Miracle-dz/UniFAR-FTUs huggingface dataset:
Bartonella quintana in Cynomolgus Monkey (Macaca fascicularis)

We identified a Bartonella quintana strain by polymerase chain reaction amplification, cloning, and sequencing of DNA extracted from lysed erythrocytes and cultured colonies grown from peripheral blood collected from a captive-bred cynomolgus monkey (Macaca fascicularis). This report describes naturally acquired B. quintana infection in a nonhuman primate.
THE NEWFIRM MEDIUM-BAND SURVEY: PHOTOMETRIC CATALOGS, REDSHIFTS, AND THE BIMODAL COLOR DISTRIBUTION OF GALAXIES OUT TO z ∼ 3

We present deep near-IR (NIR) medium-bandwidth photometry over the wavelength range 1–1.8 μm in the All-wavelength Extended Groth strip International Survey (AEGIS) and Cosmic Evolution Survey (COSMOS) fields. The observations were carried out using the NOAO Extremely Wide-Field Infrared Imager (NEWFIRM) on the Mayall 4 m Telescope on Kitt Peak as part of the NEWFIRM Medium-Band Survey (NMBS), an NOAO survey program. In this paper, we describe the full details of the observations, data reduction, and photometry for the survey. We also present a public K-selected photometric catalog, along with accurate photometric redshifts. The redshifts are computed with 37 (20) filters in the COSMOS (AEGIS) fields, combining the NIR medium-bandwidth data with existing UV (Galaxy Evolution Explorer), visible and NIR (Canada–France–Hawaii Telescope and Subaru Telescope), and mid-IR (Spitzer/IRAC) imaging. We find excellent agreement with publicly available spectroscopic redshifts, with σz/(1 + z) ∼ 1%–2% for ∼4000 galaxies at z = 0–3. The NMBS catalogs contain ∼13,000 galaxies at z > 1.5 with accurate photometric redshifts and rest-frame colors. Due to the increased spectral resolution obtained with the five NIR medium-band filters, the median 68% confidence intervals of the photometric redshifts of both quiescent and star-forming galaxies are a factor of about two times smaller when comparing catalogs with medium-band NIR photometry to NIR broadband photometry. We show evidence for a clear bimodal color distribution between quiescent and star-forming galaxies that persists to z ∼ 3, a higher redshift than has been probed so far.
Differences in mRNA expression of calpains, calpastatin isoforms and calpain/calpastatin ratios among bovine skeletal muscles.

Messenger RNA (mRNA) expression of calpain-1 (µ-calpain), -2 (m-calpain), -3 (p94), small subunit (calpain-4; 28 kDa), and three types of calpastatin (CSTN) isoform were investigated for 10 skeletal muscles of Holstein cattle by real-time and/or semi-quantitative reverse transcription polymerase chain reaction. Noticeably, effect of muscle type was observed on 28 kDa expression (P < 0.001) with a tendency of higher 28 kDa expression in myosin heavy chain (MyHC)-2x-rich muscles compared to MyHC-slow-rich muscles. The CSTN-I and -III expression in Longissimus thoracis (LT) showed the lowest value among the muscles tested. Moreover, 28 kDa/CSTN-I ratio was higher in the diaphragm (DP), psoas major (PM), and LT than those in the lingual muscles (TN), masseter (MS) and pectoralis (PP) (P < 0.05). Calpain-1/CSTN I, calpain-2/CSTN I in LT and PM were higher than that in TN (P < 0.05). Calpain-3/CSTN-I and -III in LT and/or PM showed higher values than that in TN (P < 0.05). These results indicated that the calpain and CSTN expressions are regulated by muscle type, suggesting especially by muscle fiber type. Calpains/CSTN-I ratios, especially 28 kDa/CSTN-I, may account for higher extent of post mortem proteolysis previously observed in LT and PM muscles.
High-performance complex event processing over XML streams

Much research attention has been given to delivering high-performance systems that are capable of complex event processing (CEP) in a wide range of applications. However, many current CEP systems focus on processing efficiently data having a simple structure, and are otherwise limited in their ability to support efficiently complex continuous queries on structured or semi-structured information. However, XML streams represent a very popular form of data exchange, comprising large portions of social network and RSS feeds, financial records, configuration files, and similar applications requiring advanced CEP queries. In this paper, we present the XSeq language and system that support CEP on XML streams, via an extension of XPath that is both powerful and amenable to an efficient implementation. Specifically, the XSeq language extends XPath with natural operators to express sequential and Kleene-* patterns over XML streams, while remaining highly amenable to efficient implementation. XSeq is designed to take full advantage of recent advances in the field of automata on Visibly Pushdown Automata (VPA), where higher expressive power can be achieved without compromising efficiency (whereas the amenability to efficient implementation was not demonstrated in XPath extensions previously proposed). We illustrate XSeq's power for CEP applications through examples from different domains, and provide formal results on its expressiveness and complexity. Finally, we present several optimization techniques for XSeq queries. Our extensive experiments indicate that XSeq brings outstanding performance to CEP applications: two orders of magnitude improvement are obtained over the same queries executed in general-purpose XML engines.
Introducing English and German Versions of the Adolescent Time Attitude Scale

In this study, the authors report on the development of English and German versions of the Adolescent Time Attitude Scale (ATAS). The ATAS consists of six subscales assessing Past Positive, Past Negative, Present Positive, Present Negative, Future Positive, and Future Negative time attitudes. The authors describe the development of the scales and present data on the reliability and structural validity of ATAS scores in samples of American (N = 300) and German (N = 316) adolescents. Internal consistency estimates for scores on the English and German versions of the ATAS were in the . 70 to . 80 range. Confirmatory factor analyses indicated that a six-factor structure yielded the best fit for scores and that the scores were invariant across samples.
Generalized analytical approach of the calculation of the harmonic effects of single phase multilevel PWM inverters

This paper introduces a generalized analytical approach for calculating the total harmonic distortion THD and its weighted value WTHD for multilevel PWM inverters. The calculation considers one single phase and it can apply to any number of levels of the inverter in general. Although the analysis is based on the assumption of a high number of pulses, the developed equations can also be applied for lower frequency ratios fs/f1. The analytical formulas require the characteristic parameters of the PWM only, which are the modulation factor m, the switching frequency fs, the fundamental frequency f1, the effective inductance L and the DC link voltage inverters with a number of levels N are considered. It must be noticed that some differences appear between the case of N odd and N even. Several parametric curves arc calculated to define the specifications of an inverter with N levels in order to fulfill the harmonic voltage recommendations trying to reduce the output signal filtering.
Analysis of spatial count data using Kalman smoothing

This paper considers spatial count data from an agricultural field experiment. Counts of weed plants in a field have been recorded in a project on precision farming. Interest is in mapping the weed intensity so that the dose of herbicide applied at any location can be adjusted to the amount of weed present at the location. We elaborate on a link between state space models and Markov random fields. The observations are modelled as independent Poisson counts conditional on a Gaussian Markov random field. We employ the fact that the model may be written as a state space model which may be analysed by combining approximate Kalman filter techniques with importance sampling.
Organisational justice, trust and the management of change: An exploration

This paper explores employees’ trust as a reaction to the management of change using the constructs of organisational justice. Following a review of organisational justice theory in relation to trust and change, employees’ reactions are considered using a case study of a UK public sector organisation. Drawing on 28 in‐depth interviews with employees, the nature of trust is explored. Little difference is found between trusting and mistrustful employees’ perceptions of distributive justice. Supporting earlier findings regarding the relationship between procedural justice and trust, the research also reveals the distinct importance of fairness of treatment (interactional justice) in enabling trust.
Modeling site‐based decision making: School practices in the age of accountability

Purpose – The primary purpose is to present empirical measures of variables relating to practices engaged in by site‐based teams, and then to use these variables to test a model predicting significant outcomes of site‐based decision making. The practice variables of site‐based management (SBM) teams are essential in promoting research within a distributed leadership framework.Design/methodology/approach – A path model is computed to test the relationships between factors relating to the support received by site‐based teams; site team communication and decision‐making practice, and perceived outcomes of SBM. Measures are based on survey data collected from 367 team members in 50 schools from fifteen school districts in a northeastern state in the US.Findings – Results show that different factors relating to the support provided to site‐based teams and practices employed by these teams emerge as statistically significant predictors of various outcomes. Results suggest that the resources provided to support .
Diversity of viruses associated with acute gastroenteritis in children hospitalized with diarrhea in Ho Chi Minh City, Vietnam

A molecular epidemiological study on common diarrheal viruses was conducted in Ho Chi Minh City, Vietnam between October 2002 and September 2003. Fecal samples were collected from 1,010 hospitalized children with acute gastroenteritis. Those samples were screened for groups A, B, and C rotavirus, adenovirus, genogroups I and II norovirus (NoV), sapovirus (SaV), and human astrovirus (HAstV) by RT‐multiplex PCR, and the positive specimens were characterized further by ELISA, nested PCR, or sequencing. Among the diarrheal viruses detected, group A rotavirus was the most common, with a proportion of 67.4%, whereas NoV GII, adenovirus, SaV, and HAstV were also found in 5.5, 3.2, 0.8, and 0.6%, respectively. It is noteworthy that the group C rotavirus was first reported in Vietnam, with a proportion of 0.5% in this study. Fifty‐six of 1,010 (5.5%) samples were found positive with more than one viral agent, in which 25 samples contained both group A rotavirus and NoV GII. Group A rotavirus could be identified throughout year with the peaks in both the dry and rainy season, whereas other viruses prevailed mainly in the rainy season. G‐typing for the group A rotavirus showed that genotype 1 was still the most prevailing (33.0%), but interestingly, serotype 9 was emergent and became the third most common rotavirus G‐type in these samples (13.7%). The four most common G–P combinations globally, G1P[8], G2P[4], G3P[8], and G4P[8] were found in 46.8% of rotavirus‐positive samples, and it is of interest that one unusual rotavirus G9P[19] strain was first detected in Vietnam. The majority of NoV strains belonged to GII/4, and SaV strains mainly clustered with the Manchester strain (GI/1). Twenty‐seven out of 32 adenovirus strains were identified as serotype 41. All HAstVs belonged to genotype 1. The results indicated clearly the impact of viral agents causing gastroenteritis and the importance of vaccination against diarrhea in Vietnam. J. Med. Virol. 79:582–590, 2007. © 2007 Wiley‐Liss, Inc.
MHC class II beta sequence diversity in the deer mouse (Peromyscus maniculatus): implications for models of balancing selection

We studied population polymorphism at a major histocompatibility complex (MHC) class II beta gene in the deer mouse (Peromyscusmaniculatus). We found that: (i) a single population of P. maniculatus has significantly higher levels of DNA and protein sequence diversity than worldwide samples from homologous genes in other taxa, including humans and mice; and (ii) the genealogy of allelic sequences in P. maniculatus deviates significantly from theoretical expectation under a model of symmetric balancing selection, in that alleles are relatively more divergent than expected. We suggest that the observation of high levels of pairwise allelic sequence divergence and deviation of the genealogy from theoretical expectation in P. maniculatus together provide support for a divergent allele advantage model for the maintenance of MHC polymorphism.
Groups and Individuals: Explanations in Social Psychology

Foreword to the English edition Preface Serge Moscovici Part I. The Integration of Psychology and Sociology: 1. The psychological approach 2. The sociological approach 3. The social psychological aprroach Part II. Intergroup Relations and Category Differentiation: 1. Experiments on intergroup relations 2. Category differentiation 3. Recent experimental support Bibliography Index Acknowledgements.
Increased epicardial fat volume quantified by 64-multidetector computed tomography is associated with coronary atherosclerosis and totally occlusive lesions.

BACKGROUND The relationship between the epicardial fat volume measured by 64-slice multidetector computed tomography (MDCT) and the extension and severity of coronary atherosclerosis was investigated. METHODS AND RESULTS Both MDCT and conventional coronary angiography (CAG) were performed in 71 consecutive patients who presented with effort angina. The volume of epicardial adipose tissue (EAT) was measured by MDCT. The severity of coronary atherosclerosis was assessed by evaluating the extension of coronary plaques in 790 segments using MDCT data, and the percentage diameter stenosis in 995 segments using CAG data. The estimated volume of EAT indexed by body surface area was defined as VEAT. Increased VEAT was associated with advanced age, male sex, degree of metabolic alterations, a history of acute coronary syndrome (ACS) and the presence of total occlusions, and showed positive correlation with the stenosis score (r=0.28, P=0.02) and the atheromatosis score (r=0.67, P<0.0001) of the coronary arteries. Multiple logistic regression analysis revealed an increased VEAT (>or=50 cm(3)/m(2)) to be the strongest independent determinant of the presence of total occlusions (odds ratio 4.64, P=0.02). CONCLUSIONS VEAT correlates with the degree of metabolic alterations and coronary atheromatosis. Excessive accumulation of EAT might contribute to the development of ACS and coronary total occlusions.
Breaking the Silence: Art Therapy With Children From Violent Homes

Foreword Acknowledgments Introduction 1. The Role of Art Therpay in Assessment and Treatment of Children from Violent Homes: An Overview 2. Working with Children from Violent Homes 3. Art Evaluation with Children from Violent Homes 4. bArt Intervention with Children from Violent Homes 5. Child Sexual Abuse 6. Developing Art Therapy Programs for Children from Violent Homes Epilogue Resource List References Name Index Subject Index
Binarization With Boosting and Oversampling for Multiclass Classification

Using a set of binary classifiers to solve multiclass classification problems has been a popular approach over the years. The decision boundaries learnt by binary classifiers (also called base classifiers) are much simpler than those learnt by multiclass classifiers. This paper proposes a new classification framework, termed binarization with boosting and oversampling (BBO), for efficiently solving multiclass classification problems. The new framework is devised based on the one-versus-all (OVA) binarization technique. Unlike most previous work, BBO employs boosting for solving the hard-to-learn instances and oversampling for handling the class-imbalance problem arising due to OVA binarization. These two features make BBO different from other existing works. Our new framework has been tested extensively on several multiclass supervised and semi-supervised classification problems using five different base classifiers, including neural networks, C4.5, k-nearest neighbor, repeated incremental pruning to produce error reduction, support vector machine, random forest, and learning with local and global consistency. Experimental results show that BBO can exhibit better performance compared to its counterparts on supervised and semi-supervised classification problems.
Deciphering the Spike Train of a Sensory Neuron: Counts and Temporal Patterns in the Rat Whisker Pathway

Rats achieve remarkable texture discriminations by sweeping their facial whiskers along surfaces. This work explores how neurons at two levels of the sensory pathway, trigeminal ganglion and barrel cortex, carry information about such stimuli. We identified two biologically plausible coding mechanisms, spike counts and patterns, and used “mutual information” to quantify how reliably neurons in anesthetized rats reported texture when “decoded” according to these candidate mechanisms. For discriminations between surfaces of different coarseness, spike counts could be decoded reliably and rapidly (within 30 ms after stimulus onset in cortex). Information increased as responses were considered as spike patterns with progressively finer temporal precision. At highest temporal resolution (spike sequences across six bins of 4 ms), the quantity of “information” in patterns rose 150% for ganglion neurons and 110% for cortical neurons above that in spike counts. In some cases, patterns permitted discriminations not supported by spike counts alone.
Extratropical cyclones in a warmer, moister climate: A recent Atlantic analogue

Current climate model projections do not exhibit a large change in the intensity of extratropical cyclones. However, there are concerns that current models represent moist processes poorly, and this provides motivation for investigating observational evidence for how cyclones behave in warmer climates. In the North Atlantic in particular, recent decades provide a clear contrast between warm and cold climates due to Atlantic Multidecadal Variability. In this paper we investigate these periods as analogues which may provide a guide to future cyclone behavior. While temperature and moisture rise in recent warm periods as in the projections, differences in energetics and temperature gradients imply that these periods are only partial analogues. The main result from current reanalyses is that while increased cyclone‐associated precipitation is seen in the recent warm periods, there is no robust evidence of an increase in cyclone intensity by other measures, such as maximum wind speed or vorticity. A set of low‐ and high‐resolution model simulations are also studied, suggesting that changes in cyclone intensity may be different in higher‐resolution reanalyses.
Characterisation of Botrytis species associated with neck rot of onion in Australia

Neck rot of onion has commonly been attributed to two fungal pathogens, Botrytis aclada (syn. B. allii) and B. byssoidea. However, in other countries, a recently developed PCR technique using sequence characterised amplified region (SCAR) primers (BA2f/BA1r) followed by ApoI digestion of the amplification product, has shown the presence of two groups within B. aclada, B. aclada AI and B. aclada AII syn. B. allii. This method was used to characterise Botrytis spp. of the B. aclada/B. allii complex associated with onion seed and bulbs in Australia. A total of 24 Botrytis isolates, including two from seed and ten from bulbs (Tasmania), five from seed (South Australia), and one from seed and six from a culture collection originally isolated from five bulbs and one stipe (New South Wales), were characterised. Of the 24 isolates, one was identified as B. cinerea, one as B. aclada AI, and 22 as B. aclada All syn. B. allii.
BI-RADS lexicon for US and mammography: interobserver variability and positive predictive value.

PURPOSE To retrospectively evaluate interobserver variability between breast radiologists by using terminology of the fourth edition of the Breast Imaging Reporting and Data System (BI-RADS) to categorize lesions on mammograms and sonograms and to retrospectively determine the positive predictive value (PPV) of BI-RADS categories 4a, 4b, and 4c. MATERIALS AND METHODS Institutional review board approval was obtained; informed consent was not required. This study was HIPAA compliant. Ninety-four consecutive lesions in 91 women who underwent image-guided biopsy comprised 59 masses, 32 calcifications, and three masses with calcification. Five radiologists retrospectively reviewed these lesions. Each observer described each lesion with BI-RADS terminology and assigned a final BI-RADS category. Interobserver variability was assessed with the Cohen kappa statistic. A pathologic diagnosis was available for all 94 lesions; 30 (32%) were malignant and 64 (68%) were benign. Pathologic analysis of benign lesions was performed on tissue obtained with image-guided core-needle biopsy. In cases referred for excisional biopsy after needle biopsy because of atypia or discordance, final surgical pathologic analysis was used for correlation with imaging findings. PPV for category 4 or 5 lesions was determined for all readers combined. RESULTS For ultrasonographic (US) descriptors, substantial agreement was obtained for lesion orientation, shape, and boundary (kappa = 0.61, 0.66, and 0.69, respectively). Moderate agreement was obtained for lesion margin and posterior acoustic features (kappa = 0.40 for both). Fair agreement was obtained for lesion echo pattern (kappa = 0.29). For mammographic descriptors, moderate agreement was obtained for mass shape, mass margin, and calcification distribution (kappa = 0.48, 0.48, and 0.50, respectively). Fair agreement was obtained for calcification description (kappa = 0.32). Slight agreement was obtained for mass density (kappa = 0.18). Fair agreement was obtained for final assessment category (kappa = 0.28). PPVs of BI-RADS category 4 and 5 assignments were as follows: category 4a, six (6%) of 102; category 4b, 17 (15%) of 110; category 4c, 48 (53%) of 91; and category 5, 71 (91%) of 78. CONCLUSION Interobserver agreement with the new BI-RADS terminology is good and validates the US lexicon. Subcategories 4a, 4b, and 4c are useful in predicting the likelihood of malignancy.
Comparing XML path expressions

XPath is the standard declarative language for navigating XML data and returning a set of matching nodes. In the context of XSLT/XQuery analysis, query optimization, and XML type checking, XPath decision problems arise naturally. They notably include XPath comparisons such as equivalence (whether two queries always return the same result), and containment (whether for any tree the result of a particular query is included in the result of a second one). XPath decision problems have attracted a lot of research attention, especially for studying the computational complexity of various XPath fragments. However, what is missing at present is the constructive use of an expressive logic which would allow capturing these decision problems, while providing practically effective decision procedures.In this paper, we propose a logic-based framework for the static analysis of XPath. Specifically, we propose the alternation free modal μ-calculus with converse as the appropriate logic for effectively solving XPath decision problems. We present a translation of a large XPath fragment into μ-calculus, together with practical experiments on the containment using a state-of-the-art EXPTIME decision procedure for μ-calculus satisfiability. These preliminary experiments shed light, for the first time, on the cost of checking the containment in practice. We believe they reveal encouraging results for further static analysis of XML transformations.