Miracle-dz/UniFAR-FTUs huggingface dataset:
Fundamentals and Recent Developments in Approximate Bayesian Computation

&NA; Bayesian inference plays an important role in phylogenetics, evolutionary biology, and in many other branches of science. It provides a principled framework for dealing with uncertainty and quantifying how it changes in the light of new evidence. For many complex models and inference problems, however, only approximate quantitative answers are obtainable. Approximate Bayesian computation (ABC) refers to a family of algorithms for approximate inference that makes a minimal set of assumptions by only requiring that sampling from a model is possible. We explain here the fundamentals of ABC, review the classical algorithms, and highlight recent developments. [ABC; approximate Bayesian computation; Bayesian inference; likelihood‐free inference; phylogenetics; simulator‐based models; stochastic simulation models; tree‐based models. ]
Unmanned aerial vehicle navifation system based on IEEE 802.15.4 standard radiounits

Modern unmanned aerial vehicle navigation systems are highly dependent on Global Positioning System signals. Since Global Positioning System signals in dense urban housing areas, in tunnels or indoors may be unreliable, unmanned aerial vehicle will not be able to fulfill its tasks if needed to pass such zones. An unmanned aerial vehicle navigation system based on the increasingly popular radio standard IEEE 802.15. 4 / ZigBee is proposed. A description of such networks and their advantages for unmanned aerial vehicle positioning are given.
Imperfect Replacement of Native Species by Non‐Native Species as Pollinators of Endemic Hawaiian Plants

Native plant species that have lost their mutualist partners may require non‐native pollinators or seed dispersers to maintain reproduction. When natives are highly specialized, however, it appears doubtful that introduced generalists will partner effectively with them. We used visitation observations and pollination treatments (experimental manipulations of pollen transfer) to examine relationships between the introduced, generalist Japanese White‐eye (Zosterops japonicus) and 3 endemic Hawaiian plant species (Clermontia parviflora, C. montis‐loa, and C. hawaiiensis). These plants are characterized by curved, tubular flowers, apparently adapted for pollination by curve‐billed Hawaiian honeycreepers. Z. japonicus were responsible for over 80% of visits to flowers of the small‐flowered C. parviflora and the midsize‐flowered C. montis‐loa. Z. japonicus‐visited flowers set significantly more seed than did bagged flowers. Z. japonicus also demonstrated the potential to act as an occasional Clermontia seed disperser, although ground‐based frugivory by non‐native mammals likely dominates seed dispersal. The large‐flowered C. hawaiiensis received no visitation by any birds during observations. Unmanipulated and bagged C. hawaiiensis flowers set similar numbers of seeds. Direct examination of Z. japonicus and Clermontia morphologies suggests a mismatch between Z. japonicus bill morphology and C. hawaiiensis flower morphology. In combination, our results suggest that Z. japonicus has established an effective pollination relationship with C. parviflora and C. montis‐loa and that the large flowers of C. hawaiiensis preclude effective visitation by Z. japonicus.
Serum Angiopoietin-1 and -2 Levels Discriminate Cerebral Malaria from Uncomplicated Malaria and Predict Clinical Outcome in African Children

Background Limited tools exist to identify which individuals infected with Plasmodium falciparum are at risk of developing serious complications such as cerebral malaria (CM). The objective of this study was to assess serum biomarkers that differentiate between CM and non-CM, with the long-term goal of developing a clinically informative prognostic test for severe malaria. Methodology/Principal Findings Based on the hypothesis that endothelial activation and blood-brain-barrier dysfunction contribute to CM pathogenesis, we examined the endothelial regulators, angiopoietin-1 (ANG-1) and angiopoietin-2 (ANG-2), in serum samples from P. falciparum-infected patients with uncomplicated malaria (UM) or CM, from two diverse populations – Thai adults and Ugandan children. Angiopoietin levels were compared to tumour necrosis factor (TNF). In both populations, ANG-1 levels were significantly decreased and ANG-2 levels were significantly increased in CM versus UM and healthy controls (p<0.001). TNF was significantly elevated in CM in the Thai adult population (p<0.001), but did not discriminate well between CM and UM in African children. Receiver operating characteristic curve analysis showed that ANG-1 and the ratio of ANG-2∶ANG-1 accurately discriminated CM patients from UM in both populations. Applied as a diagnostic test, ANG-1 had a sensitivity and specificity of 100% for distinguishing CM from UM in Thai adults and 70% and 75%, respectively, for Ugandan children. Across both populations the likelihood ratio of CM given a positive test (ANG-1<15 ng/mL) was 4.1 (2.7–6.5) and the likelihood ratio of CM given a negative test was 0.29 (0.20–0.42). Moreover, low ANG-1 levels at presentation predicted subsequent mortality in children with CM (p = 0.027). Conclusions/Significance ANG-1 and the ANG-2/1 ratio are promising clinically informative biomarkers for CM. Additional studies should address their utility as prognostic biomarkers and potential therapeutic targets in severe malaria.
Resumos neste número* The application of the Global Trigger Tool: a systematic review

Os estudos foram realizados em 16 países. Mais de metade não seguiu o protocolo padrão GTT sobre o número de revisores utilizados. Foram incluídos os "atos de omissão" num quarto dos estudos. Os relatórios de Incidente detetaram entre 2–8% dos EAs que foram identificados com o GTT. Taxas de EAs variaram, nos estudos de doentes internados, entre 7 a 40%. As infeções, os problemas com procedimentos cirúrgicos e as ocorrências relacionadas com medicamentos foram os tipos de incidentes mais comuns.
Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway

Abundance of most EGFR-MAPK pathway proteins is conserved across cell types, revealing adaptors as rate-limiting nodes. Adaptors are the conductors in the signaling symphony Just as there are rate-limiting enzymes in biochemical process, there are rate-limiting steps in cell signaling networks. These rate-limiting proteins direct the signal through specific molecular cascades to dictate the response. Shi et al. sought to identify the proteins in the epidermal growth factor receptor (EGFR) signaling network that serve as the conductors or directors of the EGF signal. They found that the abundance of most core pathway proteins was very similar between cells and rather that the very low abundance of the adaptor proteins made them rate-limiting for EGFR-MAPK pathway signaling in normal and malignant cells. The findings suggest that adaptor proteins serve as the directors of the signaling script. Various genetic mutations associated with cancer are known to alter cell signaling, but it is not clear whether they dysregulate signaling pathways by altering the abundance of pathway proteins. Using a combination of RNA sequencing and ultrasensitive targeted proteomics, we defined the primary components—16 core proteins and 10 feedback regulators—of the epidermal growth factor receptor (EGFR)–mitogen-activated protein kinase (MAPK) pathway in normal human mammary epithelial cells and then quantified their absolute abundance across a panel of normal and breast cancer cell lines as well as fibroblasts. We found that core pathway proteins were present at very similar concentrations across all cell types, with a variance similar to that of proteins previously shown to display conserved abundances across species. In contrast, EGFR and transcriptionally controlled feedback regulators were present at highly variable concentrations. The absolute abundance of most core proteins was between 50,000 and 70,000 copies per cell, but the adaptors SOS1, SOS2, and GAB1 were found at far lower amounts (2000 to 5000 copies per cell). MAPK signaling showed saturation in all cells between 3000 and 10,000 occupied EGFRs, consistent with the idea that adaptors limit signaling. Our results suggest that the relative stoichiometry of core MAPK pathway proteins is very similar across different cell types, with cell-specific differences mostly restricted to variable amounts of feedback regulators and receptors. The low abundance of adaptors relative to EGFR could be responsible for previous observations that only a fraction of total cell surface EGFR is capable of rapid endocytosis, high-affinity binding, and mitogenic signaling.
Real-time sign languages recognition based on hausdorff distance, Hu invariants and neural network

In this paper, a universal sign languages recognition system is proposed using two different approaches. Although a variety of sign languages exist in use, the proposed system recognizes three widely used sign languages as the American Sign Language, British Sign Language and Turkish Sign Language to make the recognition universal. One of the proposed approach is primarily based on Hausdorff distance and Hu invariants as the feature vectors and the system first focuses on how to process the hand movements and then it recognizes the different letters by the help of Hausdorff distance and Hu invariants measurements. The second approach is implemented by a feed forward neural network structure and recognition is provided with training data as three different sign language alphabets. It is shown that both approaches operate successfully while experimental results demonstrate that neural network based method provides superior performance.
Effect of a Standardised Dietary Restriction Protocol on Multiple Laboratory Strains of Drosophila melanogaster

Background Outcomes of lifespan studies in model organisms are particularly susceptible to variations in technical procedures. This is especially true of dietary restriction, which is implemented in many different ways among laboratories. Principal Findings In this study, we have examined the effect of laboratory stock maintenance, genotype differences and microbial infection on the ability of dietary restriction (DR) to extend life in the fruit fly Drosophila melanogaster. None of these factors block the DR effect. Conclusions These data lend support to the idea that nutrient restriction genuinely extends lifespan in flies, and that any mechanistic discoveries made with this model are of potential relevance to the determinants of lifespan in other organisms.
Relationship between occupational stress and cardiovascular diseases risk factors in drivers.

OBJECTIVES Of all work stressors, occupational stress is the leading cause of many disorders among workers. Drivers are classified as a high risk group for work related stress. This study set out to determine the relationship between risk factors of cardiovascular diseases and occupational stress among drivers. MATERIAL AND METHODS Two hundred and twenty two Ilam's intercity drivers were selected for the study. For measuring work stress, the Osipow work stress questionnaire was used. After a 10-h fasting period, systolic and diastolic blood pressure was recorded. Intravenous blood samples were taken to determine cholesterol, triglyceride and blood glucose levels. The independent samples t-test and Pearson's correlation test were used to assess the relationship between variables and occupational stress. RESULTS Seventy-one percent of the intercity drivers suffered from average to acute stress, and 3.1% of them suffered from acute stress. There was no significant relationship between occupational stress and diastolic blood pressure (p = 0.254) among the drivers. Nevertheless, the Pearson's correlation test demonstrated a strong relationship between work stress and blood glucose (p < 0.01), while no strong correlation was found for blood triglycerides and cholesterol levels. CONCLUSIONS Based on the results, high rates of occupational stress were observed in the Ilam's intercity drivers. Occupational stress may have effect on blood glucose levels but the results did not suggest a considerable relationship between risk factors of cardiovascular diseases and occupational stress among intercity drivers. Int J Occup Med Environ Health 2016;29(6):895-901.
More than Counting: An Intraindividual Variability Approach to Categorical Repeated Measures

Objectives Age-related differences in daily experiences are often described using summaries of categorical repeated measures, including typologies of stressors, activities, social partners, and coping strategies. This paper illustrates how an intraindividual variability (IIV) framework can be used to extract additional meaning from categorical IIV data. Method Using 8-occasion categorical data on daily stressors from the National Study of Daily Experiences (N = 1,499, MAge = 46.74, SDAge= 12.91), we derive and compute six IIV metrics that invoke numeric and nominal measurement of the central tendency, dispersion, and asymmetry of individuals' stressor experiences and examine how these metrics, relative dominance, diversity, log-skew and mode, spread, order, are related to age and interindividual differences in negative affect. Results Results demonstrate the utility of the numeric and nominal categorical IIV metrics, with theoretically meaningful age gradients in the three numeric IIV stressor metrics and five of six IIV metrics mapping differences in negative affect. Discussion Findings highlight how the unique constructs measured by these six metrics of categorical IIV may be used to examine dynamic process, study interindividual and age-related differences, and expand the variety of developmental research questions that may be answered using categorical repeated measures data.
The Combined Use of Schizosaccharomyces pombe and Lachancea thermotolerans—Effect on the Anthocyanin Wine Composition

The most popular methodology to make red wine is through the combined use of Saccharomyces cerevisiae yeast and lactic acid bacteria, for alcoholic fermentation and malolactic fermentation respectively. This classic winemaking practice produces stable red wines from a microbiological point of view. This study aims to investigate a recent red winemaking biotechnology, which through the combined use of Lachancea thermotolerans and Schizosaccharomyces pombe is used as an alternative to the classic malolactic fermentation. In this new methodology, Schizosaccharomyces pombe totally consumes malic acid, while Lachancea thermotolerans produces lactic acid, avoiding excessive deacidification of musts with low acidity in warm viticulture areas such as Spain. This new methodology has been reported to be a positive alternative to malolactic fermentation in low acidity wines, since it has the advantage to produce wines with a more fruity flavor, less acetic acid, less ethyl carbamate originators and less biogenic amines than the traditional wines produced via conventional fermentation techniques. The study focuses on unexplored facts related to this novel biotechnology such as color and anthocyanin profile.
BDNF Activates mTOR to Regulate GluR1 Expression Required for Memory Formation

Background The mammalian target of Rapamycin (mTOR) kinase plays a key role in translational control of a subset of mRNAs through regulation of its initiation step. In neurons, mTOR is present at the synaptic region, where it modulates the activity-dependent expression of locally-translated proteins independently of mRNA synthesis. Indeed, mTOR is necessary for different forms of synaptic plasticity and long-term memory (LTM) formation. However, little is known about the time course of mTOR activation and the extracellular signals governing this process or the identity of the proteins whose translation is regulated by this kinase, during mnemonic processing. Methodology/Principal Findings Here we show that consolidation of inhibitory avoidance (IA) LTM entails mTOR activation in the dorsal hippocampus at the moment of and 3 h after training and is associated with a rapid and rapamycin-sensitive increase in AMPA receptor GluR1 subunit expression, which was also blocked by intra-hippocampal delivery of GluR1 antisense oligonucleotides (ASO). In addition, we found that pre- or post-training administration of function-blocking anti-BDNF antibodies into dorsal CA1 hampered IA LTM retention, abolished the learning-induced biphasic activation of mTOR and its readout, p70S6K and blocked GluR1 expression, indicating that BDNF is an upstream factor controlling mTOR signaling during fear-memory consolidation. Interestingly, BDNF ASO hindered LTM retention only when given into dorsal CA1 1 h after but not 2 h before training, suggesting that BDNF controls the biphasic requirement of mTOR during LTM consolidation through different mechanisms: an early one involving BDNF already available at the moment of training, and a late one, happening around 3 h post-training that needs de novo synthesis of this neurotrophin. Conclusions/Significance In conclusion, our findings demonstrate that: 1) mTOR-mediated mRNA translation is required for memory consolidation during at least two restricted time windows; 2) this kinase acts downstream BDNF in the hippocampus and; 3) it controls the increase of synaptic GluR1 necessary for memory consolidation.
Virological Surveillance of Influenza in Four Recent Post-Pandemic Seasons (2010/11 to 2013/14) in Bulgaria.

AIM Influenza virological surveillance is an essential tool for studying the evolution of influenza viruses as well as for annual updating of the vaccine composition. The aim of the present study is to analyse the circulation of the influenza viruses in Bulgaria during the four recent post-pandemic seasons. METHODS A total of 3,681 respiratory samples from patients with influenza like illness (ILI) or acute respiratory illness (ARI) were tested for influenza viruses using Real Time RT-PCR. RESULTS Influenza viruses were detected in 1,367 (37%) samples. Of those viruses, 941 (69%) were of type A and 426 (31%) of type B. Among the subtyped A viruses, 543 (60%) were A(H1N1)pdm09 and 369 (40%) A(H3N2). Co-circulation of all seasonal influenza types/subtypes was registered during each season, with the exception of A(H1N1)pdm09 virus in the 2011/12 season. In this study, data gathered from the antigenic and genetic analyses of influenza viruses, their antiviral susceptibility, and the epidemiological and clinical characteristics of the infections are presented. CONCLUSIONS Yearly variations in the distribution and frequency of influenza types/subtypes and an annual shift of the predominant type/subtype were observed. In the seasons with predominant spread of A(H1N1)pdm09 virus - 2010/11 and 2013/14, a greater number of influenza-related pneumonia cases, ICU admissions and fatal cases was registered (p<0.05). The results of the present study confirm the need for continuous and comprehensive influenza surveillance.
Memory Access Analysis of Many-core System with Abundant Bandwidth

Many-core system is main architecture trend currently. One of the dominating challenges for on-chip manycore system is the memory wall. However traditional research primarily focus on the limited bandwidth. To solve this problem, many-core system is aided with large cache, and a lot of complex approaches about memory and cache are adopted aiming at relaxing the pressure of bandwidth and improving the efficiency of cache. All these methods generate much cost of area and power. In this paper, we are motivated by the feature of abundant bandwidth and low latency of optical interconnect. We analyze the characteristics of memory access on 64 cores system under the case of high bandwidth which can be assumed to benefit from optical interconnect, considering the sensibility with bandwidth and cache for different benchmarks. Finally, we discuss about promising basic frameworks suitable for manycore system with optical interconnect.
Designing a Generic Research Data Infrastructure Architecture with Continuous Software Engineering

Long-living software systems undergo a continuous development including adaptions due to altering requirements or the addition of new features. This is an even greater challenge if neither all users nor requirements are known at an initial design phase. In such a context, complex restructuring activities are much more probable, if the challenges are not taken into account from the beginning. We introduce a combination of the concepts of domain-driven design and self-contained systems to meet these challenges within the system’s architecture design. We show the merits of this approach by designing an architecture for a generic research data infrastructure, a use case where the mentioned challenges can be found. Embedding this approach within continuous software engineering, allows to implement and integrate changes continuously, without neglecting other crucial properties such as maintainability and scalability.
Photoacoustic needle: minimally invasive guidance to biopsy

Abstract. We introduce a needle probe based on photoacoustics (PA) to extend the scope of optical needle methods in guiding biopsies. Pulsed light is coupled to an optical fiber in a needle to be inserted in tissue, and PA signals are detected using an ultrasound imager used for needle guidance. This PA needle samples large volumes and possesses an imaging component so that sites forward and off-axis of the fiber are surveyed. This allows navigation of those regions for optical characterization and direct biopsy in a subsequent step. The concept is explored on simple phantoms and biological specimens.
Software Application Profile: PHESANT: a tool for performing automated phenome scans in UK Biobank

Abstract Motivation Epidemiological cohorts typically contain a diverse set of phenotypes such that automation of phenome scans is non-trivial, because they require highly heterogeneous models. For this reason, phenome scans have to date tended to use a smaller homogeneous set of phenotypes that can be analysed in a consistent fashion. We present PHESANT (PHEnome Scan ANalysis Tool), a software package for performing comprehensive phenome scans in UK Biobank. General features PHESANT tests the association of a specified trait with all continuous, integer and categorical variables in UK Biobank, or a specified subset. PHESANT uses a novel rule-based algorithm to determine how to appropriately test each trait, then performs the analyses and produces plots and summary tables. Implementation The PHESANT phenome scan is implemented in R. PHESANT includes a novel Javascript D3.js visualization and accompanying Java code that converts the phenome scan results to the required JavaScript Object Notation (JSON) format. Availability PHESANT is available on GitHub at [https://github.com/MRCIEU/PHESANT]. Git tag v0.5 corresponds to the version presented here.