Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical Evaluation and Cost-Effectiveness Analysis of Serum Tumor Markers in Lung Cancer

The detection of serum tumor markers is valuable for the early diagnosis of lung cancer. Tumor markers are frequently used for the management of cancer patients. However, single markers are less efficient but marker combinations increase the cost, which is troublesome for clinics. To find an optimal serum marker combination panel that benefits the patients and the medical management system as well, four routine lung cancer serum markers (SCCA, NSE, CEA, and CYFRA21-1) were evaluated individually and in combination. Meanwhile, the costs and effects of these markers in clinical practice in China were assessed by cost-effectiveness analysis. As expected, combinations of these tumor markers improved their sensitivity for lung cancer and different combination panels had their own usefulness. NSE + CEA + CYFRA21-1 was the optimal combination panel with highest Youden's index (0.64), higher sensitivity (75.76%), and specificity (88.57%), which can aid the clinical diagnosis of lung cancer. Nevertheless, the most cost-effective combination was SCCA + CEA, which can be used to screen the high-risk group.
Microbiological, Epidemiological, and Clinical Characteristics and Outcomes of Patients with Cryptococcosis in Taiwan, 1997–2010

Background Among members of Cryptococcus neoformans- Cryptococcus gattii species complex, C. neoformans is distributed worldwide whereas C. gattii is considered to be more prevalent in the subtropics and tropics including Taiwan. This nationwide study was undertaken to determine the distribution of genotypes, clinical characteristics and outcomes of 219 patients with proven cryptococcosis at 20 hospitals representative of all geographic areas in Taiwan during 1997–2010. Methods and Findings Of 219 isolates analyzed, C. neoformans accounted for 210 isolates (95.9%); nine isolates were C. gattii (4.1%). The predominant genotype was VNI (206 isolates). The other genotypes included VNII (4 isolates), VGI (3 isolates) and VGII (6 isolates). Antifungal minimal inhibition concentrations higher than epidemiologic cutoff values (ECVs) were found in nine VNI isolates (7 for amphotericin B). HIV infection was the most common underlying condition (54/219, 24.6%). Among HIV-negative patients, liver diseases (HBV carrier or cirrhosis) were common (30.2%) and 15.4% did not have any underlying condition. Meningoencephalitis was the most common presentation (58.9%), followed by pulmonary infection (19.6%) and “others” (predominantly cryptococcemia) (18.7%). The independent risk factors for 10-week mortality, by multivariate analysis, were cirrhosis of liver (P = 0.014) and CSF cryptococcal antigen titer ≥512 (P = 0.020). All except one of 54 HIV-infected patients were infected by VNI genotype (98.1%). Of the 13 isolates of genotypes other than VNI, 12 (92.3%) were isolated from HIV-negative patients. HIV-infected patients compared to HIV-negative patients were more likely to have meningoencephalitis and serum cryptococcal antigen ≥1∶512. Patients infected with C. gattii compared to C. neoformans were younger, more likely to have meningoencephalitis (100% vs. 57%), reside in Central Taiwan (56% vs. 31%), and higher 10-week crude mortality (44.4% vs. 22.2%). Conclusions Cryptococcus neoformans in Taiwan, more prevalent than C. gatii, has a predominant VNI genotype. Isolates with antifungal MIC higher than ECVs were rare.
Analysis of Enterovirus 68 Strains from the 2014 North American Outbreak Reveals a New Clade, Indicating Viral Evolution

Enterovirus 68 (EVD68) causes respiratory illness, mostly in children. Despite a reported low-level of transmission, the occurrence of several recent outbreaks worldwide including the 2014 outbreak in North America has raised concerns regarding the pathogenesis and evolution of EVD68. To elucidate the phylogenetic features of EVD68 and possible causes for the 2014 outbreak, 216 EVD68 strain sequences were retrieved from Genbank, including 22 from the 2014 outbreak. Several geographic and genotypic origins were established for these 22 strains, 19 of which were classified as Clade B. Of these 19 strains, 17 exhibited subsequent clustering and variation in protein residues involved in host-receptor interaction and/or viral antigenicity. Approximately 18 inter-clade variations were detected in VP1, which led to the identification of a new Clade D in EVD68 strains. The classification of this new clade was also verified by the re-construction of a Neighbor-Joining tree during the phylogenetic analysis. In addition, our results indicate that members of Clade B containing highly specific alterations in VP1 protein residues were the foremost contributors to the 2014 outbreak in the US. Altered host-receptor interaction and/or host immune recognition may explain the evolution of EVD68 as well as the global emergence and ongoing adaptation of this virus.
The effect of student attributes on success in programming

This paper examines the relationship between student results in a first year programming course and predisposition factors of gender, prior computing experience, learning style and academic performance to date. While the study does not suggest that any dominant attributes are related to success in programming, there are some interesting outcomes which will have implications for teaching and learning.
Stability of optimal-order approximation by bivariate splines over arbitrary triangulations

Let A be a triangulation of some polygonal domain in R2 and Skr(A) the space of all bivariate Cr piecewise polynomials of total degree 3r + 2, that can be used to provide the highest order of approximation, with the property that the approximation constant of this order is independent of the geometry of A with the exception of the smallest angle in the partition. This result is obtained by means of a careful choice of locally supported basis functions which, however, require a very technical proof to justify their stability in optimal-order approximation. A new formulation of smoothness conditions for piecewise polynomials in terms of their B-net representations is derived for this purpose.
Race, ethnicity and the strength of Facebook ties

ABSTRACT This study investigates the role of race and ethnicity in the self-reported strength of the social ties of young adolescents on Facebook. Based on the social diversification hypothesis, which argues that in multicultural societies, race and ethnicity are key factors that shape the nature of associations, we examine whether there are ethnic and racial differences in the size and strength of the ties of adolescent Facebook users and the role of the strength of these ties in several positive outcomes. Using data from the U.S. Teens’ Social Media and Privacy Survey conducted by the Pew Research Center’s Internet & American Life project among 802 teens ages 12–17, we found no differences in the total number of ties that adolescents from different ethnic and racial groups reported. However, African Americans reported significantly higher number of weak ties, while White Americans had a significantly higher number of strong ties. The results are consistent with the social diversification hypothesis. The implications of the findings are discussed.
Structure of Urban Movements: Polycentric Activity and Entangled Hierarchical Flows

The spatial arrangement of urban hubs and centers and how individuals interact with these centers is a crucial problem with many applications ranging from urban planning to epidemiology. We utilize here in an unprecedented manner the large scale, real-time ‘Oyster’ card database of individual person movements in the London subway to reveal the structure and organization of the city. We show that patterns of intraurban movement are strongly heterogeneous in terms of volume, but not in terms of distance travelled, and that there is a polycentric structure composed of large flows organized around a limited number of activity centers. For smaller flows, the pattern of connections becomes richer and more complex and is not strictly hierarchical since it mixes different levels consisting of different orders of magnitude. This new understanding can shed light on the impact of new urban projects on the evolution of the polycentric configuration of a city and the dense structure of its centers and it provides an initial approach to modeling flows in an urban system.
Emulating the Visual Receptive-Field Properties of MST Neurons with a Template Model of Heading Estimation

We have proposed previously a computational neural-network model by which the complex patterns of retinal image motion generated during locomotion (optic flow) can be processed by specialized detectors acting as templates for specific instances of self-motion. The detectors in this template model respond to global optic flow by sampling image motion over a large portion of the visual field through networks of local motion sensors with properties similar to those of neurons found in the middle temporal (MT) area of primate extrastriate visual cortex. These detectors, arranged within cortical-like maps, were designed to extract self-translation (heading) and self-rotation, as well as the scene layout (relative distances) ahead of a moving observer. We then postulated that heading from optic flow is directly encoded by individual neurons acting as heading detectors within the medial superior temporal (MST) area. Others have questioned whether individual MST neurons can perform this function because some of their receptive-field properties seem inconsistent with this role. To resolve this issue, we systematically compared MST responses with those of detectors from two different configurations of the model under matched stimulus conditions. We found that the characteristic physiological properties of MST neurons can be explained by the template model. We conclude that MST neurons are well suited to support self-motion estimation via a direct encoding of heading and that the template model provides an explicit set of testable hypotheses that can guide future exploration of MST and adjacent areas within the superior temporal sulcus.
The shared principalship: invitation at the top

Abstract A school principal’s workload is recognised as being heavy, with an imbalance between demands and resources. This paper contributes to the development of collective leadership. The principalship constellations of six schools in Sweden were studied with the aim of strengthening the current knowledge about structures and experiences of shared principalship. The empirical basis is qualitative data from interviews with principals and vice-principals. The analytical focus was on how the sharing structures were organised and how the shared principalship was experienced. The results point to a considerable variation in the organisational structures of shared principalship. Despite the type of model, form and constellation, the principals and vice-principals voiced a striking sense of relief in not feeling alone in their duties, as problems and troubles became manageable. An intensified interaction level in the principalship constellation created opportunities to develop competence. Theoretically, this study broadens the invited leadership concept to include horizontal invitations across unit boundaries between principals in different units within the same school. The knowledge contribution of this study is useful in discussing the legal possibilities for shared principalship, which may be especially relevant in times when the Swedish school system is being criticised for not delivering good student outcomes.
The M-triangle of generalised non-crossing partitions for the types E7 and E8

The M-triangle of a ranked locally finite poset P is the generating function P u,w2P µ(u,w)x rk u y rk w , where µ(.,.) is the Mobius function of P. We compute the M- triangle of Armstrong's poset of m-divisible non-crossing partitions for the root systems of type E7 and E8. For the other types except Dn this had been accomplished in the earlier paper "The F-triangle of the generalised cluster complex" (in: "Topics in Discrete Mathematics," M. Klazar, J. Kratochvil, M. Loebl, J. Matousek, R. Thomas and P. Valtr, eds., Springer- Verlag, Berlin, New York, 2006, pp. 93-126). Altogether, this almost settles Armstrong's F = M Conjecture, predicting a surprising relation between the M-triangle of the m-divisible partitions poset and the F-triangle (a certain refined face count) of the generalised cluster complex of Fomin and Reading, the only gap remaining in type Dn. Moreover, we prove a reciprocity result for this M-triangle, again with the possible exception of type Dn. Our results are based on the calculation of certain decomposition numbers for the reflection groups of types E7 and E8, which carry in fact finer information than the M-triangle does. The decomposition numbers for the other exceptional reflection groups had been computed in the earlier paper. As an aside, we show that there is a closed form product formula for the type An decomposition numbers, leaving the problem of computing the type Bn and type Dn decomposition numbers open.
Violence in the name of god? A framing processes approach to the Islamic State in Iraq and Syria

Abstract Since summer 2014, the insurgent group ‘Islamic State in Iraq and Syria’ (ISIS) has become a major concern for international politics and global security due to its rapid territorial gains, violent operations and the propagation of Salafi-jihadist ideology. This study aims to enhance the academic understanding of ISIS by demystifying the ideological reasoning behind its use of violence. It therefore investigates the link between structural factors that served ISIS’s evolution, its ideological outlook and the significance of this ideology to legitimize violent action. As its theoretical basis, the study employs framing processes within the study of social movements. Methodologically, discursive frame analysis serves to explore the relation of ISIS’s ideology to structural events and experiences to better understand how the group justifies violence. Therefore, the study draws on audio speeches and issues of the magazines Dabiq and Dar al-Islam published by ISIS, which are examined on the rhetoric of othering, collective identity and justifying violence. It is argued that ISIS constructs a collective action frame which creates a social reality that bestows the group with a rationale for action. ISIS’s ideology, based on Islamic symbolism, presents an interpretative lens which assigns meaning to the structural environment of ISIS’s emergence. In this context, violence is justified as a necessity to defend Islam and as an obligation for the true Muslim believer. The discussion concludes that ISIS’s ideology legitimizes the very existence of the group and conceals its mundane struggle for power, territory and wealth through reference to divine authority.
VISUALIZING SCIENTIFIC COMPUTATIONS: A SYSTEM BASED ON LATTICE-STRUCTURED DATA AND DISPLAY MODELS by WILLIAM LOUIS HIBBARD

In this thesis we develop a system that makes scientific computations visible and enables physical scientists to perform visual experiments with their computations. Our approach is unique in the way it integrates visualization with a scientific programming language. Data objects of any user-defined data type can be displayed, and can be displayed in any way that satisfies broad analytic conditions, without requiring graphics expertise from the user. Furthermore, the system is highly interactive. In order to achieve generality in our architecture, we first analyze the nature of scientific data and displays, and the visualization mappings between them. Scientific data and displays are usually approximations to mathematical objects (i.e., variables, vectors and functions) and this provides a natural way to define a mathematical lattice structure on data models and display models. Lattice-structured models provide a basis for integrating certain forms of scientific metadata into the computational and display semantics of data, and also provide a rigorous interpretation of certain expressiveness conditions on the visualization mapping from data to displays. Visualization mappings satisfying these expressiveness conditions are lattice isomorphisms. Applied to the data types of a scientific programming language, this implies that visualization mappings from data aggregates to display aggregates can always be decomposed into mappings of data primitives to display primitives. These results provide very flexible data and display models, and provide the basis for flexible and easy-to-use visualization of data objects occurring in scientific computations. Charles R. Dyer, Professor, Computer Sciences, University of Wisconsin Madison
The Pain in Neuropathy Study (PiNS): a cross-sectional observational study determining the somatosensory phenotype of painful and painless diabetic neuropathy

Abstract Disabling neuropathic pain (NeuP) is a common sequel of diabetic peripheral neuropathy (DPN). We aimed to characterise the sensory phenotype of patients with and without NeuP, assess screening tools for NeuP, and relate DPN severity to NeuP. The Pain in Neuropathy Study (PiNS) is an observational cross-sectional multicentre study. A total of 191 patients with DPN underwent neurological examination, quantitative sensory testing, nerve conduction studies, and skin biopsy for intraepidermal nerve fibre density assessment. A set of questionnaires assessed the presence of pain, pain intensity, pain distribution, and the psychological and functional impact of pain. Patients were divided according to the presence of DPN, and thereafter according to the presence and severity of NeuP. The DN4 questionnaire demonstrated excellent sensitivity (88%) and specificity (93%) in screening for NeuP. There was a positive correlation between greater neuropathy severity (r = 0.39, P < 0.01), higher HbA1c (r = 0.21, P < 0.01), and the presence (and severity) of NeuP. Diabetic peripheral neuropathy sensory phenotype is characterised by hyposensitivity to applied stimuli that was more marked in the moderate/severe NeuP group than in the mild NeuP or no NeuP groups. Brush-evoked allodynia was present in only those with NeuP (15%); the paradoxical heat sensation did not discriminate between those with (40%) and without (41.3%) NeuP. The “irritable nociceptor” subgroup could only be applied to a minority of patients (6.3%) with NeuP. This study provides a firm basis to rationalise further phenotyping of painful DPN, for instance, stratification of patients with DPN for analgesic drug trials.
Bcl-xL inhibition by molecular-targeting drugs sensitizes human pancreatic cancer cells to TRAIL

Tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) induces apoptosis in various types of cancer cells without damaging normal cells. However, in terms of pancreatic cancer, not all cancer cells are sensitive to TRAIL. In this study, we examined a panel of human pancreatic cancer cell lines for TRAIL sensitivity and investigated the effects of Bcl-2 family inhibitors on their response to TRAIL. Both ABT-263 and ABT-737 inhibited the function of Bcl-2, Bcl-xL, and Bcl-w. Of the nine pancreatic cancer cell lines tested, six showed no or low sensitivity to TRAIL, which correlated with protein expression of Bcl-xL. ABT-263 significantly sensitized four cell lines (AsPC-1, Panc-1, CFPAC-1, and Panc10.05) to TRAIL, with reduced cell viability and increased apoptosis. Knockdown of Bcl-xL, but not Bcl-2, by siRNA transfection increased the sensitivity of AsPC-1 and Panc-1 cells to TRAIL. ABT-263 treatment had no effect on protein expression of Bcl-2, Bcl-xL, or c-FLIPs. In Panc-1 cells, ABT-263 increased the surface expression of death receptor (DR) 5; the NF-κB pathway, but not endoplasmic reticulum stress, participated in the increase. In xenograft mouse models, the combination of TRAIL and ATB-737 suppressed the in vivo tumor growth of AsPC-1 and Panc-1 cells. These results indicate that Bcl-xL is responsible for TRAIL resistance in human pancreatic cancer cells, and that Bcl-2 family inhibitors could represent promising reagents to sensitize human pancreatic cancers in DR-targeting therapy.
A multimodal approach to visual thinking: the scientific sketchnote

There is a growing interest in the use of visual thinking techniques for promoting conceptual thinking in problem solving tasks as well as for reducing the complexity of ideas expressed in scientific and technical formats. The products of visual thinking, such as sketchnotes, graphics and diagrams, consist of ‘multimodal complexes’ that combine language, images, mathematical symbolism and various other semiotic resources. This article adopts a social semiotic perspective, more specifically a Systemic Functional Multimodal Discourse Analysis approach, to study the underlying semiotic mechanisms through which visual thinking makes complex scientific content accessible. To illustrate the approach, the authors analyse the roles of language, images, and mathematical graphs and symbolism in four sketchnotes based on scientific literature in physics. The analysis reveals that through the process of resemiotization, where meanings are transformed from one semiotic system to another, the abstractness of specialized discourses such as physics and mathematics is reduced by multimodal strategies which include reformulating the content in terms of entities which participate in observable (i.e. tangible) processes and enhancing the reader/viewer’s engagement with the text. Moreover, the compositional arrangement creates clear stages in the development of the ideas and arguments that are presented. In this regard, visual thinking is a form of cultural communication through which abstract ideas are translated and explained using a multimodal outline or summary of essential parts by adapting resources (e.g. linguistic resources and mathematical graphs), using new resources (e.g. stick figures and other simple schematic drawings) and maintaining others from the original text (e.g. mathematical symbolic notation), resulting in a congruent (or concrete) depiction of abstract concepts and ideas for a non-specialist audience.
Particle-in-Cell Simulations of a Nonlinear Transverse Electromagnetic Wave in a Pulsar Wind Termination Shock

A 2.5-dimensional particle-in-cell code is used to investigate the propagation of a large-amplitude, superluminal, nearly transverse electromagnetic (TEM) wave in a relativistically streaming electron-positron plasma with and without a shock. In the free-streaming, unshocked case, the analytic TEM dispersion relation is verified, and the streaming is shown to stabilize the wave against parametric instabilities. In the confined, shocked case, the wave induces strong, coherent particle oscillations, heats the plasma, and modifies the shock density profile via ponderomotive effects. The wave decays over ≳102 skin depths; the decay length scale depends primarily on the ratio between the wave frequency and the effective plasma frequency, and on the wave amplitude. The results are applied to the termination shock of the Crab pulsar wind, where the decay length-scale (≳0.″05 pc) might be comparable to the thickness of filamentary, variable substructure observed in the optical and X-ray wisps and knots.