Miracle-dz/UniFAR-FTUs huggingface dataset:
Nottingham Prognostic Index Plus: Validation of a clinical decision making tool in breast cancer in an independent series

The Nottingham Prognostic Index Plus (NPI+) is a clinical decision making tool in breast cancer (BC) that aims to provide improved patient outcome stratification superior to the traditional NPI. This study aimed to validate the NPI+ in an independent series of BC. Eight hundred and eighty five primary early stage BC cases from Edinburgh were semi‐quantitatively assessed for 10 biomarkers [Estrogen Receptor (ER), Progesterone Receptor (PgR), cytokeratin (CK) 5/6, CK7/8, epidermal growth factor receptor (EGFR), HER2, HER3, HER4, p53, and Mucin 1] using immunohistochemistry and classified into biological classes by fuzzy logic‐derived algorithms previously developed in the Nottingham series. Subsequently, NPI+ Prognostic Groups (PGs) were assigned for each class using bespoke NPI‐like formulae, previously developed in each NPI+ biological class of the Nottingham series, utilising clinicopathological parameters: number of positive nodes, pathological tumour size, stage, tubule formation, nuclear pleomorphism and mitotic counts. Biological classes and PGs were compared between the Edinburgh and Nottingham series using Cramer's V and their role in patient outcome prediction using Kaplan–Meier curves and tested using Log Rank. The NPI+ biomarker panel classified the Edinburgh series into seven biological classes similar to the Nottingham series (p > 0.01). The biological classes were significantly associated with patient outcome (p < 0.001). PGs were comparable in predicting patient outcome between series in Luminal A, Basal p53 altered, HER2+/ER+ tumours (p > 0.01). The good PGs were similarly validated in Luminal B, Basal p53 normal, HER2+/ER− tumours and the poor PG in the Luminal N class (p > 0.01). Due to small patient numbers assigned to the remaining PGs, Luminal N, Luminal B, Basal p53 normal and HER2+/ER− classes could not be validated. This study demonstrates the reproducibility of NPI+ and confirmed its prognostic value in an independent cohort of primary BC. Further validation in large randomised controlled trial material is warranted.
Differential Effects of Brain Disorders on Structural and Functional Connectivity

Different measures of brain connectivity can be defined based on neuroimaging read-outs, including structural and functional connectivity. Neurological and psychiatric conditions are often associated with abnormal connectivity, but comparing the effects of the disease on different types of connectivity remains a challenge. In this paper, we address the problem of quantifying the relative effects of brain disease on structural and functional connectivity at a group level. Within the framework of a graph representation of connectivity, we introduce a kernel two-sample test as an effective method to assess the difference between the patients and control group. Moreover, we propose a common representation space for structural and functional connectivity networks, and a novel test statistics to quantitatively assess differential effects of the disease on different types of connectivity. We apply this approach to a dataset from BTBR mice, a murine model of Agenesis of the Corpus Callosum (ACC), a congenital disorder characterized by the absence of the main bundle of fibers connecting the two hemispheres. We used normo-callosal mice (B6) as a comparator. The application of the proposed methods to this data-set shows that the two types of connectivity can be successfully used to discriminate between BTBR and B6, meaning that both types of connectivity are affected by ACC. However, our novel test statistics shows that structural connectivity is significantly more affected than functional connectivity, consistent with the idea that functional connectivity has a robust topology that can tolerate substantial alterations in its structural connectivity substrate.
Denture Stomatitis and Candida Albicans in Iranian Population: A Systematic Review and Meta-Analysis

Statement of the Problem: Denture stomatitis is the common form of oral candidiasis, which is seen in the form of diffused inflammation in the areas covered by dentures. Many primary studies report the prevalence of denture stomatitis and candida albicans among patients in the Iranian population; therefore, using meta-analysis is valuable for health policy makers. Purpose: The purpose of the present study is to determine the prevalence of denture stomatitis and candida albicans in Iran. Materials and Method: Using relevant keywords, national and international databases were searched. After limiting the search strategy and deleting the duplicates, the remaining papers were screened by examining the title and abstract. In order to increase the sensitivity of search reference lists of papers were examined. Finally the index of heterogeneity between studies was defined using Cochran test (Q) and I-squared (I2). According to heterogeneity, the random effects model was used to estimate the prevalence of denture stomatitis and candida albicans in Iran. Result: The prevalence of denture stomatitis in 12 studies, and the prevalence of candida albicans in patients with denture stomatitis have been reported in 6 studies. The number of sample under investigated and its age range among primary studies included meta- analysis was 2271 individuals and 32.7 till 87.5 years respectively. The prevalence of denture stomatitis in preliminary studies imported to a meta-analysis varied from 1.9% to 54.6%, and its rate in Iran using the meta-analysis was estimated 28.9 % (CI 95%: 18.2-39.6). Also the overall prevalence of candida albicans in patients with denture stomatitis in Iran was estimated 60.6% (CI 95%:50.1-71.2). Conclusion: This study showed that the prevalence of denture stomatitis and candida albicans among patient infected denture stomatitis is relatively significant in Iran.
The Variable O VIII Warm Absorber in MCG-6-30-15

We present the results of a 4 day ASCA observation of the Seyfert galaxy MCG-6-30-15, focussing on the nature of the X-ray absorption by the warm absorber, characterizd by the K-edges of the intermediately ionized oxygen, OVII and OVIII. We confirm that the column density of OVIII changes on a timescale of $\sim 10^4$~s when the X-ray continuum flux decreases. The significant anti-correlation of column density with continuum flux gives direct evidence that the warm absorber is photoionized by the X-ray continuum. From the timescale of the variation of the OVIII column density, we estimate that it originates from gas within a radius of about $10^{17}\cm$ of the central engine. In contrast, the depth of the OVII edge shows no response to the continuum flux, which indicates that it originates in gas at larger radii. Our results strongly suggest that there are two warm absorbing regions; one located near or within the Broad Line Region, the other associated with the outer molecular torus, scattering medium or Narrow Line Region.
Estimating the Euler Equation for Output

New Keynesian macroeconomic models have generally emphasized that expectations of future output are a key factor in determining current output. The theoretical motivation for such forward-looking behavior relies on a straightforward generalization of the well-known Euler equation for consumption. In this paper, we use maximum likelihood and generalized method of moments (GMM) methods to explore the empirical importance of output expectations. We find little evidence that rational expectations of future output help determine current output, especially after taking into account the small-sample bias in GMM.
Model-Based Segmentation of Pathological Lungs in Volumetric CT Data

Segmentation of pathological lungs is a non-trivial problem. We present a new approach for the segmentation of lungs with high-density pathologies like lung cancer. Our method consists of two main processing steps. First, a novel robust active shape model matching method is applied to roughly segment the outline of the lungs. Second, an optimal surface finding approach is utilized to refine the initial segmentation result. Left and right lungs are segmented separately. A comparison to an independent reference on eleven abnormal (lung cancer) and nine normal test cases resulted in an average Dice coefficient of 0.9741 and 0.9758, respectively. Our algorithm was specifically designed for general-purpose computation on graphics processing units (GPGPU) and requires on average 116 seconds for segmenting a left or right lung.
Coding, Recording and Incidence of Different Forms of Coronary Heart Disease in Primary Care

Objectives To evaluate the coding, recording and incidence of coronary heart disease (CHD) in primary care electronic medical records. Methods Data were drawn from the UK General Practice Research Database. Analyses evaluated the occurrence of 271 READ medical diagnostic codes, including categories for ‘Angina’, ‘Myocardial Infarction’, ‘Coronary Artery Bypass Grafting’ (CABG), ‘percutaneous transluminal coronary angioplasty’ (PCTA) and ‘Other Coronary Heart Disease’. Time-to-event analyses were implemented to evaluate occurrences of different groups of codes after the index date. Results Among 300,020 participants aged greater than 30 years there were 75,197 unique occurrences of coronary heart disease codes in 24,244 participants, with 12,495 codes for incident events and 62,702 for prevalent events. Among incident event codes, 3,607 (28.87%) were for angina, 3,262 (26.11%) were for MI, 514 (4.11%) for PCTA, 161 (1.29%) for CABG and 4,951 (39.62%) were for ‘Other CHD’. Among prevalent codes, 20,254 (32.30%) were for angina, 3,644 (5.81%) for MI, 34,542 (55.09%) for ‘Other CHD’ and 4,262 (6.80%) for CABG or PCTA. Among 3,685 participants initially diagnosed exclusively with ‘Other CHD’ codes, 17.1% were recorded with angina within 5 years, 5.6% with myocardial infarction, 6.3% with CABG and 8.6% with PCTA. From 2000 to 2010, the overall incidence of CHD declined, as did the incidence of angina, but the incidence of MI did not change. The frequency of CABG declined, while PCTA increased. Conclusion In primary care electronic records, a substantial proportion of coronary heart disease events are recorded with codes that do not distinguish between different clinical presentations of CHD. The results draw attention to the need to improve coding practice in primary care. The results also draw attention to the importance of code selection in research studies and the need for sensitivity analyses using different sets of codes.
Hierarchical language models for one-stage speech interpretation

This paper presents a robust semantic model for one-stage interpretation of natural speech. Our semantic analysis uses no explicit syntactic and morphologic knowledge, which seems sufﬁcient for narrow application domains. In contrast to previous approaches, our semantic model is embedded in a uniform, hierarchical, stochastic modeling framework together with acoustic-phonetic and lexical knowledge, and semantic representations are computed directly from acoustic observations through a one-stage decoding process. The decoder produces a hierarchical (tree) structure of words and semantic category symbols by use of the so-called hierarchical language model (HLM). We discuss generation of HLM by mixing rule-based and data-driven language model (LM) generation techniques, namely weighted regular expressions, n -grams and exact LM. Different HLM conﬁgurations with varying discounting techniques, n-gram orders and scaling factors are examined. Experiments were conducted with an airport information dialogue application. The evaluation results are based on HLM perplexity and our previously published semantic tree accuracy.
Parathyroid Hormone Mediates Hematopoietic Cell Expansion through Interleukin-6

Parathyroid hormone (PTH) stimulates hematopoietic cells through mechanisms of action that remain elusive. Interleukin-6 (IL-6) is upregulated by PTH and stimulates hematopoiesis. The purpose of this investigation was to identify actions of PTH and IL-6 in hematopoietic cell expansion. Bone marrow cultures from C57B6 mice were treated with fms-like tyrosine kinase-3 ligand (Flt-3L), PTH, Flt-3L plus PTH, or vehicle control. Flt-3L alone increased adherent and non-adherent cells. PTH did not directly impact hematopoietic or osteoclastic cells but acted in concert with Flt-3L to further increase cell numbers. Flt-3L alone stimulated proliferation, while PTH combined with Flt-3L decreased apoptosis. Flt-3L increased blasts early in culture, and later increased CD45+ and CD11b+ cells. In parallel experiments, IL-6 acted additively with Flt-3L to increase cell numbers and IL-6-deficient bone marrow cultures (compared to wildtype controls) but failed to amplify in response to Flt-3L and PTH, suggesting that IL-6 mediated the PTH effect. In vivo, PTH increased Lin- Sca-1+c-Kit+ (LSK) hematopoietic progenitor cells after PTH treatment in wildtype mice, but failed to increase LSKs in IL-6-deficient mice. In conclusion, PTH acts with Flt-3L to maintain hematopoietic cells by limiting apoptosis. IL-6 is a critical mediator of bone marrow cell expansion and is responsible for PTH actions in hematopoietic cell expansion.
Biased random walks on random combs

We develop rigorous, analytic techniques to study the behaviour of biased random walks on combs. This enables us to calculate exactly the spectral dimension of random comb ensembles for any bias scenario in the teeth or spine. Two specific examples of random comb ensembles are discussed: the random comb with nonzero probability of an infinitely long tooth at each vertex on the spine and the random comb with a power-law distribution of tooth lengths. We also analyse transport properties along the spine for these probability measures.
The acute cognitive benefits of casual exergame play

Acute cognitive benefits, such as temporary improvements in concentration, can result from as few as ten minutes of exercise; however, most people do not take exercise breaks throughout the day. To motivate people to receive the cognitive benefits of exercising in short bursts multiple times per day, we designed an engaging casual exergame. To determine whether there are cognitive benefits after playing our game, we conducted two studies to compare playing ten minutes of our casual exergame to a sedentary version of the game or exercise on a treadmill. We found acute cognitive benefits of the casual exergame over the sedentary version (but not treadmill exercise), demonstrated by significantly improved performance on two cognitive tests that require focus and concentration. Significant improvements were also found in participants' affective states after playing the casual exergame. Finally, our casual exergame produces similar exertion levels to treadmill exercise, but is perceived as more fun.
Dissociable Effects of Natural Image Structure and Color on LFP and Spiking Activity in the Lateral Prefrontal Cortex and Extrastriate Visual Area V4

Visual perception is mediated by unique contributions of the numerous brain regions that constitute the visual system. We performed simultaneous recordings of local field potentials (LFPs) and single unit activity (SUA) in areas V4 and lateral prefrontal cortex to characterize their contribution to visual processing. Here, we trained monkeys to identify natural images at different degradation levels in a visual recognition task. We parametrically varied color and structural information of natural images while the animals were performing the task. We show that the visual-evoked potential (VEP) of the LFP in V4 is highly sensitive to color, whereas the VEP in prefrontal cortex predominantly depends on image structure. When examining the relationship between VEP and SUA, we found that stimulus sensitivity for SUA was well predicted by the VEP in PF cortex but not in V4. Our results first reveal a functional specialization in both areas at the level of the LFP and further suggest that the degree to which mesoscopic signals, such as the VEP, are representative of the underlying SUA neural processing may be brain region specific within the context of visual recognition.
Discrete Bayesian Network Classifiers

We have had to wait over 30 years since the naive Bayes model was first introduced in 1960 for the so-called Bayesian network classifiers to resurge. Based on Bayesian networks, these classifiers have many strengths, like model interpretability, accommodation to complex data and classification problem settings, existence of efficient algorithms for learning and classification tasks, and successful applicability in real-world problems. In this article, we survey the whole set of discrete Bayesian network classifiers devised to date, organized in increasing order of structure complexity: naive Bayes, selective naive Bayes, seminaive Bayes, one-dependence Bayesian classifiers, k-dependence Bayesian classifiers, Bayesian network-augmented naive Bayes, Markov blanket-based Bayesian classifier, unrestricted Bayesian classifiers, and Bayesian multinets. Issues of feature subset selection and generative and discriminative structure and parameter learning are also covered.
Nitrogen cycling in shallow low-oxygen coastal waters off Peru from nitrite and nitrate nitrogen and oxygen isotopes

Abstract. O2 deficient zones (ODZs) of the world's oceans are important locations for microbial dissimilatory nitrate (NO3−) reduction and subsequent loss of combined nitrogen (N) to biogenic N2 gas. ODZs are generally coupled to regions of high productivity leading to high rates of N-loss as found in the coastal upwelling region off Peru. Stable N and O isotope ratios can be used as natural tracers of ODZ N-cycling because of distinct kinetic isotope effects associated with microbially mediated N-cycle transformations. Here we present NO3− and nitrite (NO2−) stable isotope data from the nearshore upwelling region off Callao, Peru. Subsurface oxygen was generally depleted below about 30 m depth with concentrations less than 10 µM, while NO2− concentrations were high, ranging from 6 to 10 µM, and NO3− was in places strongly depleted to near 0 µM. We observed for the first time a positive linear relationship between NO2−δ15N and δ18O at our coastal stations, analogous to that of NO3− N and O isotopes during NO3− uptake and dissimilatory reduction. This relationship is likely the result of rapid NO2− turnover due to higher organic matter flux in these coastal upwelling waters. No such relationship was observed at offshore stations where slower turnover of NO2− facilitates dominance of isotope exchange with water. We also evaluate the overall isotope fractionation effect for N-loss in this system using several approaches that vary in their underlying assumptions. While there are differences in apparent fractionation factor (e) for N-loss as calculated from the δ15N of NO3−, dissolved inorganic N, or biogenic N2, values for e are generally much lower than previously reported, reaching as low as 6.5 ‰. A possible explanation is the influence of sedimentary N-loss at our inshore stations which incurs highly suppressed isotope fractionation.
The Rho-mDia1 Pathway Regulates Cell Polarity and Focal Adhesion Turnover in Migrating Cells through Mobilizing Apc and c-Src

ABSTRACT Directed cell migration requires cell polarization and adhesion turnover, in which the actin cytoskeleton and microtubules work critically. The Rho GTPases induce specific types of actin cytoskeleton and regulate microtubule dynamics. In migrating cells, Cdc42 regulates cell polarity and Rac works in membrane protrusion. However, the role of Rho in migration is little known. Rho acts on two major effectors, ROCK and mDia1, among which mDia1 produces straight actin filaments and aligns microtubules. Here we depleted mDia1 by RNA interference and found that mDia1 depletion impaired directed migration of rat C6 glioma cells by inhibiting both cell polarization and adhesion turnover. Apc and active Cdc42, which work together for cell polarization, localized in the front of migrating cells, while active c-Src, which regulates adhesion turnover, localized in focal adhesions. mDia1 depletion impaired localization of these molecules at their respective sites. Conversely, expression of active mDia1 facilitated microtubule-dependent accumulation of Apc and active Cdc42 in the polar ends of the cells and actin-dependent recruitment of c-Src in adhesions. Thus, the Rho-mDia1 pathway regulates polarization and adhesion turnover by aligning microtubules and actin filaments and delivering Apc/Cdc42 and c-Src to their respective sites of action.
Motion cues for illustration of skeletal motion capture data

There are many applications for which it is necessary to illustrate motion in a static image using visual cues which do not represent a physical entity in the scene, yet are widely understood to convey motion. For example, consider the task of illustrating the desired movements for exercising, dancing, or a given sport technique. Traditional artists have developed techniques to specify desired movements precisely (technical illustrators) and suggest motion (cartoonists) in an image. In this paper, we present an interactive system to synthesize a 2D image of an animated character by generating artist-inspired motion cues derived from 3D skeletal motion capture data. The primary cues include directed arrows, noise waves, and stroboscopic motion. First, the user decomposes the animation into short sequences containing individual motions which can be represented by visual cues. The system then allows the user to determine a suitable viewpoint for illustrating the movement, to select the proper level in the joint hierarchy, as well as to fine-tune various controls for the depiction of the cues themselves. While the system does provide adapted default values for each control, extracted from the motion capture data, it allows fine-tuning for greater expressiveness. Moreover, these cues are drawn in real time, and maintain a coherent display with changing viewpoints. We demonstrate the benefit of our interactive system on various motion capture sequences.
Susceptibility status of Aedes aegypti (L.) (Diptera: Culicidae) to temephos from three districts of Tamil Nadu, India.

BACKGROUND & OBJECTIVES Dengue is the most rapidly expanding arboviral disease in India. Aedes aegypti is the primary vector of dengue fever. Chemical insecticides have long been used in the vector control programmes along with other control measures. However, continuous use of insecticides targeting Ae. aegypti may lead to development of insecticide resistance. Though resistance in Ae. aegypti has been reported, the mutation in ace-1 gene associated with temephos resistance is not reported in natural populations. The present study aims to evaluate the susceptibility/resistance status of Ae. aegypti to temephos from three districts of Tamil Nadu. METHODS Ae. aegypti larvae were sampled from different locations in three districts, viz., Dharmapuri, Salem and Namakkal. The standard WHO larval bioassay, biochemical assays and spotting of specific mutation (G119S) in the acetylcholinesterase gene, which is associated with organophosphate resistance, were carried out by PCR and sequencing. RESULTS The results showed that larvae from Namakkal (NKL) population had an alteration in their susceptibility status (RR = 6.9 fold), while the other populations were moderately susceptible to insecticides. Biochemical assay showed increased activity for α- and β-esterase in NKL, as well as evidence of acetylcholinesterase insensitivity. G119S mutation was detected in this population with high frequency of 0.24. INTERPRETATION & CONCLUSION The high activity of esterase, mixed-function oxidase (MFO) and ace-1 mutation frequency were closely associated with temephos resistance. Early detection of resistance alleles in natural vector population could be useful for the successful implementation of insecticide resistance management strategies. The results of this study provide baseline data on temephos resistance in Ae. aegypti populations.