Miracle-dz/UniFAR-FTUs huggingface dataset:
Physical disability in rheumatoid arthritis is associated with cartilage damage rather than bone destruction

Background Joint destruction in rheumatoid arthritis is comprised of cartilage and bone damage, which can be evaluated radiographically separately by the joint space narrowing (JSN) and erosion (ERO) scores. It is currently unclear to which extent these components affect irreversible functional disability. The aim of the present work was to determine these contributions. Methods Data, kindly provided by the sponsors, was evaluated from several randomised controlled clinical trials on adalimumab, etanercept, infliximab and leflunomide. Patients who reached stringent remission according to the Simplified Disease Activity Index (SDAI≤3.3) were extracted to eliminate the activity related (ie, reversible) component of disability. In these patients, residual Health Assessment Questionnaire Disability Index (HAQ-DI) score at the time of remission (to reflect the level of ‘irreversible’ disability) was determined and related to baseline measures of ERO and JSN scores univariately, by stratification and in adjusted regression models. Results A total of 748 patients who achieved a state of remission were analysed (16.3% of the total pooled population of 4602 patients). In the univariate analyses, mean residual HAQ-DI values in remission were significantly larger in higher tertiles of JSN and ERO (ERO: 0.21, 0.25, 0.35; JSN: 0.19, 0.24, 0.39; p<0.001 for both). In stratified analyses, mean residual HAQ-DI scores were larger in higher tertiles of JSN within the first tertile of ERO (0.18, 0.25, 0.29; p=0.05), as well as the second (0.21, 0.24, 0.29; p=0.19) and the third (0.12, 0.23, 0.42; p<0.001). In contrast, there was no such trend across ERO tertiles within the first JSN tertile (0.18, 0.21, 0.12; p=0.99) and the second tertile (0.25, 0.24, 0.23; p=0.77), and only marginally within the third tertile of JSN (0.29, 0.29, 0.42; p=0.07). Adjusted multivariate regression models supported the significant association of JSN on residual disability. Conclusions Cartilage damage appears to be the more clearly associated with irreversible physical disability than bony damage. These data suggest that particular attention should be given to therapeutic interference with cartilage destruction.
O(√log n) approximation algorithms for min UnCut, min 2CNF deletion, and directed cut problems

We give O(√log n)-approximation algorithms for the MIN UNCUT, MIN 2CNF DELETION, DIRECTED BALANCED SEPERATOR, and DIRECTED SPARSEST CUT problems. The previously best known algorithms give an O(log n)-approximation for MIN UNCUT [9], DIRECTED BALANCED SEPERATOR [17], DIRECTED SPARSEST CUT [17], and an O(log n log log n)-approximation for MIN 2CNF DELETION [14]. We also show that the integrality gap of an SDP relaxation of the MINIMUM MULTICUT problem is Ω(log n).
Application of a Bilayer TiO2 Nanofiber Photoanode for Optimization of Dye‐Sensitized Solar Cells

Figure 1 . Schematic diagram of fabrication procedure and SEM images of the bilayer TiO 2 nanofi bers photoanode. Since it was introduced in 1991, the lowcost, high-effi ciency, dye-sensitized solar cell (DSSC) has attracted intensive interest as a promising candidate for future green energy. [ 1 ] The respective record high power conversion effi ciency (PCE) of 11% has persisted for more than a decade, [ 2 ] and this needs to be further improved before the technology can be commercialized. The overall sunlight-to-electric-power conversion process of a DSSC can be summarized as the combination of photogeneration, charge-carriers transport, and collection. Considerable efforts have been made to increase the light harvesting, such as increasing the surface area of the semiconductor, [ 1 ] the development of new dyes and dyes mixture with strong and broad absorption spectra, [ 3 ] the introduction of photonic crystal, [ 4,5 ] or inclusion of a lightscattering layer [ 6–8 ] to trap more light in the device. To improve the charge-carrier transport capability of active layer, employment of functional nanostructured photoanodes such as 1D nanostructures (nanotubes, nanowires, and nanofi bers), nanotrees, and nanoforests [ 12–14 ] have been used in DSSC. Using single-walled carbon nanotube-TiO 2 as photoanode, Dang et al. [ 15 ] recently improved the electron collection and thus the power effi ciency up to 10.6%. While these methods improve the effi ciency of DSSC to a certain extent, these processes are complicated and costly because they involve surface modifi cations, synthesis of composite nanostructure, or combining different types of dyes. One promising method to improve the PCE of DSSCs is to use a 1D nanostructure photoanode with high surface area and excellent electron transport properties to harvest and collect effectively photogenerated electrons. Here, an innovative bilayer TiO 2 nanofi ber photoanode was investigated combining both smallerand larger-diameter TiO 2 nanofi bers that are readily fabricated in one step by simple, cost-effective, nozzleless
Adaptive Algorithm for Minimizing Cloud Task Length with Prediction Errors

Compared to traditional distributed computing like grid system, it is non-trivial to optimize cloud task's execution performance due to its more constraints like user payment budget and divisible resource demand. In this paper, we analyze in-depth our proposed optimal algorithm minimizing task execution length with divisible resources and payment budget: 1) We derive the upper bound of cloud task length, by taking into account both workload prediction errors and hostload prediction errors. With such state-of-the-art bounds, the worst-case task execution performance is predictable, which can improve the quality of service in turn. 2) We design a dynamic version for the algorithm to adapt to the load dynamics over task execution progress, further improving the resource utilization. 3) We rigorously build a cloud prototype over a real cluster environment with 56 virtual machines, and evaluate our algorithm with different levels of resource contention. Cloud users in our cloud system are able to compose various tasks based on off-the-shelf web services. Experiments show that task execution lengths under our algorithm are always close to their theoretical optimal values, even in a competitive situation with limited available resources. We also observe a high level of fair treatment on the resource allocation among all tasks.
Frontotemporal dementias: Recent advances and current controversies

Frontotemporal dementia (FTD) syndromes comprise a heterogeneous group of neurodegenerative conditions characterized by atrophy in the frontal and temporal lobes. Three main clinical variants are recognized: Behavioral variant (bv-FTD), Semantic dementia (SD), and Progressive nonfluent aphasia (PNFA). However, logopenic/phonological (LPA) variant has been recently described, showing a distinctive pattern of brain atrophy and often associated to Alzheimer’s disease pathology. The diagnosis of FTD is challenging, since there is clinical, pathological, and genetic overlap between the variants and other neurodegenerative diseases, such as motoneuron disease (MND) and corticobasal degeneration (CBD). In addition, patients with gene mutations (tau and progranulin) display an inconsistent clinical phenotype and the correspondence between the clinical variant and its pathology is unpredictable. New cognitive tests based on social cognition and emotional recognition together with advances in molecular pathology and genetics have contributed to an improved understanding. There is now a real possibility of accurate biomarkers for early diagnosis. The present review concentrates on new insights and debates in FTD.
Path-dependent gaze control for obstacle avoidance in vision guided humanoid walking

This article presents a novel gaze control strategy for obstacle avoidance in the context of vision guided humanoid walking. The generic strategy is based on the maximization of the predicted visual information. For information/uncertainty management a new hybrid formulation of an extended Kalman filter is employed. The performance resulting from this view direction control scheme shows the dependence of the intelligent gazing behavior on the pre-planned local path.
Beyond Topoisomerase Inhibition: Antitumor 1,4‐Naphthoquinones as Potential Inhibitors of Human Monoamine Oxidase

Monoamine oxidase (MAO) action has been involved in the regulation of neurotransmitters levels, cell signaling, cellular growth, and differentiation as well as in the balance of the intracellular polyamine levels. Although so far obscure, MAO inhibitors are believed to have some effect on tumors progression. 1,4‐naphthoquinone (1,4‐NQ) has been pointed out as a potential pharmacophore for inhibition of both MAO and DNA topoisomerase activities, this latter associated with antitumor activity. Herein, we demonstrated that certain antitumor 1,4‐NQs, including spermidine‐1,4‐NQ, lapachol, and nor‐lapachol display inhibitory activity on human MAO‐A and MAO‐B. Kinetic studies indicated that these compounds are reversible and competitive MAO inhibitors, being the enzyme selectivity greatly affected by substitutions on 1,4‐NQ ring. Molecular docking studies suggested that the most potent MAO inhibitors are capable to bind to the MAO active site in close proximity of flavin moiety. Furthermore, ability to inhibit both MAO‐A and MAO‐B can be potentialized by the formation of hydrogen bonds between these compounds and FAD and/or the residues in the active site. Although spermidine‐1,4‐NQs exhibit antitumor action primarily by inhibiting topoisomerase via DNA intercalation, our findings suggest that their effect on MAO activity should be taken into account when their application in cancer therapy is considered.
Materials and methods Plant materials : The present study included new mat

The chloroplast gene matK, located in the intron of chloroplast trnK, encodes maturase, and variations of matK provide substantial resolution for phylogenetic analyses at intergeneric levels. Sequence data from 127 species (including subspecies and varieties) of Brassicaceae and one outgroup specie (Cleome gynandra) were used to construct the phylogeny of this family and elucidate the phylogenetic relationships therein using the neighbor-joining, maximum parsimony, and maximum likelihood methods. The phylogenetic results generally confirmed recently established tribal alignments and indicated that most of the 27 tribes were assigned to Lineages I–III. We found that the Orychophragmus violaceus complex, including O. violaceus, O. taibaiensis, O. hupehensis, and O. diffuses, which are native to China, should be subsumed under Lineage II, and was most closely associated with the tribe Brassiceae. Arabis was confirmed to be polyphyletic and one subclade shared a sister relationship with Boechereae, while A. alpine related species formed the other clade, which was not associated with any tribes. Previous analyses placed Conringia planisiliqua in tribe Brassiceae, but it was included within Isatideae in the current analyses, supporting previous hypotheses that it was a member of this tribe.
Using Gene Essentiality and Synthetic Lethality Information to Correct Yeast and CHO Cell Genome-Scale Models

Essentiality (ES) and Synthetic Lethality (SL) information identify combination of genes whose deletion inhibits cell growth. This information is important for both identifying drug targets for tumor and pathogenic bacteria suppression and for flagging and avoiding gene deletions that are non-viable in biotechnology. In this study, we performed a comprehensive ES and SL analysis of two important eukaryotic models (S. cerevisiae and CHO cells) using a bilevel optimization approach introduced earlier. Information gleaned from this study is used to propose specific model changes to remedy inconsistent with data model predictions. Even for the highly curated Yeast 7.11 model we identified 50 changes (metabolic and GPR) leading to the correct prediction of an additional 28% of essential genes and 36% of synthetic lethals along with a 53% reduction in the erroneous identification of essential genes. Due to the paucity of mutant growth phenotype data only 12 changes were made for the CHO 1.2 model leading to an additional correctly predicted 11 essential and eight non-essential genes. Overall, we find that CHO 1.2 was 76% less accurate than the Yeast 7.11 metabolic model in predicting essential genes. Based on this analysis, 14 (single and double deletion) maximally informative experiments are suggested to improve the CHO cell model by using information from a mouse metabolic model. This analysis demonstrates the importance of single and multiple knockout phenotypes in assessing and improving model reconstructions. The advent of techniques such as CRISPR opens the door for the global assessment of eukaryotic models.
A High Performance Reconfigurable Core for Motif Searching Using Profile HMM

A common task in bioinformatics is the comparison of biological sequences to probabilistic models in order to evaluate their similarity. The HMMer software is a popular tool for aligning biological sequences to HMM models that represent biologic motifs. The results of these comparisons can be used to annotate domains of an unknown sequence or locate new members of a modelled family. But as the size of sequence and model repositories increases the time required to perform searches between entire databases becomes impractical. The HMMer engine is an example of this where extended searches can take up to days even with algorithmic improvements and software enhancements. This work describes the acceleration of the Viterbi decoding process by means of parallelizing the algorithm and mapping it to a systolic array. The concurrency of the arraypsilas processing elements is realized by implementing the engine on off-the-self FPGA hardware. Our implementation offers a 247times speedup over a software implementation of the HMMer tool on a standard desktop computer.
Estimating Conditional Densities of Structured Outputs in RKHS

In this paper we study the problem of estimating conditional probability distributions for structured output prediction tasks in Reproducing Kernel Hilbert Spaces. More specifically, we prove decomposition results for undirected graphical models, give constructions for kernels, and show connections to Gaussian Process classification. Finally we present efficient means of solving the optimization problem and apply this to label sequence learning. Experiments on named entity recognition and pitch accent prediction tasks demonstrate the competitiveness of our approach.
Purified Protein Derivative Response in Juvenile Idiopathic Arthritis

Objective. To examine the purified protein derivative (PPD) response that develops depending upon Th1 immune response in children with juvenile idiopathic arthritis (JIA). Methods. PPD skin test was performed in 115 children with JIA who were vaccinated with bacillus Calmette-Guerin (BCG), and then they were compared to the PPD response of 45 healthy children of the same age who were vaccinated with BCG. Children with a PPD induration ≥ 5 mm were accepted as PPD-positive. PPD induration ≥ 10 mm was accepted as a limit for suspecting tuberculosis. Results. PPD induration size and PPD positivity rates (PPD ≥ 5 mm) of children with JIA were significantly lower than those of healthy children. The mean of PPD induration size was significantly lower (p < 0.0001) in patients with either 1 BCG vaccine (3.7 ± 3.6) or more than 1 BCG vaccine than controls with either 1 BCG vaccine (7.10 ± 3.2) or more than 1 BCG vaccine (10.05 ± 4.1). PPD was positive in 35.9% of patients with JIA vaccinated once (n = 32), in 50% of patients with JIA vaccinated more than once (n = 13), in 82.1% of controls vaccinated once (n = 23), and in 88.2% of controls vaccinated more than once. This result was statistically significant (patients, p = 0.03; controls, p = 0.039). It was determined that neither the activity of the disease nor the use of corticosteroid and methotrexate affected the PPD response. Conclusion. The response to PPD, which is one of the Th1 cell-type responses, was significantly lower in BCG-vaccinated children with JIA compared to healthy children.
Clinical and mycological predictors of cryptococcosis-associated immune reconstitution inflammatory syndrome

Objective:HIV-infected patients with treated cryptococcal meningitis are at risk for further neurological deterioration after commencing combination antiretroviral therapy (cART), mostly because of cryptococcosis-associated immune reconstitution inflammatory syndrome (C-IRIS). Identifying predictors of C-IRIS could enable risk stratification. Design:Prospective, longitudinal cohort study for 24 weeks. Setting:Durban, South Africa. Participants:One hundred and thirty HIV-infected patients with first cryptococcal meningitis episode Intervention:Antifungal therapy (amphotericin 1 mg/kg median 14 days, followed by consolidation and maintenance fluconazole) and cART (commenced median of 18 days from cryptococcal meningitis diagnosis). Main outcome measure:Clinical, blood, and cerebrospinal fluid (CSF) markers associated with C-IRIS before and during cART and clinical significance of CSF cryptococcal culture negativity pre-cART commencement. Results:Of 106 patients commencing cART, 27 (25.5%) developed C-IRIS, 16 (15.1%) neurological deterioration-not C-IRIS, and 63 (59.4%) no neurological deterioration. On multivariable analysis, C-IRIS was associated with persistent CSF cryptococcal growth [hazard ratio (HR) 0.27, P = 0.026] and lower CSF protein (HR 0.53, P = 0.059) prior to cART and lower CD4+ T-cell increases (HR 0.99, P = 0.026) but not change in HIV viral load during cART. Using survival analysis, patients with a negative cryptococcal culture pre-cART commencement (n = 51; 48.1%) experienced fewer episodes of neurological deterioration, C-IRIS, and cryptococcal relapse/persistence than patients with culture positivity (n = 55; 51.9%, HR 0.33, 0.33, and 0.12 and P = 0.0003, 0.0042, and 0.0004, respectively). Conclusion:Persistent CSF cryptococcal growth at cART initiation and poor CD4+ T-cell increases on cART are strong predictors of C-IRIS. Approaches aimed at achieving CSF culture negativity prior to cART should be evaluated as a strategy to reduce rates of C-IRIS.
On the Relative Strengths of Model-Based and Dynamic Event Extraction-Based GUI Testing Techniques: An Empirical Study

Many software systems rely on graphical-user interfaces (GUIs) to support user interactions. The correctness of these GUIs affects the overall quality of the systems, and thus, it is important that GUIs be tested. To support such testing, GUI test case generation techniques based on graph models such as event flow graphs (EFGs) have been used to generate test cases in the form of sequences of events. Models, however, are abstractions of dynamic behavior and may not accurately reflect actual system behavior, thus, test case generation techniques based on models may create nonexecutable test cases and miss important events. Test case generation techniques based on dynamic event extraction-based approaches, in contrast, may suffer less from these effects. As a consequence, we expect that the two approaches will differ in terms of cost and effectiveness. In this paper, we report the results of an empirical study comparing the cost and effectiveness of model-based and dynamic event extraction-based test case generation approaches. Our results show that event extraction-based approaches, though more expensive than model-based approaches, are indeed more effective in terms of their ability to achieve code coverage and to cover events, but at additional cost, with implications for both researchers and practitioners.
Phylogenetic convergence and multiple shell shape optima for gliding scallops (Bivalvia: Pectinidae)

An important question in evolutionary biology is how often, and to what extent, do similar ecologies elicit distantly related taxa to evolve towards the same phenotype? In some scenarios, the repeated evolution of particular phenotypes may be expected, for instance when species are exposed to common selective forces that result from strong functional demands. In bivalved scallops (Pectinidae), some species exhibit a distinct swimming behaviour (gliding), which requires specific biomechanical attributes to generate lift and reduce drag during locomotive events. Further, a phylogenetic analysis revealed that gliding behaviour has independently evolved at least four times, which raises the question as to whether these independent lineages have also converged on a similar phenotype. Here, we test the hypothesis that gliding scallops display shell shape convergence using a combination of geometric morphometrics and phylogenetic comparative methods that evaluate patterns of multivariate trait evolution. Our findings reveal that the gliding species display less morphological disparity and significant evolutionary convergence in morphospace, relative to expectations under a neutral model of Brownian motion for evolutionary phenotypic change. Intriguingly, the phylomorphospace patterns indicate that gliding lineages follow similar evolutionary trajectories to not one, but two regions of morphological space, and subsequent analyses identified significant differences in their biomechanical parameters, suggesting that these two groups of scallops accomplish gliding in different ways. Thus, whereas there is a clear gliding morphotype that has evolved convergently across the phylogeny, functionally distinct morphological subforms are apparent, suggesting that there may be two optima for the gliding phenotype in the Pectinidae.
Controlled synthesis and characteristics of large‐area and high‐filling nickel nanowires arrays in AAO template

The regular and uniform size of nickel nanowires arrays has been successfully fabricated inside the nanochannels of anodic aluminium oxide (AAO) template by a simple paired cell method. The morphology, composition and structure of the nanowire arrays were characterised by field emission scanning electron microscopy, X-ray diffraction and transmission electron microscopy. The results show that Ni nanowires possess smooth surface and high aspect ratio up to 15 with a diameter of 70-80 nm. Nearly 100% of the pores were filled by Ni nanowires, which have face centre cubic structure and [111] preferential orientation. Magnetisation measurement revealed that the nickel nanowires arrays have a unique soft magnetic property with small coercivity (Hc) of 11.38 Oe. A 3D self-seed nucleation coalescent process was proposed for the formation of nickel nanowires structures. The simple synthetic route is expected to be applied to the synthesis of other highly ordered metal nanowires arrays.
Gender-Dependent Survival of Allogeneic Trophoblast Stem Cells in Liver

In view of the well-known phenomenon of trophoblast immune privilege, trophoblast stem cells (TSCs) might be expected to be immune privileged, which could be of interest for cell or gene therapies. Yet in the ectopic sites tested so far, TSC transplants fail to show noticeable immune privilege and seem to lack physiological support. However, we show here that after portal venous injection, green fluorescent protein (GFP)-labeled TSCs survive for several months in the livers of allogeneic female but not male mice. Gonadectomy experiments revealed that this survival does not require the presence of ovarian hormones but does require the absence of testicular factors. By contrast, GFP-labeled allogeneic embryonic stem cells (ESCs) are reliably rejected; however, these same ESCs survive when mixed with unlabeled TSCs. The protective effect does not require immunological compatibility between ESCs and TSCs. Tumors were not observed in animals with either successfully engrafted TSCs or coinjected ESCs. We conclude that in a suitable hormonal context and location, ectopic TSCs can exhibit and confer immune privilege. These findings suggest applications in cell and gene therapy as well as a new model for studying trophoblast immunology and physiology.