Miracle-dz/UniFAR-FTUs huggingface dataset:
Ribosomal RNA as molecular barcodes: a simple correlation analysis without sequence alignment

MOTIVATION We explored the feasibility of using unaligned rRNA gene sequences as DNA barcodes, based on correlation analysis of composition vectors (CVs) derived from nucleotide strings. We tested this method with seven rRNA (including 12, 16, 18, 26 and 28S) datasets from a wide variety of organisms (from archaea to tetrapods) at taxonomic levels ranging from class to species. RESULT Our results indicate that grouping of taxa based on CV analysis is always in good agreement with the phylogenetic trees generated by traditional approaches, although in some cases the relationships among the higher systemic groups may differ. The effectiveness of our analysis might be related to the length and divergence among sequences in a dataset. Nevertheless, the correct grouping of sequences and accurate assignment of unknown taxa make our analysis a reliable and convenient approach in analyzing unaligned sequence datasets of various rRNAs for barcoding purposes. AVAILABILITY The newly designed software (CVTree 1.0) is publicly available at the Composition Vector Tree (CVTree) web server http://cvtree.cbi. pku.edu. cn.
Performance and Accuracy of LAPACK's Symmetric Tridiagonal Eigensolvers

We compare four algorithms from the latest LAPACK 3.1 release for computing eigenpairs of a symmetric tridiagonal matrix. These include QR iteration, bisection and inverse iteration (BI), the divide-and-conquer method (DC), and the method of multiple relatively robust representations (MR). Our evaluation considers speed and accuracy when computing all eigenpairs and additionally subset computations. Using a variety of carefully selected test problems, our study includes a variety of today's computer architectures. Our conclusions can be summarized as follows. (1) DC and MR are generally much faster than QR and BI on large matrices. (2) MR almost always does the fewest floating point operations, but at a lower MFlop rate than all the other algorithms. (3) The exact performance of MR and DC strongly depends on the matrix at hand. (4) DC and QR are the most accurate algorithms with observed accuracy $O(\sqrt{n} \varepsilon)$. The accuracy of BI and MR is generally $O(n \varepsilon)$. (5) MR is preferable to BI for subset computations.
Interest of Presbyopes in Contact Lens Correction and Their Success with Monovision

The presbyopic population is seen as a large potential source of contact lens wearers. The aims of this study were: (1) to estimate the percentage of presbyopes interested in contact lenses, (2) to ascertain the success of interested presbyopes with monovision correction, and (3) to determine the percentage willing to continue wearing monovision lenses after 1 month's trial. Seven practitioners in Sydney surveyed consecutive presbyopes attending their practices about their interest in contact lenses. Of the 1133 presbyopes surveyed, 314 (28%) were interested in trying monovision lenses. A total of 72 patients were subsequently fitted with monovision in high water content hydrogel form. After 1 month, 46 of these patients (64%) were still wearing the lenses, and 39 (54%) expressed willingness to continue with monovision correction. The major reasons for discontinuation from lens wear during the 1-month trial were inadequate vision and difficulty in lens handling.
Notice of RetractionStudy of 3C Streamlined Service Model

With intensifying competition of products homogenization, differentiated services become a favorable weapon to enterprises. This paper presents the concept of streamlined services, and builds a 3C streamlined service model of service-oriented enterprises based on the three-tier model,. The model stresses customer-centric and marketing-oriented. Departments of enterprises interrelate through three levels (contact, communication and control), achieve integration with enterprise atmosphere, and eventually achieve satisfaction of both enterprise and common customer.
Mammaglobin expression in lymph nodes is an important marker of metastatic breast carcinoma.

CONTEXT Organ specificity is a desirable property of a tumor marker, especially in metastatic adenocarcinomas of unknown primary origin. Mammaglobin, a mammary-specific member of the uteroglobin family, is known to be overexpressed in human breast cancer. OBJECTIVE We investigated mammaglobin A expression in metastatic carcinomas of lymph nodes from the breast and various other organs and its usefulness in identifying metastatic carcinoma of the breast. For comparative purposes, we also investigated BRST-1 and BRST-2 expression. DESIGN We produced recombinant mammaglobin and polyclonal antimammaglobin antibodies. Mammaglobin expression was analyzed by immunohistochemical staining using a tissue microarray and by reverse transcription-polymerase chain reaction in 210 carcinomas, including those of the breast (n = 70), lung (n = 30), stomach (n = 30), colorectum (n = 25), hepatobiliary tract (n = 20), urinary tract (n = 10), thyroid gland (n = 10), ovary and endometrium (n = 10), and salivary gland (n = 5). RESULTS Mammaglobin expression was observed in 59 cases (84.3%) of breast cancer and in 21 cases (15.0%) of nonbreast cancer. The BRST-1 and BRST-2 expression rates were 75.7% and 44.3% in breast cancer and 26.4% and 2.1% in nonbreast cancer, respectively. Mammaglobin is superior to BRST-1 for both specificity and sensitivity and is superior to BRST-2 for sensitivity. CONCLUSION Our data suggest that mammaglobin is one of the first relatively mammary-specific and mammary-sensitive markers. Mammaglobin and BRST-2 appear to represent useful markers for breast cancer and should be used as a component of panels evaluating tumors of unknown primary sites.
Fuzzy computer-aided diagnosis of Alzheimer's disease using MRI and PET statistical features

In this paper, MRI and PET image features from selected brain regions are used as inputs in a fuzzy inference classification system for automatic diagnosis of Alzheimer's Disease (AD). Mean values of voxel intensity in spatial regions of interest which are extracted from normalized MRI and PET scans of brain gray matter were used as features. Area under receiver operating characteristic (AUC) was used as a classification performance measure, being function of the number of brain anatomical and functional regions of interest from which the features were extracted. In the result, combination of features from 7 MRI regions and 39 PET regions gave the highest performance of classification (AUC=0.94).
Nasal nitric oxide in cystic fibrosis with and without humming

Background Nasal nitric oxide (nNO) values are reduced in patients with cystic fibrosis (CF). Humming during nNO measurement increases nNO values in healthy subjects. Nasal NO is reduced in patients with CF, sinus disease or nasal polyps. Humming nNO values have not been reported in CF patients yet. Our aim was to explore humming nNO values in CF patients and assess whether nNO during humming is a better discriminator than silent nNO measurements in this patient group.
Synthesis of Control Protocols for Autonomous Systems

This article provides a review of control protocol synthesis techniques that incorporate methodologies from formal methods and control theory to provide correctness guarantee for different types of autonomous systems, including those with discrete and continuous state space. The correctness of the system is defined with respect to a given specification expressed as a formula in linear temporal logic to precisely describe the desired properties of the system. The formalism presented in this article admits nondeterminism, allowing uncertainties in the system to be captured. A particular emphasis is on alleviating some of the difficulties, e.g., heterogeneity in the underlying dynamics and computational complexity, that naturally arise in the construction of control protocols for autonomous systems.
Chronic exposure of Sprague-Dawley rats to 20 kHz triangular magnetic fields

Purpose: As a continuing study of 20 kHz triangular magnetic fields (MF) [Lee et al. ], we investigated the chronic toxicity and possible health effects of exposure to 20 kHz MF at the flux density of 30 μT, which is the limit standard for the occupational population in South Korea, with the use of Sprague-Dawley rats. Materials and methods: Rats were exposed to 20 kHz triangular MF at 30 μT Root Mean Square for 8 h/day for 18 months. Body and organ weights were measured and urinalysis, hematological and blood biochemistry analyses were performed in individual animals. Histopathological evaluation was also performed for the brain, thymus, lung, heart, liver, kidney, intestine and reproductive organs, including tumour tissue. Results: The mortality patterns in male or female rats exposed to magnetic fields were compared to the mortality patterns found in sex-matched sham control animals. Significant alteration of body weight was not observed with MF exposure. No significant differences were seen in sham-exposed and MF-exposed animals based on urological factors, hematological factors and blood biochemistry. Total tumour incidence was not different between sham-exposed and MF-exposed animals. Conclusion: Our results suggest that chronic exposure to 20 kHz triangular MF with 30 μT flux density did not increase toxicity in rats.
Genetics, evolution and conservation of Bromeliaceae

Bromeliaceae is a morphologically distinctive and ecologically diverse family originating in the New World. Three centers of diversity, 58 genera, and about 3,140 bromeliad species are currently recognized. We compiled all of the studies related to the reproductive biology, genetic diversity, and population structure of the Bromeliaceae, and discuss the evolution and conservation of this family. Bromeliads are preferentially pollinated by vertebrates and show marked variation in breeding systems, from predominant inbreeding to predominant outcrossing, as well as constancy in chromosome number (2n = 2x = 50). Autogamous or mixed mating system bromeliads have a high inbreeding coefficient (FIS), while outcrossing species show low FIS. The degree of differentiation among populations (FST)of species ranges from 0.043 to 0.961, which can be influenced by pollen and seed dispersal effects, clonal growth, gene flow rates, and connectivity among populations. The evolutionary history of the Bromeliaceae is poorly known, although some studies have indicated that the family arose in the Guayana Shield roughly 100 Mya. We believe that genetic, cytogenetic, and reproductive data will be essential for diagnosing species status and for assisting conservation programs.
Comparing OECD PISA Reading in English to Other Languages: Identifying Potential Sources of Non-Invariance

The use of the Programme for International Student Assessment (PISA) across nations, cultures, and languages has been criticized. The key criticisms point to the linguistic and cultural biases potentially underlying the design of reading comprehension tests, raising doubts about the legitimacy of comparisons across economies. Our research focused on the type and magnitude of invariance or non-invariance in the PISA Reading Comprehension test by language, culture, and economic development relative to performance of the Australian English-speaking reference group used to develop the tests. Multi-Group Confirmatory Factor Analysis based on means and covariance structure (MACS) modeling was used to establish a dMACS effect size index for each economy for the degree of non-invariance. Only three wealthy, English-speaking countries had scalar invariance with Australia. Moderate or large effects were observed in just 31% of the comparisons. PISA index of economic, social and cultural status had a moderate inverse correlation with dMACS suggesting that socioeconomic resourcing of education played a significant role in measurement invariance, while educational practice and language factors seemed to play a further small role in non-invariance. Alternative approaches to reporting PISA results consistent with non-invariance are suggested.
CMBPol Mission Concept Study: Foreground Science Knowledge and Prospects

We report on our knowledge of Galactic foregrounds, as well as on how a CMB satellite mission aiming at detecting a primordial B-mode signal (CMBPol) will contribute to improving it. We review the observational and analysis techniques used to constrain the structure of the Galactic magnetic field, whose presence is responsible for the polarization of Galactic emissions. Although our current understanding of the magnetized interstellar medium is somewhat limited, dramatic improvements in our knowledge of its properties are expected by the time CMBPol flies. Thanks to high resolution and high sensitivity instruments observing the whole sky at frequencies between 30 GHz and 850 GHz, CMBPol will not only improve this picture by observing the synchrotron emission from our galaxy, but also help constrain dust models. Polarized emission from interstellar dust indeed dominates over any other signal in CMBPol's highest frequency channels. Observations at these wavelengths, combined with ground-based studies of starlight polarization, will therefore enable us to improve our understanding of dust properties and of the mechanism(s) responsible for the alignment of dust grains with the Galactic magnetic field. CMBPol will also shed new light on observations that are presently not well understood. Morphological studies of anomalous dust and synchrotron emissions will indeed constrain their natures and properties, while searching for fluctuations in the emission from heliospheric dust will test our understanding of the circumheliospheric interstellar medium. Finally, acquiring more information on the properties of extra-Galactic sources will be necessary in order to maximize the cosmological constraints extracted from CMBPol's observations of CMB lensing. (abridged)
Non-invasive Measurement of Perfusion: a Critical Review of Arterial Spin Labelling Techniques

The non-invasive nature of arterial spin labelling (ASL) has opened a unique window into human brain function and perfusion physiology. High spatial and temporal resolution makes the technique very appealing not only for the diagnosis of vascular diseases, but also in basic neuroscience where the aim is to develop a more comprehensive picture of the physiological events accompanying neuronal activation. However, low signal-to-noise ratio and the complexity of flow quantification make ASL one of the more demanding disciplines within MRI. In this review, the theoretical background and main implementations of ASL are revisited. In particular, the perfusion quantification methods, including the problems and pitfalls involved, are thoroughly discussed in this article. Finally, a brief summary of applications is provided. Perfusion, or the steady state nutritive delivery of blood to the tissue capillary bed, is vital for the homeostasis, and thereby survival, of an organ. Accurate perfusion measurement can provide important diagnostic information on pathological conditions, e.g. whether an ischaemic organ is viable or not. Among other methods, MRI has emerged as a powerful tool for assessing tissue perfusion and possesses strong diagnostic and prognostic capabilities, especially when combined with additional MRI modalities such as T 1 , T 2 and diffusion-weighted images. Historically, radiology has principally offered morphological imaging techniques; however, these new MRI perfusion techniques will add routine physiological imaging to its portfolio. This information is not only valuable in clinical settings, but is of great importance for basic physiological science and drug development, where, for example, perfusion changes due to a pharmacological stimulus might be monitored over time. There exist two main MRI perfusion methods: bolus tracking after the injection of an exogenous endovascular tracer and arterial spin labelling (ASL), which uses magnetically labelled water protons as an endogenous tracer. The complete non-invasiveness of ASL makes it very suitable for perfusion studies of healthy volunteers and in patient groups requiring repetitive follow-ups. This is especially important in patients with particular conditions, such as kidney failure, or in paediatric populations where the use of radioactive tracers or exogenous contrast agents may be restricted. Recently, ASL has gained more clinical acceptance partly due to these advantages, but also as a result of the recently introduced technique for imaging the perfusion territory of individual blood vessels in the brain. In addition, the increased availability of high-field (> 3 T) clinical scanners has moved ASL from the research and development stage towards …
Character-based Neural Embeddings for Tweet Clustering

In this paper we show how the performance of tweet clustering can be improved by leveraging character-based neural networks. The proposed approach overcomes the limitations related to the vocabulary explosion in the word-based models and allows for the seamless processing of the multilingual content. Our evaluation results and code are available on-line: https://github.com/vendi12/tweet2vec_clustering.
Behavioral and Brain Functions

Background: In the light of the ongoing debate about lowering the cut-off for acceptable blood lead level to <5 μg/dL from the currently recommended level of <10 μg/dL, we considered whether prenatal exposure to varying levels of lead is associated with similar or disparate effects on neonatal behavior. Methods: Using Brazelton's Neonatal Behavioral Assessment Scale (NBAS), an epidemiological approach and robust statistical techniques like multivariate linear regression, logistic regression, Poisson regression and structural equations modeling analyses we estimated the simultaneous indirect effects of umbilical cord blood lead (CBL) levels and other neonatal covariates on the NBAS clusters. Results: We observed that when analyzed in all study subjects, the CBL levels independently and strongly influenced autonomic stability and abnormal reflexes clusters. However, when the analysis was restricted to neonates with CBL <10 μg/dL, CBL levels strongly influenced the range of state, motor and autonomic stability clusters. Abnormal walking reflex was consistently associated with an increased CBL level irrespective of the cut-off for CBL, however, only at the lower cut-offs were the predominantly behavioral effects of CBL discernible. Conclusion: Our results further endorse the need to be cognizant of the detrimental effects of blood lead on neonates even at a low-dose prenatal exposure. Background There is an ongoing debate over the appropriate cut-off of blood lead concentration to detect lead poisoning [1-6]. Starting from 60 μg/dL the cut-off recommended by the Centers for Disease Control (CDC) receded to 25 μg/dL and then to the currently used value of 10 μg/dL[5]. This was essentially due to a series of studies showing that even at low doses of exposure, environmental lead continues to be a biological and social toxicant [4,5,7,8]. Recently, there is a burgeoning recognition that even at low doses exposure to lead has serious implications on a child's behavior pattern. For example, lead exposure in low doses has been convincingly implicated in juvenile delinquency [9,10], intelligence quotient (IQ) patterns [4,11-18] and Published: 27 June 2006 Behavioral and Brain Functions 2006, 2:22 doi:10.1186/1744-9081-2-22 Received: 18 April 2006 Accepted: 27 June 2006 This article is available from: http://www.behavioralandbrainfunctions. com/content/2/1/22 © 2006 Patel et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
urrent state of digital signal processing in myoelectric interfaces and elated applications

This review discusses the critical issues and recommended practices from the perspective of myoelectric interfaces. The major benefits and challenges of myoelectric interfaces are evaluated. The article aims to fill gaps left by previous reviews and identify avenues for future research. Recommendations are given, for example, for electrode placement, sampling rate, segmentation, and classifiers. Four groups of applications where myoelectric interfaces have been adopted are identified: assistive technology, rehabilitation technology, input devices, and silent speech interfaces. The state-of-the-art applications
Are You Efficient, Trendy or Skillfull? An Exploratory Segmentation of Mobile Service Users

In the study at hand we describe users of mobile phones and mobile services, based on a random sample describing the Finnish general population. A lot of attention has been paid recently to investigating users of mobile phones because mobile services demand has not developed as expected in the Finnish market. We add to this body of knowledge through offering a description of Finnish mobile consumers, and a look at different users’ future interest to use different services.
A multicomponent nonpharmacological intervention improves activity rhythms among nursing home residents with disrupted sleep/wake patterns.

BACKGROUND Sleep and circadian rhythms are disrupted among many nursing home (NH) residents. We examined the impact of a multicomponent nonpharmacological intervention on 24-hour rest/activity rhythms among long-stay NH residents. METHODS The study was a randomized controlled trial in which, following a 3-day baseline, participants received 5 days of either usual care (control condition) or the active intervention. The intervention combined increased exposure to outdoor bright light, efforts to keep residents out of bed during the day, structured physical activity, institution of a bedtime routine, and efforts to reduce nighttime noise and light in residents' rooms. For 100 residents with baseline and follow-up wrist actigraphy data (mean age = 87 years; 76% women), rest/activity rhythms were modeled to determine the rhythm acrophase (peak time), nadir (trough time), midline estimating statistic of rhythm (MESOR) (midpoint), amplitude (height of peak), slope, and the rest period/active period ratio (alpha). RESULTS The intervention led to an increase in the duration of the "active" portion of the rhythm, which was primarily accounted for by a shift in the rest/activity rhythm rise to an earlier time. Findings persisted when analyses were adjusted for age, cognitive functioning, medical comorbidities, and behavioral disturbances. CONCLUSIONS These findings suggest that the intervention may effectively improve the robustness of rest/activity rhythms in NH residents. Further research is needed to examine the impact of similar interventions on other measures of circadian rhythms (e.g., body temperature, melatonin) among NH residents.