Miracle-dz/UniFAR-FTUs huggingface dataset:
Lipids trigger changes in the elasticity of the cytoskeleton in plant cells: a cell optical displacement assay for live cell measurements

An assay has been developed to quantitatively measure the tension and elasticity of the cytoskeleton in living plant cells. The cell optical displacement assay (CODA) uses a focused laser beam to optically trap and displace transvacuolar and cortical strands through a defined distance within the cell. Results from these experiments provide evidence for the classification of at least two rheologically distinct cytoskeletal assemblies, cortical and transvacuolar, that differ in their tension and response to both signaling molecules and reagents that perturb the cytoskeleton. It is further demonstrated that the tension of the transvacuolar strands can be significantly decreased by the addition of either linoleic acid, 1,2 dioctanoyl-sn-glycerol, or 1,3 dioctanoylglycerol. These decreases in tension could also be induced by lowering the cytoplasmic pH. In contrast, addition of Ca2+, Mg2+, or the ionophore A23187 to the cells caused a considerable increase in the tension of the transvacuolar strands. The data provides evidence that: (a) linoleic acid may be a signaling molecule in plant cells; (b) diacylglycerol functions as a signaling molecule through a protein kinase C-independent pathway mediated by PLA2; and (c) Ca2+ and pH have regulatory roles for controlling cytoskeleton tension and organization.
Estimating the location and shape of hybrid zones

We propose a new model to make use of georeferenced genetic data for inferring the location and shape of a hybrid zone. The model output includes the posterior distribution of a parameter that quantifies the width of the hybrid zone. The model proposed is implemented in the GUI and command‐line versions of the Geneland program versions ≥3.3. 0. Information about the program can be found on http://www2.imm. dtu.dk/gigu/Geneland/.
Novel C8orf37 Mutations in Patients with Early-onset Retinal Dystrophy, Macular Atrophy, Cataracts, and High Myopia

ABSTRACT Purpose: More than 50 genes are reported as causative genes of autosomal recessive (ar) retinitis pigmentosa (RP) and cone-rod dystrophy (CRD). It is challenging to identify causative mutations for arRP and arCRD. The purpose of the present study was to investigate clinical and genetic features of two siblings with early-onset retinal dystrophy. Methods: Whole-exome sequencing was conducted for the two affected siblings and their unaffected brother and mother from a Japanese family. We performed complete ophthalmic examinations, including visual acuity, funduscopy, visual-field testing, electroretinography and optical coherence tomography. Results: Whole-exome sequencing analysis identified novel compound heterozygous mutations, a splice site mutation (c.374 + 2T > C in intron 4) and a deletion mutation (c.575delC [p.T192MfsX28] in exon 6) of chromosome 8 open reading frame 37 (C8orf37) gene, which encodes a ciliary protein, in both patients. The mother carried the truncating mutation, and the brother carried neither mutation. Ophthalmic examinations revealed diffuse retinal degeneration, macular atrophy, non-recordable electroretinography responses, cataracts, and high myopia in both patients, who could not be diagnosed with either RP or CRD because of the severe retinal degeneration and early onset disease. Longitudinal follow-up of the patients revealed highly progressive retinal degeneration, macular atrophy, and visual field loss. Conclusions: Recessive C8orf37 mutations have been identified in early to adolescent-onset arRP and arCRD with macular involvement. Our study identified two novel truncating mutations of the C8orf37 gene in siblings with early-onset retinal dystrophy, macular atrophy, cataracts, and high myopia.
Optimization of the Radiating Performances for the High-Frequency Devices Used in the MEMS Applications

Two types of antennas, which are used as the radiating devices in the microwave technique, are examined. The amplitude radiation characteristics of antennas are optimized in a wide frequency band. These characteristics are obtained by means of statement and solution of the appropriate synthesis problems. The variational statement of problems allows to take into account the requirements to the amplitude radiation pattern and front-to-rear factor in the operating frequency band as well as outside of this band. The methods of successive approximations are applied for solving the received nonlinear integral equations, as well as the direct optimization of the used functional is carried out. The results of numerical modeling are shown
Active Learning for Delineation of Curvilinear Structures

Many recent delineation techniques owe much of their increased effectiveness to path classification algorithms that make it possible to distinguish promising paths from others. The downside of this development is that they require annotated training data, which is tedious to produce. In this paper, we propose an Active Learning approach that considerably speeds up the annotation process. Unlike standard ones, it takes advantage of the specificities of the delineation problem. It operates on a graph and can reduce the training set size by up to 80% without compromising the reconstruction quality. We will show that our approach outperforms conventional ones on various biomedical and natural image datasets, thus showing that it is broadly applicable.
Natural Capital, Ecological Scarcity and Rural Poverty

Much of the rural poor -- who are growing in number -- are concentrated in ecologically fragile and remote areas. The key ecological scarcity problem facing such poor households is a vicious cycle of declining livelihoods, increased ecological degradation and loss of resource commons, and declining ecosystem services on which the poor depend. In addition, developing economies with high concentrations of their populations on fragile lands and in remote areas not only display high rates of rural poverty, but also are some of the poorest countries in the world today. Policies to eradicate poverty therefore need to be targeted at the poor where they live, especially the rural poor clustered in fragile environments and remote areas. The specific elements of such a strategy include involving the poor in payment for ecosystem services schemes and other measures that enhance the environments on which the poor depend; targeting investments directly to improving the livelihoods of the rural poor, thus reducing their dependence on exploiting environmental resources; tackling the lack of access of the rural poor in less favored areas to well-functioning and affordable markets for credit, insurance, and land; and reducing the high transportation and transaction costs that prohibit the poorest households in remote areas from engaging in off-farm employment and limit smallholder participation in national and global markets.
The Sierpinski Object in the Scott Realizability Topos

We study the Sierpinski object $\Sigma$ in the realizability topos based on Scott's graph model of the $\lambda$-calculus. Our starting observation is that the object of realizers in this topos is the exponential $\Sigma ^N$, where $N$ is the natural numbers object. We define order-discrete objects by orthogonality to $\Sigma$. We show that the order-discrete objects form a reflective subcategory of the topos, and that many fundamental objects in higher-type arithmetic are order-discrete. Building on work by Lietz, we give some new results regarding the internal logic of the topos. Then we consider $\Sigma$ as a dominance; we explicitly construct the lift functor and characterize $\Sigma$-subobjects. Contrary to our expectations the dominance $\Sigma$ is not closed under unions. In the last section we build a model for homotopy theory, where the order-discrete objects are exactly those objects which only have constant paths.
An Efficient Load Balancing Method for Tree Algorithms

Nowadays, multiprocessing is mainstream with exponentially increasing number of processors. Load balancing is, therefore, a critical operation for the efficient execution of parallel algorithms. In this paper we consider the fundamental class of tree-based algorithms that are notoriously irregular,, hard to load-balance with existing static techniques. We propose a hybrid load balancing method using the utility of statistical random sampling in estimating the tree depth, node count distributions to uniformly partition an input tree. To conduct an initial performance study, we implemented the method on an Intel Xeon Phi accelerator system. We considered the tree traversal operation on both regular, irregular unbalanced trees manifested by Fibonacci, unbalanced (biased) randomly generated trees, respectively. The results show scalable performance for up to the 60 physical processors of the accelerator, as well as an extrapolated 128 processors case.
Printed Low-Voltage Fuse Memory on Paper

A printed lateral resistive fuse-type write-once-read-many (WORM) memory on paper substrate is demonstrated. The memory writing process is based on breaking of a silver nanoparticle conductor. Low-voltage and low-current writability demonstrated with printed batteries are enabled by a μm2-range cross-sectional bit area that are achieved by super-fine inkjet technology. Supported by the statistical distribution of the writing times, the bit writing process is attributed to electromigration of silver and the required current density for fusing is found to be 34 mA/μm2. The results show an improvement in memory retention time when compared with structurally similar printed antifuse-type WORM memories.
On maximum-likelihood detection and decoding for space-time coding systems

Space-time coding (STC) schemes for communication systems employing multiple transmit and receive antennas have been attracting increased attention. In this paper, we address two interrelated problems: detection of space-time codes under various interference conditions and information transfer from the STC detector to an error-correcting channel decoder. By taking a systematic maximum-likelihood (ML) approach to the joint detection and decoding problem, we show how to design optimal detectors and how to integrate them with a channel decoder. We also discuss various aspects of channel modeling for STC communication receivers. In particular, while many previous works on space-time coding assume that the channel is a stochastic quantity, we find that a deterministic channel model can have some advantages for the receiver design. Finally, we illustrate our results by numerical examples. Index Terms-Interference suppression, maximum-likelihood estimation, maximum-likelihood sequence detection, MIMO systems, space-time coding, soft information.
An Algorithm for Identifying Cognates in Bilingual Wordlists and its Applicability to Machine Translation

Abstract This article describes and discusses the theoretical model and the practical algorithm behind the program COGNATE which has been available since December 1991 in the pc/linguistics subdirectory of the anonymous ftp site garbo.uwasa. fi of the University of Vaasa, Finland, and at mirror sites. Given a list of words in any two languages transcribed in a phonemic or loosely phonemic alphabetical system, the program identifies probable letter correspondences and estimates how likely the members of each word pair are to be related or unrelated. The algorithm attempts to bring the beginning of a solution to two problems which are equivalent under the model used:
Physiological and Psychological Responses to Outdoor vs. Laboratory Cycling

Abstract Mieras, ME, Heesch, MWS, and Slivka, DR. Physiological and psychological responses to outdoor vs. laboratory cycling. J Strength Cond Res 28(8): 2324–2329, 2014—The purpose of this study was to determine the physiological and psychological responses to laboratory vs. outdoor cycling. Twelve recreationally trained male cyclists participated in an initial descriptive testing session and 2 experimental trials consisting of 1 laboratory and 1 outdoor session, in a randomized order. Participants were given a standardized statement instructing them to give the same perceived effort for both the laboratory and outdoor 40-km trials. Variables measured include power output, heart rate (HR), core temperature, skin temperature, body weight, urine specific gravity (USG), Rating of Perceived Exertion (RPE), attentional focus, and environmental conditions. Wind speed was higher in the outdoor trial than in the laboratory trial (2.5 ± 0.6 vs. 0.0 ± 0.0 m·s−1, p = 0.02) whereas all other environmental conditions were similar. Power output (208.1 ± 10.2 vs. 163.4 ± 11.8 W, respectively, p < 0.001) and HR (152 ± 4 and 143 ± 6 b·min−1, respectively, p = 0.04) were higher in the outdoor trial than in the laboratory trial. Core temperature was similar, whereas skin temperature was cooler during the outdoor trial than during the laboratory trial (31.4 ± 0.3 vs. 33.0 ± 0.2° C, respectively, p < 0.001), thus creating a larger thermal gradient between the core and skin outdoors. No significant differences in body weight, USG, RPE, or attentional focus were observed between trials. These data indicate that outdoor cycling allows cyclists to exercise at a higher intensity than in laboratory cycling, despite similar environmental conditions and perceived exertion. In light of this, cyclists may want to ride at a higher perceived exertion in indoor settings to acquire the same benefit as they would from an outdoor ride.
The Epidemiology of Pregnancy Complications and Outcome in a Norwegian Twin Population

Objective: To measure the contribution of genetic factors to selected pregnancy complications, including miscarriage, twinning, hypertension-toxemia, and nausea-vomiting. Methods: Information on 22,241 pregnancies of 8675 female twins or spouses of male twins was obtained by questionnaire from members of the population-based Norwegian Twin Panel. Comparisons of observed tetrachoric correlations were used to assess the importance of genetic influences on the variables examined. Results: Pregnancy history information was provided by both members of 830 monozygotic and 902 dizygotic female twin pairs and by the spouses of both members of 459 monozygotic and 464 dizygotic male twin pairs. The incidence of twin pregnancy in general, and of opposite-sexed twins in particular, found among dizygotic twin women was nearly twice that observed for any other group. Monozygotic female twin pairs were more concordant than dizygotic female twin pairs for the occurrence of miscarriage, nausea or vomiting during pregnancy, and hypertension or overt toxemia. A similar pattern of twin similarity was observed for the use of certain medications during pregnancy including vitamins, aspirin, and nausea medication. Conclusions: Maternal genetic factors make an important contribution to a predisposition for dizygotic twinning, contribute to the risk of miscarriage, and appear to determine, in part, whether a woman experiences nauseavomiting or hypertension-toxemia during pregnancy. In addition, health-seeking behaviors of women during pregnancy, as reflected by the use of several classes of medication, appear to be influenced somewhat by genetic factors. (Obstet Gynecol 1992;80:989-94)
The Automatic Creation of Lexical Entries for a Multilingual MT System

In this paper, we describe a method of extracting information from an on-line resource for the construction of lexical entries for a multi-lingual, interlingual MT system (ULTRA). We have been able to automatically generate lexical entries for interlingual concepts corresponding to nouns, verbs, adjectives and adverbs. Although several features of these entries continue to be supplied manually we have greatly decreased the time required to generate each entry and see this as a promising method for the creation of large-scale lexicons.
Sparse linear regression in unions of bases via Bayesian variable selection

In this letter, we propose an approach for sparse linear regression in unions of bases inspired by Bayesian variable selection. Conditionally upon an indicator variable that is 0 or 1, one expansion coefficient of the signal corresponding to one atom of the dictionary is either set to zero or given a Student t prior. A Gibbs sampler (a standard Markov chain Monte Carlo technique) is used to sample from the posterior distribution of the indicator variables, the expansion coefficients (corresponding to nonzero indicator variables), the hyperparameters of the Student t priors, and the variance of the residual signal. The structure of the dictionary, assumed to be a union of bases, allows for alternate sampling of the indicator variables and the expansion coefficients from each basis and avoids any large matrix inversion. Our method is applied to the denoising problem of a piano sequence, using a dual-resolution union of two modified discrete cosine transform bases
Improved SVM speaker verification through data-driven background dataset collection

The problem of background dataset selection in SVM-based speaker verification is addressed through the proposal of a new data-driven selection technique. Based on support vector selection, the proposed approach introduces a method to individually assess the suitability of each candidate impostor example for use in the background dataset. The technique can then produce a refined background dataset by selecting only the most informative impostor examples. Improvements of 13% in min. DCF and 10% in EER were found on the SRE 2006 development corpus when using the proposed method over the best heuristically chosen set. The technique was also shown to generalise to the unseen NIST 2008 SRE corpus.
Detection of Therapeutically Targetable Driver and Resistance Mutations in Lung Cancer Patients by Next-Generation Sequencing of Cell-Free Circulating Tumor DNA

Purpose: The expanding number of targeted therapeutics for non–small cell lung cancer (NSCLC) necessitates real-time tumor genotyping, yet tissue biopsies are difficult to perform serially and often yield inadequate DNA for next-generation sequencing (NGS). We evaluated the feasibility of using cell-free circulating tumor DNA (ctDNA) NGS as a complement or alternative to tissue NGS. Experimental Design: A total of 112 plasma samples obtained from a consecutive study of 102 prospectively enrolled patients with advanced NSCLC were subjected to ultra-deep sequencing of up to 70 genes and matched with tissue samples, when possible. Results: We detected 275 alterations in 45 genes, and at least one alteration in the ctDNA for 86 of 102 patients (84%), with EGFR variants being most common. ctDNA NGS detected 50 driver and 12 resistance mutations, and mutations in 22 additional genes for which experimental therapies, including clinical trials, are available. Although ctDNA NGS was completed for 102 consecutive patients, tissue sequencing was only successful for 50 patients (49%). Actionable EGFR mutations were detected in 24 tissue and 19 ctDNA samples, yielding concordance of 79%, with a shorter time interval between tissue and blood collection associated with increased concordance (P = 0.038). ctDNA sequencing identified eight patients harboring a resistance mutation who developed progressive disease while on targeted therapy, and for whom tissue sequencing was not possible. Conclusions: Therapeutically targetable driver and resistance mutations can be detected by ctDNA NGS, even when tissue is unavailable, thus allowing more accurate diagnosis, improved patient management, and serial sampling to monitor disease progression and clonal evolution. Clin Cancer Res; 22(23); 5772–82. ©2016 AACR.
Orbitofrontal Cortical Neurons Encode Expectation-Driven Initiation of Reward-Seeking

Adaptive execution and inhibition of behavior are guided by the activity of neuronal populations across multiple frontal cortical areas. The rodent medial prefrontal cortex has been well studied with respect to these behaviors, influencing behavioral execution/inhibition based on context. Other frontal regions, in particular the orbitofrontal cortex (OFC), are critical in directing behavior to obtain rewards, but the relationship between OFC neuronal activity and response execution or inhibition has been poorly characterized. In particular, little is known about OFC with respect to extinction learning, an important example of context-guided response inhibition. Here, we recorded the activity of OFC neurons while rats performed a discriminative-stimulus (DS)-driven sucrose-seeking task followed by multiple days of extinction of the DS. OFC neuronal activity was maximally responsive (1) to reward-predicting stimuli (RS) that triggered a lever press (i.e., lever-response initiation) and (2) during reward-well approach in pursuit of sucrose (i.e., well-response initiation). RS presentation that was not followed by a lever press or RS presentation during extinction produced weak activation, as did nonrewarded stimulus (NS) presentation regardless of response (press or withhold) or session (DS-sucrose or extinction). Activity related to nonrewarded well entry was minor, and activity was significantly inhibited during reward consumption. Finally, OFC neuronal activity switched selectivity to track rewarded behaviors when the RS/NS contingencies were reversed. Thus, rather than signaling variables related to extinction or response inhibition, activity in OFC was strongest at the initiation of multiple components of reward-seeking behavior, most prominently when valid reward-predicting cues drove these behaviors.
Mortality and cancer incidence among Swedish fishermen with a high dietary intake of persistent organochlorine compounds.

OBJECTIVES The objective of this study was to determine mortality and cancer incidence in two cohorts of Swedish fishermen with different dietary intakes of persistent organochlorine compounds. METHODS The following two cohorts of Swedish fishermen were established: a cohort of 2896 subjects from the Swedish east coast (on the Baltic Sea), and a cohort of 8477 subjects from the Swedish west coast. Mortality and cancer incidence were studied in these cohorts and comparisons were made both with the regional populations and between the cohorts. RESULTS The incidences of stomach and squamous cell skin cancers among the eastcoast fishermen were elevated as compared with those of the regional population [standardized incidence ratio (SIR 1.6, 95% confidence interval (95% CI) 1.0-2.4 and SIR 2.3, 95% CI 1.5-3.5 respectively] and with the westcoast cohort (IRR 2.2, 95% CI 1.3-3.5 and IRR 1.9, 95% CI 1.2-3.1, respectively), while that of colon cancer was decreased. Moreover, mortality from multiple myelomas was increased among the eastcoast fishermen as compared with that of the general population [standardized mortality ratio (SMR) 3.1, 95% CI 1.2-6.4) and the westcoast fishermen (IRR 3.2, 95% CI 1.2-8.7). A 12% decreased mortality in ischemic heart disease was found for the eastcoast cohort. A slight, but significant increase in such deaths was noted among the westcoast fishermen. CONCLUSIONS High consumers of fatty fish, contaminated with organochlorine compounds, had an increased risk for stomach and skin cancer. They also had a suggestive decrease in mortality from ischemic heart diseases.