Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic Characterization of Burkholderia pseudomallei Isolates Selected for Medical Countermeasures Testing: Comparative Genomics Associated with Differential Virulence

Burkholderia pseudomallei is the causative agent of melioidosis and a potential bioterrorism agent. In the development of medical countermeasures against B. pseudomallei infection, the US Food and Drug Administration (FDA) animal Rule recommends using well-characterized strains in animal challenge studies. In this study, whole genome sequence data were generated for 6 B. pseudomallei isolates previously identified as candidates for animal challenge studies; an additional 5 isolates were sequenced that were associated with human inhalational melioidosis. A core genome single nucleotide polymorphism (SNP) phylogeny inferred from a concatenated SNP alignment from the 11 isolates sequenced in this study and a diverse global collection of isolates demonstrated the diversity of the proposed Animal Rule isolates. To understand the genomic composition of each isolate, a large-scale blast score ratio (LS-BSR) analysis was performed on the entire pan-genome; this demonstrated the variable composition of genes across the panel and also helped to identify genes unique to individual isolates. In addition, a set of ~550 genes associated with pathogenesis in B. pseudomallei were screened against the 11 sequenced genomes with LS-BSR. Differential gene distribution for 54 virulence-associated genes was observed between genomes and three of these genes were correlated with differential virulence observed in animal challenge studies using BALB/c mice. Differentially conserved genes and SNPs associated with disease severity were identified and could be the basis for future studies investigating the pathogenesis of B. pseudomallei. Overall, the genetic characterization of the 11 proposed Animal Rule isolates provides context for future studies involving B. pseudomallei pathogenesis, differential virulence, and efficacy to therapeutics.
Effects of Ocean Acidification on Temperate Coastal Marine Ecosystems and Fisheries in the Northeast Pacific

As the oceans absorb anthropogenic CO2 they become more acidic, a problem termed ocean acidification (OA). Since this increase in CO2 is occurring rapidly, OA may have profound implications for marine ecosystems. In the temperate northeast Pacific, fisheries play key economic and cultural roles and provide significant employment, especially in rural areas. In British Columbia (BC), sport (recreational) fishing generates more income than commercial fishing (including the expanding aquaculture industry). Salmon (fished recreationally and farmed) and Pacific Halibut are responsible for the majority of fishery-related income. This region naturally has relatively acidic (low pH) waters due to ocean circulation, and so may be particularly vulnerable to OA. We have analyzed available data to provide a current description of the marine ecosystem, focusing on vertical distributions of commercially harvested groups in BC in the context of local carbon and pH conditions. We then evaluated the potential impact of OA on this temperate marine system using currently available studies. Our results highlight significant knowledge gaps. Above trophic levels 2–3 (where most local fishery-income is generated), little is known about the direct impact of OA, and more importantly about the combined impact of multi-stressors, like temperature, that are also changing as our climate changes. There is evidence that OA may have indirect negative impacts on finfish through changes at lower trophic levels and in habitats. In particular, OA may lead to increased fish-killing algal blooms that can affect the lucrative salmon aquaculture industry. On the other hand, some species of locally farmed shellfish have been well-studied and exhibit significant negative direct impacts associated with OA, especially at the larval stage. We summarize the direct and indirect impacts of OA on all groups of marine organisms in this region and provide conclusions, ordered by immediacy and certainty.
Relationship of the Perceived Social and Physical Environment with Mental Health-Related Quality of Life in Middle-Aged and Older Adults: Mediating Effects of Physical Activity

Background Mental health conditions are among the leading non-fatal diseases in middle-aged and older adults in Australia. Proximal and distal social environmental factors and physical environmental factors have been associated with mental health, but the underlying mechanisms explaining these associations remain unclear. The study objective was to examine the contribution of different types of physical activity in mediating the relationship of social and physical environmental factors with mental health-related quality of life in middle-aged and older adults. Methods Baseline data from the Wellbeing, Eating and Exercise for a Long Life (WELL) study were used. WELL is a prospective cohort study, conducted in Victoria, Australia. Baseline data collection took place in 2010. In total, 3,965 middle-aged and older adults (55–65 years, 47.4% males) completed the SF-36 Health Survey, the International Physical Activity Questionnaire, and a questionnaire on socio-demographic, social and physical environmental attributes. Mediation analyses were conducted using the MacKinnon product-of-coefficients test. Results Personal safety, the neighbourhood physical activity environment, social support for physical activity from family or friends, and neighbourhood social cohesion were positively associated with mental health-related quality of life. Active transportation and leisure-time physical activity mediated 32.9% of the association between social support for physical activity from family or friends and mental health-related quality of life. These physical activity behaviours also mediated 11.0%, 3.4% and 2.3% respectively, of the relationship between the neighbourhood physical activity environment, personal safety and neighbourhood social cohesion and mental health-related quality of life. Conclusions If these results are replicated in future longitudinal studies, tailored interventions to improve mental health-related quality of life in middle-aged and older adults should use a combined strategy, focusing on increasing physical activity as well as social and physical environmental attributes.
Genome-Wide Association Study (GWAS) for Growth Rate and Age at Sexual Maturation in Atlantic Salmon (Salmo salar)

Early sexual maturation is considered a serious drawback for Atlantic salmon aquaculture as it retards growth, increases production times and affects flesh quality. Although both growth and sexual maturation are thought to be complex processes controlled by several genetic and environmental factors, selection for these traits has been continuously accomplished since the beginning of Atlantic salmon selective breeding programs. In this genome-wide association study (GWAS) we used a 6.5K single-nucleotide polymorphism (SNP) array to genotype ∼480 individuals from the Cermaq Canada broodstock program and search for SNPs associated with growth and age at sexual maturation. Using a mixed model approach we identified markers showing a significant association with growth, grilsing (early sexual maturation) and late sexual maturation. The most significant associations were found for grilsing, with markers located in Ssa10, Ssa02, Ssa13, Ssa25 and Ssa12, and for late maturation with markers located in Ssa28, Ssa01 and Ssa21. A lower level of association was detected with growth on Ssa13. Candidate genes, which were linked to these genetic markers, were identified and some of them show a direct relationship with developmental processes, especially for those in association with sexual maturation. However, the relatively low power to detect genetic markers associated with growth (days to 5 kg) in this GWAS indicates the need to use a higher density SNP array in order to overcome the low levels of linkage disequilibrium observed in Atlantic salmon before the information can be incorporated into a selective breeding program.
Planar Graph Perfect Matching Is in NC

Is perfect matching in NC? That is, is there a deterministic fast parallel algorithm for it? This has been an outstanding open question in theoretical computer science for over three decades, ever since the discovery of RNC matching algorithms. Within this question, the case of planar graphs has remained an enigma: On the one hand, counting the number of perfect matchings is far harder than finding one (the former is #P-complete and the latter is in P), and on the other, for planar graphs, counting has long been known to be in NC whereas finding one has resisted a solution. In this paper, we give an NC algorithm for finding a perfect matching in a planar graph. Our algorithm uses the above-stated fact about counting matchings in a crucial way. Our main new idea is an NC algorithm for finding a face of the perfect matching polytope at which many new conditions, involving constraints of the polytope, are simultaneously satisfied. Several other ideas are also needed, such as finding a point in the interior of the minimum weight face of this polytope and finding a balanced tight odd set in NC.
Obstructive Hydrocephalus Due to Intraventricular Hemorrhage After Incidental Durotomy During Lumbar Spine Surgery

Study Design. Case report and review of literature. Objective. To present an exceedingly rare occurrence of obstructive hydrocephalus secondary to intraventricular hemorrhage after incidental durotomy during lumbar spine surgery. Summary of Background Data. Incidental durotomies are uncommon but well recognized complications associated with spine surgery. Whereas mostly considered benign with no untoward clinical sequele, it can be symptomatic and present with spinal headaches, pseudomeningoceles, wound infection, meningitis and rarely intracerebral hemorrhage. Methods. A 76-year-old woman underwent L3-S1 laminectomies and fusion for lumbar spondylosis and stenosis. Intraoperatively, a small incidental durotomy was encountered and primarily repaired. Results. The patient developed altered mental status on postoperative day 2. Computed tomography of the brain revealed obstructive hydrocephalus and intraventricular hemorrhage. The patient was immediately transferred to the neurosurgery intensive care unit and an external ventricular drain was placed emergently with high opening pressure. Her mental status improved immediately after cerebral spinal fluid diversion. The external ventricular drain was successfully removed after 8 days. The patient made a full recovery and was discharged in stable condition. Conclusion. Obstructive hydrocephalus after intraventricular hemorrhage is an exceptionally rare but potentially life-threatening complication of incidental durotomies. Spine surgeons should be aware of this rare but serious complication. Level of Evidence: 4
Traffic Off-Loading With Energy-Harvesting Small Cells and Coded Content Caching

We consider content delivery to users in a system consisting of a macro base station (BS), several energy-harvesting small cells (SCs), and many users. Each SC has a large cache and stores a copy of all contents in the BS. A user’s content request can be either handled by the SC for free if it has enough energy, or by the BS that has a cost. Each user has a finite cache and can store some most popular contents. We propose an efficient coded content caching schemes and an optimal transmission schemes for this system to maximally off-load the data traffic from the macro BS to the energy-harvesting SCs, and therefore minimize the power consumption from the grid. Specifically, the proposed coded caching scheme stores fractions of some most popular contents, such that contents requested from multiple users can be simultaneously delivered by the BS or SC. Moreover, the optimal transmission policy is formulated and solved as a Markov decision process. Extensive simulation results are provided to demonstrate that the proposed coded caching and transmission schemes can provide significantly higher traffic off-loading capability compared with systems with no caching or with uncoded caching, as well as systems that employ heuristic-based transmission schemes.
A Reverse Taxonomic Approach to Assess Macrofaunal Distribution Patterns in Abyssal Pacific Polymetallic Nodule Fields

Heightened interest in the exploitation of deep seafloor minerals is raising questions on the consequences for the resident fauna. Assessing species ranges and determination of processes underlying current species distributions are prerequisites to conservation planning and predicting faunal responses to changing environmental conditions. The abyssal central Pacific nodule belt, located between the Clarion and Clipperton Fracture Zones (CCZ), is an area prospected for mining of polymetallic nodules. We examined variations in genetic diversity and broad-scale connectivity of isopods and polychaetes across the CCZ. Faunal assemblages were studied from two mining claims (the eastern German and French license areas) located 1300 km apart and influenced by different productivity regimes. Using a reverse taxonomy approach based on DNA barcoding, we tested to what extent distance and large-scale changes in environmental parameters lead to differentiation in two macrofaunal taxa exhibiting different functions and life-history patterns. A fragment of the mitochondrial gene Cytochrome Oxidase Subunit 1 (COI) was analyzed. At a 97% threshold the molecular operational taxonomic units (MOTUs) corresponded well to morphological species. Molecular analyses indicated high local and regional diversity mostly because of large numbers of singletons in the samples. Consequently, variation in composition of genotypic clusters between sites was exceedingly large partly due to paucity of deep-sea sampling and faunal patchiness. A higher proportion of wide-ranging species in polychaetes was contrasted with mostly restricted distributions in isopods. Remarkably, several cryptic lineages appeared to be sympatric and occurred in taxa with putatively good dispersal abilities, whereas some brooding lineages revealed broad distributions across the CCZ. Geographic distance could explain variation in faunal connectivity between regions and sites to some extent, while assumed dispersal capabilities were not as important.
Enhancement of monocyte transendothelial migration by granulocyte‐macrophage colony‐stimulating factor: requirement for chemoattractant and CD11a / CD18 mechanisms

Granulocyte‐macrophage colony‐stimulating factor (GM‐CSF) enhances and primes monocyte functions, but its role in monocyte migration is poorly understood. We examined monocyte migration across human umbilical vein endothelial cells (HUVEC) grown on filters. GM‐CSF had no chemotactic or chemokinetic effect. However, GM‐CSF enhanced monocyte transendothelial migration (TEM) through unstimulated and IL‐1‐activated (5 h) HUVEC in response to C5a or monocyte chemoattractant protein‐1 in a dose‐dependent fashion, increasing the migration from 28.7 ± 5.3 % to 41.8 ± 6.2 % (n = 8, p < 0.05) and from 34.8 ± 6 % to 50.3 ± 3.1 %, p < 0.05), respectively. The enhanced TEM was inhibited by monoclonal antibodies (mAb) to LFA‐1, but not by mAb to Mac‐1 or to VLA‐4. Furthermore, GM‐CSF up‐regulated and activated LFA‐1, as assessed by NKI‐L16 neoepitope expression. The results indicate that: (1) GM‐CSF can prime monocytes for increased TEM, (2) GM‐CSF enhances LFA‐1‐mediated monocyte TEM and (3) this effect is in part mediated by increasing LFA‐1 expression and activation. Thus, increased GM‐CSF production may promote monocyte accumulation in inflammation not only by inducing monocytosis, but also enhancing migration.
High-Resolution Microbial Community Succession of Microbially Induced Concrete Corrosion in Working Sanitary Manholes

Microbially-induced concrete corrosion in headspaces threatens wastewater infrastructure worldwide. Models for predicting corrosion rates in sewer pipe networks rely largely on information from culture-based investigations. In this study, the succession of microbes associated with corroding concrete was characterized over a one-year monitoring campaign using rRNA sequence-based phylogenetic methods. New concrete specimens were exposed in two highly corrosive manholes (high concentrations of hydrogen sulfide and carbon dioxide gas) on the Colorado Front Range for up to a year. Community succession on corroding surfaces was assessed using Illumina MiSeq sequencing of 16S bacterial rRNA amplicons and Sanger sequencing of 16S universal rRNA clones. Microbial communities associated with corrosion fronts presented distinct succession patterns which converged to markedly low α-diversity levels (< 10 taxa) in conjunction with decreasing pH. The microbial community succession pattern observed in this study agreed with culture-based models that implicate acidophilic sulfur-oxidizer Acidithiobacillus spp. in advanced communities, with two notable exceptions. Early communities exposed to alkaline surface pH presented relatively high α-diversity, including heterotrophic, nitrogen-fixing, and sulfur-oxidizing genera, and one community exposed to neutral surface pH presented a diverse transition community comprised of less than 20% sulfur-oxidizers.
Radiation damage to permanent magnet materials: A survey of experimental results

A large fraction of the total power consumption of the CLIC machine is taken up by electromagnets. There is a proposal to replace some of the conventional electromagnets with permanent magnet (PM) versions. Prototypes of tunable versions using a movable PM section have been built. These would have several advantages over conventional electromagnets: zero power in normal usage; a very small power draw to change the ﬁ eld; reduced infrastructure costs (no large power supplies, thick current cables, or water cooling); increased beam stability (no vibration from ﬂ owing water or ripple from power converters); and drastically reduced hysteresis e ﬀ ects. Permanent magnets do have some disadvantages, however. One of these is a vulnerability to radiation. Exposure to radiation present in an accelerator beamline can have detrimental e ﬀ ects on PM blocks and can cause them to be demagnetised, reducing the overall ﬁ eld strength of the magnet and/or reducing the ﬁ eld quality. This document aims to summarise the experimental body of work done on damage to permanent magnets caused by radiation generated within an accelerator beamline. Experimental results are outlined, together with proposed models used to represent the data. Possible strategies to reduce the amount of damage caused are listed, particularly with regard to the estimated type and amount of radiation likely to be present in the CLIC drive beam.
Ecological Niche Transferability Using Invasive Species as a Case Study

Species distribution modeling is widely applied to predict invasive species distributions and species range shifts under climate change. Accurate predictions depend upon meeting the assumption that ecological niches are conserved, i.e., spatially or temporally transferable. Here we present a multi-taxon comparative analysis of niche conservatism using biological invasion events well documented in natural history museum collections. Our goal is to assess spatial transferability of the climatic niche of a range of noxious terrestrial invasive species using two complementary approaches. First we compare species’ native versus invasive ranges in environmental space using two distinct methods, Principal Components Analysis and Mahalanobis distance. Second we compare species’ native versus invaded ranges in geographic space as estimated using the species distribution modeling technique Maxent and the comparative index Hellinger’s I. We find that species exhibit a range of responses, from almost complete transferability, in which the invaded niches completely overlap with the native niches, to a complete dissociation between native and invaded ranges. Intermediate responses included expansion of dimension attributable to either temperature or precipitation derived variables, as well as niche expansion in multiple dimensions. We conclude that the ecological niche in the native range is generally a poor predictor of invaded range and, by analogy, the ecological niche may be a poor predictor of range shifts under climate change. We suggest that assessing dimensions of niche transferability prior to standard species distribution modeling may improve the understanding of species’ dynamics in the invaded range.
Designing, developing, and evaluating the future internet of personal health

Ubiquitous computing technologies have the potential to revolutionize the support of chronic health conditions: improving quality of life, reducing costs and optimizing health outcomes. Wearable networks of connected devices and sensors offer the prospect of personalized support and contextually aware advice, for those with specific chronic health conditions. However, there are many obstacles and concerns that need to be addressed before the full potential can be realized. This workshop aims to bring together those interested in developing ubiquitous health management and related personal decision support systems to identify how gaps in knowledge can be addressed and design practices can be improved to better support key communities and contexts of use in this rapidly growing field.
Finding Detours is Fixed-Parameter Tractable

We consider the following natural "above guarantee" parameterization of the classical longest path problem: For given vertices s and t of a graph G, and an integer k, the longest detour problem asks for an (s,t)-path in G that is at least k longer than a shortest (s,t)-path. Using insights into structural graph theory, we prove that the longest detour problem is fixed-parameter tractable (FPT) on undirected graphs and actually even admits a single-exponential algorithm, that is, one of running time exp(O(k)) * poly(n). This matches (up to the base of the exponential) the best algorithms for finding a path of length at least k. Furthermore, we study a related problem, exact detour, that asks whether a graph G contains an (s,t)-path that is exactly k longer than a shortest (s,t)-path. For this problem, we obtain a randomized algorithm with running time about 2.746^k * poly(n), and a deterministic algorithm with running time about 6.745^k * poly(n), showing that this problem is FPT as well. Our algorithms for the exact detour problem apply to both undirected and directed graphs.
Automatic Mobile Application Traffic Identification by Convolutional Neural Networks

Mobile network security and management are becoming important issues, due to the rapid development and widespread of the mobile network. Application traffic identification is a critical technology to resolve these issues. A variety of traffic classification methods on desktop applications are no longer effective in mobile network, because the majority of mobile traffic is carried over HTTP without distinctive features. Existing approaches to identify mobile traffic simply extract obvious features like fixed strings or regular expressions, which are not effective to capture hidden structure within the HTTP headers. In this paper, we propose a novel approach, which can identify mobile application by automatically extracting abstract features from labeled packets. Our approach is mainly based on convolutional neural networks (CNNs). The CNNs can extract the abstract statistical features between characters in HTTP and thus improve the identification accuracy. It's also able to reduce the dependence on prior knowledge and human effort in designing features. To verify the effectiveness of our method, we apply it to several identification tasks. The evaluation shows that our method can accurately identify the traffic of the target mobile application.