Miracle-dz/UniFAR-FTUs huggingface dataset:
Historic collections as a tool for assessing the global pollinator crisis

There is increasing concern about the decline of pollinators worldwide. However, despite reports that pollinator declines are widespread, data are scarce and often geographically and taxonomically biased. These biases limit robust inference about any potential pollinator crisis. Non-structured and opportunistic historical specimen collection data provide the only source of historical information which can serve as a baseline for identifying pollinator declines. Specimens historically collected and preserved in museums not only provide information on where and when species were collected, but also contain other ecological information such as species interactions and morphological traits. Here, we provide a synthesis of how researchers have used historical data to identify long-term changes in biodiversity, species abundances, morphology and pollination services. Despite recent advances, we show that information on the status and trends of most pollinators is absent, but we highlight opportunities and limitations to progress the assessment of pollinator declines globally. Finally, we demonstrate different approaches to analysing museum collection data using two contrasting case studies from distinct geographical regions (New Zealand and Spain) for which long-term pollinator declines have never been assessed. There is immense potential for museum specimens to play a central role in assessing the extent of the global pollination crisis.
Running title: Motor preparation affects ipsilateral TMS responses Title: Unilateral movement preparation causes task-specific modulation of TMS responses in the passive, opposite limb

Lilian Chye, Stephan Riek, Aymar de Rugy , Richard G. Carson, Timothy J. Carroll 1 Centre for Sensorimotor Performance, School of Human Movement and Nutrition Sciences, The University of Queensland, Australia 2 Institut de Neurosciences Cognitives et Intégratives d'Aquitaine, CNRS UMR 5287, Université de Bordeaux, France 3 Trinity College Institute of Neuroscience and School of Psychology, Trinity College Dublin, Ireland 4 School of Psychology, Queen's University Belfast, Northern Ireland, UK
Adding Trust to the Social Networking Sites:A Prominent Way of Content Filtering

This paper reviews about the internet filtering and content filtering techniques of the web pages that helps in removing particular types of encrypted data from that webpage. As soon as the social networking and the internet came into existence the transfer of various types of viruses and unauthorized data which is illegal in law have became a biggest threat to the industry. So, Saving our document from these types of unauthorized viruses and encrypted files is a major issue. Various organizations are working on it to prevent the free flow of these type of viruses from internet to our system and for that reason content filtering has gain importance in making our documentary files secure. This paper includes various types of filters, bases to select a filter and methods for filtering with the conclusion of the content filtering.
Model for breast cancer diversity and spatial heterogeneity

We present and analyze a growth model of an avascular tumor that considers the basic biological principles of proliferation, motility, death and genetic mutations of the cell. From a regulatory network analysis and an analysis of genomic data we identify two sets of genes-a set of six genes and a set of sixteen genes-that are believed to play an important role in the evolution of breast cancer. Considering that cancer cells shape the tissue microenvironment and niches to their competitive advantage, the model assumes that cancer and normal cells compete for essential nutrients and that the rate of the “driver” mutations depends on nutrient availability. To this end, we propose a coupling between the transport of nutrients and gene mutations dynamics. Gene mutation dynamics are modeled as a Yule-Furry Markovian process, while transport of nutrients is described with a system of reaction-diffusion equations. For each representative tumor we calculate its diversity, represented by the Shannon index, and its spatial heterogeneity, measured by its fractal dimension. These quantities are important in the clinical diagnosis of tumor malignancy. A tumor malignancy diagram, obtained by plotting diversity versus fractal dimension, is calculated for different values of a parameter β, which is related to the occurrence of driver mutations. It is found that when β < 1, tumors show greater diversity and more spatial heterogeneity as compared with β > 1. More importantly, it is found that the results and conclusions are similar when we use the six-gene set versus sixteen-gene set.
Mode effects in panel surveys: A comparison of CAPI and CATI *

In a methodological experiment, carried out within the framework of the Swiss Household Panel, two data collection strategies were evaluated: Computer Assisted Personal Interviews (CAPI) and Computer Assisted Telephone Interviews (CATI). The study was designed as a split-ballot in combination with repeated measurements. The participation rates in the two modes were similar and most answer distributions were the same in both modes. Moreover, it is shown that CATI saves costs and time in comparison with CAPI. Using a Multitrait-Multimethod design, estimates of reliability and validity were obtained for all data. Comparing these estimates, the conclusion must be that the choice of CATI versus CAPI has no implications for the quality of the data. Once the choice has been made, it does not make a very large difference either which type of response scale is used. What can really make a difference are the formulation and the topic of the question.
Using Community Visualization to Stimulate Participation in Online Communities

A motivational community visualization was designed to encourage users to participate more actively and to bring more contributions in an online community. The visualization is inspired by the theory of social comparison in social psychology. It evolved through two designs: a fixed and a customizable one for two different communities of students sharing papers – one of graduate students in a research lab and another one for students in an undergraduate class. The article discusses the features of the two communities, each of the two visualization designs, and their advantages and disadvantages.
Quantifying the risk of local Zika virus transmission in the continental US during the 2015-2016 ZIKV epidemic

Background Local mosquito-borne Zika virus (ZIKV) transmission has been reported in two counties of the continental United State (US), prompting the issuance of travel, prevention, and testing guidance across the continental US. Large uncertainty, however, surrounds the quantification of the actual risk of ZIKV introduction and autochthonous transmission across different areas of the US. Method We present a framework for the projection of ZIKV autochthonous transmission in the continental US during the 2015-2016 epidemic, using a data-driven stochastic and spatial epidemic model accounting for seasonal, environmental and detailed population data. The model generates an ensemble of travel-related case counts and simulate their potential to trigger local transmission at individual level. Results We estimate the risk of ZIKV introduction and local transmission at the county level and at the 0.025° x 0.025° cell level across the continental US. We provide a risk measure based on the probability of observing local transmission in a specific location during a ZIKV epidemic modeled after the one observed during the years 2015-2016. The high spatial and temporal resolutions of the model allow us to generate statistical estimates of the number of ZIKV introductions leading to local transmission in each location. We find that the risk is spatially heterogeneously distributed and concentrated in a few specific areas that account for less than 1% of the continental US population. Locations in Texas and Florida that have actually experienced local ZIKV transmission are among the places at highest risk according to our results. We also provide an analysis of the key determinants for local transmission, and identify the key introduction routes and their contributions to ZIKV spread in the continental US. Conclusions This framework provides quantitative risk estimates, fully captures the stochas-ticity of ZIKV introduction events, and is not biased by the under-ascertainment of cases due to asymptomatic infections. It provides general information on key risk determinants and data with potential uses in defining public health recommendations and guidance about ZIKV risk in the US.
The Evolution and Sequence Diversity of FhuA in Salmonella and Escherichia

The fhuACDB operon, present in a number of Enterobacteriaceae, encodes components essential for the uptake of ferric hydroxamate type siderophores. FhuA acts not only as transporter for physiologically important chelated ferric iron, but also as receptor for various bacteriophages, toxins and antibiotics, which are pathogenic to bacterial cells. In this research, the fhuA gene distribution and sequence diversity were investigated in Enterobacteriaceae, especially Salmonella and Escherichia. Comparative sequence analysis resulted in a fhuA phylogenetic tree that did not match the expected phylogeny based on housekeeping sequence analysis or trees of fhuCDB genes. The fhuA sequences showed a unique mosaic-clustering pattern. On the other hand, the gene sequences showed high conservation for strains from the same serovar or serotype. In total, six clusters were identified from FhuA proteins in Salmonella and Escherichia, among which typical peptide fragment variations could be defined. Six fragmental insertions / deletions and two substitution fragments were discovered, which could well classify the different clusters. Structure modeling demonstrated that all the six featured insertions/deletions and one substitution fragment are located at the apexes of the long loops of FhuA external pocket. These frequently mutated regions are likely under high selection pressure, and bacterial strains could have escaped from phage infection or toxin / antibiotics attack via fhuA gene mutations while maintaining the siderophore uptake activity essential for bacterial survival. The unusual fhuA clustering suggests that high frequency exchange of fhuA genes has occurred between enterobacterial strains after distinctive species were established. IMPORTANCE The enterobacterial fhuACDB operon encodes proteins which mediate the uptake of siderophores to supply the cells with iron essential for bacterial survival. Here we show different evolutionary patterns for the fhu genes within the same operon. The fhuA has a phylogenetic tree that does not match the species phylogeny, whereas the rest of the fhu genes do. The fhuA genes showed inter-species sequence convergence and conservation within specific serovars and serotypes. Nearly all of the significant sequence differences among FhuA clusters are located in potential ligand-binding sites on the extracellular surface of fhuA-encoding receptors. The unusual fhuA clustering suggests the frequent recombination and exchange of fhuA genes between enterobacterial strains in the evolutionary state after distinctive species were established. Our findings suggested either a new evolutionary mechanism or local gene recombination in fhuA that is in contrast to previous evolutionary hypotheses that have formed under the assumption of no recombination.
Precision Identification of Diverse Bloodstream Pathogens from the Gut Microbiome

Bloodstream infection is the most common infectious complication in hematopoietic cell transplantation recipients. To evaluate the genomic concordance of bloodstream pathogens and bacterial strains within the intestinal microbiome using whole genome sequencing, we developed StrainSifter, a bioinformatic pipeline to compare nucleotide variation between bacterial isolate strains and stool metagenomes. We applied StrainSifter to bloodstream isolates and stool metagenome samples from hematopoietic stem cell transplant recipients with bloodstream infections. StrainSifter is designed to identify single nucleotide variants between isolate and metagenomic short reads using stringent alignment, coverage, and variant frequency criteria for strain comparison. We identified enteric BSI isolates that were highly concordant with those in the gut microbiota, as well as highly concordant strains of typically non-enteric bacteria. These findings demonstrate the utility of StrainSifter in strain matching and provide a more precise investigation of the intestine as a reservoir of diverse pathogens capable of causing bloodstream infections.
Would an RRS by any other name sound as RAD?

Sampling markers throughout a genome with restriction enzymes emerged in the 2000s as reduced representation shotgun sequencing (RRS). Rapid advances in sequencing technology have since spurred modifications of RRS, giving rise to many derivatives with unique names, such as RADseq. But naming conventions have often been more creative than consistent, with unclear criteria for recognition as a unique method resulting in a proliferation of names characterized by ambiguity. We conducted a literature review to assess methodological and etymological relationships among 36 restriction enzyme-based methods, as well as rates of correct referencing of commonly-used methods. We identify several instances of methodological convergence or misattribution in the literature, and note that many published derivatives have modified only minor elements of parent protocols. We urge greater restraint in naming derivative methods, to strike a better balance between clarity, recognition of scientific innovation, and correct attribution.
Nesting the Neglected "R" A Design Study: Writing Instruction within a Prescriptive Literacy Program

Teaching writing has long been neglected as in schools. Findings from the National Assessment of Educational Progress (NAEP) indicated that most students have basic writing skills, but cannot write well enough to meet the needs of employers or for college. The writing programs in prescriptive literacy programs, which were adopted to ensure student achievement have not proven to be effective for developing proficient student writers. This design study is an attempt to provide teachers trained to teach in a prescriptive literacy program with the writing content and pedagogical knowledge necessary to engage elementary students in writing as a complex, intellectual activity so that they become proficient writers.From the literature on effective writing instruction and on teacher learning, I developed a theory of action to guide the design. A key feature of the design was to situate teacher learning in the context of a study group led by a facilitator with knowledge about writing instruction. The design emphasized teachers learning from writing themselves, reviewing student work, learning effective strategies and procedures of writing instruction, and developing knowledge through collaborative talk and reflections. Seven teachers, Grades 2 to 5, from a Title I urban school that required teachers follow the script of Open Court Reading (OCR) participated in the study. At the time of this study a window of opportunity had opened up to modify the OCR writing component.I framed teacher learning in two dimensions--Dimension 1: Instructional Strategies and Procedures, and Dimension 2: Writing as a Process. I investigated the impact of the design and the process of the design's development. Overall teachers' knowledge about writing content increased; their knowledge about writing pedagogy increased to a lesser degree; however their level of growth varied. Moreover growth in the elements of instructional strategies also varied. Growth ranged from 15% for teacher modeling writing and 109% for teacher referring to literature to teach writing strategies. Thus, I found the design basically sound but recommended modifications for future iterations.
Biased parasitoid sex ratios: Wolbachia, functional traits, local and landscape effects

Adult sex ratio (ASR) is a demographic key parameter, being essential for the survival and dynamics of a species populations. Biased ASR are adaptations to the environment on different scales, resulted by different mechanisms as inbreeding, mating behaviour, resource limitations, endosymbionts such as Wolbachia, and changes in density or spatial distribution. Parasitoid ASRs are also known to be strongly biased. But less information is available on large scale variable effects such as landscape composition or fragmentation. We aimed to study whether the landscape scale does affect the ASR of parasitoids belonging to the same tritrophic gall inducer community. We examined effects of characteristics on different scales as functional trait, local and landscape scale environment on parasitoid ASR. On species level ovipositor length, on local scale resource amount and density, while on landscape scale habitat amount, land use and landscape history were the examined explanatory variables. We controlled for the incidence and prevalence of Wolbachia infections. Parasitoid ASR is best explained by ovipositor length: with which increase ASR also increases; and available resource amount: with the gall diameter increase ASR decreases. On large scale the interaction of functional traits with habitat size also explained significantly the parasitoid ASRs. Our results support the hypothesis that large scale environmental characteristics affect parasitoid ASRs besides intrinsic and local characteristics.
Early candidate urine biomarkers for detecting Alzheimer’s disease before beta amyloid plaque deposition in an APP (swe)/PSEN1dE9 transgenic mouse model

Alzheimer’s disease (AD) is an incurable age-associated neurodegenerative disorder that is characterized by irreversible progressive cognitive deficits and extensive brain damage. The identification of candidate biomarkers before beta amyloid plaque deposition occurs is therefore of great importance for the early intervention of AD. Urine, which is not regulated by homeostatic mechanisms, theoretically accumulates changes associated with AD earlier than cerebrospinal fluid and blood. In this study, an APP (swe)/PSEN1dE9 transgenic mouse model was used to identify candidate biomarkers for early AD. Urine samples were collected from 4-, 6-, and 8-month-old transgenic mouse models, and the urinary proteomes were profiled using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). The levels of 33 proteins differed significantly between wild-type and 4-month-old mice, which had not started to deposit beta amyloid plaque. Among these proteins, 16 have been associated with the mechanisms of AD, while 9 have been suggested as AD biomarkers. Our results indicated that urine proteins enable detecting AD before beta amyloid plaque deposition, which may present an opportunity for intervention.
Development and Integration of a Navigation Component into an Automotive Embedded System

The purpose of this Master Thesis is the development of an car navigation software and its integration into an automotive embedded framework. The navigation software supports the planning of optimal routes from a starting position to the destination. Once a route has been calculated, it is possible to execute it in a demo mode. The software uses a digital road map for calculating routes. First, the structure of the digital road map is introduces. Afterwards the algorithm for route planning is presented. Then we focus on how the navigation software is implemented an integrated into the existing framework.
Machine-vision-based Defect Detection Using Circular Hough Transform in Laser Welding

In the field of laser welding, image processing technology is the general method to detect defects on the surface of the seam. Here the Hough Transform is introduced into the defect detection and the accuracy is greatly improved. The process is to use the industrial CCD(Chargecoupled Device) camera for image acquisition, then use Canny operator for edge detection, use Circular Hough Transform to locate the weld seam position, and finally compare the number of continuous pixels with the defect criteria to report detection results. Experimental data show that the false positive rate and false negative rate are greatly reduced after the Hough Transform is introduced into the defect detection, which has met the industrial requirements.
University of Birmingham Mobile-genetic-element-encoded hypertolerance to copper protects Staphylococcus aureus from killing by host phagocytes

Pathogens are exposed to toxic levels of copper during infection, and copper tolerance may be a general virulence mechanism used by bacteria to resist host defenses. In support of this, inactivation of copper exporter genes has been found to reduce the virulence of bacterial pathogens in vivo. Here we investigate the role of copper hypertolerance in methicillin-resistant Staphylococcus aureus (MRSA). We show that a copper hypertolerance operon (copB-mco), carried on a mobile genetic element (MGE), is prevalent in a collection of invasive S. aureus strains and more widely among clonal complex 22, 30, and 398 strains. The copB and mco genes encode a copper efflux pump and a multicopper oxidase, respectively. Isogenic mutants lacking copB or mco had impaired growth in subinhibitory concentrations of copper. Transfer of a copB-mco-carrying plasmid to a naive clinical isolate resulted in a gain of copper hypertolerance and enhanced bacterial survival inside primed macrophages. The copB and mco genes were upregulated within infected macrophages, and their expression was dependent on the copper-sensitive operon repressor CsoR. Isogenic copB and mco mutants were impaired in their ability to persist intracellularly in macrophages and were less resistant to phagocytic killing in human blood than the parent strain. The importance of copper-regulated genes in resistance to phagocytic killing was further elaborated using mutants expressing a copper-insensitive variant of CsoR. Our findings suggest that the gain of mobile genetic elements carrying copper hypertolerance genes contributes to the evolution of virulent strains of S. aureus that are better equipped to resist killing by host immune
Agent-Based Planning at the CTS Analysis and Simulation

Patient scheduling in hospitals is a complex task. Hospitals have a distributed organization and the treatment process is dynamic. In this thesis we focus on the planning of the Cardio-Thoracic Surgery patient processes from the Catharina Ziekenhuis Eindhoven. In our research, we denote two variants of the patient path, namely regular heart surgery and a short-track version of regular heart surgery. Furthermore, simulation is used to evaluate the patient planning in terms of throughput of patients. We do this from a distributed perspective, using a agent-based approach called ABOCSS. In ABOCSS, each postoperative care level is modeled as autonomous agents with their own goals. This reflects the decentralized structure in hospitals. The goal of the multi-agent system is to schedule patients through the surgery and postoperative care as quickly as possible. To reach this goal, the agents negotiate with each other. Finally, we examine the results of experiments with ABOCSS.
An Effective Approach for Cyberbullying Detection

The rapid growth of social networking is supplementing the progression of cyberbullying activities. Most of the individuals involved in these activities belong to the younger generations, especially teenagers, who in the worst scenario are at more risk of suicidal attempts. We propose an effective approach to detect cyberbullying messages from social media through a weighting scheme of feature selection. We present a graph model to extract the cyberbullying network, which is used to identify the most active cyberbullying predators and victims through ranking algorithms. The experiments show effectiveness of our approach. KeywordsSocial Networks; Cyberbullying; Text-Mining; Link Analysis