Miracle-dz/UniFAR-FTUs huggingface dataset:
Array set addressing: Enabling efficient hexagonally sampled image processing

of Dissertation Presented to the Graduate School of the University of Florida in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy ARRAY SET ADDRESSING: ENABLING EFFICIENT HEXAGONALLY SAMPLED IMAGE PROCESSING By Nicholas I. Rummelt December 2010 Chair: Joseph N. Wilson Major: Computer Engineering It has long been known that there are numerous advantages to sampling images hexagonally rather than rectangularly. However, due to various shortcomings of the addressing schemes, hexagonal sampling for digital images has not been embraced by the mainstream digital imaging community. The idea of using hexagonal sampling for digital imaging applications has been around since the early 1960s, yet no efficient addressing method for hexagonal grids has been developed in that time. This dissertation introduces a new hexagonal addressing technique called array set addressing (ASA), that solves the problems exhibited by other methods. This new approach uses three coordinates to represent the hexagonal grid as a pair of rectangular arrays. This representation supports efficient linear algebra and image processing manipulation. ASA-based implementations of several basic image processing operations are developed and shown to be efficient. A hexagonal fast Fourier transform (HFFT), based on the fact that the Fourier kernel becomes separable when using ASA coordinates, is also developed. An ASA implementation of the hexagonal discrete wavelet transform (DWT), which enjoys several advantages over the rectangular DWT due to the superior angular resolution and symmetry of the hexagonal grid, is demonstrated and shown to be efficient. The results of an experiment that quantifies and demonstrates the superior bandwidth of hexagonal sampling using real sensor hardware are presented.
Telomere length: population epidemiology and concordance in Australian children aged 11–12 years and their parents

Objectives To (1) describe the epidemiology of child and adult telomere length, and (2) investigate parent–child telomere length concordance. Design Population-based cross-sectional study within the Longitudinal Study of Australian Children. Setting Assessment centres in seven major Australian cities and eight selected regional towns; February 2015 to March 2016. Participants Of 1874 participating families, telomere data were available for analysis for 1206 children and 1343 parents, of whom 1143 were parent–child pairs. There were 589 boys and 617 girls; 175 fathers and 1168 mothers. Outcome measures Relative telomere length (T/S ratio), calculated by comparing telomeric DNA (T) level with the single copy (S) beta-globin gene in venous blood-derived genomic DNA by quantitative real-time PCR. Results Mean T/S ratio for all children, boys and girls was 1.09 (SD 0.56), 1.05 (SD 0.53) and 1.13 (SD 0.59), respectively. Mean T/S ratio for all parents, fathers and mothers was 0.81 (SD 0.37), 0.82 (SD 0.36) and 0.81 (SD 0.38), respectively. Parent–child T/S ratio concordance was moderate (correlation 0.24). In adjusted regression models, one unit higher parent T/S ratio was associated with 0.36 (estimated linear regression coefficient (β); 95% CI 0.28 to 0.45) higher child T/S ratio. Concordance was higher in the youngest parent-age tertile (β 0.49; 95% CI 0.34 to 0.64) compared with the middle (β 0.35; 95% CI 0.21 to 0.48) and oldest tertile (β 0.26; 95% CI 0.11 to 0.41; p-trend 0.04). Father–child concordance was 0.34 (95% CI 0.18 to 0.48), while mother–child was 0.22 (95% CI 0.17 to 0.28). Conclusions We provide telomere length population values for children aged 11–12 years and their mid-life parents. Relative telomere length was shorter in adults than children, as expected. There was modest evidence of parent–child concordance, which diminished with increasing parent age.
Smart Textile‐Integrated Microelectronic Systems for Wearable Applications

The programmable nature of smart textiles makes them an indispensable part of an emerging new technology field. Smart textile‐integrated microelectronic systems (STIMES), which combine microelectronics and technology such as artificial intelligence and augmented or virtual reality, have been intensively explored. A vast range of research activities have been reported. Many promising applications in healthcare, the internet of things (IoT), smart city management, robotics, etc., have been demonstrated around the world. A timely overview and comprehensive review of progress of this field in the last five years are provided. Several main aspects are covered: functional materials, major fabrication processes of smart textile components, functional devices, system architectures and heterogeneous integration, wearable applications in human and nonhuman‐related areas, and the safety and security of STIMES. The major types of textile‐integrated nonconventional functional devices are discussed in detail: sensors, actuators, displays, antennas, energy harvesters and their hybrids, batteries and supercapacitors, circuit boards, and memory devices.
Pre-treatment and acquired HIV drug resistance in Dar es Salaam, Tanzania in the era of tenofovir and routine viral load monitoring.

OBJECTIVES We investigated the prevalence and patterns of pre-treatment and acquired HIV drug resistance mutations (DRMs) in Tanzania as a 'treat all' strategy, virological monitoring and the progressive increase in usage of tenofovir are being implemented in HIV treatment programmes. METHODS Viral RNA was isolated from plasma of 60 ART-naive and 166 treated-but-viraemic (>400 copies/mL) HIV-1-infected adults attending a care and treatment clinic at Muhimbili National Hospital, Dar es Salaam, Tanzania, between June and October 2017. Viral genes encoding protease and reverse transcriptase were amplified by PCR and directly sequenced. RESULTS Viral genotyping of successfully amplified samples revealed pre-treatment DRMs in 14/47 (29.8%) ART-naive subjects. Of these, 7/47 (14.9%) harboured mutations that confer high-level resistance to at least one drug of the default first-line regimen. In treated-but-viraemic subjects, DRMs were found in 100/111 (90%), where DRMs against NNRTI, NRTI and PI were observed in 95/100 (95%), 92/100 (92%) and 13/100 (13%), respectively. Tenofovir-resistance mutations K65R and K70G/E or ≥3 thymidine analogue resistance mutations including M41L and L210W were found in 18/36 (50%) subjects on a tenofovir-containing regimen at failure. Four patients harboured multiple DRMs, which can confer resistance to all available ART regimens in Tanzania. CONCLUSIONS Taken together, pre-treatment and acquired DRMs were highly prevalent, which represents a major risk for the efficacy of ART programmes in Tanzania. Availability of a newer generation of antiretroviral drugs with a higher genetic barrier to resistance and robust treatment monitoring is warranted for effective and sustainable HIV treatment.
Reliable and Feasible Fitness Testing for Children on the Autism Spectrum

ABSTRACT Purpose: This study examined the test-retest reliability and feasibility of select fitness assessments in 7–12 year old children on the autism spectrum. Method: Participants (N = 14; n = 1 female; Mage = 9.5 ± 1.7 years) completed 7 fitness assessments, administered in a random order, on two occasions: Bruce protocol; Modified 6-minute walk test (M6MWT); Wingate anaerobic cycling test; muscle power sprint test (MPST); sit & reach; standing long jump; and grip strength. Intraclass correlations (two-way mixed with absolute agreement) were computed to examine test-retest reliability. Feasibility was assessed by questionnaire following the first administration of each test. Results: The Wingate (ICC = .956), standing long jump (ICC = .925), grip strength (ICC = .913), and sit and reach (ICC = .829) tests demonstrated good- to- excellent reliability, while the Bruce protocol (ICC = .811), M6MWT (ICC = .510), and MPST (ICC = .703) demonstrated moderate- to- good reliability based on the 95% confidence intervals of the ICC. All tests demonstrated assessor-rated feasibility scores of 70/100 or higher and child-rated feasibility scores of 66/100 or higher. Conclusion: The results demonstrate moderate- to excellent test-retest reliability for select fitness tests. Short, single-instruction (e.g., standing long jump) tests may be more reliable than lengthier assessments (e.g., M6MWT) in this population. Implications of this work include the ability of practitioners and researchers to feasibly and reliably measure the fitness of school-aged children on the autism spectrum for ongoing health and behavioural monitoring and intervention purposes.
Changes in knee extension peak torque and body composition and their relationship with change in gait speed

Slow gait speed is a powerful predictor of disability in activities of daily living and mortality. Muscle strength and body composition change over time, but their changes differ by sex. How these parameters jointly affect gait speed decline is unknown. Understanding this association could help develop and evaluate the sex‐specific effects of lifestyle interventions to delay gait speed decline in older adults. We assessed whether changes in strength (Δstrength), appendicular lean mass (ΔALM), and fat mass (Δfat) jointly relate to change in gait speed and whether the association differs by sex.
Innovation in Central Venous Access Device Security: A Pilot Randomized Controlled Trial in Pediatric Critical Care.

OBJECTIVES Central venous access devices enable many treatments during critical illness; however, 25% of pediatric central venous access devices fail before completion of treatment due to infection, thrombosis, dislodgement, and occlusion. This is frequently attributed to inadequate securement and dressing of the device; however, high-quality research evaluating pediatric central venous access device securement innovation to prevent central venous access device failure is scarce. This study aimed to establish the feasibility of a definitive randomized control trial examining the effectiveness of current and new technologies to secure central venous access devices in pediatrics. DESIGN Single-center, parallel group, superiority, pilot randomized control trial. SETTING Anesthetic and intensive care departments of a tertiary pediatric hospital SUBJECTS:: One-hundred eighty pediatric patients with nontunneled central venous access device INTERVENTIONS:: Participants were randomized to receive central venous access device securement via standard care (bordered polyurethane dressing, with prolene sutures, chlorhexidine gluconate disc), tissue adhesive (Histoacryl, B Braun, Melsungen, Germany) in addition to standard care; or integrated dressing securement (SorbaView SHIELD [Centurion Medical Products, Franklin, MA], with prolene sutures and chlorhexidine gluconate disc). OUTCOMES Primary: Feasibility (including effect size estimates, acceptability); central venous access device failure; central venous access device complications; secondary: individual central venous access device complications, skin damage, dressing performance, and product cost. MEASUREMENTS AND MAIN RESULTS Feasibility criteria were achieved as recruitment occurred with acceptable eligibility, recruitment, missing data, and attrition rates, as well as good protocol adherence. Family members and staff-reported comparable levels of acceptability between study arms; however, tissue adhesive was reported as the most difficult to apply. Overall, 6% of central venous access devices failed, including 6% (3/54; incident rate, 13.2 per 1,000 catheter days) standard care, 2% (1/56; incident rate, 3.65 per 1,000 catheter days) integrated, and 8% (5/59; 25.0 per 1,000 catheter days) tissue adhesive. CONCLUSIONS It is feasible to conduct an efficacy randomized control trial of the studied interventions. Further research is required to definitively identify clinical, cost-effective methods to prevent central venous access device failure by examining new dressing and securement technologies and techniques.
"Clinician, Heal Thyself": Decisional Conflict, Value Judgments, and Their Role in Practice Variation in Traumatic Brain Injury.

Pediatric Critical Care Medicine www.pccmjournal. org 679 5. Mohamed MA, Aly H: Transport of premature infants is associated with increased risk for intraventricular haemorrhage. Arch Dis Childh Fetal Neonatal Ed 2010; 95:F403–F407 6. Chevallier M, Debillon T, Pierrat V, et al: Leading cause of preterm delivery as risk factor for intraventricular hemorrhage in very preterm infants. Results of the EPIPAGE 2 cohort study. Am J Obstet Gynecol 2017; 518:e1 7. Amer R, Moddemann D, Seshia M, et al; Canadian Neonatal Network and Canadian Neonatal Follow-up Network Investigators: Neurodevelopmental outcomes of infants born at <29 weeks of gestation admitted to Canadian neonatal intensive care units based on location of birth. J Pediatr 2018; 196:31–37.e1 8. van Wezel-Meijler G, Steggerda SJ, Leijser LM: Cranial ultrasonography in neonates: Role and limitations. Semin Perinatol 2010; 34:28–38 9. Browning Carmo K, Lutz T, Greenhalgh M, et al: Feasibility and utility of portable ultrasound during retrieval of sick preterm infants. Acta Paediatr 2017; 106:1296–1301 10. Shipley L, Gyorkos T, Dorling J, et al: Risk of Severe Intraventricular Hemorrhage in the First Week of Life in Preterm Infants Transported Before 72 Hours of Age. Pediatr Crit Care Med 2019; 20:638–644 11. Sweet DG, Carnielli V, Greisen G, et al: European consensus guidelines on the management of respiratory distress syndrome 2016 update. Neonatology 2017; 111:107–125 12. Plaisier A, Raets MMA, Ecury-Goossen GM, et al: Serial cranial ultrasonography or early MRI for detecting preterm brain injury? Arch Dis Childh Fetal Neonatal Ed 2015; 100:F293–F300 13. Dorner RA, Burton VJ, Allen MC, et al: Preterm neuroimaging and neurodevelopmental outcome: A focus on intraventricular hemorrhage, post-hemorrhagic hydrocephalus, and associated brain injury. J Perinatol 2018; 38:1431–1443
Whole-Genome Sequencing of the Giant Devil Catfish, Bagarius yarrelli

Abstract As one economically important fish in the southeastern Himalayas, the giant devil catfish (Bagarius yarrelli) has been known for its extraordinarily large body size. It can grow up to 2 m, whereas the non-Bagarius sisorids only reach 10–30 cm. Another outstanding characteristic of Bagarius species is the salmonids-like reddish flesh color. Both body size and flesh color are interesting questions in science and also valuable features in aquaculture that worth of deep investigations. Bagarius species therefore are ideal materials for studying body size evolution and color depositions in fish muscles, and also potential organisms for extensive utilization in Asian freshwater aquaculture. In a combination of Illumina and PacBio sequencing technologies, we de novo assembled a 571-Mb genome for the giant devil catfish from a total of 153.4-Gb clean reads. The scaffold and contig N50 values are 3.1 and 1.6 Mb, respectively. This genome assembly was evaluated with 93.4% of Benchmarking Universal Single-Copy Orthologs completeness, 98% of transcripts coverage, and highly homologous with a chromosome-level-based genome of channel catfish (Ictalurus punctatus). We detected that 35.26% of the genome assembly is composed of repetitive elements. Employing homology, de novo, and transcriptome-based annotations, we annotated a total of 19,027 protein-coding genes for further use. In summary, we generated the first high-quality genome assembly of the giant devil catfish, which provides an important genomic resource for its future studies such as the body size and flesh color issues, and also for facilitating the conservation and utilization of this valuable catfish.
Do Arabidopsis Squamosa promoter binding Protein‐Like genes act together in plant acclimation to copper or zinc deficiency?

The genome of Arabidopsis thaliana encodes approximately 260 copper (Cu)-dependent proteins, which include enzymes in central pathways of photosynthesis, respiration and responses to environmental stress. Under Cu-deficient growth conditions, Squamosa promoter binding Protein-Like 7 (SPL7) activates the transcription of genes encoding Cu acquisition systems and mediates a metabolic reorganization to economize on Cu. The transcription factor SPL7 groups among comparably large proteins in the SPL family, which additionally comprises a second group of small SPL proteins targeted by miRNA156 with roles in plant development. SPL7 shares extended regions of sequence homology with SPL1 and SPL12. Therefore, we investigated the possibility of a functional overlap between these three members of the group of large SPL family proteins. We compared the spl1 spl12 double mutant and the spl1 spl7 spl12 triple mutant with the wild type and the spl7 single mutant under normal and Cu-deficient growth conditions. Biomass production, chlorophyll content and tissue elemental composition at the seedling stage, as well as plant and flower morphology during reproductive stages, confirmed the involvement of SPL7, but provided no indication for important roles of SPL1 or SPL12, in the acclimation of Arabidopsis to Cu deficiency. Furthermore, we analyzed the effects of zinc (Zn) deficiency on the same set of mutants. Different from what is known in the green alga Chlamydomonas reinhardtii, Arabidopsis did not activate Cu deficiency responses under Zn deficiency, and there was no Cu overaccumulation in either shoot or root tissues of Zn-deficient wild-type plants. Known Zn deficiency responses were unaltered in spl7, spl1 spl12 and spll spl7 spl12 mutants. We observed that CuZnSOD activity is strongly downregulated in Zn-deficient A. thaliana, in association with an about 94% reduction in the abundance of the CDS2 transcript, a known target of miR398. However, different from the known Cu deficiency responses of Arabidopsis, this Zn deficiency response was independent of SPL7and not associated with an upregulation of MIR398b primary transcript levels. Our data suggest that there is no conservation in A. thaliana of the crosstalk between Zn and Cu homeostasis mediated by the single SPL family protein CRR1 in Chlamydomonas. In the future, resolving how the specificity of SPL protein activation and recognition of target gene promoters is achieved will advance our understanding of the specific functions of different SPL family proteins in either Cu deficiency response regulation or growth and development of land plants.
Ultrasonic assessment of carotid intima-media thickness in migraine: a meta-analysis

Objective Migraine is believed to be a risk factor for cerebrovascular diseases, and previous studies have indicated an association between migraine and cerebral atherosclerosis. Carotid artery intima-media thickness (IMT) is considered to be a biomarker of atherosclerosis pathology. This study aimed to investigate the relationship between carotid IMT and migraine by conducting a meta-analysis. Methods We searched Web of Science, PubMed, and the Cochrane Library for eligible studies assessing carotid IMT in patients with migraine and controls. Data were extracted independently by two reviewers and analyzed using Review Manager 5.3 software. Results The meta-analysis included seven articles with 555 subjects (279 migraine patients, 276 controls). Carotid IMT was significantly greater in patients with migraine compared with controls. However, there were no significant differences in IMT between patients with migraine with aura (MA) and controls, migraine without aura (MO) and controls, and patients with MA and MO. Conclusion Patients with migraine have greater carotid IMT than individuals without migraine, suggesting an association between atherosclerosis and migraine. However, further studies with more samples are needed to confirm this finding.
Genome-wide characterization and expression profiling of the MAPKKK genes in Gossypium arboreum L.

Mitogen-activated protein kinase kinase kinases (MAPKKKs) are important components of MAPK cascades, which have different functions during developmental processes and stress responses. To date, there has been no systematic investigation of this gene family in the diploid cotton Gossypium arboreum L. In this study, a genome-wide survey was performed which identified 78 MAPKKK genes in G. arboreum. Phylogenetic analysis classified these genes into three subgroups: 14 belonged to ZIK, 20 to MEKK, and 44 to Raf. Chromosome location, phylogeny, and the conserved protein motifs of the MAPKKK gene family in G. arboreum were analyzed. The MAPKKK genes had a scattered genomic distribution across 13 chromosomes. The members in the same subfamily shared similar conserved motifs. The MAPKKK expression patterns were analyzed in mature leaves, stems, roots, and at different ovule developmental stages, as well as under salt, and drought stresses. Transcriptome analysis showed that 76 MAPKKK genes had different transcript accumulation patterns in the tested tissues and 38 MAPKKK genes were differentially expressed in response to salt and drought stresses. These results lay the foundation for understanding the complex mechanisms behind MAPKKK-mediated developmental processes and abiotic stress-signaling transduction pathways in cotton.
Apical membrane protein 1‐specific antibody profile and temporal changes in peripheral blood B‐cell populations in Plasmodium vivax malaria

Plasmodium falciparum‐specific antibodies tend to be short‐lived, but their cognate memory B cells (MBCs) circulate in the peripheral blood of exposed subjects for several months or years after the last infection. However, the time course of antigen‐specific antibodies and B‐cell responses to the relatively neglected parasite Plasmodium vivax remains largely unexplored. Here, we showed that uncomplicated vivax malaria elicits short‐lived antibodies but long‐lived MBC responses to a major blood‐stage P vivax antigen, apical membrane protein 1 (PvAMA‐1), in subjects exposed to declining malaria transmission in the Amazon Basin of Brazil. We found that atypical (CD19+CD10−CD21−CD27−) MBCs, which appear to share a common precursor with classical MBCs but are unable to differentiate into antibody‐secreting cells, significantly outnumbered classical MBCs by 5:1 in the peripheral blood of adult subjects currently or recently infected with P vivax and by 3:1 in healthy residents in the same endemic communities. We concluded that malaria can drive classical MBCs to differentiate into functionally impaired MBCs not only in subjects repeatedly exposed to P falciparum, but also in subjects living in areas with low levels of P vivax transmission in the Amazon, leading to an impaired B‐cell memory that may affect both naturally acquired and vaccine‐induced immunity.