Miracle-dz/UniFAR-FTUs huggingface dataset:
Loss of Intranetwork and Internetwork Resting State Functional Connections with Alzheimer's Disease Progression

Alzheimer's disease (AD) is the most common cause of dementia. Much is known concerning AD pathophysiology but our understanding of the disease at the systems level remains incomplete. Previous AD research has used resting-state functional connectivity magnetic resonance imaging (rs-fcMRI) to assess the integrity of functional networks within the brain. Most studies have focused on the default-mode network (DMN), a primary locus of AD pathology. However, other brain regions are inevitably affected with disease progression. We studied rs-fcMRI in five functionally defined brain networks within a large cohort of human participants of either gender (n = 510) that ranged in AD severity from unaffected [clinical dementia rating (CDR) 0] to very mild (CDR 0.5) to mild (CDR 1). We observed loss of correlations within not only the DMN but other networks at CDR 0.5. Within the salience network (SAL), increases were seen between CDR 0 and CDR 0.5. However, at CDR 1, all networks, including SAL, exhibited reduced correlations. Specific networks were preferentially affected at certain CDR stages. In addition, cross-network relations were consistently lost with increasing AD severity. Our results demonstrate that AD is associated with widespread loss of both intranetwork and internetwork correlations. These results provide insight into AD pathophysiology and reinforce an integrative view of the brain's functional organization.
Review of advances in the thin layer chromatography of pesticides: 2012–2014

Publications reporting techniques and applications of thin layer chromatography (planar chromatography) for the separation, detection, qualitative, and quantitative determination, and preparative isolation of pesticides and their metabolites are reviewed for the period from November 1, 2012 to November 1, 2014. Analyses are described for a variety of sample types and pesticide classes. In addition to references on residue analysis, studies such as pesticide structure – retention relationships, identification and characterization of natural and synthesized pesticides, metabolism, bioactivity, degradation, soil mobility, and lipophilicity are covered.
Quantitative Expression of Toll-Like Receptor 1–10 mRNA in Cellular Subsets of Human Peripheral Blood Mononuclear Cells and Sensitivity to CpG Oligodeoxynucleotides1

The Toll-like receptor (TLR)9 is critical for the recognition of immunostimulatory CpG motifs but may cooperate with other TLRs. We analyzed TLR1–10 mRNA expression by using quantitative real-time PCR in highly purified subsets of human PBMC and determined the sensitivity of these subsets to CpG oligodeoxynucleotides (ODN). TLR1 and TLR6 were expressed in all cell types examined. TLR10 was highly expressed in B cells and weakly expressed in plasmacytoid dendritic cells (PDC). High expression of TLR2 was characteristic for monocytes. PDC and B cells expressed marked levels of TLR7 and TLR9 and were directly sensitive to CpG ODN. In CpG ODN-stimulated PDC and B cells, TLR9 expression rapidly decreased, as opposed to TLR7, which was up-regulated in PDC and decreased in B cells. In monocytes, NK cells, and T cells, TLR7 was absent. Despite low expression of TLR9, monocytes, NK cells, and T cells did not respond to CpG ODN in the absence of PDC but were activated in the presence of PDC. In conclusion, our studies provide evidence that PDC and B cells, but not monocytes, NK cells, or T cells, are primary targets of CpG ODN in peripheral blood. The characteristic expression pattern of TLR1–10 in cellular subsets of human PBMC is consistent with the concept that TLR9 is essential in the recognition of CpG ODN in PDC and B cells. In addition, selective regulation of TLR7 expression in PDC and B cells by CpG ODN revealed TLR7 as a candidate TLR potentially involved in modulating the recognition of CpG motifs.
Wastewater Treatment Using Vertical Flow Constructed Wetland Dr .

Water is one of the most important elements involved in the creation and development of healthy life. Disposal of untreated wastewater from households as well as institutions & industry is causing deterioration of water bodies in urban areas in the developing world. A high level of responsibility towards water usage is required, & it must be recycled according to its pollution content in order to maintain water quality and protect our environment. One of the methods of the treatment is constructed wetland. Constructed wetland system for wastewater treatment has been proven to be effective & sustainable alternative for conventional wastewater treatment technologies. The removal of pollutants in this system relies on a combination of physical, chemical and biological processes that naturally occur in wetland & are associated with vegetation, and their microbial communities. The present study undertaken by fabricating the lab scale model of constructed wetland. The effluent of Amba Nala Amravati is treated with this system and wastewater characteristic like pH, DO, TS, BOD, COD with & without plant species studied. Using sandy soil as substrate, it was found that BOD, COD removal 61 % and 51 % for unplanted constructed wetland whereas for planted constructed wetland it was 74% and 61%.
Sources from shading

The authors assume a Lambertian shading model with unknown light source directions. It is shown that information on the occluding boundary puts strong constraints on the light source directions. For a small number of light sources, from sufficiently different directions, additional information from intensity extrema will be sufficient to determine the source directions. If there are two, or three, views of the object then the light sources can be determined without extrema information. The authors report experiments performed on synthesized images. <<ETX>>
Hierarchical Clustering of Time-Series Data Streams

This paper presents and analyzes an incremental system for clustering streaming time series. The Online Divisive-Agglomerative Clustering (ODAC) system continuously maintains a tree-like hierarchy of clusters that evolves with data, using a top-down strategy. The splitting criterion is a correlation-based dissimilarity measure among time series, splitting each node by the farthest pair of streams. The system also uses a merge operator that reaggregates a previously split node in order to react to changes in the correlation structure between time series. The split and merge operators are triggered in response to changes in the diameters of existing clusters, assuming that in stationary environments, expanding the structure leads to a decrease in the diameters of the clusters. The system is designed to process thousands of data streams that flow at a high rate. The main features of the system include update time and memory consumption that do not depend on the number of examples in the stream. Moreover, the time and memory required to process an example decreases whenever the cluster structure expands. Experimental results on artificial and real data assess the processing qualities of the system, suggesting a competitive performance on clustering streaming time series, exploring also its ability to deal with concept drift.
Isolation of a new high molecular weight protein associated with desmin and vimentin filaments from avian embryonic skeletal muscle

Filaments with a diameter of 80-120 A have been prepared from 14-d-old chick embryonic skeletal muscle, using a physiological salt solution and gel filtration chromatography. The filaments obtained are composed of the two known muscle intermediate-filament proteins, vimentin and desmin, as well as the vimentin- and desmin-associated high molecular weight protein, synemin (230,000 mol. wt). In addition, they contain a previously unidentified high molecular weight protein (280,000 mol wt) which differs from synemin by isoelectric point, molecular weight, and immunological reactivity. Immunofluorescence on cultured myogenic cells,using antisera to the 280,000-dalton polypeptide, has revealed that this protein has the same spatial distribution as desmin, vimentin, and synemin in both early myotubes, where it associates with cytoplasmic filaments, and late in myotubes, where it is associated with myofibril Z lines. Examination by immunofluorescence of frozen sections of developing embryonic skeletal muscle reveals a gradual diminution in the presence of the 280,000-dalton protein. The 280,000-dalton protein is undetectable in adult skeletal and smooth muscle, as shown by immunofluorescence and immunoautoradiography. In chick embryonic fibroblasts grown in tissue culture, only a subpopulation of the cells is reactive with antibodies to the 280,000-dalton protein even though all these cells contain vimentin. In the reactive cells, vimentin and the 280,000-dalton polypeptide exhibit an indistinguishable cytoplasmic filamentous network, which aggregates into filamentious bundles when the cells are exposed to colcemid. These results suggest that this newly identified high molecular weight protein is closely associated with intermediate filaments containing either vimentin alone or vimentin, desmin and synemin. The expression of this protein appears to be developmentally regulated and does not appear to parallel the expression of any of the other three intermediate-filament proteins. The absence of the 280,000-dalton polypeptide in adult muscle cells and its gradual reduction during development implies that is probably not required for the maintenance of Z-disk structure after the assembly of the sarcomere.
From coarse‐grain to all‐atom: Toward multiscale analysis of protein landscapes

Multiscale methods are becoming increasingly promising as a way to characterize the dynamics of large protein systems on biologically relevant time‐scales. The underlying assumption in multiscale simulations is that it is possible to move reliably between different resolutions. We present a method that efficiently generates realistic all‐atom protein structures starting from the Cα atom positions, as obtained for instance from extensive coarse‐grain simulations. The method, a reconstruction algorithm for coarse‐grain structures (RACOGS), is validated by reconstructing ensembles of coarse‐grain structures obtained during folding simulations of the proteins src‐SH3 and S6. The results show that RACOGS consistently produces low energy, all‐atom structures. A comparison of the free energy landscapes calculated using the coarse‐grain structures versus the all‐atom structures shows good correspondence and little distortion in the protein folding landscape. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Molecular control of ciliary neuron development: BMPs and downstream transcriptional control in the parasympathetic lineage

The generation of noradrenergic sympathetic neurons is controlled by BMPs and the downstream transcription factors Mash1, Phox2b, Phox2a and dHand. We examined the role of these signals in developing cholinergic parasympathetic neurons. The expression of Mash1 (Cash1), Phox2b and Phox2a in the chick ciliary ganglion is followed by the sequential expression of panneuronal, noradrenergic and cholinergic marker genes. BMPs are expressed at the site where ciliary ganglia form and are essential and sufficient for ciliary neuron development. Unlike sympathetic neurons, ciliary neurons do not express dHand; noradrenergic gene expression is eventually lost but can be maintained by ectopic dHand expression. Together, these results demonstrate a common BMP dependence of sympathetic neurons and parasympathetic ciliary neurons and implicate dHand in the maintenance of noradrenergic gene expression in the autonomic nervous system.
Childhood Atopic Diseases and Early Life Circumstances: An Ecological Study in Cuba

Background Children are especially vulnerable during periods of resource shortage such as economic embargoes. They are likely to suffer most from poor nutrition, infectious diseases, and other ensuing short-term threats. Moreover, early life circumstances can have important consequences for long-term health. We examined the relationship between early childhood exposure to the Cuban economic situation in the nineties and the occurrence of atopic diseases later in childhood. Methodology/Principal Findings A cross-sectional study of 1321 primary schoolchildren aged 4–14 was conducted in two Cuban municipalities. Asthma, allergic rhinoconjunctivitis and atopic dermatitis were diagnosed using the International Study of Asthma and Allergies in Childhood questionnaire. Children were divided into three groups of exposure to the economic situation in the nineties according to birth date: (1) unexposed; (2) exposed during infancy; (3) exposed during infancy and early childhood. Associations were assessed using multiple logistic regression models. Exposure during infancy had a significant inverse association with the occurrence of asthma (OR 0.56, 95%CI 0.33–0.94) and allergic rhinoconjunctivitis (OR 0.46, 95%CI 0.25–0.85). The associations were stronger after longer exposure, i.e. during infancy and early childhood, for asthma (OR 0.40, 95% CI 0.17–0.95) and allergic rhinoconjunctivitis (OR 0.29, 95%CI 0.11–0.77). No significant associations were found for atopic dermatitis. Conclusions/Significance Exposure to the economic situation in the nineties during infancy and early childhood was inversely associated with asthma and allergic rhinoconjunctivitis occurrence later in childhood. We hypothesize that factors related to this period, such as infectious diseases and undernutrition, may have an attenuating effect on atopic disease development. The exact cause and underlying mechanisms need to be further elucidated.
Modified Ant Colony Clustering Method in Long-term Electrocardiogram Processing

The paper presents an application of a clustering technique inspired by ant colony metaheuristics. The paper addresses the problem of long-term (Holter) electrocardiogram data processing. Long-term recording produces a huge amount of biomedical data, which must be preprocessed prior to its presentation to the specialist. The paper also discusses relevant aspects improving the robustness, stability and convergence criteria of the method. The method is compared with well known clustering techniques (both classical and nature-inspired), first testing on the known dataset and finally applying them to the real ECG data records from the MIT-BIH database and outperforms the standard methods. Electrocardiogram data clustering can effectively reduce the amount of data presented to the cardiologist: cardiac arrhythmia and significant morphology changes in the ECG can be visually emphasized in a reasonable time. The final evaluation of the ECG recording must still be made by an expert.
Bacterial infection in scarring trachoma.

PURPOSE To assess whether non-chlamydial bacterial infection is associated with trachomatous scarring in adults. METHODS This was a case-control study of 360 cases with trachomatous scarring but without trichiasis, and 360 controls without scarring. All participants underwent clinical examination, and a swab was taken from the inferior conjunctival fornix. Samples were inoculated onto blood and chocolate agar later that day. RESULTS Bacterial isolates were identified in 54.0% of cases compared with 34.6% of controls (P < 0.001). A multivariate logistic regression model adjusted for age and lack of education showed that scarring was associated with the presence of commensal organisms (odds ratio [OR], 1.46; 95% confidence interval [CI], 1.01-2.09) and was strongly associated with the presence of pathogenic organisms (OR, 4.08; 95% CI, 1.59-10.45). There was an increasing prevalence of all bacterial isolates with increasing severity of scarring (P(trend) < 0.001). CONCLUSIONS Trachomatous scarring is strongly associated with non-chlamydial bacterial infection compared with controls. The role of such infection with regard to scarring progression should be investigated and may have important implications for trachoma control strategies and prevention of blindness.
Sargassum fusiforme Polysaccharide Rejuvenat es the Small Intestine in Mice Through Altering its Physiol ogy and Gut Microbiota Composition.

BACKGROUND AND OBJECTIVE Aging can result in a progressive decline in cellular protection and physiological function. The physiological status and microbiota of the intestine are intensively linked to the aging process. Numerous studies have suggested that Sargassum fusiforme polysaccharides possess antioxidant and antiaging activities. However, it remains unclear as to whether S. fusiforme polysaccharides can prevent the insult of oxidant and aging through modulating the physiological status and microbiota of the intestine. METHODS To assess the cytoprotective effect of S. fusiforme polysaccharides (SFPS) in the small intestine of mice embarking on the aging process, we compared the expressions of Nrf2 and several representative markers (SOD-2, CAT, NQO1 and HO-1) of the Nrf2/ARE signaling pathway in the small intestine of male ICR mice fed with a control diet with those of mice fed with a SFPS-containing diet. In addition, the overall compositional changes in the small intestine microbiota were determined by 16s rDNA sequencing followed by alpha and beta diversity analyses. RESULTS The results showed that dietary intake of SFPS could ameliorate the declined cytoprotective capacity of the small intestine by upregulating the Nrf2/ARE signaling pathway. Moreover, SFPS could partially rejuvenate the overall status of the small intestine microbiota. CONCLUSION The results suggested that dietary SFPS may promote the health condition of the small intestine, consequently leading to a healthy aging.
Evaluating environmental impacts of alternative construction waste management approaches using supply-chain-linked life-cycle analysis

Waste management in construction is critical for the sustainable treatment of building-related construction and demolition (C&D) waste materials, and recycling of these wastes has been considered as one of the best strategies in minimization of C&D debris. However, recycling of C&D materials may not always be a feasible strategy for every waste type and therefore recycling and other waste treatment strategies should be supported by robust decision-making models. With the aim of assessing the net carbon, energy, and water footprints of C&D recycling and other waste management alternatives, a comprehensive economic input–output-based hybrid life-cycle assessment model is developed by tracing all of the economy-wide supply-chain impacts of three waste management strategies: recycling, landfilling, and incineration. Analysis results showed that only the recycling of construction materials provided positive environmental footprint savings in terms of carbon, energy, and water footprints. Incineration is a better option as a secondary strategy after recycling for water and energy footprint categories, whereas landfilling is found to be as slightly better strategy when carbon footprint is considered as the main focus of comparison. In terms of construction materials’ environmental footprint, nonferrous metals are found to have a significant environmental footprint reduction potential if recycled.
Information as a Manifestation of Development

Information manifests a reduction in uncertainty or indeterminacy. As such it can emerge in two ways: by measurement, which involves the intentional choices of an observer; or more generally, by development, which involves systemically mutual (‘self-organizing’) processes that break symmetry. The developmental emergence of information is most obvious in ontogeny, but pertains as well to the evolution of ecosystems and abiotic dissipative structures. In this review, a seminal, well-characterized ontogenetic paradigm—the sea urchin embryo—is used to show how cybernetic causality engenders the developmental emergence of biological information at multiple hierarchical levels of organization. The relevance of information theory to developmental genomics is also discussed.
State estimation of walking phase and functional electrical stimulation by wearable device

Functional electrical stimulation (FES) is useful to improve the gait of patients with peroneal nerve palsy or spastic hemiparesis after stroke. So as to apply FES to such patients, we have to have estimators for detecting the timing of phase switching in walking motion. We designed a wearable device for state estimating of walking and functional electrical stimulation. We consider the implementation of artificial neural network (ANN) into the device, and propose a method for supervised learning of the ANN. Two experiments have been conducted to show the effectiveness of the wearable device. The accuracy of estimating the timing for FES is good enough for the practical application.
Shared workspace applications for collaboration in the large : A product – centered approach

Shared workspaces are often based on the presumption that the state of the work is cognitively accessible to all the workers. This assumption makes it difficult to use them for collaboration in the large. On the other hand, other support systems for collaboration in the large generally focus on the organizational aspects of the work and neglect the group–level requirements. In this paper we first introduce a classification of services provided by the existing shared workspace applications along three dimensions: group, activity, and product. We then motivate a product–centered approach to building SWAs. Using such an approach, the product dimension is in focus and the product is used to guide and support the collaborative work. We also introduce a list of services for product–centered SWAs that can improve the support provided for collaboration in the large.
Example-Based Logical Labeling of Document Title Page Images

This paper presents a flexible and effective example- based approach for labeling title pages which can be used for automated extraction of bibliographic data. The labels of interest are "title", "author", "abstract" and "affiliation". The method takes a set of labeled document layouts and a single unlabeled document layout as input and finds the best matching layout in the set. The labels of this layout are used to label the new layout. The similarity measure for layouts combines structural layout similarity and textural similarity on the block-level. Experimental results yield accuracy rates from 94.8% to 99.6% obtained on the publicly available MARG dataset. This shows that our lightweight method has equivalent and partially better performance when compared to other more complex labeling methods known from the literature.
Allosteric ring assembly and chemo-mechanical melting by the interaction between 5′-phosphate and λ exonuclease

Phosphates along the DNA function as chemical energy frequently used by nucleases to drive their enzymatic reactions. Exonuclease functions as a machine that converts chemical energy of the phosphodiester-chain into mechanical work. However, the roles of phosphates during exonuclease activities are unknown. We employed λ exonuclease as a model system and investigated the roles of phosphates during degradation via single-molecule fluorescence resonance energy transfer (FRET). We found that 5′ phosphates, generated at each cleavage step of the reaction, chemo-mechanically facilitate the subsequent post-cleavage melting of the terminal base pairs. Degradation of DNA with a nick requires backtracking and thermal fraying at the cleavage site for re-initiation via the formation of a catalytically active complex. Unexpectedly, we discovered that a phosphate of a 5′ recessed DNA acts as a hotspot for an allosteric trimeric-ring assembly without passing through the central channel. Our study provides new insight into the versatile roles of phosphates during the processive enzymatic reaction.