Miracle-dz/UniFAR-FTUs huggingface dataset:
Extracellular conversion of adiponectin hexamers into trimers

Adiponectin is an adipocyte-secreted hormone that exists as trimers, hexamers and larger species collectively referred to as HMW (high-molecular-weight) adiponectin. Whether hexamers or HMW adiponectin serve as precursors for trimers outside the circulation is currently unknown. Here, we demonstrate that adiponectin trimers can be generated from larger oligomers secreted from primary rat adipose cells or differentiated 3T3-L1 adipocytes. Purified hexameric, but not HMW, adiponectin converted into trimers in conditioned media separated from 3T3-L1 adipocytes or, more efficiently, when enclosed in the dialysis membrane in the presence of adipocytes. Several lines of evidence indicate that the conversion is mediated by an extracellular redox system. First, N-terminal epitope-tagged hexamers converted into trimers without proteolytic removal of the tag. Secondly, appearance of trimers was associated with conversion of disulfide-bonded dimers into monomers. Thirdly, thiol-reactive agents inhibited conversion into trimers. Consistent with a redox-based mechanism, purified hexamers reductively converted into trimers in defined glutathione redox buffer with reduction potential typically found in the extracellular environment while the HMW adiponectin remained stable. In addition, conversion of hexamers into trimers was enhanced by NADPH, but not by NADP+. Collectively, these data strongly suggest the presence of an extracellular redox system capable of converting adiponectin oligomers.
Top Carnivores in the Suburbs? Ecological and Conservation Issues Raised by Colonization of North eastern North America by Coyotes

J a handful of individual members of a population of top predators—wolves and tigers, orcas, and great white sharks, for example—hold the potential to disproportionately influence animal and plant communities. The importance of this phenomenon, known as a “top-down”effect, has been demonstrated in several recent studies. For example, as few as four killer whales may be responsible for a shift in 800 kilometers of Alaskan near-shore community structure, from a structure dominated by kelp forests with few herbivores to one with high numbers of sea urchins and low kelp densities (Estes et al. 1998). Similarly, just two or three wolf packs indirectly control tree community organization by regulating moose numbers in 544-km2 Isle Royale, Michigan (Post et al. 1999). In coastal southern California, the presence or absence of coyotes in patches of sage–scrub habitat directly controls the distribution and abundance of smaller carnivores, which in turn alter scrub-breeding bird communities (Crooks and Soule 1999). Today in northeastern North America, the top terrestrial predator is the coyote, Canis latrans, an immigrant to the region that is anything but rare. Historically, the species was unknown to European settlers of eastern North America, who were more concerned with the presence of wolves and cougars. Coyotes were a predator of the Great Plains. Lewis and Clark didn’t catch their first glimpse of a coyote until 1804, when they reached the eastern edge of present-day Nebraska (Ambrose 1996). Times have changed. Over the past two centuries the coyote has dramatically expanded its geographical range and is now ubiquitous throughout northeastern North America (Figure 1; Parker 1995, Gompper 2002). It has even colonized seemingly isolated geographical regions such as Cape Cod and the Elizabeth Islands of Massachusetts, Cape Breton Island, Prince Edward Island, and Newfoundland of Atlantic Canada, as well as urban habitats such as parts of New York City. The culmination of this range expansion may arguably be the capture of a wild coyote in Central Park in the heart of Manhattan in 1999 (Martin 1999).
The Cytokine Odyssey 2001, a joint meeting of the Society of Leukocyte Biology and the International Cytokine Society

The Cytokine Odyssey 2001 was held at the Outrigger Wailea Resort in Maui, Hawaii, USA. The meeting, jointly sponsored by the International Cytokine Society (ICS, 9th Annual Meeting) and the Society of Leukocyte Biology (SLB, 35th Annual Meeting), was organised by Carl Ware (Chair) from the La Jolla Institute for Allergy and Immunology (La Jolla, USA) and Thomas Hamilton (Co-Chair) from the Cleveland Clinic Foundation (Cleveland, USA). This international conference was designed to bring together leading investigators in molecular and cellular biology, physiology and genetics, interested in cytokines and cells of the immune system. This forum was aimed to assess the impact of this expanding science on new approaches to disease intervention [1].
Strain-Dependent Induction of Enterocyte Apoptosis by Giardia lamblia Disrupts Epithelial Barrier Function in a Caspase-3-Dependent Manner

ABSTRACT We recently demonstrated that Giardia lamblia rearranges cytoskeletal proteins and reduces transepithelial electrical resistance. The effect of G. lamblia on enterocyte apoptosis is unknown, and a possible link between microbially induced enterocyte apoptosis and altered epithelial permeability has yet to be established. The aim of this study was to assess whether G. lamblia induces enterocyte apoptosis in duodenal epithelial monolayers and whether this effect increases epithelial permeability. Monolayers of nontransformed human duodenal epithelial cells were incubated with sonicated or live G. lamblia trophozoites (NF, S2, WB, or PB strains) for 8, 24, and 48 h. Cell cultures were assessed for apoptosis by Hoechst fluorescence staining, enzyme-linked immunosorbent assay for apoptotic nucleosomes, and electron microscopy. In separate experiments, monolayers were pretreated with or without 120 μM caspase-3 inhibitor (Z-DEVD-FMK) for 1 h and were assessed for production of apoptotic nucleosomes, tight junctional integrity (with fluorescent ZO-1 staining followed by confocal laser microscopy), and transepithelial permeability for fluorescein isothiocyanate-dextran. G. lamblia strains NF and S2, but not strains WB or PB, induced enterocyte apoptosis within the monolayers, and this effect was inhibited by Z-DEVD-FMK pretreatment. Using the G. lamblia NF isolate, additional experiments investigated the possible link between enterocyte apoptosis and altered epithelial permeability. G. lamblia NF disrupted tight junctional ZO-1 and increased epithelial permeability, but these effects were also prevented by pretreatment with the caspase-3 inhibitor. These findings indicate that strain-dependent induction of enterocyte apoptosis may contribute to the pathogenesis of giardiasis. This effect is responsible for a loss of epithelial barrier function by disrupting tight junctional ZO-1 and increasing permeability in a caspase-3-dependent manner.
Joint Transport, Routing and Spectrum Sharing Optimization for Wireless Networks with Frequency-Agile Radios

In this paper, we describe and analyze the design of a joint Transport, routing and spectrum sharing (TRSS) optimization algorithm for wireless networks with frequency- agile radios. We capitalize on the spectrum agility of modern radios which can configure both the central frequency and spectrum width of their channels. TRSS is fully distributed and is executed in two phases. In the first phase a dual driven optimizer is used to jointly adjust end-to-end transmission rate, flow-routing and spectrum width allocation. In the second phase, an innovative timing-window based spectrum access scheme is used for link layer scheduling. Analytical and simulation results show the effectiveness of our design.
Hodge integrals, partition matrices, and the λ g conjecture

We prove a closed formula for integrals of the cotangent line classes against the top Chern class of the Hodge bundle on the moduli space of stable pointed curves. These integrals are computed via relations obtained from virtual localization in Gromov-Witten theory. An analysis of several natural matrices indexed by partitions is required.
Factorization of EMG via muscle synergies in walking task: Evaluation of intra-subject and inter-subject variability

Muscle synergies have reached great popularity in the last years, to explain how the central nervous system (CNS) reduces the dimensionality of muscle activation in the execution of a specific motor task. The aim of the present paper is the quantification of the intra-subject and inter-subject variability related to the factorization of EMG data via muscle synergies. The activity of twelve muscles of the dominant leg were recorded in six healthy subjects, who were asked to perform five repetitions of level walking task at self-selected speed. A non-negative matrix factorization was performed to extract the muscle synergies. The goodness of the EMG reconstruction was assessed via the Variability Account For (VAF) between acquired and reconstructed data, for both global data and each muscle. The reliability of these parameters was evaluated through the Intra-class Correlation Coefficient (ICC) and the intra-subject and inter-subject variability of the same parameters via the Coefficient of Variation (CoV). Three, four and five muscle resulted the number of synergies selected at least in one repetition for one subject. ICC was excellent for the global reconstruction, while from poor to excellent reliability was shown for the reconstruction of each muscle. The CoV of the global reconstruction was always lower than 1.8%, decreasing with the number of synergies. By considering each muscle individually, the intra-subject variability was rarely above the 10.0% and only for the 3-synergies model. The same trend was confirmed by computing the inter-subject variability, never above the 12.6%, 6.0 % and 4.8 % and related to mean values greater than 77.8 %, 81.9 % and 92.3 % for 3-, 4- and 5- synergies models, respectively. Consequently, 4- and 5- synergies models allow to consistently reconstruct the EMG signals across repetitions and subjects. These results strengthen the possibility to use the EMG factorization via muscle synergies to describe the behavior of the CNS in the achievement of a motor task.
Imaging the Endothelial Glycocalyx In Vitro by Rapid Freezing/Freeze Substitution Transmission Electron Microscopy

Objective—Recent publications questioned the validity of endothelial cell (EC) culture studies of glycocalyx (GCX) function because of findings that GCX in vitro may be substantially thinner than GCX in vivo. The assessment of thickness differences is complicated by GCX collapse during dehydration for traditional electron microscopy. We measured in vitro GCX thickness using rapid freezing/freeze substitution (RF/FS) transmission electron microscopy (TEM), taking advantage of the high spatial resolution provided by TEM and the capability to stably preserve the GCX in its hydrated configuration by RF/FS. Methods and Results—Bovine aortic EC (BAEC) and rat fat pad EC were subjected to conventional or RF/FS-TEM. Conventionally preserved BAEC GCX was ≈0.040 &mgr;m in thickness. RF/FS-TEM revealed impressively thick BAEC GCX of ≈11 &mgr;m and rat fat pad EC GCX of ≈5 &mgr;m. RF/FS-TEM also discerned GCX structure and thickness variations due to heparinase III enzyme treatment and extracellular protein removal, respectively. Immunoconfocal studies confirmed that the in vitro GCX is several micrometers thick and is composed of extensive and well-integrated heparan sulfate, hyaluronic acid, and protein layers. Conclusion—New observations by RF/FS-TEM reveal substantial GCX layers on cultured EC, supporting their continued use for fundamental studies of GCX and its function in the vasculature.
Regret and the rationality of choices

Regret helps to optimize decision behaviour. It can be defined as a rational emotion. Several recent neurobiological studies have confirmed the interface between emotion and cognition at which regret is located and documented its role in decision behaviour. These data give credibility to the incorporation of regret in decision theory that had been proposed by economists in the 1980s. However, finer distinctions are required in order to get a better grasp of how regret and behaviour influence each other. Regret can be defined as a predictive error signal but this signal does not necessarily transpose into a decision-weight influencing behaviour. Clinical studies on several types of patients show that the processing of an error signal and its influence on subsequent behaviour can be dissociated. We propose a general understanding of how regret and decision-making are connected in terms of regret being modulated by rational antecedents of choice. Regret and the modification of behaviour on its basis will depend on the criteria of rationality involved in decision-making. We indicate current and prospective lines of research in order to refine our views on how regret contributes to optimal decision-making.
Sliding mode control for a flexible transmission system

In this paper, a robust sliding mode control for a flexible transmission system is presented. This system has two very oscillatory vibration modes subject to large load variation which makes the control of it difficult. A set of design specification in time domain is to be met by a single controller on each of the three main plant models. Furthermore the tracking problem in the presence of disturbance and load variation is investigated. Results show good performance of the proposed controller. In this approach, in order to estimate the hidden states of the flexible transmission system, an observer based on sliding mode control is used.
Polymorphisms in Catechol-O-Methyltransferase Modify Treatment Effects of Aspirin on Risk of Cardiovascular Disease

Objective— Catechol-O-methyltransferase (COMT), a key enzyme in catecholamine metabolism, is implicated in cardiovascular, sympathetic, and endocrine pathways. This study aimed to confirm preliminary association of COMT genetic variation with incident cardiovascular disease (CVD). It further aimed to evaluate whether aspirin, a commonly used CVD prevention agent, modified the potential association of COMT with incident CVD. Approach and Results— We examined COMT polymorphism rs4680 (MAF [minor allele frequency], 0.47), encoding a nonsynonymous methionine-to-valine substitution, in the Women’s Genome Health Study (WGHS), a large population-based cohort of women with randomized allocation to aspirin or vitamin E when compared with placebo and 10-year follow-up. Rs4680 effects were confirmed with COMT polymorphism rs4818 and also examined in Coronary ARtery DIsease Genome-wide Replication and Meta-analysis/The Coronary Artery Disease Genetics Consortium, consortia for genome-wide association studies of coronary artery disease. Among WGHS women allocated to placebo (135 events/n=5811), the rs4680 valine allele was protective against incident CVD relative to the methionine (hazard ratio [HR; 95% confidence interval {CI}], 0.66 [0.51–0.84]; P=0.0007); an association also observed in Coronary ARtery DIsease Genome-wide Replication and Meta-analysis and The Coronary Artery Disease Genetics Consortium (combined P=2.4×10−5). In the WGHS, the rs4680 association was abolished by randomized allocation to aspirin, such that valine/valine women experienced higher CVD rates with aspirin allocation when compared with placebo (HR [95% CI], 1.85 [1.05–3.25]; P=0.033), whereas methionine/methionine women experienced lower rates (HR [95% CI], 0.60 [0.39–0.93]; P=0.023). Allocation to vitamin E also conferred higher but nonsignificant CVD rates on valine/valine (HR [95% CI], 1.50 [0.83–2.70]; P=0.180) when compared with significantly lower rates on methionine/methionine (HR [95% CI], 0.53 [0.34–0.84]; P=0.006) women. Rs4818 results were similar. Conclusions— Common COMT polymorphisms were associated with incident CVD, and this association was modified by randomized allocation to aspirin or vitamin E. Replication of these findings is required.
Clustering Distributed Short Time Series with Dense Patterns

The clustering of genes with similar temporal profiles is an important task in gene expression data analysis. Current approaches to the clustering of sparse gene expression data with temporal information suffer from their at least quadratic complexity in the number of clusters, the number of genes, or both, and are not distributed. In this paper, we present the first distributed and density-based approach to short time series clustering, called DTSCluster, which is suitable for gene expression data. DTSCluster identifies dense patterns in the distributed datasets and uses them to generate the time series clusters. The comparative experimental results revealed that DTSCluster is scalable in the dataset size with linear complexity in time and space, and outperforms other representative approaches in terms of cluster validation with the silhouette index as well. The distributed scenario also opens up the opportunity for collaborative data mining between different gene expression data holders.
Co-Occurring Psychiatric Symptoms in Opioid-Dependent Women: The Prevalence of Antenatal and Postnatal Depression

Background: Despite the high prevalence of psychiatric symptoms in substance-dependent women, little evidence is available on postpartum depression in this population. Objectives: To determine whether demographic variables and prenatal depression predict postpartum depression and select substance abuse treatment outcomes in a sample of pregnant women. Methods: A retrospective chart review was conducted on 125 pregnant women enrolled in a comprehensive substance abuse treatment program. Data on demographic variables, prenatal care attendance, urine drug screen (UDS) results, and psychiatric symptoms were abstracted from patient medical and substance abuse treatment charts. The Postpartum Depression Screening Scale (PDSS) was administered 6 weeks post-delivery. Multiple linear regression was conducted to identify predictors of prenatal care attendance and total PDSS scores at 6 weeks postpartum. Multiple logistic regression was used to examine predictors of positive UDS at delivery. Results: Nearly one-third (30.4%) of the sample screened positive for moderate or severe depression at treatment entry. Psychiatric symptoms did not predict either prenatal care compliance or UDS results at delivery. Almost half of the sample (43.7%) exhibited postpartum depression at 6 weeks post-delivery. No demographic variables correlated with incidence of postnatal depression. Only antenatal depression at treatment entry predicted PDSS scores. Conclusion: Prevalence of antenatal psychiatric disorders and postpartum depression was high in this sample of women seeking substance abuse treatment. Results support prior history of depression as a predictor of risk for developing postpartum depression. Scientific Significance: Routine screening for perinatal and postpartum depression is indicated for women diagnosed with substance abuse disorders.
Protein Surface Matching by Combining Local and Global Geometric Information

Comparison of the binding sites of proteins is an effective means for predicting protein functions based on their structure information. Despite the importance of this problem and much research in the past, it is still very challenging to predict the binding ligands from the atomic structures of protein binding sites. Here, we designed a new algorithm, TIPSA (Triangulation-based Iterative-closest-point for Protein Surface Alignment), based on the iterative closest point (ICP) algorithm. TIPSA aims to find the maximum number of atoms that can be superposed between two protein binding sites, where any pair of superposed atoms has a distance smaller than a given threshold. The search starts from similar tetrahedra between two binding sites obtained from 3D Delaunay triangulation and uses the Hungarian algorithm to find additional matched atoms. We found that, due to the plasticity of protein binding sites, matching the rigid body of point clouds of protein binding sites is not adequate for satisfactory binding ligand prediction. We further incorporated global geometric information, the radius of gyration of binding site atoms, and used nearest neighbor classification for binding site prediction. Tested on benchmark data, our method achieved a performance comparable to the best methods in the literature, while simultaneously providing the common atom set and atom correspondences.
3D illustrative effects for animating line drawings

Most illustrative techniques used in non-photorealistic rendering to date apply a rendering style to objects or a scene and alter the appearance of this style by employing illumination or depth cueing. However for generating high quality illustrations this approach relies almost entirely on smart placement of light sources. We introduce the concept of illustrative effects to describe the workings of illustrative techniques that rely on spatial location rather than just illumination or depth. Although the rendering style is still object-dependent, this technique allows us to visualize or emphasize parts of objects or the whole scene without being limited by the scene's object decomposition. The approach also enforces the decoupling of the model and its animation from the visualization task. We demonstrate our approach using a sample collection of illustrative effects applied to line drawings. A uniform set of tools to manipulate these effects is provided.
Frontiers in Integrative Neuroscience Integrative Neuroscience Materials and Methods Subjects

These data suggest that NA, along with ABL and afferent regions in lateral OFC, might be part of a circuit critical for the use of cue-evoked information about expected outcomes to guide behavior. We tested this hypothesis by using a Pavlovian reinforcer devaluation task. In the critical extinction probe test, rats must use a representation of the outcome evoked by the CS+. To adaptively guide behavior, this CS+ evoked representation must be updated to reflect the current value of the outcome. Previous evidence has demonstrated that OFC and ABL are essential to updating and using the current value of the outcome to guide behavior. Here, we tested the role of NA core and shell in the Pavlovian reinforcer devaluation task and found pre-training lesions disrupted the ability of the animal to alter conditioned responding based on the current value of the outcome. weighing between 275 to 325 g on arrival, were individually housed and were given ad libitum access to food and water, except during testing. Beginning 5 days before testing and continuing until testing ended, rats were food deprived to 85% of their baseline body weight. The animals were placed on a 12-h light/ dark cycle and tested only during the light cycle. Rats were tested
A feasible region for meeting aperiodic end-to-end deadlines in resource pipelines

This paper generalizes the notion of utilization bounds for schedulability of aperiodic tasks to the case of distributed resource systems. In the basic model, aperiodically arriving tasks are processed by multiple stages of a resource pipeline within end-to-end deadlines. The authors consider a multidimensional space in which each dimension represents the instantaneous utilization of a single stage. A feasible region is derived in this space such that all tasks meet their deadlines as long as pipeline resource consumption remains within the feasible region. The feasible region is a multidimensional extension of the single-resource utilization bound giving rise to a bounding surface in the utilization space rather than a scalar bound. Extensions of the analysis are provided to nonindependent tasks and arbitrary task graphs. We evaluate the performance of admission control using simulation, as well as demonstrate the applicability of these results to task schedulability analysis in the total ship computing environment envisioned by the US navy.