Miracle-dz/UniFAR-FTUs huggingface dataset:
MorphoCatcher: a multiple-alignment based web tool for target selection and designing taxon-specific primers in the loop-mediated isothermal amplification method

Background Advantages of loop-mediated isothermal amplification in molecular diagnostics allow to consider the method as a promising technology of nucleic acid detection in agriculture and medicine. A bioinformatics tool that provides rapid screening and selection of target nucleotide sequences with subsequent taxon-specific primer design toward polymorphic orthologous genes, not only unique or conserved common regions of genome, would contribute to the development of more specific and sensitive diagnostic assays. However, considering features of the original software for primer selection, also known as the PrimerExplorer (Eiken Chemical Co. LTD, Tokyo, Japan), the taxon-specific primer design using multiple sequence alignments of orthologs or even viral genomes with conservative architecture is still complicated. Findings Here, MorphoCatcher is introduced as a fast and simple web plugin for PrimerExplorer with a clear interface. It enables an execution of multiple-alignment based search of taxon-specific mutations, visual screening and selection of target sequences, and easy-to-start specific primer design using the PrimerExplorer software. The combination of MorphoCatcher and PrimerExplorer allows to perform processing of the multiple alignments of orthologs for informative sliding-window plot analysis, which is used to identify the sequence regions with a high density of taxon-specific mutations and cover them by the primer ends for better specificity of amplification. Conclusions We hope that this new bioinformatics tool developed for target selection and taxon-specific primer design, called the MorphoCatcher, will gain more popularity of the loop-mediated isothermal amplification method for molecular diagnostics community. MorphoCatcher is a simple web plugin tool for the PrimerExplorer software which is freely available only for non-commercial and academic users at http://morphocatcher.ru.
Rendezvous trajectory generation for energy trophallaxis

This paper presents a novel approach of rendezvous trajectory generation for mobile robots. Rendezvous is a special study of two robots or more moving to meet at a previously agreed location. In multi-robot systems, rendezvous plays a significant role in carrying out different missions such as formation performance, collective tasks, swarming behaviours, self-assembly, self-sharing energy, self-recharging energy, etc. In this paper, we investigate a method of trajectory generation, which makes robot performing energy trophallaxis. The proposed method is a kinematic-based model that fully satisfies dynamic constraints of mobile robots as well as desirability of the final robot postures at the rendezvous point. Simulation results of the generated trajectory are provided to demonstrate the possibility of this approach.
Cross-Border Risk Factors of Cloud Services: Risk Assessment of IS Outsourcing to Foreign Cloud Service Providers

This paper identifies specific risk factors of cross-border outsourcing to cloud environments and discusses methods of evaluation. Many approaches lack in comparability between costs and risks. Therefore, we present two evaluation approaches based on the capital value (costs) and Analytical Network Process (risks) to support the assessment of outsourcing decisions under special consideration of cross-border risk factors. Although the integration of the two approaches needs further research, we present an early attempt to combine these two methods.
Being and Literature: The Disclosure of Place in Modernity

Irven, Donovan Ph.D., Purdue University, August 2016. Being and Literature: The Disclosure of Place in Modernity. Major Professor: Daniel W. Smith. The dissertation develops an original ontology of place by reading Modernist literature (1864-1950) as a critical reaction to Modern philosophy (1641-1800), and builds a platform upon movements implicit in literature from which future metaphysical and epistemological inquiries can begin. Western metaphysics and epistemology have been conditioned by the Cartesian commitment to the ego cogito, primarily understood as a subject to which the world appears as represented in concepts or ideas. The postmodern and deconstructive criticisms of such philosophical foundations – and indeed, on the very notion of foundation itself – have become well worn, but have failed to offer a viable alternative, everywhere heralding the “end of metaphysics” while simultaneously carrying on metaphysical discourse as if unaware of their own dictum! Being and Literature: The Disclosure of Place in Modernity offers the ontology of place as an alternative to postmodern anti-realism, showing that Modernist literature prefigures the postmodern critical project and implicitly leads the way toward an ontology of place that would de-center the cogito subject from the heart of Western metaphysics and epistemology. We avoid anti-realism through the reading of Modernism, while developing the alternative placial ontology capable of responding the weaknesses of postmodern anti-realism.
Complexity of VC-classes of sequences with long repetitive runs ∗

The Vapnik-Chervonenkis (VC) dimension (also known as the trace number) and the Sauer-Shelah lemma have found applications in numerous areas including set theory, combinatorial geometry, graph theory and statistical learning theory. Estimation of the complexity of discrete structures associated with the search space of algorithms often amounts to estimating the cardinality of a simpler class which is effectively induced by some restrictive property of the search. In this paper we study the complexity of Boolean-function classes of finite VC-dimension which satisfy a local ‘smoothness’ property expressed as having long runs of repeated values. As in Sauer’s lemma, a bound is obtained on the cardinality of such classes.
Acyclic colouring of graphs

A vertex colouring of a graph G is called acyclic if no two adjacent vertices have the same colour and there is no two-coloured cycle in G. The acyclic chromatic number of G, denoted by A(G), is the least number of colours in an acyclic colouring of G. We show that if G has maximum degree d then A(G) = O(d 4 3 ) as d → ∞. This settles a problem of Erdős who conjectured, in 1976, that A(G) = o(d2) as d →∞. We also show that there are graphs G with maximum degree d for which A(G) = Ω(d 4 3 /(log d) 1 3 ); and that the edges of any graph with maximum degree d can be coloured by O(d) colours so that no two adjacent edges have the same colour and there is no two-coloured cycle. All the proofs rely heavily on probabilistic arguments.
3D morphological analysis of brain MRI using wavelets

This article describes the use of the 2D wavelet transform to estimate the multiscale gradient of two types of cortical sulci, from which two potentially discriminating features, namely the gradient mean magnitude and entropy of its orientation distributions, are calculated. The obtained results corroborate the potential of such multiscale geometrical features for identification of narrow and wide cortical sulci, and important problem in medical imaging. The spatial scale leading to better discrimination is also identified.
Immunogenetic Mechanisms Leading to Thyroid Autoimmunity: Recent Advances in Identifying Susceptibility Genes and Regions

The autoimmune thyroid diseases (AITD) include Graves’ disease (GD) and Hashimoto’s thyroiditis (HT), which are characterised by a breakdown in immune tolerance to thyroid antigens. Unravelling the genetic architecture of AITD is vital to better understanding of AITD pathogenesis, required to advance therapeutic options in both disease management and prevention. The early whole-genome linkage and candidate gene association studies provided the first evidence that the HLA region and CTLA-4 represented AITD risk loci. Recent improvements in; high throughput genotyping technologies, collection of larger disease cohorts and cataloguing of genome-scale variation have facilitated genome-wide association studies and more thorough screening of candidate gene regions. This has allowed identification of many novel AITD risk genes and more detailed association mapping. The growing number of confirmed AITD susceptibility loci, implicates a number of putative disease mechanisms most of which are tightly linked with aspects of immune system function. The unprecedented advances in genetic study will allow future studies to identify further novel disease risk genes and to identify aetiological variants within specific gene regions, which will undoubtedly lead to a better understanding of AITD patho-physiology.
Tense Trees as the “Fine Structure” of Discourse

We present a new compositional tense-aspect deindexing mechanism that makes use of tense trees as components of discourse contexts. The mechanism allows reference episodes to be correctly identified even for embedded clauses and for discourse that involves shifts in temporal perspective, and permits deindexed logical forms to be automatically computed with a small number of deindexing rules.
Detection of a population gradient in the Sagittarius stream

We present a quantitative comparison between the Horizontal Branch morphology in the core of the Sagittarius dwarf spheroidal galaxy (Sgr) and in a wide field sampling a portion of its tidal stream (Sgr Stream), located tens of kpc away from the center of the parent galaxy. We find that the Blue Horizontal Branch (BHB) stars in that part of the Stream are five times more abundant than in the Sgr core, relative to Red Clump stars. The difference in the ratio of BHB to RC stars between the two fields is significant at the $\ga$$4.8\sigma$ level. This indicates that the old and metal-poor population of Sgr was preferentially stripped from the galaxy in past peri-Galactic passages with respect to the intermediate-age metal rich population that presently dominates the bound core of Sgr, probably due to a strong radial gradient that was settled within the galaxy before its disruption. The technique adopted in the present study allows to trace population gradients along the whole extension of the Stream.
Neural Stem Cells in Drosophila: Molecular Genetic Mechanisms Underlying Normal Neural Proliferation and Abnormal Brain Tumor Formation

Neural stem cells in Drosophila are currently one of the best model systems for understanding stem cell biology during normal development and during abnormal development of stem cell-derived brain tumors. In Drosophila brain development, the proliferative activity of neural stem cells called neuroblasts gives rise to both the optic lobe and the central brain ganglia, and asymmetric cell divisions are key features of this proliferation. The molecular mechanisms that underlie the asymmetric cell divisions by which these neuroblasts self-renew and generate lineages of differentiating progeny have been studied extensively and involve two major protein complexes, the apical complex which maintains polarity and controls spindle orientation and the basal complex which is comprised of cell fate determinants and their adaptors that are segregated into the differentiating daughter cells during mitosis. Recent molecular genetic work has established Drosophila neuroblasts as a model for neural stem cell-derived tumors in which perturbation of key molecular mechanisms that control neuroblast proliferation and the asymmetric segregation of cell fate determinants lead to brain tumor formation. Identification of novel candidate genes that control neuroblast self-renewal and differentiation as well as functional analysis of these genes in normal and tumorigenic conditions in a tissue-specific manner is now possible through genome-wide transgenic RNAi screens. These cellular and molecular findings in Drosophila are likely to provide valuable genetic links for analyzing mammalian neural stem cells and tumor biology.
Intensive versus Guideline Blood Pressure and Lipid Lowering in Patients with Previous Stroke: Main Results from the Pilot ‘Prevention of Decline in Cognition after Stroke Trial’ (PODCAST) Randomised Controlled Trial

Background Stroke is associated with the development of cognitive impairment and dementia. We assessed the effect of intensive blood pressure (BP) and/or lipid lowering on cognitive outcomes in patients with recent stroke in a pilot trial. Methods In a multicentre, partial-factorial trial, patients with recent stroke, absence of dementia, and systolic BP (SBP) 125–170 mmHg were assigned randomly to at least 6 months of intensive (target SBP <125 mmHg) or guideline (target SBP <140 mmHg) BP lowering. The subset of patients with ischaemic stroke and total cholesterol 3.0–8.0 mmol/l were also assigned randomly to intensive (target LDL-cholesterol <1.3 mmol/l) or guideline (target LDL-c <3.0 mmol/l) lipid lowering. The primary outcome was the Addenbrooke’s Cognitive Examination-Revised (ACE-R). Results We enrolled 83 patients, mean age 74.0 (6.8) years, and median 4.5 months after stroke. The median follow-up was 24 months (range 1–48). Mean BP was significantly reduced with intensive compared to guideline treatment (difference –10·6/–5·5 mmHg; p<0·01), as was total/LDL-cholesterol with intensive lipid lowering compared to guideline (difference –0·54/–0·44 mmol/l; p<0·01). The ACE-R score during treatment did not differ for either treatment comparison; mean difference for BP lowering -3.6 (95% CI -9.7 to 2.4), and lipid lowering 4.4 (95% CI -2.1 to 10.9). However, intensive lipid lowering therapy was significantly associated with improved scores for ACE-R at 6 months, trail making A, modified Rankin Scale and Euro-Qol Visual Analogue Scale. There was no difference in rates of dementia or serious adverse events for either comparison. Conclusion In patients with recent stroke and normal cognition, intensive BP and lipid lowering were feasible and safe, but did not alter cognition over two years. The association between intensive lipid lowering and improved scores for some secondary outcomes suggests further trials are warranted. Trial Registration ISRCTN ISRCTN85562386
Behavioral Correlates of Complex Spike Synchrony in Cerebellar Microzones

The olivo-cerebellar system is crucial for smooth and well timed execution of movements based on sensory and proprioceptive cues. The inferior olive (IO) plays a pivotal role in this process by synchronizing its activity across neurons internally through connexin36 gap junctions and providing a timing and/or learning signal to the cerebellum. Even though synchrony achieved through electrical coupling in IO cells is generally thought to be important in timing motor output, a direct relation between timing of movement and synchrony of olivary discharges has never been demonstrated within functional microcomplexes using transgenics. Here we combined in vivo, two-photon calcium imaging of complex spikes in microcomplexes of Purkinje cell (PC) dendrites with high-speed filming of tail, trunk, and limb movements in awake wild-type and connexin36-deficient mice. In wild types at rest, functional clusters of PCs were poorly defined with synchrony correlations that were relatively small and spatially limited to mediolateral distances of ∼50 μm, whereas during locomotion synchrony of the same PCs increased in strength and extended over distances spanning multiple microzones that could be correlated to specific components of sharp and well bounded movements. Instead, connexin36-deficient mice exhibited prolonged and desynchronized complex spike activity within PC microcomplexes both at rest and during behavior. Importantly, the mutants also showed concomitant abnormalities in the execution of spinocerebellar reflexes, which were significantly slower and more gradual than in wild-type littermates, particularly following sensory perturbations. Our results highlight the importance of modulation of synchronous activity within and between cerebellar microcomplexes in on-line temporal processing of motor output.
MFS transporters required for multidrug/multixenobiotic (MD/MX) resistance in the model yeast: understanding their physiological function through post-genomic approaches

Multidrug/Multixenobiotic resistance (MDR/MXR) is a widespread phenomenon with clinical, agricultural and biotechnological implications, where MDR/MXR transporters that are presumably able to catalyze the efflux of multiple cytotoxic compounds play a key role in the acquisition of resistance. However, although these proteins have been traditionally considered drug exporters, the physiological function of MDR/MXR transporters and the exact mechanism of their involvement in resistance to cytotoxic compounds are still open to debate. In fact, the wide range of structurally and functionally unrelated substrates that these transporters are presumably able to export has puzzled researchers for years. The discussion has now shifted toward the possibility of at least some MDR/MXR transporters exerting their effect as the result of a natural physiological role in the cell, rather than through the direct export of cytotoxic compounds, while the hypothesis that MDR/MXR transporters may have evolved in nature for other purposes than conferring chemoprotection has been gaining momentum in recent years. This review focuses on the drug transporters of the Major Facilitator Superfamily (MFS; drug:H+ antiporters) in the model yeast Saccharomyces cerevisiae. New insights into the natural roles of these transporters are described and discussed, focusing on the knowledge obtained or suggested by post-genomic research. The new information reviewed here provides clues into the unexpectedly complex roles of these transporters, including a proposed indirect regulation of the stress response machinery and control of membrane potential and/or internal pH, with a special emphasis on a genome-wide view of the regulation and evolution of MDR/MXR-MFS transporters.
Requirements within the Ebola Viral Glycoprotein for Tetherin Antagonism

Tetherin is an interferon-induced, intrinsic cellular response factor that blocks release of numerous viruses, including Ebola virus, from infected cells. As with many viruses targeted by host factors, Ebola virus employs a tetherin antagonist, the viral glycoprotein (EboGP), to counteract restriction and promote virus release. Unlike other tetherin antagonists such as HIV-1 Vpu or KSHV K5, the features within EboGP needed to overcome tetherin are not well characterized. Here, we describe sequences within the EboGP ectodomain and membrane spanning domain (msd) as necessary to relieve tetherin restriction of viral particle budding. Fusing the EboGP msd to a normally secreted form of the glycoprotein effectively promotes Ebola virus particle release. Cellular protein or lipid anchors could not substitute for the EboGP msd. The requirement for the EboGP msd was not specific for filovirus budding, as similar results were seen with HIV particles. Furthermore trafficking of chimeric proteins to budding sites did not correlate with an ability to counter tetherin. Additionally, we find that a glycoprotein construct, which mimics the cathepsin-activated species by proteolytic removal of the EboGP glycan cap and mucin domains, is unable to counteract tetherin. Combining these results suggests an important role for the EboGP glycan cap and msd in tetherin antagonism.
Deep bite: a case report with chewing pattern and electromyographic activity before and after therapy with function generating bite.

AIM The purpose of this case report is the concurrent evaluation of the masticatory pattern and the electromyographic activity, recorded during mastication, before and after therapy of deep bite malocclusion. CASE REPORT An 11-year-old boy, affected by deep bite (overbite = 5 mm) was treated by the use of a functional appliance (Function Generating Bite for Deep bite correction = FGB-D). Mandibular movements during mastication of a soft and a hard bolus were recorded both before and 10 months after correction of the malocclusion. Electromyographic activity (EMG) of the masseters and anterior temporalis muscles were recorded at the same time. Chewing cycles and EMG activity were recorded with the K7 I kinesiograph (Myotronics Inc., Seattle, WA-USA). Before therapy a higher EMG activity was recorded for both masseters and anterior temporalis muscles in comparison with the results after therapy. RESULTS The results showed a great decrease of the EMG activity of masseter and anterior temporalis muscles. Moreover, the height and width of the chewing cycles in the frontal plane increased after therapy. CONCLUSION The functional improvement showed after therapy with FGB-D showed that the functional appliance is able to correct the dental malocclusion and the masticatory function. The orthodontic treatment should consider not only the repositioning of teeth within the dental arches but also the effects on function, especially when the malocclusion involves the muscular and skeletal structures.
MEASUREMENTS OF FISH TARGET STRENGTH : A REVIEW

The concept of target strength and its application to the quantitative assessment of fishery resources are discussed. Methods of determining the echo characteristics of fish are reviewed and a number of results presented. Among the more important of these results are: (1) practically every case of interest to the fishing industry is in an acoustic region in which the target strength varies widely with fish size and aspect and acoustic frequency, (2) the major contributors to target strength in this region have been determined to be the swim bladder, flesh, and skeleton, ancl (3) the average maximum side-aspect and dorsal-aspect target strength of an individual fish have been determined for this region. (4) (2) 10 7' 10 where 10 is the intensity of the sound striking the target and II is the intensity of the reflected sound measured at 1 m from the acoustic center of the target. If IT is the intensity of the reflected sound measured at some distance r from the target, then, assuming that the sound spreads spherically, and there are no losses, IT will be directly proportional to 10 : T = 10 log (~). Now if Is is the intensity of the projected sound 1 m from the source, U' is defined as the acoustic cross-section of the target, and 47Tr 2 is the spherical surface area through which all the incident energy is reflected. (T depends on the size, shape, and orientation of the target, and, in general, will vary with the angle between the incident direction and the direction of the receiver. In all present fisheries work, this angle is zero and therefore in this paper (T will be the acoustic cross-section of a target for the case in which the source and receiver are located at the same point. By letting r in equation (2) be equal to 1 m and combining equations (1) and (2), Active sonars project acoustic energy into the water in an effort to detect objects by the echoes they return, the intensity of the echo depending on the proportion of the sound reflected back to the receiver. The target strength of the echo-producing object is a quantitative measure of its reflecting characteristics and is defined as T = 10 log (~:) , TARGET STRENGTH Quantitative assessment of fishery resources is a difficult task, and many groups have turned to acoustic techniques to conduct assessment surveys. Present …