Miracle-dz/UniFAR-FTUs huggingface dataset:
Accurately Assessing the Risk of Schizophrenia Conferred by Rare Copy-Number Variation Affecting Genes with Brain Function

Investigators have linked rare copy number variation (CNVs) to neuropsychiatric diseases, such as schizophrenia. One hypothesis is that CNV events cause disease by affecting genes with specific brain functions. Under these circumstances, we expect that CNV events in cases should impact brain-function genes more frequently than those events in controls. Previous publications have applied “pathway” analyses to genes within neuropsychiatric case CNVs to show enrichment for brain-functions. While such analyses have been suggestive, they often have not rigorously compared the rates of CNVs impacting genes with brain function in cases to controls, and therefore do not address important confounders such as the large size of brain genes and overall differences in rates and sizes of CNVs. To demonstrate the potential impact of confounders, we genotyped rare CNV events in 2,415 unaffected controls with Affymetrix 6.0; we then applied standard pathway analyses using four sets of brain-function genes and observed an apparently highly significant enrichment for each set. The enrichment is simply driven by the large size of brain-function genes. Instead, we propose a case-control statistical test, cnv-enrichment-test, to compare the rate of CNVs impacting specific gene sets in cases versus controls. With simulations, we demonstrate that cnv-enrichment-test is robust to case-control differences in CNV size, CNV rate, and systematic differences in gene size. Finally, we apply cnv-enrichment-test to rare CNV events published by the International Schizophrenia Consortium (ISC). This approach reveals nominal evidence of case-association in neuronal-activity and the learning gene sets, but not the other two examined gene sets. The neuronal-activity genes have been associated in a separate set of schizophrenia cases and controls; however, testing in independent samples is necessary to definitively confirm this association. Our method is implemented in the PLINK software package.
Accepted for Publication in Ieee Transactions on Automatic Control Analysis of Interconnected Oscillators by Dissipativity Theory

— The paper employs dissipativity theory for global analysis of limit cycles in particular dynamical systems of possibly high dimension. Oscillators are regarded as open systems that satisfy a particular dissipation inequality. It is shown that this characterization has implications for global stability analysis of limit cycle oscillations (i) in isolated oscillators, (ii) in intercon-nections of oscillators, and (iii) for global synchrony analysis in interconnections of identical oscillators.
Effect of casein phosphopeptide and 25-hydroxycholecalciferol on tibial dyschondroplasia in growing broiler chickens

1. An experiment was conducted to investigate the influence of dietary casein phosphopeptides and 25-hydroxycholecalciferol on the incidence of tibial dyschondroplasia (TD) in 14-d-old commercial broiler chickens. 2. Three hundred and twenty broiler chicks (one day old) were randomly allocated to one of 4 dietary treatments. A standard broiler diet was used as the control with the three experimental treatments receiving the control diet supplemented with 10 g casein phosphopeptide/kg, 14 g casein phosphopeptide/kg or 69 µg 25-hydroxycholecalciferol/kg. 3. Those birds fed the diets supplemented with 14 g casein phosphopeptide/kg or 25-hydroxycholecalciferol had a lower incidence of TD than both the control and 10 g casein phosphopeptide/kg treatments when assessed grossly. 4. The body weight of birds fed the 10 g casein phosphopeptide/kg diet or the 25-hydroxycholecalciferol diet was higher than birds fed the control diet. Although not significant, the body weight of birds fed the 14 g casein phosphopeptide/kg diet was also greater than the control birds. 5. The current experiment demonstrated that both casein phosphopeptide and 25-hydroxycholecalciferol can reduce the incidence of TD in the young broiler chicken. More research is required to explain the unexpected increase in body weight described above.
CHAPTER 3. DEFINING SPECIES IN THE FUNGI

The species concept is central to biology and has received considerable debate, yet a universal definition of a species has not found widespread agreement. Much of the discussion has centered on animals and plants, while mycologists and their organisms have generally been peripheral to the debate. A recent symposium dedicated to species concepts in clonal organisms (Mishler and Budd, 1990) did not include the fungi, though they probably have more apomictic taxa than any other major group of organisms (Blackwell, 1993). Inclusion of the fungal kingdom, with its broad array of reproductive strategies, may complicate the debate, but new insights could be gained by using fungal models. This chapter attempts to bring fungi into the debate and aims to arrive at a workable definition for fungal species.
How (and Why) Emotion Enhances the Subjective Sense of Recollection

A growing body of evidence suggests emotion boosts memory accuracy to an extent but affects the subjective sense of recollection even more. The result is vivid memories for emotional events that are held with confidence but that may be surprisingly inaccurate in their details. We examine the neural circuitry underlying emotion's impact on memory and the subjective sense of recollection to provide insight into this puzzling phenomenon. This research suggests that for emotional stimuli the quality and strength of memory for a few details may mediate judgments of recollection, whereas for neutral stimuli the quantity of contextual details may be more important. Finally, we speculate that the enhanced subjective sense of recollection with emotion, in the absence of absolute veridicality, may have evolved to enable fast and unambiguous decision making in emotional situations.
The X‐ray structure of an atypical homeodomain present in the rat liver transcription factor LFB1/HNF1 and implications for DNA binding.

The transcription factor LFB1/HNF1 from rat liver nuclei is a 628 amino acid protein that functions as a dimer binding to the inverted palindrome GTTAATN‐ATTAAC consensus site. We have crystallized a 99 residue protein containing the homeodomain portion of LFB1, and solved its structure using X‐ray diffraction data to 2.8 A resolution. The topology and orientation of the helices is essentially the same as that found in the engrailed, MAT alpha 2 and Antennapedia homeodomains, even though the LFB1 homeodomain contains 21 more residues. The 21 residue insertion is found in an extension of helix 2 and consequent lengthening of the connecting loop between helix 2 and helix 3. Comparison with the engrailed homeodomain‐DNA complex indicates that the mode of interaction with DNA is similar in both proteins, with a number of conserved contacts in the major groove. The extra 21 residues of the LFB1 homeodomain are not involved in DNA binding. Binding of the LFB1 dimer to a B‐DNA palindromic consensus sequence requires either a conformational change of the DNA (presumably bending), or a rearrangement of the subunits relative to the DNA.
Elastic mobility: stretching interaction

Based on a consideration of usage and technological computing trends, we reflect on the implications of cloud computing on mobile interaction with applications, data and devices. We argue that by extending the interaction capabilities of the mobile device by connecting it to external peripherals, new mobile contexts of personal (and social) computing can emerge, thus creating novel contexts of mobile interaction. In such a scenario, mobile devices can act as context-adaptive information filters. We then present Focus, our work in progress on a context-adaptive UI, which we can demonstrate at the MobileHCI demo session as a clickable dummy on a mobile device.
Social-aware D2D communications: qualitative insights and quantitative analysis

With emerging demands for local area services, device-to-device communication is conceived as a vital component for the next-generation cellular networks to improve spectral reuse, bring hop gains, and enhance system capacity. Ripening these benefits depends on efficiently solving several main technical problems, including mode selection, resource allocation, and interference management. Aiming to establish a new paradigm for solving these challenging problems in D2D communication, in this article we propose a social-aware enhanced D2D communication architecture that exploits social networking characteristics for system design. By developing a profound understanding of the interplay between social networks' properties and mobile communication problems, we qualitatively analyze how D2D communications can benefit from social features, and quantitatively assess the achievable gains in a social-aware D2D communication system.
Starch Serves as Carbohydrate Storage in Nematode-Induced Syncytia1[W][OA]

The plant parasitic nematode Heterodera schachtii induces specific syncytial feeding sites in the roots of Arabidopsis thaliana from where it withdraws all required nutrients. Therefore, syncytia have to be well supplied with assimilates and generate strong sinks in the host plant's transport system. Import mechanisms and consequent accumulation of sucrose in syncytia were described recently. In this work, we studied the starch metabolism of syncytia. Using high-performance liquid chromatography and microscopic analyses, we demonstrated that syncytia store carbohydrates by starch accumulation. Further, we monitored the expression of genes involved in the starch metabolic pathway by gene chip analysis and quantitative reverse transcription-PCR. Finally, we provide functional proof of the importance of starch synthesis for nematode development using T-DNA insertion lines. We conclude that syncytia accumulate starch as a carbohydrate buffer to compensate for changing solute uptake by the nematode and as long-term storage during juvenile development.
Extension of Quickest Spectrum Sensing to Multiple Antennas and Rayleigh Channels

In this letter, we study quickest spectrum sensing for cognitive radios with multiple receive antennas in Gaussian and Rayleigh channels. We derive the probability density function for the fading case and analytically compute the upper bound and asymptotic worst-case detection delay for both of the cases. The extension into multiple antennas allows us to gain insights into the reduction in detection delay that multiple antennas can provide. Although sensing in a Rayleigh channel is more challenging, good sensing performance is still demonstrated.
Application of combined PD sensor for GIS PD detection and condition monitoring

It was reported previously that partial discharge (PD) existing in GIS can be localized with a PD localization method based on the time difference of PD detection, in which more than one pulse current sensors are installed at the GIS sealing end or cable termination. However, the localization accuracy is not satisfactory since the PD propagation speed is too high and not average inside GIS. To increase the accuracy combined PD sensors to detect pulse current and to catch the acoustic signal were applied for the on-site PD localization. The result shows that higher location accuracy can be obtained.
Imaging and Analysis Platform for Automatic Phenotyping and Trait Ranking of Plant Root Systems1[W][OA]

The ability to nondestructively image and automatically phenotype complex root systems, like those of rice (Oryza sativa), is fundamental to identifying genes underlying root system architecture (RSA). Although root systems are central to plant fitness, identifying genes responsible for RSA remains an underexplored opportunity for crop improvement. Here we describe a nondestructive imaging and analysis system for automated phenotyping and trait ranking of RSA. Using this system, we image rice roots from 12 genotypes. We automatically estimate RSA traits previously identified as important to plant function. In addition, we expand the suite of features examined for RSA to include traits that more comprehensively describe monocot RSA but that are difficult to measure with traditional methods. Using 16 automatically acquired phenotypic traits for 2,297 images from 118 individuals, we observe (1) wide variation in phenotypes among the genotypes surveyed; and (2) greater intergenotype variance of RSA features than variance within a genotype. RSA trait values are integrated into a computational pipeline that utilizes supervised learning methods to determine which traits best separate two genotypes, and then ranks the traits according to their contribution to each pairwise comparison. This trait-ranking step identifies candidate traits for subsequent quantitative trait loci analysis and demonstrates that depth and average radius are key contributors to differences in rice RSA within our set of genotypes. Our results suggest a strong genetic component underlying rice RSA. This work enables the automatic phenotyping of RSA of individuals within mapping populations, providing an integrative framework for quantitative trait loci analysis of RSA.
Measuring coarticulation and variability in tongue contact patterns

Instrumental assessment of pathological speech is of limited use unless normal variability can be quantitatively defined. An attempt was made to quantify the variability of tongue contact patterns at certain stages during the pronunciation of VCV sequences by a normal speaker, in terms of the contact totals registered by an electropalatograph system. Of specific interest were the total contact area during the vowels and the rate of change of contact for consonant closures and releases. The results are discussed in the light of some current theories of coarticulation and their implications for speech assessment.
Effect of Rj-genotype and cultivation temperature on the 3 community structure of soybean-nodulating bradyrhizobia 4 5 6

23 The nodulation tendency and community structure of indigenous bradyrhizobia on 24 Rj-genotype soybean cultivars at cultivation temperatures of 33/28°C, 28/23°C and 23/18°C, 25 16/8 h (day/night degrees, hours) were investigated using 780 bradyrhizobial DNA samples 26 from an Andosol with 13 soybean cultivars of four Rj-genotypes (non-Rj, Rj2Rj3, Rj4 and 27 Rj2Rj3Rj4). A dendrogram was constructed based on restriction fragment length polymorphism 28 of the polymerase chain reaction products (PCR-RFLP) of the 16S-23S rRNA gene internal 29 transcribed spacer (ITS) region. Eleven Bradyrhizobium USDA strains were used as a 30 reference. The dendrogram indicated seven clusters based on similarities among the reference 31 strains. The occupancy rate of Bj123-cluster decreased with increasing cultivation temperature, 32 while the occupancy rates of Bj110-cluster, Be76-cluster and Be94-cluster increased with 33 increasing cultivation temperature. Especially, the Rj2Rj3Rj4-genotype soybeans were infected 34 with a number of Bj110-cluster, regardless of the increasing cultivation temperature, compared 35 with other Rj-genotype soybean cultivars. The ratio of beta diversity to gamma diversity 36 (H’β/H’γ), which represents differences in the bradyrhizobial communities by pair-wise 37 comparison among cultivation temperature sets within the same soybean cultivar, indicated 38 that the bradyrhizobial communities tended to be different among cultivation temperatures. 39 Multidimensional scaling (MDS) analysis indicated that the infection of Bj110-cluster and 40 Bj123-cluster by host soybean genotype and cultivation temperature affected the 41 bradyrhizobial communities. These results suggested that the Rj-genotypes and cultivation 42 temperatures affected the nodulation tendency and community structures of 43 soybean-nodulating bradyrhizobia. 44 on N ovem er 4, 2017 by gest ht://aem . sm . rg/ D ow nladed fom
Phosphoflow-Based Evaluation of Mek Inhibitors as Small-Molecule Therapeutics for B-Cell Precursor Acute Lymphoblastic Leukemia

Upstream mutations that lead to constitutive activation of Erk in B-cell precursor acute lymphoblastic leukemia (BCP-ALL) are relatively common. In the era of personalized medicine, flow cytometry could be used as a rapid method for selection of optimal therapies, which may include drugs that target the Erk pathway. Here, we evaluated the utility of phospho-flow, compared to Western blotting, to monitor Erk pathway activation and its inhibition by targeted Mek kinase inhibitors in human BCP ALL. Because the Erk pathway is not only activated endogenously, by mutations, but also by normal extracellular stimulation through stromal contact and serum growth factors, we compared Erk activation ex vivo in ALL cells in the presence and absence of stroma and serum. Phospho-flow was able to readily detect changes in the pool of pErk1/2 that had been generated by normal microenvironmental stimuli in patient-derived BCP-ALL cells passaged in NSG mice, in viably frozen primary patient samples, and in fresh patient samples. Treatment with the Mek1/2 inhibitor selumetinib resulted in a rapid, complete and persistent reduction of microenvironment-generated pErk1/2. Imaging flow cytometry confirmed reduction of nuclear pErk1/2 upon selumetinib treatment. An ALL relapsing with an activating KRasG12V mutation contained higher endogenous as well as serum/stromal-stimulated levels of pErk1/2 than the matched diagnosis sample which lacked the mutation, but selumetinib treatment reduced pErk1/2 to the same level in both samples. Selumetinib and trametinib as Mek inhibitors were mainly cytostatic, but combined treatment with the PI3K∂ inhibitor CAL101 increased cytotoxicity. Thus phospho-flow cytometry could be used as a platform for rapid, individualized in vitro drug sensitivity assessment for leukemia patients at the time of diagnosis.
Improving Beat Tracking in the presence of highly predominant vocals using source separation techniques: Preliminary study

The automatic beat tracking from audio is still an open re- search task in the Music Information Retrieval (MIR) community. The goal of this paper is to show and discuss a work-in-progress of how audio source separation can be used for improving beat tracking estimations in dicult cases of music audio signal with highly predominant vocals. The audio source separation using FASST (Flexible Audio Source Separa- tion Toolbox) had an average improvement of beat tracking of {14,15%, 17,74%} in the F-measure and {14,21%, 25,70%} in the Amlt of Klapuri and Degara systems respectably in a dataset of 20 songs excerpt.
Ruminative Thinking

Impairments in cognitive processes have been theorized to play a critical role in rumination, a well-established risk factor for depression. In this review, we outline central theories that present cognitive impairments as causal contributors to ruminative thinking and review relevant findings from cross-sectional and prospective studies. We then focus on experimental evidence gathered within the paradigm of cognitive bias modification (CBM). Although CBM has generated considerable interest in relation to anxiety and depression, it has only recently emerged in the field of rumination. After considering the purpose and possible advantages of CBM procedures, we review CBM work related to rumination and discuss key limitations and implications within this developing area of research. Among our recommendations, we outline ways to contrast and integrate cognitive theories of rumination, as well as to obtain stronger bias modification procedures.
Dose‐Response Relationships with Nimodipine Against Electroshock Seizures in Mice

Summary: The anticonvulsant effect of the dihydropyridine calcium channel blocker, nimodipine (NMD) was evaluated against electroshock‐induced seizures in mice. At 1 h postdosing, NMD elicited a dose‐dependent reduction in the occurrence of tonic hindlimb extension (THE) after maximal electroshock (MES). The calculated ED50 for NMD was 87 mg/kg. A single dose of NMD (75 mg/kg) produced a significant (p < 0.05) reduction in occurrence of THE for 12 h postdosing. NMD was detectable for 6 h, and plasma and brain drug concentrations correlated well (r= 0.677, p < 0.01) for that period. At 1 h postdose, a single dose of NMD (75 mg/kg) produced a 40% increase (p < 0.001) in the threshold for tonic seizures as determined by minimal electroshock (Min‐ES). NMD is an effective anticonvulsant against experimental seizures induced by electroshock. The pharmacodynamic effect of NMD appears to extend beyond the time anticipated from the pharmacokinetic profile.
Causes of blindness and visual impairment in Nigeria: the Nigeria national blindness and visual impairment survey.

PURPOSE Determine causes of blindness and visual impairment among adults aged >or=40 years. METHODS Multistage, stratified, cluster random sampling with probability proportional to size procedures were used to identify a nationally representative sample of 15,027 persons >or=40 years of age. Distance vision was measured with a reduced logMAR tumbling E-chart. Clinical examination included a basic eye examination of all subjects and a more detailed examination of those who had presenting vision <6/12 in either eye. Cause for vision loss was assigned to all subjects with presenting vision <6/12 in any eye. RESULTS Of the 15,122 persons aged >or=40 years who were enumerated, 13,599 (89.9%) were examined. In 84%, blindness was avoidable. Uncorrected refractive errors were responsible for 57.1% of moderate (<6/18-6/60) visual impairment. Cataract (43%) was the commonest cause of blindness (<3/60). Prevalence of cataract-related blindness was 1.8% (95% CI: 1.57-2.05) and glaucoma-related blindness was 0.7% (95% CI: 0.55-0.88). Increasing age was associated with increasing prevalence of all major blinding conditions. Females, illiterate persons, and residents in the North East geopolitical zone had significantly higher odds of cataract-induced blindness and severe visual impairment. CONCLUSIONS The high proportion of avoidable blindness, with half being attributable to cataract alone and uncorrected refractive errors being responsible for 57% of moderate visual impairment, means that appropriate and accessible refraction and surgical services need to be provided. If priority attention is not given, the number of blind and severely visually impaired adults in Nigeria will increase by >40% over the next decade.
Compact Convolutional Neural Network Cascade for Face Detection

The problem of faces detection in images or video streams is a classical problem of computer vision. The multiple solutions of this problem have been proposed, but the question of their optimality is still open. Many algorithms achieve a high quality face detection, but at the cost of high computational complexity. This restricts their application in the real-time systems. This paper presents a new solution of the frontal face detection problem based on compact convolutional neural networks cascade. The test results on FDDB dataset show that it is competitive with state-of-the-art algorithms. This proposed detector is implemented using three technologies: SSE/AVX/AVX2 instruction sets for Intel CPUs, Nvidia CUDA, OpenCL. The detection speed of our approach considerably exceeds all the existing CPU-based and GPU-based algorithms. Because of high computational efficiency, our detector can processing 4K Ultra HD video stream in real time (up to 27 fps) on mobile platforms (Intel Ivy Bridge CPUs and Nvidia Kepler GPUs) in searching objects with the dimension 60x60 pixels or higher. At the same time its performance weakly dependent on the background and number of objects in scene. This is achieved by the asynchronous computation of stages in the cascade.