Miracle-dz/UniFAR-FTUs huggingface dataset:
Reconstruction of Spatiotemporally Continuous MODIS-Band Reflectance in East and South Asia from 2012 to 2015

To reconstruct Moderate Resolution Imaging Spectroradiometer (MODIS) band reflectance with optimal spatiotemporal continuity, three bidirectional reflectance distribution function (BRDF) models—the Ross-Thick-Li-Sparse Reciprocal (RTLSR) model, Gao model, and adjusted BF model—were used to retrieve MODIS-band reflectance for cloudy MODIS pixels according to different inversion conditions with a proposed filling algorithm. Then, a spatiotemporally continuous MODIS-band reflectance dataset for most of Asia with more than 98% spatiotemporal coverage was reconstructed from 2012 to 2015. The validation highlighted an evident improvement in filling cloudy MODIS observations; a reasonable spatial distribution, such as in South Asia and Southeast Asia; and acceptable precision for the filled MODIS pixels, with the root mean square error percentage (RMSE%) at 9.7–9.8% and 12–16% for the Gao and adjusted BF models, respectively. In the course of reconstructing the spatiotemporal continuous MODIS-band reflectance, the differences among the three models were discussed further. For a 16-day period with a stable and unchanged land surface, the RTLSR model, as a basic model, accurately derived land surface reflectance (no more than 10% RMSE% for MCD43C1 V006 band 1) and outperformed the other two models. When the inversion period is sufficiently long (e.g., 108 days, 188 days, 268 days, or a full year), the Gao/adjusted BF model provides better precision than the RTLSR model by considering the normalized difference vegetation index (NDVI) and soil moisture/NDVI as intermediate variables used to adjust the BRDF parameters in real time. The Gao model is optimal when the inversion period is sufficiently long. Based on combining the RTLSR model and Gao/adjusted BF model, we proposed a filling algorithm to derive a dataset of MODIS-band reflectance with optimal spatiotemporal continuity.
Comparison of Cloud-Filling Algorithms for Marine Satellite Data

Marine remote sensing provides comprehensive characterizations of the ocean surface across space and time. However, cloud cover is a significant challenge in marine satellite monitoring. Researchers have proposed various algorithms to fill data gaps “below the clouds”, but a comparison of algorithm performance across several geographic regions has not yet been conducted. We compared ten basic algorithms, including data-interpolating empirical orthogonal functions (DINEOF), geostatistical interpolation, and supervised learning methods, in two gap-filling tasks: the reconstruction of chlorophyll a in pixels covered by clouds, and the correction of regional mean chlorophyll a concentrations. For this purpose, we combined tens of cloud-free images with hundreds of cloud masks in four study areas, creating thousands of situations in which to test the algorithms. The best algorithm depended on the study area and task, and differences between the best algorithms were small. Ordinary Kriging, spatiotemporal Kriging, and DINEOF worked well across study areas and tasks. Random forests reconstructed individual pixels most accurately. We also found that high levels of cloud cover led to considerable errors in estimated regional mean chlorophyll a concentration. These errors could, however, be reduced by about 50% to 80% (depending on the study area) with prior cloud-filling.
Semi-parametric Learning of Structured Temporal Point Processes

We propose a general framework of using multi-level log-Gaussian Cox process to model repeatedly observed point processes with complex structures; such type of data have become increasingly available in various areas including medical research, social sciences, economics and finance due to technological advances. A novel nonparametric approach is developed to efficiently and consistently estimate the covariance functions of the latent Gaussian processes at all levels. To predict the functional principal component scores, we propose a consistent estimation procedure by maximizing the conditional likelihood of super-positions of point processes. We further extend our procedure to the bivariate point process case in which potential correlations between the processes can be assessed. Asymptotic properties of the proposed estimators are investigated, and the effectiveness of our procedures is illustrated through a simulation study and an application to a stock trading dataset.
Cardiac calcium handling in the mouse model of Duchenne Muscular Dystrophy

The dystrophinopathies are a group of disorders characterised by cellular absence of the membrane stabilising protein, dystrophin. Duchenne muscular dystrophy is the most severe disorder clinically. The deficiency of dystrophin, in the muscular dystrophy X-linked (mdx) mouse causes an elevation in intracellular calcium in cardiac myocytes. Potential mechanisms contributing to increased calcium include enhanced influx, sarcoplasmic reticular calcium release and\or reduced sequestration or sarcolemmal efflux. This dissertation examined the potential mechanisms that may contribute to an intracellular calcium overload in a murine model of muscular dystrophy. The general cardiomyopathy of the mdx myocardium was evident, with the left atria from mdx consistently producing less force than control atria. This was associated with delayed relaxation. The role of the L-type calcium channels mediating influx was initially investigated. Dihydropyridines had a lower potency in contracting left atria corresponding to a redued dihydropyridine receptor affinity in radioligand binding studies of mdx ventricular homogenates (P<0.05). This was associated with increased ventricular dihydropyridine receptor protein and mRNA levels (P<0.05). The function of the sarcoplasmic reticulum in terms of release and also sequestration of calcium via the sarco-endoplasmic reticulum ATPase were investigated. A lower force of contraction was evident in mdx left atria in response to a range of stimulation frequencies (P<0.05) and concentrations of extracellular calcium (P<0.05). However, in the presence of 1 nM Ryanodine to block sarcoplasmic reticular calcium release, increased stimulation frequency caused similar forces to those obtained in control mice suggesting enhanced calcium influx via L-type calcium channels in mdx. Rapid cooling contractures showed a reduced contracture in mdx compared to control in response to cooling. This suggests some dysfunction in SR storage, which may be associated with the delayed relaxation time. Concentration-response curves to inhibitors of the sarco-endoplasmic reticulum showed no difference in function of the enzyme responsible for calcium uptake into the sarcoplasmic reticulum. Although sarco-endoplasmic reticulum ATPase mRNA was upregulated, no functional benefit was evident. This study indicates that a deficiency of dystrophin leads to upregulation of L-type calcium channels that contribute to increased calcium influx, with no functional change in sarcoplasmic reticular sequestration. Upregulation of the influx pathway is a potential mechanism for the calcium overload observed in mdx cardiac muscle.
Volume-sensitive Conformational Changes and Multimerization of theNa-K-Cl Cotransporter Tagged with CFP and YFP

1.2 Summary The Na-K-Cl cotransporter, NKCC1, is involved in the regulation of intracellular chloride concentration and cell volume. We have tagged both the N terminus and a non-conserved loop in the C terminus of shark NKCC1 with ECFP and EYFP and expressed these constructs in HEK cells. The constructs are fluorescent and correctly trafficked to the cell membrane. We show that NKCC1 with either the N-terminal or the C-terminal tag, as well as NKCC1 with both tags, are active and regulated by intracellular chloride. There is a significant amount of FRET between the two dyes in all cell lines, including cell lines coexpressing two NKCC1s, one fused with a single CFP, and the other one with YFP. The latter result indicates cotransporter multimerization. There is an increase in FRET upon cell shrinkage. In order to assess the mechanism of the observed FRET changes we have cotransfected NKCC1 with two tags and untagged 'wt NKCC1'. We can show that the amount of FRET is dependent on the ratio of wt NKCC1 to tagged NKCC1. This confirms that part of the FRET signal is due to multimerization of NKCC1 rather than dimerization of GFP. The FRET changes are of the same magnitude in cell lines cotransfected with untagged NKCC1, suggesting that they reflect a conformational change rather than an increase in the tendency to form multimers. The FRET studies have been carried out with the Q69M mutant of YFP, which has a low chloride sensitivity (Griesbeck et al., 2001). The constructs using regular YFP are quenched by chloride in the 0 to 100 mM range, CFP is not chloride sensitive. The ratio of YFP to CFP fluorescence in cell lines transfected with double-tagged NKCC1 is a dye concentration independent measure of the intracellular chloride concentration in HEK cells.
An Improved Spatiotemporal Data Fusion Method Using Surface Heterogeneity Information Based on ESTARFM

The use of the spatiotemporal data fusion method as an effective data interpolation method has received extensive attention in remote sensing (RS) academia. The enhanced spatial and temporal adaptive reflectance fusion model (ESTARFM) is one of the most famous spatiotemporal data fusion methods, as it is widely used to generate synthetic data. However, the ESTARFM algorithm uses moving windows with a fixed size to get the information around the central pixel, which hampers the efficiency and precision of spatiotemporal data fusion. In this paper, a modified ESTARFM data fusion algorithm that integrated the surface spatial information via a statistical method was developed. In the modified algorithm, the local variance of pixels around the central one was used as an index to adaptively determine the window size. Satellite images from two regions were acquired by employing the ESTARFM and modified algorithm. Results showed that the images predicted using the modified algorithm obtained more details than ESTARFM, as the frequency of pixels with the absolute difference of mean value of six bands’ reflectance between true observed image and predicted between 0 and 0.04 were 78% by ESTARFM and 85% by modified algorithm, respectively. In addition, the efficiency of the modified algorithm improved and the verification test showed the robustness of the modified algorithm. These promising results demonstrated the superiority of the modified algorithm to provide synthetic images compared with ESTARFM. Our research enriches the spatiotemporal data fusion method, and the automatic selection of moving window strategy lays the foundation of automatic processing of spatiotemporal data fusion on a large scale.
Physiological variation of the vertebral bone marrow water T2 relaxation time

The aim of this study was to investigate physiological variations of the water T2 relaxation time in vertebral bone marrow with respect to age, body mass index (BMI), sex and proton density fat fraction (PDFF) based on single‐voxel magnetic resonance spectroscopy (MRS) at 3 T. Multi‐TE single‐voxel STEAM MRS data of a single lumbar vertebra (L4 or L5) from 260 subjects (160/100 female/male, age: 0.7/37.1/77.7 years, BMI: 13.6/26.2/44.5 kg/m2 [min./median/max.]) with no history of vertebral bone marrow pathologies were retrospectively included. All data were processed using a joint series T2‐constrained time domain‐based water–fat model. Water T2 and PDFF data were analyzed using (a) Pearson's correlation r and (b) multiple linear regression without interactions of the independent variables. Min./median/max. water T2 and PDFF were 11.2/21.1/42.5 ms and 4.0%/36.8%/82.0%, respectively. Pearson's correlation coefficients were significant (P < .05) for water T2 versus age (r = −0.429/−0.210 female/male) and for water T2 versus PDFF (r = −0.580/−0.546 female/male) for females and males, respectively. Females showed significant higher water T2 values compared with males (P < .001). Multiple linear regression for water T2 without interactions revealed a R2 = 0.407 with PDFF (P < .001) and sex (P < .001) as significant predictors. The current study suggests that under physiological conditions vertebral bone marrow water T2 is negatively correlated with age and PDFF and shows significant differences between females and males. The observed systematic trends are of relevance for the evaluation of T2 values and T2‐weighted bone marrow parameters. Further research on the exact mechanisms and drivers of the observed water T2 behavior is required.
Initiation and maintenance of behaviour change to support memory and brain health in older adults: A randomized controlled trial

ABSTRACT The implementation of healthy lifestyle and memory behaviours has the potential to mitigate the impact of age-related memory changes on the lives of older adults. The objective of this study was to examine whether a 10–hour multi-component memory intervention improves the initiation and maintenance of targeted, adaptive behaviour changes. Sixty-seven cognitively-normal, community-dwelling older adults, age 50–91 (72% female) participated in a randomized controlled trial with outcomes assessed at baseline, post-intervention, and six-week follow-up. Participants were allocated to a five-week, in-person, facilitator-led group intervention (n = 34) versus treatment as usual (n = 33). The intervention was associated with significant changes in participant-reported primary outcomes, including increased initiation and maintenance of health-promoting lifestyle behaviours (personal health responsibility, stress management, physical activity, and nutrition) and use of evidence-based behavioural memory strategies in everyday situations. Individualized goals were attained in both the intervention and control conditions. Secondary outcomes replicated prior findings (increased knowledge and improved memory-related confidence, affect, and self-rated ability), but were null with respect to benefits on general health and well-being. Group interventions that target positive adaptation to age-related cognitive decline via behaviour change are a promising avenue to enhance the health and wellness of our aging population. Trial registration ClinicalTrials.gov identifier: NCT02087137.
Bioremediation potentials of sunflower and Pseudomonas species in soil contaminated with lead and zinc

This study was conducted to assess the ability of sunflower (Tithonia diversifolia) inoculated with Pseudomonas species to remediate soils contaminated with heavy metals (lead and zinc). The contaminants were added to 20 kg soil in pots as lead nitrate (Pb (NO3)2) and zinc nitrate (Zn (NO3)2); 400 mg/l metal concentrations were added to 20 kg soil in pots. The experimental design was a randomized complete block design (RCBD) with the two metal types (lead, zinc) and three species of Pseudomonas replicated thrice. The results reveal that all the Pseudomonas sp. (P. putida ATCC 29352, P. cepacia ATCC 29351 and P. fluorescens F113) used showed the potential for remediating zinc and lead. However, P. fluorescens inoculated sunflower remediate zinc (Zn) the best, followed by sunflower inoculated with P. putida ATCC 29352, and sunflower inoculated with P. cepacia ATCC 29351 at 8 Weeks After Planting (WAP). The order of remediation ability of sunflower inoculated with Pseudomonas spp. in soil polluted with lead (Pb) is in the order of sunflower inoculated with P. cepacia ATCC 29351 ˃ sunflower inoculated with P. putida ATCC 29352 > sunflower inoculated with P. fluorescens F113. The shoot and root of the plant were analysed for Zn and Pb uptake after 8 weeks. The bio-concentration factor (BCF) and translocation factor (TF) assessed at 8WAP showed that translocation of Zn from root to shoot by sunflower with Pseudomonas spp. , was higher than Pb. In conclusion this research suggests that sunflower inoculated with Pseudomonas spp. , has phytoextraction ability and could be used to remediate soil contaminated with Zn and Pb. Key words: Bioremediation, phytoremediation, Pseudomonas spp. , heavy metals.
The Effects of Shared e-Book Reading With Dynamic Text and Speech Output on the Single-Word Reading Skills of Young Children With Developmental Disabilities.

Purpose This study investigated the use of a new software feature, namely, dynamic text with speech output, on the acquisition of single-word reading skills by six children with developmental disabilities during shared e-book reading experiences with six typically developing peers. Method A single-subject, multiple-probe design across participants was used to evaluate the effects of the software intervention. Six children with developmental delays were the primary focus for intervention, while six children with typical development participated as peer partners in intervention activities. e-Books were created with the new software feature, in which a child selects a picture from the e-book and the written word is presented dynamically and then spoken out. These e-books were then used in shared reading activities with dyads including a child with a disability and a peer with typical development. Participants engaged in the shared reading activity for an average of 13 sessions over a 6-week time period, an average of 65 min of intervention for each dyad. Results Participants with disabilities acquired an average of 73% of the words to which they were exposed, a gain of 4.3 words above the baseline average of 1.7 correct responses. The average effect size (Tau-U) was . 94, evidence of a very large effect. Conclusion The results provide evidence that the use of e-books with the dynamic text and speech output feature during inclusive shared reading activities can be an effective and socially valid method to develop the single-word reading skills of young children with developmental disabilities.
Optimization of the experimental parameters of the ligase cycling reaction

The ligase cycling reaction (LCR) is a scarless and efficient method to assemble plasmids from fragments of DNA. This assembly method is based on the hybridization of DNA fragments with complementary oligonucleotides, so-called bridging oligos (BOs), and an experimental procedure of thermal denaturation, annealing and ligation. In this study, we explore the effect of molecular crosstalk of BOs and various experimental parameters on the LCR by utilizing a fluorescence-based screening system. The results indicate an impact of the melting temperatures of BOs on the overall success of the LCR assembly. Secondary structure inhibitors, such as DMSO and betaine, are shown to negatively impact the number of correctly assembled plasmids. Adjustments of the annealing, ligation and BO-melting temperature further improved the LCR. The optimized LCR was confirmed by validation experiments. Based on these findings, a step-by-step protocol is offered within this study to ensure a routine for high efficient LCR assemblies.
Assise: Performance and Availability via Client-local NVM in a Distributed File System

The adoption of low latency persistent memory modules (PMMs) upends the long-established model of remote storage for distributed ﬁle systems. Instead, by colocating computation with PMM storage, we can provide applications with much higher IO performance, sub-second application failover, and strong consistency. To demonstrate this, we built the As-sise distributed ﬁle system, based on a persistent, replicated coherence protocol that manages client-local PMM as a lin-earizable and crash-recoverable cache between applications and slower (and possibly remote) storage. Assise maximizes locality for all ﬁle IO by carrying out IO on process-local, socket-local, and client-local PMM whenever possible. Assise minimizes coherence overhead by maintaining consistency at IO operation granularity, rather than at ﬁxed block sizes. We compare Assise to Ceph/BlueStore, NFS, and Octopus on a cluster with Intel Optane DC PMMs and SSDs for common cloud applications and benchmarks, such as LevelDB, Postﬁx, and FileBench. We ﬁnd that Assise improves write latency up to 22 × , throughput up to 56 × , fail-over time up to 103 × , and scales up to 6 × better than its counterparts, while providing stronger consistency semantics.
Identifying the Substrate Specificities of SENP1 and SENP2 in Recognition of Sumoylated Thymine-DNA Glycosylase

SUMO is an essential post-translational protein modifiation regulated in part by the aitivity of a family of SUMO-speiifi proteases known as SENPs. Mammalian iells express six different SENPs with essential and non-redundant funitions. The moleiular meihanisms that determine the substrate speiifiities of individual SENPs and their unique funitions, however, remain unknown. Thymine-DNA glyiosylase (TDG) is an important enzyme that reiognizes and repairs G/U and G/T mismatihes in the genome during the initial stages of base exiision repair (BER), and this role is iritiial in genome integrity and also DNA demethylation. TDG is sumoylated in vivo and we are interested in exploring the funitional importanie and regulation of its modifiation. We previously found that SENP1 preferentially deionjugates sumoylated TDG in vivo, iompared with SENP2, and that speiifiity is determined by the SENP1 iatalytii domain (iSENP1). Here, we have used in vitro studies to further explore this speiifiity by iomparing the aitivities of the SENP1 and SENP2 iatalytii domains using multiple substrates, iniluding AMC, RanGAP1 and TDG. Beiause TDG iontains a SUMO interaition motif (SIM) that affeits its modifiation in vivo, we hypothesized that non-iovalent, intramoleiular SUMO-SIM interaitions impede TDG deionjugation. We also hypothesized that the iSENP1 is more effiient at disrupting the TDG SIM-SUMO interaition, thus explaining speiifiity. To test these hypotheses, we measured deionjugation rates of iSENP1 and iSENP2 over time for SUMO-modifed RanGAP1, wild type and SIM mutant TDG. Our result supported a role for SIM binding in impeding