Miracle-dz/UniFAR-FTUs huggingface dataset:
Accurate position control of a pneumatic actuator using on/off solenoid valves

The development of a fast, accurate and inexpensive position controlled pneumatic actuator that may be applied to a variety of robotic applications is described. A novel PWM valve pulsing algorithm allowed on/off solenoid valves to be used in place of costly servo valves. A linear process model was obtained from experimental data using system identification. A PID controller with added friction compensation and position feedforward was successfully implemented. A worst case steady state accuracy of 0.21 mm was achieved with a rise time of 180 ms for step inputs from 0.11 mm to 64 mm. Following errors to 64 mm s-curve profiles were less than 2.0 mm. The controller was robust to a six fold increase in the system mass. The actuator's overall performance is comparable to that achieved by other researchers using servo valves.
Impact of sputum bacteria on airway inflammation and health status in clinical stable COPD

Chronic obstructive pulmonary disease (COPD) is characterised by sputum production, bacterial colonisation, neutrophilic bronchial airway inflammation and poor health status. The aim of this study was to determine the impact of sputum potentially pathogenic microorganisms (PPMs) on bronchial airway inflammation, health status and plasma fibrinogen levels in subjects with moderate-to-severe COPD during the clinical stable state. Sputum total cell and neutrophil counts, supernatant interleukin‐8, leukotriene B4, tumour necrosis factor‐α and neutrophil elastase levels, neutrophil chemotaxis and plasma fibrinogen levels were estimated. Health status was determined using the St George's Respiratory Questionnaire and the 36‐item Short-Form Health Survey questionnaire. Twenty-seven (40%) subjects had PPMs and 40 (60%) non‐PPMs in their sputum. Both groups were of similar age, body mass index, smoking history and lung function. The PPMs group showed significantly higher levels of interleukin‐8, leukotriene B4, tumour necrosis factor‐α, neutrophil elastase and increased neutrophil chemotaxis. They also exhibited worse health status and raised plasma fibrinogen levels compared to the non‐PPMs group. In conclusion, subjects with clinically stable moderate-to-severe chronic obstructive pulmonary disease who had potentially pathogenic microorganisms in their sputum demonstrated an exaggerated airway inflammatory response, poorer health status and increased plasma fibrinogen levels than those who had nonpotentially pathogenic microorganisms.
Angry facial expressions bias gender categorization in children and adults: behavioral and computational evidence

Angry faces are perceived as more masculine by adults. However, the developmental course and underlying mechanism (bottom-up stimulus driven or top-down belief driven) associated with the angry-male bias remain unclear. Here we report that anger biases face gender categorization toward “male” responding in children as young as 5–6 years. The bias is observed for both own- and other-race faces, and is remarkably unchanged across development (into adulthood) as revealed by signal detection analyses (Experiments 1–2). The developmental course of the angry-male bias, along with its extension to other-race faces, combine to suggest that it is not rooted in extensive experience, e.g., observing males engaging in aggressive acts during the school years. Based on several computational simulations of gender categorization (Experiment 3), we further conclude that (1) the angry-male bias results, at least partially, from a strategy of attending to facial features or their second-order relations when categorizing face gender, and (2) any single choice of computational representation (e.g., Principal Component Analysis) is insufficient to assess resemblances between face categories, as different representations of the very same faces suggest different bases for the angry-male bias. Our findings are thus consistent with stimulus-and stereotyped-belief driven accounts of the angry-male bias. Taken together, the evidence suggests considerable stability in the interaction between some facial dimensions in social categorization that is present prior to the onset of formal schooling.
Body mass index and cholesterol level predict surgical outcome in patients with hepatocellular carcinoma in Taiwan - a cohort study

Curative surgical resection (CSR) remains the most effective therapeutic intervention for patients with hepatocellular carcinoma (HCC); however, frequent post-surgical recurrence leads to high cancer related mortality. This study aimed to clarify the role of body mass index (BMI) and serum cholesterol level in predicting post-surgical outcomes in HCC patients after CSR. A total of 484 HCC patients including 213 BMIhigh and 271 BMIlow patients were included. Overall survival (OS) and recurrence-free survival (RFS) rates were examined in patients with differential BMI and serum cholesterol level. The analysis showed that significant different 1-, 3- and 5-year cumulative OS rates (P-value=0.015) and RFS rate (P-value=0.010) between BMIlow and BMIhigh patients. Further analysis in groups with differential serum cholesterol levels among BMIlow and BMIhigh patients indicated that the BMIlow/Chollow patients exhibited the significant lower cumulative OS and RFS rates in comparison with the remaining subjects (P-value=0.007 and 0.039 for OS and RFS rates, respectively). In conclusion, the coexistence of low BMI and low serum cholesterol level could serve as prognostic factors to predict post-operative outcomes in HCC patients undergoing surgical hepatectomy.
The Crystal Structure of a Cockroach Pheromone-binding Protein Suggests a New Ligand Binding and Release Mechanism*

Pheromone-binding proteins (PBPs) are small helical proteins found in sensorial organs, particularly in the antennae, of moth and other insect species. They were proposed to solubilize and carry the hydrophobic pheromonal compounds through the antennal lymph to receptors, participating thus in the peri-receptor events of signal transduction. The x-ray structure of Bombyx mori PBP (BmorPBP), from male antennae, revealed a six-helix fold forming a cavity that contains the pheromone bombykol. We have identified a PBP (LmaPBP) from the cockroach Leucophaea maderae in the antennae of the females, the gender attracted by pheromones in this species. Here we report the crystal structure of LmaPBP alone or in complex with a fluorescent reporter (amino-naphthalen sulfonate, ANS) or with a component of the pheromonal blend, 3-hydroxy-butan-2-one. Both compounds bind in the internal cavity of LmaPBP, which is more hydrophilic than BmorPBP cavity. LmaPBP structure ends just after the sixth helix (helix F). BmorPBP structure extends beyond the sixth helix with a stretch of residues elongated at neutral pH and folding as a seventh internalized helix at low pH. These differences between LmaPBP and BmorPBP structures suggest that different binding and release mechanism may be adapted to the hydrophilicity or hydrophobicity of the pheromonal ligand.
A fast triangle to triangle intersection test for collision detection

The triangle‐to‐triangle intersection test is a basic component of all collision detection data structures and algorithms. This paper presents a fast method for testing whether two triangles embedded in three dimensions intersect. Our technique solves the basic sets of linear equations associated with the problem and exploits the strong relations between these sets to speed up their solution. Moreover, unlike previous techniques, with very little additional cost, the exact intersection coordinates can be determined. Finally, our technique uses general principles that can be applied to similar problems such as rectangle‐to‐rectangle intersection tests, and generally to problems where several equation sets are strongly related. We show that our algorithm saves about 20% of the mathematical operations used by the best previous triangle‐to‐triangle intersection algorithm. Our experiments also show that it runs 18.9% faster than the fastest previous algorithm on average for typical scenarios of collision detection (on Pentium 4). Copyright © 2006 John Wiley & Sons, Ltd.
Salmonella Pathogenicity Island 2 Is Expressed Prior to Penetrating the Intestine

Salmonella enterica serovar Typhimurium is a facultative intracellular pathogen that causes disease in mice that resembles human typhoid. Typhoid pathogenesis consists of distinct phases in the intestine and a subsequent systemic phase in which bacteria replicate in macrophages of the liver and spleen. The type III secretion system encoded by Salmonella pathogenicity island 2 (SPI-2) is a major virulence factor contributing to the systemic phase of typhoid pathogenesis. Understanding how pathogens regulate virulence mechanisms in response to the environment, including different host tissues, is key to our understanding of pathogenesis. A recombinase-based in vivo expression technology system was developed to assess SPI-2 expression during murine typhoid. SPI-2 expression was detectable at very early times in bacteria that were resident in the lumen of the ileum and was independent of active bacterial invasion of the epithelium. We also provide direct evidence for the regulation of SPI-2 by the Salmonella transcription factors ompR and ssrB in vivo. Together these results demonstrate that SPI-2 expression precedes penetration of the intestinal epithelium. This induction of expression precedes any documented SPI-2-dependent phases of typhoid and may be involved in preparing Salmonella to successfully resist the antimicrobial environment encountered within macrophages.
Hyaline cartilage engineered by chondrocytes in pellet culture: histological, immunohistochemical and ultrastructural analysis in comparison with cartilage explants

Cartilage engineering is a strategic experimental goal for the treatment of multiple joint diseases. Based on the process of embryonic chondrogenesis, we hypothesized that cartilage could be engineered by condensing chondrocytes in pellet culture and, in the present study, examined the quality of regenerated cartilage in direct comparison with native cartilage. Chondrocytes isolated from the sterna of chick embryos were cultured in pellets (4 × 106 cells per pellet) for 2 weeks. Cartilage explants from the same source were cultured as controls. After 2 weeks, the regenerated cartilage from pellet culture had a disc shape and was on average 9 mm at the longest diameter. The chondrocyte phenotype was stabilized in pellet culture as shown by the synthesis of type II collagen and aggrecan, which was the same intensity as in the explant after 7 days in culture. During culture, chondrocytes also continuously synthesized type IX collagen. Type X collagen was negatively stained in both pellets and explants. Except for fibril orientation, collagen fibril diameter and density in the engineered cartilage were comparable with the native cartilage. In conclusion, hyaline cartilage engineered by chondrocytes in pellet culture, without the transformation of cell phenotypes and scaffold materials, shares similarities with native cartilage in cellular distribution, matrix composition and density, and ultrastructure.
Mitochondria are required for pro‐ageing features of the senescent phenotype

Cell senescence is an important tumour suppressor mechanism and driver of ageing. Both functions are dependent on the development of the senescent phenotype, which involves an overproduction of pro‐inflammatory and pro‐oxidant signals. However, the exact mechanisms regulating these phenotypes remain poorly understood. Here, we show the critical role of mitochondria in cellular senescence. In multiple models of senescence, absence of mitochondria reduced a spectrum of senescence effectors and phenotypes while preserving ATP production via enhanced glycolysis. Global transcriptomic analysis by RNA sequencing revealed that a vast number of senescent‐associated changes are dependent on mitochondria, particularly the pro‐inflammatory phenotype. Mechanistically, we show that the ATM, Akt and mTORC1 phosphorylation cascade integrates signals from the DNA damage response (DDR) towards PGC‐1β‐dependent mitochondrial biogenesis, contributing to a ROS‐mediated activation of the DDR and cell cycle arrest. Finally, we demonstrate that the reduction in mitochondrial content in vivo, by either mTORC1 inhibition or PGC‐1β deletion, prevents senescence in the ageing mouse liver. Our results suggest that mitochondria are a candidate target for interventions to reduce the deleterious impact of senescence in ageing tissues.
The Contribution of Occult Precipitation to Nutrient Deposition on the West Coast of South Africa

The Strandveld mediterranean-ecosystem of the west coast of South Africa supports floristically diverse vegetation growing on mostly nutrient-poor aeolian sands and extending from the Atlantic Ocean tens of kilometers inland. The cold Benguela current upwelling interacts with warm onshore southerly winds in summer causing coastal fogs in this region. We hypothesized that fog and other forms of occult precipitation contribute moisture and nutrients to the vegetation. We measured occult precipitation over one year along a transect running inland in the direction of the prevailing wind and compared the nutrient concentrations with those in rainwater. Occult deposition rates of P, N, K, Mg, Ca, Na, Al and Fe all decreased with distance from the ocean. Furthermore, ratios of cations to Na were similar to those of seawater, suggesting a marine origin for these. In contrast, N and P ratios in occult precipitation were higher than in seawater. We speculate that this is due to marine foam contributing to occult precipitation. Nutrient loss in leaf litter from dominant shrub species was measured to indicate nutrient demand. We estimated that occult precipitation could meet the demand of the dominant shrubby species for annual N, P, K and Ca. Of these species, those with small leaves intercepted more moisture and nutrients than those with larger leaves and could take up foliar deposits of glycine, NO3-, NH4 + and Li (as tracer for K) through leaf surfaces. We conclude that occult deposition together with rainfall deposition are potentially important nutrient and moisture sources for the Strandveld vegetation that contribute to this vegetation being floristically distinct from neighbouring nutrient-poor Fynbos vegetation.
Pseudo-Exhaustive Testing for Software

Pseudo-exhaustive testing uses the empirical observation that, for broad classes of software, a fault is likely triggered by only a few variables interacting. The method takes advantage of two relatively recent advances in software engineering: algorithms for efficiently generating covering arrays to represent software interaction test suites, and automated generation of test oracles using model checking. An experiment with a module of the traffic collision avoidance system (TCAS) illustrates the approach testing pairwise through 6-way interactions. We also outline current and future work applying the test methodology to a large real-world application, the personal identity verification (PIV) smart card
The Global Burden of Mental, Neurological and Substance Use Disorders: An Analysis from the Global Burden of Disease Study 2010

Background The Global Burden of Disease Study 2010 (GBD 2010), estimated that a substantial proportion of the world’s disease burden came from mental, neurological and substance use disorders. In this paper, we used GBD 2010 data to investigate time, year, region and age specific trends in burden due to mental, neurological and substance use disorders. Method For each disorder, prevalence data were assembled from systematic literature reviews. DisMod-MR, a Bayesian meta-regression tool, was used to model prevalence by country, region, age, sex and year. Prevalence data were combined with disability weights derived from survey data to estimate years lived with disability (YLDs). Years lost to premature mortality (YLLs) were estimated by multiplying deaths occurring as a result of a given disorder by the reference standard life expectancy at the age death occurred. Disability-adjusted life years (DALYs) were computed as the sum of YLDs and YLLs. Results In 2010, mental, neurological and substance use disorders accounted for 10.4% of global DALYs, 2.3% of global YLLs and, 28.5% of global YLDs, making them the leading cause of YLDs. Mental disorders accounted for the largest proportion of DALYs (56.7%), followed by neurological disorders (28.6%) and substance use disorders (14.7%). DALYs peaked in early adulthood for mental and substance use disorders but were more consistent across age for neurological disorders. Females accounted for more DALYs in all mental and neurological disorders, except for mental disorders occurring in childhood, schizophrenia, substance use disorders, Parkinson’s disease and epilepsy where males accounted for more DALYs. Overall DALYs were highest in Eastern Europe/Central Asia and lowest in East Asia/the Pacific. Conclusion Mental, neurological and substance use disorders contribute to a significant proportion of disease burden. Health systems can respond by implementing established, cost effective interventions, or by supporting the research necessary to develop better prevention and treatment options.
Proactive self-adaptation under uncertainty: a probabilistic model checking approach

Self-adaptive systems tend to be reactive and myopic, adapting in response to changes without anticipating what the subsequent adaptation needs will be. Adapting reactively can result in inefficiencies due to the system performing a suboptimal sequence of adaptations. Furthermore, when adaptations have latency, and take some time to produce their effect, they have to be started with sufficient lead time so that they complete by the time their effect is needed. Proactive latency-aware adaptation addresses these issues by making adaptation decisions with a look-ahead horizon and taking adaptation latency into account. In this paper we present an approach for proactive latency-aware adaptation under uncertainty that uses probabilistic model checking for adaptation decisions. The key idea is to use a formal model of the adaptive system in which the adaptation decision is left underspecified through nondeterminism, and have the model checker resolve the nondeterministic choices so that the accumulated utility over the horizon is maximized. The adaptation decision is optimal over the horizon, and takes into account the inherent uncertainty of the environment predictions needed for looking ahead. Our results show that the decision based on a look-ahead horizon, and the factoring of both tactic latency and environment uncertainty, considerably improve the effectiveness of adaptation decisions.
Teriparatide Increases Bone Formation in Modeling and Remodeling Osteons and Enhances IGF‐II Immunoreactivity in Postmenopausal Women With Osteoporosis

Transiliac bone biopsies were obtained from 55 women treated with teriparatide or placebo for 12–24 months. We report direct evidence that modeling bone formation at quiescent surfaces was present only in teriparatide‐treated patients and bone formation at remodeling sites was higher with teriparatide than placebo.
Improved Classification of Mass Spectrometry Database Search Results Using Newer Machine Learning Approaches*

Manual analysis of mass spectrometry data is a current bottleneck in high throughput proteomics. In particular, the need to manually validate the results of mass spectrometry database searching algorithms can be prohibitively time-consuming. Development of software tools that attempt to quantify the confidence in the assignment of a protein or peptide identity to a mass spectrum is an area of active interest. We sought to extend work in this area by investigating the potential of recent machine learning algorithms to improve the accuracy of these approaches and as a flexible framework for accommodating new data features. Specifically we demonstrated the ability of boosting and random forest approaches to improve the discrimination of true hits from false positive identifications in the results of mass spectrometry database search engines compared with thresholding and other machine learning approaches. We accommodated additional attributes obtainable from database search results, including a factor addressing proton mobility. Performance was evaluated using publically available electrospray data and a new collection of MALDI data generated from purified human reference proteins.
Motion texture: a two-level statistical model for character motion synthesis

In this paper, we describe a novel technique, called motion texture, for synthesizing complex human-figure motion (e.g., dancing) that is statistically similar to the original motion captured data. We define motion texture as a set of motion textons and their distribution, which characterize the stochastic and dynamic nature of the captured motion. Specifically, a motion texton is modeled by a linear dynamic system (LDS) while the texton distribution is represented by a transition matrix indicating how likely each texton is switched to another. We have designed a maximum likelihood algorithm to learn the motion textons and their relationship from the captured dance motion. The learnt motion texture can then be used to generate new animations automatically and/or edit animation sequences interactively. Most interestingly, motion texture can be manipulated at different levels, either by changing the fine details of a specific motion at the texton level or by designing a new choreography at the distribution level. Our approach is demonstrated by many synthesized sequences of visually compelling dance motion.
Patients with ALS can use sensorimotor rhythms to operate a brain-computer interface

People with severe motor disabilities can maintain an acceptable quality of life if they can communicate. Brain-computer interfaces (BCIs), which do not depend on muscle control, can provide communication. Four people severely disabled by ALS learned to operate a BCI with EEG rhythms recorded over sensorimotor cortex. These results suggest that a sensorimotor rhythm–based BCI could help maintain quality of life for people with ALS.