Miracle-dz/UniFAR-FTUs huggingface dataset:
Methylation of glucocorticoid receptor gene promoter modulates morphine dependence and accompanied hypothalamus–pituitary–adrenal axis dysfunction

Previous studies demonstrated that dysfunction of the hypothalamus–pituitary–adrenal (HPA) axis played an important role in morphine dependence. Nonetheless, the molecular mechanism underlying morphine‐induced HPA axis dysfunction and morphine dependence remains unclear. In the current study, 5′‐aza‐2′‐deoxycytidine (5‐aza), an inhibitor of DNA methyltransferases (DNMTs), was used to examine the effects of glucocorticoid receptor (GR) promoter 17 methylation on chronic morphine–induced HPA axis dysfunction and behavioral changes in rats and the underlying mechanism. Our results showed that chronic but not acute morphine downregulated the expression of nuclear GR protein and GR exon 17 variant mRNA, and upregulated the methylation of GR 17 exon promoter in the hippocampus of rats. Meanwhile, 5‐aza per se had no effect on observed molecular and behavior change. In contrast, pretreatment of 5‐aza into rat hippocampus reversed chronic morphine–induced hypermethylation of GR 17 promoter and decrease in GR expression. Moreover, pretreatment of 5‐aza attenuated chronic morphine‐enhanced HPA axis reactivity and the naloxone‐precipitated somatic signs in morphine‐dependent rats. Our results suggest that chronic morphine induced hypermethylation of GR 17 promoter, which then downregulated the expression of hippocampal GR, and was thus involved in chronic morphine–induced dysfunction of the HPA axis and the modulation of morphine dependence. Moreover, chronic morphine–induced hypermethylation of GR 17 promoter may be at least partially due to the increase in hippocampal DNMT 1 expression and its binding at GR 17 promoter in the rat hippocampus. © 2016 Wiley Periodicals, Inc.
Shedding Light on Vampires: The Phylogeny of Vampyrellid Amoebae Revisited

With the advent of molecular phylogenetic techniques the polyphyly of naked filose amoebae has been proven. They are interspersed in several supergroups of eukaryotes and most of them already found their place within the tree of life. Although the ‘vampire amoebae’ have attracted interest since the middle of the 19th century, the phylogenetic position and even the monophyly of this traditional group are still uncertain. In this study clonal co-cultures of eight algivorous vampyrellid amoebae and the respective food algae were established. Culture material was characterized morphologically and a molecular phylogeny was inferred using SSU rDNA sequence comparisons. We found that the limnetic, algivorous vampyrellid amoebae investigated in this study belong to a major clade within the Endomyxa Cavalier-Smith, 2002 (Cercozoa), grouping together with a few soil-dwelling taxa. They split into two robust clades, one containing species of the genus Vampyrella Cienkowski, 1865, the other containing the genus Leptophrys Hertwig & Lesser, 1874, together with terrestrial members. Supported by morphological data these clades are designated as the two families Vampyrellidae Zopf, 1885, and Leptophryidae fam. nov. Furthermore the order Vampyrellida West, 1901 was revised and now corresponds to the major vampyrellid clade within the Endomyxa, comprising the Vampyrellidae and Leptophryidae as well as several environmental sequences. In the light of the presented phylogenetic analyses morphological and ecological aspects, the feeding strategy and nutritional specialization within the vampyrellid amoebae are discussed.
Inventory changes in anthropogenic carbon from 1997–2003 in the Atlantic Ocean between 20°S and 65°N

The oceans absorb and store a significant portion of anthropogenic CO2 emissions, but large uncertainties remain in the quantification of this sink. An improved assessment of the present and future oceanic carbon sink is therefore necessary to provide recommendations for long‐term global carbon cycle and climate policies. The formation of North Atlantic Deep Water (NADW) is a unique fast track for transporting anthropogenic CO2 into the ocean's interior, making the deep waters rich in anthropogenic carbon. Thus the Atlantic is presently estimated to hold 38% of the oceanic anthropogenic CO2 inventory, although its volume makes up only 25% of the world ocean. Here we analyze the inventory change of anthropogenic CO2 in the Atlantic between 1997 and 2003 and its relationship to NADW formation. For the whole region between 20°S and 65°N the inventory amounts to 32.5 ± 9.5 Petagram carbon (Pg C) in 1997 and increases up to 36.0 ± 10.5 Pg C in 2003. This result is quite similar to earlier studies. Moreover, the overall increase of anthropogenic carbon is in close agreement with the expected change due to rising atmospheric CO2 levels of 1.69% a−1. On the other hand, when considering the subpolar region only, the results demonstrate that the recent weakening in the formation of Labrador Sea Water, a component of NADW, has already led to a decrease of the anthropogenic carbon inventory in this water mass. As a consequence, the overall inventory for the total water column in the western subpolar North Atlantic increased only by 2% between 1997 and 2003, much less than the 11% that would be expected from the increase in atmospheric CO2 levels.
Mammalian Glutaminase Gls2 Gene Encodes Two Functional Alternative Transcripts by a Surrogate Promoter Usage Mechanism

Background Glutaminase is expressed in most mammalian tissues and cancer cells, but the regulation of its expression is poorly understood. An essential step to accomplish this goal is the characterization of its species- and cell-specific isoenzyme pattern of expression. Our aim was to identify and characterize transcript variants of the mammalian glutaminase Gls2 gene. Methodology/Principal Findings We demonstrate for the first time simultaneous expression of two transcript variants from the Gls2 gene in human, rat and mouse. A combination of RT-PCR, primer-extension analysis, bioinformatics, real-time PCR, in vitro transcription and translation and immunoblot analysis was applied to investigate GLS2 transcripts in mammalian tissues. Short (LGA) and long (GAB) transcript forms were isolated in brain and liver tissue of human, rat and mouse. The short LGA transcript arises by a combination of two mechanisms of transcriptional modulation: alternative transcription initiation and alternative promoter. The LGA variant contains both the transcription start site (TSS) and the alternative promoter in the first intron of the Gls2 gene. The full human LGA transcript has two in-frame ATGs in the first exon, which are missing in orthologous rat and mouse transcripts. In vitro transcription and translation of human LGA yielded two polypeptides of the predicted size, but only the canonical full-length protein displayed catalytic activity. Relative abundance of GAB and LGA transcripts showed marked variations depending on species and tissues analyzed. Conclusions/Significance This is the first report demonstrating expression of alternative transcripts of the mammalian Gls2 gene. Transcriptional mechanisms giving rise to GLS2 variants and isolation of novel GLS2 transcripts in human, rat and mouse are presented. Results were also confirmed at the protein level, where catalytic activity was demonstrated for the human LGA protein. Relative abundance of GAB and LGA transcripts was species- and tissue-specific providing evidence of a differential regulation of GLS2 transcripts in mammals.
An Double Hidden HMM and an CRF for Segmentation Tasks with Pinyin’s Finals

In this paper, we present the proposed method of participating SIGHAN-2010 Chinese word segmentation bake-off. In this year, our focus aims to quick train and test the given data. Unlike the most structural learning algorithms, such as conditional random fields, we design an in-house development conditional support vector Markov model (CMM) framework. The method is very quick to train and also show better performance in accuracy than CRF. To give a fair comparison, we compare our method to CRF with three additional tasks, namely, CoNLL-2000 chunking, SIGHAN-3 Chinese word segmentation. The results were encourage and indicated that the proposed CMM produces better not only accuracy but also training time efficiency. The official results in SIGHAN-2010 also demonstrates that our method perform very well in traditional Chinese with fine-tuned features set.
Why are there more same-sex than opposite-sex dizygotic twins?

STUDY QUESTION Are there more same-sex (SS) than opposite-sex (OS) pairs among dizygotic twins? SUMMARY ANSWER In violation of Weinberg's Differential Rule, there are significantly more SS than OS pairs among dizygotic twins in nationally representative samples both in the UK and the USA. WHAT IS KNOWN ALREADY Since at least 1874, twin researchers have assumed that dizygotic twins were equally likely to be SS or OS (later formalized as Weinberg's Differential Rule). However, recent research on the sex-specific nature of breastmilk suggests that OS twins might be at a developmental disadvantage relative to SS twins. There may therefore be evolutionary selection for the tendency to have SS twins and against the tendency to have OS twins. STUDY DESIGN, SIZE, DURATION We analyze two population samples (not subject to Lykken's rule of two-thirds): the National Child Development Study in the UK (n = 17 419) from 1958 to present, and the National Longitudinal Study of Adolescent Health in the USA (n = 20 745) from 1994 to present. PARTICIPANTS/MATERIALS, SETTING, METHODS We performed a one-sample t-test of the proportion of SS dizygotic twins against the theoretical null value of 0.5022. MAIN RESULTS AND THE ROLE OF CHANCE The proportion of SS pairs among dizygotic twins was 0.6043 (t(325) = 3.838, P = 0.00015) in the UK and 0.5739 (t(520) = 3.398, P = 0.00073) in the USA. LIMITATIONS, REASONS FOR CAUTION Twin type (monozygotic versus dizygotic) was classified by the mother, not by DNA typing, although supplementary data suggest that misclassification was negligible and supplementary analysis shows that potential misclassifications do not change our main conclusions. WIDER IMPLICATIONS OF THE FINDINGS Weinberg's Differential Rule may be incorrect in its assumption of independence of sexes within dizygotic pairs, and there may be evolutionary selection for SS, and against OS, dizygotic pairs. STUDY FUNDING/COMPETING INTERESTS None.
Personality assessment and model comparison with behavioral data: A statistical framework and empirical demonstration with bonobos (Pan paniscus)

Interest in quantifying consistent among‐individual variation in primate behavior, also known as personality, has grown rapidly in recent decades. Although behavioral coding is the most frequently utilized method for assessing primate personality, limitations in current statistical practice prevent researchers’ from utilizing the full potential of their coding datasets. These limitations include the use of extensive data aggregation, not modeling biologically relevant sources of individual variance during repeatability estimation, not partitioning between‐individual (co)variance prior to modeling personality structure, the misuse of principal component analysis, and an over‐reliance upon exploratory statistical techniques to compare personality models across populations, species, and data collection methods. In this paper, we propose a statistical framework for primate personality research designed to address these limitations. Our framework synthesizes recently developed mixed‐effects modeling approaches for quantifying behavioral variation with an information‐theoretic model selection paradigm for confirmatory personality research. After detailing a multi‐step analytic procedure for personality assessment and model comparison, we employ this framework to evaluate seven models of personality structure in zoo‐housed bonobos (Pan paniscus). We find that differences between sexes, ages, zoos, time of observation, and social group composition contributed to significant behavioral variance. Independently of these factors, however, personality nonetheless accounted for a moderate to high proportion of variance in average behavior across observational periods. A personality structure derived from past rating research receives the strongest support relative to our model set. This model suggests that personality variation across the measured behavioral traits is best described by two correlated but distinct dimensions reflecting individual differences in affiliation and sociability (Agreeableness) as well as activity level, social play, and neophilia toward non‐threatening stimuli (Openness). These results underscore the utility of our framework for quantifying personality in primates and facilitating greater integration between the behavioral ecological and comparative psychological approaches to personality research.
A checkpoint protocol for an entry consistent shared memory system

Workstation clusters are becoming an interesting alternative to dedicated multiprocessors. In this environment, the probability of a failure, during an application’s execution, increases with the execution time and the number of workstations used. If no provision is made for handling failures, it is unlikely that long running applications will terminate successfully. One solution to this problem is process checkpointing. This paper presents a checkpoint protocol for a multithreaded distributed shared memory system based on the entry consistency memory model. The protocol allows transparent recovery from single node failures and, in some cases, from multiple node failures. A simple mechanism is used to determine if the system can be brought to a consistent state in the event of multiple machine crashes. The protocol keeps a distributed log of shared data accesses in the volatile memory of the processes, taking advantage of the independent failure characteristics of workstation clusters. Periodically, or whenever the log reaches a highwater mark, each process checkpoints its state, independently from the others. The protocol needs no extra messages during the failure-free period, since all checkpoint control information is piggybacked on the memory coherence protocol messages.
Kidney Stone Disease: An Update on Current Concepts

Kidney stone disease is a crystal concretion formed usually within the kidneys. It is an increasing urological disorder of human health, affecting about 12% of the world population. It has been associated with an increased risk of end-stage renal failure. The etiology of kidney stone is multifactorial. The most common type of kidney stone is calcium oxalate formed at Randall's plaque on the renal papillary surfaces. The mechanism of stone formation is a complex process which results from several physicochemical events including supersaturation, nucleation, growth, aggregation, and retention of urinary stone constituents within tubular cells. These steps are modulated by an imbalance between factors that promote or inhibit urinary crystallization. It is also noted that cellular injury promotes retention of particles on renal papillary surfaces. The exposure of renal epithelial cells to oxalate causes a signaling cascade which leads to apoptosis by p38 mitogen-activated protein kinase pathways. Currently, there is no satisfactory drug to cure and/or prevent kidney stone recurrences. Thus, further understanding of the pathophysiology of kidney stone formation is a research area to manage urolithiasis using new drugs. Therefore, this review has intended to provide a compiled up-to-date information on kidney stone etiology, pathogenesis, and prevention approaches.
Mean-Square Asymptotic Synchronization Control of Discrete-Time Neural Networks With Restricted Disturbances and Missing Data

The problem of controller design is investigated to achieve the mean-square asymptotic synchronization of discrete-time neural networks with time-varying delay and restricted disturbances. The unreliable communication links between the neural networks, which are modeled as stochastic dropouts satisfying the Bernoulli distributions, are taken into account. By applying the Lyapunov function, a synchronization controller design method is proposed in the form of linear matrix inequalities. The design method is also extended to neural networks including modeling uncertainties. Two numerical examples are given to illustrate the effectiveness of the proposed methods.
Antibody-Based Agents in the Management of Antibiotic-Resistant Staphylococcus aureus Diseases

Staphylococcus aureus is a human pathogen that can cause a wide spectrum of diseases, including sepsis, pneumonia, arthritis, and endocarditis. Ineffective treatment of a number of staphylococcal infections with antibiotics is due to the development and spread of antibiotic-resistant strains following decades of antibiotic usage. This has generated renewed interest within the scientific community in alternative therapeutic agents, such as anti-S. aureus antibodies. Although the role of antibodies in the management of S. aureus diseases is controversial, the success of this pathogen in neutralizing humoral immunity clearly indicates that antibodies offer the host extensive protection. In this review, we report an update on efforts to develop antibody-based agents, particularly monoclonal antibodies, and their therapeutic potential in the passive immunization approach to the treatment and prevention of S. aureus infections.
Power-Efficient Linear Precoding for MU-MISO VLC Systems With Channel Uncertainty

In this letter, we consider a multi-user multiple-input single-output visible light communication system. A power-efficient linear precoding for zero-forcing (ZF) detection is developed with channel uncertainty, i.e., noisy channel state information (CSI) and outdated CSI. With the constraint of a dynamic current range of light-emitting diodes, the proposed method is capable of minimizing total optical power and guaranteeing user performance. Simulation results demonstrate that the proposed precoding can achieve a lower power consumption than the pseudo-inverse ZF precoding with the same user performance.
Correlation Preserving Sparse Coding Over Multi-level Dictionaries for Image Denoising

In this letter, we propose a novel image denoising method based on correlation preserving sparse coding. Because the instable and unreliable correlations among basis set can limit the performance of the dictionary-driven denoising methods, two effective regularized strategies are employed in the coding process. Specifically, a graph-based regularizer is built for preserving the global similarity correlations, which can adaptively capture both the geometrical structures and discriminative features of textured patches. In particular, edge weights in the graph are obtained by seeking a nonnegative low-rank construction. Besides, a robust locality-constrained coding can automatically preserve not only spatial neighborhood information but also internal consistency present in noisy patches while learning overcomplete dictionary. Experimental results demonstrate that our proposed method achieves state-of-the-art denoising performance in terms of both PSNR and subjective visual quality.
Stability in a novel 3-D chaotic system using optimal generalized back-stepping method

This paper investigates on control and stabilization of a novel 3_D chaotic system. The chaotic system is stabilized using Generalized Back-stepping Method (GBM); it's similarity to Back-stepping and more applications in systems than it. Back-stepping method is used only to strictly feedback systems but GBM expand this class. The Generalized Back-stepping approach consists of parameters which accept positive value, the system responses differently for each value, It's necessary to select proper parameter to obtain a good response because inappropriate selection lead to the improper responses or even the system unstable for this reason in this text. A series of optimization techniques were applied. To achieve optimal parameters. These optimization techniques are to Genetic Algorithm (GA), Artificial Bee Colony (ABC) And Shuffled Frog Leaping Algorithm (SFLA). In these Algorithms using a minimum squared error cost function. Cost function enforces the system error to decay to zero rapidly. Finally, according to the results of simulations and numerical calculations, we discuss which one of the above algorithms is the best performance and efficiency in the control of the aforementioned system.
A Hybrid Quantum-Classical Paradigm to Mitigate Embedding Costs in Quantum Annealing

Despite rapid recent progress towards the development of quantum computers capable of providing computational advantages over classical computers, it seems likely that such computers will, initially at least, be required to run in a hybrid quantum-classical regime. This realization has led to interest in hybrid quantum-classical algorithms allowing, for example, quantum computers to solve large problems despite having very limited numbers of qubits. Here we propose a hybrid paradigm for quantum annealers with the goal of mitigating a different limitation of such devices: the need to embed problem instances within the (often highly restricted) connectivity graph of the annealer. This embedding process can be costly to perform and may destroy any computational speedup. In order to solve many practical problems, it is moreover necessary to perform many, often related, such embeddings. We will show how, for such problems, a raw speedup that is negated by the embedding time can nonetheless be exploited to give a real speedup. As a proof-of-concept example we present an in-depth case study of a simple problem based on the maximum-weight independent set problem. Although we do not observe a quantum speedup experimentally, the advantage of the hybrid approach is robustly verified, showing how a potential quantum speedup may be exploited and encouraging further efforts to apply the approach to problems of more practical interest.
K‐MING: A mobile proxy handoff control scheme for proximate group‐based geodata sharing

This work adopts a mobile social network in proximity (MSNP)–centric group touring service concept to share geo–points of interest's (POIs') data among mobile users belonging to the same touring group. In a group‐based touring service, a mobile user can create a group in the MSNP that can consist of some clusters in which some members having the 3G/3.5G/4G cellular network service are selected as cluster leaders to enable their Wi‐Fi hot spot functions as mobile proxies. After that, each group member can join one of the clusters by connecting with a cluster leader's Wi‐Fi hot spot. Thereafter, each cluster leader downloads geo‐POIs' data using 3G/3.5G/4G cellular network and then shares the downloaded POIs' data with its cluster members through its Wi‐Fi hot spot. This work proposed a handoff mechanism such that each mobile user can handoff from its currently connected cluster to the other one that belongs to the same MNSP group. The main handoff concern is that each handheld device only allows a limited number of handheld devices to connect with its Wi‐Fi hot spot at the same time. This work proposed a K‐member‐limited MSNP‐based INter Group handoff scheme called K‐MING to tackle the handoff problem. The performance analysis shows that K‐MING for the group touring scenario has better performance for the sharing of geo‐POIs' data downloading in terms of average power consumption and average downloaded data volume from 3G/3.5G/4G cellular network than that of the individual touring scenario.