Miracle-dz/UniFAR-FTUs huggingface dataset:
Nonlinear Mutual Prediction Test for Synchronization of Stock Markets

The methodologies and assumptions in cross-country financial integration studies are problematic and may lead to spurious empirical results. Using surrogate data analysis and mutual prediction method of testing for nonlinear interdependence, it is feasible for an analyst, with a scant knowledge of the underlying dynamics of two dynamical systems, to show whether the systems are interdependent. This study applies these techniques on three Chinese stock market data: Shanghai, Shenzhen, and Hong Kong. The empirical results of the present study indicate that all three stock market series are nonlinear and that the Chinese stock exchanges are nonlinearly interdependent. These findings have important implications for empirical finance, investment decisions, pricing of financial derivatives, portfolio optimization, and cross-market transmission of volatility. Classification Code : C14, C22, F36
A Hybrid Technique for Creating Meaningful Abstractions of Dynamic 3D Scenes in Real-Time

We present an approach for creating non-photorealistic renderings of 3D scenes in real-time. We employ a hybrid system which uses both image-space and object-space techniques for creating fast and effective results. A reliable method of edge detection is presented to find all important edges within a scene. This edge detection technique is combined with a painterly renderer to render the scene using different levels of abstraction. This is used to increase the saliency of important objects and remove extraneous detail. 3D object information is used to apply an object-based segmentation technique which allows each scene object to be rendered using a single abstraction level depending on its scene importance. The abstraction techniques are implemented on the GPU which helps the system achieve interactive rates.
Ambiguous Melanocytic Tumors With Loss of 3p21

Germline loss-of-function mutations in BAP1 are associated with the development of cutaneous melanocytic tumors with some histopathologic characteristics seen in Spitz nevi. Similar melanocytic tumors occurring in a sporadic setting have been demonstrated to have biallelic loss of BAP1. In some of these sporadic tumors, loss of BAP1 occurs through mutation of 1 allele and genomic loss of the other. We screened our database of comparative genomic hybridization profiles of ambiguous melanocytic tumors to identify cases with a single genomic event involving loss of the BAP1 locus. The prevalence of tumors with a single genomic event involving loss of BAP1 was 6.7% in our study population. We further characterized the BAP1 status in 17 of these tumors with available additional material, confirming loss of BAP1 in all cases. We describe BAP1 loss in a blue nevus–like melanoma and further expand the histopathologic spectrum of spitzoid melanocytic neoplasms with BAP1 loss.
Functional gene pyrosequencing reveals core proteobacterial denitrifiers in boreal lakes

Denitrification is an important microbial process in aquatic ecosystems that can reduce the effects of eutrophication. Here, quantification and pyrosequencing of nirS, nirK, and nosZ genes encoding for nitrite and nitrous oxide reductases was performed in sediment samples from four boreal lakes to determine the structure and seasonal stability of denitrifying microbial populations. Sediment quality and nitrate concentrations were linked to the quantity and diversity of denitrification genes, the abundance of denitrifying populations (nirS and nosZ genes) correlated with coupled nitrification-denitrification (Dn), and the denitrification of the overlying water NO3- (Dw) correlated with the nirS/nirK ratio. The number of core nirS, nirK, and nosZ operational taxonomical units (OTUs) was low (6, 7, and 3, respectively), and most of these core OTUs were shared among the lakes. Dominant nirK sequences matched best with those of the order Rhizobiales, which was one of the main bacterial orders present in the sediment microbiomes, whereas the dominant nirS sequences were affiliated with the order Burkholderiales. Over half of the nosZ sequences belonged to a single OTU of the order Burkholderiales, but coupled nitrification–denitrification rate correlated with another dominant nosZ OTU assigned to the order Rhodospirillales. The study indicates that a few core proteobacterial clusters may drive denitrification in boreal lake sediments, as the same Alpha- and Betaproteobacteria denitrifier clusters were present in different lakes and seasons.
In response: Current evidence and implications—An academic perspective

There is clear evidence that wild pollinators, particularly bees, have undergone long-term decline in North America, Europe, China, and Japan [1]. These are not the only organisms in decline; in Europe, there is strong evidence that populations of birds, butterflies, andmoths (all of the groups for which we have good data) are also falling (e.g., Burns et al. [2]). Despite substantial payouts to farmers in the European Union to deploy agrienvironmental schemes specifically intended to increase biodiversity, wildlife on farmland has declined more than elsewhere [2–4]. In short, it is clear that modern farming systems are a major factor driving wildlife declines. One reason that intensively farmed land becomes less suitable for wildlife is believed to be the use of agrochemicals, especially pesticides [5]. At present, crop insecticides are not species-specific, so they may have effects on nonpest members of the insect fauna that become exposed. Because crop insecticides are imperfectly contained, exposure of organisms in the wider environment is possible. Previously, the risk-assessment schemes for the effect of agrochemicals on bees have been inadequate. Typically, the safety of agrochemicals is examined by conducting acute toxicity tests for each compound on domesticated honeybees and comparing the sensitivity of the response to plausible exposure scenarios in the field, often using ratios between the maximum expected exposure and the dose required to kill 50% of test subjects. The strengths of this approach include its feasibility and its capacity to enable comparative analysis of novel chemicals with large historical data sets comprising active ingredients of known impact, but it suffers several evident weaknesses. First, it misses effects that emerge only from longterm exposures, such as those arising from persistent toxicants. Second, it fails to consider interactions among chemicals (or among chemicals and other stressors), with the current riskassessment process focusing on the risks from exposure to a single product. In actuality, bees (and other wildlife groups) present in farmed areas encounter multiple agrochemicals throughout their lives. Therefore, synergistic interactions between agrochemicals would be discovered only when the chemicals have been approved and are in widespread use, which is far too late if one wishes to prevent environmental harm. Third, it assumes that honeybees are an appropriate sentinel species for impacts on wild bees, whereas in actuality they may be unrepresentatively resilient [6]. Finally, mortality can be a much less sensitive measure of impact than other relevant endpoints, such as fecundity [7]. Some of these shortcomings are being addressed in the new European Union data requirements and imminent new riskassessment scheme [8], which set out clearly defined protection goals, extend testing to a more representative set of bee species, In This Issue:
Transcriptome and small RNA deep sequencing reveals deregulation of miRNA biogenesis in human glioma

Altered expression of oncogenic and tumour‐suppressing microRNAs (miRNAs) is widely associated with tumourigenesis. However, the regulatory mechanisms underlying these alterations are poorly understood. We sought to shed light on the deregulation of miRNA biogenesis promoting the aberrant miRNA expression profiles identified in these tumours. Using sequencing technology to perform both whole‐transcriptome and small RNA sequencing of glioma patient samples, we examined precursor and mature miRNAs to directly evaluate the miRNA maturation process, and examined expression profiles for genes involved in the major steps of miRNA biogenesis. We found that ratios of mature to precursor forms of a large number of miRNAs increased with the progression from normal brain to low‐grade and then to high‐grade gliomas. The expression levels of genes involved in each of the three major steps of miRNA biogenesis (nuclear processing, nucleo‐cytoplasmic transport, and cytoplasmic processing) were systematically altered in glioma tissues. Survival analysis of an independent data set demonstrated that the alteration of genes involved in miRNA maturation correlates with survival in glioma patients. Direct quantification of miRNA maturation with deep sequencing demonstrated that deregulation of the miRNA biogenesis pathway is a hallmark for glioma genesis and progression. Copyright © 2012 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Prevention of Intra-Abdominal Adhesion by Bi-Layer Electrospun Membrane

The aim of this study was to compare the anti-adhesion efficacy of a bi-layer electrospun fibrous membrane consisting of hyaluronic acid-loaded poly(ɛ-caprolactone) (PCL) fibrous membrane as the inner layer and PCL fibrous membrane as the outer layer with a single-layer PCL electrospun fibrous membrane in a rat cecum abrasion model. The rat model utilized a cecal abrasion and abdominal wall insult surgical protocol. The bi-layer and PCL membranes were applied between the cecum and the abdominal wall, respectively. Control animals did not receive any treatment. After postoperative day 14, a visual semiquantitative grading scale was used to grade the extent of adhesion. Histological analysis was performed to reveal the features of adhesion tissues. Bi-layer membrane treated animals showed significantly lower adhesion scores than control animals (p < 0.05) and a lower adhesion score compared with the PCL membrane. Histological analysis of the bi-layer membrane treated rat rarely demonstrated tissue adhesion while that of the PCL membrane treated rat and control rat showed loose and dense adhesion tissues, respectively. Bi-layer membrane can efficiently prevent adhesion formation in abdominal cavity and showed a significantly decreased adhesion tissue formation compared with the control.
Paying for performance--risks and recommendations.

Congress recently called on the Centers for Medicare and Medicaid Services to implement a pay-for-performance system for hospitals, and there is strong interest in expanding such programs to individual physicians. Dr. Elliott Fisher writes that the rush to adopt pay-for-performance programs, however, has raised a number of concerns among physicians and policy analysts.
A Self-Configuring Schema Matching System

Mapping complex metadata structures is crucial in a number of domains such as data integration, ontology alignment or model management. To speed up the generation of such mappings, automatic matching systems were developed to compute mapping suggestions that can be corrected by a user. However, constructing and tuning match strategies still requires a high manual effort by matching experts as well as correct mappings to evaluate generated mappings. We therefore propose a self-configuring schema matching system that is able to automatically adapt to the given mapping problem at hand. Our approach is based on analyzing the input schemas as well as intermediate matching results. A variety of matching rules use the analysis results to automatically construct and adapt an underlying matching process for a given match task. We comprehensively evaluate our approach on different mapping problems from the schema, ontology and model management domains. The evaluation shows that our system is able to robustly return good quality mappings across different mapping problems and domains.
A Fast Direct Solver for the Biharmonic Problem in a Rectangular Grid

We present a fast direct solver methodology for the Dirichlet biharmonic problem in a rectangle. The solver is applicable in the case of the second order Stephenson scheme [J. W. Stephenson, J. Comput. Phys., 55 (1984), pp. 65-80] as well as in the case of a new fourth order scheme, which is discussed in this paper and is based on the capacitance matrix method ([B. L. Buzbee and F. W. Dorr, SIAM J. Numer. Anal., 11 (1974), pp. 1136-1150], [P. Bjorstad, SIAM J. Numer. Anal. , 20 (1983), pp. 59-71]). The discrete biharmonic operator is decomposed into two components. The first is a diagonal operator in the eigenfunction basis of the Laplacian, to which the FFT algorithm is applied. The second is a low-rank perturbation operator (given by the capacitance matrix), which is due to the deviation of the discrete operators from diagonal form. The Sherman-Morrison formula [G. H. Golub and C. F. Van Loan, Matrix Computations, 3rd ed., John Hopkins University Press, Baltimore, MD, 1996] is applied to obtain a fast solution of the resulting linear system of equations.
Reassessing the Facebook experiment: critical thinking about the validity of Big Data research

ABSTRACT The Facebook experiment of 2014 manipulated the contents of nearly 700,000 users’ News Feeds to induce changes in their emotions. This experiment was widely criticized on ethical grounds regarding informed consent. This controversy, however, diverted attention from a more important concern the experiment was intended to address, which is the impact of Facebook use on well-being. In this paper, I explore the well-being concerns raised by prior research and argue that the experiment does not alleviate them, owing to poor research design. As the question of Facebook's impact on well-being is of great importance, both to Facebook and to society overall, there is a pressing need for more experimental research that is both sensitive to informed consent and carefully designed to yield reliable results. In turn, the lessons of this case have implications for general issues of validity that emerge in Big Data research, now in vogue at major scientific venues.
Structuration bridging diffusion of innovations and gender relations theories: a case of paradigmatic pluralism in IS research

This paper discusses the adoption of a pluralist theoretical framework – one that is also multiparadigmatic – for conducting and publishing information system (IS) research. The discussion is illustrated by a single case study involving the Australian cotton industry. The theoretical framework is informed by three sociological theories, each with its particular paradigmatic assumptions: structuration theory as a meta‐theory, and diffusion of innovations and gender relations as lower‐level theories from notionally opposing paradigms. Theoretical pluralism helped to produce rich findings, illuminating both the social nature of women farmers' roles, the materiality of the cotton farming context, the characteristics of the decision support systems in use and the recursive way in which human agency and institutional pressures shape each other. Because users of so‐called divergent paradigms often face criticism based on the incommensurability issue, one of the main contributions of this paper is to discuss the value of a pluralist and multiparadigmatic theoretical framework in dealing with complex IS social phenomena.
Comparison of entropy measures for estimating severity of obstructive sleep apnea from overnight pulse oximetry data

Regularity of overnight pulse oximetry data, which can be quantified using entropy, may be used to characterize severity of obstructive sleep apnea syndrome (OSAS). In this paper three entropy measures, namely Shannon-, approximate-and sample entropy, were compared in terms of their ability to discriminate between mild and severe OSAS. In a group of 5 mild OSAS subjects, with apnea hypopnea index (AHI) <10, and 20 severe OSAS subjects, with AHI>10, approximate and sample entropy, but not Shannon entropy, produced significantly higher values in the severe OSAS group. More importantly, it was shown that parameters, including the data sampling frequency, the window length m and the tolerance r, may considerably affect the estimated entropy values. It is concluded that approximate as well as sample entropy can both be efficiently used to estimate severity of OSAS from pulse oximetry, provided the above mentioned parameters are carefully defined.
Light curves and colours of the faint Uranian irregular satellites Sycorax, Prospero, Stephano, Setebos, and Trinculo

Context. After the work of Gladman et al. (1998, Nature, 392, 897), it is now assessed that many irregular satellites are orbiting around Uranus. Aims. Despite many studies performed in past years, very little is know about the light-curves of these objects and inconsistencies are present between colours derived by different authors. This situation motivated our effort to improve both the knowledge of colours and light curves. Methods. We present and discuss, the time series observations of Sycorax, Prospero, Stephano, Setebos, and Trinculo, five faint, irregular satellites of Uranus, which were carried out at VLT, ESO Paranal (Chile) on the nights between 29 and 30 July, 2005 and 25 and 30 November, 2005. Results. We derive light curves for Sycorax and Prospero and colours for all of these these bodies. Conclusions. For Sycorax we obtain colours B −V = 0.839 ± 0.014, V −R = 0.531 ± 0.005, and a light-curve which is suggestive of a periodical variation with period ≈3.6 h and amplitude ≈0.067 ± 0.004 mag. The periods and colours we derive also for Sycorax are in agreement with our previous determination in 1999 using NTT. We also derive a light-curve for Prospero which suggests an amplitude of about 0.2 mag and a periodicity of about 4 h. However, the sparseness of our data, prevents a more precise characterization of the light-curves, and we can not determine whether they are one-peaked or two-peaked. Hence, these periods and amplitudes have to be considered preliminary estimates. As for Setebos, Stephano, and Trinculo the present data do not allow us to derive any unambiguous periodicity, despite the fact that Setebos displays a significant variability with amplitude about as large as that of Prospero. Colours for Prospero, Setebos, Stephano, and Trinculo are in marginal agreement with the literature.
A chemiosmotic mechanism of symport

Lactose permease (LacY), a paradigm for the largest family of membrane transport proteins, catalyzes the coupled translocation of a galactoside and an H+ across the Escherichia coli membrane (galactoside/H+ symport). Initial X-ray structures reveal N- and C-terminal domains, each with six largely irregular transmembrane helices surrounding an aqueous cavity open to the cytoplasm. Recently, a structure with a narrow periplasmic opening and an occluded galactoside was obtained, confirming many observations and indicating that sugar binding involves induced fit. LacY catalyzes symport by an alternating access mechanism. Experimental findings garnered over 45 y indicate the following: (i) The limiting step for lactose/H+ symport in the absence of the H+ electrochemical gradient (∆µ̃H+) is deprotonation, whereas in the presence of ∆µ̃H+, the limiting step is opening of apo LacY on the other side of the membrane; (ii) LacY must be protonated to bind galactoside (the pK for binding is ∼10.5); (iii) galactoside binding and dissociation, not ∆µ̃H+, are the driving forces for alternating access; (iv) galactoside binding involves induced fit, causing transition to an occluded intermediate that undergoes alternating access; (v) galactoside dissociates, releasing the energy of binding; and (vi) Arg302 comes into proximity with protonated Glu325, causing deprotonation. Accumulation of galactoside against a concentration gradient does not involve a change in Kd for sugar on either side of the membrane, but the pKa (the affinity for H+) decreases markedly. Thus, transport is driven chemiosmotically but, contrary to expectation, ∆µ̃H+ acts kinetically to control the rate of the process.
Resolving Holliday Junctions with Escherichia coli UvrD Helicase*

Background: The ability of UvrD, a DNA helicase, to unwind a Holliday junction has not been directly tested. Results: UvrD catalyzed robust unwinding of a Holliday junction producing a forked structure. Conclusion: UvrD unwinds a Holliday junction by binding to the junction and translocating along opposite arms. Significance: This result is likely to have relevance in recombination and replication. The Escherichia coli UvrD helicase is known to function in the mismatch repair and nucleotide excision repair pathways and has also been suggested to have roles in recombination and replication restart. The primary intermediate DNA structure in these two processes is the Holliday junction. UvrD has been shown to unwind a variety of substrates including partial duplex DNA, nicked DNA, forked DNA structures, blunt duplex DNA and RNA-DNA hybrids. Here, we demonstrate that UvrD also catalyzes the robust unwinding of Holliday junction substrates. To characterize this unwinding reaction we have employed steady-state helicase assays, pre-steady-state rapid quench helicase assays, DNaseI footprinting, and electron microscopy. We conclude that UvrD binds initially to the junction compared with binding one of the blunt ends of the four-way junction to initiate unwinding and resolves the synthetic substrate into two double-stranded fork structures. We suggest that UvrD, along with its mismatch repair partners, MutS and MutL, may utilize its ability to unwind Holliday junctions directly in the prevention of homeologous recombination. UvrD may also be involved in the resolution of stalled replication forks by unwinding the Holliday junction intermediate to allow bypass of the blockage.
“We don't Talk about that Around Here”: religion, Spirituality and Mental Health in Northern Ireland

Since the early 1970s, Northern Ireland has experienced violent conflict, the boundaries of which are shaped by religious identification. Although the violence has significantly decreased since the late 1990s, its legacy remains. Research evidences a complex relationship between religious and spiritual beliefs and mental well-being, there is a lack of research about how political conflict, in which religion plays a dominant role, may shape how beliefs may shape the impact of faith on mental health. This article draws upon the views and experiences of mental health service users’ from a qualitative study about religion, spirituality, mental health and social work practice. Participants’ accounts state that while the role of religion and spirituality within mental health was recognised, its exploration was marked with questions of legitimacy. This article proposes that support is needed for service users to both acknowledge this aspect of their mental well-being and promote their having choice about its inclusion in their mental health care.