Miracle-dz/UniFAR-FTUs huggingface dataset:
Helicobacter heilmannii gastritis: a histological and immunohistochemical trait.

AIM Biopsies of the gastric antrum were reviewed over a period of 10 years to determine the prevalence of Helicobacter heilmannii in symptomatic subjects from this geographical area and to relate its presence to distinctive histopathological and immunohistochemical features. METHODS Biopsies from 7926 symptomatic patients were reviewed. Ten serial sections were stained with haematoxylin and eosin for conventional histology. Another 10 sections were stained with the Gram method for spiral bacteria. When H heilmannii was suspected, 10 additional serial sections were stained with methylene blue to obtain homogeneous colouring. An equal number of sections from patients affected by isolated H heilmannii or H pylori gastritis were analysed by immunohistochemistry to evaluate lymphoid aggregate/mucosal lymphocyte clonality (CD20 and CD3) and tumour necrosis factor alpha (TNF-alpha) in stromal cells. RESULTS The prevalence of H heilmannii was 0.1% (eight of 7926), whereas H pylori was present in 60.7% of patients (4813 of 7926). In two of the eight H heilmannii positive patients both helicobacters were found. In all subjects infected by H heilmannii only, distinctive histology (lymphocyte exudation into gastric foveolae) was seen. Lymphoid aggregates, chronic mucosal inflammation with patchy activity, and the absence of epithelial mucus depletion were regular features of H heilmannii gastritis. Immunohistochemistry did not reveal different lymphocyte clonal patterns between H pylori and H heilmannii gastritis: CD20 positive cells were predominant in the centre of aggregates and mucosal infiltrates, whereas CD3 positive cells were prevalent at the periphery of follicles. Only H pylori gastritis showed a significant increase in TNF-alpha positive stromal cells. CONCLUSION These data suggest that an unusual lymphocyte reaction, with the tendency to invade the foveolar lumen, is a distinctive histopathological aspect of H heilmannii chronic gastritis, although further studies in a larger series are necessary to confirm this fact. Nevertheless, lymphocyte clones do not differ qualitatively from those found in H pylori infection. Moreover, compared with H heilmannii, H pylori provokes a more intense release of TNF-alpha, suggesting that different inflammatory responses exist to these two organisms.
Circadian rhythms and sleep in bipolar disorder.

OBJECTIVE Biological rhythm pathways are highlighted in a number of etiological models of bipolar disorder, and the management of circadian instability appears in consensus treatment guidelines. There are, however, significant conceptual and empirical limitations on our understanding of a hypothesised link between circadian, sleep, and emotion regulation processes in bipolar disorder. The aim of this article is to articulate the limits of scientific knowledge in relation to this hypothesis. METHODS A critical evaluation of various literatures was undertaken. The basic science of circadian and sleep processes, their involvement in normal emotion regulation, and the types of evidence suggesting circadian/sleep involvement in bipolar disorder are reviewed. RESULTS Multiple lines of evidence suggest that circadian and sleep-wake processes are causally involved in bipolar disorder. These processes demonstrably interact with other neurobiological pathways known to be important in bipolar disorder, but are unique in that they are open to behavioural manipulation. CONCLUSION Further research into biological rhythm pathways to bipolar disorder is warranted. Person-environment feedback loops are fundamental to circadian adaptation, and models of circadian pathogenesis (and treatment) should recognize this complexity.
Adaptive Newton Method for Empirical Risk Minimization to Statistical Accuracy

We consider empirical risk minimization for large-scale datasets. We introduce Ada Newton as an adaptive algorithm that uses Newton's method with adaptive sample sizes. The main idea of Ada Newton is to increase the size of the training set by a factor larger than one in a way that the minimization variable for the current training set is in the local neighborhood of the optimal argument of the next training set. This allows to exploit the quadratic convergence property of Newton's method and reach the statistical accuracy of each training set with only one iteration of Newton's method. We show theoretically and empirically that Ada Newton can double the size of the training set in each iteration to achieve the statistical accuracy of the full training set with about two passes over the dataset.
TIPE2 Inhibits Hypoxia-Induced Wnt/β-Catenin Pathway Activation and EMT in Glioma Cells

Hypoxia-induced epithelial-to-mesenchymal transition (EMT) could facilitate tumor progression. TIPE2, the tumor necrosis factor-α (TNF-α)-induced protein 8-like 2 (also known as TNFAIP8L2), is a member of the TNF-α-induced protein 8 (TNFAIP8, TIPE) family and has been involved in the development and progression of several tumors. However, the effects of TIPE2 on the EMT process in glioma cells and the underlying mechanisms of these effects have not been previously reported. In our study, we assessed the roles of TIPE2 in the EMT process in glioma cells in response to hypoxia. Our results indicated that TIPE2 expression was significantly decreased in human glioma cell lines. TIPE2 overexpression significantly inhibited hypoxia-induced migration and invasion, as well as suppressed the EMT process in glioma cells. Furthermore, TIPE2 overexpression prevented hypoxia-induced expression of β-catenin, cyclin D1, and c-myc in human glioma cells. In summary, these data suggest that TIPE2 overexpression inhibited hypoxia-induced Wnt/β-catenin pathway activation and EMT in glioma cells.
THE STABILITY OF A “UNIFORM” AMPLITUDE WAVETRAIN

A narrow-banded spectrum of gravity waves propagating in one horizontal direction 4 at the surface of water with finite depth may be governed by a nonlinear Schrödinger equation 5 (NLSE). If the depth is non-uniform, the coefficients in the NLSE are variable and an additional 6 linear term due to conservation of wave action flux is present, which may act as a dissipative term 7 that causes the wave envelope to broaden and decrease in amplitude or which may act as a growth 8 term that causes the wave envelope to focus and increase in amplitude. The addition of linear, viscous 9 dissipation either enhances the dissipative process or competes with the growth effect. Here we 10 consider such a variable-coefficient, dissipative NLSE. We find a solution that has uniform amplitude 11 in the appropriate reference frame and examine its stability. We find that for waves propagating 12 into shallower water, both bathymetry and viscous dissipation act to stabilize the modulational 13 instability. For waves propagating into deeper water, bathymetry acts to enhance instability, but 14 viscous dissipation eventually causes stabilization. For a special bathymetry, these two effects balance 15 so that the waves are governed by an inviscid NLSE and are consequently unstable to modulational 16 perturbations; this situation is considered for waves on oceanographic and laboratory scales. 17
Role of Pulmonary Artery Reactivity and Nitric Oxide in Injury and Inflammation Following Lung Contusion

ABSTRACT The mechanisms contributing to hypoxia in lung contusion (LC) remain unclear and not temporally associated with the peak onset of acute inflammation. We investigated the role of oxidative stress in alteration of pulmonary arterial (PA) reactivity following LC. In addition, the role of antioxidants in reversing this process was examined. PaO2 and PA reactivity were measured in rats subjected to bilateral LC. Rings were pretreated with a nitric oxide synthase (NOS) inhibitor, L-nitro arginine (10−3 M), or PEG–superoxide dismutase (SOD) and PEG-catalase (CAT), or both (L-nitro arginine + SOD/CAT). Rings were constricted with norepinephrine and relaxed with an NOS agonist (A23187) or NO donor (SNAP [S-nitrosyl amino penicillamine]). Immunochemical and mass spectrometric quantification for nitrotyrosine was performed. Rats were hypoxemic at 4 h after contusion compared with controls, but recovered by 24 h (PaO2/FIO2 ratio: baseline, 443 ± 28; 4 h, 288 ± 46; and 24 h, 417 ± 23). Pulmonary arterial constriction to NOS inhibition and relaxation to A23187 were impaired 4 h after LC. Pulmonary arterial relaxation to SNAP was decreased at 4 and 24 h after LC. These alterations in PA reactivity were reversed by SOD/CAT pretreatment. SOD1 and 2 mRNA were upregulated, and soluble guanylyl cyclase mRNA was downregulated 24 h after LC. Immunohistochemistry and mass spectrometry revealed that levels of 3-nitrotyrosine were increased markedly at 4 h following LC consistent with superoxide generation and formation of peroxynitrite. Collectively, these data suggest that consumption of NO due to excess superoxide resulting in peroxynitrite formation leads to diminished vascular reactivity following LC.
Stop Chasing Trends: Discovering High Order Models in Evolving Data

Many applications are driven by evolving data - patterns in Web traffic, program execution traces, network event logs, etc., are often non-stationary. Building prediction models for evolving data becomes an important and challenging task. Currently, most approaches work by "chasing trends", that is, they keep learning or updating models from the evolving data, and use these impromptu models for online prediction. In many cases, this proves to be both costly and ineffective - much time is wasted on re-learning recurring concepts, yet the classifier may remain one step behind the current trend all the time. In this paper, we propose to mine high-order models in evolving data. More often than not, there are a limited number of concepts, or stable distributions, in the data stream, and concepts switch between each other constantly. We mine all such concepts offline from a historical stream, and build high quality models for each of them. At run time, combining historical concept change patterns and cues provided by an online training stream, we find the most likely current concept and use its corresponding models to classify data in an unlabeled stream. The primary advantage of the high-order model approach is its high accuracy. Experiments show that in benchmark datasets, classification error of the high-order model is only a small fraction of that of the current best approaches. Another important benefit is that, unlike state-of-the-art approaches, our approach does not require users to tune any parameters to achieve a satisfying result on streams of different characteristics.
Zeno: Eventually Consistent Byzantine-Fault Tolerance

Many distributed services are hosted at large, shared, geographically diverse data centers, and they use replication to achieve high availability despite the unreachability of an entire data center. Recent events show that non-crash faults occur in these services and may lead to long outages. While Byzantine-Fault Tolerance (BFT) could be used to withstand these faults, current BFT protocols can become unavailable if a small fraction of their replicas are unreachable. This is because existing BFT protocols favor strong safety guarantees (consistency) over liveness (availability). This paper presents a novel BFT state machine replication protocol called Zeno that trades consistency for higher availability. In particular, Zeno replaces strong consistency (linearizability) with a weaker guarantee (eventual consistency): clients can temporarily miss each other's updates but when the network is stable the states from the individual partitions are merged by having the replicas agree on a total order for all requests. We have built a prototype of Zeno and our evaluation using micro-benchmarks shows that Zeno provides better availability than traditional BFT protocols.
Consciousness and Action Control

One of the key questions that guide and organise research on human consciousness is functional in nature: What is consciousness good for? Many answers to this question are possible , but the one that I shall be dealing with in this chapter is particularly popular. Although many laypeople and researchers would be willing to grant that many perceptual, to some degree even attentional processes occur outside of conscious awareness, the decision how to react to a given stimulus or situation is often assumed to be either necessarily or at least preferentially conscious. This idea is nicely captured by the blurb for the book Better Than Conscious? edited by Engel and Singer (2008): 'Conscious control enables human decision makers to override routines, to exercise willpower, to find innovative solutions, to learn by instruction, to decide collectively, and to justify their choices'. If correct, the implications of this characterisation are that decision making and action control are particularly promising targets of human consciousness, as they support and improve the quality of the way we deal with environmental challenges. One of the origins of this widely held view is rooted in the psychoanalytic approach of Sigmund Freud. He claimed that both conscious and unconscious processes can contribute to the control of human action and considered control to emerge from the interplay between unconscious, automatic action tendencies generated by the pleasure‐seeking Id and socially acceptable considerations provided by the rational Ego (Freud, 1923). Whereas processes initiated by the Id were assumed to be inaccessible to consciousness in principle, some, but not all, Ego operations were considered to be conscious. According to Freud, leaving action control to the Id would be problematic in modern societies, which calls for moderation by the Ego, whose task is to seek compromise between the Id's pleasure‐driven urges and the strict requirements of the Superego, which represents societal norms, expectations, and principles. More modern approaches still buy into this psychoanalytic scenario and the idea that socially responsible action requires conscious mediation. Indeed, so‐called 'dual‐route' or 'dual‐process' models can be found in almost all psychological and cognitive‐neuroscientific research areas (for an overview, see Evans & Stanovich, 2013), and even in the theoretical foundations and everyday practices of modern law (e.
FUSION: a system allowing dynamic Web service composition and automatic execution

Service portals are systems which expose a bundle of Web services to the user, allowing the specification and subsequent execution of complex tasks defined over these individual services. Examples of situations where service portals would be valuable include making travel plans or purchasing a home. Service portals must be capable of converting an abstract user goal into a correct and optimal concrete execution plan, executing according to the plan, verifying the result against a user's stated satisfaction criteria, and in the case of satisfaction failure, initiating the appropriate recovery procedures. The basic framework needed to support this functionality, from gathering the input to generating an optimal plan and executing that plan, is a prerequisite for all service portals, yet there are currently no such commercial systems in existence, and the research literature has given only cursory treatment to some of these issues. In this paper, we describe FUSION, a comprehensive software system which provides the underlying framework for a service portal. We show how using the elements of this framework, service portal designers and architects can easily create domain-specific service portals, e.g., a travel service portal. We also present the Web services execution specification language (WSESL), a language that we have developed to describe execution plans in the context of the FUSION services model. Finally, we develop a set of data structures and algorithms for generating correct and optimal execution plans.
Adaptive Ant Colony Optimization Considering Intensification and Diversification

paper discusses a new adaptive ant colony optimization algorithm and its characteristics are as follows: (1) a novel cranky ant who behaves strangely is introduced to prevent from trapping at the local optima, (2) a new observation technique for searching status is adopted to judge whether it is trapping at local optima. Experimental results using benchmark data prove that the proposed algorithm with the cranky ants and the observation technique enables to control the trade-off between intensification and diversification, in comparison with conventional ACO.
Sensitivity of Southern Hemisphere climate to zonal asymmetry in ozone

Climate model simulations of past and future climate invariably contain prescribed zonal mean stratospheric ozone. While the effects of zonal asymmetry in ozone have been examined in the Northern Hemisphere, much greater zonal asymmetry occurs in the Southern Hemisphere during the break up of the Antarctic ozone hole. We prescribe a realistic three‐dimensional distribution of ozone in a high vertical resolution atmospheric model and compare results with a simulation containing zonal mean ozone. Prescribing the three dimensional ozone distribution results in a cooling of the stratosphere and upper troposphere comparable to that caused by ozone depletion itself. Our results suggest that changes in the zonal asymmetry of ozone have had important impacts on Southern Hemisphere climate, and will continue to do so in the future.
A linear regression-based delay-bounded multicast protocol for vehicular ad hoc networks

Vehicles may inform emergent events or car accidents by using a routing protocol in vehicular ad-hoc networks VANETs. Many researches focus on minimising the end-to-end delay instead of reducing the usage of radio. Recently, delay bounded routing protocol is designed for minimising the usage of radio within user-defined delay time. In this paper, we focus on linear regression-based delay-bounded multicast, whose goal is to deliver messages to many destination regions within user-defined delay of each region by minimising the usage of radio. In our protocol, the message can be delivered to the destination regions by the hybrid of data mulling, which carried by a vehicle, when the available time is enough and the other forwarding, which delivered through radio. There are two schemes the greedy and the centralised in our protocol. Simulation results show that the proposed multicasts protocol performs better than existed research in terms of total transmitted bytes.
Entropies from Markov Models as Complexity Measures of Embedded Attractors

This paper addresses the problem of measuring complexity from embedded attractors as a way to characterize changes in the dynamical behavior of different types of systems with a quasi-periodic behavior by observing their outputs. With the aim of measuring the stability of the trajectories of the attractor along time, this paper proposes three new estimations of entropy that are derived from a Markov model of the embedded attractor. The proposed estimators are compared with traditional nonparametric entropy measures, such as approximate entropy, sample entropy and fuzzy entropy, which only take into account the spatial dimension of the trajectory. The method proposes the use of an unsupervised algorithm to find the principal curve, which is considered as the “profile trajectory”, that will serve to adjust the Markov model. The new entropy measures are evaluated using three synthetic experiments and three datasets of physiological signals. In terms of consistency and discrimination capabilities, the results show that the proposed measures perform better than the other entropy measures used for comparison purposes.
Should All Pregnant Women be Screened for Syphilis?

In industrialized countries, the incidence of syphilis has decreased dramatically since the discovery of penicillin in the 1940s. However, syphilis and congenital syphilis are far from eradicated, especially in low- and middle-income countries. Syphilis in pregnant women is a cause of adverse pregnancy outcomes that can be prevented by screening for syphilis and early treatment in pregnancy. Several studies have found screening of pregnant women for syphilis to be a highly cost-effective intervention, even if the prevalence of syphilis is low. Obstacles to universal screening of pregnant women include low awareness of syphilis and low quality of antenatal care and healthcare in general in many low- and middle-income countries. For these settings, we need simpler and more reliable serological tests for syphilis, but we also need to strengthen health services in general to ensure sustainable antenatal care services to ensure sustainability of syphilis screening programmes.
(re)Considering Bertin in the age of big data and visual analytics

ABSTRACT This paper highlights a selection of core ideas articulated by Bertin and leveraged by many researchers over time, with particular attention to how the ideas relate to developments in cartography, big data, and visual analytics. A primary contribution is a bibliometric analysis of the impact of Bertin’s Semiology of Graphics at its 50th anniversary. A briefer bibliometric assessment of Graphics and Graphic Information Processing impacts is also provided. The bibliometric analysis includes exploration of citations to Semiology of Graphics over the entire time span (in both English and French editions) as well as more focused analysis by topic and outlet since the advent of visual analytics as a research domain. Then, very recent research related to cartography, visual analytics, and big data is examined in detail to determine if and how Bertin’s ideas continue to be leveraged and extended for current data representation and analysis challenges. After outlining some limitations of the bibliometric analysis, discussion reflects on the current relevance of Bertin’s ideas, potential applications in visual analytics, and the need for a complement to Sémiologie Graphique focused on interactive visual interfaces to an increasingly diverse array of display forms. The paper concludes with thoughts on next steps.
A Problem Concerning a Character Sum

Let p be a prime congruent to −1 modulo 4, (n/p) the Legendre symbol and \(S(k) = \Sigma _{n = 1}^{p - 1} {\text{ }}n^k \left( {\tfrac{n}{p}} \right)\). The problem of finding a prime p such that S(3) > 0 was one of the motivating forces behind the development of several of Shanks' ideas for computing in algebraic number fields, although neither he nor D. H. and Emma Lehmer were ever successful in finding such a p. In this extended abstract we summarize some techniques which were successful in producing, for each k such that 3 ≤ k ≤ 2000, a value for p such that S(k) > 0.