Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Diversity of Arginine Catabolic Mobile Element in Staphylococcus epidermidis

Background The methicillin-resistant Staphylococcus aureus clone USA300 contains a novel mobile genetic element, arginine catabolic mobile element (ACME), that contributes to its enhanced capacity to grow and survive within the host. Although ACME appears to have been transferred into USA300 from S. epidermidis, the genetic diversity of ACME in the latter species remains poorly characterized. Methodology/Principal Findings To assess the prevalence and genetic diversity of ACME, 127 geographically diverse S. epidermidis isolates representing 86 different multilocus sequence types (STs) were characterized. ACME was found in 51% (65/127) of S. epidermidis isolates. The vast majority (57/65) of ACME-containing isolates belonged to the predominant S. epidermidis clonal complex CC2. ACME was often found in association with different allotypes of staphylococcal chromosome cassette mec (SCCmec) which also encodes the recombinase function that facilities mobilization ACME from the S. epidermidis chromosome. Restriction fragment length polymorphism, PCR scanning and DNA sequencing allowed for identification of 39 distinct ACME genetic variants that differ from one another in gene content, thereby revealing a hitherto uncharacterized genetic diversity within ACME. All but one ACME variants were represented by a single S. epidermidis isolate; the singular variant, termed ACME-I.02, was found in 27 isolates, all of which belonged to the CC2 lineage. An evolutionary model constructed based on the eBURST algorithm revealed that ACME-I.02 was acquired at least on 15 different occasions by strains belonging to the CC2 lineage. Conclusions/Significance ACME-I.02 in diverse S. epidermidis isolates were nearly identical in sequence to the prototypical ACME found in USA300 MRSA clone, providing further evidence for the interspecies transfer of ACME from S. epidermidis into USA300.
Multi-objective optimization for a reliable localization scheme in wireless sensor networks

In many wireless sensor network (WSN) applications, the information transmitted by an individual entity or node is of limited use without the knowledge of its location. Research in node localization is mostly geared towards multi-hop range-free localization algorithms to achieve accuracy by minimizing localization errors between the node's actual and estimated position. The existing localization algorithms are focused on improving localization accuracy without considering efficiency in terms of energy costs and algorithm convergence time. In this work, we show that our proposed localization scheme, called DV-maxHop, can achieve good accuracy and efficiency. We formulate the multi-objective optimization functions to minimize localization errors as well as the number of transmission during localization phase. We evaluate the performance of our scheme using extensive simulation on several anisotropic and isotropic topologies. Our scheme can achieve dual objective of accuracy and efficiency for various scenarios. Furthermore, the recently proposed algorithms require random uniform distribution of anchors. We also utilized our proposed scheme to compare and study some practical anchor distribution schemes.
CONTROLLERS DEPENDABILITY VERIFICATION USING A PLANT MODEL

This paper focuses on usefulness of a plant model for model-checking of untimed properties of logic controllers. Verification results obtained on a case study by using the symbolic model-checker NuSMV and three methods: verification of the only controller, constraints-based verification, in which the plant is simply modeled as a set of physical constraints, and model-based verification, that relies on a detailed model of the plant, are presented. The results yielded by these approaches enable to draw up application rules for formal verification of logic controllers.
Evaluation of Three Algorithms for the Segmentation of Overlapping Cervical Cells

In this paper, we introduce and evaluate the systems submitted to the first Overlapping Cervical Cytology Image Segmentation Challenge, held in conjunction with the IEEE International Symposium on Biomedical Imaging 2014. This challenge was organized to encourage the development and benchmarking of techniques capable of segmenting individual cells from overlapping cellular clumps in cervical cytology images, which is a prerequisite for the development of the next generation of computer-aided diagnosis systems for cervical cancer. In particular, these automated systems must detect and accurately segment both the nucleus and cytoplasm of each cell, even when they are clumped together and, hence, partially occluded. However, this is an unsolved problem due to the poor contrast of cytoplasm boundaries, the large variation in size and shape of cells, and the presence of debris and the large degree of cellular overlap. The challenge initially utilized a database of <inline-formula><tex-math notation="LaTeX">$16$</tex-math></inline-formula> high-resolution (<inline-formula><tex-math notation="LaTeX">$\times$</tex-math></inline-formula>40 magnification) images of complex cellular fields of view, in which the isolated real cells were used to construct a database of <inline-formula><tex-math notation="LaTeX">$945$</tex-math></inline-formula> cervical cytology images synthesized with a varying number of cells and degree of overlap, in order to provide full access of the segmentation ground truth. These synthetic images were used to provide a reliable and comprehensive framework for quantitative evaluation on this segmentation problem. Results from the submitted methods demonstrate that all the methods are effective in the segmentation of clumps containing at most three cells, with overlap coefficients up to 0.3. This highlights the intrinsic difficulty of this challenge and provides motivation for significant future improvement.
Adolescent Reading Improvement: A Phenomenology of High School Students’ Perspectives

The purpose of this phenomenological study was to explore the experience of improvement in reading comprehension of adolescent readers who have made gains greater than what might be predicted based on previous growth in reading comprehension measures. These research questions guided this study: What influences have impacted the lived experiences of these improving readers? What barriers to reading improvement existed for these students? In addition, what school-related reading experiences, if any, hold meaning for these readers? What characteristics are shared among adolescent readers who have experienced better-than-expected growth? Interviews, story chart artifacts created by participants, and observations of students’ process and self-talk while reading short passages were collected from 12 students at Placid High School (pseudonym). Analysis was conducted using Hycner’s framework and hermeneutic analysis in order to discover the essence of these students’ experiences as improving readers. Methodologically, this study ascertained shared characteristics and experiences that influenced the reading comprehension growth of these adolescents through inductive study of all data. Four themes emerged through the data analysis: Reading as Provocation, Reading as Displacement, Reading as Relationship, and Reading as Confluence.
A Viterbi decoder

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The effect of propagule size on the invasion of an alien insect

1. The movement of species from their native ranges to alien environments is a serious threat to biological diversity. The number of individuals involved in an invasion provides a strong theoretical basis for determining the likelihood of establishment of an alien species. 2. Here a field experiment was used to manipulate the critical first stages of the invasion of an alien insect, a psyllid weed biocontrol agent, Arytainilla spartiophila Forster, in New Zealand and to observe the progress of the invasion over the following 6 years. 3. Fifty-five releases were made along a linear transect 135 km long: 10 releases of two, four, 10, 30 and 90 psyllids and five releases of 270 psyllids. Six years after their original release, psyllids were present in 22 of the 55 release sites. Analysis by logistic regression showed that the probability of establishment was significantly and positively related to initial release size, but that this effect was important only during the psyllids' first year in the field. 4. Although less likely to establish, some of the releases of two and four psyllids did survive 5 years in the field. Overall, releases that survived their first year had a 96% chance of surviving thereafter, providing the release site remained secure. The probability of colony loss due to site destruction remained the same throughout the experiment, whereas the probability of natural extinction reduced steeply over time. 5. During the first year colonies were undergoing a process of establishment and, in most cases, population size decreased. After this first year, a period of exponential growth ensued. 6. A lag period was observed before the populations increased dramatically in size. This was thought to be due to inherent lags caused by the nature of population growth, which causes the smaller releases to appear to have a longer lag period.
Dispositional and Situational Emotion Regulation in Younger and Older Adults

Younger and older adults (N = 207) viewed a film scene eliciting strong negative emotions and then indicated how they had regulated their emotions. Dispositional emotion regulation was measured prior to stimulus presentation. Older adults showed higher levels of dispositional suppression than younger adults. Furthermore, individual differences in dispositional expressive suppression were predictive of reappraisal and suppression in the given situation. However, dispositional suppression was more strongly related to situational suppression among older adults than among younger adults. Future directions concerning the importance of and possible implications for age differences in coping with stressful situations are discussed.
Major Chromosomal Rearrangements Distinguish Willow and Poplar After the Ancestral “Salicoid” Genome Duplication

Populus (poplar) and Salix (willow) are sister genera in the Salicaceae family. In both lineages extant species are predominantly diploid. Genome analysis previously revealed that the two lineages originated from a common tetraploid ancestor. In this study, we conducted a syntenic comparison of the corresponding 19 chromosome members of the poplar and willow genomes. Our observations revealed that almost every chromosomal segment had a parallel paralogous segment elsewhere in the genomes, and the two lineages shared a similar syntenic pinwheel pattern for most of the chromosomes, which indicated that the two lineages diverged after the genome reorganization in the common progenitor. The pinwheel patterns showed distinct differences for two chromosome pairs in each lineage. Further analysis detected two major interchromosomal rearrangements that distinguished the karyotypes of willow and poplar. Chromosome I of willow was a conjunction of poplar chromosome XVI and the lower portion of poplar chromosome I, whereas willow chromosome XVI corresponded to the upper portion of poplar chromosome I. Scientists have suggested that Populus is evolutionarily more primitive than Salix. Therefore, we propose that, after the “salicoid” duplication event, fission and fusion of the ancestral chromosomes first give rise to the diploid progenitor of extant Populus species. During the evolutionary process, fission and fusion of poplar chromosomes I and XVI subsequently give rise to the progenitor of extant Salix species. This study contributes to an improved understanding of genome divergence after ancient genome duplication in closely related lineages of higher plants.
Best Practices in Teaching International Students in Higher Education: Issues and Strategies

Regardless of their level of academic preparedness, international students face distinct challenges that arise from language issues as well as ones of a personal and social nature, all of which can lead to frustration and failure (Bossio & Bylyna, 2006b). This article discusses an online survey carried out in a Canadian college that identified academic and sociocultural issues faced by international students and highlighted current or potential strategies from the input of 229 international students, 343 domestic students, and 125 professors. Findings reveal that counterproductive behavior may obstruct academic achievement and communication, and there is evidence of disagreement about international students’ academic strengths. A disconnect between participants was also found regarding academic expectations. Moreover, findings reveal that English language abilities are not the sole hindrance to academic success. Responses highlight the need for, and list steps toward, a more proactive and continual pedagogical evolution for faculty and postsecondary institutions to enhance the academic experience and success of international students.
'Good' Organisational Reasons for 'Bad' Software Testing: An Ethnographic Study of Testing in a Small Software Company

In this paper we report on an ethnographic study of a small software house to discuss the practical work of software testing. Through use of two rich descriptions, we discuss that 'rigour' in systems integration testing necessarily has to be organisationally defined. Getting requirements 'right', defining 'good' test scenarios and ensuring 'proper' test coverage are activities that need to be pragmatically achieved taking account of organisational realities and constraints such as: the dynamics of customer relationships; using limited effort in an effective way; timing software releases; and creating a market. We discuss how these organisational realities shape (1) requirements testing; (2) test coverage; (3) test automation; and (4) test scenario design.
Borderline over-sampling for imbalanced data classification

Traditional classification algorithms usually provide poor accuracy on the prediction of the minority class of imbalanced data sets. This paper proposes a new method for dealing with imbalanced data sets by over-sampling the borderline minority class instances. A Support Vector Machine (SVM) classifier is then trained to predict future instances. Compared with other over-sampling methods, the proposed method focuses only on the minority class instances residing along the decision boundary, due to the fact that this region is the most crucial for establishing the decision boundary. Furthermore, the artificial minority instances are generated in such a way that the regions of the minority class with fewer majority class instances would be expanded by extrapolation, otherwise the current boundary of the minority class would be consolidated by interpolation. Experimental results show that the proposed method achieves a better performance than other over-sampling methods.
An Empirical Comparison of A ffi ne and NonA ffi ne Models for Equity Index Options

The existing literature on equity index option valuation largely focuses on affine models, because they lead to closed-form solutions for option prices. This paper investigates the empirical biases associated with affine models, using data on S&P500 call options. We find that the root mean squared dollar error for a simple non-affine continuous-time stochastic volatility model is 17.4% lower than that of the benchmark continuous-time affine stochastic volatility model in-sample, and almost 20% out-of-sample. The analytical convenience of affine option valuation models therefore comes at a price, and non-affine models ought to be investigated more extensively. We also compare the empirical performance of affine and non-affine discrete-time models. While the performance of the discrete-time non-affine model is similar to that of the continuous-time non-affine model, the discrete-time affine model outperforms the continuous-time affine model. These findings have some interesting implications for the interpretation of existing limit results. At the methodological level, our analysis uses a novel technique based on the Auxiliary Particle Filter. This technique allows for an analysis of option valuation models using options data that imposes consistency with underlying equity returns. It is more straightforward to implement than existing methods and can be used in a variety of applications and on various loss functions. JEL Classification: G12
Identifiability in penalized function-on-function regression models

Regression models with functional covariates for functional responses constitute a powerful and increasingly important model class. However, regression with functional data poses challenging problems of non-identifiability. We describe these identifiability issues in realistic applications of penalized linear function-on-function-regression and delimit the set of circumstances under which they arise. Specifically, functional covariates whose empirical covariance has lower effective rank than the number of marginal basis function used to represent the coefficient surface can lead to unidentifiability. Extensive simulation studies validate the theoretical insights, explore the extent of the problem and allow us to evaluate its practical consequences under varying assumptions about the data generating processes. Based on theoretical considerations and our empirical evaluation, we provide easily verifiable criteria for lack of identifiability and provide actionable advice for avoiding spurious estimation artifacts. Applicability of our strategy for mitigating non-identifiability is demonstrated in a case study on the Canadian Weather data set.
Inhibition of activator protein-1 binding activity and phosphatidylinositol 3-kinase pathway by nobiletin, a polymethoxy flavonoid, results in augmentation of tissue inhibitor of metalloproteinases-1 production and suppression of production of matrix metalloproteinases-1 and -9 in human fibrosarcoma

Medicinal plants contain pharmacological substances including flavonoids, and their extracts have been therapeutically administered for cancer therapy in vitro and in vivo. We investigated the efficacy of a polymethoxy flavonoid, nobiletin, from Citrus depressa on tumor invasion in vitro. Nobiletin inhibited the tumor-invasive activity of human fibrosarcoma HT-1080 cells in the Matrigel model, whereas a similar inhibition was observed upon exogenously adding tissue inhibitors of metalloproteinases (TIMPs)-1 and -2. The gene expression and production of pro-matrix metalloproteinase 9 (proMMP-9)/progelatinase B and proMMP-1/interstitial procollagenase were specifically suppressed by nobiletin in 12-O-tetradecanoylphorbol 13-acetate-stimulated HT-1080 cells. In contrast, the gene expression and production of TIMP-1, but not TIMP-2, were enhanced by nobiletin. We also demonstrated that nobiletin suppressed the 12-O-tetradecanoylphorbol 13-acetate-induced binding activity of activator protein-1. Furthermore, a phosphatidylinositol 3-kinase inhibitor, LY-294002, was found to mimic the different actions of nobiletin on the production of proMMP-9 and TIMP-1. These results suggest that nobiletin inhibits tumor cell invasive activity not only by suppressing the expression of MMPs but also augmenting TIMP-1 production in tumor cells, and that the nobiletin-mediated inhibition of activator protein-1 binding activity is at least partly involved in the suppression of MMP expression. Furthermore, we suggest a possible mechanism by which nobiletin may interfere in the phosphatidylinositol 3-kinase pathway, which divergently regulates the production of MMP and TIMP-1.
Biochemical oxidative stress-related markers in patients with obstructive sleep apnea

Summary Background Obstructive sleep apnea (OSA) is a condition contributing to oxidative stress. The aim of this study was to ascertain if there is any connection between OSA and novel oxidative stress-related markers. Matrix metalloproteinases 2 and 9 (MMP-2, MMP-9), high sensitive C-reactive protein (hsCRP), pregnancy-associated plasma protein-A (PAPP-A), soluble receptors for advanced glycation end-products (sRAGE), zinc (Zn) and copper (Cu) were measured. Further biochemical markers were evaluated. Material/Methods Fifty-one men suspected for OSA indicated for night polygraphy were included. Apnea/hypopnea index (AHI), oxygen desaturation index (ODI), mean blood hemoglobin oxygen saturation (SpO2) and time of blood hemoglobin oxygen saturation below 90% (SpO2 <90%) were measured. Morning venous blood samples were taken. Results For body mass index (BMI) we found strong positive correlation with levels of Cu, MMP-9, hsCRP and fibrinogen, and negative correlation with sRAGE. Concerning ventilation parameters, we found positive correlation of ODI and SpO2 <90% with markers MMP-9 and hsCRP. sRAGE level correlated with AHI and ODI negatively. SpO2 correlated negatively with Cu, MMP-9, hsCRP and fibrinogen. There was no correlation between ventilation parameters and markers MMP-2, PAPP-A and Zn. Compared to severity of OSA, there was significant difference in levels of hsCRP and Cu between patients with AHI ≤5 and AHI ≥30 independent of BMI. Conclusions MMP-9, hsCRP, sRAGE and Cu seem to be strong predictors of oxidative stress in OSA patients. The strong correlation between oxidative stress-related markers and OSA is elucidated by connection of these to BMI, which is probably a primary condition of oxidative stress, but OSA is an additive condition.
Is Early-onset in Major Depression a Predictor of Specific Clinical Features with More Impaired Social Function?

Background:Early-onset major depressive disorder (MDD) (EOD) is often particularly malignant due to its special clinical features, accompanying impaired social function, protracted recovery time, and frequent recurrence. This study aimed to observe the effects of age onset on clinical characteristics and social function in MDD patients in Asia. Methods:In total, 547 out-patients aged 18–65 years who were from 13 study sites in five Asian countries were included. These patients had MDD diagnose according to the Diagnostic and Statistical Manual of Mental Disorders, 4th Edition criteria. Clinical features and social function were assessed using Symptom Checklist-90-revised (SCL-90-R) and Sheehan Disability Scale (SDS). Quality of life was assessed by a 36-item Short-form Health Survey (SF-36). Analyses were performed using a continuous or dichotomous (cut-off: 30 years) age-of-onset indicator. Results:Early-onset MDD (EOD, <30 years) was associated with longer illness (P = 0.003), unmarried status (P < 0.001), higher neuroticism (P ⩽ 0.002) based on the SCL-90-R, and more limited social function and mental health (P = 0.006, P = 0.007) based on the SF-36 and SDS. The impairment of social function and clinical severity were more prominent at in-patients with younger onset ages. Special clinical features and more impaired social function and quality of life were associated with EOD, as in western studies. Conclusions:EOD often follows higher levels of neuroticism. Age of onset of MDD may be a predictor of clinical features and impaired social function, allowing earlier diagnosis and treatment.