Miracle-dz/UniFAR-FTUs huggingface dataset:
Relative roles of TGF-β1 and Wnt in the systemic regulation and aging of satellite cell responses

Muscle stem (satellite) cells are relatively resistant to cell‐autonomous aging. Instead, their endogenous signaling profile and regenerative capacity is strongly influenced by the aged P‐Smad3, differentiated niche, and by the aged circulation. With respect to muscle fibers, we previously established that a shift from active Notch to excessive transforming growth factor‐beta (TGF‐β) induces CDK inhibitors in satellite cells, thereby interfering with productive myogenic responses. In contrast, the systemic inhibitor of muscle repair, elevated in old sera, was suggested to be Wnt. Here, we examined the age‐dependent myogenic activity of sera TGF‐β1, and its potential cross‐talk with systemic Wnt. We found that sera TGF‐β1 becomes elevated within aged humans and mice, while systemic Wnt remained undetectable in these species. Wnt also failed to inhibit satellite cell myogenicity, while TGF‐β1 suppressed regenerative potential in a biphasic fashion. Intriguingly, young levels of TGF‐β1 were inhibitory and young sera suppressed myogenesis if TGF‐β1 was activated. Our data suggest that platelet‐derived sera TGF‐β1 levels, or endocrine TGF‐β1 levels, do not explain the age‐dependent inhibition of muscle regeneration by this cytokine. In vivo, TGF‐β neutralizing antibody, or a soluble decoy, failed to reduce systemic TGF‐β1 and rescue myogenesis in old mice. However, muscle regeneration was improved by the systemic delivery of a TGF‐β receptor kinase inhibitor, which attenuated TGF‐β signaling in skeletal muscle. Summarily, these findings argue against the endocrine path of a TGF‐β1‐dependent block on muscle regeneration, identify physiological modalities of age‐imposed changes in TGF‐β1, and introduce new therapeutic strategies for the broad restoration of aged organ repair.
Digital elevation model generation from satellite interferometric synthetic aperture radar

An accurate digital elevation model (DEM) is a critical data set for characterizing the natural landscape, monitoring natural hazards, and georeferencing satellite imagery. The ideal interferometric synthetic aperture radar (InSAR) configuration for DEM production is a single-pass two-antenna system. Repeat-pass single-antenna satellite InSAR imagery, however, also can be used to produce useful DEMs. DEM generation from InSAR is advantageous in remote areas where the photogrammetric approach to DEM generation is hindered by inclement weather conditions. There are many sources of errors in DEM generation from repeat-pass InSAR imagery, for example, inaccurate determination of the InSAR baseline, atmospheric delay anomalies, and possible surface deformation because of tectonic, volcanic, or other sources during the time interval spanned by the images. This chapter presents practical solutions to identify and remove various artifacts in repeat-pass satellite InSAR images to generate a high-quality DEM.
Multiple Apoptotic Caspase Cascades Are Required in Nonapoptotic Roles for Drosophila Spermatid Individualization

Spermatozoa are generated and mature within a germline syncytium. Differentiation of haploid syncytial spermatids into single motile sperm requires the encapsulation of each spermatid by an independent plasma membrane and the elimination of most sperm cytoplasm, a process known as individualization. Apoptosis is mediated by caspase family proteases. Many apoptotic cell deaths in Drosophila utilize the REAPER/HID/GRIM family proapoptotic proteins. These proteins promote cell death, at least in part, by disrupting interactions between the caspase inhibitor DIAP1 and the apical caspase DRONC, which is continually activated in many viable cells through interactions with ARK, the Drosophila homolog of the mammalian death-activating adaptor APAF-1. This leads to unrestrained activity of DRONC and other DIAP1-inhibitable caspases activated by DRONC. Here we demonstrate that ARK- and HID-dependent activation of DRONC occurs at sites of spermatid individualization and that all three proteins are required for this process. dFADD, the Drosophila homolog of mammalian FADD, an adaptor that mediates recruitment of apical caspases to ligand-bound death receptors, and its target caspase DREDD are also required. A third apoptotic caspase, DRICE, is activated throughout the length of individualizing spermatids in a process that requires the product of the driceless locus, which also participates in individualization. Our results demonstrate that multiple caspases and caspase regulators, likely acting at distinct points in time and space, are required for spermatid individualization, a nonapoptotic process.
Melatonin administration does not alter muscle glycogen concentration during recovery from exhaustive exercise in rats

Abstract The purpose of this study was to investigate the effect of melatonin administration on muscle glycogen concentration during recovery after exhaustive swimming exercise in sedentary and trained rats. Male Wistar rats were assigned to one of four groups: sedentary control (C), sedentary melatonin-injected (M), exercise-trained (T), and trained and melatonin-injected (MT) groups. Exercise-trained groups were subjected to six weeks of swimming exercise. All rats completed an exhaustive swimming exercise. Two daily subcutaneous injections of melatonin at a dose of 3 mg·kg−1 were given to the rats in the M and MT groups immediately after the exhaustive exercise. Plasma melatonin, glucose and lactate concentrations, and glycogen concentrations of the soleus and epitrochlearis muscle tissues were measured after exhaustive exercise. Plasma lactate concentration was significantly lower in the T and MT groups than in the C group. Plasma melatonin concentration was higher in the supplemented groups than in the C group. Plasma glucose concentration was significantly higher in the T and MT groups than in the C group. Both epitrochlearis and soleus muscle glycogen concentrations were higher in the trained groups than in the C group. In conclusion, although exercise training results in improvement in muscle glycogen, exogenous melatonin administration after exhaustive exercise did not restore the glycogen concentrations in fast- or slow-twitch muscle tissues.
Robust mesh reconstruction from unoriented noisy points

We present a robust method to generate mesh surfaces from unoriented noisy points in this paper. The whole procedure consists of three steps. Firstly, the normal vectors at points are evaluated by a highly robust estimator which can fit surface corresponding to less than half of the data points and fit data with multi-structures. This benefits us with the ability to well reconstruct the normal vectors around sharp edges and corners. Meanwhile, clean point cloud equipped with piecewise normal is obtained by projecting points according to the robust fitting. Secondly, an error-minimized subsampling is applied to generate a well-sampled point cloud. Thirdly, a combinatorial approach is employed to reconstruct a triangular mesh connecting the down-sampled points, and a polygonal mesh which preserves sharp features is constructed by the dual-graph of triangular mesh. Parallelization method of the algorithm on a consumer PC using the architecture of GPU is also given.
Domain-specific vs. Uniform Modeling for Coreference Resolution

Several corpora annotated for coreference have been made available in the past decade. These resources differ with respect to their size and the underlying structure: the number of domains and their similarity. Our study compares domain-specific models, learned from small heterogeneous subsets of the investigated corpora, against uniform models, that utilize all the available data. We show that for knowledge-poor baseline systems, domain-specific and uniform modeling yield same results. Systems, relying on large amounts of linguistic knowledge, however, exhibit differences in their performance: with all the designed features in use, domain-specific models suffer from over-fitting, whereas with pre-selected feature sets they tend to outperform union models.
Single voltage‐dependent potassium channels in rat peripheral nerve membrane.

1. Voltage‐dependent potassium channels were investigated in rat axonal membrane by means of the patch‐clamp recording technique. Three different types of channels (F, I and S) have been characterized on the basis of their single‐channel conductance, activation, deactivation and inactivation properties. 2. The fast (F) channels were activated smoothly at potentials (E) between ‐50 and 50 mV (E50 = 4.6 mV). They had a conductance of 55 pS for inward current and 30 pS for outward current in solutions containing 155 mM K+ (high K+) on both sides of the membrane at 21‐23 degrees C. The F‐channels demonstrated the fastest deactivation, within 1‐2 ms, and inactivated in a few hundreds of milliseconds. The time constant of inactivation was 143 ms at E = +40 mV. 3. The intermediate (I) channels activated steeply between E = ‐70 and ‐50 mV (E50 = ‐64.2 mv) and had a single‐channel conductance of 33 pS for inward and 18 ps for outward currents. The I‐channels deactivated with intermediate kinetics with the time constants of 20.4 ms and 10.1 ms at E = ‐80 mV and E = ‐100 mV, respectively. Complete inactivation of the channels developed over tens of seconds. The time constant of inactivation was 7.4 s at E = +40 mV. 4. The slow (S) channels were active at potentials positive to ‐90 mV. Their conductance was 10 pS for inward currents. The time constant of activation of the S‐channels was strongly potential dependent. At a holding potential of ‐100 mV the channels deactivated during a long time interval between 30 ms and 1 s, producing long‐lasting tail currents. The mean time constant of deactivation for S‐channels was 129 ms. 5. The conductances of F‐ and I‐channels measured under normal physiological conditions (Ringer solution in bath) were 17 and 10 pS, respectively. 6. Tetraethylammonium (TEA), the classic blocker of potassium channels, suppressed F‐, I‐ and S‐channels. It gradually reduced the apparent amplitude of unitary currents in a dose‐dependent manner with IC50 equal to 1.2 mM for F‐channels, 0.6 mM for I‐channels and 1.4 mM for S‐channels. Dendrotoxin (DTX), a toxin from the green mamba snake, considerably inhibited the I tail currents at nanomolar concentrations (IC50 = 2.8 nM) while the amplitudes of single I‐channel currents were not affected. 7. The K+ channels of F, I and S types form the basis of the potassium conductivity in mammalian peripheral myelinated axon. (ABSTRACT TRUNCATED AT 400 WORDS)
Changes in Rat Adipocyte and Liver Glucose Metabolism Following Repeated Restraint Stress

Rats exposed to repeated restraint weigh less than controls even 8 weeks after stress. Stress-induced weight loss is lean tissue, but the post-stress difference in weight between control and restrained rats is lean and fat mass. Whole-body glucose clearance is enhanced 1 day after stress, but adipocyte glucose utilization is inhibited and muscle glucose transport is unchanged. The studies described here demonstrated that glucose transport was increased in both restrained and pair-fed rats, but that glycogen synthesis was increased only in restrained rats, which may account for the improved whole-body glucose clearance. Adipocyte glucose transport was inhibited and adipose plasma membrane β-adrenergic receptor number was increased 1 day post-stress in restrained rats when weight loss was lean tissue, but were not different from control rats 5 days post-stress, when both fat and lean tissue were reduced. Thus, repeated restraint induces reversible changes in adipocyte metabolism that may represent a transition from the catabolic state of stress to a new energetic equilibrium in rats that maintain a reduced body weight for an extended period of time.
Design of Broadband Mushroom Antenna Using Machine-Learning-Based Optimization

This paper presents an optimization method using machine learning for a broadband metasurface mushroom antenna. The proposed antenna evolves from the metasurface mushroom antenna with an array of patch cells. By cutting the patch cells and changing the positions of shorting vias, the impedance bandwidth of the proposed antenna is broadened. An artificial neural network (ANN) is proposed to build a model for antenna optimization. The input data of the proposed ANN model are the desired reflection coefficients, and the output data are geometry parameters of the metasurface mushroom antenna. The proposed ANN model can predict the geometry parameters, which make the antenna reach the targeted performance. Measurement results show that the $\vert \mathrm{S}_{\mathbf{11}}\vert \lt \mathrm{-10-dB}$ impedance bandwidth of the proposed antenna is 38.6%, ranging from 4.6 GHz to 6.8 GHz. Compared to the original metasurface mushroom antenna, the impedance bandwidth of the optimized antenna is improved from 25% to 38.6%.
Intimate Communities: Representation and Social Transformation in Women's College Fiction, 1895–1910

The many popular representations of student life at women s colleges produced in the United States during the Progressive Era are examined. The college woman was described and defined in a period when women s higher education was still socially suspect. While other scholars have argued that the Progressive Era was the golden age for women s single-sex education, pointing to the many positive depictions of the women s college student, Inness suggests that these representations actually helped to perpetuate the status quo and did little to advance women s social rights. "
Estimating Error in Using Residential Outdoor PM2.5 Concentrations as Proxies for Personal Exposures: A Meta-analysis

Background Studies examining the health effects of particulate matter ≤ 2.5 μm in aerodynamic diameter (PM2.5) commonly use ambient PM2.5 concentrations measured at distal monitoring sites as proxies for personal exposure and assume spatial homogeneity of ambient PM2.5. An alternative proxy—the residential outdoor PM2.5 concentration measured adjacent to participant homes—has few advantages under this assumption. Objectives We systematically reviewed the correlation between residential outdoor PM2.5 and personal PM2.5 (r̄j) as a means of comparing the magnitude and sources of measurement error associated with their use as exposure surrogates. Methods We searched seven electronic reference databases for studies of the within-participant residential outdoor-personal PM2.5 correlation. Results The search identified 567 candidate studies, nine of which were abstracted in duplicate, that were published between 1996 and 2008. They represented 329 nonsmoking participants 6–93 years of age in eight U.S. cities, among whom r̄j was estimated (median, 0.53; range, 0.25–0.79) based on a median of seven residential outdoor-personal PM2.5 pairs per participant. We found modest evidence of publication bias (symmetric funnel plot; pBegg = 0.4; pEgger = 0.2); however, we identified evidence of heterogeneity (Cochran’s Q-test p = 0.05). Of the 20 characteristics examined, earlier study midpoints, eastern longitudes, older mean age, higher outdoor temperatures, and lower personal-residential outdoor PM2.5 differences were associated with increased within-participant residential outdoor-personal PM2.5 correlations. Conclusions These findings were similar to those from a contemporaneous meta-analysis that examined ambient-personal PM2.5 correlations (r̄j = median, 0.54; range, 0.09–0.83). Collectively, the meta-analyses suggest that residential outdoor-personal and ambient-personal PM2.5 correlations merit greater consideration when evaluating the potential for bias in studies of PM2.5-mediated health effects.
Nitric Oxide Inhibits IFN-α Production of Human Plasmacytoid Dendritic Cells Partly via a Guanosine 3′,5′-Cyclic Monophosphate-Dependent Pathway1

NO, a free radical gas, is known to be critically involved not only in vascular relaxation but also in host defense. Besides direct bactericidal effects, NO has been shown to inhibit Th1 responses and modulate immune responses in vivo, although the precise mechanism is unclear. In this study, we examined the effect of NO on human plasmacytoid dendritic cells (pDCs) to explore the possibility that NO might affect innate as well as adaptive immunity through pDCs. We found that NO suppressed IFN-α production of pDCs partly via a cGMP-dependent mechanism, which was accompanied by down-regulation of IFN regulatory factor 7 expression. Furthermore, treatment of pDCs with NO decreased production of IL-6 and TNF-α and up-regulated OX40 ligand expression. In accordance with these changes, pDCs treated with NO plus CpG-oligodeoxynucleotide AAC-30 promoted differentiation of naive CD4+ T cells into a Th2 phenotype. Moreover, pDCs did not express inducible NO synthase even after treatment with AAC-30, LPS, and several cytokines. These results suggest that exogenous NO and its second messenger, cGMP, alter innate as well as adaptive immune response through modulating the functions of pDCs and may be involved in the pathogenesis of certain Th2-dominant allergic diseases.
Toxicity Testing in the 21st Century: Defining New Risk Assessment Approaches Based on Perturbation of Intracellular Toxicity Pathways

The approaches to quantitatively assessing the health risks of chemical exposure have not changed appreciably in the past 50 to 80 years, the focus remaining on high-dose studies that measure adverse outcomes in homogeneous animal populations. This expensive, low-throughput approach relies on conservative extrapolations to relate animal studies to much lower-dose human exposures and is of questionable relevance to predicting risks to humans at their typical low exposures. It makes little use of a mechanistic understanding of the mode of action by which chemicals perturb biological processes in human cells and tissues. An alternative vision, proposed by the U.S. National Research Council (NRC) report Toxicity Testing in the 21st Century: A Vision and a Strategy, called for moving away from traditional high-dose animal studies to an approach based on perturbation of cellular responses using well-designed in vitro assays. Central to this vision are (a) “toxicity pathways” (the innate cellular pathways that may be perturbed by chemicals) and (b) the determination of chemical concentration ranges where those perturbations are likely to be excessive, thereby leading to adverse health effects if present for a prolonged duration in an intact organism. In this paper we briefly review the original NRC report and responses to that report over the past 3 years, and discuss how the change in testing might be achieved in the U.S. and in the European Union (EU). EU initiatives in developing alternatives to animal testing of cosmetic ingredients have run very much in parallel with the NRC report. Moving from current practice to the NRC vision would require using prototype toxicity pathways to develop case studies showing the new vision in action. In this vein, we also discuss how the proposed strategy for toxicity testing might be applied to the toxicity pathways associated with DNA damage and repair.
treeClust: An R Package for Tree-Based Clustering Dissimilarities

This paper describes treeClust, an R package that produces dissimilarities useful for clustering. These dissimilarities arise from a set of classification or regression trees, one with each variable in the data acting in turn as a the response, and all others as predictors. This use of trees produces dissimilarities that are insensitive to scaling, benefit from automatic variable selection, and appear to perform well. The software allows a number of options to be set, affecting the set of objects returned in the call; the user can also specify a clustering algorithm and, optionally, return only the clustering vector. The package can also generate a numeric data set whose inter-point distances relate to the treeClust ones; such a numeric data set can be much smaller than the vector of inter-point dissimilarities, a useful feature in big data sets.
A LONGITUDINAL ANALYSIS OF THE IMPACT OF WORKPLACE EMPOWERMENT ON STAFF NURSES' WORK SATISFACTION.

A longitudinal design was used to test Kanter's (1977) work empowerment theory in a random sample of185 staff nurses. Kanter argues that work environments which provide access to information, support, resources, and opportunity to learn and develop are empowering and influence employee work attitudes and organizational effectiveness. A model linking changes in structural and psychological empowerment to changes in job satisfaction at two time periods was proposed to test these relationships over time. The Conditions of Work Effectiveness Questionnaire-II, Psychological Empowerment Scale and a global measure of job satisfaction were used. Structural equation modeling analyses revealed a good fit of the data to the hypothesized model. Changes in perceptions of structural empowerment had direct effects on changes in psychological empowerment (.38) and on changes in job satisfaction (.70). Changes in psychological empowerment did not directly affect changes in job satisfaction (-.08). That is, changes in nurs.
Exploiting Latent Attack Semantics for Intelligent Malware Detection

Behavioral malware detectors promise to expose previously unknown malware and are an important security primitive. However, even the best behavioral detectors suffer from high false positives and negatives. In this paper, we address the challenge of aggregating weak per-device behavioral detectors in noisy communities (i.e., ones that produce alerts at unpredictable rates) into an accurate and robust global anomaly detector (GD). Our system - Shape GD - combines two insights: Structural: actions such as visiting a website (waterhole attack) or membership in a shared email thread (phishing attack) by nodes correlate well with malware spread, and create dynamic neighborhoods of nodes that were exposed to the same attack vector; and Statistical: feature vectors corresponding to true and false positives of local detectors have markedly different conditional distributions. We use neighborhoods to amplify the transient low-dimensional structure that is latent in high-dimensional feature vectors - but neighborhoods vary unpredictably, and we use shape to extract robust neighborhood-level features that identify infected neighborhoods. Unlike prior works that aggregate local detectors' alert bitstreams or cluster the feature vectors, Shape GD analyzes the feature vectors that led to local alerts (alert-FVs) to separate true and false positives. Shape GD first filters these alert-FVs into neighborhoods and efficiently maps a neighborhood's alert-FVs' statistical shapes into a scalar score. Shape GD then acts as a neighborhood level anomaly detector - training on benign program traces to learn the ShapeScore of false positive neighborhoods, and classifying neighborhoods with anomalous ShapeScores as malicious. Shape GD detects malware early (~100 infected nodes in a ~100K node system for waterhole and ~10 of 1000 for phishing) and robustly (with ~100% global TP and ~1% global FP rates).