Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatiotemporal Data Clustering: A Survey of Methods

Large quantities of spatiotemporal (ST) data can be easily collected from various domains such as transportation, social media analysis, crime analysis, and human mobility analysis. The development of ST data analysis methods can uncover potentially interesting and useful information. Due to the complexity of ST data and the diversity of objectives, a number of ST analysis methods exist, including but not limited to clustering, prediction, and change detection. As one of the most important methods, clustering has been widely used in many applications. It is a process of grouping data with similar spatial attributes, temporal attributes, or both, from which many significant events and regular phenomena can be discovered. In this paper, some representative ST clustering methods are reviewed, most of which are extended from spatial clustering. These methods are broadly divided into hypothesis testing-based methods and partitional clustering methods that have been applied differently in previous research. Research trends and the challenges of ST clustering are also discussed.
Coextirpation of host–affiliate relationships in rivers: the role of climate change, water withdrawal, and host‐specificity

The role of climate‐related disturbances on complex host–affiliate relationships remains understudied, largely because affiliate species vary in host use and are often differentially susceptible to disturbance relative to their hosts. Here we report the first set of host–affiliate species–discharge relationships (SDR) in freshwater and examine how anticipated shifts in water availability (flow) will impact coextirpations. We used SDR for freshwater mussels and fish across 11 regions (over 350 rivers) in the continental United States that we coupled to future water availability (2070) to model mussel and fish coextirpations. We also used river‐specific host–affiliate matrices (presence–absence) to evaluate how host‐specificity (mean number of hosts used by an affiliate) and host‐overlap (extent to which affiliates share hosts) relate to extirpation vulnerability. We found that the strength and predictability of SDR models vary geographically and that mussels were more susceptible to flow alterations than fish. These patterns of extirpations were strongest in the southeast where: (1) flow reductions are expected to be greatest; (2) more species are lost per unit flow; (3) and more mussels are expected to be lost per unit of fish. We also found that overall mussel losses associated with reduction in habitat (water availability) were greater than those associated with loss of fish hosts which we assumed to be a function of host redundancy. These findings highlight the utility of SDR as a tool for conservation efforts but they also demonstrate the potential severity of reductions in mussel and fish richness as consequence of climate change and water use. Mussels provide key ecosystem services but face multiple pronged attacks from reductions in flow, habitat, and fish hosts. These losses in biodiversity and ecosystem functions can translate into major effects on food webs and nutrient recycling.
A revised mechanism for (p)ppGpp synthesis by Rel proteins: The critical role of the 2′-OH of GTP

Bacterial Rel proteins synthesize hyperphosphorylated guanosine nucleotides, denoted as (p)ppGpp, which by inhibiting energy requiring molecular pathways help bacteria to overcome the depletion of nutrients in its surroundings. (p)ppGpp synthesis by Rel involves transferring a pyrophosphate from ATP to the oxygen of 3′-OH of GTP/GDP. Initially, a conserved glutamate at the active site was believed to generate the nucleophile necessary to accomplish the reaction. Later this role was alluded to a Mg2+ ion. However, no study has unequivocally established a catalytic mechanism for (p)ppGpp synthesis. Here we present a revised mechanism, wherein for the first time we explore a role for 2′-OH of GTP and show how it is important in generating the nucleophile. Through a careful comparison of substrate-bound structures of Rel, we illustrate that the active site does not discriminate GTP from dGTP, for a substrate. Using biochemical studies, we demonstrate that both GTP and dGTP bind to Rel, but only GTP (but not dGTP) can form the product. Reactions performed using GTP analogs substituted with different chemical moieties at the 2′ position suggest a clear role for 2′-OH in catalysis by providing an indispensable hydrogen bond; preliminary computational analysis further supports this view. This study elucidating a catalytic role for 2′-OH of GTP in (p)ppGpp synthesis allows us to propose different mechanistic possibilities by which it generates the nucleophile for the synthesis reaction. This study underscores the selection of ribose nucleotides as second messengers and finds its roots in the old RNA world hypothesis.
Subjective Family Socioeconomic Status and Adolescents’ Attention: Blacks’ Diminished Returns

Background: Racial minorities, particularly non-Hispanic blacks (NHBs) in the US, experience weaker effects from their families’ socioeconomic status on tangible outcomes, a pattern called the Minorities’ Diminished Returns (MDRs) theory. These MDRs are frequently shown in the effects of the families’ socioeconomic status (SES) on NHB adolescents’ school performance. As a result of these MDRs, NHB adolescents from high SES families show a worse than expected school performance. The existing knowledge is, however, minimal about the role of attention in explaining the diminished returns of the families’ SES with regard to the adolescents’ outcomes. Aim: To investigate the racial differences in the effects of the subjective family SES on adolescents’ attention, we compared non-Hispanic white (NHW) and NHB adolescents to assess the effect of the subjective family SES on adolescents’ attention. Methods: This was a cross-sectional analysis that included 4188 adolescents from the Adolescent Brain Cognitive Development (ABCD) Study. The independent variable was the subjective family SES. The primary outcome was the adolescents’ attention to be measured by the stop-signal task (SST). The attention domain of the Child Behavior Checklist (CBCL) was also measured. Results: Overall, a high subjective family SES was associated with a higher task-based and CBCL-based attention. Race showed statistically significant interactions with subjective family SES in terms of adolescents’ attention outcomes. These interactions suggested that a high subjective family SES has smaller tangible effects on increasing the attention of NHB than NHW adolescents. Conclusion: The boosting effect of subjective family SES on attention is diminished for NHB rather than NHW adolescents. To minimize the racial gap in attention-related behaviors, such as school performance, we need to address the diminished returns of resources in the lives of NHB families. Not only should we equalize SES, but also increase the marginal returns of SES for racial minorities, particularly NHB families. Such efforts require public policies that empower NHB families to better leverage their SES resources and turn them into tangible outcomes. In addition, social policies should directly aim to alter the societal barriers that limit NHB families’ ability to effectively utilize their resources. Discrimination, segregation, and racism should be targets of our policy solutions.
Correlation between Tribological Properties and the Quantified Structural Changes of Lysozyme on Poly (2-hydroxyethyl methacrylate) Contact Lens

The ocular discomfort is the leading cause of contact lens wear discontinuation. Although the tear proteins as a lubricant might improve contact lens adaptation, some in vitro studies suggested that the amount of adsorbed proteins could not simply explain the lubricating performance of adsorbed proteins. The purpose of this study was to quantify the structural changes and corresponding ocular lubricating properties of adsorbed protein on a conventional contact lens material, poly (2-hydroxyethyl methacrylate) (pHEMA). The adsorption behaviors of lysozyme on pHEMA were determined by the combined effects of protein–surface and protein–protein interactions. Lysozyme, the most abundant protein in tear, was first adsorbed onto the pHEMA surface under widely varying protein solution concentrations to saturate the surface, with the areal density of the adsorbed protein presenting different protein–protein effects within the layer. These values were correlated with the measured secondary structures, and corresponding friction coefficient of the adsorbed and protein covered lens surface, respectively. The decreased friction coefficient value was an indicator of the lubricated surfaces with improved adaptation. Our results indicate that the protein–protein effects help stabilize the structure of adsorbed lysozyme on pHEMA with the raised friction coefficient measured critical for the innovation of contact lens material designs with improved adaptation.
Safety of exercise therapy after acute pulmonary embolism

Objective The role of exercise therapy after acute pulmonary embolism (PE) is unknown. Exercise therapy is safely used after myocardial infarction and chronic obstructive pulmonary disease. The aim of this study was to investigate the safety of exercise therapy after acute PE. Methods We implemented a 3-month exercise program after acute PE. Outcomes were death, bleeding, readmissions, recurrent events, changes in peak VO2 and quality of life (QoL). Results A total of 23 patients were enrolled and received anticoagulation; no adverse events were reported during the exercise period. One death, 1 DVT and 5 readmissions were reported due to non-exercise related reasons. Functional capacity improved as evidenced by an increased peak VO2 at 3 months (+3.9 ± 5.6 mL/kg/min; p = 0.05). Improvement in QoL was observed at 6-months on the functional (+17.0 ± 22.6, p = 0.03) and physical health factor scales (+0.9 ± 4.6, p = 0.03). Conclusion Exercise therapy is feasible and safe in appropriately anticoagulated patients after PE.
Urban distribution of Rhytisma acerinum (Pers.) Fries (tar spot) on sycamore.

This study examined ecological aspects of the distribution of tar spot disease caused by the fungus Rhytisma acerinum (Pers.) Fries on Acer pseudoplatanus L. (sycamore). The host is abundant in Edinburgh and surrounding areas yet no tar spots were found in the city, although they were abundant on sycamore in the surrounding countryside, especially at sheltered sites. The vertical distribution from a localized source of leaf litter from infected sycamore showed an approximately linear relationship between tar spot index of attached leaves (TSI = no. of tar spots per 100 cm2 of leaf) and the log of height of such infected foliage above the ground. The distribution of tar spots was controlled primarily by the presence or absence of overwintered sycamore leaves infected with R. acerinum. In Edinburgh these leaves are actively removed by man and passively by wind, so reducing the potential source of inoculum by the following spring. The presence of SO2 was unimportant in the distribution of R. acerinum. An experiment to study the relative importance of current air concentrations of SO2 on the incidence of infection by R. acerinum showed that the average SO2 concentration of < 50 μg m-3 hail no effect. The observed distribution of tar spot throughout the city and surrounding countryside could be explained entirely by distance from the nearest source of inoculum without involving a role for air pollutants.
Interoperability in semantic Web of Things: Design issues and solutions

The significant improvement in processing power, communication, energy consumption, and the size of computational devices has led to the emergence of the Internet of Things (IoT). IoT projects raise many challenges, such as the interoperability between IoT applications because of the high number of sensors, actuators, services, protocols, and data associated with these systems. Semantics solves this problem by using annotations that define the role of each IoT element and reduces the ambiguity of information exchanged between the devices. This work presents SWoTPAD, a semantic framework that helps in the development of IoT projects. The framework is designer oriented and provides a semantic language that is more user‐friendly than OWL‐S and WSML and allows the IoT designer to specify devices, services, environment, and requests. Following this, it makes use of these specifications and maps them for RESTful services. Additionally, it generates an automatic service composition engine that is able to combine services needed to handle complex user requests. We validated this approach with two case studies. The former concerns a residential security system and the latter, the cloud application deployment. The average time required for service discovery and automatic service composition corresponds to 72.9% of the service execution time in the case study 1 and 64.4% in the case study 2.
Drought Impacts Survivorship and Reproductive Strategies of an Epiphyllous Leafy Liverwort in Central Amazonia

Understanding how changing precipitation patterns impact the population dynamics of Amazonian plants is necessary for predicting their long‐term survival. Most terrestrial plants are characterized by life cycles intractably slow for evaluating such demographic consequences. Due to the demands of surviving on an ephemeral substrate such as a leaf surface, epiphyllous (leaf‐inhabiting) bryophytes have some of the fastest generation times for terrestrial plants. Considering these advantages, we investigated the demographic consequences of seasonality in precipitation during one‐year of the epiphyllous bryophyte Radula flaccida Gott. (Radulaceae) in a central Amazonian rain forest. In a 1‐ha sized study area, 154 epiphyll colonies from 18 phorophytes of the understory shrub Naucleopsis ulei (Warb.) Ducke (Moraceae) were marked and colony growth, extinction, recolonization, as well as rates of sexual and asexual expression were measured in nine demographic censuses. The probability of survivorship decreased in the dry season due to the synergistic effects of both increased leaf fall (e.g., loss of occupied patches) and colony mortality on persisting leaves. Asexual expression also declined significantly during the driest months; however, sexual expression, as measured by sporophyte density, was not related to seasonality. Logistic regression probabilities also indicate a minimum threshold colony size for optimal sporophyte expression. Lower survivorship and colony growth in the dry season along with reduced sporophyte production in smaller colonies implies that both demographic stability as well as population structure of Amazonian epiphyll species may be compromised whether climate models projecting prolonged droughts for the region are accurate.
Optimization of low-dose scan parameters in dual-energy computed tomography for displaying the anterior cruciate ligament

Objective This study was performed to assess low-dose scan parameters in dual-energy computed tomography (CT) for displaying the anterior cruciate ligament. Methods Dual-energy CT scans with low and standard dose parameters, respectively, were performed in nine human knee joint specimens. Eighteen imaging data sets for cruciate ligament specimens were obtained and processed. Statistical analysis was performed for signal-to-noise ratios of the CT images and subjective scores. Results Comparable signal-to-noise ratios and subjective image quality scores by evaluators in dual-energy CT anterior cruciate ligament images between the low and standard-dose groups were observed. Conclusion Low-dose scan parameters do not compromise the outcomes of anterior cruciate ligament imaging.
Isolation and Characterization of Campylobacter jejuni from Broiler Chickens in Malaysia

Very few studies on Campylobacter in chickens were done in Malaysia. This study was carried out to determine the prevalence of Campylobacter in broiler chickens and to characterize the isolates to species level, their antibiotic resistance patterns and plasmid profiles. Ten broiler chicken farms were studied. The chickens in nine of the farms were found colonized with campylobacters; the prevalence rates ranged from 46.3 to 93.3%, with a mean of 72.6%; one farm was negative. Campylobacter jejuni was the predominant species. Antibiotic susceptibility test revealed that all the 76 C. jejuni isolates tested were resistant to tetracycline; 82.9, 55.3 and 34.2% were resistant to streptomycin, kanamycin and ampicillin, respectively while resistance to gentamicin, erythromycin and chloramphenicol ranged from 26.3 to 22.4%. It was also found that 22.4% of the isolates were resistant to one antibiotic while 13.1% to all seven antibiotics. 59% of C. jejuni isolates harboured between one to four plasmids, demonstrating 14 plasmid profiles with size of the plasmids ranged from 4.5 to 70.3 kb. More isolates containing plasmids were observed to be resistant to tetracycline, chloramphenicol and kanamycin than those isolates without plasmids. The numbers of plasmid bands present were not consistent with the antibiotic resistance patterns.
High environmental stress and productivity increase functional diversity along a deep-sea hydrothermal vent gradient.

Productivity and environmental stress are major drivers of multiple biodiversity facets and faunal community structure. Little is known on their interacting effects on early community assembly processes in the deep sea (>200 m), the largest environment on Earth. However, at hydrothermal vents productivity correlates, at least partially, with environmental stress. Here, we studied the colonization of rock substrata deployed along a deep-sea hydrothermal vent gradient at four sites with and without direct influence of vent fluids at 1700 m depth in the Lucky Strike vent field (Mid-Atlantic Ridge, MAR). We examined in detail the composition of faunal communities (>20 µm) established after two years and evaluated species and functional patterns. We expected the stressful hydrothermal activity to (1) limit functional diversity and (2) filter for traits clustering functionally similar species. However, our observations did not support our hypotheses. On the contrary, our results show that hydrothermal activity enhanced functional diversity. Moreover, despite high species diversity, environmental conditions at surrounding sites appear to filter for specific traits, thereby reducing functional richness. In fact, diversity in ecological functions may relax the effect of competition allowing several species to coexist in high densities in the reduced space of the highly-productive vent habitats under direct fluid emissions. We suggest that the high productivity at fluid-influenced sites supports higher functional diversity and traits that are more energetically expensive. The presence of exclusive species and functional entities led to a high turnover between surrounding sites. As a result, some of these sites contributed more than expected to the total species and functional β-diversities. The observed faunal overlap and energy links (exported productivity) suggest that rather than operating as separate entities, habitats with and without influence of hydrothermal fluids may be considered as interconnected entities. Low functional richness and environmental filtering suggests that surrounding areas, with their very heterogeneous species and functional assemblages, may be especially vulnerable to environmental changes related to natural and anthropogenic impacts, including deep-sea mining.
Iterative CT image reconstruction using neural network optimization algorithms

Stochastic or model-based iterative reconstruction is able to account for the stochastic nature of the CT imaging process and some artifacts and is able to provide better reconstruction quality. It is also, however, computationally expensive. In this work, we investigated the use of some of the neural network training algorithms such as momentum and Adam for iterative CT image reconstruction. Our experimental results indicate that these algorithms provide better results and faster convergence than basic gradient descent. They also provide competitive results to coordinate descent (a leading technique for iterative reconstruction) but, unlike coordinate descent, they can be implemented as parallel computations, hence can potentially accelerate iterative reconstruction in practice.
Enhancing Extensive and Remote LoRa Deployments through MEC-Powered Drone Gateways

The distribution of Internet of Things (IoT) devices in remote areas and the need for network resilience in such deployments is increasingly important in smart spaces covering scenarios, such as agriculture, forest, coast preservation, and connectivity survival against disasters. Although Low-Power Wide Area Network (LPWAN) technologies, like LoRa, support high connectivity ranges, communication paths can suffer from obstruction due to orography or buildings, and large areas are still difficult to cover with wired gateways, due to the lack of network or power infrastructure. The proposal presented herein proposes to mount LPWAN gateways in drones in order to generate airborne network segments providing enhanced connectivity to sensor nodes wherever needed. Our LoRa-drone gateways can be used either to collect data and then report them to the back-office directly, or store-carry-and-forward data until a proper communication link with the infrastructure network is available. The proposed architecture relies on Multi-Access Edge Computing (MEC) capabilities to host a virtualization platform on-board the drone, aiming at providing an intermediate processing layer that runs Virtualized Networking Functions (VNF). This way, both preprocessing or intelligent analytics can be locally performed, saving communications and memory resources. The contribution includes a system architecture that has been successfully validated through experimentation with a real test-bed and comprehensively evaluated through computer simulation. The results show significant communication improvements employing LoRa-drone gateways when compared to traditional fixed LoRa deployments in terms of link availability and covered areas, especially in vast monitored extensions, or at points with difficult access, such as rugged zones.
Molecular Dynamics Study of the Effect of Abrasive Grains Orientation and Spacing during Nanogrinding

Grinding at the nanometric level can be efficiently employed for the creation of surfaces with ultrahigh precision by removing a few atomic layers from the substrate. However, since measurements at this level are rather difficult, numerical investigation can be conducted in order to reveal the mechanisms of material removal during nanogrinding. In the present study, a Molecular Dynamics model with multiple abrasive grains is developed in order to determine the effect of spacing between the adjacent rows of abrasive grains and the effect of the rake angle of the abrasive grains on the grinding forces and temperatures, ground surface, and chip formation and also, subsurface damage of the substrate. Findings indicate that nanogrinding with abrasive grains situated in adjacent rows with spacing of 1 Å leads directly to a flat surface and the amount of material remaining between the rows of grains remains minimal for spacing values up to 5 Å. Moreover, higher negative rake angle of the grains leads to higher grinding forces and friction coefficient values over 1.0 for angles larger than −40°. At the same time, chip formation is suppressed and plastic deformation increases with larger negative rake angles, due to higher compressive action of the abrasive grains.