bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterisations of testing preorders for a finite probabilistic
π
-calculus
Authors: Deng Yuxin , Tiu Alwen 
Published: June 2012

Abstract

We consider two characterisations of the may and must testing preorders for a probabilistic extension of the finite
π
-calculus: one based on notions of probabilistic weak simulations, and the other on a probabilistic extension of a fragment of Milner–Parrow–Walker modal logic for the
π
-calculus. We base our notions of simulations on similar concepts used in previous work for probabilistic CSP. However, unlike the case with CSP (or other non-value-passing calculi), there are several possible definitions of simulation for the probabilistic
π
-calculus, which arise from different ways of scoping the name quantification. We show that in order to capture the testing preorders, one needs to use the “earliest” simulation relation (in analogy to the notion of early (bi)simulation in the non-probabilistic case). The key ideas in both characterisations are the notion of a “characteristic formula” of a probabilistic process, and the notion of a “characteristic test” for a formula. As in an earlier work on testing equivalence for the
π
-calculus by Boreale and De Nicola, we extend the language of the
π
-calculus with a mismatch operator, without which the formulation of a characteristic test will not be possible.
External and internal choice with event groups in Event-B
Authors: Butler Michael 
Published: June 2012

Abstract
Abrial’s Event-B formalism for refinement-based system development is influenced by Back’s action system approach. Morgan has defined a CSP-like failures-divergence semantics for action systems that distinguishes internal and external choice of actions. Morgan’s semantics has the characteristic that the choice between enabled actions is external while internal choice is represented less directly through nondeterministic effect of actions. Practical experience with Event-B has demonstrated the need to be able to represent both internal and external choice between enabled events more explicitly. In this paper, Morgan’s failures semantics for action systems is modified to allow both internal and external choice to be represented directly. This is achieved by grouping events so that external choice is between event groups and internal choice is within event groups. This leads to a refinement rule for preservation of choice between event groups while allowing for reduction of choice within event groups. We also provide a refinement rule for splitting event groups in order to increase external choice. The refinement rules are justified in terms of failures refinement.
Dijkstra, Floyd and Warshall meet Kleene
Authors: Höfner Peter , Möller Bernhard 
Published: June 2012

Abstract
Around 1960, Dijkstra, Floyd and Warshall published papers on algorithms for solving single-source and all-sources shortest path problems, respectively. These algorithms, nowadays named after their inventors, are well known and well established. This paper sheds an algebraic light on these algorithms. We combine the shortest path problems with Kleene algebra, also known as Conway’s regular algebra. This view yields a purely algebraic version of Dijkstra’s shortest path algorithm and the one by Floyd/Warshall. Moreover, the algebraic abstraction yields applications of these algorithms to structures different from graphs and pinpoints the mathematical requirements on the underlying cost algebra that ensure their correctness.
Architectural refinement and notions of intransitive noninterference
Authors: van der Meyden Ron 
Published: June 2012

Abstract
This paper deals with architectural designs that specify components of a system and the permitted flows of information between them. In the process of systems development, one might refine such a design by viewing a component as being composed of subcomponents, and specifying permitted flows of information between these subcomponents and others in the design. The paper studies the soundness of such refinements with respect to a spectrum of different semantics for information flow policies, including Goguen and Meseguer’s purge-based definition, Haigh and Young’s intransitive purge-based definition, and some more recent notions TA-security, TO-security and ITO-security defined by van der Meyden. It is shown that all these definitions support the soundness of architectural refinement, for both a state- and an action-observed model of systems. A notion of systems refinement in which the information content of observations is reduced is also studied. It is also shown that refinement preserves weak access control structure, an implementation mechanism that ensures TA-security.
Leptin and dementia over 32 years—The Prospective Population Study of Women
Authors: Gustafson Deborah R. , Bäckman Kristoffer , Lissner Lauren , Carlsson Lena , Waern Margda , Östling Svante , Guo Xinxin , Bengtsson Calle , Skoog Ingmar 
Published: June 2012

AbstractBackgroundWe have shown that high mid‐life central adiposity may increase the risk for dementia after 32 years. Leptin, an adipose tissue hormone, is correlated with adiposity measures and may contribute to a better etiological understanding of the relationship between high adiposity and dementia. We explored the relationship between serum leptin in mid‐life and dementia, which is a late‐life outcome.MethodsA longitudinal cohort study, the Prospective Population Study of Women, in Gothenburg, Sweden, includes a representative sample of 1462 women followed from mid‐life ages of 38 to 60 years to late‐life ages of 70 to 92 years. Women were examined in 1968, 1974, 1980, 1992, and 2000 using neuropsychiatric, anthropometric, clinical, and other measurements. Serum leptin was measured on samples collected at the 1968 baseline examination, after storage at −20°C for 29 years. Cox proportional hazards regression models estimated incident dementia risk by baseline leptin. Logistic regression models related leptin levels to dementia among surviving participants 32 years later. All models were adjusted for multiple potential confounders.ResultsMid‐life leptin was not related to dementia risk using Cox or logistic regression models. This was observed despite positive baseline correlations between leptin and adiposity measures, and given our previous report of high mid‐life waist‐to‐hip ratio being related to a twofold higher dementia risk.ConclusionsLeptin is not a mid‐life marker of late‐life dementia risk in this population sample of Swedish women born between 1908 and 1930.
Generic top-down discrimination for sorting and partitioning in linear time
Authors: HENGLEIN FRITZ 
Published: June 2012

AbstractWe introduce the notion ofdiscriminationas a generalization of both sorting and partitioning, and show thatdiscriminators(discrimination functions) can be definedgenerically, by structural recursion on representations oforderingandequivalence relations. Discriminators improve the asymptotic performance of generic comparison-based sorting and partitioning, and can be implemented not to expose more information than the underlying ordering, respectively equivalence relation. For a large class of order and equivalence representations, including all standard orders for regular recursive first-order types, the discriminators execute in the worst-case linear time. The generic discriminators can be coded compactly using list comprehensions, with order and equivalence representations specified using Generalized Algebraic Data Types. We give some examples of the uses of discriminators, including the most-significant digit lexicographic sorting, type isomorphism with an associative-commutative operator, and database joins. Source code of discriminators and their applications in Haskell is included. We argue that built-in primitive types, notably pointers (references), should come with efficient discriminators, not just equality tests, since they facilitate the construction of discriminators for abstract types that are both highly efficient and representation-independent.
Lake microbial communities are resilient after a whole-ecosystem disturbance
Authors: Shade Ashley , Read Jordan S , Youngblut Nicholas D , Fierer Noah , Knight Rob , Kratz Timothy K , Lottig Noah R , Roden Eric E , Stanley Emily H , Stombaugh Jesse , Whitaker Rachel J , Wu Chin H , McMahon Katherine D 
Published: June 2012

Abstract
Disturbances act as powerful structuring forces on ecosystems. To ask whether environmental microbial communities have capacity to recover after a large disturbance event, we conducted a whole-ecosystem manipulation, during which we imposed an intense disturbance on freshwater microbial communities by artificially mixing a temperate lake during peak summer thermal stratification. We employed environmental sensors and water chemistry analyses to evaluate the physical and chemical responses of the lake, and bar-coded 16S ribosomal RNA gene pyrosequencing and automated ribosomal intergenic spacer analysis (ARISA) to assess the bacterial community responses. The artificial mixing increased mean lake temperature from 14 to 20 °C for seven weeks after mixing ended, and exposed the microorganisms to very different environmental conditions, including increased hypolimnion oxygen and increased epilimnion carbon dioxide concentrations. Though overall ecosystem conditions remained altered (with hypolimnion temperatures elevated from 6 to 20 °C), bacterial communities returned to their pre-manipulation state as some environmental conditions, such as oxygen concentration, recovered. Recovery to pre-disturbance community composition and diversity was observed within 7 (epilimnion) and 11 (hypolimnion) days after mixing. Our results suggest that some microbial communities have capacity to recover after a major disturbance.
Functional responses of methanogenic archaea to syntrophic growth
Authors: Walker Christopher B , Redding-Johanson Alyssa M , Baidoo Edward E , Rajeev Lara , He Zhili , Hendrickson Erik L , Joachimiak Marcin P , Stolyar Sergey , Arkin Adam P , Leigh John A , Zhou Jizhong , Keasling Jay D , Mukhopadhyay Aindrila , Stahl David A 
Published: June 2012

Abstract
Methanococcus maripaludis grown syntrophically with Desulfovibrio vulgaris was compared with M. maripaludis monocultures grown under hydrogen limitation using transcriptional, proteomic and metabolite analyses. These measurements indicate a decrease in transcript abundance for energy-consuming biosynthetic functions in syntrophically grown M. maripaludis, with an increase in transcript abundance for genes involved in the energy-generating central pathway for methanogenesis. Compared with growth in monoculture under hydrogen limitation, the response of paralogous genes, such as those coding for hydrogenases, often diverged, with transcripts of one variant increasing in relative abundance, whereas the other was little changed or significantly decreased in abundance. A common theme was an apparent increase in transcripts for functions using H2 directly as reductant, versus those using the reduced deazaflavin (coenzyme F420). The greater importance of direct reduction by H2 was supported by improved syntrophic growth of a deletion mutant in an F420-dependent dehydrogenase of M. maripaludis. These data suggest that paralogous genes enable the methanogen to adapt to changing substrate availability, sustaining it under environmental conditions that are often near the thermodynamic threshold for growth. Additionally, the discovery of interspecies alanine transfer adds another metabolic dimension to this environmentally relevant mutualism.
Roseobacter clade bacteria are abundant in coastal sediments and encode a novel combination of sulfur oxidation genes
Authors: Lenk Sabine , Moraru Cristina , Hahnke Sarah , Arnds Julia , Richter Michael , Kube Michael , Reinhardt Richard , Brinkhoff Thorsten , Harder Jens , Amann Rudolf , Mußmann Marc 
Published: June 2012

Abstract
Roseobacter clade bacteria (RCB) are abundant in marine bacterioplankton worldwide and central to pelagic sulfur cycling. Very little is known about their abundance and function in marine sediments. We investigated the abundance, diversity and sulfur oxidation potential of RCB in surface sediments of two tidal flats. Here, RCB accounted for up to 9.6% of all cells and exceeded abundances commonly known for pelagic RCB by 1000-fold as revealed by fluorescence in situ hybridization (FISH). Phylogenetic analysis of 16S rRNA and sulfate thiohydrolase (SoxB) genes indicated diverse, possibly sulfur-oxidizing RCB related to sequences known from bacterioplankton and marine biofilms. To investigate the sulfur oxidation potential of RCB in sediments in more detail, we analyzed a metagenomic fragment from a RCB. This fragment encoded the reverse dissimilatory sulfite reductase (rDSR) pathway, which was not yet found in RCB, a novel type of sulfite dehydrogenase (SoeABC) and the Sox multi-enzyme complex including the SoxCD subunits. This was unexpected as soxCD and dsr genes were presumed to be mutually exclusive in sulfur-oxidizing prokaryotes. This unique gene arrangement would allow a metabolic flexibility beyond known sulfur-oxidizing pathways. We confirmed the presence of dsrA by geneFISH in closely related RCB from an enrichment culture. Our results show that RCB are an integral part of the microbial community in marine sediments, where they possibly oxidize inorganic and organic sulfur compounds in oxic and suboxic sediment layers.
Effective equidistribution of the real part of orbits on hyperbolic surfaces
Authors: Truelsen Jimi 
Published: June 2012

For non-cocompact Fuchsian groups with finite covolume we prove that the real part of the orbit of a point in the upper half-plane is equidistributed with an effective error term. This extends previous results by A. Good, M. Risager, and Z. Rudnick. We use the equidistribution result to generalize a theorem by F. Chamizo.
Pentraxin‐3 in chronic heart failure: the CORONA and GISSI‐HF trials
Authors: Latini Roberto , Gullestad Lars , Masson Serge , Nymo Ståle Haugset , Ueland Thor , Cuccovillo Ivan , Vårdal Mari , Bottazzi Barbara , Mantovani Alberto , Lucci Donata , Masuda Nobuhito , Sudo Yukio , Wikstrand John , Tognoni Gianni , Aukrust Pål , Tavazzi Luigi ,   on behalf of the Investigators of the Controlled Rosuvastatin Multinational Trial in Heart Failure (CORONA) and GISSI‐Heart Failure (GISSI‐HF) trials
Published: June 2012

AimsPentraxin‐3 (PTX3) is a component of the humoral arm of innate immunity which can regulate inflammatory processes. Since the role of inflammation in the progression of chronic heart failure (HF) is debated, we investigated the prognostic value of PTX3 and the effect of a statin in two large populations of patients with HF.Methods and resultsPlasma levels of PTX3 were measured at randomization and after 3 months in 1457 patients enrolled in the Controlled Rosuvastatin Multinational Trial in HF (CORONA) and 1233 patients enrolled in the GISSI‐Heart Failure trial (GISSI‐HF). The relationships between baseline PTX3 levels or their changes over time and mortality were evaluated with multivariable Cox proportional hazard models including clinical factors, high sensitivity C‐reactive protein (hsCRP), and N‐terminal pro brain natriuretic peptide (NT‐proBNP). PTX3 concentration [median (Q1–Q3) = 5.34 (3.55–7.64) ng/mL, n = 2690] was higher in females, in older patients, and those with lower body mass index. Baseline elevated PTX3 was associated with a higher risk of all‐cause mortality [759 events, hazard ratio (HR) for 1 SD increase 1.20, 95% confidence interval (CI) 1.12–1.30, P < 0.0001], cardiovascular mortality (587 events, HR 1.27, 95% CI 1.17–1.38, P < 0.0001), or hospitalization for worsening HF (720 events, HR 1.21, 95% CI 1.12–1.30, P < 0.0001), and marginally improved discrimination. Three‐month changes in PTX3 were associated with fatal events after adjustment for hsCRP or NT‐proBNP. Rosuvastatin lowered hsCRP levels but significantly raised PTX3.ConclusionIn two independent clinical trials that enrolled patients with chronic HF, PTX3 was consistently associated with outcomes. The opposite effects of a statin on hsCRP and PTX3 call for further investigation.Trial registrationNCT00336336 (GISSI‐HF), NCT00206310 (CORONA).
The High-Affinity Phosphate Transporter GmPT5 Regulates Phosphate Transport to Nodules and Nodulation in Soybean
Authors: Qin Lu , Zhao Jing , Tian Jiang , Chen Liyu , Sun Zhaoan , Guo Yongxiang , Lu Xing , Gu Mian , Xu Guohua , Liao Hong 
Published: June 2012

AbstractLegume biological nitrogen (N) fixation is the most important N source in agroecosystems, but it is also a process requiring a considerable amount of phosphorus (P). Therefore, developing legume varieties with effective N2 fixation under P-limited conditions could have profound significance for improving agricultural sustainability. We show here that inoculation with effective rhizobial strains enhanced soybean (Glycine max) N2 fixation and P nutrition in the field as well as in hydroponics. Furthermore, we identified and characterized a nodule high-affinity phosphate (Pi) transporter gene, GmPT5, whose expression was elevated in response to low P. Yeast heterologous expression verified that GmPT5 was indeed a high-affinity Pi transporter. Localization of GmPT5 expression based on β-glucuronidase staining in soybean composite plants with transgenic roots and nodules showed that GmPT5 expression occurred principally in the junction area between roots and young nodules and in the nodule vascular bundles for juvenile and mature nodules, implying that GmPT5 might function in transporting Pi from the root vascular system into nodules. Overexpression or knockdown of GmPT5 in transgenic composite soybean plants altered nodulation and plant growth performance, which was partially dependent on P supply. Through both in situ and in vitro 33P uptake assays using transgenic soybean roots and nodules, we demonstrated that GmPT5 mainly functions in transporting Pi from roots to nodules, especially under P-limited conditions. We conclude that the high-affinity Pi transporter, GmPT5, controls Pi entry from roots to nodules, is critical for maintaining Pi homeostasis in nodules, and subsequently regulates soybean nodulation and growth performance.
Inducible Repression of Multiple Expansin Genes Leads to Growth Suppression during Leaf Development
Authors: Goh Hoe-Han , Sloan Jennifer , Dorca-Fornell Carmen , Fleming Andrew 
Published: June 2012

Abstract
Expansins are cell wall proteins implicated in the control of plant growth via loosening of the extracellular matrix. They are encoded by a large gene family, and data linked to loss of single gene function to support a role of expansins in leaf growth remain limited. Here, we provide a quantitative growth analysis of transgenics containing an inducible artificial microRNA construct designed to down-regulate the expression of a number of expansin genes that an expression analysis indicated are expressed during the development of Arabidopsis (Arabidopsis thaliana) leaf 6. The results support the hypothesis that expansins are required for leaf growth and show that decreased expansin gene expression leads to a more marked repression of growth during the later stage of leaf development. In addition, a histological analysis of leaves in which expansin gene expression was suppressed indicates that, despite smaller leaves, mean cell size was increased. These data provide functional evidence for a role of expansins in leaf growth, indicate the importance of tissue/organ developmental context for the outcome of altered expansin gene expression, and highlight the separation of the outcome of expansin gene expression at the cellular and organ levels.
Prosaposin, a regulator of estrogen receptor alpha, promotes breast cancer growth
Authors: Wu Yihong , Sun Linlin , Zou Weiying , Xu Jiejie , Liu Haiou , Wang Wenzhong , Yun Xiaojing , Gu Jianxin 
Published: June 2012

Prosaposin, a secreted protein, is a well‐known pleiotropic growth factor. Although a previous report has indicated that prosaposin is overexpressed in breast cancer cell lines, the role of prosaposin in the development of breast cancer remains to be identified. Here, we first revealed that prosaposin upregulated estrogen receptor alpha expression, nuclear translocation and transcriptional activity by western blot, immunofluorescence assay and dual luciferase reporter gene assay, respectively. Furthermore, we demonstrated prosaposin upregulated estrogen receptor alpha expression through MAPK‐signaling pathway using MAPK inhibitor. Proliferation assay and tumor xenograft experiments in nude mice (n = 6 per group) further confirmed prosaposin could promote breast cancer growth significantly in vitro and in vivo. These findings suggested that prosaposin might enhance estrogen receptor alpha‐mediated signaling axis and play a role in breast cancer development and progression.
Temporal and spatial Bean pod mottle virus‐induced gene silencing in soybean
Authors: Juvale Parijat S. , Hewezi Tarek , Zhang Chunquan , Kandoth Pramod Kaitheri , Mitchum Melissa G. , Hill John H. , Whitham Steven A. , Baum Thomas J. 
Published: June 2012

SummaryVirus‐induced gene silencing (VIGS) is a powerful reverse genetics tool in plant science. In this study, we investigated the temporal and spatial silencing patterns achieved by Bean pod mottle virus (BPMV)‐based VIGS in soybean using virus constructs targeting green fluorescence protein (GFP). Silencing GFP enabled an in‐depth analysis of silencing in soybean tissues over time in a transgenic line constitutively expressing GFP. We discovered evidence for variable GFP silencing based on insert orientation and targeted region in the coding sequence. A 3′ sequence in reverse orientation produced the strongest silencing phenotypes. Furthermore, we documented that BPMV VIGS can achieve widespread silencing in a broad range of tissues, including leaves, stems, flowers and roots. Near‐complete silencing was attained in leaves and flowers. Although weaker than in shoots, the observed gene silencing in soybean roots will also allow reverse genetics studies in this tissue. When GFP fluorescence was assayed in cross‐sections of stems and leaf petioles, near‐complete and uniform silencing was observed in all cell types. Silencing was observed from as early as 2 weeks post‐virus inoculation in leaves to 7 weeks post‐virus inoculation in flowers, suggesting that this system can induce and maintain silencing for significant durations.