Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of a porosity measurement method for wet calcium phosphate cements

The porosity of a calcium phosphate cement is a key parameter as it affects several important properties of the cement. However, a successful, non-destructive porosity measurement method that does not include drying has not yet been reported for calcium phosphate cements. The aim of this study was to evaluate isopropanol solvent exchange as such a method. Two different types of calcium phosphate cements were used, one basic (hydroxyapatite) and one acidic (brushite). The cements were allowed to set in an aqueous environment and then immersed in isopropanol and stored under three different conditions: at room temperature, at room temperature under vacuum (300 mbar) or at 37℃. The specimen mass was monitored regularly. Solvent exchange took much longer time to reach steady state in hydroxyapatite cements compared to brushite cements, 350 and 18 h, respectively. Furthermore, the immersion affected the quasi-static compressive strength of the hydroxyapatite cements. However, the strength and phase composition of the brushite cements were not affected by isopropanol immersion, suggesting that isopropanol solvent exchange can be used for brushite calcium phosphate cements. The main advantages with this method are that it is non-destructive, fast, easy and the porosity can be evaluated while the cements remain wet, allowing for further analysis on the same specimen.
Wireless power transfer system based on high-index dielectric resonators

We have experimentally demonstrated two magnetic resonant wireless power transfer (WPT) systems based on dielectric spherical and disk resonators implemented with high permittivity microwave ceramics. We investigated the power transfer efficiency as a function of separation and rotation angle of the receiver and the transmitter with respect to one another. For the WPT system with spherical resonators, the maximal power transfer efficiency of 63% and 80% were obtained for the magnetic dipole mode and the magnetic quadrupole mode, respectively. With the matched impedance, the power transfer efficiency of the WPT system based on dielectric disk resonators can be as high as 80% for the separation less than 10 cm (2.4 radii of resonator) and more than 50% within separation of 16 cm (3.8 radii of resonator).
Therapeutic Assessment With Children: Intervening With Parents “Behind the Mirror”

All the steps in the model of therapeutic assessment used with children (TA–C) are designed to involve and impact the child's parents. However, a distinctive process that parallels and accompanies the testing sessions with the child might be the most significant in helping parents shift their story of their child and family. In this process, parents are invited to observe their child's testing sessions (in an adjacent room through a live video feed, through a 1-way mirror, or in the corner of the testing room) and process the experience with the assessor (either simultaneously in the case of the 2-assessor model or after the fact in the 1-assessor model). We discuss the development and evolution of what we have come to call the “behind the mirror” method. We describe the therapeutic intent of the method and delineate 13 techniques utilized to enlist parents as active collaborators. We illustrate each technique using the case study of a 10-year-old boy where the 2-assessor model and live video feed method were used. We also provide research findings from the case study that address the parents’ experience of the assessment and their changed view of their child.
An evolutionary metaheuristic algorithm to optimise solutions to NES games

Recently, it has been shown that lexicographic orderings and time travel can be used to automate the play of Nintendo Entertainment System (NES) games. In this work, we present a method for optimizing solutions to NES games. Since many of these classic Nintendo games are NP-hard, we propose a metaheuristic algorithm that works by borrowing operators from evolutionary algorithms. By using a search based heuristic, the algorithm is able to create basic solutions to the games and then iteratively improve upon them until it converges towards a local maximum. The optimum game solutions found by this algorithm are shown to be competitive to human players and are close to the best known times achieved by them.
Practical downlink transmission schemes for future LTE systems with many base-station antennas

We consider downlink multi-user MIMO transmission of a wireless system in which the base station is equipped with a large number of antennas. We propose two downlink schemes based on random beamforming and subspace tracking and show that while reducing signaling overhead, these schemes can improve the system performance compared to conventional systems with a smaller number of antennas at the base station.
Genetically encoding thioacetyl‐lysine as a non‐deacetylatable analog of lysine acetylation in Escherichia coli

Reversible lysine acetylation is one of the most widely distributed post‐translational modifications; it is involved in a variety of biological processes and can be found in all three domains of life. Acetyltransferases and deacetylases work coordinately to control levels of protein acetylation. In this work, we applied the genetic code expansion strategy to site‐specifically incorporate Nε‐thioacetyl‐l‐lysine (TAcK) as an analog of Nε‐acetyl‐l‐lysine (AcK) into green fluorescent protein and malate dehydrogenase in Escherichia coli. We showed that TAcK could serve as an ideal functional mimic for AcK. It could also resist the bacterial sirtuin‐type deacetylase CobB. Thus, genetic incorporation of TAcK as a non‐deacetylatable analog of AcK into proteins will facilitate in vivo studies of protein acetylation.
Dynamic River Masks from Multi-Temporal Satellite Imagery: An Automatic Algorithm Using Graph Cuts Optimization

Our knowledge of the spatio-temporal variation of river hydrological parameters is surprisingly poor. In situ gauge stations are limited in spatial and temporal coverage, and their number has been decreasing during the past decades. On the other hand, remote sensing techniques have proven their ability to measure different parameters within the Earth system. Satellite imagery, for instance, can provide variations in river area with appropriate temporal sampling. In this study, we develop an automatic algorithm for water body area monitoring based on maximum a posteriori estimation of Markov random fields. The algorithm considers pixel intensity, spatial correlation between neighboring pixels, and temporal behavior of the water body to extract accurate water masks. We solve this optimization problem using the graph cuts technique. We also measure the uncertainty associated with the determined water masks. Our method is applied over three different river reaches of Niger and Congo rivers with different hydrological characteristics. We validate the obtained river area time series by comparing with in situ river discharge and satellite altimetric water level time series. Along the Niger River, we obtain correlation coefficients of 0.85–0.96 for river reaches and 0.65 for the Congo River, which is demonstrably an improvement over other river mask retrieval algorithms.
Transcription regulation mechanisms of bacteriophages

Phage diversity significantly contributes to ecology and evolution of new bacterial species through horizontal gene transfer. Therefore, it is essential to understand the mechanisms underlying phage-host interactions. After initial infection, the phage utilizes the transcriptional machinery of the host to direct the expression of its own genes. This review presents a view on the transcriptional regulation mechanisms of bacteriophages, and its contribution to phage diversity and classification. Through this review, we aim to broaden the understanding of phage-host interactions while providing a reference source for researchers studying the regulation of phage transcription.
Revealing the Socio-Technical Context of Design Settings: Toward Participatory IS Design

This research proposes a participatory sociotechnical design approach to making explicit issues in collaborative information system design in a multidisciplinary context. The approach proposes the Socio-Technical Evaluation (STE) Matrix as a conceptual tool to address the lack of a technical and methodological instrument to expose cultural differences, boundaries, and conflicts in multidisciplinary research. STE Matrix was born within the context of the Village eScience for Life (VeSeL) project and adopts an empirical sociotechnical experimentation to initially explore the context of the stakeholders, including that of the end-users. These contexts are then revisited through information system design theories to rationalize the STE Matrix paradigm. Subsequent experiments and exposure to communities of practice provide validity to the approach by revealing the different frames of interpretation within the VeSeL project. Furthermore, STE Matrix provided a platform to truly observe participatory design by equally involving end-users and design partners in the subsequent phases of the VeSeL project.
Multiplexed genetic profiling of human blood platelets using fluorescent microspheres

Summary Human platelets have unique and reproducible mRNA profiles, with evidence for distinct profiles in haematopoietic stem cell disorders associated with thrombocytosis. Platelet transcript profiling is traditionally studied by microarray analysis, quantitative reverse transcription-PCR or serial analysis of gene ex-pression,techniques that are labor- and technically-intensive.We have now applied a novel multiplex-based platform for quantitative transcript profiling of human platelets.Simultaneous quantification of 17 platelet transcripts was assayed using intact platelet-rich plasma or gel-filtered platelets lysed in vitro.Accurate and reproducible profiles could be obtained from as few as 5 X 107 platelets (a platelet mass corresponding to ∼100 µl of whole blood), even for the low-abundant platelet transcripts. Correlation coefficients of this 17-member gene set to platelet Affymetrix microarrays were excellent (r2 = 0.949, p < 1 X 10–10), with no correlation to in kind-derived leukocyte profiles, highlighting the cell-specificity of the platform.These data demonstrate that transcript multiplexing using fluorescent micro-spheres can be adapted for rapid molecular profiling using intact platelets (bypassing the need for RNA isolation methods), with potential applicability irrespective of baseline platelet counts.
The core planar cell polarity gene, Vangl2, maintains apical‐basal organisation of the corneal epithelium

The role of the core planar cell polarity (PCP) pathway protein, Vangl2, was investigated in the corneal epithelium of the mammalian eye, a paradigm anatomical model of planar cell migration. The gene was conditionally knocked out in vivo and knocked down by siRNA, followed by immunohistochemical, behavioural and morphological analysis of corneal epithelial cells. The primary defects observed in vivo were of apical‐basal organisation of the corneal epithelium, with abnormal stratification throughout life, mislocalisation of the cell membrane protein, Scribble, to the basal side of cells, and partial loss of the epithelial basement membrane. Planar defects in migration after wounding and in the presence of an applied electric field were noted. However, knockdown of Vangl2 also retarded cell migration in individual cells that had no contact with their neighbours, which precluded a classic PCP mechanism. It is concluded that some of the planar polarity phenotypes in PCP mutants may arise from disruption of apical‐basal polarity.
Molecular genetic analysis of enoyl‐acyl carrier protein reductase inhibition by diazaborine

Diazaborine and isoniazid are, at first sight, unrelated anti‐bacterial agents that inhibit the enoyl‐ACP reductase (ENR) of Escherichia coli and Mycobacterium tuberculosis respectively. The crystal structures of these enzymes including that of the diazaborine‐inhibited E. coli ENR have been obtained at high resolution. Site‐directed mutagenesis was used to study the importance of amino acid residues in diazaborine susceptibility and enzyme function. The results show that drug binding and inhibition require the presence of a glycine residue at position 93 of E. coli ENR or at the structurally equivalent position in the plant homologue, which is naturally resistant to the drug. The data confirm the hypothesis that any amino acid side‐chain other than hydrogen at this position within the three‐dimensional structure of these enzymes will affect diazaborine resistance by encroaching into the drug binding site. Substitutions of Gly‐93 by amino acids with small side‐chains, such as serine, alanine, cysteine and valine, hardly affected the catalytic parameters and rendered the bacterial host resistant to the drug. Larger amino acid side‐chains, such as that of arginine, histidine, lysine and glutamine, completely inactivated the activity of the enzyme.
Within- and Across-Subject Variability of Repeated Measurements of Medial Olivocochlear-Induced Changes in Transient-Evoked Otoacoustic Emissions

Objectives: Measurement of changes in transient-evoked otoacoustic emissions (TEOAEs) caused by activation of the medial olivocochlear reflex (MOCR) may have clinical applications, but the clinical utility is dependent in part on the amount of variability across repeated measurements. The purpose of this study was to investigate the within- and across-subject variability of these measurements in a research setting as a step toward determining the potential clinical feasibility of TEOAE-based MOCR measurements. Design: In 24 normal-hearing young adults, TEOAEs were elicited with 35 dB SL clicks and the MOCR was activated by 35 dB SL broadband noise presented contralaterally. Across a 5-week span, changes in both TEOAE amplitude and phase evoked by MOCR activation (MOC shifts) were measured at four sessions, each consisting of four independent measurements. Efforts were undertaken to reduce the effect of potential confounds, including slow drifts in TEOAE amplitude across time, activation of the middle-ear muscle reflex, and changes in subjects’ attentional states. MOC shifts were analyzed in seven 1/6-octave bands from 1 to 2 kHz. The variability of MOC shifts was analyzed at the frequency band yielding the largest and most stable MOC shift at the first session. Within-subject variability was quantified by the size of the standard deviations across all 16 measurements. Across-subject variability was quantified as the range of MOC shift values across subjects and was also described qualitatively through visual analyses of the data. Results: A large majority of MOC shifts in subjects were statistically significant. Most subjects showed stable MOC shifts across time, as evidenced by small standard deviations and by visual clustering of their data. However, some subjects showed within- and across-session variability that could not be explained by changes in hearing status, middle ear status, or attentional state. Simulations indicated that four baseline measurements were sufficient to predict the expected variability of subsequent measurements. However, the measured variability of subsequent MOC shifts in subjects was often larger than expected (based on the variability present at baseline), indicating the presence of additional variability at subsequent sessions. Conclusions: Results indicated that a wide range of within- and across-subject variability of MOC shifts was present in a group of young normal-hearing individuals. In some cases, very large changes in MOC shifts (e.g., 1.5 to 2 dB) would need to occur before one could attribute the change to either an intervention or pathology, rather than to measurement variability. It appears that MOC shifts, as analyzed in the present study, may be too variable for clinical use, at least in some individuals. Further study is needed to determine the extent to which changes in MOC shifts can be reliably measured across time for clinical purposes.
Acupuncture for Amnestic Mild Cognitive Impairment: A Meta-Analysis of Randomised Controlled Trials

Objective Mild cognitive impairment (MCI) is a pre-dementia state; 5–10% of cases per year will evolve into dementia. MCI can be amnestic (AMCI) or non-amnestic. AMCI is associated with a higher risk of progression. In recent years, interest in acupuncture as a potential treatment for AMCI has grown. The aim of this meta-analysis was to estimate the clinical effectiveness and safety of acupuncture for AMCI. Methods Randomised controlled trials (RCTs) of acupuncture versus medical treatment for AMCI were identified using the following databases from inception to July 2015: PubMed; Medline; CENTRAL; Chinese Scientific Journal Database; The Chinese Acupuncture Trials Register; China National Knowledge Infrastructure (CNKI); and Wanfang database. Data were extracted from RCTs meeting the inclusive criteria according to Cochrane methods. Meta-analyses were conducted using Rev Man V.5. 3 software. Results Five trials involving 568 subjects were included. Meta-analysis showed that participants receiving acupuncture had better outcomes than those receiving nimodipine with greater clinical efficacy rates (odds ratio (OR) 1.78, 95% CI 1.19 to 2.65; p<0.01), mini-mental state examination (MMSE) scores (mean difference (MD) 0.99, 95% CI 0.71 to 1.28; p<0.01), and picture recognition score (MD 2.12, 95% CI 1.48 to 2.75; p<0.01). Meta-analysis also showed acupuncture in conjunction with nimodipine significantly improved MMSE scores (MD 1.09, 95% CI 0.29 to 1.89; p<0.01) compared to nimodipine alone. Three trials reported adverse events. Methodological quality of the included studies was judged to be generally poor. Conclusions Acupuncture appears effective for AMCI when used as an alternative or adjunctive treatment; however, caution must be exercised given the low methodological quality of included trials. Further, more rigorously designed studies are needed.
A Mathematical Theory of Evidence

Both in science and in practical affairs we reason by combining facts only inconclusively supported by evidence. Building on an abstract understanding of this process of combination, this book constructs a new theory of epistemic probability. The theory draws on the work of A. P. Dempster but diverges from Depster's viewpoint by identifying his "lower probabilities" as epistemic probabilities and taking his rule for combining "upper and lower probabilities" as fundamental. The book opens with a critique of the well-known Bayesian theory of epistemic probability. It then proceeds to develop an alternative to the additive set functions and the rule of conditioning of the Bayesian theory: set functions that need only be what Choquet called "monotone of order of infinity. " and Dempster's rule for combining such set functions. This rule, together with the idea of "weights of evidence," leads to both an extensive new theory and a better understanding of the Bayesian theory. The book concludes with a brief treatment of statistical inference and a discussion of the limitations of epistemic probability. Appendices contain mathematical proofs, which are relatively elementary and seldom depend on mathematics more advanced that the binomial theorem.
Temporal and Spatial Evolution of Somatic Chromosomal Alterations: A Case-Cohort Study of Barrett's Esophagus

All cancers are believed to arise by dynamic, stochastic somatic genomic evolution with genome instability, generation of diversity, and selection of genomic alterations that underlie multistage progression to cancer. Advanced esophageal adenocarcinomas have high levels of somatic copy number alterations. Barrett's esophagus is a risk factor for developing esophageal adenocarcinoma, and somatic chromosomal alterations (SCA) are known to occur in Barrett's esophagus. The vast majority (∼95%) of individuals with Barrett's esophagus do not progress to esophageal adenocarcinoma during their lifetimes, but a small subset develop esophageal adenocarcinoma, many of which arise rapidly even in carefully monitored patients without visible endoscopic abnormalities at the index endoscopy. Using a well-designed, longitudinal case-cohort study, we characterized SCA as assessed by single-nucleotide polymorphism arrays over space and time in 79 “progressors” with Barrett's esophagus as they approach the diagnosis of cancer and 169 “nonprogressors” with Barrett's esophagus who did not progress to esophageal adenocarcinoma over more than 20,425 person-months of follow-up. The genomes of nonprogressors typically had small localized deletions involving fragile sites and 9p loss/copy neutral LOH that generate little genetic diversity and remained relatively stable over prolonged follow-up. As progressors approach the diagnosis of cancer, their genomes developed chromosome instability with initial gains and losses, genomic diversity, and selection of SCAs followed by catastrophic genome doublings. Our results support a model of differential disease dynamics in which nonprogressor genomes largely remain stable over prolonged periods, whereas progressor genomes evolve significantly increased SCA and diversity within four years of esophageal adenocarcinoma diagnosis, suggesting a window of opportunity for early detection. Cancer Prev Res; 7(1); 114–27. ©2013 AACR.
Tumor and Stem Cell Biology High Fidelity Patient-Derived Xenografts for Accelerating Prostate Cancer Discovery and Drug Development

Standardized and reproducible preclinical models that recapitulate the dynamics of prostate cancer are urgently needed.We established a bank of transplantable patient-derived prostate cancer xenografts that capture the biologic and molecular heterogeneity currently confounding prognostication and therapy development. Xenografts preserved the histopathology, genome architecture, and global gene expression of donor tumors. Moreover, their aggressiveness matched patient observations, and their response to androgen withdrawal correlated with tumor subtype. The panel includes the first xenografts generated from needle biopsy tissue obtained at diagnosis. This advance was exploited to generate independent xenografts from different sites of a primary site, enabling functional dissection of tumor heterogeneity. Prolonged exposure of adenocarcinoma xenografts to androgenwithdrawal led to castration-resistant prostate cancer, including thefirst-in-fieldmodel of complete transdifferentiation into lethal neuroendocrine prostate cancer. Further analysis of thismodel supports the hypothesis that neuroendocrine prostate cancer can evolve directly from adenocarcinoma via an adaptive response and yielded a set of genes potentially involved in neuroendocrine transdifferentiation. We predict that these next-generation models will be transformative for advancing mechanistic understanding of disease progression, response to therapy, and personalized oncology. Cancer Res; 74(4); 1272–83. 2013 AACR.
Building FLOW: federating libraries on the web

Individuals, teams, organizations, and networks can be thought of as tiers or classes within the complex grid of technology and practice in which research documentation is both consumed and generated. The panoply of possible classes share with the others a common need for document management tools and practices. The distinctive document management tools and practices used within each represent boundaries across which information could flow openly if technology and metadata standards were to provide an accessible digital framework. The CERN Document Server (CDS), implemented by a research partnership at the San Diego Supercomputer Center (SDSC), establishes a prototype tiered repository system for such a panoply. Research suggests modifications to enable cross-domain information flow and is represented as a metadata grid.