Miracle-dz/UniFAR-FTUs huggingface dataset:
Should the Statistical Analyses of Twinning-Rate Data be Improved?

Abstract Every statistical model is based on explicitly or implicitly formulated assumptions. In this study we address new techniques of calculation of variances and confidence intervals, analyse some statistical methods applied to modelling twinning rates, and investigate whether the improvements give more reliable results. For an observed relative frequency, the commonly used variance formula holds exactly with the assumptions that the repetitions are independent and that the probability of success is constant. The probability of a twin maternity depends not only on genetic predisposition, but also on several demographic factors, particularly ethnicity, maternal age and parity. Therefore, the assumption of constancy is questionable. The effect of grouping on the analysis of regression models for twinning rates is also considered. Our results indicate that grouping influences the efficiency of the estimates but not the estimates themselves. Recently, confidence intervals for proportions of low-incidence events have been a target for revived interest and we present the new alternatives. These confidence intervals are slightly wider and their midpoints do not coincide with the maximum-likelihood estimate of the twinning rate, but their actual coverage is closer to the nominal one than the coverage of the traditional confidence interval. In general, our findings indicate that the traditional methods are mainly satisfactorily robust and give reliable results. However, we propose that new formulae for the confidence intervals should be used. Our results are applied to twin-maternity data from Finland and Denmark.
Convolutional neural networks pretrained on large face recognition datasets for emotion classification from video

In this paper we describe a solution to our entry for the emotion recognition challenge EmotiW 2017. We propose an ensemble of several models, which capture spatial and audio features from videos. Spatial features are captured by convolutional neural networks, pretrained on large face recognition datasets. We show that usage of strong industry-level face recognition networks increases the accuracy of emotion recognition. Using our ensemble we improve on the previous best result on the test set by about 1 %, achieving a 60.03 % classification accuracy without any use of visual temporal information.
Noninvasive Approach to Focal Cortical Dysplasias: Clinical, EEG, and Neuroimaging Features

Purpose. The main purpose is to define more accurately the epileptogenic zone (EZ) with noninvasive methods in those patients with MRI diagnosis of focal cortical dysplasia (FCD) and epilepsy who are candidates of epilepsy surgery. Methods. Twenty patients were evaluated prospectively between 2007 and 2010 with comprehensive clinical evaluation, video-electroencephalography, diffusion tensor imaging (DTI), and high-resolution EEG to localize the equivalent current dipole (ECD). Key Findings. In 11 cases with white matter asymmetries in DTI the ECDs were located next to lesion on MRI with mean distance of 14.63 millimeters with topographical correlation with the EZ. Significance. We could establish a hypothesis of EZ based on Video-EEG, high-resolution EEG, ECD method, MRI, and DTI. These results are consistent with the hypothesis that the EZ in the FCD is complex and is often larger than visible lesion in MRI.
Characterization of a Novel G3P[3] Rotavirus Isolated from a Lesser Horseshoe Bat: a Distant Relative of Feline/Canine Rotaviruses

ABSTRACT Bats are considered important animal reservoirs for many viruses pathogenic to humans. An approach based on viral metagenomics was used to study gut specimens from 78 insectivorous bats in Yunnan Province, China. Seventy-four reads were found to be related to group A rotavirus (RVA). Further reverse transcription-PCR screening and viral isolation on cell cultures confirmed the presence of a novel RVA strain, named RVA/Bat-tc/MSLH14/2012/G3P[3], in 1 (6%) of 16 lesser horseshoe bats. Full genomic sequencing analyses showed that MSLH14 possessed the genotype constellation G3-P[3]-I8-R3-C3-M3-A9-N3-T3-E3-H6, which is akin to human and animal rotaviruses believed to be of feline/canine origin. Phylogenetic analysis indicated that VP7 was most closely related to bovine RVA strains from India, whereas VP4 was most closely related to an unusual human RVA strain, CMH222, with animal characteristics isolated in Thailand. The remaining gene segments were only distantly related to a range of animal RVA strains, most of which are believed to be related to feline/canine RVAs. Experimental infection showed that bat RVA strain MSLH14 was highly pathogenic to suckling mice, causing 100% mortality when they were inoculated orally with a titer as low as 5 × 102 50% tissue culture infective doses. As this virus is not closely related to any known RVA strain, it is tempting to speculate that it is a true bat RVA strain rather than a virus transmitted between species. However, further screening of bat populations, preferably juvenile animals, will be crucial in determining whether or not this virus is widely distributed in the bat population.
Histological Evidence of Increased Osteoclast Cell Number and Asymmetric Bone Resorption Activity in the Tibiae of Interleukin-6-Deficient Mice

Interleukin-6 (IL-6) is a multifunctional cytokine considered to modulate bone homeostasis. Based on previous contradictory studies, we aimed to verify the influence of IL-6 deficiency on bone remodeling using an IL-6 knockout (IL-6-/-) murine model. Eight-month-old male mice, homozygous for the disrupted IL-6 gene, and their wild type (WT) littermates (control), were used. After transcardiac perfusion, tibiae were removed for histochemical analysis. Compared with the control group, IL-6 deficiency increased tartrate resistant acid phosphatase (TRAP)-positive osteoclast numbers and up-regulated the alkaline phosphatase (ALP) activity of osteoblasts in the metaphysis of the tibia. However, further analysis of serial histological sections from IL-6-/- mice found a significant discrepancy in osteoclast number, with the higher number of TRAP-positive osteoclasts conflicting with the lower number of cathepsin K-positive osteoclasts. Moreover, TUNEL staining identified a significantly higher rate of osteoclast apoptosis in IL-6-/- mice as compared with their WT controls. IL-6 deficiency induced abundant TRAP-positive osteoclasts but delayed bone remodeling by significantly inhibiting the bone resorption activity of osteoclasts and promoting osteoclast apoptosis.
Efficient and Effective Visual Codebook Generation Using Additive Kernels

Common visual codebook generation methods used in a bag of visual words model, for example, k-means or Gaussian Mixture Model, use the Euclidean distance to cluster features into visual code words. However, most popular visual descriptors are histograms of image measurements. It has been shown that with histogram features, the Histogram Intersection Kernel (HIK) is more effective than the Euclidean distance in supervised learning tasks. In this paper, we demonstrate that HIK can be used in an unsupervised manner to significantly improve the generation of visual codebooks. We propose a histogram kernel k-means algorithm which is easy to implement and runs almost as fast as the standard k-means. The HIK codebooks have consistently higher recognition accuracy over k-means codebooks by 2-4% in several benchmark object and scene recognition data sets. The algorithm is also generalized to arbitrary additive kernels. Its speed is thousands of times faster than a naive implementation of the kernel k-means algorithm. In addition, we propose a one-class SVM formulation to create more effective visual code words. Finally, we show that the standard k-median clustering method can be used for visual codebook generation and can act as a compromise between the HIK / additive kernel and the k-means approaches.
Photolabeling a Nicotinic Acetylcholine Receptor (nAChR) with an (α4)3(β2)2 nAChR-Selective Positive Allosteric Modulator

Positive allosteric modulators (PAMs) of nicotinic acetylcholine (ACh) receptors (nAChRs) have potential clinical applications in the treatment of nicotine dependence and many neuropsychiatric conditions associated with decreased brain cholinergic activity, and 3-(2-chlorophenyl)-5-(5-methyl-1-(piperidin-4-yl)-1H-pyrrazol-4-yl)isoxazole (CMPI) has been identified as a PAM selective for neuronal nAChRs containing the α4 subunit. In this report, we compare CMPI interactions with low-sensitivity (α4)3(β2)2 and high-sensitivity (α4)2(β2)3 nAChRs, and with muscle-type nAChRs. In addition, we use the intrinsic reactivity of [3H]CMPI upon photolysis at 312 nm to identify its binding sites in Torpedo nAChRs. Recording from Xenopus oocytes, we found that CMPI potentiated maximally the responses of (α4)3(β2)2 nAChR to 10 μM ACh (EC10) by 400% and with an EC50 of ∼1 µM. CMPI produced a left shift of the ACh concentration-response curve without altering ACh efficacy. In contrast, CMPI inhibited (∼35% at 10 µM) ACh responses of (α4)2(β2)3 nAChRs and fully inhibited human muscle and Torpedo nAChRs with IC50 values of ∼0.5 µM. Upon irradiation at 312 nm, [3H]CMPI photoincorporated into each Torpedo [(α1)2β1γδ] nAChR subunit. Sequencing of peptide fragments isolated from [3H]CMPI-photolabeled nAChR subunits established photolabeling of amino acids contributing to the ACh binding sites (αTyr190, αTyr198, γTrp55, γTyr111, γTyr117, δTrp57) that was fully inhibitable by agonist and lower-efficiency, state-dependent [3H]CMPI photolabeling within the ion channel. Our results establish that CMPI is a potent potentiator of nAChRs containing an α4:α4 subunit interface, and that its intrinsic photoreactivy makes it of potential use to identify its binding sites in the (α4)3(β2)2 nAChR.
Improving Family Involvement for Juvenile Offenders with Emotional/Behavioral Disorders and Related Disabilities

Youth with emotional and behavioral (E/BD) and other disorders, who in many cases have not received needed interventions and supports in school, are overrepresented in the juvenile justice system. This article considers how parents of youth with E/BDs can become more involved in the process when their child is referred to juvenile court, thereby decreasing the likelihood of recidivism. Despite the existing barriers to parental involvement in the juvenile justice system, parents should be informed of their youth's educational rights in school, juvenile court, and out-of-home correctional settings. In addition, increasing parent involvement and reducing recidivism is an achievable goal; several family- and youth-centered strategies and programs have shown success in keeping youth with E/BDs out of the justice system.
Carrier of Wingless (Cow), a Secreted Heparan Sulfate Proteoglycan, Promotes Extracellular Transport of Wingless

Morphogens are signaling molecules that regulate growth and patterning during development by forming a gradient and activating different target genes at different concentrations. The extracellular distribution of morphogens is tightly regulated, with the Drosophila morphogen Wingless (Wg) relying on Dally-like (Dlp) and transcytosis for its distribution. However, in the absence of Dlp or endocytic activity, Wg can still move across cells along the apical (Ap) surface. We identified a novel secreted heparan sulfate proteoglycan (HSPG) that binds to Wg and promotes its extracellular distribution by increasing Wg mobility, which was thus named Carrier of Wg (Cow). Cow promotes the Ap transport of Wg, independent of Dlp and endocytosis, and this function addresses a previous gap in the understanding of Wg movement. This is the first example of a diffusible HSPG acting as a carrier to promote the extracellular movement of a morphogen.
Gamma-aminobutyric acid system genes--no evidence for a role in alcohol use and abuse in a community-based sample.

BACKGROUND While twin and adoption studies point to substantial genetic influence upon alcohol use, dependence, and other alcohol-related phenotypes, few of the genes underlying variation in these phenotypes have been identified. Markers in genes related to GABAergic activity-a system integral to many of alcohol's biological effects-have been implicated in alcohol use and alcohol-related psychopathology in linkage and association studies. METHODS Using multiple methods, we conducted a comprehensive examination of the effects of markers in γ-aminobutyric acid (GABA) system genes in a community-based sample of 7,224 individuals assessed in early and middle adulthood. In addition to testing the effect of individual single nucleotide polymorphism (SNP) markers on alcohol-related phenotypes, we computed a polygenic score reflecting the aggregated effects of multiple GABA system SNPs. We also estimated the variance in alcohol-related phenotypes attributable to all GABA system markers considered simultaneously and conducted gene-based association tests. RESULTS No method produced results indicative of an effect of GABA system variants on measures of alcohol use or misuse. CONCLUSIONS These results reflect alcohol-related behaviors in a population-representative sample, many of whom are still in adolescence, and in which the incidence of heavy drinking and alcohol-related symptomatology are relatively low. Contrasted with existing studies of the association between alcohol use and GABA system genes, our results suggest that the relationship may be limited to particular contexts, such as when accompanied by polysubstance abuse or a familial history of alcoholism.
Sustained Improvement of Arterial Stiffness and Blood Pressure after Long-Term Rosuvastatin Treatment in Patients with Inflammatory Joint Diseases: Results from the RORA-AS Study

Objective Patients with inflammatory joint diseases (IJD) have a high prevalence of hypertension and increased arterial stiffness. The aim of the present study was to evaluate the effect of long-term rosuvastatin treatment on arterial stiffness, measured by augmentation index (AIx) and aortic pulse wave velocity (aPWV), and blood pressure (BP) in IJD patients with established atherosclerosis. Methods Eighty-nine statin naïve IJD patients with carotid atherosclerotic plaque(s) (rheumatoid arthritis n = 55, ankylosing spondylitis n = 23, psoriatic arthritis n = 11) received rosuvastatin for 18 months to achieve low-density lipoprotein cholesterol goal ≤1.8 mmol/L. Change in AIx (ΔAIx), aPWV (ΔaPWV), systolic BP (ΔsBP) and diastolic BP (ΔdBP) from baseline to study end was assessed by paired samples t-tests. Linear regression was applied to evaluate associations between cardiovascular disease (CVD) risk factors, rheumatic disease specific variables and medication, and ΔAIx, ΔaPWV, ΔsBP and ΔdBP. Results AIx, aPWV, sBP and dBP were significantly reduced from baseline to study end. The mean (95%CI) changes were: ΔAIx: -0.34 (-0.03, -0.65)% (p = 0.03), ΔaPWV: -1.69 (-0.21, -3.17)m/s2 (p = 0.03), ΔsBP: -5.27 (-1.61, -8.93)mmHg (p = 0.004) and ΔdBP -2.93 (-0.86, -5.00)mmHg (p = 0.01). In linear regression models, ∆aPWV was significantly correlated with ΔsBP and ΔdBP (for all: p<0.001). Conclusions There is an unmet need of studies evaluating CVD prevention in IJD patients. We have shown for the first time that long-term intensive lipid lowering with rosuvastatin improved arterial stiffness and induced a clinically significant BP reduction in patients with IJD. These improvements were linearly correlated and may represent novel insight into the pleiotropic effects by statins. Trial Registration ClinicalTrials.gov NCT01389388
Intravenous Grafts Of Amniotic Fluid-Derived Stem Cells Induce Endogenous Cell Proliferation and Attenuate Behavioral Deficits in Ischemic Stroke Rats

We recently reported isolation of viable rat amniotic fluid-derived stem (AFS) cells [1]. Here, we tested the therapeutic benefits of AFS cells in a rodent model of ischemic stroke. Adult male Sprague-Dawley rats received a 60-minute middle cerebral artery occlusion (MCAo). Thirty-five days later, animals exhibiting significant motor deficits received intravenous transplants of rat AFS cells or vehicle. At days 60–63 post-MCAo, significant recovery of motor and cognitive function was seen in stroke animals transplanted with AFS cells compared to vehicle-infused stroke animals. Infarct volume, as revealed by hematoxylin and eosin (H&E) staining, was significantly reduced, coupled with significant increments in the cell proliferation marker, Ki67, and the neuronal marker, MAP2, in the dentate gyrus (DG) [2] and the subventricular zone (SVZ) of AFS cell-transplanted stroke animals compared to vehicle-infused stroke animals. A significantly higher number of double-labeled Ki67/MAP2-positive cells and a similar trend towards increased Ki67/MAP2 double-labeling were observed in the DG and SVZ of AFS cell-transplanted stroke animals, respectively, compared to vehicle-infused stroke animals. This study reports the therapeutic potential of AFS cell transplantation in stroke animals, possibly via enhancement of endogenous repair mechanisms.
Changes in Vascular Distensibility during Angiotensin-Converting Enzyme Inhibition Involve Bradykinin Type 2 Receptors

Changes in arterial stiffness and structure occur during cardiovascular diseases and can be modified by angiotensin-converting enzyme (ACE) inhibitors. In the present study we investigated the role of membrane-bound ACE (t-ACE) in the regulation of arterial structure and mechanics. Large and small arteries of t-ACE–/– mice were isolated to determine the passive pressure-diameter relationship. We observed that t-ACE–/– mice exhibit a reduced arterial distensibility compared to t-ACE+/+ mice. This reduced arterial distensibility was also observed after 9 weeks of captopril treatment (80 mg/kg/ day). We hypothesized that bradykinin type 2 receptor (BK2) stimulation might be involved in the regulation of arterial stiffness. t-ACE–/– and t-ACE+/+ mice were treated with Hoe 140 (1 mg/kg/day) for 14 days. After Hoe 140 treatment, both the structural and mechanical changes observed in the t-ACE–/– carotid artery were abolished. Although Hoe 140 administration increased blood pressure in both groups by approximately 10 mm Hg, the pressure difference between the two groups did not change. Thus, t-ACE is involved in the regulation of arterial distensibility. The changes observed in t-ACE–/– mice are not caused by an altered fetal development. Moreover, it is likely that the regulation of arterial distensibility by ACE involves stimulation of the BK2 receptor.
Molecular Detection of Genomic Islands Associated With Class 1 and 2 Integron in Haemophilus influenzae Isolated in Iran

Background: High levels of multidrug resistance are usually associated with mobile genetic elements that encode specific resistance genes. Integrons are important genetic elements involved in spreading antibiotic multi-resistance. In special cases, large exogenous segments in bacterial genomes form genomic islands, and one of the functions of these genomic islands is antibiotic resistance. Due to geographical heterogeneity in antibiotic resistance pattern, it is mandatory to determine resistance patterns that are region-specific rather than generalized. Objectives: The objective of this study was to detect class 1 and 2 integrons in clinical isolates of Haemophilus influenzae. Patients and Methods: Antibiogram tests were carried out for twenty clinical isolates collected from different patients admitted to the Milad hospital. The PCR reactions were performed using universal primers specified for Int1 and Int2 genes attributed to class 1 and 2 integrons. Also amplification of integrase genes related to genomic islands was investigated by designing specific primers. Results: Of the twenty isolates, all (100%) were resistant to clindamycin, chloramphenicol and tetracycline, 95% to amoxicillin, 50% to ceftriaxone, 45% to ciprofloxacin and 5% to azithromycin. Also, all isolates (100%) were sensitive to trimethoprim/sulfamethoxazole. Class 1 and 2 integrons were not detected in any of the isolates; however the integrase gene attributed to genomic islands was identified in twelve isolates. Conclusions: Antibiotic resistance gene cassettes may be carried on integron or other genetic elements. The purpose of this study was to detect integron or genomic islands involved in antibiotic resistance profile of the isolates of H. influenzae collected in this study.
Towards Optimal Binary Code Learning via Ordinal Embedding

Binary code learning, a.k. a. , hashing, has been recently popular due to its high efficiency in large-scale similarity search and recognition. It typically maps high-dimensional data points to binary codes, where data similarity can be efficiently computed via rapid Hamming distance. Most existing unsupervised hashing schemes pursue binary codes by reducing the quantization error from an original real-valued data space to a resulting Hamming space. On the other hand, most existing supervised hashing schemes constrain binary code learning to correlate with pairwise similarity labels. However, few methods consider ordinal relations in the binary code learning process, which serve as a very significant cue to learn the optimal binary codes for similarity search. In this paper, we propose a novel hashing scheme, dubbed Ordinal Embedding Hashing (OEH), which embeds given ordinal relations among data points to learn the ranking-preserving binary codes. The core idea is to construct a directed unweighted graph to capture the ordinal relations, and then train the hash functions using this ordinal graph to preserve the permutation relations in the Hamming space. To learn such hash functions effectively, we further relax the discrete constraints and design a stochastic gradient decent algorithm to obtain the optimal solution. Experimental results on two large-scale benchmark datasets demonstrate that the proposed OEH method can achieve superior performance over the state-of-the-arts approaches.At last, the evaluation on query by humming dataset demonstrates the OEH also has good performance for music retrieval by using user's humming or singing.
Sandeel recruitment in the North Sea: demographic, climatic and trophic effects

The lesser sandeel Ammodytes marinus, which is one of the most abundant fish in the North Sea, has highly variable recruitment dynamics. We evaluate potential associations between their recruitment and some key biological and physical factors. Population data were analysed at the North Sea scale (years 1983 to 1999) and at the regional scale (southwestern section and northeast- ern section; years 1984 to 1996/7). Relationships between recruitment and spawning stock biomass were weak, but Age-1 sandeels (non-spawners) were related negatively with recruitment, implying that demographic effects are important. A negative relationship was detected between recruitment and the winter index of the North Atlantic Oscillation, which affects sea temperatures during the egg and larval period. Warmer sea temperatures correlated with poorer than average recruitment. This effect was most pronounced in the southwestern part of the North Sea, which is near the southern limit of the species' distribution. There was a positive association between recruitment and Calanus copepod (Stages V and VI) abundance around the time of larval hatching, suggesting that the avail- ability of this prey species is important for young sandeel survival. Our findings suggest that climate change may impact upon sandeel populations in the North Sea.