Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogeny and Biogeography of Cyanobacteria and Their Produced Toxins

Phylogeny is an evolutionary reconstruction of the past relationships of DNA or protein sequences and it can further be used as a tool to assess population structuring, genetic diversity and biogeographic patterns. In the microbial world, the concept that everything is everywhere is widely accepted. However, it is much debated whether microbes are easily dispersed globally or whether they, like many macro-organisms, have historical biogeographies. Biogeography can be defined as the science that documents the spatial and temporal distribution of a given taxa in the environment at local, regional and continental scales. Speciation, extinction and dispersal are proposed to explain the generation of biogeographic patterns. Cyanobacteria are a diverse group of microorganisms that inhabit a wide range of ecological niches and are well known for their toxic secondary metabolite production. Knowledge of the evolution and dispersal of these microorganisms is still limited, and further research to understand such topics is imperative. Here, we provide a compilation of the most relevant information regarding these issues to better understand the present state of the art as a platform for future studies, and we highlight examples of both phylogenetic and biogeographic studies in non-symbiotic cyanobacteria and cyanotoxins.
RPAP3 interacts with Reptin to regulate UV‐induced phosphorylation of H2AX and DNA damage

We have previously reported that Monad, a novel WD40 repeat protein, potentiates apoptosis induced by tumor necrosis factor‐α and cycloheximide. By affinity purification and mass spectrometry, RNA polymerase II‐associated protein 3 (RPAP3) was identified as a Monad binding protein and may function with Monad as a novel modulator of apoptosis pathways. Here we report that Reptin, a highly conserved AAA + ATPase that is part of various chromatin‐remodeling complexes, is also involved in the association of RPAP3 by immunoprecipitation and confocal microscopic analysis. Overexpression of RPAP3 induced HEK293 cells to death after UV‐irradiation. Loss of RPAP3 by RNAi improved HeLa cell survival after UV‐induced DNA damage and attenuated the phosphorylation of H2AX. Depletion of Reptin reduced cell survival and facilitated the phosphorylation on H2AX. These results suggest that RPAP3 modulates UV‐induced DNA damage by regulating H2AX phosphorylation. J. Cell. Biochem. 106: 920–928, 2009. © 2009 Wiley‐Liss, Inc.
Online Anomaly Detection for Service-Oriented Components in OSGi-based Applications

OSGi has become one of the most promising frameworks for managingservice-oriented and component-based applications. The OSGi-based service-oriented components delivered by different vendors are usually black-box program units which lack source code and design documents. Thus, it is difficult to evaluate their quality by s tatic code analysis, and the defective components may lead to the failure of the whole system eventually. In this paper, we propose an online method for detecting anomalous service-oriented components in OSGi-based applications. A thread-tracing method is presented to monitor resource utilization and interactions between components. The method considers both the dynamic service invocation and static method invocation. Furthermore, according to the monitored data, we detect anomalous components by control charts, which can detect the anomalous trend of resource utilization without prior knowledge. A prototype tool was implemented and applied to a real application server. The experimental results show that our method 1) is of high accuracy for monitoring resource utilization in component perspective; 2) does not introduce significant overhead; 3) and can detect anomalous components effectively.
Maternal and Paternal Perception of Child Vulnerability and Behaviour Problems in Very Preterm Born Children

Preterm born children have more behaviour problems than term born children. Perinatal risks, current child functioning, sociodemographic characteristics, parental psychological distress and parental perceptions of child vulnerability (PCV) have been shown to be risk factors for behaviour problems. However, the role of maternal and paternal PCV is unclear, as these have not been investigated as a risk factor for behaviour problems, with all other risk factors taken into account. Aim of this study is to investigate whether maternal and paternal PCV are independent risk factors for behaviour problems in very preterm (VP) and term born children. The present study is a single centre prospective cohort study. Preterm children (n = 104), born at <30 weeks' gestation and/or birth weight <1000 g, and term children (n = 95) were assessed at age 5. Results showed that risk factors for parent-rated behaviour problems were low/middle parental education, VP birth, parental stress and, in VP children, maternal PCV. Risk factors for teacher-rated behaviour problems were low/middle parental education, foreign parental country of birth, intrauterine growth restriction and objective child vulnerabilities. It can be concluded that maternal PCV is a risk factor for parent-rated behaviour problems in VP children. When VP children are presented with behavioural problems, clinicians ought to be aware of the possibility that parents might still perceive their child as vulnerable. The neonatal history of the child, the way parents experienced that period, their perceptions of the child and possible consequences of these perceptions could be subjects for conversation during visits at follow-up clinics. Copyright © 2015 John Wiley & Sons, Ltd.
Big Five personality traits as predictors of the academic success of university and college students in early childhood education

Academic success in early childhood teacher education is important because it provides a foundation for occupational development in terms of professional competence, the quality of educational practices, as well as career success. Consequently, identifying factors that can explain differences in academic success is an important research task. Previous research has indicated that the Big Five personality traits can predict academic success in tertiary education even when other predictors have been accounted for. However, there is a lack of research regarding students in early childhood education. Therefore, this study investigated the effects of the Big Five on the academic success of college and university students in Germany who were studying early childhood education. Data from 567 college students and 270 university students were used. Several socio-demographic variables and the school-leaving Grade Point Average (GPA) served as controls. As hypothesised, students with higher conscientiousness also had better college and university GPAs. Furthermore, higher conscientiousness was associated with higher study satisfaction but only for college students. Unexpectedly, neuroticism was not negatively related to study satisfaction. In addition, there were exploratory findings concerning the effects of agreeableness, extraversion, neuroticism and openness. The findings are discussed with respect to implications for research and practice. In particular, the consequences with regard to the preparation of students in early childhood education are discussed.
Acoustic Cues to Speech Segmentation in Spoken French: Native and Non-native Strategies

In spoken French, the phonological processes of liaison and resyllabification can render word and syllable boundaries ambiguous. In the case of liaison, for example, the final /n/ of the masculine indefinite article un [œ] is latent in isolation or before word beginning with a consonant (un stylo [œ.sti.lo] 'a pen'); however, when followed by a vowel-initial word the /n/ surfaces and is resyllabified as the onset of that word (un ami [œ.na.mi] 'a pen'). Thus, the phrases un air 'a melody' and un nerf 'a nerve' are produced with identical phonemic content and syllable boundaries [œ. nɛʁ]. Some research has suggested that speakers of French give listeners acoustic cues to word boundaries by varying the duration of consonants that surface in liaison environments relative to consonant produced word-initially. Production studies (e.g. Wauquier-Gravelines 1996; Spinelli et al. 2003) have demonstrated that liaison consonants (e.g. /n/ in un air) are significantly shorter than the same consonant in initial position (e.g. /n/ in un nerf). Studies on the perception of spoken French have suggested that listeners exploit these durational differences in the segmentation of running speech (e.g. Gaskell et al. 2002; Spinelli et al. 2003), though no study to date has tested this hypothesis directly. The current study employs a direct test of the exploitation of duration as a segmentation cue by manipulating this single acoustic factor while holding all other factors in the signal constant. Thirty-six native speakers of French and 54 adult learners of French as a second language (L2) were tested on both an AX discrimination task and a forced-choice identification task which employed stimuli in which the durations of pivotal consonants (e.g. /n/ in [œ.nɛʁ]) were instrumentally shortened and lengthened. The results suggest that duration alone can indeed modulate the lexical interpretation of ambiguous sequences in spoken French. Shortened stimuli elicited a significantly larger proportion of vowel-initial (liaison) responses, while lengthened stimuli elicited a significantly larger proportion of consonant-initial responses, indicating that both native and (advanced) non-native speakers are indeed sensitive to this acoustic cue. These results add to a growing body of work demonstrating that listeners use extremely fined-grained acoustic detail to modulate lexical access (e.g. Salverda et al. 2003; Shatzman & McQueen 2006). In addition, the current results have manifest ramifications for study of the upper limits of L2 acquisition and the plasticity of the adult perceptual system in that several advanced learners of French showed evidence nativelike perceptual sensitivity to non-contrastive phonological variation.
Implementing homeostatic plasticity in VLSI networks of spiking neurons

Homeostatic plasticity acts to stabilize firing activity in neural systems, ensuring a homogeneous computational substrate despite the inherent differences among neurons and their continuous change. These types of mechanisms are extremely relevant for any physical implementation of neural systems. They can be used in VLSI pulse-based neural networks to automatically adapt to chronic input changes, device mismatch, as well as slow systematic changes in the circuitpsilas functionality (e.g. due to temperature drifts). In this paper we propose analog circuits for implementing homeostatic plasticity mechanisms in VLSI spiking neural networks, compatible with local spike-based learning mechanisms. We show experimental results where a homeostatic control is implemented as a hybrid SoftWare/HardWare (SW/HW) solution, and present analog circuits for a complete on-chip stand-alone solution, validated by circuit simulations.
Changing Use of Surgical Antibiotic Prophylaxis in Thika Hospital, Kenya: A Quality Improvement Intervention with an Interrupted Time Series Design

Introduction In low-income countries, Surgical Site Infection (SSI) is a common form of hospital-acquired infection. Antibiotic prophylaxis is an effective method of preventing these infections, if given immediately before the start of surgery. Although several studies in Africa have compared pre-operative versus post-operative prophylaxis, there are no studies describing the implementation of policies to improve prescribing of surgical antibiotic prophylaxis in African hospitals. Methods We conducted SSI surveillance at a typical Government hospital in Kenya over a 16 month period between August 2010 and December 2011, using standard definitions of SSI and the extent of contamination of surgical wounds. As an intervention, we developed a hospital policy that advised pre-operative antibiotic prophylaxis and discouraged extended post-operative antibiotics use. We measured process, outcome and balancing effects of this intervention in using an interrupted time series design. Results From a starting point of near-exclusive post-operative antibiotic use, after policy introduction in February 2011 there was rapid adoption of the use of pre-operative antibiotic prophylaxis (60% of operations at 1 week; 98% at 6 weeks) and a substantial decrease in the use of post-operative antibiotics (40% of operations at 1 week; 10% at 6 weeks) in Clean and Clean-Contaminated surgery. There was no immediate step-change in risk of SSI, but overall, there appeared to be a moderate reduction in the risk of superficial SSI across all levels of wound contamination. There were marked reductions in the costs associated with antibiotic use, the number of intravenous injections performed and nursing time spent administering these. Conclusion Implementation of a locally developed policy regarding surgical antibiotic prophylaxis is an achievable quality improvement target for hospitals in low-income countries, and can lead to substantial benefits for individual patients and the institution.
Eğitim Fakültesinde Görevli Öğretim Elemanlarının Yapılandırmacı Öğretmen Algıları

This study was carried out to explore the perceptions that academicians working at faculties of education in Turkey have regarding ‘constructivist teacher’. The participants of this phenomenological study included 323 academicians at 71 Faculties of Education in the spring of the 2013-2014 academic year. In the study, purposive sampling method was used among the sampling methods. Academicians completed the sentence “Constructivist teacher is like . because . ” and the data gathered is analyzed with qualitative method. The results indicated that academicians produced 94 different metaphors regarding the constructivist teacher. These metaphors are categorized into 14 conceptual categories with regard to their common features. The metaphors indicated by all academicians and mostly-indicated ones are the following: Guide, master, maestro, director, architect, artist and democratic leader
Behavioral Bias within the Decision Making Process

Behavioral finance studies how subjective behavioral elements introduce distortions in the individual’s decision-making process. The empirical study of systematic errors in cognitive reasoning and perception, and ultimately what these errors reveal about the individual’s underlying thought processes, is often referred to as investor heuristics and biases. This paper investigates the cognitive biases and heuristics to which business students are subject. This was achieved by administering a questionnaire and collecting empirical evidence about both undergraduate and graduate business students’ own perceptions of bias. The psychological phenomenon known as bias and its presence in human decision making, both financial and nonfinancial will provide additional insight on the subject of investor irrationality and broaden the ideals of rationality assumed in classical financial theory.
The Role of Production Frequency in the Sharing of Simian Immunodeficiency Virus-Specific CD8+ TCRs between Macaques1

In some epitope-specific responses, T cells bearing identical TCRs occur in many MHC-matched individuals. The sharing of public TCRs is unexpected, given the enormous potential diversity of the TCR repertoire. We have previously studied the sharing of TCR β-chains in the CD8+ T cell responses to two influenza epitopes in mice. Analysis of these TCRβ repertoires suggests that, even with unbiased V(D)J recombination mechanisms, some TCRβs can be produced more frequently than others, by a process of convergent recombination. The TCRβ production frequency was shown to be a good predictor of the observed sharing of epitope-specific TCRβs between mice. However, this study was limited to immune responses in an inbred population. In this study, we investigated TCRβ sharing in CD8+ T cell responses specific for the immunodominant Mamu-A*01-restricted Tat-SL8/TL8 and Gag-CM9 epitopes of SIV in rhesus macaques. Multiple data sets were used, comprising a total of ∼6000 TCRβs sampled from 20 macaques. We observed a spectrum in the number of macaques sharing epitope-specific TCRβs in this outbred population. This spectrum of TCRβ sharing was negatively correlated with the minimum number of nucleotide additions required to produce the sequences and strongly positively correlated with the number of observed nucleotide sequences encoding the amino acid sequences. We also found that TCRβ sharing was correlated with the number of times, and the variety of different ways, the sequences were produced in silico via random gene recombination. Thus, convergent recombination is a major determinant of the extent of TCRβ sharing.
Capturing Flexibility of Information Technology Infrastructure: A Study of Resource Characteristics and their Measure

Abstract:Information technology (IT) infrastructure has been identified in recent years in some businesses as having a critical impact on the firm’s ability to use IT competitively. Although a flexible infrastructure is considered highly valuable under certain circumstances, it is difficult to plan and to measure because there is no common, operational definition. This paper addresses the problem at two levels. First, it presents and explores various efforts to define or describe infrastructure flexibility in the literature. It identifies basic components of IT infrastructure and previously proposed characteristics of flexibility. The discussion considers concepts of IT resource management, including technological architecture, alignment of planning, and human resource skills, all of which have also been linked to definitions of infrastructure flexibility. Second, the paper explores how the concept of infrastructure flexibility is viewed among IT executives. The characteristics of infrastructure may vary .
Simultaneous Semi-Coupled Dictionary Learning for Matching RGBD Data

Matching with hidden information which is available only during training and not during testing has recently become an important research problem. Matching data from two different modalities, known as cross-modal matching is another challenging problem due to the large variations in the data coming from different modalities. Often, these are treated as two independent problems. But for applications like matching RGBD data, when only one modality is available during testing, it can reduce to either of the two problems. In this work, we propose a framework which can handle both these scenarios seamlessly with applications to matching RGBD data of Lambertian objects. The proposed approach jointly uses the RGB and depth data to learn an illumination invariant canonical version of the objects. Dictionaries are learnt for the RGB, depth and the canonical data, such that the transformed sparse coefficients of the RGB and the depth data is equal to that of the canonical data. Given RGB or depth data, their sparse coefficients corresponding to their canonical version is computed which can be directly used for matching using a Mahalanobis metric. Extensive experiments on three datasets, EURECOM, VAP RGB-D-T and Texas 3D Face Recognition database show the effectiveness of the proposed framework.
High gene flow on a continental scale in the polyandrous Kentish plover Charadrius alexandrinus

Gene flow promotes genetic homogeneity of species in time and space. Gene flow can be modulated by sex‐biased dispersal that links population genetics to mating systems. We investigated the phylogeography of the widely distributed Kentish plover Charadrius alexandrinus. This small shorebird has a large breeding range spanning from Western Europe to Japan and exhibits an unusually flexible mating system with high female breeding dispersal. We analysed genetic structure and gene flow using a 427‐bp fragment of the mitochondrial (mtDNA) control region, 21 autosomal microsatellite markers and a Z microsatellite marker in 397 unrelated individuals from 21 locations. We found no structure or isolation‐by‐distance over the continental range. However, island populations had low genetic diversity and were moderately differentiated from mainland locations. Genetic differentiation based on autosomal markers was positively correlated with distance between mainland and each island. Comparisons of uniparentally and biparentally inherited markers were consistent with female‐biased gene flow. Maternally inherited mtDNA was less structured, whereas the Z‐chromosomal marker was more structured than autosomal microsatellites. Adult males were more related than females within genetic clusters. Taken together, our results suggest a prominent role for polyandrous females in maintaining genetic homogeneity across large geographic distances.
Staying Relevant and Current with Online Learning in an Increasingly Global and Competitive Environment

This paper outlines the success of online learning in the workplace with corporate partners through Open Universities Australia (OUA). OUA is recognized as the national leader in online higher education in Australia with over 200,000 students studying with OUA since 1993. The corporate program helps employees formalize or extend their current skills, reach the next level in their organization or pursue relevant interests through tertiary studies. The business sector sees OUA as a highly attractive solution to fostering a culture of professional development, engagement and inclusiveness.
Transcriptome Sequencing of the Blind Subterranean Mole Rat, Spalax galili: Utility and Potential for the Discovery of Novel Evolutionary Patterns

The blind subterranean mole rat (Spalax ehrenbergi superspecies) is a model animal for survival under extreme environments due to its ability to live in underground habitats under severe hypoxic stress and darkness. Here we report the transcriptome sequencing of Spalax galili, a chromosomal type of S. ehrenbergi. cDNA pools from muscle and brain tissues isolated from animals exposed to hypoxic and normoxic conditions were sequenced using Sanger, GS FLX, and GS FLX Titanium technologies. Assembly of the sequences yielded over 51,000 isotigs with homology to ∼12,000 mouse, rat or human genes. Based on these results, it was possible to detect large numbers of splice variants, SNPs, and novel transcribed regions. In addition, multiple differential expression patterns were detected between tissues and treatments. The results presented here will serve as a valuable resource for future studies aimed at identifying genes and gene regions evolved during the adaptive radiation associated with underground life of the blind mole rat.