Miracle-dz/UniFAR-FTUs huggingface dataset:
Facial nerve image enhancement from CBCT using supervised learning technique

Facial nerve segmentation plays an important role in surgical planning of cochlear implantation. Clinically available CBCT images are used for surgical planning. However, its relatively low resolution renders the identification of the facial nerve difficult. In this work, we present a supervised learning approach to enhance facial nerve image information from CBCT. A supervised learning approach based on multi-output random forest was employed to learn the mapping between CBCT and micro-CT images. Evaluation was performed qualitatively and quantitatively by using the predicted image as input for a previously published dedicated facial nerve segmentation, and cochlear implantation surgical planning software, OtoPlan. Results show the potential of the proposed approach to improve facial nerve image quality as imaged by CBCT and to leverage its segmentation using OtoPlan.
Effective Fusion of Multi-Modal Remote Sensing Data in a Fully Convolutional Network for Semantic Labeling

In recent years, Fully Convolutional Networks (FCN) have led to a great improvement of semantic labeling for various applications including multi-modal remote sensing data. Although different fusion strategies have been reported for multi-modal data, there is no in-depth study of the reasons of performance limits. For example, it is unclear, why an early fusion of multi-modal data in FCN does not lead to a satisfying result. In this paper, we investigate the contribution of individual layers inside FCN and propose an effective fusion strategy for the semantic labeling of color or infrared imagery together with elevation (e.g., Digital Surface Models). The sensitivity and contribution of layers concerning classes and multi-modal data are quantified by recall and descent rate of recall in a multi-resolution model. The contribution of different modalities to the pixel-wise prediction is analyzed explaining the reason of the poor performance caused by the plain concatenation of different modalities. Finally, based on the analysis an optimized scheme for the fusion of layers with image and elevation information into a single FCN model is derived. Experiments are performed on the ISPRS Vaihingen 2D Semantic Labeling dataset (infrared and RGB imagery as well as elevation) and the Potsdam dataset (RGB imagery and elevation). Comprehensive evaluations demonstrate the potential of the proposed approach.
Can voluntary pooled procurement reduce the price of antiretroviral drugs? a case study of Efavirenz

Purpose : A number of strategies have aimed to assist countries in procuring antiretroviral therapy (ARV) at lower prices. In 2009, as the Global Fund to Fight AIDS, Tuberculosis and Malaria (GFATM) commenced a voluntary pooled procurement scheme, however, the impact of the scheme on ARV prices remains uncertain. This study aims to estimate the effect of VPP on drug prices using Efavirenz as a case study. Methods This analysis uses WHO Global price report mechanism (GPRM) data from 2004 to 2013. Due to the highly skewed distribution of drug Prices, a generalized linear model (GLM) was used to conduct a difference-in-difference estimation of drug price changes over time. Results These analyses found that voluntary pooled procurement reduced both the ex-works price of generic Efavirenz and the incoterms price by 16.2 and 19.1%, respectively ( P < 0.001) in both cases). The year dummies were also statistically significant from 2006 to 2013 ( P < 0.001), indicating a strong decreasing trend in the price of Efavirenz over that period. Conclusion Voluntary pooled procurement significantly reduced the price of 600 mg generic Efavirenz between 2009 and 2013. Voluntary pooled procurement therefore offers a potentially effective strategy for the reduction in HIV drug prices and the improvement of technical efficiency in HIV programming. Further work is required to establish if these findings hold also for other drugs.
A Psychometric Analysis of the Italian Version of the eHealth Literacy Scale Using Item Response and Classical Test Theory Methods

Background The eHealth Literacy Scale (eHEALS) is a tool to assess consumers’ comfort and skills in using information technologies for health. Although evidence exists of reliability and construct validity of the scale, less agreement exists on structural validity. Objective The aim of this study was to validate the Italian version of the eHealth Literacy Scale (I-eHEALS) in a community sample with a focus on its structural validity, by applying psychometric techniques that account for item difficulty. Methods Two Web-based surveys were conducted among a total of 296 people living in the Italian-speaking region of Switzerland (Ticino). After examining the latent variables underlying the observed variables of the Italian scale via principal component analysis (PCA), fit indices for two alternative models were calculated using confirmatory factor analysis (CFA). The scale structure was examined via parametric and nonparametric item response theory (IRT) analyses accounting for differences between items regarding the proportion of answers indicating high ability. Convergent validity was assessed by correlations with theoretically related constructs. Results CFA showed a suboptimal model fit for both models. IRT analyses confirmed all items measure a single dimension as intended. Reliability and construct validity of the final scale were also confirmed. The contrasting results of factor analysis (FA) and IRT analyses highlight the importance of considering differences in item difficulty when examining health literacy scales. Conclusions The findings support the reliability and validity of the translated scale and its use for assessing Italian-speaking consumers’ eHealth literacy.
Antibody Neutralization of CXCL10 in Vivo Is Dependent on Binding to Free and Not Endothelial-bound Chemokine

To improve our understanding of properties that confer successful inhibition of chemokines in vivo, we analyzed anti-murine CXCL10 monoclonal antibodies (mAb) having different characteristics. 1B6 displayed potent inhibition of cell recruitment in vitro with an IC50 of 0.5 nm but demonstrated little efficacy in various animal models of human disease. On the contrary, 1F11 showed efficacy in several models of inflammation yet was less potent at inhibiting chemotaxis in vitro with an IC50 of 21 nm. Furthermore, we observed that 1B6 displayed a rapid dose-dependent clearance (t½ 10–60 h) in contrast to 1F11, which presented a dose-proportional pharmacokinetic profile and a half-life of 12 days. Moreover, 1B6 recognized glycosaminoglycan (GAG)-bound CXCL10, resulting in target-mediated clearance, which was corroborated using CXCL10-deficient mice. In contrast to 1B6, 1F11 inhibited the interaction of CXCL10 with GAGs, did not recognize GAG-bound CXCL10, and did not display target-mediated drug disposition. Confirming previous animal studies, 1B6 was poor at reversing glycemia in a model of type 1 diabetes, whereas 1F11 induced early and prolonged control of diabetes. Furthermore, when using 1A4, a subsequently generated anti-mCXCL10 mAb that shares the property with 1F11 of being unable to recognize CXCL10 immobilized on GAG, we observed a similar superior control of diabetes as compared with 1B6. We therefore concluded that targeting chemokines with antibodies such as 1B6 that recognize the more abundant GAG-bound form of the chemokine may not be the optimal strategy to achieve disease control.
Bubble-TV: Live Visual Feedback for Social TV Broadcast

Live visualizations connected to Twitter are an opportunity to engage television (TV) viewers by providing them with visual feedback, social awareness and the possibility to interact with others. In this paper we describe our experience in deploying Bubble-TV, an extension of Bubble-T [3], intended for live visualization of TV viewers' tweets. It was used as a permanent background for the french TV show: "Le grand Webze", allowing its hosts to explore and comment the social activity that took place around the show. In addition, we found that Bubble-TV impacted the viewers' experience, since half of all the viewers who tweeted actively used the system guidelines that were given to them.Yet as effective as Bubble-TV was, we believe more research and different applications are needed to identify best practices and develop general guidelines.
Continuous Interaction Data Acquisition and Evaluation: A Process Applied within a Smart, Robot Inhabited Apartment

Intelligent agents need to perceive and correctly interpret the social signals of their interaction partners. In order to support the development of these skills, we establish a process of long-term data acquisition, annotation and continuous model evaluation. We facilitate automatic recording and annotation of unconstrained, multicentric interactions in a smart environment. Finally, we simplify manual ground truth annotation and allow continuous evaluation of our recognition models on a growing set of interactions.
Inferring the Ancient History of the Translation Machinery and Genetic Code via Recapitulation of Ribosomal Subunit Assembly Orders

Universally conserved positions in ribosomal proteins have significant biases in amino acid usage, likely indicating the expansion of the genetic code at the time leading up to the most recent common ancestor(s) (MRCA). Here, we apply this principle to the evolutionary history of the ribosome before the MRCA. It has been proposed that the experimentally determined order of assembly for ribosomal subunits recapitulates their evolutionary chronology. Given this model, we produce a probabilistic evolutionary ordering of the universally conserved small subunit (SSU) and large subunit (LSU) ribosomal proteins. Optimizing the relative ordering of SSU and LSU evolutionary chronologies with respect to minimizing differences in amino acid usage bias, we find strong compositional evidence for a more ancient origin for early LSU proteins. Furthermore, we find that this ordering produces several trends in specific amino acid usages compatible with models of genetic code evolution.
Integration of Vessel-Based Hyperspectral Scanning and 3D-Photogrammetry for Mobile Mapping of Steep Coastal Cliffs in the Arctic

Remote and extreme regions such as in the Arctic remain a challenging ground for geological mapping and mineral exploration. Coastal cliffs are often the only major well-exposed outcrops, but are mostly not observable by air/spaceborne nadir remote sensing sensors. Current outcrop mapping efforts rely on the interpretation of Terrestrial Laser Scanning and oblique photogrammetry, which have inadequate spectral resolution to allow for detection of subtle lithological differences. This study aims to integrate 3D-photogrammetry with vessel-based hyperspectral imaging to complement geological outcrop models with quantitative information regarding mineral variations and thus enables the differentiation of barren rocks from potential economic ore deposits. We propose an innovative workflow based on: (1) the correction of hyperspectral images by eliminating the distortion effects originating from the periodic movements of the vessel; (2) lithological mapping based on spectral information; and (3) accurate 3D integration of spectral products with photogrammetric terrain data. The method is tested using experimental data acquired from near-vertical cliff sections in two parts of Greenland, in Karrat (Central West) and Sondre Stromfjord (South West). Root-Mean-Square Error of (6.7, 8.4) pixels for Karrat and (3.9, 4.5) pixels for Sondre Stromfjord in X and Y directions demonstrate the geometric accuracy of final 3D products and allow a precise mapping of the targets identified using the hyperspectral data contents. This study highlights the potential of using other operational mobile platforms (e.g., unmanned systems) for regional mineral mapping based on horizontal viewing geometry and multi-source and multi-scale data fusion approaches.
Predictors of Cold and Pressure Pain Tolerance in Healthy South African Adults

Background Studies on relationships between sex, ethnicity, and pain have largely emanated from the United States and Europe. We compared cold (CPT) and pressure pain tolerance (PPT) in male and female South Africans of African and European ancestry and assessed whether psychosocial factors (including pain beliefs) predicted differences in pain tolerance. Methods We recruited 106 (62 female) students of African ancestry and 106 (55 female) of European ancestry and subjected them to a cold-pressor test and pressure algometry. Socioeconomic status (SES), pain catastrophizing, depression, anxiety, and pain beliefs were assessed as predictors of pain tolerance. Results CPT was lower in students of African compared with European ancestry (for both sexes), and PPT was lower in female than male students (for both ethnicities). Females were very accepting of men expressing pain and males less so. Males of African ancestry were least accepting but still tolerant. Multivariate analysis identified African ancestry, and particularly being a female of African ancestry, as strong predictors of lower CPT. Anxiety was a weak predict or of CPT. Sex was the only strong predictor of PPT on multivariate analysis (PPT females < males), and catastrophizing was a weak predictor. Female sex and African ancestry were strong predictors of acceptance of expression of pain in males. SES was a weak predictor of the Appropriate Pain Behavior Questionnaire-Malescore. Conclusions Despite different cultural and social backgrounds from US and European cohorts, we saw similar patterns of sex and ethnic differences in CPT and PPT in an African cohort. Traditional psychosocial predictors of pain sensitivity predicted variation in the outcome variables but were not strong predictors.
Phase error analysis in CMOS injection‐coupled LC quadrature oscillator (IC‐QO)

This paper presents a novel approach to study the phase error in source injection coupled quadrature oscillators (QOs). Like other LC QOs, the mismatches between LC tanks are the main source of phase error in this oscillator. The QO is analyzed where the phase error and oscillation frequency are derived in terms of circuit parameters. The proposed analysis shows that the output phase error is a function of injection current and the current of source equivalent capacitor. As a result, it is shown that increasing of tail current and LC tank quality factor decreases the phase error. Derived equations show that the phase error can be cancelled and even controlled by adjusting bias currents. To evaluate the proposed analysis and consequent designed QO, a 5.5 GHz CMOS QO is designed and simulated using the practical 0.18 µm TSMC CMOS technology. The experiments show good agreement between analytical equations and simulation results. Copyright © 2013 John Wiley & Sons, Ltd.
Rotavirus Vaccine Schedules and Vaccine Response Among Infants in Low- and Middle-Income Countries: A Systematic Review

Abstract Background Rotavirus vaccine schedules may impact vaccine response among children in low- and middle-income countries (LMICs). Our objective was to review the literature evaluating the effects of monovalent (RV1) or pentavalent rotavirus vaccines schedules on vaccine response. Methods We searched PubMed, Web of Science, Embase, and ClinicalTrials.gov for eligible trials conducted in LMICs comparing ≥2 vaccine schedules and reporting immunologic response or efficacy. We calculated seroconversion proportion differences and geometric mean concentration (GMC) ratios with 95% confidence intervals. Results We abstracted data from 8 eligible trials of RV1. The point estimates for seroconversion proportions difference ranged from −0.25 to −0.09 for the 6/10-week schedule compared with 10/14. The range for the 6/10/14- compared with 10/14-week schedule was −0.02 to 0.10. Patterns were similar for GMC ratios and efficacy estimates. Conclusions The commonly used 6/10-week RV1 schedule in LMICs may not be optimal. Further research on the effect of rotavirus schedules using clinical endpoints is essential.
Implicit memory in amnesic patients: When is auditory priming spared?

Abstract Amnesic patients often exhibit spared priming effects on implicit memory tests despite poor explicit memory. In previous research, we found normal auditory priming in amnesic patients on a task in which the magnitude of priming in control subjects was independent of whether speaker's voice was same or different at study and test, and found impaired voice-specific priming on a task in which priming in control subjects is higher when speaker's voice is the same at study and test than when it is different. The present experiments provide further evidence of spared auditory priming in amnesia, demonstrate that normal priming effects are not an artifact of low levels of baseline performance, and provide suggestive evidence that amnesic patients can exhibit voice-specific priming when experimental conditions do not require them to interactively bind together word and voice information. (JINS, 1995, I, 434–442.)
Automated age-related macular degeneration classification in OCT using unsupervised feature learning

Age-related Macular Degeneration (AMD) is a common eye disorder with high prevalence in elderly people. The disease mainly affects the central part of the retina, and could ultimately lead to permanent vision loss. Optical Coherence Tomography (OCT) is becoming the standard imaging modality in diagnosis of AMD and the assessment of its progression. However, the evaluation of the obtained volumetric scan is time consuming, expensive and the signs of early AMD are easy to miss. In this paper we propose a classification method to automatically distinguish AMD patients from healthy subjects with high accuracy. The method is based on an unsupervised feature learning approach, and processes the complete image without the need for an accurate pre-segmentation of the retina. The method can be divided in two steps: an unsupervised clustering stage that extracts a set of small descriptive image patches from the training data, and a supervised training stage that uses these patches to create a patch occurrence histogram for every image on which a random forest classifier is trained. Experiments using 384 volume scans show that the proposed method is capable of identifying AMD patients with high accuracy, obtaining an area under the Receiver Operating Curve of 0:984. Our method allows for a quick and reliable assessment of the presence of AMD pathology in OCT volume scans without the need for accurate layer segmentation algorithms.
ABCMdb reloaded: updates on mutations in ATP binding cassette proteins

Abstract ABC (ATP-Binding Cassette) proteins with altered function are responsible for numerous human diseases. To aid the selection of positions and amino acids for ABC structure/function studies we have generated a database, ABCMdb (Gyimesi et al., ABCMdb: a database for the comparative analysis of protein mutations in ABC transporters, and a potential framework for a general application. Hum Mutat 2012; 33:1547–1556.), with interactive tools. The database has been populated with mentions of mutations extracted from full text papers, alignments and structural models. In the new version of the database we aimed to collect the effect of mutations from databases including ClinVar. Because of the low number of available data, even in the case of the widely studied disease-causing ABC proteins, we also included the possible effects of mutations based on SNAP2 and PROVEAN predictions. To aid the interpretation of variations in non-coding regions, the database was supplemented with related DNA level information. Our results emphasize the importance of in silico predictions because of the sparse information available on variants and suggest that mutations at analogous positions in homologous ABC proteins have a strong predictive power for the effects of mutations. Our improved ABCMdb advances the design of both experimental studies and meta-analyses in order to understand drug interactions of ABC proteins and the effects of mutations on functional expression. Database URL: http://abcm2.hegelab. org
SEISMIC RETROFIT OF RC BRIDGE COLUMNS USING COMBINATION OFCARBON FIBER REINFORCED POLYMER SHEET AND STEEL JACKETING

本研究は，炭素繊維シート（CFRPシート）巻立て工法によって主鉄筋段落し部の補強対策が既に実施された鉄筋コンクリート（RC）橋脚を対象とし，その2段階目のアップグレード補強工法の一つとしてCFRPシートを主要補強材とする耐震補強工法を構築するための検討を行ったものである．本検討では，地震時に塑性ヒンジとなる橋脚基部に鋼板，基部以外の躯体部にCFRPシートを適用する併用工法を考案するとともに，その要素技術となるCFRPシートと鋼板の付着特性を把握するための付着実験および補強効果を検証するためのRC橋脚模型の正負交番載荷実験等を実施した．これらの一連の検討より，考案するアップグレード補強工法の有効性を確認するとともに，CFRPシートと鋼板の接着接合部の設計手法を提案した．
Multiplexed transposon-mediated stable gene transfer in human cells

Generation of cultured human cells stably expressing one or more recombinant gene sequences is a widely used approach in biomedical research, biotechnology, and drug development. Conventional methods are not efficient and have severe limitations especially when engineering cells to coexpress multiple transgenes or multiprotein complexes. In this report, we harnessed the highly efficient, nonviral, and plasmid-based piggyBac transposon system to enable concurrent genomic integration of multiple independent transposons harboring distinct protein-coding DNA sequences. Flow cytometry of cell clones derived from a single multiplexed transfection demonstrated approximately 60% (three transposons) or approximately 30% (four transposons) stable coexpression of all delivered transgenes with selection for a single marker transposon. We validated multiplexed piggyBac transposon delivery by coexpressing large transgenes encoding a multisubunit neuronal voltage-gated sodium channel (SCN1A) containing a pore-forming subunit and two accessory subunits while using two additional genes for selection. Previously unobtainable robust sodium current was demonstrated through 38 passages, suitable for use on an automated high-throughput electrophysiology platform. Cotransfection of three large (up to 10.8 kb) piggyBac transposons generated a heterozygous SCN1A stable cell line expressing two separate alleles of the pore-forming subunit and two accessory subunits (total of four sodium channel subunits) with robust functional expression. We conclude that the piggyBac transposon system can be used to perform multiplexed stable gene transfer in cultured human cells, and this technology may be valuable for applications requiring concurrent expression of multiprotein complexes.
Genome sequence of the small brown planthopper, Laodelphax striatellus

Abstract Background Laodelphax striatellus Fallén (Hemiptera: Delphacidae) is one of the most destructive rice pests. L. striatellus is different from 2 other rice planthoppers with a released genome sequence, Sogatella furcifera and Nilaparvata lugens, in many biological characteristics, such as host range, dispersal capacity, and vectoring plant viruses. Deciphering the genome of L. striatellus will further the understanding of the genetic basis of the biological differences among the 3 rice planthoppers. Findings A total of 190 Gb of Illumina data and 32.4 Gb of Pacbio data were generated and used to assemble a high-quality L. striatellus genome sequence, which is 541 Mb in length and has a contig N50 of 118 Kb and a scaffold N50 of 1.08 Mb. Annotated repetitive elements account for 25.7% of the genome. A total of 17 736 protein-coding genes were annotated, capturing 97.6% and 98% of the BUSCO eukaryote and arthropoda genes, respectively. Compared with N. lugens and S. furcifera, L. striatellus has the smallest genome and the lowest gene number. Gene family expansion and transcriptomic analyses provided hints to the genomic basis of the differences in important traits such as host range, migratory habit, and plant virus transmission between L. striatellus and the other 2 planthoppers. Conclusions We report a high-quality genome assembly of L. striatellus, which is an important genomic resource not only for the study of the biology of L. striatellus and its interactions with plant hosts and plant viruses, but also for comparison with other planthoppers.