Miracle-dz/UniFAR-FTUs huggingface dataset:
Plasma physics computations on emerging hardware architectures

This thesis explores the potential of emerging hardware architectures to increase the impact of high performance computing in fusion plasma physics research. For next generation tokamaks like ITER, realistic simulations and data-processing tasks will become significantly more demanding of computational resources than current facilities. It is therefore essential to investigate how emerging hardware such as the graphics processing unit (GPU) and field-programmable gate array (FPGA) can provide the required computing power for large data-processing tasks and large scale simulations in plasma physics specific computations. The use of emerging technology is investigated in three areas relevant to nuclear fusion: (i) a GPU is used to process the large amount of raw data produced by the synthetic aperture microwave imaging (SAMI) plasma diagnostic, (ii) the use of a GPU to accelerate the solution of the Bateman equations which model the evolution of nuclide number densities when subjected to neutron irradiation in tokamaks, and (iii) an FPGA-based dataflow engine is applied to compute massive matrix multiplications, a feature of many computational problems in fusion and more generally in scientific computing. The GPU data processing code for SAMI provides a 60x acceleration over the previous IDL-based code, enabling inter-shot analysis in future campaigns and the data-mining (and therefore analysis) of stored raw data from previous MAST campaigns. The feasibility of porting the whole Bateman solver to a GPU system is demonstrated and verified against the industry standard FISPACT code. Finally a dataflow approach to matrix multiplication is shown to provide a substantial acceleration compared to CPU-based approaches and, whilst not performing as well as a GPU for this particular problem, is shown to be much more energy efficient. Emerging hardware technologies will no doubt continue to provide a positive contribution in terms of performance to many areas of fusion research and several exciting new developments are on the horizon with tighter integration of GPUs and FPGAs with their host central processor units. This should not only improve performance and reduce data transfer bottlenecks, but also allow more user-friendly programming tools to be developed. All of this has implications for ITER and beyond where emerging hardware technologies will no doubt provide the key to delivering the computing power required to handle the large amounts of data and more realistic simulations demanded by these complex systems.
Imaging of the Axon Initial Segment

The axon initial segment (AIS) is the first 20‐ to 60‐μm segment of the axon proximal to the soma of a neuron. This highly specialized subcellular domain is the initiation site of the action potential and contains a high concentration of voltage‐gated ion channels held in place by a complex nexus of scaffolding and regulatory proteins that ensure proper electrical activity of the neuron. Studies have shown that dysfunction of many AIS channels and scaffolding proteins occurs in a variety of neuropsychiatric and neurodegenerative diseases, raising the need to develop accurate methods for visualization and quantification of the AIS and its protein content in models of normal and disease conditions. In this article, we describe methods for immunolabeling AIS proteins in cultured neurons and brain slices as well as methods for quantifying protein expression and pattern distribution using fluorescent labeling of these proteins. © 2019 by John Wiley & Sons, Inc.
Headgear does not improve neurocogntivie function and balance performance following acute bouts of soccer heading

Objective: The main objective of this study was to investigate the effects of an acute bout of soccer heading on neurocognitive function and balance performance, as well as, the impact of the Full90 TM protective headgear. Design: This was a repeated measures study where subjects reported on a total of 3 occasions. The first session was baseline, where neurocognitive function and balance performance was assessed. Subjects completed a heading protocol during each of the next 2 sessions, once while wearing headgear, and the other time without the apparatus. Setting: Field setting (indoor Astroturf facility) Participants: A total of 29 college-aged club and competitive division intramural athletes Interventions: A 10 minute protocol consisting of 20 linear headers was completed twice by all
Bacteria associated with flowers affect the reproductive success of Brassica napus L. via scent-mediated interactions with pollinators

Flowers are colonized by specific bacterial communities that have been shown to affect floral scent emission and pollinator behavior. Whether these effects translate into changes in the plants’ reproductive success remains unknown. In our study, flowers of Brassica napus were inoculated with the phyllospheric bacteria Pantoea agglomerans and Pseudomonas syringae. Next-generation 16S rRNA gene amplicon sequencing of bacterial communities associated with flowers showed that inoculation was efficient and affected bacterial communities throughout the flowering time of individual flowers. Flowers of B. napus inoculated with P. agglomerans and P. syringae were preferred by pollinators in the field or in olfactometer assays. Presumably due to the increased visitation rates, inoculated plants produced more seeds of tendentially higher quality per flower. Floral scent emissions were affected by time after inoculation and by treatment with bacterial strains, potentially explaining the behavioral responses of pollinators. Controlled laboratory experiments showed that bacteria emit volatiles through their own metabolism and that the concentrations of some floral volatiles can be reduced by bacteria. Furthermore, our results also suggest that bacteria can use floral scent compounds as carbon sources. Our results demonstrate a significant effect of floral bacteria on the pollination and reproduction of entomophilous plants that is at least partly mediated by their effects on floral chemical signaling.
A Postoperative Pain Management Mobile App (Panda) for Children at Home After Discharge: Usability and Feasibility

Background Emphasis on outpatient pediatric surgical procedures places the burden of responsibility for postoperative pain management on parents or guardians. Panda is a mobile phone app that provides scheduled medication alerts and allows parents to track their child’s pain and medication administration. We have previously tested and optimized the usability and feasibility of Panda within the hospital setting. Objective The purpose of this study was to evaluate and optimize the usability and feasibility of Panda for use at home based on alert response adherence (response to any medication notification within 1 hour) and parents’ satisfaction. Methods Parents or guardians of children aged 3 to 18 years undergoing day surgery were recruited to use Panda at home for 1 to 7 days to manage their scheduled medications and to assess their child’s pain. After the surgical procedure, a research assistant guided parents through app setup before independent use at home. We aimed to recruit 10 child-caregiver pairs in each of three rounds of evaluation. Each user’s adherence with the recommended medication alerts was analyzed through audit-trail data generated during the use of the app. We used the Computer System Usability Questionnaire and a poststudy phone interview to evaluate the app’s ease of use and identify major barriers to adoption. Suggestions provided during the interviews were used to improve the app between each round. Results Twenty-nine child-caregiver pairs participated in three rounds, using the app for 1 to 5 days. Alert response adherence (response to any medication notification within 1 hour) improved as the study progressed: participants responded to a median 30% (interquartile range [IQR] 22%-33%) of alerts within 1 hour in round 1, and subsequently to median 60% (IQR 44%-64%) in round 2 and median 64% (IQR 56%-72%) in round 3 (P=.005). Similarly, response times decreased from median 131 (IQR 77-158) minutes in round 1 to median 31 (IQR 18-61) minutes in round 2 and median 10 (IQR 2-14) minutes in round 3 (P=.002). Analysis of interview feedback from the first two rounds revealed usability issues, such as complaints of too many pages and trouble hearing app alerts, which were addressed to streamline app function, as well as improve visual appearance and audible alerts. Conclusions It is feasible for parents or guardians to use Panda at home to manage their child’s medication schedule and track their pain. Simple modifications to the app’s alert sounds and user interface improved response times.
Small-scale distribution of metazoan meiofauna and sedimentary organic matter in subtidal sandy sediments (Mediterranean Sea)

While variations in sedimentary organic matter (OM) quantity, biochemical composition and nutritional quality as well as in meiofaunal abundance and assemblage composition at the macro- and mesoscale are relatively well known, information about variations at the microscale is much scarcer. To shed some light on this issue, we tested the null hypothesis by which abundance and composition of the meiofaunal assemblages, and the quantity, biochemical composition and nutritional quality of sedimentary organic matter in coastal shallow environments do not vary within a frame of 1 m2. No significant variation within the frame emerged for OM quantity, nutritional quality, biochemical composition and the abundance of meiofaunal assemblages. On the other hand, the composition of meiofaunal assemblages varied significantly within the frame and exhibited a clear segregation of assemblages farther to the shore, as a likely result of local micro-hydrodynamic conditions. Spatial autocorrelation analysis revealed that lipid and protein sedimentary contents had a random distribution, whereas carbohydrate and biopolymeric C contents and meiofaunal total abundance were characterized by a patchy distribution, with discrete peaks within the sub-frame squares (ca. 0.1 m2). Phytopigments showed a spatial positive autocorrelation distribution, following the micro-hydrodynamic pattern, with patches larger than the sub-frame square, but smaller than the entire one (1 m2). Overall, our results suggest that, within 1 m2 of subtidal sandy sediments, three replicates could be sufficient to assess correctly OM attributes and the abundance of meiofauna, but could be possibly inadequate for assessing meiofaunal assemblages’ composition at a finer scale (<1 m2).
The role of telomere dysfunction in modulating disease progression and response to treatment in chronic lymphocytic leukaemia.

In Chronic lymphocytic leukaemia (CLL), short telomere length (TL) and dysfunction and is a powerful predictor of patient survival. The aim of this project was to understand the dynamics of TL in CLL and the relationship between TL in CLL B-cells and autologous T-cells. Normal B-cells from CLL patients showed TL erosion that was indistinguishable from normal ageing. In contrast, T-cells showed rapid TL shortening. Using serial sampling and longterm follow-up, the change in CLL B-cell TL correlated strongly with starting TL. Patients with CLL B-cell TL above the fusogenic threshold displayed TL erosion, whereas patients below the threshold showed no change. There was no lower limit to the mean TL in CLL B-cells suggesting a dysfunctional DNA-damage response allowing on-going cell division and stabilisation of TL. T-cell TL demonstrated marked erosion over the same timescale and the degree of erosion correlated with longevity of diagnosis. Mean T-cell TL did not reach the same degree of shortening as CLL B-cells, consistent with the induction of replicative senescence. T-cell TL was associated with immunophenotypic changes indicating T-cell exhaustion. Furthermore, TCR repertoires showed evidence of clonality and a skewed reliance on certain V gene segments. Longterm co-culture of PBMC from CLL patients, showed survival and proliferation for up to 154 days in-vitro. Despite proliferation, little change in CLL B-cell TL was observed. Surprisingly T-cell TL increased probably due to the selective loss of shorter TL T-cells during the culture. This study shows that the telomeres of CLL B-cells show distinct dynamics over the course of the disease, suggesting that the TL may be pre-determined at the initiation of disease. In contrast, the TL of T-cells showed significant erosion, evidence of replicative senescence, and a phenotype that, together with the associated T-cell exhaustion, may have consequences for the therapeutic use of autologous T-cells.
Genetic diversity analysis of Jatropha by Random Amplified Polymorphic DNA (RAPD)

Genetic diversity analysis of Jatropha and intraspecific level of J. curcas were studied using RAPD technique. Six out of one hundred and seven primers produced polymorphic DNA patterns. A total of 144 bands were scored ranging at 0.25-3.0 kb. Genetic similarity was estimated by the Jaccard coefficient from NTSYSpc 2.20e version and ranged between 0.46-1.000. A dendrogram was constructed using Unweighted Pair Group Method with Arithmetic Mean (UPGMA) which divided Jatropha into two major clusters. The first group comprised all the 18 J. curcas accessions. J. curcas (Myanmar), J. curcas (Lumpang) and J. curcas (Chiang Mai) were grouped together with high similarity index (1.000), while J. curcas (Mukdahan) and J. curcas (India) were also clustered together. The second clade included 5 samples of Jatropha as J. gossypifolia , J. podagrica , J. multifida , J. integerrima (1) and J. integerrima (2), with the latter two clustered together and showing genetic similarity according to their morphological character.
First record of the bacterial endosymbiont Wolbachia for phytophagous hoverflies from genus Merodon (Diptera: Syrphidae)

Wolbachia is a widespread bacterial endosymbiont among arthropod species. It influences the reproduction of the host species and also mitochondrial DNA diversity. Until now there were only a few studies that detected Wolbachia infections in hoverflies (Diptera: Syrphidae), and this is the first broader study with the aim of examining the incidence of Wolbachia in the hoverfly genus Merodon. The obtained results indicate an infection rate of 96% and the presence of both Wolbachia supergroup A and B, which are characteristic for most of the infected arthropod species. Additionally, the presence of multiple Wolbachia strains in the Merodon aureus group species was detected and the mitochondrial DNA COI‐based relationships of the group are discussed in the light of infection. Finally, we discuss plant‐mediated horizontal transmission of Wolbachia strains among the studied hoverfly species.
Effects of Saddle Height and Workrate on Frontal Plane Knee Joint Biomechanics

Cycling is one of the most popular exercises for knee osteoarthritis (OA) or total knee replacement (TKR) rehabilitation. It is known for reduced loading to lower extremity joints compared to walking. One way to fit a bicycle to an individual is adjusting saddle height. There have been limited studies on effects of saddle height on frontal-plane knee joint loading. PURPOSE: To determine the effects of saddle height and workrate on the knee joint biomechanics. METHODS: Fourteen experienced cyclists (age 50-70 years) were recruited from bicycle shops and clubs. Subjects participated in a single testing session that included six test conditions of three saddle heights at two workrates. Saddle heights were set at 20°, 30°, and 40° of knee flexion while the crank was at the bottom position. Workrate was electronically controlled at 80 and 120 watts. Three-dimensional kinematic (240 Hz, Vicon) and pedal reaction force (1200 Hz, Customized instrumented pedal) data were recorded for five successful cycles in each condition. Joint kinematics and kinetics were calculated and compared using a 3x2 ANOVA and paired t-tests with a Bonferroni correction. RESULTS: There were no significant interactions or saddle height main effect for peak knee abduction moment. There was a significant effect of saddle height on knee extension ROM, peak knee extension moment, and peak knee flexion moment (all p <0.012). The post hoc comparisons showed that the knee extension ROM was different from one another between 20°, 30°, and 40° saddle heights (80.1° vs. 73.7° vs. 67.6°, respectively). The peak knee extension moment for 20° saddle height (19.9 Nm) was different from 30° and 40° saddle heights (22.6 Nm and 23.6 Nm, respectively). Additionally, the peak knee flexion moment was different between all three saddle heights (-33.4 Nm vs. -23.4 Nm vs. -18.9 Nm). There was a significant workrate main effect on knee extension ROM, peak knee extension moment, and peak knee abduction moment (all p < 0.008). CONCLUSIONS: Although decreased saddle height increased the knee extension moment, the knee abduction moment was not affected. These results suggest that saddle height adjustment could be a potential and safe method to modulate knee joint loading without concern of impacting frontal-plane knee loading in rehabilitation for patients with knee OA or TKR.
Validation of a quantitative trait locus for the white-core expression rate of grain on chromosome 6 in a brewing rice cultivar and development of DNA markers for marker-assisted selection

Sake-brewing cultivars among varieties of Japanese rice (Oryza sativa L.) have traits adapted to the sake-brewing process, such as a high white-core expression rate (WCE). Our previous study detected putative quantitative trait loci (QTLs) associated with a high WCE derived from Yamadanishiki, a popular brewing rice cultivar. Because the occurrence of white-core grains depends on air temperature and the position of the grain on the panicle, phenotyping of WCE must consider these variable conditions. In this study, qWCE6, a QTL for the WCE on chromosome 6, was validated for the first time, and the phenotyping method examined for its suitability in fine-mapping. A clear tendency towards high WCE was observed in late-heading substituted lines which headed under low daily mean temperature at the experimental location. White-core grains were often expressed by the primary spikelets on the upper panicle, producing a high percentage of superior grains. The segregating population for qWCE6 in late heading revealed a distinct difference in WCE between the Koshihikari and Yamadanishiki homozygous alleles at qWCE6 as determined from that locality. Further, two insertion/deletion markers were developed for the marker-assisted selection of qWCE6. Our results will be useful for informing the breeding of sake-brewing rice cultivars.
Frost maintains forests and grasslands as alternate states in a montane tropical forest–grassland mosaic; but alien tree invasion and warming can disrupt this balance

Forest–grassland mosaics, with abrupt boundaries between the two vegetation types, occur across the globe. Fire and herbivory are widely considered primary drivers that maintain these mosaics by limiting tree establishment in grasslands, while edaphic factors and frosts are generally considered to be secondary factors that reinforce these effects. However, the relative importance of these drivers likely varies across systems. In particular, although frost is known to occur in many montane tropical mosaics, experimental evidence for its role as a driving factor is limited. We used replicated in situ transplant and warming experiments to examine the role of microclimate (frost and freezing temperatures) and soil in influencing germination and seedling survival of both native forest trees and alien invasive Acacia trees in grasslands of a tropical montane forest–grassland mosaic in the Western Ghats of southern India. Seed germination of both native and alien tree species was higher in grasslands regardless of soil type, indicating that germination was not the limiting stage to tree establishment. However, irrespective of soil type, native seedlings in grasslands incurred high mortality following winter frosts and freezing temperatures relative to native seedlings in adjoining forests where freezing temperatures did not occur. Seedling survival through the tropical winter was thus a primary limitation to native tree establishment in grasslands. In contrast, alien Acacia seedlings in grasslands incurred much lower levels of winter mortality. Experimental night‐time warming in grasslands significantly enhanced over‐winter survival of all tree seedlings, but increases were much greater for alien Acacia than for native tree seedlings. Synthesis. Our results provide evidence for a primary role for frost and freezing temperatures in limiting tree establishment in grasslands of this tropical montane forest–grassland mosaic. Future increases in temperature are likely to release trees from this limitation and favour tree expansion into grasslands, with rates of expansion of non‐native Acacia likely to be much greater than that of native trees. We suggest that studies of frost limitation to plant establishment are needed across a range of tropical ecosystems to re‐evaluate the general importance of frost as a driver of vegetation transitions in the tropics.
Machine Learning Approach for Content Based Image Retrieval

Developments in technology and the Internet have led to an increase in number of digital images and videos. Thousands of images are added to WWW every day. Content based Image Retrieval (CBIR) system typically consists of a query example image, given by the user as an input, from which low-level image features are extracted. These low level image features are used to find images in the database which are most similar to the query image and ranked according their similarity. This chapter evaluates various CBIR techniques based on fuzzy logic and neural networks and proposes a novel fuzzy approach to classify the colour images based on their content, to pose a query in terms of natural language and fuse the queries based on neural networks for fast and efficient retrieval. A number of experiments were conducted for classification, and retrieval of images on sets of images and promising results were obtained.
User Log Based Image Re-ranking and Retrieval

Digital world has developed tremendously. Initially textual information associated with images is used to do image based search. From user’s perspective the final result contains both relevant as well irrelevant images. The expected yield from such a system is to get pertinent result. Satisfaction of the client will be enhanced if re-ranking is used as critical parameter. Images are displayed based on the category selected and reranked according to the query image opted by user. Image re-ranking based on user log technique is used to overcome the issues and to achieve efficient result. Expanding the keyword and clustering is done at offline mode which is also important parameters for the performance of the system. The performance of re-ranked image retrieval is improved with a reduction of time in seconds as compared to existing re-ranking method. The maintained user log helps to produce the relevant search results. The proposed user log system reduces the image retrieval and re-ranking duration from 17 seconds to 4 seconds.