Miracle-dz/UniFAR-FTUs huggingface dataset:
Age and mortality associated DNA methylation patterns on the X-chromosome in male and female samples

Background Multiple epigenetic association studies on human aging have been performed reporting large numbers of sites differentially methylated across ages on the autosomal chromosomes. The X-chromosome has been studied little, due to analytical difficulties in dealing with sex differences in X-chromosome content and X-inactivation in females. Based on large collections of genome-wide DNA methylation data on two Danish cohorts of identical twins (mean ages, 66 and 79 years) and the Lothian Birth Cohort 1921 (mean age 79 years), we conducted a chromosome-wide association analysis on male and female samples separately with equal sample sizes to discover age-dependent X-linked DNA methylation patterns using chromosome 20 with about same number of CpGs analysed as an autosomal reference, and compare the age-related changes in DNA methylation between the two sexes. In addition, age-related methylation sites were assessed for their associations with mortality. Results We identified more age-related DNA methylation sites (FDR<0.05) in females than in males. Among them, predominantly more sites were hypermethylated in the older as compared with the younger cohorts, a pattern similar to that observed on chromosome 20. Among the age-related sites, 13 CpGs in males and 24 CpGs in females were found significant (FDR<0.05) in all cohorts. Survival analysis showed that there are more age-methylated CpGs that contribute to reduce mortality than those that increase mortality in male but not in female samples. Conclusion The X-chromosome displays significant age-and sex-dependent methylation patterns which might be differentially associated with mortality in the two sexes.
Facilitating Online Learning

This paper examines three online postgraduate degree programs in the School of Information and Communication Technologies (the School) at the University of Paisley, Scotland. Two of the programs were taught in both online and F2F formats. Comparison of students’ results revealed the online students performed better than their F2F counterparts. This paper examines the online teaching and learning methods that we believe contributed to the greater success of the online students.
Isolation, expression and function analysis of a bZIP transcription factor IbbZIP37 in sweetpotato (Ipomoea batatas L. [Lam])

bZIP transcription factor play an important regulatory role in the response to multiple abiotic stresses. However, our knowledge of the stress tolerance functions of bZIP family genes in sweetpotato (Ipomoea batatas [L.] Lam) remains limited. In the present study, we isolated and functionally characterized an IbbZIP37 gene encoding an abiotic stress-inducible bZIP group A transcription factor. Sequence analysis showed that the IbbZIP37 contained a typical bZIP domain and five conserved Ser/Thr kinase phosphorylation sites (RXXS/T). The IbbZIP37 protein was localized in the nucleus and possessed transcriptional activation activity. The results of electrophoretic mobility shift assays indicated that IbbZIP37 can bind to the ABRE cis-element, not do to DRE cis-element in vitro. The IbbZIP37 gene showed the highest level of constitutive expression in root, especially in fibrous root and storage root body. Gene expression was induced by ABA and several environmental stresses including drought, salt and heat shock. Our results suggest that IbbZIP37 is a positive transcription regulator of the abiotic stresses response, which can be used as an excellent candidate for improving the stress tolerance of different crop plants.
Mechanical Design of a Hybrid Leg Exoskeleton to Augment Load-Carrying for Walking

An innovative lower extremity exoskeleton, SJTU-EX, is demonstrated in Shanghai JiaoTong University, which mainly aims to help soldiers and workers to support a payload in motion. This paper summarizes the mechanical design of SJTU-EX. Each pseudo-anthropomorphic leg of SJTU-EX has four active joints and two passive joints, and the joint ranges are optimized in consideration of both safety factors and the realization of typical motions. Springs are applied in the leg to eliminate the effect of gravity. The results of dynamic simulations are used to determine the actuated joints and the passive joints. Novel Hy-Mo actuators are introduced for SJTU-EX and the layout of the actuator for Diamond Side 2 is described in detail as a design example.
A New Method of Solving Nonlinear Simultaneous Equations

The method of solving nonlinear simultaneous equations here discussed consists of a particular form of Broyden's method used in conjunction with a particular form of Davidenko's method. The only information required of the user, apart from the procedure to compute the residuals, is an initial estimate of the solution. (First received July 1968 and in revised form September 1968)
A Proposal for Agent Simulation of Peer Review

Peer review lies at the core of current scientific research. It is composed of a set of social norms, practices and processes that connect the abstract scientific method with the society of people that apply the method. As a social construct, peer review should be understood by building theory-informed models and comparing them with data collection. Both these activities are evolving in the era of automated computation and communication: new modeling tools and large bodies of data become available to the interested researcher. In this paper, starting from abstract principles, we develop and present a model of the peer review process. We also propose a working implementation of a subset of the general model, developed with Jason, a language that implements the BDI architecture for multi agent systems. After running a set of simulations, varying the initial distribution of reviewer skill, we compare the aggregates that our simplified model produces with recent findings, showing how the model can generate data with comparable statistical signatures. We conclude with a list of research questions that could be addressed in future work.
Basis of Graph Theory on Brain Imaging Study

Brain is a complex network, which shows dynamic changes depending on the state and traits of an individual. Graph theory is able to characterize such brain networks by providing neurobiological meaning and easily computable measures. In this article, I have discussed the construction of networks based on data about brain connectivity and described common network measures that can quantify functional segregation and integration, as well as the centrality of brain architecture. Finally, I have introduced software for conducting analyses based on the graph theory.
Silencing of SmAgo2 increases abundance of retrotransposons in the parasitic flatworm Schistosoma mansoni

1 Transposable elements (TEs) are mobile parts of the genome that can jump or self2 replicate, posing a threat to the stability and integrity of the host genome. TEs are 3 prevented from causing damage to the host genome by defense mechanisms such as 4 epigenetic changes and through nuclear silencing of TE transcripts in an RNAi-like 5 fashion. These pathways are well known in model organisms but very little is known 6 about them in other species. Parasitic flatworms present an interesting opportunity to 7 investigate evolutionary novelties in TE control because they lack canonical pathways 8 identified in model organisms (such as the piRNA pathways, etc) but have conserved 9 central players such as DICER and AGO (argonaute) enzymes. Notably, parasitic 10 flatworm AGOs are phylogenetically distinct from classical AGOs, raising the question of 11 whether they play special roles in these organisms. In this report, we investigate the role 12 of one of these flatworm-specific AGOs, AGO2, in the parasitic flatworm Schistosoma 13 mansoni. We show that transcript abundance of retrotransposable elements significantly 14 increased upon silencing of SmAGO2. We further demonstrate that SmAGO2 protein is 15 localised in the nucleus and the cytosol of adult worms. This is the first evidence of the 16 presence of a nuclear silencing mechanism in schistosomes. 17
A Trend-based Prediction System for Web User Behavior

Since web applications make great progress, the latency of Internet owing to the network bandwidth becomes an urge problem in the cyber world. It is very important to deliberate on how to construct a prediction model to predict web users traveling path for adapting the website structure and improving the website performance. A trend based prediction model without extra information is proposed in this paper to generate prediction models with a sequence of pages for a proxy server prefetcting the suitable pages. The trend similarity is the core of our proposed model which considers not only the page similarity but also position similarity. Two measures include page correctness rate and order correctness rate are proposed to evaluate accuracy of our prediction system.
NMDA Receptor in Vasopressin 1b Neurons Is Not Required for Short-Term Social Memory, Object Memory or Aggression

The vasopressin 1b receptor (Avpr1b) plays an important role in social behaviors including aggression, social learning and memory. Genetic removal of Avpr1b from mouse models results in deficits in aggression and short-term social recognition in adults. Avpr1b gene expression is highly enriched in the pyramidal neurons of the hippocampal cornu ammonis 2 (CA2) region. Activity of the hippocampal CA2 has been shown to be required for normal short-term social recognition and aggressive behaviors. Vasopressin acts to enhance synaptic responses of CA2 neurons through a NMDA-receptor dependent mechanism. Genetic removal of the obligatory subunit of the NMDA receptor (Grin1) within distinct hippocampal regions impairs non-social learning and memory. However, the question of a direct role for NMDA receptor activity in Avpr1b neurons to modulate social behavior remains unclear. To answer this question, we first created a novel transgenic mouse line with Cre recombinase knocked into the Avpr1b coding region to genetically target Avpr1b neurons. We confirmed this line has dense Cre expression throughout the dorsal and ventral CA2 regions of the hippocampus, along with scattered expression within the caudate-putamen and olfactory bulb. Conditional removal of the NMDA receptor was achieved by crossing our line to an available floxed Grin1 line. The resulting mice were measured on a battery of social and memory behavioral tests. Surprisingly, we did not observe any differences between Avpr1b-Grin1 knockout mice and their wildtype siblings. We conclude that mice without typical NMDA receptor function in Avpr1b neurons can develop normal aggression as well as short-term social and object memory performance. Significance Statement Activity of neurons that express vasopressin 1b receptor are essential for aggressive and social recognition behaviors. We created a novel transgenic mouse to allow selective targeting of vasopressin 1b neurons. Our studies indicate that NMDA receptor expression in vasopressin 1b neurons (including most CA2 neurons) are not required for development of the typical expression of aggression or recognition memory. Thus, CA2 neurons may have a unique way of incorporating novel stimuli into memory that deserves further investigation.
Time Label Topic Model

Most of the models not aware of these dependencies on document time stamps. Not modeling time can confound co-occurrence patters and results in exchangeability of topic problem, which is important factor to deal with when finding dynamic topic discovery. This limitation has thus motivated work on developing a generalized framework for incorporating time information into topic models. Consequently, a topic model named Topics over Time (TOT) is proposed, which introduces a time node in topic model to handle the exchangeability of topics problem. However it lacks the capability to accommodate data type of side information. In this paper, we present a generative time LDA-style topic model with a variety of side information named Time Label Topic(TLT), which can find not only how the latent low-dimensional structure of document-response pairs changes over time, but also overcome the exchangeability of topics problem. Empirical results demonstrate significant improvements accuracy of time stamp and response variable prediction, and lower perplexity of our proposed model and dominance over other models.
GGE biplot and AMMI model to evaluate spine gourd (Momordica dioica Roxb.) for genotype × environment interaction and seasonal adaptation

A investigation was carried out to ascertain the GEI, the yield stability and adaptability of 12 advanced spine gourd genotypes (G) in one environments over three crop years (2013, 2014 and 2015). The AMMI and GGE biplot model were used to study the nature of GEI on the fruit yield. First and second component of AMMI model totally explained more than 99% of GEI variations. G7 having maximum trait value with specific adaptation while G2 and G3 were having general adoptability. AMMI 2 biplot revealed high stability of G5 and G2 across environments. Results of GGE biplot model showed that the G4 with the environment of E3 and G7 with the environment of E1 and E2, respectively showed a special adaptability. G7 could be recommended for Northern hill zone of Chhattisgarh. Considering both graphical analysis models of AMMI and GGE biplot could be recommended. The ideal environment, according to both the models, was E2. The results indicated that AMMI and GGE biplot are facilitated visual comparison and informative methods to detect genotypes stability and in the preferential genotypes recommendations.
Self-nominating: a robust affordable routing for wireless sensor networks

In this paper we present a new routing approach, self-nominating, for wireless sensor networks. A time-based self-maintained mechanism is used to improve the routing efficiency in terms of both delay and power consumption. It guarantees one and only one of the most promising next-hop nodes to relay broadcasted data packets. Each sensor node passively supervises all its neighbors' behavior and decides its own activity in the routing process accordingly to achieve a resource-aware routing. Analyses and simulation results show that the self-nominating achieves affordability in terms of resource consumptions, and robustness in dealing with node failures.
Low complexity synchronisation, equalisation and diversity combining for home-based Hiperlan/1 transceivers

This paper discusses the development of a Hiperlan/1 radio modem for the simultaneous transmission of video, voice and data in the home environment. In particular, the performance of the wireless modem has been optimised to support MPEG II video streams. The modem will eventually be integrated with digital set-top box equipment to support wireless Internet and digital television applications around the home. This paper describes a number of enhanced architectures and algorithms that enable an efficient FPGA implementation of the baseband digital equaliser, synchroniser and diversity combiner. Results show that the entire baseband receiver can easily fit within a single Xilinx Virtex device and that error-free packet rates in excess of 99% are possible, even in worst case radio channels.
Isoform Specificity of PKMs during Long-Term Facilitation in Aplysia Is Mediated through Stabilization by KIBRA

Persistent activity of protein kinase M (PKM), the truncated form of protein kinase C (PKC), can maintain long-term changes in synaptic strength in many systems, including the hermaphrodite marine mollusk, Aplysia californica. Moreover, different types of long-term facilitation (LTF) in cultured Aplysia sensorimotor synapses rely on the activities of different PKM isoforms in the presynaptic sensory neuron and postsynaptic motor neuron. When the atypical PKM isoform is required, the kidney and brain expressed adaptor protein (KIBRA) is also required. Here, we explore how this isoform specificity is established. We find that PKM overexpression in the motor neuron, but not the sensory neuron, is sufficient to increase synaptic strength and that this activity is not isoform-specific. KIBRA is not the rate-limiting step in facilitation since overexpression of KIBRA is neither sufficient to increase synaptic strength, nor to prolong a form of PKM-dependent intermediate synaptic facilitation. However, the isoform specificity of dominant-negative-PKMs to erase LTF is correlated with isoform-specific competition for stabilization by KIBRA. We identify a new conserved region of KIBRA. Different splice isoforms in this region stabilize different PKMs based on the isoform-specific sequence of an α-helix “handle” in the PKMs. Thus, specific stabilization of distinct PKMs by different isoforms of KIBRA can explain the isoform specificity of PKMs during LTF in Aplysia. SIGNIFICANCE STATEMENT Long-lasting changes in synaptic plasticity associated with memory formation are maintained by persistent protein kinases. We have previously shown in the Aplysia sensorimotor model that distinct isoforms of persistently active protein kinase Cs (PKMs) maintain distinct forms of long-lasting synaptic changes, even when both forms are expressed in the same motor neuron. Here, we show that, while the effects of overexpression of PKMs are not isoform-specific, isoform specificity is defined by a “handle” helix in PKMs that confers stabilization by distinct splice forms in a previously undefined domain of the adaptor protein KIBRA. Thus, we define new regions in both KIBRA and PKMs that define the isoform specificity for maintaining synaptic strength in distinct facilitation paradigms.
Dynamic scene modelling and representation from video and depth

Recent advances in sensor technology have introduced low-cost video+depth sensors, such as the Microsoft Kinect, which enable simultaneous acquisition of colour and depth images at video rates. The aim of this research is to investigate representations which support integration of noisy, partial surface measurements over time to form more complete, temporally coherent models of dynamic scenes with enhanced detail and reduced noise. The initial focus of this work is on the restricted case of rigid geometry for which online GPU-accelerated volumetric fusion is implemented and tested. An alternative fusion approach based on dense surface elements (surfels) is also explored and compared to the volumetric approach. As a first step towards handling non-rigid scenes, the static volumetric approach is extended to treat articulated (semi-rigid) geometry with a focus on humans. The human body is segmented into piece-wise rigid volumetric parts and part tracking is aided by depth-based skeletal motion data. To address scenes containing more general non-rigid geometry beyond people and isolated rigid shapes, a more flexible approach is required. A piece-wise modelling approach using a sparse surfel graph and repeated alternation between part segmentation, motion and shape estimation is proposed. The method is designed to incorporate methods for noise reduction and handling of missing data. Finally, a hybrid approach is proposed which leverages the advantages of the surfel graph segmentation and coarse surface modelling with the higher-resolution surface reconstruction capability of volumetric fusion. The hybrid method is able to produce a seamless skinned mesh structure to efficiently represent a temporally consistent dynamic scene. The hybrid framework can be considered a unification of rigid and non-rigid reconstruction techniques, for which static scenes are a special case. It allows arbitrary dynamic scenes to be efficiently represented with enhanced levels of detail and completeness where possible, but gracefully falls back to raw measurements where no structure can be inferred. The representation is shown to facilitate creative manipulation of real scene data which would previously require more complex capture setups or extensive manual processing.
SAROTUP: a suite of tools for finding potential target-unrelated peptides from phage display data

SAROTUP (Scanner And Reporter Of Target-Unrelated Peptides) 3.1 is a significant upgrade to the widely used SAROTUP web server for the rapid identification of target-unrelated peptides (TUPs) in phage display data. At present, SAROTUP has gathered a suite of tools for finding potential TUPs and other purposes. Besides the TUPScan, the motif-based tool, and three tools based on the BDB database, i.e., MimoScan, MimoSearch, and MimoBlast, three predictors based on support vector machine, i.e., PhD7Faster, SABinder and PSBinder, are integrated into SAROTUP. The current version of SAROTUP contains 27 TUP motifs and 823 TUP sequences. We also developed the standalone SAROTUP application with graphical user interface (GUI) and command line versions for processing deep sequencing phage display data and distributed it as an open source package, which can perform perfectly locally on almost all systems that support C++ with little or no modification. The web interfaces of SAROTUP have also been redesigned to be more self-evident and user-friendly. The latest version of SAROTUP is freely available at http://i.uestc. edu.cn/sarotup3.
Devibursaphelenchus wangi sp. n. (Nematoda: Ektaphelenchinae) feeding on Aphelenchoides sp.

Summary. Devibursaphelenchus wangi sp. n. is described and figured. The new species was isolated from pine packaging wood from the USA and inspected in Ningbo harbour, China in 2009. The new species is characterised by relatively slender body (a = 36.5 and 37.1 for males and females, respectively); three lines in the lateral field; stylet with relatively wide lumen but lacking basal knobs; vulval flap absent, very short post-uterine sac; non-functional and indistinct female rectum and anus; spicules relatively small (14.2-15.6 μm) with a flattened cucullus; two pairs of caudal papillae. The new species is morphologically close to D. eproctatus and D. hunanensis and can be distinguished by shape and size of spicules and smaller stylet. The separate species status is supported by ITS-RFLP patterns and molecular phylogenetic analysis based on ITS1/2 and partial LSU sequences, which revealed that the new species is close to D. hunanensis . The feeding habit of the new species is also observed and discussed.