Miracle-dz/UniFAR-FTUs huggingface dataset:
Two New Recursive Likelihood Calculation Methods for Genetic Analysis

Recursive likelihood calculations for genetic analysis with ungenotyped pedigree data employ variations of the Elston-Stewart (ES) or the Lander-Green (LG) algorithms. With the ES algorithm, the number of loci may be limited but not the pedigree size. With the LG algorithm, the reverse is the case. We introduce two new algorithms for the computation of regressive likelihoods for pedigrees with multivariate traits. The first is an alternative formulation of our existing model, which leads to a simpler form in the binary trait, polygenic and mixed model cases. The second is an approximation model, which is computationally efficient. These methods apply to both continuous and binary traits, in the oligogenic and polygenic cases. Both methods coincide in the binary case. We considered these methods for cases in which all the traits are controlled by a single locus, with each trait controlled by one locus independent to the others. Simulation studies and analysis of a real data are presented for segregation analysis as illustrations. These methods can also be used in other model-based analyses. These methods are implemented in G.E. M.S., the genetic epidemiology models software.
The Efficacy of Phonological Awareness Intervention for Children With Spoken Language Impairment.

PURPOSE This study investigated the efficacy of an integrated phonological awareness intervention approach for children with spoken language impairment (SLI) who demonstrated early reading delay. Ninety-one, 5- to 7-year-old New Zealand children participated in this study: 61 children with SLI and 30 children with typically developing speech and language skills. All of the children with language impairment exhibited expressive phonological difficulties and some also had delayed semantic and syntactic development. METHOD The children with SLI participated in either: (a) an integrated phonological awareness program, (b) a more traditional speech-language intervention control program that focused on improving articulation and language skills, or (c) a minimal intervention control program over a 4 1/2-month time period. RESULTS Effects of the interventions on phonological awareness ability, reading performance, and speech production were examined. The children who received phonological awareness intervention made significantly more gains in their phonological awareness ability and reading development than the children receiving the other types of speech and language intervention. Despite significant delays in phonological awareness prior to training, children who received the phonological awareness intervention reached levels of performance similar to children with typically developing speech and language skills at post-test assessment. The phonological awareness intervention also improved the children's speech articulation. CLINICAL IMPLICATIONS The findings suggest that integrated phonological awareness intervention may be an efficient method to improve phonological awareness, speech production, and reading development of children with SLI. Findings are discussed with reference to a speech-literacy link model.
Extended tuning range in sampled grating DBR lasers

The authors demonstrate, for the first time, successful implementation of a distributed Bragg reflector laser with two sampled grating mirrors, which they previously predicted should give tuning range in excess of 50 nm. This device uses a uniform grating pitch throughout the structure, and relies on the same fabrication technology as a standard DBR laser. Initial results show 57 nm of mathematical tuning at 1.475 mu m with side-mode suppression ratio (SMSR)>30 dB over much of the tuning range. The observed change in operating wavelength versus mirror currents along with below threshold spectra agree with theoretical expectations. <<ETX>>
Honey Collected from Different Floras of Chandigarh Tricity: A Comparative Study Involving Physicochemical Parameters and Biochemical Activities

ABSTRACT Background: Different monofloral honeys have a distinctive flavor and color because of differences in physicochemical parameters because of their principal nectar sources or floral types. Methods: Honey samples were collected from Apis mellifera colonies forged on 10 floras to analyze the quality of honey in terms of standards laid by Honey Grading and Marking Rules (HGMR), India, 2008 and Codex Alimentarious Commission (CAC), . The honey samples were analyzed for various physicochemical parameters of honey quality control, i.e., pH, total acidity, moisture, reducing sugars, non-reducing sugars, total sugars, water insoluble solids (WIS), ash content, 5-hydroxymethylfurfural content, and diastase value. The antioxidant potential was estimated using Folin–Ciocalteu reagent. Further, honey samples were assayed for antibacterial activities against clinical isolates of Staphylococcus aureus and Escherichia coli using the hole-plate diffusion method. Results: The physicochemical variation in the composition of honey because of floral source shows Ziziphus honey with high pH and diastase values along with low acidity, whereas Helianthus honey contained high reducing sugar and low moisture content. Amomum, Brassica, Acacia, and Citrus contained lowest amount of non-reducing sugars, ash, WIS, and moisture, respectively. Lowest 5-hydroxymethylfurfural (HMF) value was detected in Amomum honey, while highest HMF value was observed with Eucalyptus. The maximum antibacterial and antioxidant potential was observed in Azadirachta and Citrus, respectively. Conclusion: The quality of honey produced by local beekeepers met HGMR and CAC standards, and the chemical composition and biological properties of honey were dependent on the floral source from which it was produced.
Naval Structural Antenna Systems for Broadband HF Communications—Part II: Design Methodology for Real Naval Platforms

Recently, it was shown how to make a multipurpose broadband HF antenna system out of existing naval super-structures such as the funnel or a big mast. The idea was discussed by means of canonical structures, e.g., a cylindrical body of circular or square cross-section, placed onto an infinite ground plane. This paper investigates the critical aspects concerning the extension of naval structural antenna concept to real ship platforms with the aim to define a general design methodology for impedance matching and radiation pattern control. The method is described with reference to a realistic frigate model, whose big mast is transformed into a broadband HF antenna system able to perform communications by both sea-wave and sky-wave links. It is demonstrated that, even in a real environment, the multiport strategy permits to increase the system efficiency and to moderately shape the radiation pattern in order to overcome the shadowing effect due to other large objects
Resource partition for real-time systems

We investigate an approach to implement the open system environment idea by means of temporal resource partitions. In this approach, application task groups with hard timing constraints may share the same physical resource and yet be free from the interference of one another. Each resource partition uses only a fraction of the time on the resource. Partitions are specified by two models, a static partition model and a bounded-delay partition model. Both models achieve a clean separation of concerns between task group level scheduling and resource level partition scheduling. The schedulability problems for both preemptive fixed priority and dynamic priority scheduling policies are analyzed.
The Quality of Governance and Economic Growth in Croatia

The objective of this paper is to show the justification and importance of explicit inclusion of quality of governance in the debate on economic growth in Croatia. Governance is defined as the manner in which the state employs its power in handling the institutional environment, thus affecting the accumulation of economic growth factors. Although there are numerous elements in the quality of governance, this paper places the emphasis on the whole on two of them: the rule of law and the quality of the public administration. In pursuit of its objective, the paper first of all considers the links between governance and economic growth in growth theory and empirical research to date. After that an econometric (panel) analysis of quality of governance and economic growth on a sample of EU countries and Croatia, Bulgaria and Romania (EU accession candidate countries) is performed, and then changes in the quality of governance in Croatia are considered. From a comparison of the values of indicators of the rule of law and quality of the public administration, and the dynamics and nature of reform in the administration of justice and the civil service, it appears that those in whom power is vested in Croatia are more focused on rent-seeking than is the case in the average of EU countries. Institutional shortcomings have affected the current level of real per capita GDP in Croatia, and more rapid and effective reforms of the justice and public administration sectors, as well as fighting corruption and boosting democracy (as mechanism for controlling those in whom power is vested) would have a positive effect on future economic growth.
L-type calcium channels mediate transmitter release in isolated, wide-field retinal amacrine cells

Transmitter release in neurons is triggered by intracellular Ca2+ increase via the opening of voltage-gated Ca2+ channels. Here we investigated the voltage-gated Ca2+ channels in wide-field amacrine cells (WFACs) isolated from the white-bass retina that are functionally coupled to transmitter release. We monitored transmitter release through the measurement of the membrane capacitance (Cm). We found that 500-ms long depolarizations of WFACs from −70 mV to 0 mV elicited about a 6% transient increase in the Cm or membrane surface area. This Cm jump could be eliminated either by intracellular perfusion with 10 mM BAPTA or by extracellular application of 4 mM cobalt. WFACs possess N-type and L-type voltage-gated Ca2+ channels. Depolarization-evoked Cm increases were unaffected by the specific N-type channel blocker ω-conotoxin GVIA, but they were markedly reduced by the L-type blocker diltiazem, suggesting a role for the L-type channel in synaptic transmission. Further supporting this notion, in WFACs the synaptic protein syntaxin always colocalized with the pore-forming subunit of the retinal specific L-type channels (CaV1.4 or α1F), but never with that of the N-type channels (CaV2.2 or α1B).
Prism-like effect of nanotubes and nanowires made of noble metals

The scattering of the H-polarized plane electromagnetic wave by circular gold and silver nanotubes and nanowires with concentric dielectric covers in the visible range of the wavelengths is studied. In each case, the mathematical model is based on the Maxwell equations in the polar coordinates, and the analytical solution of the wave-scattering problem is obtained by the separation of variables. In computations, the complex permittivity of gold or silver is taken from the published experimental data. Unlike previous studies, the focus is on the "prism-like" effect: it is demonstrated that these nanoobjects can scatter specific wavelength bands at different angles.
Endogenous Shifts in OPEC Market Power: A Stackelberg Oligopoly with Fringe

This article proposes a two-stage oligopoly model for the crude oil market. In a game of several Stackelberg leaders, market power increases endogenously as the spare capacity of the competitive fringe goes down. This effect is due to the specific cost function characteristics of extractive industries. The model captures the increase of OPEC market power before the financial crisis and its drastic reduction in the subsequent turmoil at the onset of the global recession. The two-stage model better replicates the price path over the years 2003-2011 compared to a standard simultaneous-move, onestage Nash-Cournot model with a fringe. This article also discusses how most large-scale numerical equilibrium models, widely applied in the energy sector, over-simplify and potentially misinterpret market power exertion.
Pre-training Attention Mechanisms

Recurrent neural networks with differentiable attention mechanisms have had success in generative and classification tasks. We show that the classification performance of such models can be enhanced by guiding a randomly initialized model to attend to salient regions of the input in early training iterations. We further show that, if explicit heuristics for guidance are unavailable, a model that is pretrained on an unsupervised reconstruction task can discover good attention policies without supervision. We demonstrate that increased efficiency of the attention mechanism itself contributes to these performance improvements. Based on these insights, we introduce bootstrapped glimpse mimicking, a simple, theoretically task-general method of more effectively training attention models. Our work draws inspiration from and parallels results on human learning of attention.
Baseline Differences in Social Support Among Treatment-Seeking Alcoholics With and Without Social Phobia

Differences on demographics and seven measures of social support between matched, treatment-seeking alcoholics with and without social phobia (SP and NSP groups, respectively) were examined. The groups did not differ on most demographic variables, although the SP group (n = 397) had a lower occupational status and had fewer years of education (both p's < .01) than the NSP group (n = 397). On social support measures, the SP group had less perceived social support from friends and had a lower performance on the social behavior role scale than the NSP group (both p's < .001). The two groups were unexpectedly more similar than different on the measures of interest in this study; however, the differences identified are meaningful for treatment planning. It is important to ascertain the quantity and sources of social support which are available to these clients in order to maximize positive treatment outcomes.
Impact of Steroids on the Inflammatory Response after Ischemic Acute Kidney Injury in Rats

Inflammation plays a crucial role in acute kidney injury (AKI). The current study was designed to analyze the influence of prednisolone treatment on the inflammatory reaction during the first 96 h after AKI induction in a rat model. AKI was induced by unilateral clipping of the renal vessels. The treatment group received prednisolone 5 mg/kg s.c. daily. Infiltration rates of macrophages, leukocytes, and T-cells (24, 96 h) as well as plasma concentrations of the inflammatory markers intercellular adhesion molecule, interleukin-1 beta (IL-1β), IL-18, IL-6, and tumor necrosis factor-alpha (0, 6, 24, 96 h) were determined by fluorescence-activated cell sorting (FACS) analysis only. Ninety-six hours after AKI induction, the prednisolone group demonstrated significantly lower creatinine concentrations compared to the control group (P < 0.05). Twenty-four hours after induction of AKI, a significantly higher rate of infiltrating leukocytes was detectable with FACS analysis in the control group (P < 0.01) with a corresponding significantly higher rate of macrophages after 96 h (P < 0.01). IL-6 and IL-1β demonstrated a peak after 6 h with a significantly higher release in the control group (IL-6: P < 0.01; IL-1β: P < 0.05). In contrast to the control group, the prednisolone group demonstrated no further incline of IL-18 after 24 h. The results demonstrate the importance of stretching the observation period in an ischemia-reperfusion-induced AKI setting beyond the first 24 h. Despite the demonstrated protective effects of a continuous prednisolone application, it seems that this single anti-inflammatory agent will not be able to completely suppress the inflammatory response after an ischemia-reperfusion-induced AKI.
Genetic Dynamic Analysis of the Influenza A H5N1 NS1 Gene in China

The direct precursors of the A/Goose/Guangdong/1/1996 (GS/GD) virus lineage and its reassortants have been established geographically and ecologically. To investigate the variation and evolutionary dynamics of H5N1 viruses, whole-genome viral sequences (n = 164) were retrieved from the NCBI Influenza Virus Resource. Here, we present phylogenetic evidence for intrasubtype reassortments among H5N1 viruses isolated from China during 1996–2012. On the basis of phylogenetic analysis, we identified four major groups and further classified the reassortant viruses into three subgroups. Putative mosaic structures were mostly found in the viral ribonucleoprotein (vRNP) complexes and 91.0% (10/11) mosaics were obtained from terrestrial birds. Sequence variability and selection pressure analyses revealed that both surface glycoproteins (HA and NA) and nonstructural protein 1 (NS1) have higher dN/dS ratio and variability than other internal proteins. Furthermore, we detected 47 positively selected sites in genomic segments with the exception of PB2 and M1 genes. Hemagglutinin (HA) and neuraminidase (NA) are considered highly variable due to host immune pressure, however, it is not known what drives NS1 variability. Therefore, we performed a thorough analysis of the genetic variation and selective pressure of NS1 protein (462 available NS1 sequences). We found that most of positively selected sites and variable amino acids were located in the C-terminal effector domain (ED) of NS1. In addition, we focused on the NS1–RNA and NS1–protein interactions that were involved in viral replication mechanisms and host immune response. Transcriptomic analysis of H5N1-infected monkey lungs showed that certain PI3K-related genes were up-regulated.
Predicting the mortality in geriatric patients with dengue fever

Abstract Geriatric patients have high mortality for dengue fever (DF); however, there is no adequate method to predict mortality in geriatric patients. Therefore, we conducted this study to develop a tool in an attempt to address this issue. We conducted a retrospective case–control study in a tertiary medical center during the DF outbreak in Taiwan in 2015. All the geriatric patients (aged ≥65 years) who visited the study hospital between September 1, 2015, and December 31, 2015, were recruited into this study. Variables included demographic data, vital signs, symptoms and signs, comorbidities, living status, laboratory data, and 30-day mortality. We investigated independent mortality predictors by univariate analysis and multivariate logistic regression analysis and then combined these predictors to predict the mortality. A total of 627 geriatric DF patients were recruited, with a mortality rate of 4.3% (27 deaths and 600 survivals). The following 4 independent mortality predictors were identified: severe coma [Glasgow Coma Scale: ⩽8; adjusted odds ratio (AOR): 11.36; 95% confidence interval (CI): 1.89–68.19], bedridden (AOR: 10.46; 95% CI: 1.58–69.16), severe hepatitis (aspartate aminotransferase >1000 U/L; AOR: 96.08; 95% CI: 14.11–654.40), and renal failure (serum creatinine >2 mg/dL; AOR: 6.03; 95% CI: 1.50–24.24). When we combined the predictors, we found that the sensitivity, specificity, positive predictive value, and negative predictive value for patients with 1 or more predictors were 70.37%, 88.17%, 21.11%, and 98.51%, respectively. For patients with 2 or more predictors, the respective values were 33.33%, 99.44%, 57.14%, and 98.51%. We developed a new method to help decision making. Among geriatric patients with none of the predictors, the survival rate was 98.51%, and among those with 2 or more predictors, the mortality rate was 57.14%. This method is simple and useful, especially in an outbreak.
AN IMPLANTABLE VENTRICULAR ASSIST SYSTEM EMPLOYING A RADIALLY CONTROLLED MAGLEV CENTRIFUGAL BLOOD PUMP WITH CAPABILITY TO MEASURE BLOOD FLOW RATE WITHOUT ADDITIONAL SENSORS

In order to solve the problems of lack of heart donors for transplant, implantable ventricular assist systems (VAS) have been developed to assist the failing heart ventricle. One of the components of a VAS is a blood pump that connects the left ventricle to the aorta. Therefore, the pump flow rate is influenced by the cardio-vascular system. To control the flow rate through the blood pump, real-time measurement of flow rate is required. However, the use of conventional flow sensors is not desirable due to issues of compactness and durability. In a magnetically levitated (maglev) rotary blood pump, the radial thrust acting on the maglev impeller depends on the pump flow rate. In this study, we present a centrifugal blood pump (CBP), incorporating a radial-controlled magnetic bearing (MB) and a brushless DC motor to be used in an implantable VAS. We also present a method for estimating average pump flow rate during ventricular assistance, based on the radial thrust estimated by a disturbance force observer of the MB. The magnetic bearing of the CBP is composed of two pairs of electromagnets located in the stator and a sandwich of two iron rings and a permanent magnet (PM) ring embedded in the impeller. To design the observer, parameters of the dynamic model of a maglev impeller were identified under different flow conditions, assuming the density and viscosity of water to be constant. The disturbance force observers were designed based on linear models that were obtained for a given rotational speed. The relationship between pump flow rate and radial thrust was first identified experimentally under continous flow conditions. Then, using this relationship and the measured radial thrust, the pump average flow rate was estimated under pulsatile flow conditions. The maglev CBP is 69.0 mm in diameter, 28.5 mm in height, 50.0 mm in impeller’s diameter and the pump priming volume is 20 ml. The pump mass is 370 g, while the impeller mass is 98 g. Under rotational speed of 1700 rpm, the operating point (5 L/min, 100 mmHg) can be achieved. Using the proposed estimation method, the pump average flow rate estimation error was less than 11% (0.4L/min).
MEL-IRIS: An Online Tool for Audio Analysis and Music Indexing

Chroma is an important attribute of music and sound, although it has not yet been adequately defined in literature. As such, it can be used for further analysis of sound, resulting in interesting colorful representations that can be used in many tasks: indexing, classification, and retrieval. Especially in Music Information Retrieval (MIR), the visualization of the chromatic analysis can be used for comparison, pattern recognition, melodic sequence prediction, and color-based searching. MEL-IRIS is the tool which has been developed in order to analyze audio files and characterize music based on chroma. The tool implements specially designed algorithms and a unique way of visualization of the results. The tool is network-oriented and can be installed in audio servers, in order to manipulate large music collections. Several samples from world music have been tested and processed, in order to demonstrate the possible uses of such an analysis.