Miracle-dz/UniFAR-FTUs huggingface dataset:
Distribution, abundance, social and genetic structuresof Indo-Pacific bottlenose dolphins (Tursiops aduncus)in Perth metropolitan waters, Western Australia

In heterogeneous coastal and estuarine environments, dolphins are exposed to varying levels of human activities. Consequently, it is important to identify and characterise fine-scale population structuring based on ecological, social, spatial and genetic data to develop appropriate conservation and management strategies. This thesis focused on identifying subpopulations of Indo-Pacific bottlenose dolphins (Tursiops aduncus) inhabiting Perth waters, Western Australia (WA). Using spatial and social data collected over four years of boat-based photo-identification surveys, I: i) estimated abundances, survival and movement rates using a Multistate Closed Robust Design approach; and ii) examined the social structure and home range using social association and network analyses. I used microsatellite loci and mtDNA markers to investigate the genetic population structure of dolphins at metropolitan (Perth) and regional (c. 1000 km of coastline) scales. High capture probabilities, high survival and constant abundances described a subpopulation with high fidelity in an estuary. In contrast, low captures, emigration and fluctuating abundances suggested transient use and low fidelity in an open coastline region. Overall, dolphins formed four socially and geographically distinct, mixed-sex subpopulations that varied in association strength, site fidelity and residency patterns. Curiously, home range overlap and genetic relatedness did not affect the association patterns. In Perth metropolitan waters, a source-sink relationship was suggested between a subpopulation inhabiting a semi-enclosed embayment and three other subpopulations, including the estuarine subpopulation. On a broader scale, the Perth metapopulation was genetically distinct from other populations along the WA southwestern coastline, with little to no migration from and into other populations. The subpopulations present in Perth waters should each be regarded as a distinct management unit, with a particular focus on protecting the estuarine subpopulation, which is small, has limited connection with adjacent subpopulations and is more vulnerable because of the intensity and diversity of anthropogenic threats present in the estuary.
Giving a hand to the eyes: leveraging input accuracy for subpixel interaction

We argue that the current practice of using integer positions for pointing events artificially constrains human precision capabilities. The high sensitivity of current input devices can be harnessed to enable precise direct manipulation ""in between"" pixels, called subpixel interaction. We provide detailed analysis of subpixel theory and implementation, including the critical component of revised control-display gain transfer functions. A prototype implementation is described with several illustrative examples. Guidelines for subpixel domain applicability are provided and an overview of required changes to operating systems and graphical user interface frameworks are discussed.
A Study on Distributed Frequent Co-occurrence Patterns Algorithms across Multiple Data Streams

With the era of big data coming, the data streams are fast, continuous, and unbounded. The real-time requirements of the data streams processing results are very high. A large number of researches have been on Frequent Co-occurrence Patterns across multiple data streams. But those algorithms are centralized, which is worked on a single compute node. The memory of a single compute node and CPU calculation can be limited, which is difficult to deal with the increasing data streams. Using the distributed server cluster is an effective way. However, the centralized algorithm cannot be directly deployed to distributed server cluster. This paper designs a Distributed Frequent Co-occurrence Pattern across multiple data streams to solve these problems. Through a lot of experiments to evaluate it, the algorithm can detect all the objects that meet the conditions in real time, and have good scalability. In order to save memory, this paper also improves the algorithm, and proposes Modified Distributed Frequent Co-occurrence Pattern based on P-condition deletion strategy. The improved algorithm can delete element combinations which can not constitute Frequent Co-occurrence Patterns in the initial stage, so as to effectively save memory.
The Glycobiome of the Rumen Bacterium Butyrivibrio proteoclasticus B316T Highlights Adaptation to a Polysaccharide-Rich Environment

Determining the role of rumen microbes and their enzymes in plant polysaccharide breakdown is fundamental to understanding digestion and maximising productivity in ruminant animals. Butyrivibrio proteoclasticus B316T is a Gram-positive, butyrate-forming rumen bacterium with a key role in plant polysaccharide degradation. The 4.4Mb genome consists of 4 replicons; a chromosome, a chromid and two megaplasmids. The chromid is the smallest reported for all bacteria, and the first identified from the phylum Firmicutes. B316 devotes a large proportion of its genome to the breakdown and reassembly of complex polysaccharides and has a highly developed glycobiome when compared to other sequenced bacteria. The secretion of a range of polysaccharide-degrading enzymes which initiate the breakdown of pectin, starch and xylan, a subtilisin family protease active against plant proteins, and diverse intracellular enzymes to break down oligosaccharides constitute the degradative capability of this organism. A prominent feature of the genome is the presence of multiple gene clusters predicted to be involved in polysaccharide biosynthesis. Metabolic reconstruction reveals the absence of an identifiable gene for enolase, a conserved enzyme of the glycolytic pathway. To our knowledge this is the first report of an organism lacking an enolase. Our analysis of the B316 genome shows how one organism can contribute to the multi-organism complex that rapidly breaks down plant material in the rumen. It can be concluded that B316, and similar organisms with broad polysaccharide-degrading capability, are well suited to being early colonizers and degraders of plant polysaccharides in the rumen environment.
Dengue Vaccine: Considerations before Rollout in Colombia

Dengue has become an increasing public health concern in tropical and subtropical countries with worsening societal and financial burdens. Dengue causes considerable suffering and loss of productivity despite the typical, relatively short, weeklong duration of illness. Furthermore, people keep dying from dengue in the absence of early clinical recognition of severe infection and adequate supportive care. The World Health Organization estimates that 50–100 million dengue infections occur annually. However, estimates based on cartographic modelling approaches suggest that up to 390 million dengue infections occur annually (95% CI 284–528) [1]. The Pan American Health Organization (PAHO) reported in the region of the Americas a total of 1,181 deaths in 2015. Dengue costs are substantial because of the cost of hospital care and the loss in earnings by incapacitation or premature death [2]. Estimates are probably conservative because most studies do not include budgets directed to vector control, loss in tourism, and other costs.
Gossip-Based Dissemination of Time

Time synchronization between computers within a very large, highly dynamic network is a challenging task. Current solutions operate mostly in a hierarchical client-server mode based on a static configuration of logical connections, which tends to lack the scalability and robustness to failures. In this thesis, the author presents the Gossiping Time Protocol (GTP) — an approach to time synchronization employing the theory of epidemics. GTP is a completely decentralized solution in which all the hosts form a peer-to-peer network. They gossip with each other in order to propagate accurate time. The algorithms constituting GTP have desired properties of scalability and robustness, while offering fast and quite accurate synchronization. Experimental results obtained with a prototype implementation on an emulated network of more than 64,000 hosts scattered across the machines of a wide-area cluster computer confirm the above claim.
Effect of night-time temperatures on cause and age-specific mortality in London

Background: High ambient temperatures are associated with an acute increase in mortality risk. Although heat exposure during the night is anecdotally cited as being important, this has not been rigorously demonstrated in the epidemiological literature. Methods: We quantified the contribution of nighttime temperatures using time-series quasi-Poisson regression on cause and age-specific daily mortality in London between 1993 and 2015. Daytime and nighttime exposures were characterized by average temperatures between 9 am and 9 pm and between 4 am and 8 am, respectively, lagged by 7 days. We also examined the differential impacts of hot and cool nights preceded by very hot days. All models were adjusted for air quality, season, and day of the week. Nighttime models were additionally adjusted for daytime exposure. Results: Effects from nighttime exposure persisted after adjusting for daytime exposure. This was highest for stroke, RR (relative risk) = 1.65 (95% confidence interval (CI) = 1.27 to 2.14) estimated by comparing mortality risk at the 80th and 99th temperature percentiles. Compared to daytime exposure, nighttime exposure had a higher mortality risk on chronic ischemic and stroke and in the younger age groups. Respiratory mortality was most sensitive to daytime temperatures. Hot days followed by hot nights had a greater mortality risk than hot days followed by cool nights. Conclusions: Nighttime exposures make an additional important contribution to heat-related mortality. This impact was highest on warm nights that were preceded by a hot day, which justifies the alert criteria in heat–health warning system that is based on hot days followed by hot nights. The highest mortality risk was from stroke; targeted interventions would benefit patients most susceptible to stroke.
Automating Second Language Acquisition Research: Integrating Information Visualisation and Machine Learning

We demonstrate how data-driven approaches to learner corpora can support Second Language Acquisition research when integrated with visualisation tools. We present a visual user interface supporting the investigation of a set of linguistic features discriminating between pass and fail 'English as a Second or Other Language' exam scripts. The system displays directed graphs to model interactions between features and supports exploratory search over a set of learner scripts. We illustrate how the interface can support the investigation of the co-occurrence of many individual features, and discuss how such investigations can shed light on understanding the linguistic abilities that characterise different levels of attainment and, more generally, developmental aspects of learner grammars.
Histone deacetylase activity is essential for the expression of HoxA9 and for endothelial commitment of progenitor cells

The regulation of acetylation is central for the epigenetic control of lineage-specific gene expression and determines cell fate decisions. We provide evidence that the inhibition of histone deacetylases (HDACs) blocks the endothelial differentiation of adult progenitor cells. To define the mechanisms by which HDAC inhibition prevents endothelial differentiation, we determined the expression of homeobox transcription factors and demonstrated that HoxA9 expression is down-regulated by HDAC inhibitors. The causal involvement of HoxA9 in the endothelial differentiation of adult progenitor cells is supported by the finding that HoxA9 overexpression partially rescued the endothelial differentiation blockade induced by HDAC inhibitors. Knockdown and overexpression studies revealed that HoxA9 acts as a master switch to regulate the expression of prototypical endothelial-committed genes such as endothelial nitric oxide synthase, VEGF-R2, and VE-cadherin, and mediates the shear stress–induced maturation of endothelial cells. Consistently, HoxA9-deficient mice exhibited lower numbers of endothelial progenitor cells and showed an impaired postnatal neovascularization capacity after the induction of ischemia. Thus, HoxA9 is regulated by HDACs and is critical for postnatal neovascularization.
The Social Web of Things (SWoT)- Structuring an Integrated Social Network for Human, Things and Services

In recent years, the development of IoT (Internet of Things) technology has given people many ways to obtain information through various types of physical devices. In parallel with that trend, people rely more on context-aware service and devices in many aspects, such as health care and elderly home care. However, traditional sensors are typically locked into closed systems, which hinder the access to such sensors that can be available in other information systems. Establishing free communication between human and physical things will help build a network with hybrid intelligence and amazing services. In order to share information and enable the communication between both physical devices and human, we proposed a SWoT (Social Web of Thing) framework in this paper that establishes social networking between embedded devices, services and human. Through the supernetwork approach, we discussed the service discovery in the SWoT system with heterogeneous social relations. At last, we introduced the MagicHome prototype of SWoT.
Simulating searches from transaction logs

Computer simulations have become key to modeling human behavior in many disciplines. They can be used to explore, and deepen our understanding of, new algorithms and interfaces, especially when real-world data is too costly to obtain or unavailable due to privacy or competitiveness reasons. In information retrieval, simulators can be used to generate inputs from simulated users -- including queries, clicks, reformulations, judgments -- which can then be used to develop a deeper understanding of user behavior and to evaluate (interactive) retrieval systems. The trust that we put in simulators depends on their validity, which, in turn, depends on the data sources used to inform them. In this paper we present our views on future directions and challenges for simulation of queries and clicks from transaction logs.
Genome-Wide Analysis of Epstein-Barr Virus Rta DNA Binding

ABSTRACT The Epstein-Barr virus (EBV) lytic transactivator Rta activates promoters through direct binding to cognate DNA sites termed Rta response elements (RREs). Rta also activates promoters that apparently lack Rta binding sites, notably Zp and Rp. Chromatin immunoprecipitation (ChIP) of endogenous Rta expressed during early replication in B95-8 cells was performed to identify Rta binding sites in the EBV genome. Quantitative PCR (qPCR) analysis showed strong enrichment for known RREs but little or no enrichment for Rp or Zp, suggesting that the Rta ChIP approach enriches for direct Rta binding sites. Rta ChIP combined with deep sequencing (ChIP-seq) identified most known RREs and several novel Rta binding sites. Rta ChIP-seq peaks were frequently upstream of Rta-responsive genes, indicating that these Rta binding sites are likely functioning as RREs. Unexpectedly, the BALF5 promoter contained an Rta binding peak. To assess whether BALF5 might be activated by an RRE-dependent mechanism, an Rta mutant (Rta K156A), deficient for DNA binding and RRE activation but competent for Zp/Rp activation, was used. Rta K156A failed to activate BALF5p, suggesting this promoter can be activated by an RRE-dependent mechanism. Rta binding to late gene promoters was not seen at early time points but was specifically detected at later times within the Rta-responsive BLRF2 and BFRF3 promoters, even when DNA replication was inhibited. Our results represent the first characterization of Rta binding to the EBV genome during replication, identify previously unknown RREs, such as one in BALF5p, and highlight the complexity of EBV late gene promoter activation by Rta.
An Empirical Study of Execution-Data Classification Based on Machine Learning

As it may be difficult for users to distinguish a passing execution from a failing execution for a released software system, researchers have proposed to apply the Random Forest algorithm to classify remotely-collected program execution data. In general, execution-data classification can be viewed as a machine-learning problem, in which a trained learner needs to classify whether each execution is a passing execution or a failing execution. In this paper, we report an empirical study that further investigates various issues in execution-data classification based on machine learning. Compared with previous research, our study further investigates the impact of the following issues: different machinelearning algorithms, the numbers of training instances to construct a classification model, and different types of exe-
The role of vegetation in the CO[subscript 2] flux from a tropical urban neighbourhood

Urban surfaces are usually net sources of CO 2. Vegetation can potentially have an important role in reducing the CO2 emitted by anthropogenic activities in cities, particularly when vegetation is extensive and/or evergreen. A direct and accurate estimation of carbon uptake by urban vegetation is difficult due to the particular characteristics of the urban ecosystem and high variability in tree distribution and species. Here, we investigate the role of urban vegetation in the CO2 flux from a residential neighbourhood in Singapore using two different approaches. CO 2 fluxes measured directly by eddy covariance are compared with emissions estimated from emissions factors and activity data. The latter includes contributions from vehicular traffic, household combustion, soil respiration and human breathing. The difference between estimated emissions and measured fluxes should approximate the flux associated with the aboveground vegetation. In addition, a tree survey was conducted to estimate the annual CO2 sequestration using allometric equations and an alternative model of the metabolic theory of ecology for tropical forests. Palm trees, banana plants and turfgrass were also included in the survey with their annual CO 2 uptake obtained from published growth rates. Both approaches agree within 2 % and suggest that vegetation sequesters 8 % of the total emitted CO2 in the residential neighbourhood studied. An uptake of 1.4 ton km−2 day−1 (510 ton km−2 yr−1) was estimated as the difference between assimilation by photosynthesis minus the aboveground biomass respiration during daytime (4.0 ton km−2 day−1) and release by plant respiration at night (2.6 ton km−2 day−1). However, when soil respiration is added to the daily aboveground flux, the biogenic component becomes a net source amounting to 4 % of the total CO2 flux and represents the total contribution of urban vegetation to the carbon flux to the atmosphere.
The first technique for non-invasive measurements of volumetric ophthalmic artery blood flow in humans

Aim: To validate the first non-invasive measurements of volumetric ophthalmic artery blood flow in humans. Methods: The ophthalmic arteries of healthy normal adults were examined by Advanced Technology Laboratories (ATL, a subsidiary of Phillips Medical Systems Inc) high definition imaging (HDI) 5000 colour Doppler imaging ultrasound with a 5–12 MHZ probe. A group of 14 subjects for experiment 1 and a group of 10 subjects for experiments 2 and 3 were selected, with the examined eye chosen randomly. Peak systolic velocities (PSV) and end diastolic velocities (EDV) of the ophthalmic artery and central retinal artery were measured and recorded. Cineloops (cinegraphic videos) of the ophthalmic arteries were then recorded with the ATL HDI 5000 and values for ophthalmic artery blood flow were produced offline using experimental analysis software. Multiple regression analysis was used to compare blood flow measurements with PSV and EDV measurements in the ophthalmic artery. In two follow up experiments, intraobserver variation in obtaining cineloops and the interanalyser variability in cineloop analysis were studied. Results: Volumetric flow correlated with ophthalmic artery PSV and EDV (p = 0.02, r2 = 0.5). There was no correlation with the cental retinal artery. The intraobserver coefficient of variation in obtaining cineloops was 29.89% for blood flow, 19.07% for diameter, and 22.27% for velocity. The coefficients of variation of the measurements of the two cineloop analysers were 40.21% for blood flow, 22.71% for diameter, and 26.34% for velocity. Conclusion: Cineloop analysis produces ophthalmic artery flow measurements which correlate with PSV and EDV, suggesting validity. The intraobserver variation and cineloop analyser variation were found to be in the acceptable range.
The Binding Problem Solutions to the Spatial Binding Problem

Objects have different features such as color, shape, sound, and smell. Some, such as color and sound, are represented separately from the instant they hit our sensory receptors. Other features, such as color and shape, are initially encoded together but subsequently analyzed by separate areas of the brain. Despite this separation, in perception the brain must represent which features belong to the same object. This is the binding problem. Any case of the brain representing as associated two features or stimuli that are initially represented separately can be called binding, but this entry will focus on a subset of these: the pairing of features that belong to a common object. A simple solution to the binding problem is to have a single neuron (or other representational unit) for each possible combination of features. However, considering that different feature dimensions such as color, shape, and texture may each have hundreds of values, it is impractical to dedicate a unit to each combination. Still, the visual system does contain neurons selective for certain combinations of features, and these may suffice to solve the binding problem in certain cases (Risenhuber & Poggio 1999). Wolf Singer has championed the theory that binding is represented via synchronous rhythmic firing of the neurons selective for the paired features (von der Malsburg 1981; Gray et al. 1989). The idea is that the joint activity of the feature representations allows other brain areas to process the features together, to the exclusion of features belonging to other objects. Groups of neurons in many parts of the brain frequently do synchronize their responses, and attention to visual stimuli can enhance the effect, but the precise relationship of the phenomenon to For experimental psychology researchers, two papers on binding by Anne Treisman in the 1980s set the course for nearly two decades (Treisman & Gelade 1980; Treisman & Schmidt 1982). Treisman's "feature integration theory" (FIT) became not only the most influential theory of binding, but also the most influential theory of attention. FIT posits that binding is accomplished by an act of selective attention and has three elements.