Miracle-dz/UniFAR-FTUs huggingface dataset:
The Triangle Inequality and Character Analysis

With the advent of both analytical and evolutionary models that specify complex character-transformation weights (or probabilities) and computer programs in which they are implemented, the use of multistate characters with elaborate state-transformation costs (matrix characters; Sankoff and Rousseau 1975; Sankoff and Cedergren 1983) is increasing. What has not yet appeared, however, is a general discussion of these characters as they are implemented in various analyses. Since the most prominent use of these characters comes in the phylogenetic analysis of molecular data, it is in this area that the most attention is required. In its simplest incarnation, a matrix character is one which possesses a matrix of values-each cell of which describes a unique cost for a possible character transformation. These costs are the number of steps required to transform one state into another. In a nonadditive or unordered Fitch-type analysis (Fitch 197 1; Farris 1988)) all transformations are equally costly-each constitutes a single step. Programs such as Swofford’s ( 1990) PAUP allow the definition of elaborate “step matrices” in which the number of steps required by any transformation can be specified. This matrix may be as simple as a binary character with different costs for forward changes and reversals or as complex as a multistate character with scores of specified transformations. As an example, character models such as Do110 parsimony (Farris 1977 ) and irreversibility (Camin and Sokal 1965) are, in essence, simple matrix characters, specifying asymmetries in transformation between two states. In both of these cases, changes in one direction are more costly than the reverse, yielding a quantitative polarity statement. Multistate characters allow more complex delineations. In the case of nucleic acid sequence data, there are four nucleotide bases and 12 transformations to be specified, although not all of these are necessarily unique [actually 16, but the identity transformations play no role in parsimony analysis (Wheeler 1990a)]. Most commonly, the matrix specifies only two types of transformation-transitions (purine to purine, A-G; and pyrimidine to pyrimidine, C-T/U) and transversions (purine to pyrimidine and the reverse, such as A-T) (Brown et al. 1982; Liu and Beckenbach 1992). Transition-transversion ratios are frequently specified in analyses, regardless of whether the chosen costs are internally consistent. Transformation values among character states are, in essence, distances. Distances between sequences are these character changes summed over the length of the sequences. When analyzed as such, they must conform to certain logical strictures even if the events they describe do not. Foremost among these is the triangle inequality invoked by Farris ( 198 1, 1985) and others (Swofford 198 1) in their criticisms of distances. The triangle inequality is a property of metric spaces. Distances that do not conform to this relation are nonmetric and, hence, are internally inconsistent because
Histological, Immunohistological, and Clinical Features of Merkel Cell Carcinoma in Correlation to Merkel Cell Polyomavirus Status

Merkel cell carcinoma is a rare, but highly malignant tumor of the skin with high rates of metastasis and poor survival. Its incidence rate rises and is currently about 0.6/100000/year. Clinical differential diagnoses include basal cell carcinoma, cyst, amelanotic melanoma, lymphoma and atypical fibroxanthoma. In this review article clinical, histopathological and immunhistochemical features of Merkel cell carcinoma are reported. In addition, the role of Merkel cell polyomavirus is discussed.
Shear-improved Smagorinsky model for large-eddy simulation of wall-bounded turbulent flows

A shear-improved Smagorinsky model is introduced based on results concerning mean-shear effects in wall-bounded turbulence. The Smagorinsky eddy-viscosity is modified as vT =(Csδ)2(|S|—|〈S〉|): the magnitude of the mean shear |〈S〉|is subtracted from the magnitude of the instantaneous resolved rate-of-strain tensor |S|; CS is the standard Smagorinsky constant and Δ denotes the grid spacing. This subgrid-scale model is tested in large-eddy simulations of plane-channel flows at Reynolds numbers Reτ = 395 and Reτ = 590. First comparisons with the dynamic Smagorinsky model and direct numerical simulations for mean velocity, turbulent kinetic energy and Reynolds stress profiles, are shown to be extremely satisfactory. The proposed model, in addition to being physically sound and consistent with the scale-by-scale energy budget of locally homogeneous shear turbulence, has a low computational cost and possesses a high potential for generalization to complex non-homogeneous turbulent flows.
Language universals in the brain: How linguistic are they?

Anybody’s search for language universals will depend on certain assumptions that are not themselves scientific in the strict sense of the empirical sciences, since they cannot be subjected to experimental testing. These basic assumptions are ontological, as they imply convictions of how those universals might exist, and they are epistemological because their mode of existence will determine how one can find out about them. Although I do not intend to digress into philosophical questions, it is nonetheless necessary at the outset to clarify certain preconceptions that will characterize this chapter. These are physicalist in nature and therefore the information I will provide in the discussions below will be most relevant to those who believe that minds are organized in certain ways because brains are. There are alternative positions one could take regarding universals. For example, to Saussure (1915/1972) universal principles of “langue” were communicative in nature, i.e., derived from social interaction, rather than individual minds or brains.1 In more recent cognitive science, minds have sometimes been likened to software or programs that can be implemented on just about any computational hardware (cf. Fodor, 1976; Gardner, 1987: p78f). The implication of this position would be that some universals of mind may exist without corresponding universals of brain. Conversely, Chomsky – arguably the most prominent thinker in modern linguistics – has insisted that “linguistic universals [are] principles that hold of language quite generally as a matter of biological (not logical) necessity”, which is ultimately based on a “genetically determined initial state” (Chomsky, 1980: p232). The physicalist approach taken in this chapter does not deny the possibility of universal principles of language that are not based on a unique neural architecture. In other words, different speakers (including speakers of different languages) may abide by abstract universal principles, but these principles – though universal descriptively – may be subserved by diverse types of neural processes. This universality could be called shallow because it is not found in neurocognitive architecture, but only in the description of linguistic behavior. Deep universality, on the contrary, would involve neurofunctional principles shared by all typically developing brains. I will argue below that from a developmental neuroscience point of view, it is not very likely that any deeply universal principles are specifically linguistic. Functional domains that begin to develop before the onset of language acquisition (such as visuomotor coordination, polymodal integration, joint attention, working memory) present us with much more probable roots for linguistic universals.
MDM2 Antagonist Nutlin-3 Displays Antiproliferative and Proapoptotic Activity in Mantle Cell Lymphoma

Purpose: Mantle cell lymphoma (MCL) has one of the poorest prognoses of the non-Hodgkin's lymphomas, and novel therapeutic approaches are needed. We wished to determine whether Nutlin-3, a novel small-molecule murine double minute 2 (MDM2) antagonist that efficiently activates TP53, might be effective in inducing cell death in MCL. Experimental Design: MCL cell lines with known TP53 status were treated with Nutlin-3, and biological and biochemical consequences were studied. Synergies with the prototypic genotoxic agent doxorubicin and the novel proteasome inhibitor bortezomib were assessed. Results: Nutlin-3 resulted in a reduction in cell proliferation/viability (IC50 < 10 μmol/L), an increase in the apoptotic fraction, and cell cycle arrest in wild-type (wt) TP53 Z-138 and Granta 519 cells. These effects were accompanied by TP53 accumulation and induction of TP53-dependent proteins p21, MDM2, Puma, and Noxa. Cell cycle arrest was characterized by suppression of S phase and an increase in the G0-G1 and G2-M fractions and accompanied by suppression of total and phosphorylated retinoblastoma protein and a decrease in G2-M-associated proteins cyclin B and CDC2. The combination of Nutlin-3 with doxorubicin or bortezomib was synergistic in wt-TP53 MCL cells. Nutlin-3 also induced cell cycle arrest and reduced cell viability in the mutant TP53 MINO cells but at a significantly higher IC50 (22.5 μmol/L). These effects were associated with induction of the TP53 homologue p73, slight increases in p21 and Noxa, and caspase activation. Nutlin-3 and bortezomib synergistically inhibited cell growth of MINO. Conclusion: These findings suggest that the MDM2 antagonist Nutlin-3 may be an effective agent in the treatment of MCL with or without wt-TP53.
MONTE CARLO DOSE ALGORITHM

Conventional dose calculation algorithms, such as Pencil Beam are proven effective for tumors located in homogeneous regions with similar tissue consistency such as the brain. However, these algorithms tend to overestimate the dose distribution in extracranial regions such as in the lung and head and neck regions where large inhomogeneities exist. Due to the inconsistencies seen in current calculation methods for extracranial treatments and the need for the creation and integration of improved calculation methods into treatmen software. Figure 1: The Monte Carlo (XVMC) Dose Algorithm Algorithms (left) show discretization artifacts. iPlan RT Dose with Monte Carlo from Brainlab has been developed in order to compensate for this under dosage in extracranial calculations and improve radiation treatment planning accuracy for clinical practice. The advanced dose calculation solution from Brain method of modelling the transport of radiation through the beam collimation system and through human tissue. Monte Carlo requires a 3 to create an internal model of the patien emitted by a medical linear accelerator. The present implementation is designed to model photon radiation. It can be used to calculate dose for conformal treatments including conformal beam, IMRT, static and dynamic arc and HybridArc treatment modalities. The MLC and patient models are created using interaction parameter tabulations from the National Institute of Standards and Technology (NIST) of the USA and the International Commission on Radiation Units and Measurements (ICRU). Studies have shown that Monte Carlo is more accurate for arc and dynamic IMRT treatments since the MC algorithm simulates gantry rotations and dynamic leaf movements continuously and not in discrete steps as with other algorithms. For these treatments the Monte Carlo calculation might even be faster than the pencil beam. software, Monte Carlo is designed to provide additional dose planning choice for the cl more precise radiation delivery, research has led to (right) simulates rotational treatments continuously lab is based on the Monte Carlo (MC) -dimensional CT-scan of the patient's tissue t and to calculate the dose distribution of the radiation Multileaf Collimator (MLC) As an integral part of the iPlan RT Dose tumors diagnosed in
Meta-Analysis Research and Theory Building

The problem and the solution. Although meta-analysis has been widely recognized as a powerful empirical research method, it has not been well acknowledged that it can be a valuable tool for theory-building purposes. This chapter describes common meta-analytic approaches and outlines a process of building theory in applied disciplines through this approach. Contributions of meta-analysis to theory building are discussed in terms of its unique roles in the relationshipbetween theoreti cal constructs and empirical evidences. Both merits and disadvantages of the meta-analytic approach in theory-building research are discussed.
Ethical Consumer Decision‐Making: The Role of Need for Cognition and Affective Responses

Most of the academic research in the field of consumer ethics has focused on the cognitive antecedents and processes of unethical consumer behavior. However, the specific roles of discrete emotions such as fear have not yet been investigated thoroughly. This research examines the role of the need for cognition (NFC), the three affective responses&#8212;fear, power, and excitement&#8212;and perceived issue importance on moral intensity, ethical perceptions, and ethical intentions for four types of unethical consumer behaviors. A sample of consumers from the two cities of Alexandria and Cairo, Egypt (n&#8201;=&#8201;346) participated in the survey. Most research hypotheses were supported. NFC, issue importance, and affect variables were all predictors of moral intensity, ethical perceptions, and ethical intentions in four different consumer ethics scenarios. The specific predictors varied from one consumer ethics scenario to another, however.
Event‐related fMRI: Comparison of conditions with varying BOLD overlap

Recently, event‐related fMRI‐experiments have been reported in which subsequent trials were separated by only 2 sec or less. Because the BOLD response needs 10 sec and longer to return to baseline, the event‐related signal in these experiments has to be extracted from the overlapping responses elicited by successive trials. Usually it is assumed that this convolved signal is a summation of the overlapping BOLD responses. We tested this assumption by comparing event‐related signals in conditions with little and with substantial BOLD overlap in two fMRI experiments of a task‐switching paradigm. We analyzed the difference in the activational time course elicited by a critical task and a baseline task when trials of both tasks were separated by intertrial intervals of 15 sec or when the critical trials were embedded in a stream of baseline trials with ISI = 1 sec. The change of the BOLD signal elicited by the critical trials showed a high correspondence between both experiments in five out of six cortical ROI. Our data support the view that BOLD overlap leads to largely linear signal changes. In the present study, task‐related increases in the BOLD response were detected equally well with substantial BOLD overlap as with mostly nonoverlapping BOLD responses. Hum. Brain Mapping 9:26–37, 2000. © 2000 Wiley‐Liss, Inc.
Generalized Fixed Point Algebras and Square-Integrable Group Actions

We analyze Rieffel's construction of generalized fixed point algebras in the setting of group actions on Hilbert modules. Let G be a locally compact group acting on a C*-algebra B. We construct a Hilbert module F over the reduced crossed product of G and B, using a pair (E, R), where E is an equivariant Hilbert module over B and R is a dense subspace of E with certain properties. The generalized fixed point algebra is the C*-algebra of compact operators on F. Any Hilbert module over the reduced crossed product arises by this construction for a pair (E, R) that is unique up to isomorphism. A necessary condition for the existence of R is that E be square-integrable. The consideration of square-integrable representations of Abelian groups on Hilbert space shows that this condition is not sufficient and that different choices for R may yield different generalized fixed point algebras. If B is proper in Kasparov's sense, there is a unique R with the required properties. Thus the generalized fixed point algebra only depends on E.
Analysis of teacher reinforcement practices and reprimands system at the basic education classrooms: an observation study

Access and retention are key components of the basic education programme in Nigeria. However, despite progress in access, low retention rate remains a key issue. Addressing the retention problem requires a critical review of current teacher classroom management practices. While positive reinforcement (PR) and reprimands are tools used by teachers to reinforce classroom behaviour, research suggests that retention is enhanced when PR outweighs reprimands by a ratio of 4:1. Although research has consistently shown that the use of reprimands is prevalent in Nigerian classrooms, data regarding the level of PR emission is lacking. Using a systematic observation method, this study examined the types, rate, frequency and pattern of PR system currently in use at the basic education classrooms vis-à-vis levels of reprimands with a view to providing baseline data for decision-making. Subjects included 60 teachers drawn from 20 schools (10 primary/10 junior secondary) in Lagos, southwest Nigeria. They were observed for 4 weeks during regular classroom teaching. Data collected were coded into quantitative categories and analysed with the use of frequencies, ratios, percentages, and chi-square test. Results showed that teachers delivered a low rate of PR and a high rate of reprimands at the ratio of approximately 1:6, far below the recommended level. No significant differences were found when the data were analysed by grade level and years of teaching. The findings are discussed in terms of their practical implications. To boost student retention at school, the use of PR strategies needs to be more widespread in the basic education classrooms.
Blind Feature Compensation for Time-Variant Band-Limited Speech Recognition

Mismatch in speech bandwidth between training and real operation greatly affects automatic speech recognition. This letter extends previous work on feature compensation of band-limited speech to establish a framework for blind compensation of speech data of unknown bandwidth, valid even when the distortion (band-limiting channel) changes rapidly and continuously in time. The available bandwidth of the input speech signal is automatically detected, and the band-limited feature vectors are compensated prior to being compared against full-bandwidth acoustic models. For a fixed bandwidth limitation, phoneme recognition performance using the proposed method is similar to that achieved by models adapted to match the distortion. However, compared to model adaptation approaches, this new approach can seamlessly be extended to rapidly time-varying conditions while maintaining low computational and memory costs
Maternal Urinary Bisphenol A during Pregnancy and Maternal and Neonatal Thyroid Function in the CHAMACOS Study

Background: Bisphenol A (BPA) is widely used in the manufacture of polycarbonate plastic bottles, food and beverage can linings, thermal receipts, and dental sealants. Animal and human studies suggest that BPA may disrupt thyroid function. Although thyroid hormones play a determinant role in human growth and brain development, no studies have investigated relations between BPA exposure and thyroid function in pregnant women or neonates. Objective: Our goal was to evaluate whether exposure to BPA during pregnancy is related to thyroid hormone levels in pregnant women and neonates. Methods: We measured BPA concentration in urine samples collected during the first and second half of pregnancy in 476 women participating in the CHAMACOS (Center for the Health Assessment of Mothers and Children of Salinas) study. We also measured free thyroxine (T4), total T4, and thyroid-stimulating hormone (TSH) in women during pregnancy, and TSH in neonates. Results: Associations between the average of the two BPA measurements and maternal thyroid hormone levels were not statistically significant. Of the two BPA measurements, only the one taken closest in time to the TH measurement was significantly associated with a reduction in total T4 (β = –0.13 µg/dL per log2 unit; 95% CI: –0.25, 0.00). The average of the maternal BPA concentrations was associated with reduced TSH in boys (–9.9% per log2 unit; 95% CI: –15.9%, –3.5%) but not in girls. Among boys, the relation was stronger when BPA was measured in the third trimester of pregnancy and decreased with time between BPA and TH measurements. Conclusion: Results suggest that exposure to BPA during pregnancy is related to reduced total T4 in pregnant women and decreased TSH in male neonates. Findings may have implications for fetal and neonatal development.
Inside the search process: Information seeking from the user's perspective

The article discusses the users’ perspective of information seeking. A model of the information search process is presented derived from a series of five studies investigating common experiences of users in information seeking situations. The cognitive and affective aspects of the process of information seeking suggest a gap between the users’ natural process of information use and the information system and intermediaries’ traditional patterns of information provision.
Object Recognition with Multi-Scale Pyramidal Pooling Networks

We present a Multi-Scale Pyramidal Pooling Network, featuring a novel pyramidal pooling layer at multiple scales and a novel encoding layer. Thanks to the former the network does not require all images of a given classification task to be of equal size. The encoding layer improves generalisation performance in comparison to similar neural network architectures, especially when training data is scarce. We evaluate and compare our system to convolutional neural networks and state-of-the-art computer vision methods on various benchmark datasets. We also present results on industrial steel defect classification, where existing architectures are not applicable because of the constraint on equally sized input images. The proposed architecture can be seen as a fully supervised hierarchical bag-of-features extension that is trained online and can be fine-tuned for any given task.