Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-wide association studies to identify rice salt-tolerance markers.

Salinity is an ever increasing menace that affects agriculture worldwide. Crops such as rice are salt sensitive, but its degree of susceptibility varies widely between cultivars pointing to extensive genetic diversity that can be exploited to identify genes and proteins that are relevant in the response of rice to salt stress. We used a diversity panel of 306 rice accessions and collected phenotypic data after short (6 h), medium (7 d) and long (30 d) salinity treatment (50 mm NaCl). A genome-wide association study (GWAS) was subsequently performed, which identified around 1200 candidate genes from many functional categories, but this was treatment period dependent. Further analysis showed the presence of cation transporters and transcription factors with a known role in salinity tolerance and those that hitherto were not known to be involved in salt stress. Localization analysis of single nucleotide polymorphisms (SNPs) showed the presence of several hundred non-synonymous SNPs (nsSNPs) in coding regions and earmarked specific genomic regions with increased numbers of nsSNPs. It points to components of the ubiquitination pathway as important sources of genetic diversity that could underpin phenotypic variation in stress tolerance.
SUPERTWIN: towards 100kpixel CMOS quantum image sensors for quantum optics applications

Quantum imaging uses entangled photons to overcome the limits of a classical-light apparatus in terms of image quality, beating the standard shot-noise limit, and exceeding the Abbe diffraction limit for resolution. In today experiments, the spatial properties of entangled photons are recorded by means of complex and slow setups that include either the motorized scanning of single-pixel single-photon detectors, such as Photo-Multiplier Tubes (PMT) or Silicon Photo- Multipliers (SiPM), or the use of low frame rate intensified CCD cameras. CMOS arrays of Single Photon Avalanche Diodes (SPAD) represent a relatively recent technology that may lead to simpler setups and faster acquisition. They are spatially- and time-resolved single-photon detectors, i.e. they can provide the position within the array and the time of arrival of every detected photon with <100 ps resolution. SUPERTWIN is a European H2020 project aiming at developing the technological building blocks (emitter, detector and system) for a new, all solid-state quantum microscope system exploiting entangled photons to overcome the Rayleigh limit, targeting a resolution of 40nm. This work provides the measurement results of the 2nd order cross-correlation function relative to a flux of entangled photon pairs acquired with a fully digital 8×16 pixel SPAD array in CMOS technology. The limitations for application in quantum optics of the employed architecture and of other solutions in the literature will be analyzed, with emphasis on crosstalk. Then, the specifications for a dedicated detector will be given, paving the way for future implementations of 100kpixel Quantum Image Sensors.
Experience with genomic sequencing in pediatric patients with congenital cardiac defects in a large community hospital

Congenital cardiac defects, whether isolated or as part of a larger syndrome, are the most common type of human birth defect occurring on average in about 1% of live births depending on the malformation. As there is an expanding understanding of the underlying molecular mechanisms by which a cardiac defect may occur, there is a need to assess the current rates of diagnosis of cardiac defects by molecular sequencing in a clinical setting.
Interpolation snakes for border detection in ultrasound images

Ultrasound images present major challanges to just about any segmentation algorithm, including active contour techniques, due to increased specularity, non-uniform edges along the boundaries of interest, incomplete and misleading visual support. Active contours that depend on a vector of parameters (e.g. B-splines), have been proposed in the literature, and have the advantage over traditional snakes and level-set snakes, that smoothness is built-in, which is a sine qua non requirement in border detection in medical images. We propose in this paper the use of interpolation splines as active contours for border detection in ultrasound images, which we term interpolation snakes. We argue that interpolation snakes are better suited for ultrasound than other snakes, because of the fact that the control points (parameters which control the shape of the snake) are on the curve. This allows for an initial arclength parameterization of the snake. In conjunction with interpolation snakes we define a new energy (measure of fit) which incorporates a term supposed to maintain arclength parameterization of the snake throughout the minimization process. A shape prior can also be introduced naturally, as a distribution on the control points.
Hospice and palliative social workers' experiences with clients at risk of suicide

Abstract Objective: We sought to determine the frequency with which hospice and palliative social workers encounter patients, family caregivers, and other clients at risk of suicide, and to discover the extent to which hospice and palliative social workers feel prepared to address issues related to suicide in their professional practice. Method: We conducted a cross-sectional survey of hospice and palliative social workers, recruiting a convenience sample of volunteer respondents through advertisements at professional conferences and listservs, and via social media accounts associated with national organizations, state hospice and palliative care associations, and individual healthcare professionals. Results: Most respondents reported having worked with patients, family caregivers, or other clients who had exhibited warning signs of suicide during the previous year. Fewer respondents indicated that they had worked with patients and family members who had attempted or died by suicide. While the majority of respondents believed they possessed sufficient knowledge and skills to intervene effectively with individuals at risk of suicide, they indicated that additional education on this topic would be valuable for their professional practice. Significance of results: These study results suggest that suicide-related competencies are important in the practice of hospice and palliative social work. Future education and training efforts should include skill development in addition to knowledge building.
A NOVEL HIGH DIRECTIVE EBG STRUCTURE

In this paper a high gain and directive microstrip antenna made from metamatrial superstrate and an electromagnetic band-gap (EBG) substrate has been investigated. EBG structures have two main configurations, first EBG substrate and second EBG superstrate. In first case, the patch of antenna is surrounded with EBG structure that suppress the propagation of surface wave and in second case, layer of EBG structure that call EBG superstrate or metamaterial superstrate set above the patch of antenna. The layers of EBG superstrate have near zero refraction index that concentrate radiation energy normal to superstrate. A patch antenna surrounded with novel EBG structure is used for radiation. By choosing appropriate geometrical parameters of the structures we can obtain suitable impedance matching and negative refraction. The results show that the gain of the antenna with one layer of H-Doubled split ring EBG superstrate increase up to 16dB at 14.3 GHz. In addition, pattern of microstrip antenna with EBG superstrate is more narrower than simple microstrip antenna.
Multistage Signaling Game-Based Optimal Detection Strategies for Suppressing Malware Diffusion in Fog-Cloud-Based IoT Networks

We consider the Internet of Things (IoT) with malware diffusion and seek optimal malware detection strategies for preserving the privacy of smart objects in IoT networks and suppressing malware diffusion. To this end, we propose a malware detection infrastructure realized by an intrusion detection system (IDS) with cloud and fog computing to overcome the IDS deployment problem in smart objects due to their limited resources and heterogeneous subnetworks. We then employ a signaling game to disclose interactions between smart objects and the corresponding fog node because of malware uncertainty in smart objects. To minimize privacy leakage of smart objects, we also develop optimal strategies that maximize malware detection probability by theoretically computing the perfect Bayesian equilibrium of the game. Moreover, we analyze the factors influencing the optimal probability of a malicious smart object diffusing malware, and factors influencing the performance of a fog node in determining an infected smart object. Finally, we present a framework to demonstrate a potential and practical application of suppressing malware diffusion in IoT networks.
A glycosyl transferase family 43 protein involved in xylan biosynthesis is associated with straw digestibility in Brachypodium distachyon

Summary The recalcitrance of secondary plant cell walls to digestion constrains biomass use for the production of sustainable bioproducts and for animal feed. We screened a population of Brachypodium recombinant inbred lines (RILs) for cell wall digestibility using commercial cellulases and detected a quantitative trait locus (QTL) associated with this trait. Examination of the chromosomal region associated with this QTL revealed a candidate gene that encodes a putative glycosyl transferase family (GT) 43 protein, orthologue of IRX14 in Arabidopsis, and hence predicted to be involved in the biosynthesis of xylan. Arabinoxylans form the major matrix polysaccharides in cell walls of grasses, such as Brachypodium. The parental lines of the RIL population carry alternative nonsynonymous polymorphisms in the Bd GT43A gene, which were inherited in the RIL progeny in a manner compatible with a causative role in the variation in straw digestibility. In order to validate the implied role of our candidate gene in affecting straw digestibility, we used RNA interference to lower the expression levels of the Bd GT43A gene in Brachypodium. The biomass of the silenced lines showed higher digestibility supporting a causative role of the Bd GT43A gene, suggesting that it might form a good target for improving straw digestibility in crops.
IMPLEMENTING COMBINED FSM WITH

The subject of the research in this article is the logic circuit of the combined finite state machine (CFSM), which combines the functions of the both FSM Mealy and Moore. In practice, such a model of control automata is used widely, but in the literature there is almost no theoretical description CFSM models and ways to optimize them. The article considers the problem of optimizing the logic of the combined finite state machine implemented in complex programmable logic devices (CPLD) basis. The CFSM circuit using programmable array logic (PAL) macrocells is implemented. The number of CPLD components, required to implement the logic of the automaton circuit, depends on the CFSM parameters and characteristics of element basis. Obviously, the reduction of necessary number of components leads to a decrease area occupied CFSM scheme in CPLD, thereby leads to reducing the hardware amount and power consumption in the circuit, and as result, increases the efficiency of the whole project. To solve the problem of CFSM optimization for a criterion of hardware expenses in this article it’s proposed to use the structural features of the basis CPLD, as well as the method of pseudoequivalent states. The FSM states are defined as a pseudoequivalent, if they mark some vertices linked with the input of the same next vertex in flow-chart. The proposed method includes the following steps: forming a plurality of CFSM states; encoding of states; forming a set of classes pseudoequivalent states; formation PALer blocks and tables; implementation of the CFSM scheme in a given element basis, such as CPLD. As a result, it’s possible to reduce the necessary number of PAL macro cells for implementing CFSM circuit in CPLD. The general result is a decreasing of in the total area of CFSM circuit on a chip. The advisability conditions of this method are discussed.
Structural basis of the methylation specificity of R.DpnI

R.DpnI consists of N-terminal catalytic and C-terminal winged helix domains that are separately specific for the Gm6ATC sequences in Dam-methylated DNA. Here we present a crystal structure of R.DpnI with oligoduplexes bound to the catalytic and winged helix domains and identify the catalytic domain residues that are involved in interactions with the substrate methyl groups. We show that these methyl groups in the Gm6ATC target sequence are positioned very close to each other. We further show that the presence of the two methyl groups requires a deviation from B-DNA conformation to avoid steric conflict. The methylation compatible DNA conformation is complementary with binding sites of both R.DpnI domains. This indirect readout of methylation adds to the specificity mediated by direct favorable interactions with the methyl groups and solvation/desolvation effects. We also present hydrogen/deuterium exchange data that support ‘crosstalk’ between the two domains in the identification of methylated DNA, which should further enhance R.DpnI methylation specificity.
Characterizing Alzheimer’s Disease Severity via Resting-Awake EEG Amplitude Modulation Analysis

Changes in electroencephalography (EEG) amplitude modulations have recently been linked with early-stage Alzheimer’s disease (AD). Existing tools available to perform such analysis (e.g., detrended fluctuation analysis), however, provide limited gains in discriminability power over traditional spectral based EEG analysis. In this paper, we explore the use of an innovative EEG amplitude modulation analysis technique based on spectro-temporal signal processing. More specifically, full-band EEG signals are first decomposed into the five well-known frequency bands and the envelopes are then extracted via a Hilbert transform. Each of the five envelopes are further decomposed into four so-called modulation bands, which were chosen to coincide with the delta, theta, alpha and beta frequency bands. Experiments on a resting-awake EEG dataset collected from 76 participants (27 healthy controls, 27 diagnosed with mild-AD, and 22 with moderate-AD) showed significant differences in amplitude modulations between the three groups. Most notably, i) delta modulation of the beta frequency band disappeared with an increase in disease severity (from mild to moderate AD), ii) delta modulation of the theta band appeared with an increase in severity, and iii) delta modulation of the beta frequency band showed to be a reliable discriminant feature between healthy controls and mild-AD patients. Taken together, it is hoped that the developed tool can be used to assist clinicians not only with early detection of Alzheimer’s disease, but also to monitor its progression.
Identifying Behavioral Design Flaws in Evolving Object-Oriented Software Using an Ontology-Based Approach

It is a demanding process when safeguarding superiority in software development and preservation. Understanding of reoccurring problems to enhance the quality of existing and future software development is employed in the concept of design flaws. Recurring bad design solutions or error-free source codes comprise design flaws, which are hard to comprehend and sustain. Eliminating these flaws without modifying a programs functionality while enhancing program quality at the same time are the goals of code refactoring. To identify some flaws from source code, several rules-based and metrics-based approaches can be used. However, information and consideration of these indicators of low quality software remain insufficient to answer the numerous issues they signify. An ontology-based method is offered in this research to reinforce design flaws detection. Describing the concepts and related properties of design flaws is supported by ontology. A universal understanding of these concepts among those in the software community is fostered by an ontological infrastructure. Further, it gives more succinct definitions that can prevent intersecting and inconstant accounts. When declarative meta-programming is used, detection is carried out at the meta-level. To identify various design flaws that have previously been well documented, this research employs the approach detailed. The approach is effective for detecting such flaws, as substantiated by the findings.
Usefulness of the Cytomegalovirus Antigenemia Assay in Patients With Ulcerative Colitis

Background/Aims Patients with ulcerative colitis (UC) are at high risk for cytomegalovirus (CMV) reactivation. The usefulness of the CMV antigenemia assay in active UC patients has rarely been studied. We assessed whether the assay detects CMV colitis and predicts clinical outcomes in patients with UC. Methods We retrospectively reviewed the medical records of patients hospitalized for moderate-to-severe UC from 2003 to 2012. Positive CMV antigenemia was defined as ≥1 pp65-positive cell per 2×105 polymorphonuclear neutrophils. CMV colitis was defined as the presence of inclusion bodies and/or positive immunohistochemistry in the colonic mucosa. The primary outcome was steroid refractoriness, defined as the absence of clinical improvement after intravenous high-dose steroid administration. Results A total of 43 patients were enrolled. CMV antigenemia was detected in 12 (27.9%) patients. Positive CMV antigenemia was significantly associated with CMV colitis (P =0.001). The sensitivity and specificity of positive CMV antigenemia for diagnosing CMV colitis were 66.7% and 87.1%, respectively. Steroid refractoriness was found in 11 of 12 (91.7%) and 12 of 31 (38.7%) patients with positive and negative CMV antigenemia, respectively (P =0.002). The independent predictors for steroid refractoriness were positive CMV antigenemia (adjusted odds ratio [OR], 7.73; 95% confidence interval [CI], 1.22-49.19; P =0.030) and a shorter duration from the diagnosis of UC (adjusted OR, 0.99; 95% CI, 0.98-0.99; P =0.025). Conclusions The CMV antigenemia assay shows low sensitivity but high specificity for detecting CMV colitis and may predict steroid-refractory UC. Early rescue therapy might be considered in UC patients positive for CMV antigenemia.
F eb 2 01 4 Gravitational lensing and frame dragging of light by a Kerr-Newman ( anti ) de Sitter black hole

The null geodesics that describe photon orbits in the spacetime of a rotating electrically charged black hole (Kerr-Newman) are solved exactly including the contribution from the cosmological constant. We then solve the more involved problem of treating a Kerr-Newman black hole as a gravitational lens, i.e. a KN black hole along with a static source of light and a static observer both located far away but otherwise at arbitrary positions in space. For this model we derive the analytic solutions of the lens equations in terms of Appell and Lauricella hypergeometric functions and the Weierstraß modular form. The exact solutions derived for null, spherical polar and non-polar orbits, are applied for the calculation of frame dragging for the orbit of a photon around the galactic centre, assuming that the latter is a Kerr-Newman black hole. We also apply the exact solution for the deflection angle of an equatorial light ray in the gravitational field of a Kerr-Newman black hole for the calculation of bending of light from the gravitational field of the galactic centre for various values of the Kerr parameter, electric charge and impact factor.
A novel wearable sensor device for continuous monitoring of cardiac activity during sleep

The miniaturization and energy optimization of sensors opens up new possibilities in the field of sleep research. Wearable sensors are capable of recording vital parameters during sleep in a simple and unobtrusive manner. In order to analyze sleep architecture and sleep disorders, continuous monitoring of movements and cardiorespiratory parameters in high resolution is of central importance. In this paper a novel wearable sensor device based on impedance plethysmography (IPG) is presented, which is able to continuously monitor movements and cardiac parameters at the wrist. The sensor is designed to realize high resolution measurements up to 48 hours constantly. Measurements during sleep show that up to 98% of the pulse intervals are correctly detected. Furthermore, the comparison of the heart rate variability (HRV) parameters between IPG and the gold standard ECG demonstrate the potential of the sensor as a valid tool for ambulant sleep analysis.
Mutation in sorghum LOW GERMINATION STIMULANT 1 alters strigolactones and causes Striga resistance

Significance The parasitic weed Striga is the greatest biological constraint to production of many crops in Africa and parts of Asia. Genetic control is the most feasible means of crop protection from this pest. We report on identification of a gene regulating Striga resistance in sorghum and the associated change in strigolactone chemistry. Knowing this gene and its various natural alleles, sorghum breeders can design markers within it to facilitate its transfer into improved varieties providing farmers effective control of Striga in infested fields. The gene could also be used to potentially improve Striga resistance through genome editing in crops such as maize that evolved away from Striga, and hence have a paucity of Striga resistance genes. Striga is a major biotic constraint to sorghum production in semiarid tropical Africa and Asia. Genetic resistance to this parasitic weed is the most economically feasible control measure. Mutant alleles at the LGS1 (LOW GERMINATION STIMULANT 1) locus drastically reduce Striga germination stimulant activity. We provide evidence that the responsible gene at LGS1 codes for an enzyme annotated as a sulfotransferase and show that functional loss of this gene results in a change of the dominant strigolactone (SL) in root exudates from 5-deoxystrigol, a highly active Striga germination stimulant, to orobanchol, an SL with opposite stereochemistry. Orobanchol, although not previously reported in sorghum, functions in the multiple SL roles required for normal growth and environmental responsiveness but does not stimulate germination of Striga. This work describes the identification of a gene regulating Striga resistance and the underlying protective chemistry resulting from mutation.