Miracle-dz/UniFAR-FTUs huggingface dataset:
Proteome Regulation during Olea europaea Fruit Development

Background Widespread in the Mediterranean basin, Olea europaea trees are gaining worldwide popularity for the nutritional and cancer-protective properties of the oil, mechanically extracted from ripe fruits. Fruit development is a physiological process with remarkable impact on the modulation of the biosynthesis of compounds affecting the quality of the drupes as well as the final composition of the olive oil. Proteomics offers the possibility to dig deeper into the major changes during fruit development, including the important phase of ripening, and to classify temporal patterns of protein accumulation occurring during these complex physiological processes. Methodology/Principal Findings In this work, we started monitoring the proteome variations associated with olive fruit development by using comparative proteomics coupled to mass spectrometry. Proteins extracted from drupes at three different developmental stages were separated on 2-DE and subjected to image analysis. 247 protein spots were revealed as differentially accumulated. Proteins were identified from a total of 121 spots and discussed in relation to olive drupe metabolic changes occurring during fruit development. In order to evaluate if changes observed at the protein level were consistent with changes of mRNAs, proteomic data produced in the present work were compared with transcriptomic data elaborated during previous studies. Conclusions/Significance This study identifies a number of proteins responsible for quality traits of cv. Coratina, with particular regard to proteins associated to the metabolism of fatty acids, phenolic and aroma compounds. Proteins involved in fruit photosynthesis have been also identified and their pivotal contribution in oleogenesis has been discussed. To date, this study represents the first characterization of the olive fruit proteome during development, providing new insights into fruit metabolism and oil accumulation process.
Prevention and Control of Seasonal Influenza With Vaccines: Recommendations of the Advisory Committee on Immunization Practices—United States, 2017–18 Influenza Season

For the 2017–18 season, quadrivalent and trivalent influenza vaccines will be available. Inactivated influenza vaccines (IIVs) will be available in trivalent (IIV3) and quadrivalent (IIV4) formulations. Recombinant influenza vaccine (RIV) will be available in trivalent (RIV3) and quadrivalent (RIV4) formulations. Live attenuated influenza vaccine (LAIV4) is not recommended for use during the 2017–18 season due to concerns about its effectiveness against (H1N1)pdm09 viruses during the 2013–14 and 2015–16 seasons. Recommendations for different vaccine types and specific populations are discussed. No preferential recommendation is made for one influenza vaccine product over another for persons for whom more than one licensed, recommended product is available.
RPE vs. Percentage 1RM Loading in Periodized Programs Matched for Sets and Repetitions

Purpose: To investigate differences between rating of perceived exertion (RPE) and percentage one-repetition maximum (1RM) load assignment in resistance-trained males (19–35 years) performing protocols with matched sets and repetitions differentiated by load-assignment. Methods: Participants performed squats then bench press 3x/weeks in a daily undulating format over 8-weeks. Participants were counterbalanced by pre-test 1RM then assigned to percentage 1RM (1RMG, n = 11); load-assignment via percentage 1RMs, or RPE groups (RPEG, n = 10); participant-selected loads to reach target RPE ranges. Ultrasonography determined pre and post-test pectoralis (PMT), and vastus lateralis muscle thickness at 50 (VLMT50) and 70% (VLMT70) femur-length. Results: Bench press (1RMG +9.64 ± 5.36; RPEG + 10.70 ± 3.30 kg), squat (1RMG + 13.91 ± 5.89; RPEG + 17.05 ± 5.44 kg) and their combined-total 1RMs (1RMG + 23.55 ± 10.38; RPEG + 27.75 ± 7.94 kg) increased (p < 0.05) in both groups as did PMT (1RMG + 1.59 ± 1.33; RPEG +1.90 ± 1.91 mm), VLMT50 (1RMG +2.13 ± 1.95; RPEG + 1.85 ± 1.97 mm) and VLMT70 (1RMG + 2.40 ± 2.22; RPEG + 2.31 ± 2.27 mm). Between-group differences were non-significant (p > 0.05). Magnitude-based inferences revealed 79, 57, and 72% chances of mean small effect size (ES) advantages for squat; ES 90% confidence limits (CL) = 0.50 ± 0.63, bench press; ES 90% CL = 0.28 ± 0.73, and combined-total; ES 90% CL = 0.48 ± 0.68 respectively, in RPEG. There were 4, 14, and 6% chances 1RMG had a strength advantage of the same magnitude, and 18, 29, and 22% chances, respectively of trivial differences between groups. Conclusions: Both loading-types are effective. However, RPE-based loading may provide a small 1RM strength advantage in a majority of individuals.
Group trust, communication media, and interactivity: toward an integrated model of online collaborative learning

ABSTRACT The present investigation examines the multidimensional relationships among several critical components in online collaborative learning, including group trust, communication media, and interactivity. Four hundred eleven university students from 103 groups in the United States responded survey items on online collaboration, interactivity, communication media, and group trust. Structural equation modeling was employed to examine the relationships among these variables. Results revealed that trust among group members had a positive and powerful influence on online collaboration. Results further revealed that the influence of group trust on online collaboration was mediated by communication media and the interactivity among group members. These findings are discussed in the context of existing literature in the field. Practical implications and directions for future investigation are provided.
Modeling Injury Severity of Vehicular Traffic Crashes

Data mining techniques constitute an alternative approach that has received increasing attention from researchers in recent years in road safety analysis field. In this paper Bayesian networks were used to develop models in order to identify factors that affect the injury severity of a crash within urban areas based on traffic crashes data on Jordanian roads collected for three years (2009-2011). The following variables were found to have a significant effect on classifying crashes according to their injury severity: lighting of roadway, crash type, road type, crash manner, surface condition, number of lanes, number of vehicles, gradient, type of pavement, traffic control devices, and speed limit. The results of this research can be used to determine the factors that should be taken into consideration when designing a new roadway or for improving safety of existing roads.
Chthoniobacter flavus gen. nov., sp. nov., the First Pure-Culture Representative of Subdivision Two, Spartobacteria classis nov., of the Phylum Verrucomicrobia

ABSTRACT The phylum Verrucomicrobia is increasingly recognized as an environmentally significant group of bacteria, particularly in soil habitats. At least six subdivisions of the Verrucomicrobia are resolved by comparative analysis of 16S rRNA genes, mostly obtained directly from environmental samples. To date, only two of these subdivisions (1 and 4) have characterized pure-culture representatives. We have isolated and characterized the first known pure-culture representative of subdivision 2. Strain Ellin428 is an aerobic heterotrophic bacterium that is able to grow with many of the saccharide components of plant biomass but does not grow with amino acids or organic acids other than pyruvate. Cells are yellow, rod-shaped, nonmotile, and gram-stain negative, and they contain peptidoglycan with direct cross-linkages of the A1γ meso-Dpm type. The isolate grows well at 25°C on a variety of standard biological media, including some used in the routine cultivation of bacteria from soil. The pH range for growth is 4.0 to 7.0. Low levels of menaquinones MK-10 and MK-11 were detected. The major cellular fatty acids are C14:0, a-C15:0, C16:1ω7c, and/or 2OH i-C15:0, and C16:0. The G+C content of the genomic DNA is 61 mol%. We propose a new genus and species, Chthoniobacter flavus gen. nov., sp. nov., with isolate Ellin428 as the type strain, and a new class for the subdivision to which it belongs, Spartobacteria classis nov. Environmental sequences indicate that the class Spartobacteria is largely represented by globally distributed, abundant, and active soil bacteria.
Noisy vestibular stimulation improves dynamic walking stability in bilateral vestibulopathy

Objective: To examine the effects of imperceptible levels of white noise galvanic vestibular stimulation (nGVS) on dynamic walking stability in patients with bilateral vestibulopathy (BVP). Methods: Walking performance of 13 patients with confirmed BVP (mean age 50.1 ± 5.5 years) at slow, preferred, and fast speeds was examined during walking with zero-amplitude nGVS (sham trial) and nonzero-amplitude nGVS set to 80% of the individual cutaneous threshold for GVS (nGVS trial). Eight standard gait measures were analyzed: stride time, stride length, base of support, double support time percentage as well as the bilateral phase coordination index, and the coefficient of variation (CV) of stride time, stride length, and base of support. Results: Compared to the sham trial, nGVS improved stride time CV by 26.0% ± 8.4% (p < 0.041), stride length CV by 26.0% ± 7.7% (p < 0.029), base of support CV by 27.8% ± 2.9% (p < 0.037), and phase coordination index by 8.4% ± 8.8% (p < 0.013). The nGVS effects on walking performance were correlated with subjective ratings of walking balance (ρ = 0.79, p < 0.001). Effect of nGVS on walking stability was most pronounced during slow walking. Conclusions: In patients with BVP, nGVS is effective in improving impaired gait performance, predominantly during slower walking speeds. It primarily targets the variability and bilateral coordination characteristics of the walking pattern, which are linked to dynamic walking stability. nGVS might present an effective treatment option to immediately improve walking performance and reduce the incidence of falls in patients with BVP. Classification of evidence: This study provides Class IV evidence that in patients with BVP, an imperceptible level of nGVS improves dynamic walking stability.
Neural correlates of motor recovery after robot-assisted stroke rehabilitation: a case series study

ABSTRACT Robot-assisted bilateral arm therapy (RBAT) has shown promising results in stroke rehabilitation; however, connectivity mapping of the sensorimotor networks after RBAT remains unclear. We used fMRI before and after RBAT and a dose-matched control intervention (DMCI) to explore the connectivity changes in 6 subacute stroke patients. Sensorimotor functions improved in the RBAT and DMCI groups after treatment. Enhanced activation changes were observed in bilateral primary motor cortex (M1) and bilateral supplementary motor area (SMA) after RBAT. Dynamic causal model analysis revealed that interhemispheric connections were enhanced in RBAT patients. These preliminary findings suggest that intracortical and intercortical coupling might underlie poststroke RBAT.
Urban/rural differences in diet and atopy in South Africa

Background: There are large differences in the prevalence of atopic disease between urban and rural areas of developing countries, without good explanation. Diet has been associated with atopic disease, but studies of specific nutrients are contradictory, cross‐sectional studies often being unsupported by trials. We investigated diet as an explanation for the difference in the prevalence of atopy between urban and rural areas in South Africa.
Neuronal pathophysiology featuring PrPC and its control over Ca2+ metabolism

ABSTRACT Calcium (Ca2+) is an intracellular second messenger that ubiquitously masters remarkably diverse biological processes, including cell death. Growing evidence substantiates an involvement of the prion protein (PrPC) in regulating neuronal Ca2+ homeostasis, which could rationalize most of the wide range of functions ascribed to the protein. We have recently demonstrated that PrPC controls extracellular Ca2+ fluxes, and mitochondrial Ca2+ uptake, in neurons stimulated with glutamate (De Mario et al., J Cell Sci 2017; 130:2736-46), suggesting that PrPC protects neurons from threatening Ca2+ overloads and excitotoxicity. In light of these results and of recent reports in the literature, here we review the connection of PrPC with Ca2+ metabolism and also provide some speculative hints on the physiologic outcomes of this link. In addition, because PrPC is implicated in neurodegenerative diseases, including prion disorders and Alzheimer's disease, we will also discuss possible ways by which disruption of PrPC-Ca2+ association could be mechanistically connected with these pathologies.
Imaging-Based Biomarkers of Cognitive Performance in Older Adults Constructed via High-Dimensional Pattern Regression Applied to MRI and PET

In this study, we used high-dimensional pattern regression methods based on structural (gray and white matter; GM and WM) and functional (positron emission tomography of regional cerebral blood flow; PET) brain data to identify cross-sectional imaging biomarkers of cognitive performance in cognitively normal older adults from the Baltimore Longitudinal Study of Aging (BLSA). We focused on specific components of executive and memory domains known to decline with aging, including manipulation, semantic retrieval, long-term memory (LTM), and short-term memory (STM). For each imaging modality, brain regions associated with each cognitive domain were generated by adaptive regional clustering. A relevance vector machine was adopted to model the nonlinear continuous relationship between brain regions and cognitive performance, with cross-validation to select the most informative brain regions (using recursive feature elimination) as imaging biomarkers and optimize model parameters. Predicted cognitive scores using our regression algorithm based on the resulting brain regions correlated well with actual performance. Also, regression models obtained using combined GM, WM, and PET imaging modalities outperformed models based on single modalities. Imaging biomarkers related to memory performance included the orbito-frontal and medial temporal cortical regions with LTM showing stronger correlation with the temporal lobe than STM. Brain regions predicting executive performance included orbito-frontal, and occipito-temporal areas. The PET modality had higher contribution to most cognitive domains except manipulation, which had higher WM contribution from the superior longitudinal fasciculus and the genu of the corpus callosum. These findings based on machine-learning methods demonstrate the importance of combining structural and functional imaging data in understanding complex cognitive mechanisms and also their potential usage as biomarkers that predict cognitive status.
Nonlocal Low-Rank Tensor Factor Analysis for Image Restoration

Low-rank signal modeling has been widely leveraged to capture non-local correlation in image processing applications. We propose a new method that employs low-rank tensor factor analysis for tensors generated by grouped image patches. The low-rank tensors are fed into the alternative direction multiplier method (ADMM) to further improve image reconstruction. The motivating application is compressive sensing (CS), and a deep convolutional architecture is adopted to approximate the expensive matrix inversion in CS applications. An iterative algorithm based on this low-rank tensor factorization strategy, called NLR-TFA, is presented in detail. Experimental results on noiseless and noisy CS measurements demonstrate the superiority of the proposed approach, especially at low CS sampling rates.
Location privacy in pervasive computing

Recent technological advances have made it feasible to measure and track the location of users, vehicles, and practically any mobile object. Positioning and tracking systems are then collecting a huge amount of potentially sensitive location information , which is a set of data describing a user’s location over a period of time. Since the activities of a user are often related to the locations where such activities are performed, it is natural for users to demand privacy, that is, to require control over the access to their location information. In this chapter, we focus on the privacy aspects of using location information in location-based services (LBSs). LBSs are services that take the current position of the user into consideration when performing their tasks. These services can be accessed from mobile phones, PDA, and any other mobile device. We start the chapter by characterizing the location privacy protection problem and introducing a classiﬁcation of the main techniques that have been proposed to protect the location privacy. We also survey and discuss recent proposals and ongoing work in the location-based systems area.
Industrial Big Data for Fault Diagnosis: Taxonomy, Review, and Applications

Fault diagnosis is an important topic both in practice and research. There is intense pressure on industrial systems to continue reducing unscheduled downtime, performance degradation, and safety hazards, which requires detecting and recovering from potential faults as early as possible. From the historical perspective, this paper divides fault diagnosis into previous research and industrial big data era. According to primary drivers, this paper classifies fault diagnosis into knowledge-driven, data-driven, and value-driven methods. Among them, the former two approaches belong to the previous research on fault diagnosis. They mainly depend on expert experience and shallow models to detect and extract failures from relatively small size data. With the continuous exponential growth of data, it is insufficient to mine valuable fault information from massive multi-source heterogeneous data. The huge diagnostic value embodied in industrial big data has driven the emergence of the third category, which belongs to fault diagnosis based on big data. It consists of big data processing and analysis corresponding to high efficiency, cost effectiveness, and generality, which can deal well with problems that previous methods faced. We introduce the concept of a device electrocardiogram from the perspective of applicability to outline the present status of fault diagnosis for big data, and compare it with traditional diagnostic system. We also discuss issues and challenges that need to be further considered. It would be great valuable to integrate or explore more advanced diagnostic methods to handle collected industrial big data and put them into practice to mine the huge hidden diagnostic value.
‘Just an extra pair of hands’? A qualitative study of obstetric service users’ and professionals’ views towards 24/7 consultant presence on a single UK tertiary maternity unit

Objectives To explore the views of maternity service users and professionals towards obstetric consultant presence 24 hours a day, 7 days a week. Design Semistructured interviews conducted face to face with maternity service users and professionals in March and April 2016. All responses were analysed together (ie, both service users’ and professionals’ responses) using an inductive thematic analysis. Setting A large tertiary maternity unit in the North West of England that has implemented 24/7 obstetric consultant presence. Participants Antenatal and postnatal inpatient service users (n=10), midwives, obstetrics and gynaecology specialty trainees and consultant obstetricians (n=10). Results Five themes were developed: (1) ‘Just an extra pair of hands? ’ (the consultant’s role), (2) the context, (3) the team, (4) training and (5) change for the consultant. Respondents acknowledged that obstetrics is an acute specialty, and consultants resolve intrapartum complications. However, variability in consultant experience and behaviour altered perception of its impact. Service users were generally positive towards 24/7 consultant presence but were not aware that it was not standard practice across the UK. Professionals were more pragmatic and discussed how the implementation of 24/7 working had affected their work, development of trainees and potential impacts on future consultants. Conclusions The findings raised several issues that should be considered by practitioners and policymakers when making decisions about the implementation of 24/7 consultant presence in other maternity units, including attributes of the consultants, the needs of maternity units, the team hierarchy, trainee development, consultants’ other duties and consultant absences.
An Assessment of the Accuracy of Volunteered Road Map Production in Western Kenya

The introduction of web based mapping facilities that use satellite imagery, offers local people the possibility to map their environment. However, maps need to be accurate, which is the reason why map making is assigned to professionals. In this paper, we investigated the classification accuracy of road infrastructure from high resolution satellite imagery of an urban area in western Kenya achieved by surveyors and non-surveyors alike, with and without local knowledge. Those with local knowledge classified roads with over 92% accuracy on average, irrespective of surveying background. Professional surveyors and laymen without local knowledge achieved lower accuracies of 67.7% and 42.9% respectively. We argue that local knowledge is also likely to improve the classification accuracy of many other attributes featured in topographic maps and thus conclude that there is reason to consider engaging local expertise in the production and updating of topographic maps.
Surface Enhanced Raman Spectroscopy (SERS) for the Multiplex Detection of Braf, Kras, and Pik3ca Mutations in Plasma of Colorectal Cancer Patients

In this paper, we discuss the use of a procedure based on polymerase chain reaction (PCR) and surface enhanced Raman spectroscopy (SERS) (PCR-SERS) to detect DNA mutations. Methods: This method was implemented by first amplifying DNA-containing target mutations, then by annealing probes, and finally by applying SERS detection. The obtained SERS spectra were from a mixture of fluorescence tags labeled to complementary sequences on the mutant DNA. Then, the SERS spectra of multiple tags were decomposed to component tag spectra by multiple linear regression (MLR). Results: The detection limit was 10-11 M with a coefficient of determination (R2) of 0.88. To demonstrate the applicability of this process on real samples, the PCR-SERS method was applied on blood plasma taken from 49 colorectal cancer patients to detect six mutations located at the BRAF, KRAS, and PIK3CA genes. The mutation rates obtained by the PCR-SERS method were in concordance with previous research. Fisher's exact test showed that only two detected mutations at BRAF (V600E) and PIK3CA (E542K) were significantly positively correlated with right-sided colon cancer. No other clinical feature such as gender, age, cancer stage, or differentiation was correlated with mutation (V600E at BRAF, G12C, G12D, G12V, G13D at KRAS, and E542K at PIK3CA). Visually, a dendrogram drawn through hierarchical clustering analysis (HCA) supported the results of Fisher's exact test. The clusters drawn by all six mutations did not conform to the distributions of cancer stages, differentiation or cancer positions. However, the cluster drawn by the two mutations of V600E and E542K showed that all samples with those mutations belonged to the right-sided colon cancer group. Conclusion: The suggested PCR-SERS method is multiplexed, flexible in probe design, easy to incorporate into existing PCR conditions, and was sensitive enough to detect mutations in blood plasma.