Miracle-dz/UniFAR-FTUs huggingface dataset:
Phased Whole-Genome Genetic Risk in a Family Quartet Using a Major Allele Reference Sequence

Whole-genome sequencing harbors unprecedented potential for characterization of individual and family genetic variation. Here, we develop a novel synthetic human reference sequence that is ethnically concordant and use it for the analysis of genomes from a nuclear family with history of familial thrombophilia. We demonstrate that the use of the major allele reference sequence results in improved genotype accuracy for disease-associated variant loci. We infer recombination sites to the lowest median resolution demonstrated to date (<1,000 base pairs). We use family inheritance state analysis to control sequencing error and inform family-wide haplotype phasing, allowing quantification of genome-wide compound heterozygosity. We develop a sequence-based methodology for Human Leukocyte Antigen typing that contributes to disease risk prediction. Finally, we advance methods for analysis of disease and pharmacogenomic risk across the coding and non-coding genome that incorporate phased variant data. We show these methods are capable of identifying multigenic risk for inherited thrombophilia and informing the appropriate pharmacological therapy. These ethnicity-specific, family-based approaches to interpretation of genetic variation are emblematic of the next generation of genetic risk assessment using whole-genome sequencing.
High Frequency of vacA s1m2 Genotypes Among Helicobacter pylori Isolates From Patients With Gastroduodenal Disorders in Kermanshah, Iran

Background: Helicobacter pylori infection and related diseases outcome are mediated by a complex interplay between bacterial, host and environmental factors. Several distinct virulence factors of H. pylori have been shown to be associated with different clinical outcomes. Here we focused on vacA and cagA genotypes of H. pylori strains isolated from patients with gastric disorder. Objectives: The aim of this study was to determine the frequency of two toxins and genotypes of VacA toxin in patients referred to a central hospital in the west of Iran (Imam Reza hospital, Kermanshah) during 2011 - 2012. Patients and Methods: Samples were collected from patients infected with H. pylori. Gastric biopsy specimens from the stomach antrum and corpus were cultured. PCR analysis was performed for genotyping H. pylori vacA and cagA genes. Results: Helicobacter pylori was isolated from 48% (96/200) of patients with gastroduodenal disorders. In 81/96 (84%) cases, the cagA gene was present. Among different genotypes of vacA, two s1m2 and s2m2 genotypes were dominant with frequency of 39.5% and 50%, respectively. The frequency of the s1m1 genotype was 7.2% (7/96), which is much lower than elsewhere. H. pylori isolates with positive results for cagA gene and vacA s1m2 genotypes showed statistically significant correlation with peptic ulcer (s1m2 13/34 [38.2%] P = 0.003). However, isolates of H. pylori infection with cagA gene and vacA s2m2 genotypes were significantly associated with development of gastritis (s2m2 41/42 [97.6%] P = 0.000). Conclusions: About 90% of H. pylori strains potentially contained vacA s2m2 and s1m2 genotypes. Infection with H. pylori strain containing the cagA gene or the vacA s1m1 and s1m2 genotypes was associated with increased incidence of peptic ulcer disease (PUD).
The Relationship Between Causal and Noncausal Mismatched Estimation in Continuous-Time AWGN Channels

A continuous-time finite-power process with distribution P is observed through an AWGN channel, at a given signal-to-noise ratio (SNR), and is estimated by an estimator that would have minimized the mean-square error if the process had distribution Q. We show that the causal filtering mean-square error (MSE) achieved at SNR level snr is equal to the average value of the noncausal (smoothing) MSE achieved with a channel whose SNR is chosen uniformly distributed between 0 and snr. Emerging as the bridge for equating these two quantities are mutual information and relative entropy. Our result generalizes that of Guo, Shamai, and Verdú (2005) from the nonmismatched case, where P = Q, to general P and Q. Among our intermediate results is an extension of Duncan's theorem, that relates mutual information and causal MMSE, to the case of mismatched estimation. Some further extensions and implications are discussed. Key to our findings is the recent result of Verdú on mismatched estimation and relative entropy.
Product systems of graphs and the Toeplitz algebras of higher-rank graphs | NOVA. The University of Newcastle's Digital Repository

There has recently been much interest in the C � -algebras of directed graphs. Here we consider product systems E of directed graphs over semigroups and associated C � -algebras C � (E) and T C � (E) which generalise the higher-rank graph algebras of Kumjian-Pask and their Toeplitz analogues. We study these algebras by constructing from E a product system X(E) of Hilbert bimodules, and applying re- cent results of Fowler about the Toeplitz algebras of such systems. Fowler's hypotheses turn out to be very interesting graph-theoretically, and indicate new relations which will have to be added to the usual Cuntz-Krieger relations to obtain a satisfactory theory of Cuntz-Krieger algebras for product systems of graphs; our algebras C � (E) and T C � (E) are universal for families of partial isometries satisfying these relations. Our main result is a uniqueness theorem for T C � (E) which has particularly in- teresting implications for the C � -algebras of non-row-finite higher-rank graphs. This theorem is apparently beyond the reach of Fowler's theory, and our proof requires a detailed analysis of the expectation onto the diagonal in T C � (E).
Estrogen: Friend or Foe in Pulmonary Hypertension?

identify (5). SLB remains a valuable tool in the evaluation of patients with ILD, providing important diagnostic information that guides therapy when the combination of history, physical examination, and high-resolution chest computed tomography is inadequate to provide a diagnosis, as this information cannot be obtained by any other means (6–8). However, the benefit of the additional information gained from the SLB must be weighed against the expected morbidity and mortality from the procedure. The average mortality for all patients undergoing SLB significantly underor overestimates the probability of postprocedural in-hospital mortality in an individual patient, depending on the presence or absence of specific risk factors. In an individual patient, SLB should be considered when the histopathologic pattern is expected to meaningfully alter treatment and outcome. This decision should be made in the context of the physician and patient’s desire for a definitive diagnosis and a clear understanding of and tolerance for the risks related to the procedure. Hutchinson and colleagues have improved our ability to quantify these risks. n
Ratiometric analysis of Acridine Orange staining in the study of acidic organelles and autophagy

ABSTRACT Acridine Orange is a cell-permeable green fluorophore that can be protonated and trapped in acidic vesicular organelles (AVOs). Its metachromatic shift to red fluorescence is concentration-dependent and, therefore, Acridine Orange fluoresces red in AVOs, such as autolysosomes. This makes Acridine Orange staining a quick, accessible and reliable method to assess the volume of AVOs, which increases upon autophagy induction. Here, we describe a ratiometric analysis of autophagy using Acridine Orange, considering the red-to-green fluorescence intensity ratio (R/GFIR) to quantify flow cytometry and fluorescence microscopy data of Acridine-Orange-stained cells. This method measured with accuracy the increase in autophagy induced by starvation or rapamycin, and the reduction in autophagy produced by bafilomycin A1 or the knockdown of Beclin1 or ATG7. Results obtained with Acridine Orange, considering R/GFIR, correlated with the conversion of the unlipidated form of LC3 (LC3-I) into the lipidated form (LC3-II), SQSTM1 degradation and GFP–LC3 puncta formation, thus validating this assay to be used as an initial and quantitative method for evaluating the late step of autophagy in individual cells, complementing other methods. Summary: We describe the photochemical basis of Acridine Orange (AO) and its usefulness as a probe for autophagy quantification and find that considering the red-to-green fluorescence intensity ratio of AO gives the best correlation with other autophagy assays.
Secrecy capacity of wiretap channels with additive colored Gaussian noise

Wyner has shown in his seminal paper on (discrete memoryless) wiretap channels that if the channel between the sender and an eavesdropper is a degraded version of the channel between the sender and the legitimate receiver, then the sender can reliably and securely transmit a message to the receiver, while the eavesdropper obtains absolutely no information about the message. Later, Leung-Yan-Cheong and Hellman extended Wyner's result to the case where the noise is white Gaussian. In this paper we extend the white Gaussian wiretap channel to the colored Gaussian case and show the finite block length secrecy capacity of colored Gaussian wiretap channels. We also show an asymptotic lower bound on the secrecy capacity of a specific colored Gaussian wiretap channel for which optimum power allocation can be found by water filling.
Bioaccumulation and distribution of 137Cs in tobacco cultivated under hydroponic conditions

Potential of plants to uptake metals from soil solution can be successfully applied for removal of long-lived radionuclides such as radiostrontium 90Sr or radiocaesium 137Cs. This work deals with bioaccumulation of Cs in tobacco plants (Nicotiana tabacum L.) hydroponically grown in diluted Hoagland media (HM) spiked with 137CsCl. Speciation analysis using a program Visual MINTEQ showed, that more than 97% of caesium in HM occurred in the form of Cs+ ions. We found that bioaccumulation of Cs significantly decreased from the value 100% to the value 20% removing of Cs from media after 8 days cultivation of plants with increasing HM concentration. However, the concentration ratio (CR) [Cs]shoot : [Cs]root increased with increasing HM concentration from the value 0.10 to the value 0.85. Bioaccumulation of Cs by tobacco plants significantly decreased with increasing CsCl concentration in media from the value 95% found at concentration of CsCl 10 μmol/dm3 to the value 44% at concentration of CsCl 1 000 μmol/dm3. We did not found visual symptoms of Cs toxicity on plants after 8 days cultivation or significant differences in growth rate or transpiration activity at CsCl concentration up to 0.2 mM. However, at > 0.2 mM CsCl concentration the decrease of growth rate and necrosis of young leaves or die-back of leaves (> 2 mM CsCl) were observed. The CR ([Cs]shoot : [Cs]root) increased with increasing concentration of CsCl (10 – 1 000 μmol/dm3) in media from the value 0.10 to the value 0.40. The obtained data suggest that fast growing plant species with high biomass production like tobacco might be a suitable in phytoextraction or rhizofiltration technologies used for 137Cs removing from environment.
A Path Generation Approach to Embedding of Virtual Networks

As the virtualization of networks continues to attract attention from both industry and academia, the virtual network embedding (VNE) problem remains a focus of researchers. This paper proposes a one-shot, unsplittable flow VNE solution based on column generation. We start by formulating the problem as a path-based mathematical program called the primal, for which we derive the corresponding dual problem. We then propose an initial solution which is used, first, by the dual problem and then by the primal problem to obtain a final solution. Unlike most approaches, our focus is not only on embedding accuracy but also on the scalability of the solution. In particular, the one-shot nature of our formulation ensures embedding accuracy, while the use of column generation is aimed at enhancing the computation time to make the approach more scalable. In order to assess the performance of the proposed solution, we compare it against four state of the art approaches as well as the optimal link-based formulation of the one-shot embedding problem. Experiments on a large mix of virtual network (VN) requests show that our solution is near optimal (achieving about 95% of the acceptance ratio of the optimal solution), with a clear improvement over existing approaches in terms of VN acceptance ratio and average substrate network (SN) resource utilization, and a considerable improvement (92% for a SN of 50 nodes) in time complexity compared to the optimal solution.
Parametric studies of the response decrement produced by mechanical stimuli in the protozoan, Stentor coeruleus.

SUMMARY A decrement in the probability of eliciting a response is observed during the course of repetitive stimulation in many response systems of both metazoa and protozoa. Those forms of metazoan response decrement called habituation have recently been characterized behaviorally. In the studies reported here, the response decrement of the contractile protozoan, Stentor coeruleus, to repeated mechanical stimulation was systemically characterized to provide a comparison with metazoan habituation. This change in response probability was closely approximated by a negative exponential function after the first few stimuli. Animals responded to parametric variations of stimulus amplitude, interstimulus interval and retention period in a manner paralleling that observed in metazoa. However, neither interpolated large amplitude mechanical stimuli nor suprathreshold electrical stimuli produced dishabituation in Stentor though these stimuli are among the most effective dishabituating stimuli for metazoan tactile response systems. Behavioral analysis of the response decrement proceeded on the assumption that Stentor contains receptor and effector mechanisms only. Since the response decrement was not correlated with a change in responsiveness to electrical stimuli, the ability of the animal to contract appears to be unaltered by the process producing the response decrement. On the other hand, weak mechanical prestimuli were found to increase the rate of the response decrement which suggests that a process of receptor adaption is operative.
The Hoopoe's Uropygial Gland Hosts a Bacterial Community Influenced by the Living Conditions of the Bird

Molecular methods have revealed that symbiotic systems involving bacteria are mostly based on whole bacterial communities. Bacterial diversity in hoopoe uropygial gland secretion is known to be mainly composed of certain strains of enterococci, but this conclusion is based solely on culture-dependent techniques. This study, by using culture-independent techniques (based on the 16S rDNA and the ribosomal intergenic spacer region) shows that the bacterial community in the uropygial gland secretion is more complex than previously thought and its composition is affected by the living conditions of the bird. Besides the known enterococci, the uropygial gland hosts other facultative anaerobic species and several obligated anaerobic species (mostly clostridia). The bacterial assemblage of this community was largely invariable among study individuals, although differences were detected between captive and wild female hoopoes, with some strains showing significantly higher prevalence in wild birds. These results alter previous views on the hoopoe-bacteria symbiosis and open a new window to further explore this system, delving into the possible sources of symbiotic bacteria (e.g. nest environments, digestive tract, winter quarters) or the possible functions of different bacterial groups in different contexts of parasitism or predation of their hoopoe host.
Self-adaptive TDMA protocols: a learning-automata-based approach

Due to its fixed assignment nature, the well-known TDMA protocol suffers from poor performance when the offered traffic is bursty. In this paper a learning-automata-based time division multiple access protocol, which is capable of operating efficiently under bursty traffic conditions, is introduced. According to the proposed protocol, the station which grants permission to transmit at each time slot is selected by means of learning automata. The choice probability of the selected station is updated by taking into account the network feedback information. The system which consists of the automata and the network is analyzed and it is proved that the choice probability of each station asymptotically tends to be proportional to the probability that this station is not idle. Thus, although there is no centralized control of the stations and the traffic characteristics are unknown and time-variable, each station tends to take a fraction of the bandwidth proportional to its needs. Furthermore, extensive simulation results are presented which indicate that the proposed protocol achieves a significantly higher performance that other well-known time division multiple access protocols when operating under bursty traffic conditions.
A Theory of Marital Dissolution and Stability

Research is presented on the prospective longitudinal prediction of marital dissolution. First, a cascade toward marital dissolution is described. Second, the cascade is predicted with variables from a balance theory of marriage. Third, there are process and perception (the distance and isolation cascades) cascades related to the cascade toward dissolution. The importance of "flooding" is discussed, as well as a mechanism through which negative perceptions (which are 2 dimensional) become global and stable and through which the entire history of the marriage is recast negatively. The role of physiology is outlined. A theory is presented in which a "core triad of balance" is formulated in terms of 3 weakly related thermostats (connected by catastrophe theory) and related to the distance and isolation cascade. Implications for a minimal marital therapy are discussed.
Exploiting Multi-Channel Clustering for Power Efficiency in Sensor Networks

Sensor networks typically comprise of a number of inexpensive small devices with processing, communication and sensing abilities that collaborate to perform a common task. Sensor devices use batteries as their sole power supply. The operational lifetime of a sensor network, therefore, depends entirely on the better utilization of the devices. Typically a sensor network is divided into clusters to optimize power utilization by performing division of labor and data aggregation within a cluster. This paper introduces a novel approach to naturally distributed clustering of sensor nodes in a sensor net using multi channel data planes. Our technique incorporates a virtual sense mechanism that reduces energy spent in sampling and transmission. It also decreases network traffic, thereby decreasing contention, potential collisions and retransmissions. This approach inherently implements a sleep-awake mechanism based on virtual sensing that contributes towards increasing the network lifetime by efficient utilization. The proposed technique can be used to track spreading phenomenon like forest fires and water flows. A spreading phenomenon can be represented by a field whose value changes dynamically with time over area. We focus on following the movement of such a dynamically changing field rather than obtaining the value of the field at different locations at disjoint random times
Delay to Diagnosis in Acute Pediatric Arterial Ischemic Stroke

Background and Purpose— For the clinician, the diagnosis of arterial ischemic stroke (AIS) in children is a challenge. Prompt diagnosis of pediatric AIS within 6 hours enables stroke-specific thrombolytic and neuroprotective strategies. Methods— We conducted a retrospective study of prospectively enrolled consecutive cohort of children with AIS, admitted to The Hospital for Sick Children, Toronto, from January 1992 to December 2004. The data on clinical presentation, symptom onset, emergency department arrival, neuroimaging and stroke diagnosis were recorded. The putative predictors of delayed diagnosis were selected a priori for analysis. Results— A total of 209 children with AIS were studied. The median interval from symptom onset to AIS diagnosis was 22.7 hours (interquartile range: 7.1 to 57.7 hours), prehospital delay (symptom onset to hospital arrival) was 1.7 hours (interquartile range: 49 minutes to 8.1 hours), and the in-hospital delay (presentation to diagnosis) was 12.7 hours (interquartile range: 4.5 to 33.5 hours). The initial assessment was completed in 16 minutes and initial neuroimaging in 8.8 hours. The diagnosis of AIS was suspected on initial assessment in 79 (38%) children and the initial neuroimaging diagnosed AIS in 47%. The parent’s help seeking action, nonabrupt onset of symptoms, altered consciousness, milder stroke severity, posterior circulation infarction and lack of initial neuroimaging at a tertiary hospital were predictive delayed AIS diagnosis. Conclusion— In the diagnosis of AIS, significant prehospital and in-hospital delays exist in children. Several predictors of the delayed AIS diagnosis were identified in the present study. Efforts to target these predictors can reduce diagnostic delays and optimize the management of AIS in children.
Pointwise frequency responses framework for stability analysis in periodically time-varying systems

ABSTRACT This paper explicates a pointwise frequency-domain approach for stability analysis in periodically time-varying continuous systems, by employing piecewise linear time-invariant (PLTI) models defined via piecewise-constant approximation and their frequency responses. The PLTI models are piecewise LTI state-space expressions, which provide theoretical and numerical conveniences in the frequency-domain analysis and synthesis. More precisely, stability, controllability and positive realness of periodically time-varying continuous systems are examined by means of PLTI models; then their pointwise frequency responses (PFR) are connected to stability analysis. Finally, Nyquist-like and circle-like criteria are claimed in terms of PFR's for asymptotic stability, finite-gain Lp-stability and uniformly boundedness, respectively, in linear feedbacks and nonlinear Luré connections. The suggested stability conditions have explicit and direct matrix expressions, where neither Floquet factorisations of transition matrices nor open-loop unstable poles are involved, and their implementation can be graphical and numerical. Illustrative studies are sketched to show applications of the main results.
The Welfare State and Redistribution

In the reaction of aromatic compounds with nitrating acids comprising HNO3 and, if appropriate, H2SO4 and/or H2O and/or H3PO4 to form aromatic nitro compounds, according to the invention an amount of from 0.5 to 20,000 ppm of one or more surface-active substances from the group of the anionic, cationic, zwitterionic or nonionic surface-active substances is added to the reaction mixture.