Miracle-dz/UniFAR-FTUs huggingface dataset:
Twist1 Controls a Cell-Specification Switch Governing Cell Fate Decisions within the Cardiac Neural Crest

Neural crest cells are multipotent progenitor cells that can generate both ectodermal cell types, such as neurons, and mesodermal cell types, such as smooth muscle. The mechanisms controlling this cell fate choice are not known. The basic Helix-loop-Helix (bHLH) transcription factor Twist1 is expressed throughout the migratory and post-migratory cardiac neural crest. Twist1 ablation or mutation of the Twist-box causes differentiation of ectopic neuronal cells, which molecularly resemble sympathetic ganglia, in the cardiac outflow tract. Twist1 interacts with the pro-neural factor Sox10 via its Twist-box domain and binds to the Phox2b promoter to repress transcriptional activity. Mesodermal cardiac neural crest trans-differentiation into ectodermal sympathetic ganglia-like neurons is dependent upon Phox2b function. Ectopic Twist1 expression in neural crest precursors disrupts sympathetic neurogenesis. These data demonstrate that Twist1 functions in post-migratory neural crest cells to repress pro-neural factors and thereby regulate cell fate determination between ectodermal and mesodermal lineages.
Collaborative Spectrum Sensing in the Presence of Byzantine Attacks in Cognitive Radio Networks

Cognitive radio (CR) has emerged as a solution to the problem of spectrum scarcity as it exploits transmission opportunities in the under-utilized spectrum bands of primary users. Collaborative (or distributed) spectrum sensing has been shown to have various advantages in terms of spectrum utilization and robustness. The data fusion scheme is a key component of collaborative spectrum sensing. In this paper, we analyze the performance limits of collaborative spectrum sensing under Byzantine Attacks where malicious users send false sensing data to the fusion center leading to increased probability of incorrect sensing results. We show that above a certain fraction of Byzantine attackers in the CR network, data fusion scheme becomes completely incapable and no reputation based fusion scheme can achieve any performance gain. We present optimal attacking strategies for given attacking resources and also analyze the possible counter measures at the fusion center (FC). Based on these analyses, we also propose a novel and easy to implement technique to counter Byzantine attacks in CRNs. In this approach, the FC identifies the attackers and removes them from the data fusion process. Our analysis indicates that the proposed scheme is robust against Byzantine attacks and can successfully remove the Byzantines in a short time span.
Combining RADARSAT-2 and COSMO-SkyMed data for alpine permafrost deformation monitoring

With this work, we present a method for the detection of alpine permafrost surface deformations by using DInSAR (Differential SAR Interferometry) technique, integrating RADARSAT-2 and COSMO-SkyMed data through Support Vector Machine (SVM). On our test dataset, the combination of the two sensors produces an increase of classification accuracy equal to 8.5% with respect to the case in which only one sensor is employed, leading to an overall accuracy equal to 86.9%. We are also showing here how COSMO-SkyMed data time series acquired in the snow-free period are well suited to estimate surface deformations on some particular alpine rock glaciers. The velocities estimated with the SBAS (Small BAseline Subset) algorithm are well correlated with velocity measurements obtained by means of a ground based total station, showing a root mean squared error (RMSE) and R square value equal to 3.5 cm and to 0.67 respectively.
Martılarda (Laridae spp.) Cranium’un Üç Boyutlu Modellemesi

Bu calisma, marti cranium’larina ait osteometrik ozellikleri ve diger kanatli hayvan turleri ile aralarindaki farkliliklari ortaya koymak amaciyla yapildi. Calismada, cinsiyet ve tur farki gozetilmeden toplanan 15 adet olu marti kullanildi. Diseksiyon yontemiyle govdeden ayrilan marti cranium’lari 64 dedektorlu bilgisayarli tomografi (General Electronic Revolution) cihazi ile tarandi. Elde edilen aksiyal kesitsel goruntulerden 3D formatinda goruntuler olusturuldu. Olusturulan bu uc boyutlu goruntuler uzerinde belirlenen olcum noktalarindan osteometrik olcumler alindi. Elde edilen olcum verileri ile istatistiksel degerlendirmeler yapildi. Laridae familyasina ait olan martilarin cranium’larinin Multi Dedektor Bilgisayarli Tomografi goruntuleri uzerinden alinan olcumlerinde istatistiki olarak P<0.01 ve P<0.05 duzeyinde onem iliskisi tasiyan veriler tespit edildi. Bu verilerin belirlenmesiyle marti cranium anatomisinin daha iyi anlasilacagi, taksonomik yerinin belirlenmesinde referans veriler sunacagi ve bu konuda sinirli olan literaturlere de katki saglanacagi dusunuldu.
Energy-Optimized Toed Walking on Flexible Soles for Humanoids

In this research the role of thick flexible soles in energy-efficient humanoid walking is analyzed. It is hypothesized that, the addition of underactuated degrees of freedom under the foot gives the robot the potential to execute a pseudo-passive walking motion 1, which yields a decrease in ankle torque and energy expenditure. Furthermore it is hypothesized that, if these principles are applied to toed gait walking patterns, instead of flat foot walking patterns the decreases will be larger in magnitude. To isolate the effects of adding a sole, a toe joint and both at the same time, four walking types are compared in simulation; flat foot and toed gait walking, both with and without sole. To asses the cases without sole, energy-optimized walking pattern generation is used. For walking on soles, the optimized walking patterns are used as input for a deformation estimator that calculates the sole compression. Simulation results show that the rolling motion of the sole reduces the ankle torque and the energy consumption. The results prove that the reduction effects are especially large for toed gait walking, thereby validating both the hypotheses.
Stochastic optimization-based approach for multifingered grasps synthesis

SUMMARY In this paper, we propose an approach for computing suboptimal grasps of polyhedral objects. Assuming n hard-finger contact with Coulomb friction model and based on central axes of the grasp wrench, we develop a new necessary and sufficient condition for n-finger grasps to achieve force-closure property. Accordingly, we reformulate the proposed force-closure test as a new linear programming problem, which we solve using an interior point method. Furthermore, we present an approach for finding appropriate stable grasps for a robotic hand on arbitrary objects. We use the simulated annealing technique for synthesizing suboptimal grasps of 3D objects. Through numerical simulations on arbitrary shaped objects, we show that the proposed approach is able to compute good grasps for multifingered hands within a reasonable computational time.
Genetic diversity and parentage in farmer selections of cacao from Southern Sulawesi, Indonesia revealed by microsatellite markers

Indonesia is the third largest cocoa-producing country in the world. Knowledge of genetic diversity and parentage of farmer selections is important for effective selection and rational deployment of superior cacao clones in farmers’ fields. We assessed genetic diversity and parentage of 53 farmer selections of cacao in Sulawesi, Indonesia, using 152 international clones as references. Cluster analysis, based on 15 microsatellite markers, showed that these Sulawesi farmer selections are mainly comprised of hybrids derived from Trinitario and two Upper Amazon Forastero groups. Bayesian assignment and likelihood-based parentage analysis further demonstrated that only a small number of germplasm groups, dominantly Trinitario and Parinari, contributed to these farmer selections, in spite of diverse parental clones having been used in the breeding program and seed gardens in Indonesia since the 1950s. The narrow parentage predicts a less durable host resistance to cacao diseases. Limited access of the farmers to diverse planting materials or the strong preference for large pods and large bean size by local farmers, may have affected the selection outcome. Diverse sources of resistance, harbored in different cacao germplasm groups, need to be effectively incorporated to broaden the on-farm diversity and ensure sustainable cacao production in Sulawesi.
Abnormal renal hemodynamics and pressure-natriuresis relationship in Dahl salt-sensitive rats.

The renal responses to changes in renal perfusion pressure (RPP) were compared in Dahl salt-resistant (R) rats and in prehypertensive and hypertensive Dahl salt-sensitive (S) rats to determine whether an abnormality in the pressure diuresis response is involved in the development of this form of hypertension. Possible differences in the neural and endocrine background to the kidney of S and R rats were eliminated by denervating the kidney and by holding plasma levels of vasopressin, aldosterone, corticosterone, and norepinephrine fixed by intravenous infusion. Arterial pressure averaged 124 +/- 1 mmHg in R rats, 133 +/- 1 mmHg in prehypertensive S rats, and 158 +/- 2 mmHg in hypertensive S rats. Control renal blood flows (RBF) and glomerular filtration rates (GFR) were not significantly different in the three groups. RBF was autoregulated over a range of pressures from 80 to 160 mmHg in normotensive S and R rats. GFR was autoregulated at pressures greater than 100 mmHg in R rats and greater than 120 mmHg in prehypertensive S rats. In contrast, RBF was only autoregulated at pressures greater than 110 mmHg in hypertensive Dahl S rats, and GFR was significantly reduced from control when RPP was lowered below 150 mmHg. In R rats, increasing RPP from 100 to 150 mmHg produced a fivefold increase in urine flow and sodium excretion. In prehypertensive or hypertensive Dahl S rats the slopes of the relationships between urine flow, sodium excretion, and RPP were less than half of those seen in R rats. (ABSTRACT TRUNCATED AT 250 WORDS)
Improved Half Vector Space Light Transport

In this paper, we present improvements to half vector space light transport (HSLT) [ KHD14 ], which make this approach more practical, robust for difficult input geometry, and faster. Our first contribution is the computation of half vector space ray differentials in a different domain than the original work. This enables a more uniform stratification over the image plane during Markov chain exploration. Furthermore, we introduce a new multi chain perturbation in half vector space, which, if combined appropriately with half vector perturbation, makes the mutation strategy both more robust to geometric configurations with fine displacements and faster due to reduced number of ray casts. We provide and analyze the results of improved HSLT and discuss possible applications of our new half vector ray differentials.
Intrusion Detection System based on SVM and Bee Colony

An intrusion detection system (IDS) is an active process or device that analyzes system and network activity for unauthorized entry. Nowadays many intrusion detection systems are developed based on many different machine learning techniques. Some of the models are based on single classifying techniques while some models are based on combining different classifying techniques, such as hybrid or ensemble techniques. The basic task is to classify network activities (in the network log as connection records) as normal or abnormal while minimizing misclassification. Even if different classification models have been developed for network intrusion detection, each classification technique has its vitality and vulnerability. The machine learning based SVM method is a good choice for learning with little volume of data. Whenever new information is added into a system, updating of the old model is required immediately to ensure that the system is properly protected. As retraining may take weeks, or even months, it is impractical to retrain the new model on all available data. Thus, a mechanism is needed to generate an adaptive model that can be updated by cooperation of the old model with the new information. We can take advantage of the clustering based on Bee Colony in updating the models. We propose a new approach of combining SVM and Bee Colony to achieve high quality performance of Intrusion Detection System. Our algorithm is implemented and evaluated using a standard benchmark KDD99 data set. In this paper experimental result shows that SVM with Bee colony achieves an average accuracy is 88.46%.
Runtime Checks as Nominal Types

We propose a language design where types can be enriched by tags corresponding to predicates written by the programmer. For instance, int&positive is a type, where positive is a user-defined boolean function on integers. Expressions of type int&positive are obtained by an explicit check construct, analogous to cast, e.g., (positive) 2. In this way, the fact that the value of an expression is guaranteed to succeed a runtime check is a static property which can be controlled by the type system. We formalize our proposal as an extension of the simply-typed lambda calculus, and prove, besides soundness, the fact that expressions of tagged types reduce to values which satisfy the corresponding predicates.
Diagnostic validation of selected serological tests for detecting scrub typhus

Clinical diagnosis of scrub typhus is often difficult because the symptoms are very similar to those of other febrile illness such as dengue, leptospirosis, malaria and other viral hemorrhagic fevers. Though better diagnostic tests are available for rickettsial diseases and scrub typhus elsewhere, the Weil–Felix test is still commonly used in India, mainly because microimmunofluorescence assays (M‐IFA) were not available in India till recently and relevant staff had insufficient training. The present study was performed to investigate the performance of M‐IFA, IgM ELISA, and Weil–Felix test on 546 non‐repeated serum samples from subjects suspected of having scrub typhus. One hundred and forty‐three of these 546 samples were positive by M‐IFA; these cases were also confirmed clinically to have scrub typhus based on their dramatic responses to doxycycline therapy. IgM ELISA was positive in 122 of the 143 M‐IFA positive cases and the Weil–Felix test in 96. Though the Weil–Felix test is a heterophile agglutination test, it was found in this study to have good specificity but far too little sensitivity to use as a routine diagnostic test. IgM ELISA can be a good substitute for M‐IFA. Incorporation of multiple prototype antigens on M‐IFA slides is likely one of the reasons for its superior performance. As newer and better diagnostic assays become available for scrub typhus diagnosis in developed countries, it will be imperative to also use such tests in other endemic countries to prevent over‐ or under‐diagnosis of scrub typhus.
Transcriptome Analysis of Flower Sex Differentiation in Jatropha curcas L. Using RNA Sequencing

Background Jatropha curcas is thought to be a promising biofuel material, but its yield is restricted by a low ratio of instaminate / staminate flowers (1/10-1/30). Furthermore, valuable information about flower sex differentiation in this plant is scarce. To explore the mechanism of this process in J. curcas, transcriptome profiling of flower development was carried out, and certain genes related with sex differentiation were obtained through digital gene expression analysis of flower buds from different phases of floral development. Results After Illumina sequencing and clustering, 57,962 unigenes were identified. A total of 47,423 unigenes were annotated, with 85 being related to carpel and stamen differentiation, 126 involved in carpel and stamen development, and 592 functioning in the later development stage for the maturation of staminate or instaminate flowers. Annotation of these genes provided comprehensive information regarding the sex differentiation of flowers, including the signaling system, hormone biosynthesis and regulation, transcription regulation and ubiquitin-mediated proteolysis. A further expression pattern analysis of 15 sex-related genes using quantitative real-time PCR revealed that gibberellin-regulated protein 4-like protein and AMP-activated protein kinase are associated with stamen differentiation, whereas auxin response factor 6-like protein, AGAMOUS-like 20 protein, CLAVATA1, RING-H2 finger protein ATL3J, auxin-induced protein 22D, and r2r3-myb transcription factor contribute to embryo sac development in the instaminate flower. Cytokinin oxidase, Unigene28, auxin repressed-like protein ARP1, gibberellin receptor protein GID1 and auxin-induced protein X10A are involved in both stages mentioned above. In addition to its function in the differentiation and development of the stamens, the gibberellin signaling pathway also functions in embryo sac development for the instaminate flower. The auxin signaling pathway also participates in both stamen development and embryo sac development. Conclusions Our transcriptome data provide a comprehensive gene expression profile for flower sex differentiation in Jatropha curcas, as well as new clues and information for further study in this field.
Visual Selective Attention : Insights from Brain Imaging and Neurophysiology

The contents of our minds at any given moment are not rigidly determined by the stimuli that happen to be impinging on our senses. Instead, we perceivers actively select a subset of the available perceptual information for detailed processing, relegating other information to the shadows of consciousness. This active process of perceptual selection, attention, has been the topic of extensive study for several decades, using all of the methods of cognitive neuroscience. Here we outline recent progress from brain imaging in humans and neurophysiology in monkeys, focusing on research that helps to answer three longstanding and fundamental questions about visual attention: i) what is the locus of attentional selection? , ii) what are the units of information that are selected by attention? , and iii) how exactly does neural processing differ for attended versus unattended information? In this chapter we will not review the recent imaging and electrophysiological literature on the sources of attentional signals in the frontal and parietal regions, a topic that is addressed in this volume by Humphreys and in several recent reviews (see Colby and Goldberg, 1999; (Kanwisher and Wojciulik, 2000) Gottlieb, 2002; Culham and Kanwisher, 2001; Kastner and Ungerleider, 2000; Corbetta and Shulman, 2002).
Statistical Modeling of Sea Ice Concentration Using Satellite Imagery and Climate Reanalysis Data in the Barents and Kara Seas, 1979-2012

Abstract: Extensive sea ice over Arctic regions is largely involved in heat, moisture, and momentum exchanges between the atmosphere and ocean. Some previous studies have been conducted to develop statistical models for the status of Arctic sea ice and showed considerable possibilities to explain the impacts of climate changes on the sea ice extent. However, the statistical models require improvements to achieve better predictions by incorporating techniques that can deal with temporal variation of the relationships between sea ice concentration and climate factors. In this paper, we describe the statistical approaches by ordinary least squares (OLS) regression and a time-series method for modeling sea ice concentration using satellite imagery and climate reanalysis data for the Barents and Kara Seas during 1979–2012. The OLS regression model could summarize the overall climatological characteristics in the relationships between sea ice concentration and climate variables. We also introduced autoregressive integrated moving average (ARIMA) models because the sea ice concentration is such a long-range dataset that the relationships may not be explained by a single equation of the OLS regression. Temporally varying
Identifying and Retrieving of Audio Sequences by using Wavelet Descriptors and Neural Network with User's Assistance

Audio content identifying, indexing, and retrieving are of great importance for the next generation of Internet search. The retrieval of digital audio, based on similarities between feature vectors of querying and stored audio material, is considered. We used wavelet descriptors for characterizing short music sequences and Euclidean distance as an objective similarity measure. Since music sequences may be subjectively classified in different ways, the retrieval process is upgraded by user's feedback and neural network decision. After the first pass, from the initial set of sequences ordered related to objectively measured distances from the query, the user select and mark those subjectively declared as more similar to a query. Selected sequences update the weights of radial basis function (RBF) neural network: moving the RBF center towards selected sequences and changing the width of RBF for obtaining fine-tuning. New ranking of audio sequences is then performing from RBF output. The user can repeat the process in iterative way until obtaining satisfactory results. Our simulations show that the process converges very fast: after a few iterations (1 to 4) selected fragments are just those we needed
Unexpected role of clathrin adaptor AP-1 in MHC-dependent positive selection of T cells

Trafficking of transmembrane receptors to a specific intracellular compartment is conducted by adaptor molecules that bind to target motifs within the cytoplasmic domains of cargo proteins. We generated mice containing a lymphoid-specific deficiency of AP-1 using RNAi knockdown technology. Inhibition of AP-1 expression in thymocytes blocks progression from double-positive immature thymocytes, resulting in complete absence of CD4+ single-positive thymocytes and severe reduction of CD3+CD8+ single-positive thymocytes. Analysis of the contribution of AP-1 deficiency on the interaction between mature CD4+ T cells and antigen-presenting cells revealed that AP-1 is essential to efficient immune synapse formation and associated T cell activation, suggesting a possible mechanism of AP-1 function in thymocyte development.
Analytic Solutions of Integral Moving Least Squares for Polygon Soups

This paper presents analytic solutions to the integral moving least squares (MLS) equations originally proposed by Shen et al. by choosing another specific weighting function that renders the numerator in the MLS equation unitless. In addition, we analyze the original method to show that their approximation surfaces (i.e., enveloping surfaces with nonzero \epsilon values in the weighting function) often form zero isosurfaces near concavities behind the triangle-soup models. This paper also presents error terms for the integral MLS formulations against signed distance fields. Based on our analytic solutions, we show that our method provides both interpolation and approximation surfaces faster and more efficiently. Because our method computes solutions for integral MLS equations directly, it does not rely on numerical steps that might have numerical-accuracy issues. In particular, unlike the original method that deals with incorrect approximation surfaces by iteratively adjusting parameters, this paper proposes faster and more efficient approximations to surfaces without needing iterative routines. We also present computational efficiency comparisons, in which our method is 15-fold faster in computing integrations, even with conservative assumptions. Finally, we show that the surface normal vectors on the implicit surfaces formed by our analytic solutions are identical to the angle-weighted pseudonormal vectors.