Miracle-dz/UniFAR-FTUs huggingface dataset:
Heterogeneity Confounds Establishment of “a” Model Microbial Strain

ABSTRACT Aspergillus fumigatus is a ubiquitous environmental mold and the leading cause of diverse human diseases ranging from allergenic bronchopulmonary aspergillosis (ABPA) to invasive pulmonary aspergillosis (IPA). Experimental investigations of the biology and virulence of this opportunistic pathogen have historically used a few type strains; however, it is increasingly observed with this fungus that heterogeneity among isolates potentially confounds the use of these reference isolates. Illustrating this point, Kowalski et al. (mBio 7:e01515-16, 2016, https://doi.org/10.1128/mBio.01515-16 ) demonstrated that variation in 16 environmental and clinical isolates of A. fumigatus correlated virulence with fitness in low oxygen, whereas Fuller et al. (mBio 7:e01517-16, 2016, https://doi.org/10.1128/mBio.01517-16 ) showed wide variation in light responses at a physiological and protein functionality level in 15 A. fumigatus isolates. In both studies, two commonly used type strains, Af293 and CEA10, displayed significant differences in physiological responses to abiotic stimuli and virulence in a murine model of IPA.
DECOD: fast and accurate discriminative DNA motif finding

MOTIVATION Motif discovery is now routinely used in high-throughput studies including large-scale sequencing and proteomics. These datasets present new challenges. The first is speed. Many motif discovery methods do not scale well to large datasets. Another issue is identifying discriminative rather than generative motifs. Such discriminative motifs are important for identifying co-factors and for explaining changes in behavior between different conditions. RESULTS To address these issues we developed a method for DECOnvolved Discriminative motif discovery (DECOD). DECOD uses a k-mer count table and so its running time is independent of the size of the input set. By deconvolving the k-mers DECOD considers context information without using the sequences directly. DECOD outperforms previous methods both in speed and in accuracy when using simulated and real biological benchmark data. We performed new binding experiments for p53 mutants and used DECOD to identify p53 co-factors, suggesting new mechanisms for p53 activation. AVAILABILITY The source code and binaries for DECOD are available at http://www.sb. cs.cmu. edu/DECOD CONTACT: zivbj@cs.cmu. edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Hopes of Affiliation and Fears of Rejection: The Effects of Attachment Anxiety on Behaviour and Outcomes in Initial Interactions

Research has demonstrated that attachment anxiety undermines our ongoing relationships, however, less is known about the role anxiety plays in the context of relationship initiation (Creasey & Jarvis, 2008; Mikulincer & Shaver, 2007). The present research therefore explored how attachment anxiety affects people’s behaviour and outcomes in initial interactions. The first manuscript presents two studies using a social dilemma game paradigm. In the first study, chronic attachment anxiety was associated with uncertainty about cooperation and longer decision latencies in selecting their behaviour. In the second study, the contextual activation of attachment security was used to ameliorate the effects of chronic anxiety. The next two manuscripts examined more overtly interpersonal contexts. In the second manuscript, field data collected at speed-dating demonstrated that attachment anxiety was associated with lower romantic selectivity—that is, more anxious participants made attempts to pursue further contact with a larger number of potential dating partners—and decreased romantic popularity—more anxious participants were pursued for further contact by fewer potential dating partners. In a signal detection analysis, it was shown that more anxious participants were therefore making more false alarms, or maximizing the number of failed relationship initiation attempts. Finally, the third manuscript sought to test a meditational model, wherein the link between attachment anxiety and negative social outcomes in initial interactions was mediated by theoryderived interpersonal displays. In a first study, participants filmed a video introducing themselves to an attractive, available confederate in another room; these videos were coded by peer research assistants. In a second study,
Frequency-Based Environment Matting by Compressive Sensing

Extracting environment mattes using existing approaches often requires either thousands of captured images or a long processing time, or both. In this paper, we propose a novel approach to capturing and extracting the matte of a real scene effectively and efficiently. Grown out of the traditional frequency-based signal analysis, our approach can accurately locate contributing sources. By exploiting the recently developed compressive sensing theory, we simplify the data acquisition process of frequency-based environment matting. Incorporating phase information in a frequency signal into data acquisition further accelerates the matte extraction procedure. Compared with the state-of-the-art method, our approach achieves superior performance on both synthetic and real data, while consuming only a fraction of the processing time.
High current fast Marx generator and vircator experiments

This paper describes a compact pulsed power generator. This system stores 10 kJ and is capable of delivering up to 40 GW to an electron diode. It has been optimized to drive high power microwaves devices that require high current. In order to limit the parasitic inductance and to reduce the rise time of the current to less than 100 ns, two Marx generators have been associated in parallel. Some typical results of vircator operation in S band are also presented.
A Novel Long Distance Base-pairing Interaction in Human Immunodeficiency Virus Type 1 RNA Occludes the Gag Start Codon*

The 5′-untranslated region (5′-UTR) is the most conserved part of the HIV-1 RNA genome, and it contains regulatory motifs that mediate various steps in the viral life cycle. Previous work showed that the 5′-terminal 290 nucleotides of HIV-1 RNA adopt two mutually exclusive secondary structures, long distance interaction (LDI) and branched multiple hairpin (BMH). BMH has multiple hairpins, including the dimer initiation signal (DIS) hairpin that mediates RNA dimerization. LDI contains a long distance base-pairing interaction that occludes the DIS region. Consequently, the two conformations differ in their ability to form RNA dimers. In this study, we have presented evidence that the full-length 5′-UTR also adopts the LDI and BMH conformations. The downstream 290–352 region, including the Gag start codon, folds differently in the context of the LDI and BMH structures. These nucleotides form an extended hairpin structure in the LDI conformation, but the same sequences create a novel long distance interaction with upstream U5 sequences in the BMH conformation. The presence of this U5-AUG duplex was confirmed by computer-assisted RNA structure prediction, biochemical analyses, and a phylogenetic survey of different virus isolates. The U5-AUG duplex may influence translation of the Gag protein because it occludes the start codon of the Gag open reading frame.
Statistical Bayesian Learning for Automatic Arabic Text Categorization

Problem statement: The rapid increasing of online Arabic documents necessitated applying Text Categorization techniques that are commonly used for English language to categorize them automatically. The complex morphology of Arabic language and its large vocabulary size make applying these techniques directly difficult and costly in time and effort. Approach: We have investigated Bayesian learning models in order to enhance Arabic ATC. Three classifiers based on Bayesian theorem had been implemented which are Simple Naive Bayes (NB), Multi-variant Bernoulli Naive Bayes (MBNB) and Multinomial Naive Bayes (MNB) models. TREC-2002 Light Stemmer was applied for Arabic stemming. For text representation, Bag-Of-Word and character-level n-gram with the length 3, 4 and 5 are used. In order to reduce the dimensionality of feature space, the following feature selection methods: Mutual Information, Chi-Square statistic, Odds Ratio and GSS-coefficient were used. Conclusion: MBNB classifier outperformed both of NB and MNB classifiers. BOW representation leads to the best classification performance; nevertheless, using character-level n-gram leads to satisfying results for Arabic ATC based on Bayesian learning. Moreover, the use of feature selection methods dramatically increases the categorization performance.
Moving the LD Field Ahead

Do not follow where the path may lead. Go, instead, where there is no path and leave a trail. Anonymous In this final article in the series on the future of the LD field, we reflect on ideas presented by the contributors and underscore trends for the the future that seem essential to the field's progress. Inadequacies of prevailing thinking in the field are highlighted and suggestions are offered about the way in which such thinking needs to be expanded and transformed. In this connection, we stress the importance of (a) an expanded focus on adolescents and adults, (b) broader models for understanding the patterns of behavior and learning seen in LD programs, (c) going beyond the concepts of diagnosis, treatment, remediation, and individualized instruction, (d) expansion of prevailing views of basic skills, and (e) development of interventions that focus on more than changing people. Finally, we explore implications of and ideas for reducing the large number of LD misdiagnoses. One purpose of this series has been to focus attention on the directions that have been established and where they are leading the field. Another purpose has been to encourage thought and discussion about new paths to follow. The rapid growth of the field has left precious little time for reflection, and it is easy to lose perspective under such circumstances. The series presentations provide a beginning for efforts to clarify an agenda for the immediate future; over the next year or so, we hope that the various LD journals will encourage an ongoing interchange about these and other ideas that should shape that agenda. It is from such an interchange that a new synthesis of guidelines and recommendations for theory, research, and practice can be developed by the field's advocates, representatives, and others who shape the future through then influence on policy and socialization of professionals and the general public. It is time to stimulate and broaden the dialectic process; the result should be a refreshing renewal of the spirit that prevailed when the field was born.
Genotypic-specific variance in Caenorhabditis elegans lifetime fecundity

Organisms live in heterogeneous environments, so strategies that maximze fitness in such environments will evolve. Variation in traits is important because it is the raw material on which natural selection acts during evolution. Phenotypic variation is usually thought to be due to genetic variation and/or environmentally induced effects. Therefore, genetically identical individuals in a constant environment should have invariant traits. Clearly, genetically identical individuals do differ phenotypically, usually thought to be due to stochastic processes. It is now becoming clear, especially from studies of unicellular species, that phenotypic variance among genetically identical individuals in a constant environment can be genetically controlled and that therefore, in principle, this can be subject to selection. However, there has been little investigation of these phenomena in multicellular species. Here, we have studied the mean lifetime fecundity (thus a trait likely to be relevant to reproductive success), and variance in lifetime fecundity, in recently-wild isolates of the model nematode Caenorhabditis elegans. We found that these genotypes differed in their variance in lifetime fecundity: some had high variance in fecundity, others very low variance. We find that this variance in lifetime fecundity was negatively related to the mean lifetime fecundity of the lines, and that the variance of the lines was positively correlated between environments. We suggest that the variance in lifetime fecundity may be a bet-hedging strategy used by this species.
Study on the Algorithm of Human Body Modeling

This paper studies the basic thoughts and impacts of traditional non-contact algorithms of human body modeling. The algorithms of most existing modeling methods are multiple and complex, and in this paper they are mainly classified into three types according to the optical, geometry and topology character of human body they are based on. And some brief comparisons and analyses are given among the core algorithms of different types. Finally, the conclusions and prospects for future development of these modeling algorithms are discussed.
A multicultural approach to teach sustainability

Globalization is a tendency that covers all society perspectives in general, and the high education in particular. The main traditional objective of these institutions was to prepare domestic students with a set of skills. The research competition and universities rankings, as well as the need to reach other publics pushed them towards internationalization. The exchange of students across the UE is a well-known reality which success is largely due to cultural similarities. However, a set of issues raises in importance when students from different cultures are involved. We proposed an International Summer Course with a layout specifically designed to identify those questions. In our experience the class included Korean and Portuguese students in the same proportions to develop some work under the framework of sustainability, a specific theme chosen in order to foster consensus. Aiming at a higher level of internationalization and having in mind that students could gain from an intensive and multicultural experience ISEP organized its first Engineering for Sustainable Development (E4SD) Summer Course, in July 2014. This work reports some results from this experience, which included a Problem Based Learning (PBL) approach, and points new directions. In fact, PBL seemed to be a way of promoting integration and the inclusion of multiple cultures allowed the analysis of different perspectives which otherwise would not have been considered. On the other hand, all the students had an international experience, in a non native language, which has driven them out of their confort zone
Subjective and Objective Evaluation of Speech Intelligibility Enhancement Under Constant Energy and Duration Constraints

Speakers appear to adopt strategies to improve speech intelligibility for interlocutors in adverse acoustic conditions. Generated speech, whether synthetic, recorded or live, may also benefit from context-sensitive modifications in challenging situations. The current study measured the effect on intelligibility of six spectral and temporal modifications operating under global constraints of constant input-output energy and duration. Reallocation of energy from mid-frequency regions with high local SNR produced the largest intelligibility benefits, while other approaches such as pause insertion or maintenance of a constant segmental SNR actually led to a deterioration in intelligibility. Listener scores correlated only moderately well with recent objective intelligibility estimators, suggesting that further development of intelligibility models is required to improve predictions for modified speech. Index Terms: speech intelligibility, objective measures, energy reallocation
Distinction of salvaged and infarcted myocardium within the ischaemic area-at-risk with T2 mapping.

AIM Area-at-risk (AAR) measurements often rely on T2-weighted images, but subtle differences in T2 may be overlooked with this method. To determine the differences in oedema between salvaged and infarcted myocardium, we performed quantitative T2 mapping of the AAR. We also aimed to determine the impact of reperfusion time on T2 in the AAR. METHODS Twenty-two dogs underwent 2 h of coronary occlusion followed by 4 or 48 h of reperfusion before cardiac magnetic resonance imaging at 1.5 T. Late gadolinium enhancement images were used to define the infarcted, salvaged, and remote myocardium. T2 values from T2 maps and signal intensities on T2-weighted images were measured in the corresponding areas. RESULTS At both imaging time points, the T2 of the salvaged myocardium was longer than of remote (66.0 ± 6.9 vs. 51.4 ± 3.5 ms, P < 0.001 at 4 h, and 56.7 ± 7.3 vs. 48.1 ± 3.5 ms, P < 0.001 at 48 h). The T2 was also longer in the infarcted myocardium compared with remote at both 4 and 48 h (71.4 ± 7.6 ms, P < 0.01 vs. salvage and 64.0 ± 6.9 ms, P = 0.03 vs. salvage, both P < 0.001 vs. remote). The increase in T2 in the salvaged myocardium compared with remote was greater after 4 h than after 48 h (14.7 ± 5.6 vs. 8.7 ± 5.1 ms, P = 0.02). CONCLUSIONS T2 relaxation parameters are different in the infarcted and salvaged myocardium, and both are significantly longer than remote. Furthermore, the magnitude of increase in T2 was less in the salvaged myocardium after longer reperfusion, indicating partial resolution of oedema in the first 48 h after reperfusion.
How should intergroup contact be structured to reduce bias among majority and minority group children?

This experiment examined the effectiveness of one-group and dual-identity recategorization strategies on reducing intergroup bias among 180 European Portuguese and African Portuguese 9- and 10-year-old children. Results revealed that each of these recategorization strategies, relative to one that emphasized separate group identities, was successful in producing positive attitudes toward the outgroup children present during the session, the outgroup as a whole, and the outgroup as a whole three weeks later. Consistent with a functional perspective regarding which representation would most effectively promote their group’s goals, a dual identity was more effective for the European Portuguese majority group, whereas a one-group identity was more effective for the African Portuguese minority group. Additional analyses explored a model of the process of generalization that formally links attitudes toward the outgroup as a whole to the attitudes toward outgroup members present during contact.
A Candidate Single Nucleotide Polymorphism in the 3′ Untranslated Region of Stearoyl-CoA Desaturase Gene for Fatness Quality and the Gene Expression in Berkshire Pigs

Fatness qualities in pigs measured by the amount of fat deposition and composition of fatty acids (FAs) in pork have considerable effect on current breeding goals. The stearoyl-CoA desaturase (SCD) gene plays a crucial role in the conversion of saturated FAs into monounsaturated FAs (MUFAs), and hence, is among the candidate genes responsible for pig fatness traits. Here, we identified a single nucleotide polymorphism (SNP, c.*2041T>C) in the 3′ untranslated region by direct sequencing focused on coding and regulatory regions of porcine SCD. According to the association analysis using a hundred of Berkshire pigs, the SNP was significantly associated with FA composition (MUFAs and polyunsaturated FAs [PUFAs]), polyunsaturated to saturated (P:S) FA ratio, n-6:n-3 FA ratio, and extent of fat deposition such as intramuscular fat and marbling (p<0.05). In addition, the SNP showed a significant effect on the SCD mRNA expression levels (p = 0.041). Based on our results, we suggest that the SCD c. *2041T>C SNP plays a role in the gene regulation and affects the fatness qualities in Berkshire pigs.
Adaptação cultural e validação da escala “falls efficacy scale” de Tinetti

As quedas sao os acidentes mais frequentes e incapacitantes para o idoso. A diminuicao da forca muscular, da flexibilidade e as alteracoes posturais decorrentes da idade levam a um certo receio de quedas nos idosos que nunca cairam. Este medo leva a uma deterioracao da qualidade de vida (Campbell, Robertson, Gardner, Norton e Tilyard, 1997; Feder, Cryer, Donovan e Carter, 2000). A falta de definicao e operacionalizacao do medo de cair leva Tinetti a utilizar a Teoria da Auto Eficacia de Bandura (1986) como forma de avaliacao do medo de cair, perguntando aos individuos as suas sensacoes numa variedade de determinadas tarefas relacionadas com as actividades da vida diaria (AVD). A Teoria da Auto Eficacia afirma que sao os julgamentos que as pessoas fazem acerca da sua eficacia pessoal que constituem os melhores preditores do seu envolvimento e persistencia em diferentes tarefas. Uma baixa auto eficacia leva a restricao da actividade, e consequentemente a diminuicao da capacidade fisica. Perell et al. ABSTRACT
Prospective Register Of patients undergoing repeated OFfice and Ambulatory Blood Pressure Monitoring (PROOF-ABPM): protocol for an observational cohort study

Introduction The diagnosis and management of hypertension depends on accurate measurement of blood pressure (BP) in order to target antihypertensive treatment appropriately. Most BP measurements take place in a clinic setting, but it has long been recognised that readings taken out-of-office (via home or ambulatory monitoring) estimate true underlying BP more accurately. Recent studies have shown that the change in clinic BP over multiple readings is a significant predictor of the difference between clinic and out-of-office BP. Used in combination with patient characteristics, this change has been shown to accurately predict a patient's out-of-office BP level. The present study proposes to collect real-life BP data to prospectively validate this new prediction tool in routine clinical practice. Methods and analysis A prospective, multicentre observational cohort design will be used, recruiting patients from primary and secondary care. All patients attending participating centres for ambulatory BP monitoring will be eligible to participate. Anonymised clinical data will be collected from all eligible patients, who will be invited to give informed consent to permit identifiable data to be collected for data linkage to external outcome registries. Descriptive statistics will be used to calculate the sensitivity, specificity, positive and negative predictive values of the out-of-office BP prediction tool. Area under the receiver operator characteristic curve statistics will be used to examine model performance. Ethics and dissemination Ethical approval for this study has been obtained from the National Research. Ethics Service Committee South Central—Oxford A (reference; 15/SC/0184), and site-specific R&D approval has been acquired from the relevant NHS trusts. All findings will be presented at relevant conferences and published in peer-reviewed journals, on the study website and disseminated in lay and social media where appropriate.