Miracle-dz/UniFAR-FTUs huggingface dataset:
Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data

Profound knowledge of demographic history is a prerequisite for the understanding and inference of processes involved in the evolution of population differentiation and speciation. Together with new coalescent-based methods, the recent availability of genome-wide data enables investigation of differentiation and divergence processes at unprecedented depth. We combined two powerful approaches, full Approximate Bayesian Computation analysis (ABC) and pairwise sequentially Markovian coalescent modeling (PSMC), to reconstruct the demographic history of the split between two avian speciation model species, the pied flycatcher and collared flycatcher. Using whole-genome re-sequencing data from 20 individuals, we investigated 15 demographic models including different levels and patterns of gene flow, and changes in effective population size over time. ABC provided high support for recent (mode 0.3 my, range <0.7 my) species divergence, declines in effective population size of both species since their initial divergence, and unidirectional recent gene flow from pied flycatcher into collared flycatcher. The estimated divergence time and population size changes, supported by PSMC results, suggest that the ancestral species persisted through one of the glacial periods of middle Pleistocene and then split into two large populations that first increased in size before going through severe bottlenecks and expanding into their current ranges. Secondary contact appears to have been established after the last glacial maximum. The severity of the bottlenecks at the last glacial maximum is indicated by the discrepancy between current effective population sizes (20,000–80,000) and census sizes (5–50 million birds) of the two species. The recent divergence time challenges the supposition that avian speciation is a relatively slow process with extended times for intrinsic postzygotic reproductive barriers to evolve. Our study emphasizes the importance of using genome-wide data to unravel tangled demographic histories. Moreover, it constitutes one of the first examples of the inference of divergence history from genome-wide data in non-model species.
Extracting Key Paragraph based on Topic and Event Detection Towards Multi-Document Summarization

This paper proposes a method for extracting key paragraph for multi-document summarization based on distinction between a topic and an event. A topic and an event are identified using a simple criterion called domain dependency of words. The method was tested on the TDT1 corpus which has been developed by the TDT Pilot Study and the result can be regarded as promising the idea of domain dependency of words effectively employed.
Damage Identification of Curtain Wall Cables based on Improved VMD and Hilbert Transform

Cable is an important role in Curtain wall cable structures. In order to detect cable damage in a timely and accurate manner, this paper focuses on the problem of non-stationary nonlinear vibration information and mode mixing in Empirical Mode Decomposition (EMD) itself. Based on the damage detection method combining Variational Mode Decomposition (VMD) and Hilbert Transform (HT), further parameter optimization is carried out. This method determines the penalty factor and decomposition level K by searching for the minimum envelope entropy. VMD is used to decompose the vibration information into different BIMF components, and then Hilbert transform is applied to the extracted components to obtain the corresponding marginal spectrum. cable damage identification is performed based on the modal anomaly index. This article confirms through local damage analysis of a single cable that this method can effectively identify the damage location and degree of the cable.
Shape from perspective trihedral angle constraint

A fundamental problem of determining the position and orientation of a 3-D object using a single perspective image view is defined and investigated. The technique is based on the interpretation of trihedral angle constraint information. A new closed-form solution to the problem is proposed. The method also provides a general analytic technique for dealing with a class of problem of shape from inverse perspective projection by using angle to angle correspondence information. Simulation experiments show that the authors' method is effective and robust for real application. <<ETX>>
Centralized peer-to-peer streaming with layered video

Faster computational power and higher network bandwidth facilitates Internet applications to improve the way we live, work and play. For video streaming applications, it is a challenge to provide the scalability while maintaining the central manageability and the robustness. In this paper, we propose the centralized peer-to-peer streaming protocol (P2PSP), which features the centralized management, guaranteed perceived quality of service (PQoS), while decentralized the traffic loads. To evaluate the protocol, a layered video coding technique based on 3D discrete cosine transform (DCT) is designed. This codec applies self-organizing tree map (SOTM) to generate cascaded vector quantization codebooks. We demonstrate the effectiveness of the centralized P2PSP by comparing the video streaming simulations under the proposed architecture and the client/server architecture.
OCSS: Ontology Cloud Storage System

Cloud computing is considered a booming trend in the world of information technology which depends on the idea of computing on demand. Cloud computing platform is a set of scalable data servers, providing computing and storage services. The cloud storage is a relatively basic and widely applied service which can provide users with stable, massive data storage space. Our research concerns with searching in content of different kind of files in the cloud based on ontology, this approach resolves the weaknesses that existed in Google File System that depends on metadata. In this paper, we are proposing new cloud storage architecture based on ontology that can store and retrieve files in the cloud based on its content. Our new architecture was tested on Cloud Storage Simulator and the result shows that the new architecture has better scalability, fault tolerance and performance.
Les granitoïdes calco-alcalins de la boutonnière d'Iguerda-Tayfast (Anti-Atlas, Maroc)

La boutonniere d' Iguerda-Tayfast est formee de micaschistes et de metadiorites resultant de deux episodes de plissements synmet amorphes (de la mesozone a la zone des migmatites) accompagnes de foliations (SI et S2). Apres l'intrusion de granitoides qui marqueraient la fin de l'orogenese eburneenne, une phase de deformation accompagnee par un metamorphisme retrograde avec foliation (S3), puis deux episodes de deformation marques par une schistosite de fracture (S4 et S5), pourraient etre attribues a l'orogenese pan-africaine. Ces deformations precedent la mise en place des formations volcaniques acides et volcano-sedimentaires de la fin du Proterozoique superieur (ou PI II) et des formations sedimentaires du Proterozoique terminal (Adoudounien) . Parmi les granitoides, trois groupes ont ete distingues. D'apres leur chimisme, peuvent appartenir a deux lignees calco-alcalines, la seconde a caractere peralumineux, l'une formee de diorites-granodiorites (G1A), l'autre de granites porphyroides (GIB), granites (G2) et aplo-pegmatites (G3-G4). L'evolution depuis les granites GIB, jusqu'aux aplo-pegmatites G3 est marquee par un enrichissement en Sn, Nb et Y qui chutent dans les derniers termes (G4), signe d'un partage de ces elements en faveur de liquides generateurs des aplo-pegmatites tardives.
Growth and metabolism of inositol-starved Saccharomyces cerevisiae

Upon starvation for inositol, a phospholipid precursor, an inositol-requiring mutant of Saccharomyces cerevisiae has been shown to die if all other conditions are growth supporting. The growth and metabolism of inositol-starved cells has been investigated in order to determine the physiological state leading to "inositolless death". The synthesis of the major inositol-containing phospholipid ceases within 30 min after the removal of inositol from the growth medium. The cells, however, continue in an apparently normal fashion for one generation (2 h under the growth conditions used in this study). The cessation of cell division is not preceded or accompanied by any detectable change in the rate of macromolecular synthesis. When cell division ceases, the cells remain constant in volume, whereas macromolecular synthesis continues at first at an unchanged rate and eventually at a decreasing rate. Macromolecular synthesis terminates after about 4 h of inositol starvation, at approximately the time when the cells begin to die. Cell death is also accompanied by a decline in cellular potassium and adenosine triphosphate levels. The cells can be protected from inositolless death by several treatments that block cellular metabolism. It is concluded that inositol starvation results in a imbalance between the expansion of cell volume and the accumulation of cytoplasmic constituents. This imbalance is very likely the cause of inositolless death.
Experimental investigation of thawing behavior of saline soils using resistivity method

Electrical resistivity method has been widely used to study permafrost and to monitor the process of freezing-thawing. However, a thorough understanding of the mechanism of electrical response during thawing is missing. In this study, we investigated the thawing behavior of saline soils in the temperature range ∼-10 to 15 °C considering the effects of soil type and salinity. A total of nine experiments were performed with three soil types (silica sand, sandy soil and silt) and three salinities (0.01 S/m, 0.1 S/m and 1 S/m). The results show that resistivity variations with temperature can be divided into three stages. In Stage I, tortuosity and unfrozen water content play major roles in the decrease of resistivity. In Stage Ⅱ, which is an isothermal or near isothermal process, resistivity still decreases slightly due to the thawing of residual ice and pore water movement. In Stage III, ionic mobility plays an important impact on decreasing resistivity. In addition, the isothermal process is found to only occur in silica sand which can be explained by latent heat effect. Exponential and linear models linking temperature with resistivity are used to fit the experimental data in Stage I and Stage III. The fitting parameter in different models shows great correlation with soil type and salinity. Furthermore, unfrozen water content below 0 °C is also estimated and uncertainty of estimation is analyzed.
Fast and reliable prediction of noncoding RNAs

We report an efficient method for detecting functional RNAs. The approach, which combines comparative sequence analysis and structure prediction, already has yielded excellent results for a small number of aligned sequences and is suitable for large-scale genomic screens. It consists of two basic components: (i) a measure for RNA secondary structure conservation based on computing a consensus secondary structure, and (ii) a measure for thermodynamic stability, which, in the spirit of a z score, is normalized with respect to both sequence length and base composition but can be calculated without sampling from shuffled sequences. Functional RNA secondary structures can be identified in multiple sequence alignments with high sensitivity and high specificity. We demonstrate that this approach is not only much more accurate than previous methods but also significantly faster. The method is implemented in the program rnaz, which can be downloaded from www.tbi. univie.ac. at/~wash/RNAz. We screened all alignments of length n > or = 50 in the Comparative Regulatory Genomics database, which compiles conserved noncoding elements in upstream regions of orthologous genes from human, mouse, rat, Fugu, and zebrafish. We recovered all of the known noncoding RNAs and cis-acting elements with high significance and found compelling evidence for many other conserved RNA secondary structures not described so far to our knowledge.
The large‐X effect in plants: increased species divergence and reduced gene flow on the Silene X‐chromosome

The disproportionately large involvement of the X‐chromosome in the isolation of closely related species (the large‐X effect) has been reported for many animals, where X‐linked genes are mostly hemizygous in the heterogametic sex. The expression of deleterious recessive mutations is thought to drive the frequent involvement of the X‐chromosome in hybrid sterility, as well as to reduce interspecific gene flow for X‐linked genes. Here, we evaluate the role of the X‐chromosome in the speciation of two closely related plant species – the white and red campions (Silene latifolia and S. dioica) – that hybridize widely across Europe. The two species evolved separate sexes and sex chromosomes relatively recently (~107 years), and unlike most animal species, most X‐linked genes have intact Y‐linked homologs. We demonstrate that the X‐linked genes show a very small and insignificant amount of interspecific gene flow, while gene flow involving autosomal loci is significant and sufficient to homogenize the gene pools of the two species. These findings are consistent with the hypothesis of the large‐X effect in Silene and comprise the first report of this effect in plants. Nonhemizygosity of many X‐linked genes in Silene males indicates that exposure of recessive mutations to selection may not be essential for the occurrence of the large‐X effect. Several possible causes of the large‐X effect in Silene are discussed.
Factors influencing commercialization of green maize in Nandi South, Nandi County Kenya

The purpose of this study was to assess the factors that influenced the commercialization of green maize in Nandi South, Nandi County. The Study aimed at investigating the reasons why farmers opted to sell green maize rather than wait to sell it as dry cereals. The study aimed at achieving the following objectives; to analyze policies that guide the commercialization of green maize; to assess factors that motivate farmers to sell their green maize, to evaluate the consequences of the sale of green maize and to assess the positive ant the negative results of the sale of green maize. The study utilized purposive sampling and simple random sampling technique. The study employed descriptive survey design with questionnaires and interview schedules as data collection instruments applied to sample of 188 respondents. Both qualitative and quantitative methods were used to analyze data. The findings of the study are as follows: the huge profits realized in the business motivated the farmers to sell green maize, the rising cost of farm inputs, the challenges farmers are facing in the entire business, incidences of corruption, vices and theft cases have been on the rise, lack of clear government policy on commercialization of green maize. Commercialization of green maize harvests has effects on long-term food security. It has attracted unscrupulous business men who con farmers. Government policy is not strong in protecting farmers. Based on the findings, recommendations were made to capture the benefits of commercialization of green maize and their disadvantages. There is need for clear policy framework to help the farmers. To assess the negative consequences of commercialization so as intervene on behalf of farmers.
Diagnostic and Prognostic Utility of a DNA Hypermethylated Gene Signature in Prostate Cancer

We aimed to identify a prostate cancer DNA hypermethylation microarray signature (denoted as PHYMA) that differentiates prostate cancer from benign prostate hyperplasia (BPH), high from low-grade and lethal from non-lethal cancers. This is a non-randomized retrospective study in 111 local Asian men (87 prostate cancers and 24 BPH) treated from 1995 to 2009 in our institution. Archival prostate epithelia were laser-capture microdissected and genomic DNA extracted and bisulfite-converted. Samples were profiled using Illumina GoldenGate Methylation microarray, with raw data processed by GenomeStudio. A classification model was generated using support vector machine, consisting of a 55-probe DNA methylation signature of 46 genes. The model was independently validated on an internal testing dataset which yielded cancer detection sensitivity and specificity of 95.3% and 100% respectively, with overall accuracy of 96.4%. Second validation on another independent western cohort yielded 89.8% sensitivity and 66.7% specificity, with overall accuracy of 88.7%. A PHYMA score was developed for each sample based on the state of methylation in the PHYMA signature. Increasing PHYMA score was significantly associated with higher Gleason score and Gleason primary grade. Men with higher PHYMA scores have poorer survival on univariate (p = 0.0038, HR = 3.89) and multivariate analyses when controlled for (i) clinical stage (p = 0.055, HR = 2.57), and (ii) clinical stage and Gleason score (p = 0.043, HR = 2.61). We further performed bisulfite genomic sequencing on 2 relatively unknown genes to demonstrate robustness of the assay results. PHYMA is thus a signature with high sensitivity and specificity for discriminating tumors from BPH, and has a potential role in early detection and in predicting survival.
Anticolitis activity of chinese herbal formula Yupingfeng powder via regulating colonic enterochromaffin cells and serotonin

Objective: To investigate whether traditional Chinese herbal formula Yupingfeng (YPF) powder has an anti-inflammatory effect on colonic inflammation, and to explore the mechanism involved. Materials and Methods: YPF powder was orally administrated to trinitrobenzene sulfonic acid (TNBS)-induced colitis mice at the dose of 3, 6, and 12 g/kg/d for 7 consecutive days. Body weight, stool consistency, histopathological score, and myeloperoxidase (MPO) activity were tested to evaluate the effect of YPF powder on colonic inflammation while colonic enterochromaffin (EC) cell density and serotonin 5-hydroxytryptamine (5-HT) content were investigated to identify the effect of YPF powder on colonic 5-HT availability. Results: The results showed that the body weight of colitis mice was markedly decreased by 10, 12, 14, and 17% at 1, 3, 5, and 7 days (P < 0.05), whereas stool consistency score (3.6 vs. 0.4, P < 0.05), histopathological score (3.6 vs. 0.3, P < 0.05), and MPO activity (2.7 vs. 0.1, P < 0.05) in colitis mice were significantly increased compared to that of the normal mice; YPF powder treatment dose-dependently increased the body weight (7–13% increase) and decreased the stool consistency score (0.4–1.4 decrease), histopathological score (0.2–0.7 decrease), and MPO activity (0.1–0.9 decrease) in colitis mice. Colonic EC cell density (70% increase) and 5-HT content (40% increase) were markedly increased in colitis mice (P < 0.05), YPF powder treatment dose-dependently reduced EC cell density (20–50% decrease), and 5-HT content (5–27% decrease) in colitis mice. Conclusion: The findings demonstrate that the anti-inflammatory effect of YPF powder on TNBS - induced colitis may be mediated via reducing EC cell hyperplasia and 5-HT content. The important role of YPF powder in regulating colonic EC cell number and 5-HT content may provide an alternative therapy for colonic inflammation.
Aberrant Activity in Degenerated Retinas Revealed by Electrical Imaging

In this review, I present and discuss the current understanding of aberrant electrical activity found in the ganglion cell layer (GCL) of rod-degenerated (rd) mouse retinas. The reported electrophysiological properties revealed by electrical imaging using high-density microelectrode arrays can be subdivided between spiking activity originating from retinal ganglion cells (RGCs) and local field potentials (LFPs) reflecting strong trans-membrane currents within the GCL. RGCs in rd retinas show increased and rhythmic spiking compared to age-matched wild-type retinas. Fundamental spiking frequencies range from 5 to 15 Hz in various mouse models. The rhythmic RGC spiking is driven by a presynaptic network comprising AII amacrine and bipolar cells. In the healthy retina this rhythm-generating circuit is inhibited by photoreceptor input. A unique physiological feature of rd retinas is rhythmic LFP manifested as spatially-restricted low-frequency (5–15 Hz) voltage changes. Their spatiotemporal characterization revealed propagation and correlation with RGC spiking. LFPs rely on gap-junctional coupling and are shaped by glycinergic and by GABAergic transmission. The aberrant RGC spiking and LFPs provide a simple readout of the functionality of the remaining retinal circuitry which can be used in the development of improved vision restoration strategies.
Accepted in Frontiers in Human Neuroscience for the Research Topic : Numerical cognition : Recent findings on the neural base of numerical processing and development Title : Graspable objects shape number processing

The field of numerical cognition represents an interesting case for action-based theories of cognition, since number is a special kind of abstract concept. Several studies have shown that within the parietal lobes adjacent neural regions code numerical magnitude and graspingrelated information. This anatomical proximity between brain areas involved in number and sensorimotor processes may account for interactions between numerical magnitude and action. In particular, recent studies have demonstrated a causal role of action perception on numerical magnitude processing. If objects are represented in terms of actions (affordances), the causal role of action on number processing should extend to the case of objects affordances. This study investigates the relationship between numbers and objects affordances in two experiments, without (Experiment 1) or with (Experiment 2) the requirement of an action (i.e., participants were asked to hold an object in their hands during the task). The task consisted in repeating aloud the odd or even digit within a pair depending on the type of the preceding or following object. Order of presentation (object-number vs. number-object), Object type (graspable vs. ungraspable), Object size (small vs. large), and Numerical magnitude (small vs. large) were manipulated for each experiment. Experiment 1 showed a facilitation – in terms of quicker responses for graspable over ungraspable objects preceded by numbers, and an effect of numerical magnitude after the presentation of graspable objects. Experiment 2 demonstrated that the action execution enhanced overall the sensitivity to numerical magnitude, however interfering with the effects of objects affordances on number processing. Overall, these findings demonstrate that numbers and graspable objects are strongly interrelated, supporting the view that abstract concepts may be grounded in motor experience.
Multiuser diversity and multiplexing using multiple random beams in wireless systems

In this paper, we propose a new multiple-antenna transmission scheme that can simultaneously achieve both diversity and multiplexing gain in the multiuser domain, by using multiple random beams. Multiple beams are generated so that the users encounter multiple channels at the same time, enabling the use of multiuser diversity through each channel. Although the signal-to-noise power ratio (SNR) of each channel is reduced in proportion to the number of beams, multiple beams are generated so that the multiplexing gain is larger than the decrease of SNR, increasing the overall system capacity