Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression of ATP7B in human gastric cardiac carcinomas in comparison with distal gastric carcinomas.

AIM To analyze expression of ATP7B in gastric cardiac adenocarcinomas, its clinicopathologic significance, in comparison with distal gastric adenocarcinomas. METHODS Immunohistochemical avidin-biotin peroxidase complex method was applied to detect the expression of ATP7B in 49 cases of cardiac carcinomas, the corresponding adjacent non-neoplastic epithelium and 55 cases of distal gastric carcinomas. RESULTS The proportion of ATP7B positive samples in gastric cardiac carcinomas (51.0%, 25 of 49) was significantly higher than that in the corresponding adjacent non-neoplastic epithelium (22.4%, 11 of 49) (P = 0.003). ATP7B expression in poorly differentiated gastric cardiac carcinomas was significantly higher than that in well/moderately differentiated gastric cardiac carcinomas (P = 0.030). ATP7B expression in gastric cardiac carcinomas was independent of age, tumor size, nodal stage and metastasis status. ATP7B protein was detected in 30.9% (17/55 cases) of distal gastric carcinomas, markedly lower than that in gastric cardiac carcinomas (P = 0.037). CONCLUSION ATP7B protein is frequently overexpressed in gastric cardiac carcinomas, and correlated with the differentiation of cardiac carcinoma. ATP7B expression in gastric cardiac carcinomas is significantly higher than that in distal gastric carcinomas, which might partially explain the difference of chemotherapy response and prognosis between these two gastric carcinomas.
A Localization Scheme for Wireless Sensor Networks Using Mobile Anchors With Directional Antennas

This paper proposes a range-free localization scheme for wireless sensor networks (WSNs) using mobile anchor nodes equipped with four directional antennas. In the proposed approach, each mobile anchor node determines its position via GPS, and then broadcasts its coordinates as it moves through the WSN. The sensor nodes detect these beacon messages and utilize a simple processing scheme to determine their own coordinates based on those of the anchors. The proposed approach removes the requirement for specific ranging hardware on the sensor nodes, avoids the need for communications between the sensor nodes. Moreover, the scheme is robust toward the effects of variations in the transmission range of the anchor nodes and the presence of obstacles in the sensing environment. The performance of the proposed scheme is evaluated by conducting a series of simulations using the ns-2 network simulator. The results show that the proposed localization scheme achieves a reduced localization error and a lower energy consumption than existing range-free solutions based on mobile anchor nodes over a wide range of typical network conditions.
Transcriptional Analysis of the Escherichia coli mreBCD Genes Responsible for Morphogenesis and Chromosome Segregation

The Escherichia coli mreB gene encodes an actin-like cytoskeletal protein and is required for rod shape formation of cells and chromosome segregation. Just downstream of mreB, the mreC and mreD genes are located. They are also required for rod shape formation, though their role in chromosome segregation is unclear. lacZ fusion analysis and Northern hybridization showed that the mreB, mreC, and mreD genes formed an operon. Most of the transcripts were expressed as a monocistronic mreB mRNA, and only 1–2% of the transcripts were expressed as a polycistronic mreBCD mRNA. Introduction of a frame-shift mutation in the mreB gene resulted in a significant decrease in the amount of polycistronic mreBCD mRNA but not in that of monocistronic mreB mRNA, suggesting that an attenuation-like regulation was involved in this transcriptional control. Primer extension analysis identified three transcriptional initiation sites. Three possible σD-dependent promoter-like sequences were found just upstream of these transcriptional initiation sites. lacZ fusion analysis confirmed that these three promoters contributed to the expression of mreBCD. On the basis of these findings, the essentiality of the mreB gene was confirmed.
Linking isoprene with plant thermotolerance, antioxidants and monoterpene emissions

The purpose of the present study was to test the possible plant thermotolerance role of isoprene and to study its relationship with non-enzymatic antioxidants and terpene emissions. The gas exchange, chlorophyll fluorescence, extent of photo- and oxidative stress, leaf damage, mechanisms of photo- and antioxidant protection, and terpene emission were measured in leaves of Quercus ilex seedlings exposed to a ramp of temperatures of 5 ∞ ∞ ∞ C steps from 25 to 50 ∞ ∞ ∞ C growing with and without isoprene (10 m L L - 1 ) fumigation. The results showed that isoprene actually conferred thermotolerance (shifted the decrease of net photosynthetic rates from 35 to 45 ∞ C, increased F v / F m at 50 ∞ ∞ ∞ C from 0.38 to 0.65, and decreased the leaf area damaged from 27 to 15%), that it precluded or delayed the enhancement of the antioxidant non-enzymatic defence conferred by a tocopherol, ascorbic acid or b b b -carotene consumption in response to increasing temperatures, and that it decreased by approximately 70% the emissions of monoterpenes at the highest temperatures. This suggests that there are inducible mechanisms triggered by the initial stages of thermal damage that up-regulate these antioxidant compounds at high temperatures and that these mechanisms are somehow suppressed in the presence of exogenous isoprene, which seems to already exert an antioxidant-like behaviour.
Endogenous Phenazine Antibiotics Promote Anaerobic Survival of Pseudomonas aeruginosa via Extracellular Electron Transfer

ABSTRACT Antibiotics are increasingly recognized as having other, important physiological functions for the cells that produce them. An example of this is the effect that phenazines have on signaling and community development for Pseudomonas aeruginosa (L. E. Dietrich, T. K. Teal, A. Price-Whelan, and D. K. Newman, Science 321:1203-1206, 2008). Here we show that phenazine-facilitated electron transfer to poised-potential electrodes promotes anaerobic survival but not growth of Pseudomonas aeruginosa PA14 under conditions of oxidant limitation. Other electron shuttles that are reduced but not made by PA14 do not facilitate survival, suggesting that the survival effect is specific to endogenous phenazines.
Grid Code Compatibility of VSC-HVDC Connected Offshore Wind Turbines Employing Power Synchronization Control

This paper presents an alternative control scheme for offshore wind turbines (WTs) connected to the mainland grid through high voltage dc (HVDC) links based on voltage source converters (VSCs). The proposed WT controller inherently provides rapid droop-type frequency response, without the need to implement an additional WT frequency controller. A coordinated control approach is proposed between the WT and HVDC controllers in order to achieve fault ride-through (FRT) and frequency response capabilities, relying solely on offshore frequency modulation. To demonstrate the FRT capability of the VSC-HVDC link, a detailed EMT-type model is first developed in Matlab/Simulink, where onshore grid faults are tested. Then, the offshore wind farm is connected to a study case system in order to assess the contribution of the VSC-HVDC link to frequency regulation, by exploiting the proposed WT controller along with the communication capability between the two HVDC VSCs.
Envelope Protein Requirements for the Assembly of Infectious Virions of Porcine Reproductive and Respiratory Syndrome Virus

ABSTRACT Virions of porcine reproductive and respiratory syndrome virus (PRRSV) contain six membrane proteins: the major proteins GP5 and M and the minor proteins GP2a, E, GP3, and GP4. Here, we studied the envelope protein requirements for PRRSV particle formation and infectivity using full-length cDNA clones in which the genes encoding the membrane proteins were disrupted by site-directed mutagenesis. By transfection of RNAs transcribed from these cDNAs into BHK-21 cells and analysis of the culture medium using ultracentrifugation, radioimmunoprecipitation, and real-time reverse transcription-PCR, we observed that the production of viral particles is dependent on both major envelope proteins; no particles were released when either the GP5 or the M protein was absent. In contrast, particle production was not dependent on the minor envelope proteins. Remarkably, in the absence of any one of the latter proteins, the incorporation of all other minor envelope proteins was affected, indicating that these proteins interact with each other and are assembled into virions as a multimeric complex. Independent evidence for such complexes was obtained by coexpression of the minor envelope proteins in BHK-21 cells using a Semliki Forest virus expression system. By analyzing the maturation of their N-linked oligosaccharides, we found that the glycoproteins were each retained in the endoplasmic reticulum unless expressed together, in which case they were collectively transported through the Golgi complex to the plasma membrane and were even detected in the extracellular medium. As the PRRSV particles lacking the minor envelope proteins are not infectious, we hypothesize that the virion surface structures formed by these proteins function in viral entry by mediating receptor binding and/or virus-cell fusion.
Induction of Protective Immunity against Murine Gammaherpesvirus 68 Infection in the Absence of Viral Latency

ABSTRACT Human gammaherpesviruses, Epstein-Barr virus, and human herpesvirus 8/Kaposi's sarcoma-associated herpesvirus are important pathogens associated with diseases, including lymphomas and other malignancies. Murine gammaherpesvirus 68 (MHV-68) is used as an experimental model system to study the host immune control of infection and explore novel vaccine strategies based on latency-deficient live viruses. We studied the properties and the potential of a recombinant MHV-68 (AC-RTA) in which the genes required for persistent infection were replaced by a constitutively expressed viral transcription activator, RTA, which dictates the virus to lytic replication. After intranasal infection of mice, replication of AC-RTA in the lung was attenuated, and no AC-RTA virus or viral DNA was detected in the isolated splenocytes, indicating a lack of latency in the spleen. Infection of the AC-RTA virus elicited both cellular immune responses and virus-specific IgG at a level comparable to that elicited by infection of the wild-type virus. Importantly, vaccination of AC-RTA was able to protect mice against subsequent challenge by the wild-type MHV-68. AC-RTA provides a vaccine strategy for preventing infection of human gammaherpesviruses. Furthermore, our results suggest that immunity to the major latent antigens is not required for protection.
A theoretical study of the nonintercalative binding of berenil and stilbamidine to double-stranded (dA-dT)n oligomers.

The nonintercalative binding of two diarylamidines , berenil and stilbamidine , to the minor groove of double-stranded (dA-dT)n oligomers in the B-DNA conformation was investigated by performing theoretical computations of their intermolecular interaction energies with the groove. The method consists of an additive procedure developed previously in this laboratory using empirical formulae based on ab initio computations. The objective was to assess the extent to which the particular structure of each diarylamidine bears on its binding mode and affinity to the minor groove. The results show that the intrinsically preferred configurations of the two compounds are markedly different. Owing to its slightly curved shape, berenil interacts with the groove predominantly through its concave side, the binding occurring principally with sites (O2, O1) belonging to two thymidines on the opposite strands. The binding of stilbamidine involves a more limited number of hydrogen-bonding interactions, although an appreciably large number of interatomic distances between its hydrogens and sites on the groove (O2, N3, O1) falls in the range 2.7-3.1 A. Each side of stilbamidine with respect to its long axis faces a distinct strand of DNA. The importance of the electrostatic contribution of the binding energy of the two diarylamidines is underlined. Preferential binding of berenil rather than of stilbamidine occurs only at the level of a complete helical turn of phosphates in (dA-dT)n. The energy difference increases significantly upon further buildup of phosphates. These results can be interpreted in terms of the molecular electrostatic potential in the grooves.
Enhancing Structure Learning of Markov Network Using Alternating Decision Trees

Most of the existing algorithms used for the purpose of Markov network structure learning are either restricted to learning interactions among small number of variables or are extremely slow in nature because of the large number of possible structures, as given in the literature. In this paper, we propose a novel method of using Alternating Decision (AD) trees for learning Markov network structures. The advantage in using the AD trees is that complex interactions among many variables can be represented and high prediction accuracy is obtained. Given a data set, using AD trees for structure learning involves learning an AD tree for the prediction of each variable, conversion of each tree to a set of conjunctive features and weight learning. The set of conjunctive features define the Markov network structure. In this paper, we compare Decision Tree Structure Learning (DTSL) method proposed by Lowd and Davis with the AD tree approach empirically over five data sets and find AD tree approach to be more accurate than the DTSL approach for two data sets. However, the method using AD trees is slower than the DTSL method.
Buoyancy reversal in cloud‐top mixing layers

A theoretical and numerical small‐scale study of the evaporative cooling phenomenon that might appear in the stratocumulus‐topped boundary layers is presented. An ideal configuration of a cloud‐top mixing layer is considered as defined by two non‐turbulent horizontal layers, stably stratified and with buoyancy reversal within a certain range of mixture fractions due to the evaporative cooling. Linear stability analysis of the shear‐free configuration is employed to provide a new interpretation of the buoyancy reversal parameter, namely in terms of a time‐scale ratio between the stable and the unstable modes of the system. An incompressible high‐order numerical algorithm to perform direct numerical simulation of the configuration is described and two‐dimensional simulations of single‐mode perturbations are presented. These simulations confirm the role of the different parameters identified in the linear stability analysis and show that convoluted flow patterns can be generated by the evaporative cooling even for the low levels of buoyancy reversal found in stratocumulus clouds. They also show that there is no enhancement of turbulent entrainment of upper‐layer fluid in the shear‐free configuration, and turbulent mixing enhancement by the evaporative cooling is restricted to the lower layer. Copyright © 2009 Royal Meteorological Society
Sociodemographic risk and early environmental factors that contribute to resilience in executive control: A factor mixture model of 3-year-olds

Young children at sociodemographic risk generally demonstrate lower executive control (EC), although with substantial heterogeneity across children. Given this marked variability, there may be some at-risk children who display higher EC and may be buffered from or resilient to the effects of sociodemographic risk who can be studied to identify the contributory factors. In this study, factor mixture modelling was used to determine whether subgroups of 3-year-old children existed based on their observed performance on a battery of EC tasks. Results indicated 2 latent groups: One characterized by lower EC and the other by higher EC. Both sociodemographically at-risk and low-risk children were represented in each group, yielding 4 risk-status-by-EC groups, where at-risk higher EC children were termed the resilient group. Proximal household enrichment (e.g., exposure to learning materials, varied enriching experiences, academic and language stimulation, parental responsivity) distinguished the resilient group from lower performing children of similar risk status, whereas distal financial resources and proximal social network resources did not distinguish these two groups. Results suggest potential intervention targets to promote optimal EC development, particularly among children at risk.
Explorer Abstract Data Types without the Types . Dedicated to

Data Types without the Types. Dedicated to David Turner on the occasion of his 70'th birthday Citation for published version: Wadler, P 2017, 'Abstract Data Types without the Types. Dedicated to David Turner on the occasion of his 70'th birthday', Journal of Universal Computer Sciene, vol. 23, no. 1, pp. 5-20. Link: Link to publication record in Edinburgh Research Explorer Document Version: Publisher's PDF, also known as Version of record Published In: Journal of Universal Computer Sciene General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact openaccess@ed.ac.uk providing details, and we will remove access to the work immediately and investigate your claim. Download date: 20. Mar. 2020 Abstract Data Types without the TypesData Types without the Types Philip Wadler (Edinburgh University, Scotland wadler@inf.ed.ac.uk) Dedicated to David Turner on the occasion of his 70’th birthday Abstract: The data abstraction mechanism of Miranda may be adapted to a dynamically typed programming language by applying ideas from gradual typing.
Development and Validation of an Expanded Version of the Three-Factor Levenson Self-Report Psychopathy Scale

abstract The Levenson Self-Report Psychopathy Scale (LSRP; Levenson, Kiehl, & Fitzpatrick, 1995) is a brief self-report questionnaire frequently used in psychopathy research. Although the scale has many desirable properties such as brevity and being available in the public domain, there are also several psychometric concerns associated with it, including low internal consistency, problematic construct validity, and incomplete conceptual coverage of several components of psychopathy. In 2 studies, we provide evidence that additional items can augment the LSRP to address the aforementioned concerns. In the first study, using a large sample of students and members of the general Australian community (n = 729), we found that an expanded 36-item, 3-factor version of the LSRP was associated with improvements in internal consistency and construct coverage with little degradation in model fit. In the second study, using another Australian community sample (n = 300), we replicated the results of Study 1 and demonstrated improvements in construct validity for the expanded 36-item, 3-factor scale compared to the 19-item, 3-factor scale. Our results indicate that, although slightly longer, the expanded version of the 3-factor LSRP ameliorates many of the concerns associated with its original counterpart.
Leveraging adaptive peeking window to improve self-exciting point process model for popularity prediction

Predicting the popularity of online content is an important issue. The mainstream method is to model the cumulative growth of the popularity as a temporal point process and to make predictions based on the observed initial period of information cascade. The peeking window, which will be taken into consideration in making predictions, is vitally important for the accuracy of predictions. However, the existing studies only generated hypotheses about the initial burst and maintained a consistent size of the peeking window for all content. The limited accuracy of previous approaches raises a fundamental question, i.e., How can we obtain the most effective part of the history to make an accurate prediction? In this paper, we identified the existence of a strong correlation between the peeking window and the temporal dynamic of the instantaneous relative attractiveness for a given online content. An investigation was conducted to explore the adaptive peeking window, which was used in a selfexciting point process model to predict eventual future popularity. Empirical studies on a Twitter dataset demonstrated that the proposed method significantly outperformed existing approaches.
THE ROLE OF DECISION TREES IN NATURAL LANGUAGE PROCESSING

The speech recognition and understanding systems require various kinds of linguistic knowledge to improve their performances. This requires the capture of knowledge from different linguistic levels (morphological, syntactic, semantic, etc.) and their processing using different techniques. The decision trees are one of the most frequently used techniques in natural language processing because they can model very well the grammatical structure of sentences/phrases. In this paper we present the role of the decision trees in modeling of possession relation between two nouns semantically related.
Skew-Aware Task Scheduling in Clouds

Data skew is an important reason for the emergence of stragglers in MapReduce-like cloud systems. In this paper, we propose a Skew-Aware Task Scheduling (SATS) mechanism for iterative applications in MapReduce-like systems. The mechanism utilizes the similarity of data distribution in adjacent iterations of iterative applications to reduce the straggle problem caused by data skew. It collects the data distribution information during the execution of tasks for the current iteration, and uses the information to guide data partitioning in tasks for the next iteration. We implement the mechanism in the HaLoop system and deploy it in a cluster. Experiments show that the proposed mechanism could deal with the data skew and improve the load balancing effectively.