Miracle-dz/UniFAR-FTUs huggingface dataset:
A hyperelastic biphasic fibre-reinforced model of articular cartilage considering distributed collagen fibre orientations: continuum basis, computational aspects and applications

Cartilage is a multi-phase material composed of fluid and electrolytes (68–85% by wet weight), proteoglycans (5–10% by wet weight), chondrocytes, collagen fibres and other glycoproteins. The solid phase constitutes an isotropic proteoglycan gel and a fibre network of predominantly type II collagen, which provides tensile strength and mechanical stiffness. The same two components control diffusion of the fluid phase, e.g. as visualised by diffusion tensor MRI: (i) the proteoglycan gel (giving a baseline isotropic diffusivity) and (ii) the highly anisotropic collagenous fibre network. We propose a new constitutive model and finite element implementation that focus on the essential load-bearing morphology: an incompressible, poroelastic solid matrix reinforced by an inhomogeneous, dispersed fibre fabric, which is saturated with an incompressible fluid residing in strain-dependent pores of the collagen–proteoglycan solid matrix. The inhomogeneous, dispersed fibre fabric of the solid further influences the fluid permeability, as well as an intrafibrillar portion that cannot be ‘squeezed out’ from the tissue. Using representative numerical examples on the mechanical response of cartilage, we reproduce several features that have been demonstrated experimentally in the cartilage mechanics literature.
Effects of cognitive‐behavioural therapy (CBT) and positive psychological intervention (PPI) on female offenders with psychological distress in Hong Kong

BACKGROUND Despite rapid growth in the female prison population, there is little research on effectiveness of psychological interventions for them. AIMS To test the hypotheses that (1) each of two psychological interventions administered separately - cognitive behavioural therapy (CBT) or positive psychology intervention (PPI) - would be more effective than 'treatment-as-usual' alone in reducing psychological distress and enhancing psychological well-being; (2) outcomes would differ according to intervention; and (3) combining the interventions would be more effective than delivering either alone. METHODS We recruited 40 women in a special Hong Kong prison unit for female offenders with psychological distress. Half of them received eight sessions of CBT followed by eight sessions of PPI; the other half received the same interventions in the reverse order. We recruited another 35 women who received only 'treatment as usual' (TAU) in the same unit. We used various clinical scales to assess the women's psychological distress or well-being before and after the interventions or at similar time points for the comparison women. RESULTS All intervention group women showed a significant reduction in psychological distress and enhancement in psychological well-being after each intervention alone compared to the TAU women. There were no significant differences between CBT and PPI in this respect. Receiving both treatments, however, did yield significantly more improvement than either intervention alone in reducing depressive thoughts and enhancing global judgement of life satisfaction, self-perceived strengths and hopeful thinking style. CONCLUSIONS AND IMPLICATION FOR PRACTICE Our findings provide preliminary empirical support for the effectiveness of psychological interventions with psychologically distressed women in prison. It would be important now to conduct a full, randomised trial to determine optimal length and combinations of treatment. Copyright © 2017 John Wiley & Sons, Ltd.
Hypothermic oxygenated machine perfusion reduces bile duct reperfusion injury after transplantation of donation after circulatory death livers

Dual hypothermic oxygenated machine perfusion (DHOPE) of the liver has been advocated as a method to reduce ischemia/reperfusion injury (IRI). This study aimed to determine whether DHOPE reduces IRI of the bile ducts in donation after circulatory death (DCD) liver transplantation. In a recently performed phase 1 trial, 10 DCD livers were preserved with DHOPE after static cold storage (SCS; www.trialregister.nl NTR4493). Bile duct biopsies were obtained at the end of SCS (before DHOPE; baseline) and after graft reperfusion in the recipient. Histological severity of biliary injury was graded according to an established semiquantitative grading system. Twenty liver transplantations using DCD livers not preserved with DHOPE served as controls. Baseline characteristics and the degree of bile duct injury at baseline (end of SCS) were similar between both groups. In controls, the degree of stroma necrosis (P = 0.002) and injury of the deep peribiliary glands (PBG; P = 0.02) increased after reperfusion compared with baseline. In contrast, in DHOPE‐preserved livers, the degree of bile duct injury did not increase after reperfusion. Moreover, there was less injury of deep PBG (P = 0.04) after reperfusion in the DHOPE group compared with controls. In conclusion, this study suggests that DHOPE reduces IRI of bile ducts after DCD liver transplantation. Liver Transplantation 24 655–664 2018 AASLD.
PYROLYSIS CHARACTERIZATION OF EUCALYPTUS GLOBULUS SAMPLES TROUGHT SIMULTANEUS THERMAL ANALYSIS

Thermogravimetry and differential scanning calorimetry (Simultaneus Thermal Analysis STA) tests of Eucalyptus Globulus samples, collected in Cantabria last November, were analyzed. The study includes an analysis of “a priori” two kinds of sawdust and leaves and two random combinations of leaves and sawdust. The analysis was performed at different heating rates which led the nature of the process (exothermic or endothermic). The characteristics processes of wood (hemicelluloses, cellulose and lignin) were obtained as well the qualitative energies involved in each process. Two differential isoconversional methods (Ozawa derived and Kissinger) were used to obtain the apparent activation energy to deal with a comparative analysis between the two types of sawdust from eucalyptus branches with different diameter.
Development and Validation of Risk Prediction Models for Cardiovascular Events in Black Adults: The Jackson Heart Study Cohort.

IMPORTANCE Cardiovascular risk assessment is a fundamental component of prevention of cardiovascular disease (CVD). However, commonly used prediction models have been formulated in primarily or exclusively white populations. Whether risk assessment in black adults is dissimilar to that in white adults is uncertain. OBJECTIVES To develop and validate risk prediction models for CVD incidence in black adults, incorporating standard risk factors, biomarkers, and subclinical disease. DESIGN, SETTING, AND PARTICIPANTS The Jackson Heart Study (JHS), a longitudinal community-based study of 5301 black adults in Jackson, Mississippi. Inclusive study dates were the date of a participant's first visit (September 2000 to March 2004) to December 31, 2011. The median (75th percentile) follow-up was 9.1 (9.7) years. The dates of the analysis were August 2013 to May 2015. Measurements included standard risk factors, including age, sex, body mass index, systolic and diastolic blood pressure, ratio of fasting total cholesterol to high-density lipoprotein cholesterol, estimated glomerular filtration rate, antihypertensive therapy, diabetes mellitus, and smoking; blood biomarkers; and subclinical disease measures, including ankle-brachial index, carotid intimal-medial thickness, and echocardiographic left ventricular hypertrophy and systolic dysfunction. MAIN OUTCOMES AND MEASURES Incident CVD event was defined as the first occurrence of myocardial infarction, coronary heart disease death, congestive heart failure, stroke, incident angina, or intermittent claudication. Model performance was compared with the American College of Cardiology/American Heart Association (ACC/AHA) CVD risk algorithm and the Framingham Risk Score (FHS) refitted to the JHS data and evaluated in the Atherosclerosis Risk in Communities (ARIC) and Multi-Ethnic Study of Atherosclerosis cohorts. RESULTS The study cohort comprised 3689 participants with mean (SD) age at baseline was 53 (11) years, and 64.8% (n = 2390) were female. Over a median of 9.1 years, 270 participants (166 women) experienced a first CVD event. A simple combination of standard CVD risk factors, B-type natriuretic peptide, and ankle-brachial index (model 6) yielded modest improvement over a model without B-type natriuretic peptide and ankle-brachial index (C statistic, 0.79; 95% CI, 0.75-0.83 [relative integrated discrimination improvement, 0.22; 95% CI, 0.15-0.30]). However, the reclassification improvement was not substantially different between model 6 and the ACC/AHA CVD Pooled Cohort risk equations or between model 6 and the FHS. The models discriminated reasonably well in the ARIC and Multi-Ethnic Study of Atherosclerosis data (C statistic range, 0.70-0.77). CONCLUSIONS AND RELEVANCE Our findings using the JHS data in the present study are valuable because they confirm that current FHS and ACC/AHA risk algorithms work well in black individuals and are not easily improved on. A unique risk calculator for black adults may not be necessary.
Design of reversible logic circuits using quantum dot cellular automata-based system

Abstract Shrinking transistor sizes and power dissipation are the major barriers in the development of future computational circuits. At least when the transistor size approaches the atomic scale, duplication of transistor density according to Moore’s law will not be possible. Physical limits, like quantum effects and nondeterministic behavior of small currents, and technological limits, such as high power consumption and design complexity, may hold back the future program of microelectronic conventional circuit scaling. Hence, an alternative technology is required for future design. Quantum dot-cellular automata (QCA) is a transistor-less, very promising nanotechnology that can be used to build nanocircuits. The conventional computer is an irreversible one; i.e. once a logic block generates the output bits, the input bits are lost. A possible solution is reversible computing, where no bit is lost during computation. Hence, logically reversible circuit can consume less energy than any conventional circuit. In this paper, a brief review on evolution of the QCA in reversible computing is discussed. Various reversible gates that are designed using QCA technology as well as the modification of those designs that are made in latter works are highlighted.
Impact of the Uremic Milieu on the Osteogenic Potential of Mesenchymal Stem Cells

Human mesenchymal stem cells (hMSCs), the precursors of osteoblasts during osteogenesis, play a role in the balance of bone formation and resorption, but their functioning in uremia has not been well defined. To study the effects of the uremic milieu on osteogenic properties, we applied an in vitro assay culturing hMSCs in osteogenic medium supplemented with serum from healthy donors and from uremic patients on hemodialysis. Compared to control, serum from uremic patients induces, in hMSC cultures, a modification of several key regulators of bone remodeling, in particular a reduction of the ratio Receptor Activator of Nuclear factor Kappa B Receptor (RANKL) over osteoprotegerin, indicating an adaptive response of the system to favor osteogenesis over osteoclastosis. However, the levels of osteopontin, osteocalcin, and collagen type I, are increased in cell medium, while BMP-2, and alizarin red staining were decreased, pointing to a reduction of bone formation favoring resorption. Selected uremic toxins, such as p-cresylsulfate, p-cresylglucuronide, parathyroid hormone, indoxyl sulfate, asymmetric dimethylarginine, homocysteine, were able to mimic some of the effects of whole serum from uremic patients. Serum from cinacalcet-treated patients antagonizes these effects. Hydrogen sulfide (H2S) donors as well as hemodialysis treatment are able to induce beneficial effects. In conclusion, bone modifications in uremia are influenced by the capability of the uremic milieu to alter hMSC osteogenic differentiation. Cinacalcet, H2S donors and a hemodialysis session can ameliorate the hampered calcium deposition.
Comparative Toxicity of Size-Fractionated Airborne Particulate Matter Collected at Different Distances from an Urban Highway

Background Epidemiologic studies have reported an association between proximity to highway traffic and increased cardiopulmonary illnesses. Objectives We investigated the effect of size-fractionated particulate matter (PM), obtained at different distances from a highway, on acute cardiopulmonary toxicity in mice. Methods We collected PM for 2 weeks in July–August 2006 using a three-stage (ultrafine, < 0.1 μm; fine, 0.1–2.5 μm; coarse, 2.5–10 μm) high-volume impactor at distances of 20 m [near road (NR)] and 275 m [far road (FR)] from an interstate highway in Raleigh, North Carolina. Samples were extracted in methanol, dried, diluted in saline, and then analyzed for chemical constituents. Female CD-1 mice received either 25 or 100 μg of each size fraction via oropharyngeal aspiration. At 4 and 18 hr postexposure, mice were assessed for pulmonary responsiveness to inhaled methacholine, biomarkers of lung injury and inflammation; ex vivo cardiac pathophysiology was assessed at 18 hr only. Results Overall chemical composition between NR and FR PM was similar, although NR samples comprised larger amounts of PM, endotoxin, and certain metals than did the FR samples. Each PM size fraction showed differences in ratios of major chemical classes. Both NR and FR coarse PM produced significant pulmonary inflammation irrespective of distance, whereas both NR and FR ultrafine PM induced cardiac ischemia–reperfusion injury. Conclusions On a comparative mass basis, the coarse and ultrafine PM affected the lung and heart, respectively. We observed no significant differences in the overall toxicity end points and chemical makeup between the NR and FR PM. The results suggest that PM of different size-specific chemistry might be associated with different toxicologic mechanisms in cardiac and pulmonary tissues.
A Genetic Algorithm-based Classifier Ensemble Optimization for Activity Recognition in Smart Homes

Over the last few years, one of the most common purposes of smart homes is to provide human centric services in the domain of u-healthcare by analyzing inhabitants’ daily living. Currently, the major challenges in activity recognition include the reliability of prediction of each classifier as they differ according to smart homes characteristics. Smart homes indicate variation in terms of performed activities, deployed sensors, environment settings, and inhabitants’ characteristics. It is not possible that one classifier always performs better than all the other classifiers for every possible situation. This observation has motivated towards combining multiple classifiers to take advantage of their complementary performance for high accuracy. Therefore, in this paper, a method for activity recognition is proposed by optimizing the output of multiple classifiers with Genetic Algorithm (GA). Our proposed method combines the measurement level output of different classifiers for each activity class to make up the ensemble. For the evaluation of the proposed method, experiments are performed on three real datasets from CASAS smart home. The results show that our method systematically outperforms single classifier and traditional multiclass models. The significant improvement is achieved from 0.82 to 0.90 in the F-measures of recognized activities as compare to existing methods.
D Face Recognition Using Gabor Discrete Cosine Transform

In this paper, we present a novel 2.5D face recognition method based on Gabor Discrete Cosine Transform (GDCT). In the proposed method, the Gabor filter is applied to extract feature vectors from the texture and the depth information. Then, Discrete Cosine Transform (DCT) is used for dimensionality and redundancy reduction to improve computational efficiency. The system is combined texture and depth information in the decision level, which presents higher performance compared to methods, which use texture and depth information, separately. The proposed algorithm is examined on publically available Bosphorus database including models with pose variation. The experimental results show that the proposed method has a higher performance compared to the benchmark. Keywords—Gabor filter, discrete cosine transform, 2.5D face recognition, pose.
A 3.0-Angstrom Resolution Cryo-Electron Microscopy Structure and Antigenic Sites of Coxsackievirus A6-Like Particles

ABSTRACT Coxsackievirus A6 (CVA6) has recently emerged as one of the predominant causative agents of hand, foot, and mouth disease (HFMD). The structure of the CVA6 mature viral particle has not been solved thus far. Our previous work shows that recombinant virus-like particles (VLPs) of CVA6 represent a promising CVA6 vaccine candidate. Here, we report the first cryo-electron microscopy (cryo-EM) structure of the CVA6 VLP at 3.0-Å resolution. The CVA6 VLP exhibits the characteristic features of enteroviruses but presents an open channel at the 2-fold axis and an empty, collapsed VP1 pocket, which is broadly similar to the structures of the enterovirus 71 (EV71) VLP and coxsackievirus A16 (CVA16) 135S expanded particle, indicating that the CVA6 VLP is in an expanded conformation. Structural comparisons reveal that two common salt bridges within protomers are maintained in the CVA6 VLP and other viruses of the Enterovirus genus, implying that these salt bridges may play a critical role in enteroviral protomer assembly. However, there are apparent structural differences among the CVA6 VLP, EV71 VLP, and CVA16 135S particle in the surface-exposed loops and C termini of subunit proteins, which are often antigenic sites for enteroviruses. By immunological assays, we identified two CVA6-specific linear B-cell epitopes (designated P42 and P59) located at the GH loop and the C-terminal region of VP1, respectively, in agreement with the structure-based prediction of antigenic sites. Our findings elucidate the structural basis and important antigenic sites of the CVA6 VLP as a strong vaccine candidate and also provide insight into enteroviral protomer assembly. IMPORTANCE Coxsackievirus A6 (CVA6) is becoming one of the major pathogens causing hand, foot, and mouth disease (HFMD), leading to significant morbidity and mortality in children and adults. However, no vaccine is currently available to prevent CVA6 infection. Our previous work shows that recombinant virus-like particles (VLPs) of CVA6 are a promising CVA6 vaccine candidate. Here, we present a 3.0-Å structure of the CVA6 VLP determined by cryo-electron microscopy. The overall architecture of the CVA6 VLP is similar to those of the expanded structures of enterovirus 71 (EV71) and coxsackievirus A16 (CVA16), but careful structural comparisons reveal significant differences in the surface-exposed loops and C termini of each capsid protein of these particles. In addition, we identified two CVA6-specific linear B-cell epitopes and mapped them to the GH loop and the C-terminal region of VP1, respectively. Collectively, our findings provide a structural basis and important antigenic information for CVA6 VLP vaccine development.
High altitude arterialised capillary earlobe blood gas measurement using the Abbott i-STAT

Introduction Measurement of physiological parameters in extreme environments is essential to advancing knowledge, prophylaxis and treatment of altitude sickness. Point-of-care testing facilitates investigation in non-specialist and remote settings, as well as becoming increasingly popular at the bedside for real-time results in the clinical environment. Arterialised capillary earlobe blood gases are recommended as a valid alternative to arterial sampling in research. This study aimed to test the feasibility of obtaining and analysing daily earlobe samples at high altitude. Methods From 17 to 24 January 2016, 24 participants on a research expedition to Ecuador underwent daily earlobe blood gas measurements including pH, partial pressure of oxygen and partial pressure of carbon dioxide to 5043 m. Samples were analysed using an Abbott i-STAT blood gas analyser and G3+ cartridges. Results Daily measurements were successfully obtained and analysed at the point of care in 23/24 participants and were well tolerated with no adverse events. 12% (27/220) cartridges failed and required repeat sampling. Conclusions Daily earlobe blood gas analysis using the Abbott i-STAT is feasible in a protected environment at high altitude. Participants and equipment should be kept warm before and during testing. Spare cartridges should be available. This methodology may be useful for both research and therapeutic measurements in remote, rural and wilderness medicine.
Opportunities and obstacles for deep learning in biology and medicine

Deep learning, which describes a class of machine learning algorithms, has recently showed impressive results across a variety of domains. Biology and medicine are data rich, but the data are complex and often ill-understood. Problems of this nature may be particularly well-suited to deep learning techniques. We examine applications of deep learning to a variety of biomedical problems -- patient classification, fundamental biological processes, and treatment of patients -- to predict whether deep learning will transform these tasks or if the biomedical sphere poses unique challenges. We find that deep learning has yet to revolutionize or definitively resolve any of these problems, but promising advances have been made on the prior state of the art. Even when improvement over a previous baseline has been modest, we have seen signs that deep learning methods may speed or aid human investigation. More work is needed to address concerns related to interpretability and how to best model each problem. Furthermore, the limited amount of labeled data for training presents problems in some domains, as can legal and privacy constraints on work with sensitive health records. Nonetheless, we foresee deep learning powering changes at the bench and bedside with the potential to transform several areas of biology and medicine.
Genetic Control of Differential Acetylation in Diabetic Rats

Post-translational protein modifications such as acetylation have significant regulatory roles in metabolic processes, but their relationship to both variation in gene expression and DNA sequence is unclear. We address this question in the Goto-Kakizaki (GK) rat inbred strain, a model of polygenic type 2 diabetes. Expression of the NAD-dependent deacetylase Sirtuin-3 is down-regulated in GK rats compared to normoglycemic Brown Norway (BN) rats. We show first that a promoter SNP causes down-regulation of Sirtuin-3 expression in GK rats. We then use mass-spectrometry to identify proteome-wide differential lysine acetylation of putative Sirtuin-3 protein targets in livers of GK and BN rats. These include many proteins in pathways connected to diabetes and metabolic syndrome. We finally sequence GK and BN liver transcriptomes and find that mRNA expression of these targets does not differ significantly between GK and BN rats, in contrast to other components of the same pathways. We conclude that physiological differences between GK and BN rats are mediated by a combination of differential protein acetylation and gene transcription and that genetic variation can modulate acetylation independently of expression.