Miracle-dz/UniFAR-FTUs huggingface dataset:
Hybridization and Molecular Characterization of F1 Allium Cepa × Allium Roylei Plants

We made interspecific crosses to facilitate the introgression of desirable traits of Allium roylei into the Allium cepa genome. After hand-pollination, 906 interspecific F1 Allium cepa × A. roylei plants were obtained by in vitro culture via embryo rescue. Nuclear DNA analysis showed that 97.6% of the regenerants were interspecific F1 Allium cepa × A. roylei hybrids. Genomic in situ hybridization (GISH) showed that each hybrid had 16 chromosomes, eight of which were identified as A. cepa and eight as A. roylei chromosomes.
Design of complex-valued variable FIR digital filters and its application to the realization of arbitrary sampling rate conversion for complex signals

This brief studies the design of complex-valued variable digital filters (CVDFs) and their applications to the efficient arbitrary sample rate conversion for complex signals. The design of CVDFs using either the minimax or least-squares criteria is formulated as a convex optimization problem and solved using the second-order cone programming (SOCP). In addition, linear and convex quadratic inequality constraints can be readily incorporated. Design examples are given to demonstrate the effectiveness of the proposed approach.
Mod-Müllner: an efficient algorithm for hierarchical community analysis in large networks

In this work, we propose a new efficient agglomerative algorithm for hierarchical clustering analysis (HCA) of large networks. This algorithm, called Mod-Mullner, is an adaptation of an existing algorithm proposed by Mullner in 2011 and initially dedicated to HCA of pairwise dissimilarities. Mod-Mullner performs a greedy optimisation of the modularity, a widely used measure for network partitioning. We show that thanks to adapted data structures, Mod-Mullner achieves lower running times than other agglomerative algorithms, while producing comparable solutions. Finally, Mod-Mullner is compared to the Louvain method on simulated and real-world datasets. For both methods, the improved solutions obtained through single-level and multilevel refinements are studied.
Dependable Over-the-Air Programming

The complexity of software running on wireless sensor networks has increased over the years, and the need for an over-the-air (OTA) programming tool has become prominent. The requirements for the network traffic generated by a code update and the security issues that arise from it are atypical for wireless sensor networks, thus requiring innovative solutions. In this article, we provide an integrated protocol suite for a secure and efficient code image propagation in multi-hop wireless sensor networks consisting of three main parts: i)An efficient data structure including a program memory efficient T -time signature based on Merkle’s one time signature; ii) A transmission efficient authenticated pagewise packet encoding using rateless erasure codes with security measures against denial-of-service-attacks; iii)An adaptive multi-hop propagation strategy which uses techniques from fuzzy control to mitigate the hidden terminal problem. Weaving means from fuzzy control into the propagation scheme enables exploiting the benefits of rateless erasure codes by efficiently reducing channel congestion and, thus, packet collisions.
Determining optimal signal features and parameters for HMM-based emotion classification

The recognition of emotions from speech is a challenging issue. Creating emotion recognisers needs well defined signal features, parameter sets, and a huge amount of data material. Indeed, it is influenced by several conditions. This paper focuses on a proposal of an optimal parameter set for an HMM-based recogniser. For this, we compared different signal features (MFCCs, LPCs, and PLPs) as well as several architectures of HMMs. Moreover, we evaluated our proposal on three databases (eNTERFACE, Emo-DB, and SmartKom). Different proposals for acted/naive emotion recognition are given as well as recommendations for efficient and valid validation methods.
Pulmonary and Systemic Endotoxin Tolerance in Preterm Fetal Sheep Exposed to Chorioamnionitis1

In a model of human chorioamnionitis, fetal sheep exposed to a single injection, but not repeated injections, of intra-amniotic endotoxin develop lung injury responses. We hypothesized that repeated exposure to intra-amniotic endotoxin induces endotoxin tolerance. Fetal sheep were given intra-amniotic injections of saline (control) or Escherichia coli LPS O55:B5 (10 mg) either 2 days (2-day group, single exposure), 7 days (7-day group, single exposure), or 2 plus 7 days (2- and 7-day repeat exposure) before preterm delivery at 124 days gestation (term = 150 days). Endotoxin responses were assessed in vivo in the lung and liver, and in vitro in monocytes from the blood and the lung. Compared with the single 2-day LPS exposure group, the (2 plus 7 days) repeat LPS-exposed lambs had: 1) decreased lung neutrophil and monocyte inducible NO synthase (NOSII) expression, and 2) decreased lung cytokine and liver serum amyloid A3 mRNA expression. In the lung, serum amyloid A3 mRNA expression decreased in the airway epithelial cells but not in the lung inflammatory cells. Unlike the single 7-day LPS exposure group, peripheral blood and lung monocytes from the repeat-LPS group did not increase IL-6 secretion or hydrogen peroxide production in response to in vitro LPS. Compared with controls, TLR4 expression did not change but IL-1R-associated kinase M expression increased in the monocytes from repeat LPS-exposed lambs. These results are consistent with the novel finding of endotoxin tolerance in preterm fetal lungs exposed to intra-amniotic LPS. The findings have implications for preterm infants exposed to chorioamnionitis for both responses to lung injury and postnatal nosocomial infections.
Synthesizing designs with low-cardinality minimum feedback vertex set for partial scan application

An efficient partial scan approach for cost-effective sequential ATPG is to select flip-flops (FFs) in the minimum feedback vertex set (MFVS) of the FF dependency graph, so that loops are broken. Through a comprehensive analysis of the sources of loops in the data path, this paper proposes a new high-level synthesis methodology to synthesize data paths which have low-cardinality MFVS, thereby reducing the cost of partial scan significantly. A test efficiency of 100% could be achieved for all designs synthesized by the proposed approach, requiring a significantly less number of FFs to be scanned compared to the original implementations. <<ETX>>
GOMA: Web utility for direct finding of enriched Gene Ontology terms from gene expression profile

Microarrays have become popular devices used to elucidate changes of cell status. Following microarray experiments, technicians would like to verify their observations and changes of cell status occurring because of stimuli during experiments. Currently, we validate analyses of several or hundreds of samples using clustering and visualization. However, comparison is not an easy task because knowledge of data analysis is required and hundreds of clusters might be produced. This study presents GOMA, a web-based expression enrichment checking server using Gene Ontology (GO). By putting sets of gene names and expressions into the server, which GO categoriespsila genes are enriched can be verified immediately, and changes of cell status can be detected. The server presents a graphical GO structure association of their terms to ease the checking scheme. We evaluate that our web server enables us to recognize functions associated with changes of gene expression and to elucidate effects of different stimuli. The experimental results shows that our web server detects aldo-keto reductase activity under sorbitol supplemental condition from yeast expression data automatically, and our server visualizes the functional changes between sorbitol condition and stationary phase. GOMA is available online at http://goma.sel. is.ocha. ac.jp/ .
Cross layer design approach for performance evaluation of multimedia contents

Service Performance Evaluation is usually associated with connectivity related services, such as the provisioning of an internet connection. Now operators are beginning to explore new business opportunities on the All-over-IP world and beyond. New solutions are being deployed focusing on the multimedia interactive contents. New network architectures will require extensions to provide a clear vision on the service delivery quality, and new approaches on cross-layer information will be envisioned. This paper provides an insight on the cross-layer overview of the current 3GPP networks, while featuring the analysis until the end-to-end performance and end-user perception. It employs a correlation between the most relevant parameters at each layer and underlines their contribution to the upper layers. It further provides an analytical qualitative analysis of the overall service performance by evaluating simulation results which are sustained by both network and service performance metrics.
Cardioversion differences among first detected episode, paroxysmal, and persistent atrial fibrillation patients in the RHYTHM AF registry in Poland.

BACKGROUND The aim of the publication is to show differences among patients with the first detected episode of atrial fibrillation (AF), paroxysmal, and persistent AF patients, for whom cardioversion was planned in the hospital setting in Poland. METHODS We present an analysis of the Polish cohort of the multicenter, multinational RHYTHM-AF registry. Consecutive patients in the hospital setting, aged ≥ 18 years, with documented AF at the time of enrollment, and for whom cardioversion of AF is one of the planned therapeutic options were recruited. Follow-up data was collected 60 days after enrollment. RESULTS Five-hundred-and-one patients were recruited, 483 with a defined AF type: 88 - first detected, 191 paroxysmal, and 204 persistent AF. CHA₂DS₂VASc scores were not significantly different between the groups, while treatment with vitamin K antagonists (VKA) was significantly lower in paroxysmal AF group than in persistent AF patients. Primary electrical cardioversion was most commonly performed in patients with persistent AF (90.4%), while primary pharmacological cardioversion - in the first detected AF (80.0%) and paroxysmal AF patients (76.7%). During 2 months of follow-up, the rate of rehospitalization and complications was comparable among the groups. CONCLUSIONS Despite their comparable CHA₂DS₂VASc scores, patients with persistent AF were more frequently treated with VKA antagonists than other groups. Recurrence of AF within 2 months after restoring sinus rhythm was present in about 25% of the patients, and the rate of complications was not different among the three groups.
Saliency based Person Re-Identification in Video using Colour Features

Human re-identification is to match persons observed in non-overlapping camera views with visual features for inter camera tracking. Person re-identification in a non-overlapping multi-camera scenario is an open and interesting challenge. Humans are inherently able to sample those relevant people’s details that allow us to correctly solve the problem in a fraction of a second. But the task can hardly be completed by machines. Human salience is distinctive and reliable information in matching persons across disjoint camera views. So a saliency based approach can be used to re-identify persons in video. The model includes three stages: I) input processing, ii) video processing, iii) matching. The proposed person representation combines visual features either considering or not the saliency. The proposed approach has been extensively evaluated on 3DPes public datasets.
Intensive care unit survivors have fewer hospital readmissions and readmission days than other hospitalized patients in British Columbia

ObjectiveIntensive care unit (ICU) patients who survive their hospital admission have a long-term survival that is similar to that of hospitalized patients who do not require ICU admission. The risk of future readmission to the hospital for these two patient groups is unknown. The objective of this study was to determine the association between ICU admission and number of readmissions to the hospital and number of readmission days. DesignCohort study for 3 yrs between 1994 and 1997. SettingAll acute care hospitals in British Columbia, Canada. PatientsA total of 23,859 patients admitted to the ICU and 40,052 patients admitted to the hospital but not the ICU (5% random sample of total). InterventionNone. Measurements and Main ResultsWe measured the number of readmissions to the hospital and the number of readmission days after discharge from the first admission to the hospital during the study period. For survivors to the end of the study period, patients who had been in the ICU had 0.66 readmissions per year and 5.29 readmission days per year compared with 0.73 readmissions per year and 5.48 readmission days per year for control subjects. After controlling for age, sex, socioeconomic status, number of previous ICU and hospital admissions, major clinical category during index admission, comorbidity score during index admission, length of hospital stay during index admission, size of index hospital, and period of follow-up, ICU admission was associated with fewer readmissions (survivors: rate ratio, 0.80; 95% confidence interval, 0.77–0.82; nonsurvivors: rate ratio, 0.85; 95%, confidence interval, 0.82–0.89) and readmission days (survivors: rate ratio, 0.91; 95% confidence interval, 0.87–0.95; nonsurvivors: rate ratio, 0.87; 95%, confidence interval, 0.81–0.92) than admission to the hospital but not the ICU. ConclusionsSurvivors of a hospital stay that includes admission to an ICU have fewer hospital readmissions and readmission days after their discharge than do survivors of a hospital stay without intensive care.
Suppression of fibroblast growth factor 2 expression by antisense oligonucleotides inhibits embryonic chick neural retina cell differentiation and survival in vivo

During retinal differentiation, fibroblast growth factor 2 (FGF2) expression increases in retinal neurons following the sequential appearance of the neuronal layers. The function of the developmental increase of endogenous FGF2 in the developing chick retina was investigated by using an antisense strategy, using both optic vesicle cultures and in ovo‐intravitreal microinjections. The former model allowed us to study the consequences of FGF2 down‐regulation on early ganglion cell differentiation, whereas, in the latter model, subsequent development stages and terminal maturation of the retina were studied. FGF2 inhibition resulted in reduced ganglion cell differentiation, as visualized by the expression of the ganglion cell‐specific RA4 and Islet‐1 markers in optic vesicle cultures. Eyes intravitreally injected with the FGF2‐specific antisense oligonucleotide exhibited profound retinal differentiation defects: thinning of the ganglion and outer nuclear (photoreceptors) cell layers and increased cell death in ganglion cell and inner nuclear layers. These results indicate that the loss of endogenous FGF2 cannot be compensated for in the retina and suggest that, although many other sources of FGF exist in the eye, the main role of the increase in endogenous FGF2 observed during retinal development is to intrinsically stimulate neuron differentiation and to protect neurons against cell death. Dev. Dyn. 1998;212:63–74. © 1998 Wiley‐Liss, Inc.
Interactive Kalman filtering

Data assimilation via the extended Kalman filter can become problematic when the assimilating model is strongly nonlinear, primarily in connection with sharp, "switchlike" changes between different regimes of the system. The filter seems too inert to follow those switches quickly enough, a fact that can lead to a complete failure when the switches occur often enough. In this paper we replace the key feature of the filter, the use of local linearity for the error model update, with a principle that uses a more global approach through the utilization of a set of preselected regimes. The method uses all regime error models simultaneously. Being mutually incompatible, a compromise between the different error models is found through the use of a weighting function that reflects the 'closeness' of the error model to the correct model. To test the interactive Kalman filter a series of numerical experiments is performed using the double-well system and the well-known Lorenz system, and the results are compared to the extended Kalrnan filter. It turns out that, depending on the set of preselected regimes, the performance is worse than, comparable to, or better than that of the extended Kalman filter.
Reevaluation of the digestible lysine requirement for broilers based on genetic potential

Broiler strains available in the poultry industry present different requirements for dietary lysine due to their different growth potentials as a result of their genetic makeup. This study aimed to determine the model parameters for maximum nitrogen retention (NRmaxT), the nitrogen maintenance requirement (NMR) and the efficiency of lysine utilization (bc-1) to reevaluate the lysine (Lys) requirements of male and female broilers. Nitrogen balance trials were performed during three periods (I: 6-21 days, II: 22-37 days, and III: 38-53 days). Seven treatments were used for males and females; the treatments consisted of seven diets with protein levels ranging from 61 to 364 g kg-1 dry matter, with Lys being limiting in the dietary nitrogen (4.91 g of Lys in 16 g of N). Nitrogen intake (NI), excretion (NEX), deposition (ND, ND=NI-NEX) and retention (NR, NR=ND+NMR) values were obtained. The NMR was represented by the exponential relationship between NEX and NI. The NRmax T and bc-1 were estimated by the exponential fit between ND and NI. The NRmax T, bc-1, and NMR values were combined in a model to estimate Lys intake by simulating different percentages of the NRmaxT. The Lys intake estimates were 581, 1,538, and 2,171 mg day-1 for males and 512, 1,340, and 1674 mg day-1 for females during periods I, II, and III, respectively. Due to the flexibility of the model, it is possible to calculate the Lys intake for percentages of NR in the range of practical performance data.
Imaging characteristics of a 3-dimensional GSO whole-body PET camera.

UNLABELLED A whole-body 3-dimensional PET scanner using gadolinium oxyorthosilicate (GSO) crystals has been designed to achieve high sensitivity and reduced patient scanning time. This scanner has a diameter of 82.0 cm and an axial field of view of 18 cm without interplane septa. The detector comprises of 4 x 6 x 20 mm(3) GSO crystals coupled via an optically continuous light guide to an array of 420 photomultiplier tubes (39-mm diameter) in a hexagonal arrangement. The patient port diameter is 56 cm, and 2.86-cm (1.125 in.) thick lead shielding is used to fill in the region up to the detector ring. METHODS Performance measurements on the scanner were made using the National Electrical Manufactures Association (NEMA) NU 2-2001 procedures. Additional counting rate measurements with a large phantom were performed to evaluate imaging characteristics for heavier patients. The image-quality torso phantom with hot or cold spheres was also measured as a function of counting rate to evaluate different techniques for randoms and scatter subtraction as well as to determine an optimum imaging time. RESULTS The transverse and axial resolutions near the center are 5.5 and 5.6 mm, respectively. The absolute sensitivity of this scanner measured with a 70-cm-long line source is 4.36 cps/kBq, whereas the scatter fraction is 40% with a 20 x 70 cm line source cylinder. For the same cylinder, the peak noise equivalent count (NEC) rate of 30 kcps at an activity concentration of 9.25 kBq/mL (0.25 micro Ci/mL) leads to a 7% increase in the peak NEC value. A significant reduction in the peak NEC is observed with a larger 35 x 70 cm line source cylinder. Image-quality measurements show that the small 10-mm sphere in the NEMA NU 2-2001 image-quality phantom is clearly visible in a scan time of 3 min, and there is no noticeable degradation in image contrast at high activity levels. CONCLUSION This whole-body scanner represents a new generation of 3D, high-sensitivity, and high-performance PET cameras capable of producing high-quality images in <30 min for a full patient scan. The use of a pixelated GSO Anger-logic detector leads to a high-sensitivity scanner design with good counting rate capability due to the reduced light spread in the detector and fast decay time of GSO. The light collection over the detector is fairly uniform, leading to a good energy resolution and, thus, reduced scatter in the collected data due to a tight energy gate.
A 100/spl times/100 pixels orientation-selective multi-chip vision system

We describe a multi-chip analog VLSI system which emulates the orientation selective response of the simple cell in the primary visual cortex. The system consists of two analog chips, a silicon retina and an orientation chip, which mimic the parallel and hierarchical architecture of the visual system in the brain. The spatial resolution of the system is 100/spl times/100 pixels. The silicon retina receives the input image with a Laplacian-Gaussian-like receptive field. The output image of the retina is transferred to the orientation selection chip. The image transmission between two chips is carried out using analog signals. The orientation chip selectively aggregates multiple pixels of the silicon retina, mimicking the feed-forward model proposed to explain the orientation-selective receptive field of the simple cell. The orientation chip provides three output images with different preferred orientation in parallel. The analog multi-chip architecture used in the present study is useful to mimic the responses of higher order cells in the primary visual cortex.
An oomycete effector protein induces shade avoidance in Arabidopsis and attenuates salicylate signaling by binding to host proteins of the RADICAL-INDUCED CELL DEATH1 family

The oomycete pathogen Hyaloperonospora arabidopsidis (Hpa) causes downy mildew disease on Arabidopsis. During infection, Hpa like other biotrophic pathogens, suppresses activation of plant innate immunity by translocating effector proteins into host cells. Some of these effectors localize to the host cell nucleus where they may manipulate transcriptional reprogramming of plant defense genes. Here we report that the nuclear-localized Hpa effector HaRxL106, when expressed in Arabidopsis, induces shade avoidance and attenuates the transcriptional response to the defense signaling molecule salicylic acid. HaRxL106 interacts with RADICAL-INDUCED CELL DEATH1 (RCD1) and loss of RCD1 function renders Arabidopsis resilient against HaRxL106-mediated suppression of immunity. To further characterize the molecular functions of RCD1 we solved a crystal structure of RCD1’s Poly-(ADP-ribose)-Polymerase (PARP) domain and, based on non-conservation of amino acids constituting the active site of canonical PARPs, conclude that RCD1 has no PARP activity. We report that RCD1-type proteins are phosphorylated and identified histone-modifying Mut9-like kinases (MLKs) as RCD1-interacting proteins. A mlk1,3,4 triple mutant exhibits stronger SA-induced defense marker gene expression compared to wild-type plants. Our data suggest that HaRxL106 suppresses Arabidopsis innate immunity by manipulating the function(s) of RCD1 in the host cell nucleus and point towards a role of RCD1 as a transcriptional co-regulator that integrates signals from light and pathogen sensors.