Miracle-dz/UniFAR-FTUs huggingface dataset:
CD44 and OTP Are Strong Prognostic Markers for Pulmonary Carcinoids

Purpose: Pulmonary carcinoids are well-differentiated neuroendocrine tumors showing usually a favorable prognosis. However, there is a risk for late recurrence and/or distant metastasis. Because histologic classification in typical and atypical carcinoids is difficult and its reliability to predict disease outcome varies, we evaluated three genes as potential prognostic markers, that is, orthopedia homeobox (OTP), CD44, and rearranged during transfection (RET). Experimental Design: These genes were analyzed in 56 frozen carcinoids by quantitative real-time PCR (qRT-PCR). RET was further studied by methylation and mutation analysis. Immunohistochemistry for CD44 and OTP protein expression was conducted on 292 carcinoids. Results: Low mRNA expression levels of CD44 (P = 1.8e−5) and OTP (P = 0.00054), and high levels of RET (P = 0.025), were strongly associated with a low 20-year survival of carcinoid patients. High RET expression was not related to promoter hypomethylation or gene mutations. A direct link between gene expression and protein levels was confirmed for CD44 and OTP but not for RET. Within all carcinoids as well as atypical carcinoids, absence of CD44 protein was significantly associated with low 20-year survival (P = 0.00014 and 0.00013, respectively). The absence of nuclear OTP followed by complete loss of expression was also significantly associated with unfavorable disease outcome in all carcinoids (P = 5.2−6). Multivariate analyses revealed that age at diagnosis, histopathology, stage, and cytoplasmic OTP immunoreactivity were independent predictors of prognosis. Conclusions: Our study indicates that CD44 and OTP are strong indicators of poor outcome. We therefore argue for implementation of these markers in routine diagnostics in addition to histopathology to improve subclassification of pulmonary carcinoids into prognostically relevant categories. Clin Cancer Res; 19(8); 2197–207. ©2013 AACR.
Massive-Training Artificial Neural Networks (MTANN) in Computer-Aided Detection of Colorectal Polyps and Lung Nodules in CT

Computer-aided diagnosis (CAD) (Giger and Suzuki 2007) has been an active area of study in medical image analysis, because evidence suggests that CAD can help improve the diagnostic performance of radiologists in their image interpretations (Li, Aoyama et al. 2004; Li, Arimura et al. 2005; Dean and Ilvento 2006). Many investigators have participated in and developed CAD schemes for detection/diagnosis of lesions in medical images, such as detection of lung nodules in chest radiographs (Giger, Doi et al. 1988; van Ginneken, ter Haar Romeny et al. 2001; Suzuki, Shiraishi et al. 2005) and in thoracic CT (Armato, Giger et al. 1999; Armato, Li et al. 2002; Suzuki, Armato et al. 2003; Arimura, Katsuragawa et al. 2004), detection of microcalcifications/masses in mammography (Chan, Doi et al. 1987), breast MRI (Gilhuijs, Giger et al. 1998), breast US (Horsch, Giger et al. 2004; Drukker, Giger et al. 2005), and detection of polyps in CT colonography (Yoshida and Nappi 2001; Suzuki, Yoshida et al. 2006; Suzuki, Yoshida et al. 2008). Some advanced CAD schemes employ a filter for enhancement of lesions as a preprocessing step for improving sensitivity and specificity. The filter enhances objects similar to a model employed in the filter; e.g., a blob enhancement filter based on the Hessian matrix enhances sphere-like objects (Frangi, Niessen et al. 1999). Actual lesions, however, often differ from a simple model, e.g., a lung nodule is generally modeled as a solid sphere, but there are nodules of various shapes and inhomogeneous nodules such as a spiculated nodule and a ground-glass opacity. A colorectal polyp is often modeled as a cap structure by using a shape index filter, but a sessile polyp or a flat polyp cannot be characterized well as a cap structure of the shape index. Thus, conventional filters often fail to enhance actual lesions such as lung nodules with ground-glass opacity and sessile/flat polyps. To address this issue, we developed a supervised filter for enhancement of actual lesions by use of a massive-training artificial neural network (MTANN) (Suzuki, Armato et al. 2003) filter in a CAD scheme. In this chapter, we introduce MTANN-based CAD schemes for detection of lung nodules in CT and for detection of polyps in CT colonography. To summerize, by extension of “neural filters” (Suzuki, Horiba et al. 2002) and “neural edge enhancers” (Suzuki, Horiba et al. 2003; Suzuki, Horiba et al. 2004), which are ANN-based 18
What was the ‘Kurdish opening’ all about? A qualitative text analysis of parliamentary group speeches in Turkey

This study explores the use of four discourses – socio-economic, relative deprivation, pro-Islamist and terrorism oriented – used by political parties in Turkey to address the Kurdish issue and the resulting political party strategies during the Kurdish opening in Turkey. Although the factors that influence the Kurdish issue have drawn attention, no research has analysed Turkish political parties’ perspectives on the Kurdish issue in primary political documents. By examining 188 parliamentary group speeches delivered during the Kurdish opening process with qualitative text analysis, this study reveals that the mainstream parties in the Turkish Parliament employ socio-economic, relative deprivation and regional terrorism approaches, while the ethnic parties use either regional terrorism and pro-Islamist approaches or the relative deprivation approach. Due to the overlap in their discourses, the mainstream parties have developed a new strategy: compartmentalization of the ethnic issue by creating sub-ethnic categories. This research contributes to revealing political parties’ approaches to the Kurdish question and their strategies for mobilizing the ethnic median voter.
MiR-21 Expression in the Tumor Stroma of Oral Squamous Cell Carcinoma: An Independent Biomarker of Disease Free Survival

Oral squamous cell carcinoma (OSCC) patients have a high mortality rate; thus, new clinical biomarkers and therapeutic options are needed. MicroRNAs (miRNAs) are short noncoding RNAs that regulate posttranscriptional gene expression and are commonly deregulated in OSCC and other cancers. MicroRNA-21 (miR-21) is the most consistently overexpressed miRNA in several types of cancer, and it might be a useful clinical biomarker and therapeutic target. To better understand the role of miR-21 in OSCC, paraffin-embedded tumor tissue samples from 86 patients with primary OSCC were analyzed by in situ hybridization. We found that miR-21 was primarily expressed in the tumor stroma and in some tumor-associated blood vessels with no expression in the adjacent normal epithelia or stroma. Using image analysis, we quantitatively estimated miR-21 expression levels specifically in the stroma of a cohort of OSCC samples. These miR-21 levels significantly correlated with disease free survival with the highest levels being located in the stroma. Stromal miR-21 expression was independently associated with a poorer prognosis, even after adjusting for clinical parameters (perineural invasion and N-stage) in a multivariate analysis. In summary, we have shown that miR-21 is located in the carcinoma cells, stroma and blood vessels of tumors, and its expression specifically in the stromal compartment has a negative prognostic value in OSCC.
Boundary Curves of Incompressible Surfaces

This is a Tex version, made in 2004, of a paper that appeared in Pac. J. Math. 99 (1982), 373-377, with some revisions in the exposition. Let M be an compact orientable 3 manifold whose boundary @M consists of a single torus. If a meridian and longitude in this torus are chosen, then isotopy classes of smoothly embedded circles in @M that do not bound disks correspond bijectively with elements of QP 1 E Q[f 1= 0g, regarded as slopes of these curves. We show in this paper that the set of slopes coming from boundary curves of incompressible, @ incompressible surfaces in M is finite. There is also a generalization to the case that @M consists of n tori T1;;Tn . Given a curve system in @M consisting of finitely many disjoint smoothly embedded circles that do not bound disks, then by choosing parallel orientations for the circles in each component of @M, we get an element of H 1 N@MO. Ignoring orientations amounts to factoring out multiplication by1 in each component, yielding a quotient of H 1 N@MO which can be identified with the set CSN@MO of isotopy classes of curve systems in@M. Each factorH1NTiO ofH1N@MO is the integer lattice inH1NTi;RO R 2 , and H 1 NT i ;RO= 1 is a cone, so CSN@MO can be viewed as the integer lattice in a product of cones, the space H1N@M;RO=Z n where Z n acts by inversions in the factors H 1 NT i ;RO.
Running Head : TMS ENHANCES WORKING MEMORY 1 Transcranial Magnetic Stimulation enhances working memory

Cognitive decline associated with aging affects a large proportion of America’s progressively older population. To remedy this decline, various working memory (WM) training protocols are emerging, the most novel of which utilize Transcranial Magnetic Stimulation (TMS) to excite neuronal activity, induce long-term potentiation, and enhance cognitive functioning. Ultimately aiming to remediate WM decline in aging adults by using TMS, this study first sought to establish ideal TMS parameters to induce WM improvements. Using a delayed match-to-sample (DMS) WM task with both maintenance and manipulation conditions, it was hypothesized that active TMS, relative to sham TMS, would differentially impact task performance depending on its timing of administration, either before encoding or at the end of the delay phases. Following screening and practice, subjects trained on the DMS task for 4 hours over 2 days, receiving 5s of either active 5Hz TMS at 100% of motor threshold to the dorsolateral prefrontal cortex (DLPFC) or sham TMS. The phase of active versus sham TMS stimulation was counterbalanced across participants. The results suggest that active TMS improved DMS reaction time and accuracy as compared to sham TMS. Specifically, maintenance task performance improved with TMS before encoding, while manipulation task performance was aided by TMS during the delay period. Although promising, these results should be bolstered by increased sample sizes and individualized fMRI-based DLPFC targeting before deciding on the optimal timing of TMS for each DMS task condition in aging adults. TMS ENHANCES WORKING MEMORY 3 We all have experienced the frustration of trying and failing to remember information, such as a telephone number, for short periods of time. However, imagine the feeling of debilitation involved in consistently loosing track of the topic during a conversation, forgetting where important objects like keys or medications were placed, or being unable to mentally compute basic calculations such as a tip in a restaurant. For a large proportion of America’s progressively aging population, this form of cognitive decline that particularly afflicts executive processing and working memory (WM) becomes a serious setback (Fiore et al., 2012; Salthouse, 1994).
Validation cohort results for NSPN manuscript "Adolescence is associated with genomically patterned consolidation of the hubs of the human brain connectome"

How does human brain structure mature during adolescence? We used MRI to measure cortical thickness and intracortical myelination in 297 population volunteers aged 14 – 24 y old. We found and replicated that association cortical areas were thicker and less myelinated than primary cortical areas at the internal layer of projection Adolescent cortical myelination and shrinkage coupled with a dorsoventrally patterned gene expression profile enriched for synaptic, oligodendroglial- and schizophrenia-related genes. efficient and biologically expensive hubs of the anatomical network of shrinkage/myelination associated with overexpression of the same transcriptional profile as cortical consolidation. We that normative maturation involves a genetically patterned process of consoli- anatomical network hubs. We that developmental of this consolidation process be relevant both to normal cognitive and behavioral changes and the high incidence of schizophrenia during human brain
Ruelle operator theorem for non-expansive systems

Abstract The Ruelle operator theorem has been studied extensively both in dynamical systems and iterated function systems. In this paper we study the Ruelle operator theorem for non-expansive systems. Our theorems give some sufficient conditions for the Ruelle operator theorem to be held for a non-expansive system.
Can ‘Philosophy for Children’ Improve Primary School Attainment?

There are tensions within formal education between imparting knowledge and the development of skills for handling that knowledge. In the primary school sector, the latter can also be squeezed out of the curriculum by a focus on basic skills such as literacy and numeracy. What happens when an explicit attempt is made to develop young children's reasoning—both in terms of their apparent cognitive abilities and their basic skills? This paper reports an independent evaluation of an in-class intervention called ‘Philosophy for Children’ (P4C), after just over one year of schooling. The intervention aims to help children become more willing and able to question, reason, construct arguments and collaborate with others. A group of 48 volunteer schools were randomised to receive P4C (22 schools) or act as a control for one year (26). This paper reports the CAT results for all pupils in years 4 and 5 initially, and the Key Stage 2 attainment in English and Maths for those starting in year 5. There was no school dropout. Individual attrition from a total of 3,159 pupils was around 11 percent—roughly equal between groups. There were small positive ‘effect’ sizes in favour of the P4C group in progress in reading (+0.12) and maths (+0.10), and even smaller perhaps negligible improvements in CAT scores (+0.07) and writing (+0.03). The results for the most disadvantaged (free school eligible) pupils were larger for attainment (+0.29 in reading, +0.17 writing and +0.20 maths), but not for CATs (–0.02). Observations and interviews suggest that the intervention was generally enjoyable and thought to be beneficial for pupil confidence. Our conclusion is that, for those wishing to improve attainment outcomes in the short term, an emphasis on developing reasoning is promising, especially for the poorest students, but perhaps not the most effective way forward. However, for those who value reasoning for its own sake, this evaluation demonstrates that using curriculum time in this way does not damage attainment (and may well enhance it and reduce the poverty gradient in attainment), and so suggests that something like P4C is an appropriate educational approach.
On the tautological ring of M g , n

In this section, we briefly describe the objects under consideration for the sake of non-experts. A more detailed informal exposition of these well-known ideas is given in [PV]. When studying Riemann surfaces of some given genus g, one is naturally led to study the moduli spaceMg of such objects. This space has dimension 3g−3, and has a natural compactification due to Deligne and Mumford, [DM], the moduli space Mg of stable genus g curves. More generally, one can define a moduli space of stable n-pointed genus g curves, denotedMg,n, over any given algebraically closed field (or indeed over SpecZ). We shall work over the complex numbers. A stable n-pointed genus g complex curve is a compact curve with only nodes as singularities, with n distinct labeled smooth points. There is a stability condition: each rational component has at least 3 special points, and each component of genus 1 has at least 1 special point. (A special point is a point on the normalization of the component that is either a marked point, or a branch of a node.) This stability condition is equivalent to requiring that the automorphism group of the pointed curve be finite. If a curve is stable, then a short combinatorial exercise shows that 2g − 2 + n > 0. The open subset ofMg,n corresponding to smooth curves is denotedMg,n. The curves of compact type (those with compact Jacobian, or equivalently, with a tree as dual graph) form a partial compactification, denoted Mg,n.
High Levels of Cre Expression in Neuronal Progenitors Cause Defects in Brain Development Leading to Microencephaly and Hydrocephaly

Hydrocephalus is a common and variegated pathology often emerging in newborn children after genotoxic insults during pregnancy (Hicks and D’Amato, 1980). Cre recombinase is known to have possible toxic effects that can compromise normal cell cycle and survival. Here we show, by using three independent nestin Cre transgenic lines, that high levels of Cre recombinase expression into the nucleus of neuronal progenitors can compromise normal brain development. The transgenics analyzed are the nestin Cre Balancer (Bal1) line, expressing the Cre recombinase with a nuclear localization signal, and two nestin CreERT2 (Cre recombinase fused with a truncated estrogen receptor) mice lines with different levels of expression of a hybrid CreERT2 recombinase that translocates into the nucleus after tamoxifen treatment. All homozygous Bal1 nestin Cre embryos displayed reduced neuronal proliferation, increased aneuploidy and cell death, as well as defects in ependymal lining and lamination of the cortex, leading to microencephaly and to a form of communicating hydrocephalus. An essentially overlapping phenotype was observed in the two nestin CreERT2 transgenic lines after tamoxifen mediated-CreERT2 translocation into the nucleus. Neither tamoxifen-treated wild-type nor nestin CreERT2 oil-treated control mice displayed these defects. These results indicate that some forms of hydrocephalus may derive from a defect in neuronal precursors proliferation. Furthermore, they underscore the potential risks for developmental studies of high levels of nuclear Cre in neurogenic cells.
UNDULATORY SWIMMING: HOW TRAVELING WAVES ARE PRODUCED AND MODULATED IN SUNFISH (LEPOMIS GIBBOSUS)

We have developed an experimental procedure in which the in situ locomotor muscles of dead fishes can be electrically stimulated to generate swimming motions. This procedure gives the experimenter control of muscle activation and the mechanical properties of the body. Using pumpkinseed sunfish, Lepomis gibbosus, we investigated the mechanics of undulatory swimming by comparing the swimming kinematics of live sunfish with the kinematics of dead sunfish made to swim using electrical stimulation. In electrically stimulated sunfish, undulatory waves can be produced by alternating left­right contractions of either all the axial muscle or just the precaudal axial muscle. As judged by changes in swimming speed, most of the locomotor power is generated precaudally and transmitted to the caudal fin by way of the skin and axial skeleton. The form of the traveling undulatory wave ­ as measured by tail-beat amplitude, propulsive wavelength and maximal caudal curvature ­ can be modulated by experimental control of the body's passive stiffness, which is a property of the skin, connective tissue and axial skeleton.
Lattice Diagrams Using Reed-Muller Logic

Universal Akers Arrays UAA allow to realize arbitrary Boolean function directly in cellular layout but are very area ine cient This paper presents an extension of UAAs called Lattice Diagrams in which Shannon Positive and Negative Davio expansions are used in nodes An e cient method of mappig arbitrary multi output incompletely speci ed functions to them is presented We prove that with these extensions our concept of regular layout becomes not only feasible but also e cient Regular layout is a fundamental concept in VLSI design which can have applications to submicron design and designing new ne grain FPGAs
recipes: a cross-sectional study

A government’s response to increasing incidence of lifestyle-related illnesses, such as obesity, has been to encourage people to cook for themselves. The healthiness of home cooking will, nevertheless, depend on what people cook and how they cook it. In this article, one common source of cooking inspiration—Internet-sourced recipes—is investigated in depth. The energy and macronutrient content of 5,237 main meal recipes from the food website Allrecipes.com are compared with those of 100 main meal recipes from five bestselling cookery books from popular celebrity chefs and 100 ready meals from the three leading UK supermarkets. The comparison is made using nutritional guidelines published by the World Health Organization and the UK Food Standards Agency. The main conclusions drawn from our analyses are that Internet recipes sourced from Allrecipes.com are less healthy than TV chef recipes and ready meals from leading UK supermarkets. Only 6 out of 5,237 Internet recipes fully complied with the WHO recommendations. Internet recipes were more likely to meet the WHO guidelines for protein than other classes of meal (10.88 v 7% (TV), p < 0.01; 10.86 v 9% (ready), p < 0.01). However, the Internet recipes were less likely to meet the criteria for fat (14.28 v 24 (TV) v 37% (ready); p < 0.01), saturated fat (25.05 v 33 (TV) v 34% (ready); p < 0.01), and fiber (compared to ready meals 16.50 v 56%; p < 0.01). More Internet recipes met the criteria for sodium density than ready meals (19.63 v 4%; p < 0.01), but fewer than the TV chef meals (19.32 v 36%; p < 0.01). For sugar, no differences between Internet recipes and TV chef recipes were observed (81.1 v 81% (TV); p = 0.86), although Internet recipes were less likely to meet the sugar criteria than ready meals (81.1 v 83% (ready); p < 0.01). Repeating the analyses for each year of available data shows that the results are very stable over time.
Evolution of Lithium in the Milky Way

We adopt up-to-date 7Li yields from asymptotic giant branch stars in order to study the temporal evolution of this element in the solar neighbourhood. Several lithium stellar sources are considered besides the AGBs: Type II supernovae, novae, low-mass giants. Galactic cosmic ray nucleosynthesis is taken into account as well. We conclude that AGB stars do not substantially contribute to 7Li enrichment on a Galactic scale. Therefore, a significant 7Li production from novae and low-mass stars is needed to explain the late, steep rise of the 7Li abundance in disk stars and the meteoritic 7Li abundance.
The Impact of Cognitive Trust and E-WOM on Purchase Intention in C2C E-Commerce Site

In the last few years, the number of Internet users in Indonesia was growing rapidly as many people started to use e-commerce sites. Utilization of C2C e-commerce in particular has a risk that may reduce people interest in online shopping. Of the many factors that may influence online shopping intention, trust becomes the key. This study built a model to explain the purchase intention in the C2C e-commerce environment. In the model, buyerâs trust to the seller is a major factor that influences the purchase intention. Cognitive trust and adoption of e-WOM information is used as a factor that explains how trust is formed. We tested the model by distributing online questionnaires in Kaskus forum, the largest online shopping community in Indonesia. Total 114 valid questionnaire responses were used for analysis. The analysis was conducted using PLS and Smart PLS 2.0 as the tools. Our results showed that trust have a positive and significant effect to the purchase intention. Later it was found that two cognitive trust variables, the perception of ability and integrity of the seller, along with the adoption of e-WOM information have a positive and significant impact on the trust to the seller.