robust ΔF/F responses (range: 37%–264%) to single spine uncaging stimuli that were correlated with NMDA receptor currents measured through a somatic patch pipette. One major drawback of GCaMP2 was its low baseline fluorescence. Our results show that GCaMP2 is improved from the previous versions of GCaMP and may be suited to detect bursts of high-frequency action potentials and synaptic currents in vivo.
Testing Gene-environment Interaction in Large Scale Case-control Association Studies: Possible Choices and Comparisons Running Title: Tests for Gene-environment Interaction

In the era of post genome-wide association studies, many investigators are currently searching for non-multiplicative gene-environment (G x E) interaction effects for studying complex disease phenotypes with established environmental risk factors. Several methods for screening G x E interaction have recently been proposed that address the issue of using gene-environment independence in a data-adaptive way. In this brief report, we present a comparative simulation study of power and Type I error properties of three classes of procedures: (i) The standard one-step case-control method; (ii) The case-only method which requires an assumption of gene-environment independence for the underlying population; (iii) A variety of hybrid methods, including empirical-Bayes, two-step and model averaging, that aim at gaining power by exploiting the assumption of gene-environment independence and yet can protect against false positives when the independence assumption is violated. Our studies suggest that while the case-only method generally has maximum power, it has the potential to create substantial false positives in large scale studies even when a small fraction of markers are associated with the exposure under study in the underlying population. All the hybrid methods perform well in protecting against such false positives and yet can retain substantial power advantages over standard case-control tests. The relative performance of the hybrid methods depend on the true underlying parameters for gene-environment interaction and gene-environment association. We conclude that for future genome-wide scans for G × E interactions, major power gain is possible by using alternatives to standard case-control analysis. Whether a case-only type scan or one of the hybrid methods should be used, depends on degree and direction of gene-environment association expected, the level of tolerance for false positives and the nature of replication strategies.
The multidrug ABC transporter BmrC/BmrD of Bacillus subtilis is regulated via a ribosome-mediated transcriptional attenuation mechanism

Expression of particular drug transporters in response to antibiotic pressure is a critical element in the development of bacterial multidrug resistance, and represents a serious concern for human health. To obtain a better understanding of underlying regulatory mechanisms, we have dissected the transcriptional activation of the ATP-binding cassette (ABC) transporter BmrC/BmrD of the Gram-positive model bacterium Bacillus subtilis. By using promoter-GFP fusions and live cell array technology, we demonstrate a temporally controlled transcriptional activation of the bmrCD genes in response to antibiotics that target protein synthesis. Intriguingly, bmrCD expression only occurs during the late-exponential and stationary growth stages, irrespective of the timing of the antibiotic challenge. We show that this is due to tight transcriptional control by the transition state regulator AbrB. Moreover, our results show that the bmrCD genes are co-transcribed with bmrB (yheJ), a small open reading frame immediately upstream of bmrC that harbors three alternative stem-loop structures. These stem-loops are apparently crucial for antibiotic-induced bmrCD transcription. Importantly, the antibiotic-induced bmrCD expression requires translation of bmrB, which implies that BmrB serves as a regulatory leader peptide. Altogether, we demonstrate for the first time that a ribosome-mediated transcriptional attenuation mechanism can control the expression of a multidrug ABC transporter.
Active Caspases and Cleaved Cytokeratins Are Sequestered into Cytoplasmic Inclusions in Trail-Induced Apoptosis

Tumor necrosis factor–related apoptosis- inducing ligand (TRAIL) –induced apoptosis, in transformed human breast epithelial MCF-7 cells, resulted in a time-dependent activation of the initiator caspases-8 and -9 and the effector caspase-7. Cleavage of caspase-8 and its preferred substrate, Bid, preceded processing of caspases-7 and -9, indicating that caspase-8 is the apical initiator caspase in TRAIL-induced apoptosis. Using transient transfection of COOH-terminal–tagged green fluorescent protein fusion constructs, caspases-3, -7, and -8 were localized throughout the cytoplasm of MCF-7 cells. TRAIL-induced apoptosis resulted in activation of caspases-3 and -7, and the redistribution of most of their detectable catalytically active small subunits into large spheroidal cytoplasmic inclusions, which lacked a limiting membrane. These inclusions, which were also induced in untransfected cells, contained cytokeratins 8, 18, and 19, together with both a phosphorylated form and a caspase-cleavage fragment of cytokeratin 18. Similarly, in untransfected breast HBL100 and lung A549 epithelial cells, TRAIL induced the formation of cytoplasmic inclusions that contained cleaved cytokeratin 18 and colocalized with active endogenous caspase-3. We propose that effector caspase-mediated cleavage of cytokeratins, resulting in disassembly of the cytoskeleton and formation of cytoplasmic inclusions, may be a characteristic feature of epithelial cell apoptosis.
Conceptualizing, Measuring, and Managing Customer-Based Brand Equity

The author presents a conceptual model of brand equity from the perspective of the individual consumer. Customer-based brand equity is defined as the differential effect of brand knowledge on consumer response to the marketing of the brand. A brand is said to have positive (negative) customer-based brand equity when consumers react more (less) favorably to an element of the marketing mix for the brand than they do to the same marketing mix element when it is attributed to a fictitiously named or unnamed version of the product or service. Brand knowledge is conceptualized according to an associative network memory model in terms of two components, brand awareness and brand image (i.e., a set of brand associations). Customer-based brand equity occurs when the consumer is familiar with the brand and holds some favorable, strong, and unique brand associations in memory. Issues in building, measuring, and managing customer-based brand equity are discussed, as well as areas for future research.
Massively expedited genome-wide heritability analysis (MEGHA)

Significance Practical tools for high-dimensional heritability-based screening are invaluable for prioritizing phenotypes for genetic studies with the dramatic expansion of available phenotypic data. Classical estimates of heritability require twin or pedigree data, which can be costly and difficult to acquire. Alternative methods based on whole-genome data from unrelated individuals exist but are computationally expensive. Here we present a novel, fast, and accurate statistical method for massively expedited genome-wide heritability analysis, making heritability-based prioritization of millions of phenotypes based on data from unrelated individuals tractable for the first time to our knowledge. We apply our method to large-scale heritability analyses of brain imaging measurements and demonstrate its potential for facilitating phenome-wide analyses and characterizing the genetic architecture of complex traits. The discovery and prioritization of heritable phenotypes is a computational challenge in a variety of settings, including neuroimaging genetics and analyses of the vast phenotypic repositories in electronic health record systems and population-based biobanks. Classical estimates of heritability require twin or pedigree data, which can be costly and difficult to acquire. Genome-wide complex trait analysis is an alternative tool to compute heritability estimates from unrelated individuals, using genome-wide data that are increasingly ubiquitous, but is computationally demanding and becomes difficult to apply in evaluating very large numbers of phenotypes. Here we present a fast and accurate statistical method for high-dimensional heritability analysis using genome-wide SNP data from unrelated individuals, termed massively expedited genome-wide heritability analysis (MEGHA) and accompanying nonparametric sampling techniques that enable flexible inferences for arbitrary statistics of interest. MEGHA produces estimates and significance measures of heritability with several orders of magnitude less computational time than existing methods, making heritability-based prioritization of millions of phenotypes based on data from unrelated individuals tractable for the first time to our knowledge. As a demonstration of application, we conducted heritability analyses on global and local morphometric measurements derived from brain structural MRI scans, using genome-wide SNP data from 1,320 unrelated young healthy adults of non-Hispanic European ancestry. We also computed surface maps of heritability for cortical thickness measures and empirically localized cortical regions where thickness measures were significantly heritable. Our analyses demonstrate the unique capability of MEGHA for large-scale heritability-based screening and high-dimensional heritability profile construction.
Nanocomposites Prepared by Solution Blending: Microstructure and Mechanical Properties

Composites of poly(vinyl chloride) (PVC) filled with micron‐ and nanosized calcium carbonate (CaCO3) particles were prepared by solution blending. The influences of particle size and CaCO3 content on the microstructure and mechanical properties of the PVC composites were investigated by means of polarized optical microscopy and mechanical testing. The polarized optical microscope images revealed that nanosized CaCO3 particles were more agglomerated than micron‐sized CaCO3 particles and the amount of agglomerates increased with increasing particle content. PVC/CaCO3‐0.22 composites (PVC nanocomposite filled with 220‐nm‐particle‐sized CaCO3) 5 phr CaCO3 content had the maximum tensile strength. The Young's modulus of all composites increased with increasing particle content. The energy at break of all composites showed a decreasing trend as a function of CaCO3 content and varied with particle size.