Miracle-dz/UniFAR-FTUs huggingface dataset:
Nitrogen Addition and Warming Independently Influence the Belowground Micro-Food Web in a Temperate Steppe

Climate warming and atmospheric nitrogen (N) deposition are known to influence ecosystem structure and functioning. However, our understanding of the interactive effect of these global changes on ecosystem functioning is relatively limited, especially when it concerns the responses of soils and soil organisms. We conducted a field experiment to study the interactive effects of warming and N addition on soil food web. The experiment was established in 2006 in a temperate steppe in northern China. After three to four years (2009–2010), we found that N addition positively affected microbial biomass and negatively influenced trophic group and ecological indices of soil nematodes. However, the warming effects were less obvious, only fungal PLFA showed a decreasing trend under warming. Interestingly, the influence of N addition did not depend on warming. Structural equation modeling analysis suggested that the direct pathway between N addition and soil food web components were more important than the indirect connections through alterations in soil abiotic characters or plant growth. Nitrogen enrichment also affected the soil nematode community indirectly through changes in soil pH and PLFA. We conclude that experimental warming influenced soil food web components of the temperate steppe less than N addition, and there was little influence of warming on N addition effects under these experimental conditions.
MUSTv2: An Improved De Novo Detection Program for Recently Active Miniature Inverted Repeat Transposable Elements (MITEs)

Abstract Background Miniature inverted repeat transposable element (MITE) is a short transposable element, carrying no protein-coding regions. However, its high proliferation rate and sequence-specific insertion preference renders it as a good genetic tool for both natural evolution and experimental insertion mutagenesis. Recently active MITE copies are those with clear signals of Terminal Inverted Repeats (TIRs) and Direct Repeats (DRs), and are recently translocated into their current sites. Their proliferation ability renders them good candidates for the investigation of genomic evolution. Results This study optimizes the C++ code and running pipeline of the MITE Uncovering SysTem (MUST) by assuming no prior knowledge of MITEs required from the users, and the current version, MUSTv2, shows significantly increased detection accuracy for recently active MITEs, compared with similar programs. The running speed is also significantly increased compared with MUSTv1. We prepared a benchmark dataset, the simulated genome with 150 MITE copies for researchers who may be of interest. Conclusions MUSTv2 represents an accurate detection program of recently active MITE copies, which is complementary to the existing template-based MITE mapping programs. We believe that the release of MUSTv2 will greatly facilitate the genome annotation and structural analysis of the bioOMIC big data researchers.
Spatial Distribution of Tree Species Governs the Spatio-Temporal Interaction of Leaf Area Index and Soil Moisture across a Forested Landscape

Quantifying coupled spatio-temporal dynamics of phenology and hydrology and understanding underlying processes is a fundamental challenge in ecohydrology. While variation in phenology and factors influencing it have attracted the attention of ecologists for a long time, the influence of biodiversity on coupled dynamics of phenology and hydrology across a landscape is largely untested. We measured leaf area index (L) and volumetric soil water content (θ) on a co-located spatial grid to characterize forest phenology and hydrology across a forested catchment in central Pennsylvania during 2010. We used hierarchical Bayesian modeling to quantify spatio-temporal patterns of L and θ. Our results suggest that the spatial distribution of tree species across the landscape created unique spatio-temporal patterns of L, which created patterns of water demand reflected in variable soil moisture across space and time. We found a lag of about 11 days between increase in L and decline in θ. Vegetation and soil moisture become increasingly homogenized and coupled from leaf-onset to maturity but heterogeneous and uncoupled from leaf maturity to senescence. Our results provide insight into spatio-temporal coupling between biodiversity and soil hydrology that is useful to enhance ecohydrological modeling in humid temperate forests.
Adaptive Structure Concept Factorization for Multiview Clustering

Most existing multiview clustering methods require that graph matrices in different views are computed beforehand and that each graph is obtained independently. However, this requirement ignores the correlation between multiple views. In this letter, we tackle the problem of multiview clustering by jointly optimizing the graph matrix to make full use of the data correlation between views. With the interview correlation, a concept factorization–based multiview clustering method is developed for data integration, and the adaptive method correlates the affinity weights of all views. This method differs from nonnegative matrix factorization–based clustering methods in that it can be applicable to data sets containing negative values. Experiments are conducted to demonstrate the effectiveness of the proposed method in comparison with state-of-the-art approaches in terms of accuracy, normalized mutual information, and purity.
Mechanisms of B cell activation in patients with acquired immunodeficiency syndrome and related disorders. Contribution of antibody-producing B cells, of Epstein-Barr virus-infected B cells, and of immunoglobulin production induced by human T cell lymphotropic virus, type III/lymphadenopathy-associa

Patients with acquired immunodeficiency syndrome (AIDS) and AIDS-related complex (ARC) have hyperimmunoglobulinemia and increased numbers of circulating immunoglobulin-secreting cells. In this paper, we studied the basis for this B cell hyperactivity. Limiting dilution studies of B cells from seven patients with ARC and four with AIDS revealed that some B cells spontaneously produced antibodies to human T cell lymphotropic virus, type III/lymphadenopathy-associated virus (HTLV-III/LAV) (39:10(6) and 7:10(6) B cells, respectively), suggesting that chronic antigenic stimulation by HTLV-III/LAV was one contributing factor. The patients also had an increased number of spontaneously outgrowing B cells than did normals (6:10(6) vs. less than 2:10(6) B cells), suggesting that they had an increased number of Epstein-Barr virus (EBV)-infected B cells. However, fewer B cells from patients were immortalized by exogenously added EBV than were B cells from normals. In additional studies, HTLV-III/LAV induced immunoglobulin secretion (mean 2,860 ng/ml) by peripheral blood mononuclear cells from normals; this HTLV-III/LAV-induced immunoglobulin secretion required the presence of both B and T cells. Thus, antigenic stimulation by HTLV-III/LAV, increased numbers of EBV-infected B cells, and HTLV-III/LAV-induced T cell-dependent B cell activation all contribute to the B cell hyperactivity in patients with HTLV-III/LAV disease.
Sol-gel derived optical waveguide films: technological platform for development of planar evanescent wave sensors

Plane evanescent wave sensors are being developed for over thirty years. However, their full development is somehow limited by the lack of relatively cheap and stable waveguide layers of high refractive index, low optical losses and at the same time resistance to the impact of chemical substances. The paper involves waveguide layers SiO2:TiO2 of high refractive index (∼1.81) satisfying these criteria, fabricated via sol-gel method and dip-coating technique. The parameters of the waveguide layers SiO2:TiO2 were determined using elipsometric and spectrophotometric methods. The presented waveguide layers have excellent optical properties and are suitable for the application in the planar evanescent wave sensors technology. For the best waveguide SiO2:TiO2 layers, the obtained level of optical loss was below 0.2 dB/cm.
A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo

In recent years, multielectrode arrays and large silicon probes have been developed to record simultaneously between hundreds and thousands of electrodes packed with a high density. However, they require novel methods to extract the spiking activity of large ensembles of neurons. Here, we developed a new toolbox to sort spikes from these large-scale extracellular data. To validate our method, we performed simultaneous extracellular and loose patch recordings in rodents to obtain ‘ground truth’ data, where the solution to this sorting problem is known for one cell. The performance of our algorithm was always close to the best expected performance, over a broad range of signal-to-noise ratios, in vitro and in vivo. The algorithm is entirely parallelized and has been successfully tested on recordings with up to 4225 electrodes. Our toolbox thus offers a generic solution to sort accurately spikes for up to thousands of electrodes.
A critical stress to detach cancer cells in microchannels

We present experiments involving T24 cancer cells adhering at the bottom of functionalized microchannels, and subjected to increasing shear rates. Morphological studies have been carried out at different shear stresses. Cells exhibit spreading patterns similar to the ones observed in static conditions, as long as the shear stress is not too high. At a critical value of the wall shear stress, cells start to decrease their area until detachment is achieved for the larger stresses. The influence of microchannel size is also analyzed and shows a slight effect, enhanced for high confinement. To analyze such data, we propose a model to determine the 3D-shear stress necessary to achieve cell area decrease (leading to detachment), as a function of focal adhesion contacts present at the cell-substrate interface. Using this method, the determination of typical forces exerted at each focal contact can be achieved.
Effect of rhythmic auditory cueing on gait in cerebral palsy: a systematic review and meta-analysis

Auditory entrainment can influence gait performance in movement disorders. The entrainment can incite neurophysiological and musculoskeletal changes to enhance motor execution. However, a consensus as to its effects based on gait in people with cerebral palsy is still warranted. A systematic review and meta-analysis were carried out to analyze the effects of rhythmic auditory cueing on spatiotemporal and kinematic parameters of gait in people with cerebral palsy. Systematic identification of published literature was performed adhering to Preferred Reporting Items for Systematic Reviews and Meta-Analyses and American Academy for Cerebral Palsy and Developmental Medicine guidelines, from inception until July 2017, on online databases: Web of Science, PEDro, EBSCO, Medline, Cochrane, Embase and ProQuest. Kinematic and spatiotemporal gait parameters were evaluated in a meta-analysis across studies. Of 547 records, nine studies involving 227 participants (108 children/119 adults) met our inclusion criteria. The qualitative review suggested beneficial effects of rhythmic auditory cueing on gait performance among all included studies. The meta-analysis revealed beneficial effects of rhythmic auditory cueing on gait dynamic index (Hedge’s g=0.9), gait velocity (1.1), cadence (0.3), and stride length (0.5). This review for the first time suggests a converging evidence toward application of rhythmic auditory cueing to enhance gait performance and stability in people with cerebral palsy. This article details underlying neurophysiological mechanisms and use of cueing as an efficient home-based intervention. It bridges gaps in the literature, and suggests translational approaches on how rhythmic auditory cueing can be incorporated in rehabilitation approaches to enhance gait performance in people with cerebral palsy.
Heat-Stress and Light-Stress Induce Different Cellular Pathologies in the Symbiotic Dinoflagellate during Coral Bleaching

Coral bleaching is a significant contributor to the worldwide degradation of coral reefs and is indicative of the termination of symbiosis between the coral host and its symbiotic algae (dinoflagellate; Symbiodinium sp. complex), usually by expulsion or xenophagy (symbiophagy) of its dinoflagellates. Herein, we provide evidence that during the earliest stages of environmentally induced bleaching, heat stress and light stress generate distinctly different pathomorphological changes in the chloroplasts, while a combined heat- and light-stress exposure induces both pathomorphologies; suggesting that these stressors act on the dinoflagellate by different mechanisms. Within the first 48 hours of a heat stress (32°C) under low-light conditions, heat stress induced decomposition of thylakoid structures before observation of extensive oxidative damage; thus it is the disorganization of the thylakoids that creates the conditions allowing photo-oxidative-stress. Conversely, during the first 48 hours of a light stress (2007 µmoles m−2 s−1 PAR) at 25°C, condensation or fusion of multiple thylakoid lamellae occurred coincidently with levels of oxidative damage products, implying that photo-oxidative stress causes the structural membrane damage within the chloroplasts. Exposure to combined heat- and light-stresses induced both pathomorphologies, confirming that these stressors acted on the dinoflagellate via different mechanisms. Within 72 hours of exposure to heat and/or light stresses, homeostatic processes (e.g., heat-shock protein and anti-oxidant enzyme response) were evident in the remaining intact dinoflagellates, regardless of the initiating stressor. Understanding the sequence of events during bleaching when triggered by different environmental stressors is important for predicting both severity and consequences of coral bleaching.
Eco-Evolutionary Feedback and the Tuning of Proto-Developmental Life Cycles

Multicellular organisms depend on developmental programs to coordinate growth and differentiation from single cells, but the origins of development are unclear. A possible starting point is stochastic phenotypic variation generated by molecular noise. Given appropriate environmental conditions, noise-driven differentiation could conceivably evolve so as to come under regulatory control; however, abiotic conditions are likely to be restrictive. Drawing from an experimental system, we present a model in which environmental fluctuations are coupled to population growth. We show that this coupling generates stable selection for a single optimal strategy that is largely insensitive to environmental conditions, including the number of competitors, carrying capacity of the environment, difference in growth rates among phenotypic variants, and population density. We argue that this optimal strategy establishes stabilizing conditions likely to improve the quality and reliability of information experienced by evolving organisms, thus increasing opportunity for the evolutionary emergence of developmental programs.
Altered Hub Configurations within Default Mode Network following Acupuncture at ST36: A Multimodal Investigation Combining fMRI and MEG

Acupuncture, an externally somatosensory stimulation in the Traditional Chinese Medicine, has been proposed about its modulations on the brain's default mode network (DMN). However, it is still unknown on how the internal brain resting networks are modulated and what inferences can be made about the physiological processes underlying these changes. Combining high spatial resolution of functional magnetic resonance imaging (fMRI) with high temporal resolution of magnetoencephalography (MEG), in the current multimodal study, we sought to explore spatiotemporally whether or not band-specific DMN hub configurations would be induced by verum acupuncture, compared with sham control. Spatial independent component analysis was applied to fMRI data, followed by the discrete regional sources seeded into MEG data. Partial correlation analysis was further adopted to estimate the intrinsic functional connectivity and network hub configurations. One of the most striking findings is that the posterior cingulate cortex is not only validated as a robust DMN hub, but served as a hub only within the delta and gamma bands following the verum acupuncture, compared with its consistently being a DMN hub in sham control group. Our preliminary results may provide a new perspective to lend support for the specificity of neural mechanism underlying acupuncture.
Simultaneous Event-Triggered Fault Detection and Estimation for Stochastic Systems Subject to Deception Attacks

In this paper, a synthesized design of fault-detection filter and fault estimator is considered for a class of discrete-time stochastic systems in the framework of event-triggered transmission scheme subject to unknown disturbances and deception attacks. A random variable obeying the Bernoulli distribution is employed to characterize the phenomena of the randomly occurring deception attacks. To achieve a fault-detection residual is only sensitive to faults while robust to disturbances, a coordinate transformation approach is exploited. This approach can transform the considered system into two subsystems and the unknown disturbances are removed from one of the subsystems. The gain of fault-detection filter is derived by minimizing an upper bound of filter error covariance. Meanwhile, system faults can be reconstructed by the remote fault estimator. An recursive approach is developed to obtain fault estimator gains as well as guarantee the fault estimator performance. Furthermore, the corresponding event-triggered sensor data transmission scheme is also presented for improving working-life of the wireless sensor node when measurement information are aperiodically transmitted. Finally, a scaled version of an industrial system consisting of local PC, remote estimator and wireless sensor node is used to experimentally evaluate the proposed theoretical results. In particular, a novel fault-alarming strategy is proposed so that the real-time capacity of fault-detection is guaranteed when the event condition is triggered.
Impact of Dietary Calcium Supplement on Circulating Lipoprotein Concentrations and Atherogenic Indices in Overweight and Obese Individuals: A Systematic Review

ABSTRACT Dyslipidemia is the main risk factor for developing cardiovascular disease. There are discrepancies in the effects of calcium supplementation on modulation of lipid status. Therefore, we aimed to summarize the effects of dietary calcium supplement on circulating lipoprotein concentrations and atherogenic indices in overweight and obese individuals. We conducted a systematic literature search from 2000 until July 2016. PubMed, Scopus, Cochran Library, and ISI Web of Science databases were searched for clinical trials written in English. Placebo controlled clinical trials on calcium or calcium with vitamin D supplement in overweight and obese indiciduals were considered. Finally, 11 clinical trials met the criteria and were included. Most studies (n = 9) evaluated Ca/D co-supplementation. Positive effects of calcium supplementation alone or with vitamin D were as follows: serum levels of total cholesterol (TC; n = 1), triglyceride (TG) concentrations (n = 1), serum levels of low-density lipoprotein cholesterol (LDL-C; n = 5) and high-density lipoprotein cholesterol (HDL-C; n = 3). Seven clinical trials reported atherogenic indices and three of them demonstrated beneficial effects of calcium supplementation on at least one atherogenic index. Calcium supplementation may not be helpful to reduce serum levels of TC and TG in overweight and obese individuals. However, it may modulate LDL-C and HDL-C concentration. More studies are warranted to clarify the effects of calcium supplementation on each atherogenic index.
Probiotics Protect Mice from Ovariectomy-Induced Cortical Bone Loss

The gut microbiota (GM) modulates the hosts metabolism and immune system. Probiotic bacteria are defined as live microorganisms which when administered in adequate amounts confer a health benefit on the host and can alter the composition of the GM. Germ-free mice have increased bone mass associated with reduced bone resorption indicating that the GM also regulates bone mass. Ovariectomy (ovx) results in bone loss associated with altered immune status. The purpose of this study was to determine if probiotic treatment protects mice from ovx-induced bone loss. Mice were treated with either a single Lactobacillus (L) strain, L. paracasei DSM13434 (L. para) or a mixture of three strains, L. paracasei DSM13434, L. plantarum DSM 15312 and DSM 15313 (L. mix) given in the drinking water during 6 weeks, starting two weeks before ovx. Both the L. para and the L. mix treatment protected mice from ovx-induced cortical bone loss and bone resorption. Cortical bone mineral content was higher in both L. para and L. mix treated ovx mice compared to vehicle (veh) treated ovx mice. Serum levels of the resorption marker C-terminal telopeptides and the urinary fractional excretion of calcium were increased by ovx in the veh treated but not in the L. para or the L. mix treated mice. Probiotic treatment reduced the expression of the two inflammatory cytokines, TNFα and IL-1β, and increased the expression of OPG, a potent inhibitor of osteoclastogenesis, in cortical bone of ovx mice. In addition, ovx decreased the frequency of regulatory T cells in bone marrow of veh treated but not probiotic treated mice. In conclusion, treatment with L. para or the L. mix prevents ovx-induced cortical bone loss. Our findings indicate that these probiotic treatments alter the immune status in bone resulting in attenuated bone resorption in ovx mice.
Long‐term in situ persistence of biodiversity in tropical sky islands revealed by landscape genomics

Tropical mountains are areas of high species richness and endemism. Two historical phenomena may have contributed to this: (i) fragmentation and isolation of habitats may have promoted the genetic differentiation of populations and increased the possibility of allopatric divergence and speciation and (ii) the mountain areas may have allowed long‐term population persistence during global climate fluctuations. These two phenomena have been studied using either species occurrence data or estimating species divergence times. However, only few studies have used intraspecific genetic data to analyse the mechanisms by which endemism may emerge at the microevolutionary scale. Here, we use landscape analysis of genomic SNP data sampled from two high‐elevation plant species from an archipelago of tropical sky islands (the Trans‐Mexican Volcanic Belt) to test for population genetic differentiation, synchronous demographic changes and habitat persistence. We show that genetic differentiation can be explained by the degree of glacial habitat connectivity among mountains and that mountains have facilitated the persistence of populations throughout glacial/interglacial cycles. Our results support the ongoing role of tropical mountains as cradles for biodiversity by uncovering cryptic differentiation and limits to gene flow.