Miracle-dz/UniFAR-FTUs huggingface dataset:
The Hodge filtration on nonabelian cohomology

This is partly a survey article on nonabelian Hodge theory, but we also give proofs of results that have only been announced elsewhere. In the introduction we discuss a wide range of recent work on this subject and give some references. In the body of the paper, we discuss Corlette's nonabelian Hodge theorem, Hitchin's quaternionic structure on the moduli space of representations of $\pi _1(X)$ (for a compact K\"ahler manifold $X$), and Deligne's construction of the resulting twistor space. We then mention the interpretation of Deligne's space of $\lambda$-connections as the Hodge filtration of the nonabelian de Rham cohomology $M_{DR}(X,G)= H^1(X,G)$. We go on to prove several properties of this Hodge filtration, such as Griffiths transversality and regularity of the Gauss-Manin connection; a local triviality property coming from Goldman and Millson's analysis of the singularities; and a weight property coming from Langton's theory. We construct a compactification of $M_{DR}$ using the Hodge filtration with its weight property. At the end, we define a nonabelian version of the Noether-Lefschetz locus, and prove that it is algebraic if the base of the fibration is compact. We pose the open problem of studying degenerations of nonabelian Hodge structure sufficiently well to be able to prove algebraicity of the Noether-Lefshetz locus even when the base is quasiprojective.
A detailed study of the deformation of high purity niobium single crystals

Abstract A study has been made of the stress-strain behaviour, secondary slip geometry and slip line morphology of niobium single crystals purified by annealing in ultra-high vacuum. Within favourable limits of orientation, temperature and strain rate the stress—strain curves exhibit well-defined three-stage hardening. The principal secondary slip system is not usually that bearing the highest proportion of the applied stress and this anomalous behaviour can account for the orientation dependence of overshoot. For temperatures below 250°K the stress-strain curve is non-linear and the initial hardening rate very high. The slip lines observed on crystals deformed at low temperatures belong to a {110} ⟨111⟩ system which, in extreme orientations, is only the sixth most highly stressed system. The slip appears as crystallographic lamellae, in contrast to the wavy slip observed for all other systems.
Numerical Simulation Method of Tensile Behavior of Glass Fiber Laminates

Based on the structural characteristics of glass fiber laminates, a novel finite element numerical model of the laminates was proposed and established with ANSYS software. The results from the FE analysis are compared with available test data in the literature [1], which indicate the numerical model is reasonable and reliable. At same time, tensile behavior and shear behavior of the glass fiber laminates was analyzed. This study can provide reference for glass fiber laminates design and calculation, and has important practical value.
Unsupervised Learning for Physical Interaction through Video Prediction

A core challenge for an agent learning to interact with the world is to predict how its actions affect objects in its environment. Many existing methods for learning the dynamics of physical interactions require labeled object information. However, to scale real-world interaction learning to a variety of scenes and objects, acquiring labeled data becomes increasingly impractical. To learn about physical object motion without labels, we develop an action-conditioned video prediction model that explicitly models pixel motion, by predicting a distribution over pixel motion from previous frames. Because our model explicitly predicts motion, it is partially invariant to object appearance, enabling it to generalize to previously unseen objects. To explore video prediction for real-world interactive agents, we also introduce a dataset of 59,000 robot interactions involving pushing motions, including a test set with novel objects. In this dataset, accurate prediction of videos conditioned on the robot's future actions amounts to learning a "visual imagination" of different futures based on different courses of action. Our experiments show that our proposed method produces more accurate video predictions both quantitatively and qualitatively, when compared to prior methods.
Computer assessment of the composition of a generic wound by image processing

This paper addresses the assessment of the composition of a general wound, in terms of all identifiable categories of tissue and pigmentation in an attempt to improve accuracy in assessing and monitoring wound health. Materials and Methods: A knowledgebase of clusters was built into the hue, saturation and intensity (HSI) color space and then used for assessing wound composition. Based on the observation that the clusters are fairly distinct, two different algorithms, that is, Mahalanobis distance (MD)based and the rotated coordinate system (RCS) method, were used for classification. These methods exploit the shape, spread, and orientation of each cluster. Results: The clusters in the HSI color space,built from about 9,000 (calibrated) pixels from 48 images of various wound beds, showed 8 fairly distinct regions. The inter‑cluster distances were consistent with the visual appearance. The efficacy of the MD and RCS based methods in 120 experiments taken from a set of 15 test images (in terms of average percent‑match) was found to be 91.55 and 93.71, respectively. Conclusion: Our investigations established eight categories of tissue and pigmentation in wound beds. These findings help to determine the stage of wound healing more accurately and comprehensively than typically permitted through use of the 4‑color model reported in the literature for addressing specific wound types.
GmCLC1 Confers Enhanced Salt Tolerance through Regulating Chloride Accumulation in Soybean

The family of chloride channel proteins that mediate Cl- transportation play vital roles in plant nutrient supply, cellular action potential and turgor pressure adjustment, stomatal movement, hormone signal recognition and transduction, Cl- homeostasis, and abiotic and biotic stress tolerance. The anionic toxicity, mainly caused by chloride ions (Cl-), on plants under salt stress remains poorly understood. In this work, we investigated the function of soybean Cl-/H+ antiporter GmCLC1 under salt stress in transgenic Arabidopsis thaliana, soybean, and yeast. We found that GmCLC1 enhanced salt tolerance in transgenic A. thaliana by reducing the Cl- accumulation in shoots and hence released the negative impact of salt stress on plant growth. Overexpression of GmCLC1 in the hairy roots of soybean sequestered more Cl- in their roots and transferred less Cl- to their shoots, leading to lower relative electrolyte leakage values in the roots and leaves. When either the soybean GmCLC1 or the yeast chloride transporter gene, GEF1, was transformed into the yeast gef1 mutant, and then treated with different chloride salts (MnCl2, KCl, NaCl), enhanced survival rate was observed. The result indicates that GmCLC1 and GEF1 exerted similar effects on alleviating the stress of diverse chloride salts on the yeast gef1 mutant. Together, this work suggests a protective function of GmCLC1 under Cl- stress.
Characterization of E2F8, a novel E2F-like cell-cycle regulated repressor of E2F-activated transcription

The E2F family of transcription factors are downstream effectors of the retinoblastoma protein, pRB, pathway and are essential for the timely regulation of genes necessary for cell-cycle progression. Here we describe the characterization of human and murine E2F8, a new member of the E2F family. Sequence analysis of E2F8 predicts the presence of two distinct E2F-related DNA binding domains suggesting that E2F8 and, the recently, identified E2F7 form a subgroup within the E2F family. We show that E2F transcription factors bind the E2F8 promoter in vivo and that expression of E2F8 is being induced at the G1/S transition. Purified recombinant E2F8 binds specifically to a consensus E2F-DNA-binding site indicating that E2F8, like E2F7, binds DNA without the requirement of co-factors such as DP1. E2F8 inhibits E2F-driven promoters suggesting that E2F8 is transcriptional repressor like E2F7. Ectopic expression of E2F8 in diploid human fibroblasts reduces expression of E2F-target genes and inhibits cell growth consistent with a role for repressing E2F transcriptional activity. Taken together, these data suggest that E2F8 has an important role in turning of the expression of E2F-target genes in the S-phase of the cell cycle.
Smooth-surface reconstruction in near-linear time

A surface reconstruction algorithm takes as input a set of sample points from an unknown closed and smooth surface in 3-d space, and produces a piece-wise linear approximation of the surface that contains the sample points. Recently, several algorithms with a correctness guarantee have been proposed. They have unfortunately a worst-case running time that is quadratic in the size of the input because they are based on the construction of 3-d Voronoi diagrams or Delaunay tetrahedrizations which can have quadratic size. In this paper, we describe a new algorithm that also has a correctness guarantee but whose worst-case running time is O(n log n) where n is the input size. This is actually optimal. As in some of the previous algorithms, the piece-wise linear approximation produced by the new algorithm is a triangulation which is a subset of the 3-d Delaunay tetrahedrization.
Music for medical indications in the neonatal period: a systematic review of randomised controlled trials

Objective: To conduct a systematic review of the efficacy of music for medical indications in term or preterm neonates. Methods: We searched 17 electronic databases, subject bibliographies, reference lists and trials registries. Two reviewers independently screened studies for inclusion, assessed methodological quality, and extracted data. Meta-analysis was not feasible due to heterogeneity in outcomes so a qualitative analysis is presented. Results: Nine randomised trials were included. The methodological quality was generally poor (median Jadad score = 1). The outcomes most commonly reported were physiological measures (heart rate (HR), respiratory rate, oxygen saturation (Sao2)), behavioural state and pain. Six studies evaluated music for the painful procedures circumcision (three trials) and heel prick (three trials). For circumcisions, one high quality pilot study (n = 23) showed benefits of music for the outcomes of HR, Sao2 and pain, while two low quality studies showed no difference. For heel prick, three low quality studies provided some evidence that music may be beneficial primarily for measures of behaviour and pain. The remaining studies evaluated the use of music in preterm infants to improve physiological and behavioural parameters (n = 31; benefits observed for behavioural parameters), to reinforce non-nutritive sucking via use of a pacifier activated lullaby (n = 32; significant increase in feeding rates), and to influence physiological stability and behaviours in infants with chronic lung disease (n = 22; no significant differences for outcomes assessed). Conclusions: The heterogeneity in study populations, interventions and outcomes precludes definitive conclusions around efficacy. There is preliminary evidence for some therapeutic benefits of music for specific indications; however, these findings need to be confirmed in methodologically rigorous trials.
The Elastic Properties of the Arterial Wall

HAVING found it desirable, in the course of some investigations on the form of the pulse-wave, to elucidate one or two points connected with the elasticity of the arteries, I was led to undertake a number of experiments on the subject. These observations have become more extended than was at first contemplated, so much so that I consider it advisable to describe in a separate communication the results at which I have arrived. At first I sought only to determine, by direct experiment, what is the relation which exists between the intra-arterial pressure and the cubic capacity of any given portion of artery. In the course of my work on this subject, however, a number of facts came under my notice which seemed to deserve further investigation, and I was thus led to widen the limits of my experiments.
Accommodation mechanisms for grain boundary sliding as inferred from texture evolution during superplastic deformation

To gain insight into accommodation mechanisms for local stress concentrations produced by grain boundary sliding (GBS), we systematically examined texture evolution within a superplastic magnesium alloy undergoing deformation at a relatively low deformation temperature (at which basal slip is known to be the preferred slip system in magnesium). Although we did observe an overall weakening of the initial basal texture during superplastic deformation, we also observed within the interior of the specimen a convergent evolution that depends on loading direction. We attribute this texture evolution within the bulk to the competing effects of (a) orientation divergence due to grain rotation accompanied by GBS and (b) convergent evolution due to slip, which acts primarily as an accommodation mechanism for GBS. In contrast, at the near-surface, we found the initial orientation to be preserved, indicating that slip accommodation is less important near the surface than within the bulk.
A dual neural network for redundancy resolution of kinematically redundant manipulators subject to joint limits and joint velocity limits

In this paper, a recurrent neural network called the dual neural network is proposed for online redundancy resolution of kinematically redundant manipulators. Physical constraints such as joint limits and joint velocity limits, together with the drift-free criterion as a secondary task, are incorporated into the problem formulation of redundancy resolution. Compared to other recurrent neural networks, the dual neural network is piecewise linear and has much simpler architecture with only one layer of neurons. The dual neural network is shown to be globally (exponentially) convergent to optimal solutions. The dual neural network is simulated to control the PA10 robot manipulator with effectiveness demonstrated.
Time‐resolved and spatio‐temporal analysis of complex cognitive processes and their role in disorders like developmental dyscalculia

The aim of this article is to report on the importance and challenges of a time‐resolved and spatio‐temporal analysis of fMRI data from complex cognitive processes and associated disorders using a study on developmental dyscalculia (DD). Participants underwent fMRI while judging the incorrectness of multiplication results, and the data were analyzed using a sequence of methods, each of which progressively provided more a detailed picture of the spatio‐temporal aspect of this disease. Healthy subjects and subjects with DD performed alike behaviorally, though they exhibited parietal disparities using traditional “voxel‐based” group analyses. Further and more detailed differences, however, surfaced with a “time‐resolved” examination of the neural responses during the experiment. While performing intergroup comparisons, a third group of subjects with dyslexia but with no arithmetic difficulties was included to test the specificity of the analysis and strengthen the statistical base with overall 58 subjects. Surprisingly, the analysis showed a functional dissimilarity during an initial reading phase for the group of dyslexic but otherwise normal subjects, with respect to controls, though only numerical digits and no alphabetic characters were presented. Thus, our results suggest that “time‐resolved multivariate” analysis of complex experimental paradigms has the ability to yield powerful new clinical insights about abnormal brain function. Similarly, a detailed compilation of aberrations in the functional cascade may have much greater potential to delineate the core processing problems in mental disorders. © 2012 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 22, 81–96, 2012
Seizure Onset Determination

Digital electroencephalography has greatly expanded the opportunities for data analysis. Although commercial software packages are available they seem not to be used as widely in the preoperative work-up of epilepsy patients as might be warranted. This review will demonstrate that seizure onset can be better defined by judicious use of post hoc filter settings, expanded electrode coverage, and special electrode montages. In scalp recordings, ictal baseline shifts and infraslow activity (ISA) can be evaluated with conventional EEG systems by opening the high-pass filter to 0.01 Hz; in intracranial recordings high-frequency activity (>60 Hz; HFA) can be observed in addition. Inasmuch as ISA and HFA have considerably smaller electrical fields than the conventional frequencies they may better define seizure onset than might be possible otherwise. It is recommended that to determine the clinical value of ISA and HFA for epilepsy surgery, retrospective analyses of seizure data, which include assessment of ISA and HFA, be performed from patients who have undergone surgical resections of epileptogenic tissue. These may yield information as to whether or not the epileptogenic areas of ISA and HFA had been included in the resected tissue and their relationship to surgical outcome can then be determined.
Efficacy of everolimus (RAD001) in patients with advanced NSCLC previously treated with chemotherapy alone or with chemotherapy and EGFR inhibitors.

BACKGROUND Treatment options are scarce in pretreated advanced non-small-cell lung cancer (NSCLC) patients. RAD001, an oral inhibitor of the mammalian target of rapamycin (mTOR), has shown phase I efficacy in NSCLC. METHODS Stage IIIb or IV NSCLC patients, with two or fewer prior chemotherapy regimens, one platinum based (stratum 1) or both chemotherapy and epidermal growth factor receptor tyrosine kinase inhibitors (stratum 2), received RAD001 10 mg/day until progression or unacceptable toxicity. Primary objective was overall response rate (ORR). Analyses of markers associated with the mTOR pathway were carried out on archival tumor from a subgroup using immunohistochemistry (IHC) and direct mutation sequencing. RESULTS Eighty-five patients were enrolled, 42 in stratum 1 and 43 in stratum. ORR was 4.7% (7.1% stratum 1; 2.3% stratum 2). Overall disease control rate was 47.1%. Median progression-free survivals (PFSs) were 2.6 (stratum 1) and 2.7 months (stratum 2). Common > or =grade 3 events were fatigue, dyspnea, stomatitis, anemia, and thrombocytopenia. Pneumonitis, probably or possibly related, mainly grade 1/2, occurred in 25%. Cox regression analysis of IHC scores found that only phospho AKT (pAKT) was a significant independent predictor of worse PFS. CONCLUSIONS RAD001 10 mg/day was well tolerated, showing modest clinical activity in pretreated NSCLC. Evaluation of RAD001 plus standard therapy for metastatic NSCLC continues.
Elicitation of health state utilities in metastatic renal cell carcinoma

Abstract Objective: The aim of the study was to obtain United Kingdom societal preferences for receiving newly developed treatments for metastatic renal cell carcinoma. Methods: Health states were developed based on a literature review and in-depth interviews with clinical experts. These states described the burden of both stable and progressive disease, and a variety of commonly encountered toxicities associated with first-line therapies (fatigue, diarrhoea, nausea/vomiting, mucositis, hand/foot syndrome, hypertension and anaemia). These states were further reviewed by additional clinicians and patients to ensure their validity. One hundred members of the general public rated the states using the time trade-off (TTO) methodology to determine health state utility. Results: Stable disease had a utility value of 0.795 whilst progressive disease demonstrated a significant decline with a value of 0.355. The range of toxicities showed a variable impact in line with their toxicity grading from fatigue grade I/II (0.751) to hand/foot syndrome grade III (0.469). Conclusions: This study highlights the burden associated with a number of common toxicities encountered with current first-line mRCC treatments. Practical constraints coupled with the societal nature of the valuation exercise limited the amount of direct involvement by patients. However, these utility values should better permit the consideration of toxicity profiles in establishing the cost-effectiveness of future treatments.
Relax, Cool Down and Scaffold: How to Restore Surface Expression of Folding-Deficient Mutant GPCRs and SLC6 Transporters

Many diseases arise from mutations, which impair protein folding. The study of folding-deficient variants of G protein-coupled receptors and solute carrier 6 (SLC6) transporters has shed light on the folding trajectory, how it is monitored and how misfolding can be remedied. Reducing the temperature lowers the energy barrier between folding intermediates and thereby eliminates stalling along the folding trajectory. For obvious reasons, cooling down is not a therapeutic option. One approach to rescue misfolded variants is to use membrane-permeable orthosteric ligands. Antagonists of GPCRs are—in many instances—effective pharmacochaperones: they restore cell surface expression provided that they enter cells and bind to folding intermediates. Pharmacochaperoning of SLC6 transporters is less readily achieved because the ionic conditions in the endoplasmic reticulum (ER) are not conducive to binding of typical inhibitors. The second approach is to target the heat-shock protein (HSP) relay, which monitors the folding trajectory on the cytosolic side. Importantly, orthosteric ligands and HSP-inhibitors are not mutually exclusive. In fact, pharmacochaperones and HSP-inhibitors can act in an additive or synergistic manner. This was exemplified by rescuing disease-causing, folding-deficient variants of the human dopamine transporters with the HSP70 inhibitor pifithrin-μ and the pharmacochaperone noribogaine in Drosophila melanogaster.
Heterozygosity and survival in blue tits (Cyanistes caeruleus): contrasting effects of presumably functional and neutral loci

The relationship between genetic diversity and fitness has important implications in evolutionary and conservation biology. This relationship has been widely investigated at the individual level in studies of heterozygosity–fitness correlations (HFC). General effects caused by inbreeding and/or local effects at single loci have been used as explanations of HFC, but the debate about the causes of HFC in open, natural populations is still ongoing. Study designs that control for variation in the inbreeding level of the individuals, and knowledge on the function and location of the markers used to measure heterozygosity, are fundamental to understand the causes of HFC. Here we investigated correlations between individual heterozygosity and estimates of survival at different life‐history stages in an open population of blue tits (Cyanistes caeruleus). For survival at the embryo, nestling and fledgling stage, we used a full‐sibling approach, i.e. we controlled for the level of inbreeding. We genotyped 1496 individuals with 79 microsatellites mapped across 25 chromosomes in the zebra finch (Taeniopygia guttata) that were classified either as potentially functional (58 loci) or as neutral (21 loci). We found different effects of standardized multilocus heterozygosity (SH): SHfunctional had a negative effect on the probability of hatching and local recruitment of females, whereas SHneutral had a positive effect on adult survival. The negative effects of functional loci are better explained by local effects, whereas the positive effects of neutral markers could reflect inbreeding effects in the population. Our results highlight the importance of considering the characteristics of the markers used in HFC studies and confirm the mixed effects of heterozygosity in different contexts (e.g. sex and life‐history stage).