Miracle-dz/UniFAR-FTUs huggingface dataset:
Combinatorial Control of Smooth Muscle–Specific Gene Expression

Abstract—Alterations in the differentiated state of vascular smooth muscle cells (SMCs) are known to play a key role in vascular diseases, yet the mechanisms controlling SMC differentiation are still poorly understand. In this review, we discuss our present knowledge of control of SMC differentiation at the transcriptional level, pointing out some common themes, important paradigms, and unresolved issues in SMC-specific gene regulation. We focus primarily on the serum response factor–CArG box–dependent pathway, because it has been shown to play a critical role in regulation of multiple SMC marker genes. However, we also highlight several other important regulatory elements, such as a transforming growth factor &bgr; control element, E-boxes, and MCAT motifs. We present evidence in support of the notion that SMC-specific gene regulation is not controlled by a few SMC-specific transcription factors but rather by complex combinatorial interactions between multiple general and tissue-specific proteins. Finally, we discuss the implications of chromatin remodeling on SMC differentiation.
Population‐based screening for Lynch syndrome in Western Australia

We showed earlier that routine screening for microsatellite instability (MSI) and loss of mismatch repair (MMR) protein expression in colorectal cancer (CRC) led to the identification of previously unrecognized cases of Lynch syndrome (LS). We report here the results of screening for LS in Western Australia (WA) during 1994–2012. Immunohistochemistry (IHC) for loss of MMR protein expression was performed in routine pathology laboratories, while MSI was detected in a reference molecular pathology laboratory. Information on germline mutations in MMR genes was obtained from the state's single familial cancer registry. Prior to the introduction of routine laboratory‐based screening, an average of 2–3 cases of LS were diagnosed each year amongst WA CRC patients. Following the implementation of IHC and/or MSI screening for all younger (<60 years) CRC patients, this has increased to an average of 8 LS cases diagnosed annually. Based on our experience in WA, we propose three key elements for successful population‐based screening of LS. First, for all younger CRC patients, reflex IHC testing should be carried out in accredited pathology services with ongoing quality control. Second, a state‐ or region‐wide reference laboratory for MSI testing should be established to confirm abnormal or suspicious IHC test results and to exclude sporadic cases by carrying out BRAF mutation or MLH1 methylation testing. Finally, a state or regional LS coordinator is essential to ensure that all appropriate cases identified by laboratory testing are referred to and attend a Familial Cancer Clinic for follow‐up and germline testing.
Comparative rates of growth of the Port Jackson shark throughout its southern Australian range

Port Jackson sharks are distributed throughout southern Australia, with evidence suggesting that potential subpopulations exist. If subpopulations are evident, then phenotypic variation among groups should result in differences in life-history parameters. The present study tested for patterns of spatial variability of life-history parameters among regional Port Jackson shark populations. Rates of growth from Port Jackson sharks caught in the gulf waters of South Australia were calculated on the basis of counts of vertebral increments. Growth parameters were obtained by fitting the length-at-age data to von Bertalanffy and Gompertz growth functions. While the derived growth curves fit the length-at-age data well (r2 ranged from 0.87 to 0.91), parameters showed considerable differences between the two functions, with the von Bertalanffy function providing the more realistic estimates of growth (combined sexes: k = 0.081 year–1, L∞ = 1232 mm total length and t0 = –1.937 years). Life-history parameters for South Australian Port Jackson sharks were collated with the available data for the species, facilitating comparisons among regional populations. Growth curves among populations varied significantly; however, considerable overlap in the length ranges of size at birth and sizes at maturity among populations were evident. Overall, the data presented here do not provide definitive support for the presence of subpopulations across the distribution of the Port Jackson shark, suggesting that molecular analysis maybe required to directly test for structuring.
Self-regulated reionization

Recently, we have presented the first, truly large-scale radiative transfer simulations of inhomogeneous cosmic reionization which resolve all the possible halo sources down to the dwarf galaxy mass range, M ≥ 10 9 M⊙, in a comoving volume (100 h - 1 Mpc) 3 . This is large enough to sample the global mean history, geometry and statistical properties of reionization fairly and accurately for the first time. Here we present new simulations which extend the source halo mass range downward to 10 8 M⊙, to capture the full range of halo masses thought to be primarily responsible for reionization by their star formation following atomic hydrogen radiative cooling and gravitational collapse. Haloes below about 10 9 M⊙, however, are subject to Jeans-mass filtering in the ionized regions, which suppresses their baryonic content and their ability to release ionizing radiation. By including these smaller mass haloes but accounting for their suppression, too, we find that reionization is 'self-regulating', as follows. As the mean ionized fraction rises, so does the fraction of the volume within which suppression occurs. Hence, the degree of suppression is related to the mean ionized fraction. Since low-mass haloes with high efficiency (i.e. high emissivity) achieve a given mean ionized fraction earlier than do those with low efficiency, Jeans-mass filtering compensates for the difference in the emissivity of the suppressible haloes in these two cases. As a result, in the presence of lower mass source haloes, reionization begins earlier, but the later stages of reionization and the time of overlap are dictated by the efficiency of the higher mass haloes, independent of the efficiency of the suppressible, lower mass haloes. Hence, while the lower mass haloes do not alter the overlap redshift, Z ov , they serve to boost the electron-scattering optical depth of the universe, τ es . This may explain why observations of quasar absorption spectra at high redshift find that reionization ended late (Z ov 11). We present results for the Lambda cold dark matter universe with cosmological parameters from both 1- and 3-yr data releases of Wilkinson Microwave Anisotropy Probe. Reionization histories consistent with current constraints on Z ov and τ es are shown to be achievable with standard stellar sources in haloes above 10 8 M⊙. Neither minihaloes nor exotic sources are required, and the phenomenon of 'double reionization' previously suggested does not occur.
Error Rates Analysis of MIMO Space-Time Block Codes in Generalized Shadowed Fading Channels

This paper introduces a new and unified bit error rates performance analysis of space-time block codes (STBC) deployed in wireless systems with spatial diversity in generalized shadowed fading and noise scenarios. Specifically, we derive a simple and a very accurate approximate expressions for the average error rates of coherent modulation schemes in generalized $\eta-\mu$ and $\kappa-\mu$ shadowed fading channels with multiple input multiple output (MIMO) systems. The noise in the network is assumed to be modeled using the additive white generalized Gaussian noise (AWGGN), which encompasses the classical Laplacian and the Gaussian noise environments as special cases. The derived results obviate the need to re-derive the error rates for MIMO STBC systems under many multipath fading and noise conditions while avoiding any special functions with high computational complexity. Published results from the literature, as well as numerical evaluations, corroborate the accuracy of our derived generalized expressions.
Predictors of peritonitis in patients on peritoneal dialysis: results of a large, prospective Canadian database.

BACKGROUND AND OBJECTIVES Despite the decreasing incidence of peritonitis among peritoneal dialysis (PD) patients over time, its occurrence is still associated with significant morbidity and mortality. Determining factors that are associated with PD peritonitis may facilitate the identification of patients who are at risk. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS Using data collected in the multicenter Baxter POET database between 1996 and 2005, the study population included incident Canadian PD patients. Potential predictors of peritonitis were sought using a negative binomial model and an Andersen-Gill model. Study variables included age, gender, race, cause of renal disease, diabetes status, transfer from hemodialysis (HD), previous renal transplant, and continuous ambulatory PD (CAPD) versus automated PD (APD). RESULTS Data were available for 4247 incident PD patients, including 1605 patients with a total of 2555 peritonitis episodes. Using the negative binomial regression model, factors that were independently associated with a higher peritonitis rate included age, Black race, and having transferred from HD. There was an interaction between gender and diabetes, with an increased risk for peritonitis among female patients with diabetes. The use of CAPD versus APD did not affect the peritonitis rate. The Andersen-Gill model for recurrent events yielded similar results. CONCLUSIONS Predictors of PD peritonitis included Black race, transferring from HD to PD, and diabetes among women. In contrast to previous findings, CAPD and APD were similar with regard to peritonitis risk.
Semileptonic kaon decays

We present the matrix elements for the semileptonic kaon decays $K_{l2\gamma}$ , $K_{l2l^+l^-}$, $K_{l2l'^+l'^-}$,$K_{l3}$, $K_{l3\gamma}$ and $K_{l4}$ at next-to-leading order, and $K_{e5}$ at leading order in Chiral Perturbation Theory and compare the predictions with experimental data. For $K_{l4}$ decays we estimate yet higher orders in order to reduce theoretical uncertainties in the comparison with the data. Monte Carlo event generators are used to calculate the corresponding rates at DA$\Phi$NE. We discuss the possibilities to improve our knowledge of the low-energy structure of the Standard Model at this and similar machines.
Empirical Evaluation of A New Approach to Simplifying Long Short-term Memory (LSTM)

The standard LSTM, although it succeeds in the modeling long-range dependences, suffers from a highly complex structure that can be simplified through modifications to its gate units. This paper was to perform an empirical comparison between the standard LSTM and three new simplified variants that were obtained by eliminating input signal, bias and hidden unit signal from individual gates, on the tasks of modeling two sequence datasets. The experiments show that the three variants, with reduced parameters, can achieve comparable performance with the standard LSTM. Due attention should be paid to turning the learning rate to achieve high accuracies
Elevated circulating microRNA-210 levels in patients with hereditary hemorrhagic telangiectasia and pulmonary arteriovenous malformations: a potential new biomarker

Pulmonary arteriovenous malformations (PAVMs), which can lead to life-threatening bleeding and other complications, have been reported to occur in 30–50% of patients with hereditary hemorrhagic telangiectasia (HHT). Circulating microRNAs (miRNAs) have emerged as new biomarkers for human diseases. This study was conducted to explore circulating miRNAs as biomarkers for the screening of HHT patients with PAVMs. MicroRNA array analysis revealed eight altered circulating miRNAs in patients with PAVMs. Real time RT-PCR showed that the levels of circulating miR-210 were significantly elevated in HHT patients with PAVMs but not changed in patients without PAVMs as compared with healthy controls. Circulating miR-210 therefore may be used as a new and sensitive biomarker for the screening of patients with HHT for clinically significant PAVMs.
Neurogenic Model of Migraine

Activation of peripheral trigeminal fibers induces neurogenic inflammation in rat dura mater, as well as vascular and mast cell changes. These changes parallel an increase of vasodilating and permeability promoting peptides in venous effluent of the cephalic circulation. The experimental model of electrical trigeminal ganglion stimulation or systemic capsaicin administration has proven effective in detecting cellular activation in brainstem trigeminal nuclei. Animal experimental models of trigeminovascular activation and the effects of antimigraine drugs on functional and morphological consequences of such activation provide the background for further models and for developing pharmacological strategies in this field.
Identification and Expression of Nine Oak Aquaporin Genes in the Primary Root Axis of Two Oak Species, Quercus petraea and Quercus robur

Aquaporins (AQPs) belong to the Major Intrinsic Protein family that conducts water and other small solutes across biological membranes. This study aimed to identify and characterize AQP genes in the primary root axis of two oak species, Quercus petraea and Quercus robur. Nine putative AQP genes were cloned, and their expression was profiled in different developmental root zones by real-time PCR. A detailed examination of the predicted amino acid sequences and subsequent phylogenetic analysis showed that the isolated AQPs could be divided into two subfamilies, which included six plasma membrane intrinsic proteins (PIPs) and three tonoplast intrinsic proteins (TIPs). We characterized the anatomical features of the roots and defined three developmental root zones: the immature, transition and mature zones. Expression analysis of the AQPs was performed according to these root developmental stages. Our results showed that the expression of PIP2;3 and TIP1 was significantly higher in Quercus petraea compared with Quercus robur in the three root zones. However, PIP2;1 and TIP2;1 were found to be differentially expressed in the mature zone of the two oak species. Of the nine AQP genes identified and analyzed, we highlighted four genes that might facilitate a deeper understanding of how these two closely related tree species adapted to different environments.
Malaysian Vowel Recognition Based on Spectral Envelope Using Bandwidth Approach

Automatic speech recognition (ASR) has made great strides with the development of digital signal processing hardware and software especially using English as the language of choice. In this paper, a new feature extraction method is presented to identify vowels recorded from 80 Malaysian speakers. The features are obtained from Vocal Tract Model based on Bandwidth (BW) approach. The bandwidth is determined by finding the frequency where the spectral energy is 3dB below the peak. Average gain was calculated from these bandwidths. Classification results from Bandwidth Approach were then compared with results from 14 MFCC Coefficients using BPNN (Backpropagation Neural Network), MLR (Multinomial Logistic Regression) and LDA (Linear Discriminative Analysis). Classification accuracy obtained shows Bandwidth Approach performs better than MFCC using all these classifiers.
Molecular phylogeny and evolutionary history of the tit-tyrants (Aves: Tyrannidae).

Tit-tyrants of the genus Anairetes presently consist of six species; five inhabit various regions along the Andean cordillera of South America and one is endemic to the Juan Fernandez Islands off the coast of Chile. Data from mtDNA ND2 and Cyt b sequences were used to construct a phylogeny for all Anairetes species as well as Uromyias agilis, a closely related genus, and Stigmatura as an outgroup, to determine their relationships and history of radiation in South America. Results strongly supported the following paired relationships: A. nigrocristatus-A. reguloides, A. flavirostris-A. alpinus, and A. parulus-A. fernandezianus. This dataset, however, could not resolve basal nodes; therefore relationships among these pairs remains obscure. Moreover the genus Uromyias, controversially separated on morphological criteria from Anairetes, fell within the Anairetes clade, although its exact position could not be ascertained with confidence. The molecular data indicate that this group probably radiated within the past 2 million years, concomitant with highly accentuated cycles of global climatic change. Certain high altitude areas within the Andes may have been stable during global climatic changes and may have served as refugia during the Plio-Pleistocene.
Plastid Cues Posttranscriptionally Regulate the Accumulation of Key Enzymes of the Methylerythritol Phosphate Pathway in Arabidopsis1

Plastid isoprenoids (including hormones and photosynthetic pigments) are essential for plant growth and development, but relatively little is known of how the production of their metabolic precursors via the recently elucidated methylerythritol phosphate (MEP) pathway is regulated. We have identified an Arabidopsis (Arabidopsis thaliana) mutant that survives an otherwise lethal block of the MEP pathway with fosmidomycin (FSM). In rif10 (resistant to inhibition with FSM 10) plants, the accumulation of flux-controlling enzymes of the pathway is posttranscriptionally up-regulated. Strikingly, this phenotype is linked to a lower accumulation of plastidial isoprenoid pigments such as chlorophylls and carotenoids, resulting in mutant plants that are paler and smaller than the wild type. The rif10 mutant is impaired in plastid RNA processing due to a T-DNA insertion in the coding region of the At3g03710 gene encoding the chloroplast-targeted exoribonuclease polyribonucleotide phosphorylase. FSM resistance and other rif10-like phenotypes were also observed in wild-type Arabidopsis, tomato (Lycopersicon esculentum), and rice (Oryza sativa) seedlings grown in the presence of sublethal concentrations of chloramphenicol (an inhibitor of protein synthesis in plastids). By contrast, treatment with norflurazon (an inhibitor of carotenoid biosynthesis causing a similar pale cotyledon phenotype) did not result in FSM resistance. Together, the results support that plastome-encoded proteins are involved in negatively regulating the posttranscriptional accumulation of specific nuclear-encoded MEP pathway enzymes in chloroplasts. Regulation of the MEP pathway by a mechanism dependent on plastid cues might function under physiological conditions to finely adjust plastidial isoprenoid biosynthesis to the metabolic capabilities or requirements of plastids.
An analytical model for fair rate calculation in resilient packet rings

Resilient packet ring (RPR) is a new medium access control (MAC) protocol for high-speed ring networks. It supports spatial reuse and, therefore, maintaining fairness among different nodes is a challenging task in RPR. To ensure fairness among nodes, a fairness algorithm is employed at each RPR node. In case of congestion, the fairness algorithm advertises a fair rate to all upstream nodes contributing to the congestion. In this paper, we develop an analytical model for fair rate calculation in the standard RPR fairness algorithm in the parking lot scenario. We first ignore the link propagation delay and model the system using a nonlinear discrete-time low-pass filter. We, then, consider the link propagation delay and develop a more realistic model. We verify our model by simulation results and analyze the effect of various parameters on the convergence time. Finally, we determine the low-pass filter coefficient to ensure that convergence time of the algorithm is within its minimum range
Antimicrobial drug susceptibility of Staphylococcus aureus from subclinical bovine mastitis in Coimbatore , Tamilnadu , South India

Aim: The study was carried out to investigate the prevalence and antimicrobial susceptibility of clinical pathogens isolated from Bovine Mastitis in and around Coimbatore District, Tamilnadu, South India. Materials and Methods: A total of 250 milk samples were screened and 152 isolates of Staphylococci were obtained and their susceptibility to several antimicrobial agents by agar disc diffusion method. Results: Out of 152 isolates of Staphylococcus aureus resistance was detected in 63 (41.44%), 39 (25.65%), 21(13.81%), 18 (11.84%), 6 (3.94%) and 5 (3.28%) isolates for penicillin, streptomycin, erythromycin, tetracycline, ampicillin and Cephalothin, respectively. No resistance was detected for Gentamicin. Conclusion: Results indicated that these isolates exhibited the highest degree of resistance to penicillin of all antimicrobial agents tested.
Patterns and Risks of Trichinella Infection in Humans and Pigs in Northern Laos

Several outbreaks of trichinellosis associated with the consumption of raw pork have occurred in Laos since 2004. This cross-sectional study was conducted in four provinces of northern Laos to investigate the seroepidemiology of trichinellosis in the human population and determine the prevalence and species of Trichinella infection in the domestic pig population. Serum samples and questionnaire data were obtained from 1419 individuals. Serum samples were tested for Trichinella antibodies by ELISA using larval excretory–secretory (ES) antigens and a subset of 68 positive samples were tested by western blot. The seroprevalence of Trichinella antibodies was 19.1% (95% confidence interval (CI) = 17.1–21.1%). The risk of having antibodies detected by ELISA using ES antigens increased with age, being of Lao-Tai ethnicity, living in Oudomxay province and being male. Tongue and diaphragm muscle samples were collected from 728 pigs and tested for Trichinella larvae by the artificial digestion method. Trichinella larvae were isolated from 15 pigs (2.1%) of which 13 were identified as T. spiralis by molecular typing; the species of the two remaining isolates could not be determined due to DNA degradation. Trichinella spp. are endemic in the domestic environment of northern Laos and targeted preventative health measures should be initiated to reduce the risk of further outbreaks occurring.
Realtime facial animation with on-the-fly correctives

We introduce a real-time and calibration-free facial performance capture framework based on a sensor with video and depth input. In this framework, we develop an adaptive PCA model using shape correctives that adjust on-the-fly to the actor's expressions through incremental PCA-based learning. Since the fitting of the adaptive model progressively improves during the performance, we do not require an extra capture or training session to build this model. As a result, the system is highly deployable and easy to use: it can faithfully track any individual, starting from just a single face scan of the subject in a neutral pose. Like many real-time methods, we use a linear subspace to cope with incomplete input data and fast motion. To boost the training of our tracking model with reliable samples, we use a well-trained 2D facial feature tracker on the input video and an efficient mesh deformation algorithm to snap the result of the previous step to high frequency details in visible depth map regions. We show that the combination of dense depth maps and texture features around eyes and lips is essential in capturing natural dialogues and nuanced actor-specific emotions. We demonstrate that using an adaptive PCA model not only improves the fitting accuracy for tracking but also increases the expressiveness of the retargeted character.