Miracle-dz/UniFAR-FTUs huggingface dataset:
Segmentation of Bleeding Regions in Wireless Capsule Endoscopy Images an Approach for inside Capsule Video Summarization

Wireless capsule endoscopy (WCE) is an effective means of diagnosis of gastrointestinal disorders. Detection of informative scenes by WCE could reduce the length of transmitted videos and can help with the diagnosis. In this paper we propose a simple and efficient method for segmentation of the bleeding regions in WCE captured images. Suitable color channels are selected and classified by a multi-layer perceptron (MLP) structure. The MLP structure is quantized such that the implementation does not require multiplications. The proposed method is tested by simulation on WCE bleeding image dataset. The proposed structure is designed considering hardware resource constrains that exist in WCE systems.
Periapical implant lesion: A systematic review

Background The aim of this study was to systematically review the evidence for periapical implant lesion, which makes a patient more susceptible to the periapical lesion, frequency, symptoms, signs (including radiological findings) and possible treatment options. Material and Methods A systematic literature review and analysis of publications included in PubMed, Embase and Cochrane; articles published until March 2016; with a populations, exposures and outcomes (PEO) search strategy was performed, focused on the issue: “In patients with periapical lesion to the implant during the osseointegration, what symptoms, signs, and changes in complementary examination manifested, for according to that stage, be intervened with the appropriate approach? ”. The set criteria for inclusion were peer-reviewed articles. Results From a total of 212 papers identified, 36 studies were included in this systematic review, with 15461 implants evaluated and 183 periapical implant lesions. Which 8 papers included more than 5 cases and 28 included equal or less than 5 cases. Analysis of the papers revealed that periapical implant lesion is classified according to evolution stages into acute (non-suppurated and suppurated) and subacute (or suppurated-fistulized). In the acute stage and in the subacute if there is no loss of implant stability, the correct treatment approach is implant periapical surgery. In the subacute stage associated with implant mobility the implant must be removed. Conclusions Evidence on the subject is very limited, there are few studies with small sample, without homogeneity of criteria for diagnosing the disease and without design of scientific evidence. Currently etiology lacks consensus. The early diagnosis of periapical implant periapical lesions during the osseointegration phase and early treatment, will lead to a higher survival rate of implants treated, hence preventing the need for implant extraction. Key words:Apical peri-implantitis, retrograde peri-implantitis, inflammatory peri-implantitis lesion.
A study on text classification based on stacked contractive auto-encoder

In order to improve the classification effect of text classification and reduce the error rate of classification, this paper proposes the thought of text classification based on Stacked Contractive Auto-Encoder (SCAE) by stacking network layer by layer, the SCAE constitutes the depth of the neural network by unsupervised training and learning text to improve the robustness of feature extraction, the network uses the gradient descent algorithm to optimize parameters of the network. This paper adopts an improved TFIDF method calculating the weight of feature words. Though experiments, the CAE and SAE (Sparse Auto-Encoder) are compared, the support vector machine (SVM) is used to classify text. Experiment result shows that the classification performance of single layer CAE is better than that of single layer SAE, and the classification performance of SCAE is better than that of SSAE (Stacked Sparse Auto-Encoder).
Coexpression of Escherichia coli obgE, Encoding the Evolutionarily Conserved Obg GTPase, with Ribosomal Proteins L21 and L27

ABSTRACT Multiple essential small GTPases are involved in the assembly of the ribosome or in the control of its activity. Among them, ObgE (CgtA) has been shown recently to act as a ribosome antiassociation factor that binds to ppGpp, a regulator whose best-known target is RNA polymerase. The present study was aimed at elucidating the expression of obgE in Escherichia coli. We show that obgE is cotranscribed with ribosomal protein genes rplU and rpmA and with a gene of unknown function, yhbE. We show here that about 75% of the transcripts terminate before obgE, because there is a transcriptional terminator between rpmA and yhbE. As expected for ribosomal protein operons, expression was highest during exponential growth, decreased during entry into stationary phase, and became almost undetectable thereafter. Expression of the operon was derepressed in mutants lacking ppGpp or DksA. However, regulation by these factors appears to occur post-transcription initiation, since no effects of ppGpp and DksA on rplU promoter activity were observed in vitro. IMPORTANCE The conserved and essential ObgE GTPase binds to the ribosome and affects its assembly. ObgE has also been reported to impact chromosome segregation, cell division, resistance to DNA damage, and, perhaps most interestingly, persister formation and antibiotic tolerance. However, it is unclear whether these effects are related to its role in ribosome formation. Despite its importance, no studies on ObgE expression have been reported. We demonstrate here that obgE is expressed from an operon encoding two ribosomal proteins, that the operon's expression varies with the growth phase, and that it is dependent on the transcription regulators ppGpp and DksA. Our results thus demonstrate that obgE expression is coupled to ribosomal gene expression.
n-3 Polyunsaturated fatty acids and trans fatty acids in patients with the metabolic syndrome: a case–control study in Korea

n-3 and Trans fatty acids are considered to be the important modifiable factors of the metabolic syndrome. The purpose of this study was to test the hypothesis that lower Omega-3 fatty acids and/or higher trans fatty acids of erythrocytes (RBC) are associated with the risk of the metabolic syndrome. Forty-four patients with the metabolic syndrome, defined by three or more risk factors of the modified Adult Treatment Panel III criteria, and eighty-eight age- and sex-matched controls with less than three risk factors were recruited for the study. The mean age was 54·5 (sem 0·8) years and 45 % of subjects were female. Trans fatty acids of RBC were higher in patients than controls (0·82 (sem 0·04) v. 0·73 (sem 0·03) %; P = 0·043), while their Omega-3 indexes, the sum of EPA and DHA in RBC, did not significantly differ (11·78 (sem 0·04) v. 12·39 (sem 0·02) %). Multivariable-adjusted regression analysis showed positive association between trans fatty acid and risk of the metabolic syndrome (OR 7·13; 95 % CI 1·53, 33·27; P = 0·013). Fasting serum insulin (7·9 (sem 0·7) v. 4·9 (sem 0·3) μU/ml; P < 0·001) and high sensitivity C-reactive protein (18 (sem 3) v. 11 (sem 17) mg/l; P = 0·042) were also higher in patients than controls. There were significant positive relationships between trans fatty acids and waist circumference, and between trans fatty acids and BMI. The results suggested that RBC trans fatty acids might be a predictor of increased risk for the metabolic syndrome, but n-3 fatty acids were not in this population.
Isoform-specific subcellular localization and function of protein kinase A identified by mosaic imaging of mouse brain

Protein kinase A (PKA) plays critical roles in neuronal function that are mediated by different regulatory (R) subunits. Deficiency in either the RIβ or the RIIβ subunit results in distinct neuronal phenotypes. Although RIβ contributes to synaptic plasticity, it is the least studied isoform. Using isoform-specific antibodies, we generated high-resolution large-scale immunohistochemical mosaic images of mouse brain that provided global views of several brain regions, including the hippocampus and cerebellum. The isoforms concentrate in discrete brain regions, and we were able to zoom-in to show distinct patterns of subcellular localization. RIβ is enriched in dendrites and co-localizes with MAP2, whereas RIIβ is concentrated in axons. Using correlated light and electron microscopy, we confirmed the mitochondrial and nuclear localization of RIβ in cultured neurons. To show the functional significance of nuclear localization, we demonstrated that downregulation of RIβ, but not of RIIβ, decreased CREB phosphorylation. Our study reveals how PKA isoform specificity is defined by precise localization. DOI: http://dx.doi. org/10.7554/eLife.17681. 001
Multiparameter cytometric analysis of complex cellular response

Complex analysis of cellular responses after experimental treatment is important for screening, mechanistic understanding of treatment effects, and the identification of sensitive and resistant cell phenotypes. Modern multicolor flow cytometry has demonstrated its power for such analyses. Here, we introduce a multiparametric protocol for complex analysis of cytokinetics by the simultaneous detection of seven fluorescence parameters. This analysis includes the detection of two surface markers for immunophenotyping, analysis of proliferation based on the cell cycle and the measurement of incorporated nucleoside analogue 5‐ethynyl‐2′‐deoxyuridine (EdU) in newly synthesized DNA, analysis of DNA damage using an anti‐phospho‐histone H2A.X (Ser139) antibody, and determination of cell death using a fixable viability probe and intracellular detection of caspase‐3 activation. To demonstrate the applicability of this protocol for the analysis of heterogeneous and complex cell responses, we used different treatments and model cell lines. We demonstrated that this protocol has the potential to provide complex and simultaneous analysis of cytokinetics and analyze the heterogeneity of the response at the single‐cell level. © 2017 International Society for Advancement of Cytometry
The role of refuges in the persistence of Australian dryland mammals

Irruptive population dynamics are characteristic of a wide range of fauna in the world's arid (dryland) regions. Recent evidence indicates that regional persistence of irruptive species, particularly small mammals, during the extensive dry periods of unpredictable length that occur between resource pulses in drylands occurs as a result of the presence of refuge habitats or refuge patches into which populations contract during dry (bust) periods. These small dry‐period populations act as a source of animals when recolonisation of the surrounding habitat occurs during and after subsequent resource pulses (booms). The refuges used by irruptive dryland fauna differ in temporal and spatial scale from the refugia to which species contract in response to changing climate. Refuges of dryland fauna operate over timescales of months and years, whereas refugia operate on timescales of millennia over which evolutionary divergence may occur. Protection and management of refuge patches and refuge habitats should be a priority for the conservation of dryland‐dwelling fauna. This urgency is driven by recognition that disturbance to refuges can lead to the extinction of local populations and, if disturbance is widespread, entire species. Despite the apparent significance of dryland refuges for conservation management, these sites remain poorly understood ecologically. Here, we synthesise available information on the refuges of dryland‐dwelling fauna, using Australian mammals as a case study to provide focus, and document a research agenda for increasing this knowledge base. We develop a typology of refuges that recognises two main types of refuge: fixed and shifting. We outline a suite of models of fixed refuges on the basis of stability in occupancy between and within successive bust phases of population cycles. To illustrate the breadth of refuge types we provide case studies of refuge use in three species of dryland mammal: plains mouse (Pseudomys australis), central rock‐rat (Zyzomys pedunculatus), and spinifex hopping‐mouse (Notomys alexis). We suggest that future research should focus on understanding the species‐specific nature of refuge use and the spatial ecology of refuges with a focus on connectivity and potential metapopulation dynamics. Assessing refuge quality and understanding the threats to high‐quality refuge patches and habitat should also be a priority. To facilitate this understanding we develop a three‐step methodology for determining species‐specific refuge location and habitat attributes. This review is necessarily focussed on dryland mammals in continental Australia where most refuge‐based research has been undertaken. The applicability of the refuge concept and the importance of refuges for dryland fauna conservation elsewhere in the world should be investigated. We predict that refuge‐using mammals will be widespread particularly among dryland areas with unpredictable rainfall patterns.
Multi-level droplet routing in active-matrix based digital-microfluidic biochips

Active-Matrix (AM) technology is currently being used to implement a superior class of EWOD-based biochips, which consist of a dense 2D-array of microelectrodes. These chips offer many advantages over conventional biochips such as the capability of handling variable-size droplets, more flexibility in droplet movement, precise control over droplet navigation, and as a sequel, ease of implementing complex bioprotocols on-chip. However, the new technology poses a number of challenges concerning droplet routing. In order to enhance routability, we propose, in this paper, a multi-level hierarchical approach that takes appropriate decisions on droplet splitting and reshaping. Compared to the most recent routing methods used for EWOD, the proposed multi-level router reduces maximum latest-arrivaltime by an average 18% and achieves 7% less average latest-arrival-time.
Improving information spread through modified scheduled-seeding algorithm

In this modern era, social network has become one of the primary sources of instant information. Identifying influential nodes which play a vital role in spreading information across maximum number of nodes in a quick time is very important problem. Vast majority of the work done in this field has investigated techniques for finding the most influential nodes and maximize the spread of information. Yet so far, the timing aspect, namely, the time at which the information needs to be seeded for effective information spread has not been sufficiently addressed. In this work we revisit this problem of scheduled information seeding through minimum distance clustering and try to demonstrate its efficiency with the help of simulation. The discussed algorithm increases the rate of information spread across the social network by 19% from the previously proposed algorithm. This approach has a wide range of application in social networks, where network topology is either static or is dynamically changing.
Mosaic Analysis in Drosophila

Since the founding of Drosophila genetics by Thomas Hunt Morgan and his colleagues over 100 years ago, the experimental induction of mosaicism has featured prominently in its recognition as an unsurpassed genetic model organism. The use of genetic mosaics has facilitated the discovery of a wide variety of developmental processes, identified specific cell lineages, allowed the study of recessive embryonic lethal mutations, and demonstrated the existence of cell competition. Here, we discuss how genetic mosaicism in Drosophila became an invaluable research tool that revolutionized developmental biology. We describe the prevailing methods used to produce mosaic animals, and highlight advantages and disadvantages of each genetic system. We cover methods ranging from simple “twin-spot” analysis to more sophisticated systems of multicolor labeling.
A Generalized Chirp-Scaling Algorithm for Geosynchronous Orbit SAR Staring Observations

Geosynchronous Orbit Synthetic Aperture Radar (GEO SAR) has recently received increasing attention due to its ability of performing staring observations of ground targets. However, GEO SAR staring observation has an ultra-long integration time that conventional frequency domain algorithms cannot handle because of the inaccurately assumed slant range model and existing azimuth aliasing. To overcome this problem, this paper proposes an improved chirp-scaling algorithm that uses a fifth-order slant range model where considering the impact of the “stop and go” assumption to overcome the inaccuracy of the conventional slant model and a two-step processing method to remove azimuth aliasing. Furthermore, the expression of two-dimensional spectrum is deduced based on a series of reversion methods, leading to an improved chirp-scaling algorithm including a high-order-phase coupling function compensation, range and azimuth compression. The important innovations of this algorithm are implementation of a fifth-order order slant range model and removal of azimuth aliasing for GEO SAR staring observations. A simulation of an L-band GEO SAR with 1800 s integration time is used to demonstrate the validity and accuracy of this algorithm.
A Situational Awareness Trust Evolution Model for Mobile Devices in D2D Communication

Device-to-device (D2D) communication is a promising concept for improving user experiences and resource utilization in cellular networks. This type of communication enables two or more mobile devices in proximity to establish local links, coordinated by a base station, to perform direct data exchange. The benefits of D2D communication include ubiquitous computing and communication, enhanced energy efficiency, creation of new services, and so on. However, how to establish the trust relationship between two devices is a base problem that should be solved. In this paper, we propose a situational awareness trust evolution model for mobile devices involved in D2D communication. Compared with available trust evaluation schemes, we consider the comprehensive situation that a mobile device may encounter. We use what a device wants and what it can obtain to depict the situation of the device when given a concrete interaction (transaction). We give the method to get quantitative description of such information, and then the coefficients of the new proposed trust evolution function can be determined. To demonstrate the efficiency of our method, we conduct some experiments to show the properties of our method, and the results show that our trust evolution scheme is consistent with the intuition about trust in real life. Furthermore, we compare our scheme with two state-of-the-art dynamic trust evaluation schemes in different usage scenarios of mobile devices. The results show that our scheme can perform well in all scenarios, whereas the other two schemes can perform well only in some of the tested scenarios.
TRMT10A dysfunction is associated with abnormalities in glucose homeostasis, short stature and microcephaly

Background Trm10 is a tRNA m1G9 methyltransferase, which in yeast modifies 12 different tRNA species, yet is considered non-essential for viability under standard growth conditions. In humans, there are three Trm10 orthologs, one mitochondrial and two presumed cytoplasmic. A nonsense mutation in one of the cytoplasmic orthologs (TRMT10A) has recently been associated with microcephaly, intellectual disability, short stature and adolescent onset diabetes. Methods and results The subjects were three patients who suffered from microcephaly, intellectual disability, short stature, delayed puberty, seizures and disturbed glucose metabolism, mainly hyperinsulinaemic hypoglycaemia. A homozygous Gly206Arg (G206R) mutation in the TRMT10A gene was identified using whole exome sequencing. The mutation segregated in the family and was absent from large control cohorts. Determination of the methylation activity of the expressed wild-type (WT) and variant TRMT10A enzymes with transcripts of 32P -tRNAGlyGCC as a substrate revealed a striking defect (<0.1% of WT activity) for the variant enzyme. The binding affinity of the G206R variant enzyme to tRNA, determined by fluorescence anisotropy, was similar to that of the WT enzyme. Conclusions The completely abolished m1G9 methyltransferase activity of the mutant enzyme is likely due to significant defects in its ability to bind the methyl donor S-adenosyl methionine. We propose that TRMT10A deficiency accounts for abnormalities in glucose homeostasis initially manifesting both ketotic and non-ketotic hypoglycaemic events with transition to diabetes in adolescence, perhaps as a consequence of accelerated β cell apoptosis. The seizure disorder and intellectual disability are probably secondary to mutant gene expression in neuronal tissue.
Inhibiting glutaminase in acute myeloid leukemia: metabolic dependency of selected AML subtypes

Metabolic reprogramming has been described as a hallmark of transformed cancer cells. In this study, we examined the role of the glutamine (Gln) utilization pathway in acute myeloid leukemia (AML) cell lines and primary AML samples. Our results indicate that a subset of AML cell lines is sensitive to Gln deprivation. Glutaminase (GLS) is a mitochondrial enzyme that catalyzes the conversion of Gln to glutamate. One of the two GLS isoenzymes, GLS1 is highly expressed in cancer and encodes two different isoforms: kidney (KGA) and glutaminase C (GAC). We analyzed mRNA expression of GLS1 splicing variants, GAC and KGA, in several large AML datasets and identified increased levels of expression in AML patients with complex cytogenetics and within specific molecular subsets. Inhibition of glutaminase by allosteric GLS inhibitor bis-2-(5-phenylacetamido-1, 2, 4-thiadiazol-2-yl) ethyl sulfide or by novel, potent, orally bioavailable GLS inhibitor CB-839 reduced intracellular glutamate levels and inhibited growth of AML cells. In cell lines and patient samples harboring IDH1/IDH2 (Isocitrate dehydrogenase 1 and 2) mutations, CB-839 reduced production of oncometabolite 2-hydroxyglutarate, inducing differentiation. These findings indicate potential utility of glutaminase inhibitors in AML therapy, which can inhibit cell growth, induce apoptosis and/or differentiation in specific leukemia subtypes.
Nitride-Based Materials for Flexible MEMS Tactile and Flow Sensors in Robotics

The response to different force load ranges and actuation at low energies is of considerable interest for applications of compliant and flexible devices undergoing large deformations. We present a review of technological platforms based on nitride materials (aluminum nitride and silicon nitride) for the microfabrication of a class of flexible micro-electro-mechanical systems. The approach exploits the material stress differences among the constituent layers of nitride-based (AlN/Mo, SixNy/Si and AlN/polyimide) mechanical elements in order to create microstructures, such as upwardly-bent cantilever beams and bowed circular membranes. Piezoresistive properties of nichrome strain gauges and direct piezoelectric properties of aluminum nitride can be exploited for mechanical strain/stress detection. Applications in flow and tactile sensing for robotics are described.
Measuring sample distortions in face recognition

In this paper we describe FACE (Face Analysis for Commercial Entities), a framework for face recognition, and show how the approach is made robust to both pose and light variations, thanks to suitable correction strategies. Furthermore, two separate indices are devised for the quantitative assessment of these two kinds of distortions, which allow evaluating the quality of the sample at hand before submitting it to the classifier. Moreover, FACE implements two reliability margins, which, differently from the preceding two, estimate the 'acceptability' of the single response from the classifier. Experimental results show that the overall FACE implementation is able to provide an accuracy (in terms of Recognition Rate) which is better, in some respect, than the present state of art.