Miracle-dz/UniFAR-FTUs huggingface dataset:
Gastric extremely well differentiated adenocarcinoma of gastric phenotype : as a gastric counterpart of adenoma malignum of the uterine cervix

Background: Most of gastric adenocarcinoma can be simply diagnosed by microscopic examination of biopsy specimen. Rarely the structural and cellular atypia of tumor cells is too insignificant to discriminate from benign foveolar epithelium. Case presentation: A 67-year-old male presented with a gastric mass incidentally found on the abdominal computed tomography (CT) for routine medical examination. Gastric endoscopic examination revealed a huge fungating mass at the cardia and mucosal biopsy was performed. Microscopically the biopsy specimen showed proliferation of bland looking foveolar epithelia in the inflammatory background and diagnosed as foveolar epithelial hyperplasia. Because the clinical and endoscopic features of this patient were strongly suggestive of malignancy, the patient underwent radical total gastrectomy. The resected stomach revealed a huge fungating tumor at the cardia. The cut surface of the tumor was whitish gelatinous. Microscopically the tumor was sharply demarcated from surrounding mucosa and composed of very well formed glandular structures without significant cellular atypia, which invaded into the whole layer of the gastric wall. Tumor glands were occasionally complicated or dilated, and glandular lumina were filled with abundant mucin. Immunohistochemically the tumor cells revealed no overexpression of p53 protein but high Ki-67 labeling index. The tumor cells and intraluminal mucin were diffusely expressed MUC1 and MUC5AC and only focally expressed MUC2. On abdominal CT taken after 12 months demonstrated peritoneal carcinomatosis and multiple metastatic foci in the lung. Conclusion: The clinicopathologic profiles of gastric extremely well differentiated adenocarcinoma of gastric phenotype include cardiac location, fungating gross type, very similar histology to foveolar epithelial hyperplasia, foveolar mucin phenotype, lack of p53 overexpressoin and high proliferative index. Background Most of gastric adenocarcinoma can be simply diagnosed by microscopic examination of biopsy specimen. Extremely well differentiated adenocarcinoma (EWDA) of the stomach is histologically too bland and too similar to benign foveolar epithelium to make a diagnosis as Published: 23 May 2005 World Journal of Surgical Oncology 2005, 3:28 doi:10.1186/1477-7819-328 Received: 09 March 2005 Accepted: 23 May 2005 This article is available from: http://www.wjso. com/content/3/1/28 © 2005 Ae Lee; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
A Novel Non-Lens βγ−Crystallin and Trefoil Factor Complex from Amphibian Skin and Its Functional Implications

Background In vertebrates, non-lens βγ-crystallins are widely expressed in various tissues, but their functions are unknown. The molecular mechanisms of trefoil factors, initiators of mucosal healing and being greatly involved in tumorigenesis, have remained elusive. Principal Findings A naturally existing 72-kDa complex of non-lens βγ-crystallin (α-subunit) and trefoil factor (β-subunit), named βγ-CAT, was identified from frog Bombina maxima skin secretions. Its α-subunit and β-subunit (containing three trefoil factor domains), with a non-covalently linked form of αβ2, show significant sequence homology to ep37 proteins, a group of non-lens βγ-crystallins identified in newt Cynops pyrrhogaster and mammalian trefoil factors, respectively. βγ-CAT showed potent hemolytic activity on mammalian erythrocytes. The specific antiserum against each subunit was able to neutralize its hemolytic activity, indicating that the two subunits are functionally associated. βγ-CAT formed membrane pores with a functional diameter about 2.0 nm, leading to K+ efflux and colloid-osmotic hemolysis. High molecular weight SDS-stable oligomers (>240-kDa) were detected by antibodies against the α-subunit with Western blotting. Furthermore, βγ-CAT showed multiple cellular effects on human umbilical vein endothelial cells. Low dosages of βγ-CAT (25–50 pM) were able to stimulate cell migration and wound healing. At high concentrations, it induced cell detachment (EC50 10 nM) and apoptosis. βγ-CAT was rapidly endocytosed via intracellular vacuole formation. Under confocal microscope, some of the vacuoles were translocated to nucleus and partially fused with nuclear membrane. Bafilomycin A1 (a specific inhibitor of the vacuolar-type ATPase) and nocodazole (an agent of microtuble depolymerizing), while inhibited βγ-CAT induced vacuole formation, significantly inhibited βγ-CAT induced cell detachment, suggesting that βγ-CAT endocytosis is important for its activities. Conclusions/Significance These findings illustrate novel cellular functions of non-lens βγ-cyrstallins and action mechanism via association with trefoil factors, serving as clues for investigating the possible occurrence of similar molecules and action mechanisms in mammals.
Visibility Computations: From Discrete Algorithms to Real Algebraic Geometry

We investigate visibility computations with moving viewpoints. The initial problems are of discrete and algorithmic nature, but even for simple classes of objects (such as balls and polytopes), they lead to interesting and difficult problems from real algebraic geometry. Namely, it is necessary to characterize and compute the common tangent lines to a given set of convex bodies. In particular, we present a new sweep algorithm in dimension 2, as well as survey and extend recent algebraic-geometric results on the tangent problems
Learning Causal Structures Using Regression Invariance

We study causal inference in a multi-environment setting, in which the functional relations for producing the variables from their direct causes remain the same across environments, while the distribution of exogenous noises may vary. We introduce the idea of using the invariance of the functional relations of the variables to their causes across a set of environments. We define a notion of completeness for a causal inference algorithm in this setting and prove the existence of such algorithm by proposing the baseline algorithm. Additionally, we present an alternate algorithm that has significantly improved computational and sample complexity compared to the baseline algorithm. The experiment results show that the proposed algorithm outperforms the other existing algorithms.
A 124.8Msps, 15.6mW Field-Programmable Variable-Length Codec for Multimedia Applications

Variable-length coding is one of the key compression methods for multimedia bitstreams. To accommodate new or user-defined variable-length codes (VLC) for maximal compressions in various applications, we propose a variable-length codec that supports field programmability along with very competitive performance indices. The design has 33% less transistors than its field-programmable predecessor. Moreover, measurement on the real chip demonstrates that the design is capable of processing 124.8 mega-symbols (Msym) per second for MPEG4, while consuming only 15.6mW at 1.4V. When measured by muW/Msym, the realized variable-length codec is even 5% better than the state-of-the-art non-programmable MPEG2 variable-length decoder that hardwires the entire design into random logic
A Model of Dynamic Choice, Confidence, and Motor Response

In psychology research, mathematical models have developed to explain choices and response times. More recently, researchers have begun creating models to try explaining confidence as well (e.g., Vickers, 1979; Pleskac & Busemeyer, 2010; Ratcliff & Starns, 2009; Van Zandt, 2000). I join this effort by adapting the Linear Ballistic Accumulator model (Brown & Heathcote, 2008) to account for confidence by employing the relative balance-of-evidence hypothesis (Merkle & Van Zandt, 2006) in my Ballistic Accumulator for Confidence (BAC). The goal of this research is to account for multiple components of a decision task, including choice probabilities, confidence ratings, and response times. Often in a decision experiment, researchers count the time between stimulus appearance and the press of a button for a choice simply as response time, although many different mental activities occur during that time. Their primary focus is the decision process, but other processes include movement and movement programming. Through a within-subjects experiment designed to extract movement times from response times to obtain reaction times, I show that decision times and movement times are not independent in determining response times. In some conditions, movement times vary systematically and correlate with reaction times, while in other conditions, they do not.
MicroRNAs bind to Toll-like receptors to induce prometastatic inflammatory response

MicroRNAs (miRNAs) are small noncoding RNAs, 19–24 nucleotides in length, that regulate gene expression and are expressed aberrantly in most types of cancer. MiRNAs also have been detected in the blood of cancer patients and can serve as circulating biomarkers. It has been shown that secreted miRNAs within exosomes can be transferred from cell to cell and can regulate gene expression in the receiving cells by canonical binding to their target messenger RNAs. Here we show that tumor-secreted miR-21 and miR-29a also can function by another mechanism, by binding as ligands to receptors of the Toll-like receptor (TLR) family, murine TLR7 and human TLR8, in immune cells, triggering a TLR-mediated prometastatic inflammatory response that ultimately may lead to tumor growth and metastasis. Thus, by acting as paracrine agonists of TLRs, secreted miRNAs are key regulators of the tumor microenvironment. This mechanism of action of miRNAs is implicated in tumor–immune system communication and is important in tumor growth and spread, thus representing a possible target for cancer treatment.
The evolution of bacterial resistance against bacteriophages in the horse chestnut phyllosphere is general across both space and time

Insight to the spatial and temporal scales of coevolution is key to predicting the outcome of host–parasite interactions and spread of disease. For bacteria infecting long-lived hosts, selection to overcome host defences is just one factor shaping the course of evolution; populations will also be competing with other microbial species and will themselves be facing infection by bacteriophage viruses. Here, we examine the temporal and spatial patterns of bacterial adaptation against natural phage populations from within leaves of horse chestnut trees. Using a time-shift experiment with both sympatric and allopatric phages from either contemporary or earlier points in the season, we demonstrate that bacterial resistance is higher against phages from the past, regardless of spatial sympatry or how much earlier in the season phages were collected. Similarly, we show that future bacterial hosts are more resistant to both sympatric and allopatric phages than contemporary bacterial hosts. Together, our results suggest the evolution of relatively general bacterial resistance against phages in nature and are contrasting to previously observed patterns of phage adaptation to bacteria from the same tree hosts over the same time frame, indicating a potential asymmetry in coevolutionary dynamics.
Breaking Free of Control: How Conventional T Cells Overcome Regulatory T Cell Suppression

Conventional T (Tcon) cells are crucial in shaping the immune response, whether it is protection against a pathogen, a cytotoxic attack on tumor cells, or an unwanted response to self-antigens in the context of autoimmunity. In each of these immune settings, regulatory T cells (Tregs) can potentially exert control over the Tcon cell response, resulting in either suppression or activation of the Tcon cells. Under physiological conditions, Tcon cells are able to transiently overcome Treg-imposed restraints to mount a protective response against an infectious threat, achieving clonal expansion, differentiation, and effector function. However, evidence has accumulated in recent years to suggest that Tcon cell resistance to Treg-mediated suppression centrally contributes to the pathogenesis of autoimmune disease. Tipping the balance too far in the other direction, cancerous tumors utilize Tregs to establish an overly suppressive microenvironment, preventing antitumor Tcon cell responses. Given the wide-ranging clinical importance of the Tcon/Treg interaction, this review aims to provide a better understanding of what determines whether a Tcon cell is susceptible to Treg-mediated suppression and how perturbations to this finely tuned balance play a role in pathological conditions. Here, we focus in detail on the complex array of factors that confer Tcon cells with resistance to Treg suppression, which we have divided into two categories: (1) extracellular factor-mediated signaling and (2) intracellular signaling molecules. Further, we explore the therapeutic implications of manipulating the phosphatidylinositol-3 kinase (PI3K)/Akt signaling pathway, which is proposed to be the convergence point of signaling pathways that mediate Tcon resistance to suppression. Finally, we address important unresolved questions on the timing and location of acquisition of resistance, and the stability of the “Treg-resistant” phenotype.
The Lymphoid Variant of Hypereosinophilic Syndrome

AbstractThe CD3-CD4+ aberrant T-cell phenotype is the most described in the lymphoid variant of hypereosinophilic syndrome (L-HES), a rare form of HES. Only a few cases have been reported, and data for these patients are scarce. To describe characteristics and outcome of CD3-CD4+ L-HES patients, we conducted a national multicentric retrospective study in the French Eosinophil Network. All patients who met the recent criteria of hypereosinophilia (HE) or HES and who had a persistent CD3-CD4+ T-cell subset on blood T-cell phenotyping were included. Clinical and laboratory data were retrospectively collected by chart review. CD3-CD4+ L-HES was diagnosed in 21 patients (13 females, median age 42 years [range, 5–75 yr]). Half (48%) had a history of atopic manifestations. Clinical manifestations were dermatologic (81%), superficial adenopathy (62%), rheumatologic (29%), gastrointestinal (24%), pulmonary (19%), neurologic (10%), and cardiovascular (5%). The median absolute CD3-CD4+ T-cell count was 0.35 G/L (range, 0.01–28.3), with a clonal TCR&ggr;&dgr; rearrangement in 76% of patients. The mean follow-up duration after HES diagnosis was 6.9 ± 5.1 years. All patients treated with oral corticosteroids (CS) (n = 18) obtained remission, but 16 required CS-sparing treatments. One patient had a T-cell lymphoma 8 years after diagnosis, and 3 deaths occurred during follow-up.In conclusion, clinical manifestations related to CD3-CD4+ T cell-associated L-HES are not limited to skin, and can involve all tissue or organs affected in other types of HE. Contrary to FIP1L1-PDGFRA chronic eosinophilic leukemia patients, CS are always effective in these patients, but CS-sparing treatments are frequently needed. The occurrence of T-cell lymphoma, although rare in our cohort, remains a major concern during follow-up.
Electrical Stimulation of the Human Cerebral Cortex by Extracranial Muscle Activity: Effect Quantification With Intracranial EEG and FEM Simulations

Objective: Electric fields (EF) of approx. 0.2 V/m have been shown to be sufficiently strong to both modulate neuronal activity in the cerebral cortex and have measurable effects on cognitive performance. We hypothesized that the EF caused by the electrical activity of extracranial muscles during natural chewing may reach similar strength in the cerebral cortex and hence might act as an endogenous modality of brain stimulation. Here, we present first steps toward validating this hypothesis. Methods: Using a realistic volume conductor head model of an epilepsy patient having undergone intracranial electrode placement and utilizing simultaneous intracranial and extracranial electrical recordings during chewing, we derive predictions about the chewing-related cortical EF strength to be expected in healthy individuals. Results: We find that in the region of the temporal poles, the expected EF strength may reach amplitudes in the order of 0.1-1 V/m. Conclusion: The cortical EF caused by natural chewing could be large enough to modulate ongoing neural activity in the cerebral cortex and influence cognitive performance. Significance: The present study lends first support for the assumption that extracranial muscle activity might represent an endogenous source of electrical brain stimulation. This offers a new potential explanation for the puzzling effects of gum chewing on cognition, which have been repeatedly reported in the literature.
Toward a large-scale formal theory of commonsense psychology for metacognition

Abstract : Robust intelligent systems will require a capacity for metacognitive reasoning, where intelligent systems monitor and reflect on their own reasoning processes. A large-scale study of human strategic reasoning indicates that rich representational models of commonsense psychology are available to enable human metacognition. In this paper, we argue that large-scale formalizations of commonsense psychology enable metacognitive reasoning in intelligent systems. We describe our progress toward developing 30 integrated axiomatic theories of commonsense psychology, and discuss the central representational challenges that have arisen in this work to date.
La realidad del maltrato entre iguales en los centros de secundaria españoles

Resumen A partir del estudio empírico elaborado para el Informe del Defensor del Pueblo sobre violencia escolar, se presentan nuevos datos de la incidencia de varias formas de abusos entre iguales en la enseñanza secundaria obligatoria, de las circunstancias en que ocurren así como la visión del profesorado acerca del mismo. La incidencia del maltrato estí estimada a partir de un cuestionario aplicado a una muestra representativa nacional de 3000 estudiantes de ESO, la mitad chicas, la mitad chicos, quienes contestan desde su perspectiva de posible víctima, agresor o testigo. Los datos muestran una mayor incidencia de agresiones que se manifiestan como exclusión social y agresión verbal. La variación debida a género y curso depende del tipo de agresión y del papel como víctima o agresor. En general los chicos están más implicados, salvo en agresiones indirectas. Hay más incidencia en primer ciclo de educación secundaria con algunas excepciones (maledicencia e ignorar). Las víctimas describen como autor/a a alguien del mismo grupo de clase, y con la edad aumenta la importancia del aula como escenario. Además, la ayuda que reciben las víctimas es escasa, limitada a los amigos/as. Por su parte, los/as jefes de estudio informan de agresiones entre profesores/as y alumnos/as, de la importancia que dan a las situaciones de maltrato y de las medidas adoptadas individualmentey en los centros para atajar el problema.
Time series models and its relevance to modeling TCP SYN based DoS attacks

Denial of Service (DoS) attacks are extensively modeled using linear time series models. But, the effectiveness of these models are seldom established in the literature. In particular, properties like stationarity, stability and adequacy of the model proposed, are not verified. This paper is an attempt to establish the relevance of linear time series models for detecting TCP SYN based DoS attack, by analysing the network traffic at an edge router, for three months. In the first part of the paper, higher order statistics of the difference between incoming SYN packets and outgoing SYN/ACK packets (called half-open count), accumulated over a sampling interval, are studied in detail. It is found that the half-open time series is unstable and non-stationary. In the second part of the paper, two different transformations on the half-open time series are studied, namely differencing and averaging. It is observed that the averaging pushes the process more to the region of instability, while the differencing brings back the process to stability. Further, differencing is found to be appropriate for the detection of SYN attack using linear time series model, the Auto-Regressive (AR) model in specific. Since the AR model is built on the difference series, it can also be called Auto-Regressive Integrated (ARI) model. The model proposed is tested for its adequacy, by analysing the autocorrelation of the residual error of prediction and through an N-fold cross validation. Low rate SYN attacks of the order of 10 to 20 SYN/second are simulated and studied.
Situación de la convivencia escolar en España: políticas de intervención

Este trabajo ahora el problema de la violencia escolar partiendo de una primera aproximacion doctrinal al sentido y caracteristicas de la violencia en las escuelas: que entendemos por conductas violentas, donde suelen producirse, a quienes afectan principalmente, etc. El autor se plantea tres preguntas basicas que sirven de nexo estructurador del articulo: ? cual es el problema'? es grave el problema'? que soluciones podrian aplicarse? Se anaden tambien los resultados obtenidos en una investigacion desarrollada por el autor en Galicia en la que una amplia muestra de profesores, alumnos, familias y orientadores ofrecen su vision de la situacion en las escuelas.
Criteria for measuring knowledge management performance outcomes in organisations

While many criteria for measuring KM performance outcomes have been proposed, no attempt has been made to provide a comprehensive set of widely accepted criteria and/or benefits associated with KM efforts. This paper seeks to fill the gap by investigating all the criteria proposed in previous research.A framework is proposed in which KM initiatives consist of five dimensions.The appropriate implementation of activities of these dimensions could result in the achievement of KM outcomes.The findings have important implications to organisations on how their KM efforts can be systematically managed and measured for business success.
Automatic classication of large changes into maintenance categories

Large software systems undergo significant evolution during their lifespan, yet often individual changes are not well documented. In this work, we seek to automatically classify large changes into various categories of maintenance tasks — corrective, adaptive, perfective, feature addition, and non-functional improvement — using machine learning techniques. In a previous paper, we found that many commits could be classified easily and reliably based solely on the manual analysis of the commit metadata and commit messages (i.e., without reference to the source code). Our extension is the automation of classification by training Machine Learners on features extracted from the commit metadata, such as the word distribution of a commit message, commit author, and modules modified. We validated the results of the learners via 10-fold cross validation, which achieved accuracies consistently above 50%, indicating good to fair results. We found that the identity of the author of a commit provided much information about the maintenance class of a commit, almost as much as the words of the commit message. This implies that for most large commits, the Source Control System (SCS) commit messages plus the commit author identity is enough information to accurately and automatically categorize the nature of the maintenance task.