Miracle-dz/UniFAR-FTUs huggingface dataset:
'Compensatory slippage' in the evolution of ribosomal RNA genes.

The distribution patterns of shared short repetitive motifs in the expansion segments of the large subunit rRNA genes of different species show that these segments are coevolving as a set and that in two examined vertebrate species the RNA secondary structures are conserved as a consequence of runs of motifs in one region being compensated by complementary motifs in another. These unusual processes, involving replication-slippage, have implications for the evolution of ribosomal RNA and for the use of the rDNA multigene family as a 'molecular clock' for assessing relationships between species.
Fluorescence of coral larvae predicts their settlement response to crustose coralline algae and reflects stress

Multi-coloured homologues of the green fluorescent protein generate some of the most striking visual phenomena in the ocean. Despite their natural prominence in reef-building corals and widespread use in biotechnology, their biological role remains obscure. Here, we experimented with larvae of Acropora millepora to determine what can be learned about a coral larva or recruit from its fluorescent colour. We performed 12 crosses between seven A. millepora colonies representing differing fluorescence phenotypes, the larvae of which were exposed to a natural settlement cue (crustose coralline algae) and heat–light stress. Parental effects explained 18 per cent of variation in colour and 47 per cent of variation in settlement. The colour of the larval family emerged as a predictor of the settlement success: redder families were significantly less responsive to the provided settlement cue (p = 0.006). This relationship was owing to a correlation between parental effects on settlement and colour (r2 = 0.587, p = 0.045). We also observed pronounced (16%) decline in settlement rate, as well as subtle (2%), but a statistically significant decrease in red fluorescence, as a consequence of heat–light stress exposure. Variation in settlement propensity in A. millepora is largely owing to additive genetic effects, and is thought to reflect variation in dispersal potential. Our results suggest an optical signature to discriminate between long- and short-range dispersing genotypes, as well as to evaluate stress. Further research in this direction may lead to the development of field applications to trace changes in coral life history and physiology caused by global warming.
Processing queries with expensive functions and large objects in distributed mediator systems

LeSelect is a mediator system which allows scientists to publish their resources (data and programs) so they can be transparently accessed. The scientists can typically issue queries which access distributed published data and involve the execution of expensive functions (corresponding to programs). Furthermore, the queries can involve large objects, such as images (e.g. archived meteorological satellite data). In this context, the costs of transmitting large objects and invoking expensive functions are the dominant factors of execution time. In this paper, we first propose three query execution techniques which minimize these costs by taking full advantage of the distributed architecture of mediator systems like LeSelect. Then we devise parallel processing strategies for queries including expensive functions. Based on experimentation, we show that it is hard to predict the optimal execution order when dealing with several functions. We propose a new hybrid parallel technique to solve this problem and give some experimental results.
On non-blocking switching networks

A switching network may be informally described as a collection of single-pole, single-throw switches arranged so as to connect a set of terminals called inputs to another set of terminals called outputs. It is non-blocking if, given any set of connections from some of the inputs to some of the outputs, and an idle input terminal x and idle output terminal y, then it is possible to connect x to y without disturbing any of the existing connections. Denote by σ(a, b) the minimal number of switches necessary to connect a inputs to b outputs using a non-blocking network. We are interested in studying the growth of σ(a, a) as a ∞. Results of C. Clos show that σ(a, a) ⩽ C ae2√log a·log 2. We show that σ(a, a) ⩽ 8a(log2a)2.
Automatic error detection in Russian learner language

Learner corpora, also known as interlanguage (IL) or second language (L2) corpora, have become increasingly popular resources in language research in the past decade. Learner corpora provide large volume of rich data for theoretical and applied language studies. Just as native (or L1) corpora, learner corpora are particularly useful for research when they are tagged; and learner corpora often contain tags that are more intricate than those found in L1 corpora. Metalinguistic tags, for instance, often contain information relevant both to the author of the text (language background, level, etc.) and the task (genre, format, time restriction, etc.). In regards to grammatical annotation, in addition to the usual lemmatisation and morphosyntactic tagging, L2 corpora may contain error-tags that provide information on deviant language use. Error-tagging is known to be a resourceconsuming and technologically-challenging task, more so for highly inflectional languages such as Russian, with its rich inflection, derivation, agreement, and robust syntax. Yet, the ability to conduct corpus searches by the types of errors may afford better insight into the processes of language acquisition; this goal warrants the necessity of errortagging learner corpora. The project described in the present paper attempts to develop an automatic error-tagging protocol for Russian learner language. The annotation procedures are currently tested on the materials of the Russian Learner Corpus of Academic Writing (RULEC).
Superpixel-based classification of hyperspectral data using sparse representation and conditional random fields

This paper presents a superpixel-based classifier for landcover mapping of hyperspectral image data. The approach relies on the sparse representation of each pixel by a weighted linear combination of the training data. Spatial information is incorporated by using a coarse patch-based neighborhood around each pixel as well as data-adapted superpixels. The classification is done via a hierarchical conditional random field, which utilizes the sparse-representation output and models spatial and hierarchical structures in the hyperspectral image. The experiments show that the proposed approach results in superior accuracies in comparison to sparse-representation based classifiers that solely use a patch-based neighborhood.
Resource Classification for Medical Questions

We present an approach for manually and automatically classifying the resource type of medical questions. Three types of resources are considered: patient-specific, general knowledge, and research. Using this approach, an automatic question answering system could select the best type of resource from which to consider answers. We first describe our methodology for manually annotating resource type on four different question corpora totaling over 5,000 questions. We then describe our approach for automatically identifying the appropriate type of resource. A supervised machine learning approach is used with lexical, syntactic, semantic, and topic-based feature types. This approach is able to achieve accuracies in the range of 80.9% to 92.8% across four datasets. Finally, we discuss the difficulties encountered in both manual and automatic classification of this challenging task.
Tiled 360° panoramic projection system

In order to obtain 360 degree panoramic displays, tiled video projections are often used. In this paper we present a system for cylindrical 360 degree panoramic projection based on a client-server architecture. The system performs following actions: projector calibration, image transformation and video playback. To perform above actions several problems have to be addressed. Calibration of multiple projectors is based on computing of spatial relations between cylindrical projecting surface and each projector. We do this by photographing the projected chessboard pattern of each projector using a camera with fish-eye lens. The photograph first has to be unwrapped into a rectangle shaped texture. After that, the relation between original chessboard corners and corners on the photograph has to be found. Using these corners the image transformation function has to be interpolated. The transformation of image to be projected is done using this function and also includes lightning correction to achieve smooth transitions between each projector image. If playing video, videos from all projectors have to be synchronized. In the current client-server architecture, a server performs semiautomatic projector calibration, files and configuration distribution to clients and has the ability to off-line create images for each projector. Each client handles storage, showing of already prepared images and playback and real-time transformation of videos. The projector calibration is done using Matlab, whilst the playback and real-time transformation of video is done using custom made software written in C++ and OpenGL.
Contraception for HIV-infected women.

Decisions regarding the use of contraception for HIV-infected women are complicated by changing opinions regarding prevention and treatment. In addition, there is also interplay between the two risks involved: vertical HIV transmission in the event of pregnancy, and horizontal transmission to an uninfected partner. Unfortunately, the methods of contraception that have historically best protected against HIV transmission, such as condoms, have also been least effective in preventing pregnancy. Moreover, studies have shown that HIV-positive women who use a more effective method of contraception are less likely to also use a condom, even with an uninfected partner. While two different methods of contraception are advisable to deal with the two separate risk factors, it is still unclear which methods are safest and most effective.
Autonomic Function Tests: Some Clinical Applications

Modern autonomic function tests can non-invasively evaluate the severity and distribution of autonomic failure. They have sufficient sensitivity to detect even subclinical dysautonomia. Standard laboratory testing evaluates cardiovagal, sudomotor and adrenergic autonomic functions. Cardiovagal function is typically evaluated by testing heart rate response to deep breathing at a defined rate and to the Valsalva maneuver. Sudomotor function can be evaluated with the quantitative sudomotor axon reflex test and the thermoregulatory sweat test. Adrenergic function is evaluated by the blood pressure and heart rate responses to the Valsalva maneuver and to head-up tilt. Tests are useful in defining the presence of autonomic failure, their natural history, and response to treatment. They can also define patterns of dysautonomia that are useful in helping the clinician diagnose certain autonomic conditions. For example, the tests are useful in the diagnosis of the autonomic neuropathies and distal small fiber neuropathy. The autonomic neuropathies (such as those due to diabetes or amyloidosis) are characterized by severe generalized autonomic failure. Distal small fiber neuropathy is characterized by an absence of autonomic failure except for distal sudomotor failure. Selective autonomic failure (which only one system is affected) can be diagnosed by autonomic testing. An example is chronic idiopathic anhidrosis, where only sudomotor function is affected. Among the synucleinopathies, autonomic function tests can distinguish Parkinson's disease (PD) from multiple system atrophy (MSA). There is a gradation of autonomic failure. PD is characterized by mild autonomic failure and a length-dependent pattern of sudomotor involvement. MSA and pure autonomic failure have severe generalized autonomic failure while DLB is intermediate.
Robust h ∞ networked control for systems with uncertain sampling rates

This study investigates the problem of controller design for systems with uncertain sampling rates. The system is controlled through a communication network. The sampling period, within a given interval, is assumed to be time-varying and a simplified framework for the network-induced delay is considered. The overall system is thus described by an uncertain discrete-time model with time-varying parameters inside a polytope whose vertices are obtained by means of the Cayley–Hamilton theorem. A digital robust controller that minimises an upper bound to the ℋ∞ performance of the closed-loop networked control system (NCS) is determined. The design conditions rely on a particular parameter-dependent Lyapunov function and are expressed as bilinear matrix inequalities (BMIs) in terms of extra matrix variables, which may be explored in the search for a better system behaviour. Numerical examples illustrate the results.
Sampling for Microsatellite-Based Population Genetic Studies: 25 to 30 Individuals per Population Is Enough to Accurately Estimate Allele Frequencies

One of the most common questions asked before starting a new population genetic study using microsatellite allele frequencies is “how many individuals do I need to sample from each population? ” This question has previously been answered by addressing how many individuals are needed to detect all of the alleles present in a population (i.e. rarefaction based analyses). However, we argue that obtaining accurate allele frequencies and accurate estimates of diversity are much more important than detecting all of the alleles, given that very rare alleles (i.e. new mutations) are not very informative for assessing genetic diversity within a population or genetic structure among populations. Here we present a comparison of allele frequencies, expected heterozygosities and genetic distances between real and simulated populations by randomly subsampling 5–100 individuals from four empirical microsatellite genotype datasets (Formica lugubris, Sciurus vulgaris, Thalassarche melanophris, and Himantopus novaezelandia) to create 100 replicate datasets at each sample size. Despite differences in taxon (two birds, one mammal, one insect), population size, number of loci and polymorphism across loci, the degree of differences between simulated and empirical dataset allele frequencies, expected heterozygosities and pairwise FST values were almost identical among the four datasets at each sample size. Variability in allele frequency and expected heterozygosity among replicates decreased with increasing sample size, but these decreases were minimal above sample sizes of 25 to 30. Therefore, there appears to be little benefit in sampling more than 25 to 30 individuals per population for population genetic studies based on microsatellite allele frequencies.
Generalized adaptive notch filters with frequency debiasing

Generalized adaptive notch filters are used for identification/tracking of quasi-periodically varying dynamic systems and can be considered an extension, to the system case, of classical adaptive notch filters. Belonging to the class of causal adaptive filters, the generalized adaptive notch filtering algorithms yield biased frequency estimates. We show that this bias can be removed, or at least substantially reduced. The only price paid for the resulting improvement of the filter's tracking performance is in terms of a decision delay, which must be incorporated in the adaptive loop. Since decision delay is acceptable in many practical applications, the proposed bias/delay trade-off is an attractive alternative to the classical bias/variance compromise.
Duration and exclusiveness of breastfeeding and childhood asthma-related symptoms

The aim of our study was to examine the associations of breastfeeding duration and exclusiveness with the risks of asthma-related symptoms in preschool children, and to explore whether these associations are explained by atopic or infectious mechanisms. This study was embedded in a population-based prospective cohort study of 5,368 children. Information on breastfeeding duration, exclusiveness and asthma-related symptoms, including wheezing, shortness of breath, dry cough and persistent phlegm, was obtained by questionnaires. Compared with children who were breastfed for 6 months, those who were never breastfed had overall increased risks of wheezing, shortness of breath, dry cough and persistent phlegm during the first 4 yrs (OR 1.44 (95% CI 1.24–1.66), 1.26 (1.07–1.48), 1.25 (1.08–1.44) and 1.57 (1.29–1.91), respectively). Similar associations were observed for exclusive breastfeeding. The strongest associations per symptom per year were observed for wheezing at 1 and 2 yrs. Additionally adjusted analyses showed that the associations of breastfeeding with asthma-related symptoms were not explained by eczema but partly by lower respiratory tract infections. Shorter duration and nonexclusivity of breastfeeding were associated with increased risks of asthma-related symptoms in preschool children. These associations seemed, at least partly, to be explained by infectious, but not by atopic, mechanisms.
DRAM Refresh Mechanisms, Penalties, and Trade-Offs

Ever-growing application data footprints demand faster main memory with larger capacity. DRAM has been the technology choice for main memory due to its low latency and high density. However, DRAM cells must be refreshed periodically to preserve their content. Refresh operations negatively affect performance and power. Traditionally, the performance and power overhead of refresh have been insignificant. But as the size and speed of DRAM chips continue to increase, refresh becomes a dominating factor of DRAM performance and power dissipation. In this paper, we conduct a comprehensive study of the issues related to refresh operations in modern DRAMs. Specifically, we describe the difference in refresh operations between modern synchronous DRAM and traditional asynchronous DRAM; the refresh modes and timings; and variations in data retention time. Moreover, we quantify refresh penalties versus device speed, size, and total memory capacity. We also categorize refresh mechanisms based on command granularity, and summarize refresh techniques proposed in research papers. Finally, based on our experiments and observations, we propose guidelines for mitigating DRAM refresh penalties.
Probable Early-Onset Alzheimer’s Disease in an Apolipoprotein E2 Homozygote

Objective: To describe a case of early-onset Alzheimer’s disease (AD) in an apolipoprotein (Apo) Ε2/Ε2 homozygote. Background: Apo Ε2/Ε2 is the rarest of the ApoE genotypes, representing only 1.4% of the population. Cognitive decline in ApoE Ε2 homozygotes has rarely been reported. Case Report/Methods: We report a 58-year-old Apo Ε2/Ε2 female who meets clinical criteria for probable AD as confirmed by neuropsychological testing, positron emission/computed tomography scan, CSF analysis and genetic screening for known mutations. Results: The clinical course is typical of AD, with progressive cognitive and functional decline. Conclusion: Clinically confirmed early-onset AD is atypical in ApoE2 homozygotes but can occur.
Electrical and mechanical restitution of the human heart at different rates of stimulation.

Action potential duration and contractility are reduced following premature excitations, and gradually increase as the stimulus interval is lengthened. To examine these phenomena of electrical and mechanical restitution in the human heart, we simultaneously measured action potential duration and the maximum rate of left ventricular pressure in five patients undergoing electrophysiological study. Test beats were introduced at varying intervals after the last of a series of steady state intervals. By plotting action potential duration and maximum rate of left ventricular pressure as a function of the test interval, we formed electrical and mechanical restitution curves. When the rate of steady state pacing was increased, there was a decrease in action potential duration and an increase in the maximum rate of left ventricular pressure for all test intervals; i.e., a change in pacing rate affected action potential duration and maximum rate of left ventricular pressure of test responses in a reciprocal fashion. In addition, a higher steady state pacing rate allowed action potentials and contractile responses to be elicited at shorter test intervals, thereby displacing the electrical and mechanical restitution curves to the left. The magnitude of the leftward shift of both curves corresponded closely to the shortening of the steady state action potential duration induced by the increase in pacing rate. These findings confirm for the human heart that both electrical and mechanical restitution occur after membrane repolarization, i.e., as a function of the electrical diastolic interval preceding a beat, and not the stimulus interval.
Shielding Effect Analysis of Em Waves for Oblique Incidence in Double Shields

Shielding effectiveness analysis of double shields with conductors using plane-wave theory are carried out as a function of angle of incidence. The plane wave shielding effectiveness of new combination of these materials is evaluated for the double shields. Stable highly conductive materials , with characteristics of light-weight, mechanically strong materials are considered for shielding the EMI. The analysis is done at a particular frequency for double shields of aluminum and copper polymers.
Sphingosine Kinase 1 Is Associated with Gastric Cancer Progression and Poor Survival of Patients

Purpose: The present study was to investigate the clinical significance of sphingosine kinase 1 (SPHK1), an oncoenzyme, in the development and progression of gastric cancer. Experimental Design: mRNA and protein levels of SPHK1 expression in normal gastric epithelial cells, gastric cancer cell lines, and paired gastric cancer lesions and the adjacent noncancerous tissues were examined using reverse transcription-PCR and Western blotting. Immunohistochemistry was employed to analyze SPHK1 expression in 175 clinicopathologically characterized gastric cancer cases. Statistical analyses were applied to derive prognostic and diagnostic associations. Results: Levels of SPHK1 mRNA and protein were higher in gastric cancer cell lines than in normal gastric epithelial cells. SPHK1 protein level was up-regulated in gastric cancer lesions compared with that in the paired adjacent noncancerous tissues. Gastric cancer tissues from 115 of 175 (65.7%) patients revealed high level of SPHK1 protein expression in contrast to the undetectable or marginally detectable expression of SPHK1 in the adjacent noncancerous gastric tissues. Significantly different expression levels of SPHK1 were found in patients at different clinical stages (P = 0.003), T classification (P = 0.035), and M classification (P = 0.020). Patients with higher SPHK1 expression had shorter overall survival time, whereas those with lower SPHK1 expression survived longer. Further multivariate analysis suggested that SPHK1 up-regulation was an independent prognostic indicator for the disease. Conclusions: SPHK1 protein could be a useful marker for the prognosis of gastric cancer. Further study on the potential use of SPHK1 as a therapeutic target is also warranted.