bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pan-Genome and Comparative Genome Analyses of Propionibacterium acnes Reveal Its Genomic Diversity in the Healthy and Diseased Human Skin Microbiome
Authors: Tomida Shuta , Nguyen Lin , Chiu Bor-Han , Liu Jared , Sodergren Erica , Weinstock George M. , Li Huiying 
Published: May 2013

ABSTRACT

Propionibacterium acnes
constitutes a major part of the skin microbiome and contributes to human health. However, it has also been implicated as a pathogenic factor in several diseases, including acne, one of the most common skin diseases. Its pathogenic role, however, remains elusive. To better understand the genetic landscape and diversity of the organism and its role in human health and disease, we performed a comparative genome analysis of 82
P. acnes
strains, 69 of which were sequenced by our group. This collection covers all known
P. acnes
lineages, including types IA, IB, II, and III. Our analysis demonstrated that although the
P. acnes
pan-genome is open, it is relatively small and expands slowly. The core regions, shared by all the sequenced genomes, accounted for 88% of the average genome. Comparative genome analysis showed that within each lineage, the strains isolated from the same individuals were more closely related than the ones isolated from different individuals, suggesting that clonal expansions occurred within each individual microbiome. We also identified the genetic elements specific to each lineage. Differences in harboring these elements may explain the phenotypic and functional differences of
P. acnes
in functioning as a commensal in healthy skin and as a pathogen in diseases. Our findings of the differences among
P. acnes
strains at the genome level underscore the importance of identifying the human microbiome variations at the strain level in understanding its association with diseases and provide insight into novel and personalized therapeutic approaches for
P. acnes
-related diseases.

IMPORTANCE
Propionibacterium acnes
is a major human skin bacterium. It plays an important role in maintaining skin health. However, it has also been hypothesized to be a pathogenic factor in several diseases, including acne, a common skin disease affecting 85% of teenagers. To understand whether different strains have different virulent properties and thus play different roles in health and diseases, we compared the genomes of 82
P. acnes
strains, most of which were isolated from acne or healthy skin. We identified lineage-specific genetic elements that may explain the phenotypic and functional differences of
P. acnes
as a commensal in health and as a pathogen in diseases. By analyzing a large number of sequenced strains, we provided an improved understanding of the genetic landscape and diversity of the organism at the strain level and at the molecular level that can be further applied in the development of new and personalized therapies.
Green space is associated with walking and moderate-to-vigorous physical activity (MVPA) in middle-to-older-aged adults: findings from 203 883 Australians in the 45 and Up Study
Authors: Astell-Burt Thomas , Feng Xiaoqi , Kolt Gregory S 
Published: May 2013

BackgroundGreen space is widely hypothesised to promote physical activity. Few studies, however, examine whether this is the case for walking and moderate-to-vigorous physical activity (MVPA). We investigated to what extent neighbourhood green space was associated with weekly participation and frequency of walking and MVPA in a large cross-sectional survey of Australian adults 45 years and older.MethodsLogit and negative binomial regression were used to estimate the degree of association between walking, MVPA and neighbourhood green space in a sample of 203 883 adults from the Australian 45 and Up Study. Walking and MVPA were measured using the Active Australia Survey. Green space was measured as a percentage of the total land-use within 1 km radius of residence. We controlled for a range of individual and neighbourhood characteristics.Results86.6% of the sample walked and 85.8% participated in MVPA at least once a week. These rates fell steeply with age. Compared with residents of neighbourhoods containing 0–20% green space, those in greener areas were significantly more likely to walk and participate in MVPAs at least once a week (trend for both p<0.001). Among those participating at least once a week, residents of neighbourhoods containing 80%+ green space participated with a greater frequency of walking (incidence rate ratio (IRR) 1.09, 95% CI 1.05 to 1.13) and MVPA (IRR 1.10, 95% CI 1.05 to 1.15).ConclusionsOur findings suggest that the amount of green space available to adults in middle-to-older age within their neighbourhood environments could help to promote walking and MVPA.
Semen quality of 1559 young men from four cities in Japan: a cross-sectional population-based study
Authors: Iwamoto Teruaki , Nozawa Shiari , Mieno Makiko Naka , Yamakawa Katsunori , Baba Katsuyuki , Yoshiike Miki , Namiki Mikio , Koh Eitetsu , Kanaya Jiro , Okuyama Akihiko , Matsumiya Kiyomi , Tsujimura Akira , Kanetake Hiroshi , Eguchi Jiro , Skakkebaek Niels E , Vierula Matti , Toppari Jorma , Jørgensen Niels 
Published: May 2013

ObjectivesTo provide information of semen quality among normal young Japanese men and indicate the frequency of reduced semen quality.DesignCross-sectional, coordinated studies of Japanese young men included from university areas. The men had to be 18–24 years, and both the man and his mother had to be born in Japan. Background information was obtained from questionnaires. Standardised and quality-controlled semen analyses were performed, reproductive hormones analysed centrally and results adjusted for confounding factors.SettingFour study centres in Japan (Kawasaki, Osaka, Kanazawa and Nagasaki).Participants1559 men, median age 21.1 years, included during 1999–2003.Outcome measuresSemen volume, sperm concentration, total sperm count, sperm motility, sperm morphology and reproductive hormone levels.ResultsMedian sperm concentration was 59 (95% CI 52 to 68) million/ml, and 9% and 31.9% had less than 15 and 40 million/ml, respectively. Median percentage of morphologically normal spermatozoa was 9.6 (8.8 to 10.3)%. Small, but statistically significant, differences were detected for both semen and reproductive hormone variables between men from the four cities. Overall, the semen values were lower than those of a reference population of 792 fertile Japanese men.ConclusionsAssuming that the investigated men were representative for young Japanese men, a significant proportion of the population had suboptimal semen quality with reduced fertility potential, and as a group they had lower semen quality than fertile men. However, the definitive role—if any—of low semen quality for subfertility and low fertility rates remain to be investigated.
The complexity of conservative valued CSPs
Authors: Kolmogorov Vladimir , Živný Stanislav 
Published: May 2013

We study the complexity of valued constraint satisfaction problems (VCSPs) parametrized by aconstraint language, a fixed set of cost functions over a finite domain. An instance of the problem is specified by a sum of cost functions from the language and the goal is to minimize the sum. Under the unique games conjecture, the approximability of finite-valued VCSPs is well understood, see Raghavendra [2008]. However, there is no characterization of finite-valued VCSPs, let alone general-valued VCSPs, that can be solved exactly in polynomial time, thus giving insights from a combinatorial optimization perspective.We consider the case of languages containing all possible unary cost functions. In the case of languages consisting of only {0,∞}-valued cost functions (i.e., relations), such languages have been calledconservativeand studied by Bulatov [2003, 2011] and recently by Barto [2011]. Since we study valued languages, we call a languageconservativeif it contains all finite-valued unary cost functions. The computational complexity of conservative valued languages has been studied by Cohen et al. [2006] for languages over Boolean domains, by Deineko et al. [2008] for {0,1}-valued languages (a.k.a Max-CSP), and by Takhanov [2010a] for {0,∞}-valued languages containing all finite-valued unary cost functions (a.k.a. Min-Cost-Hom).We prove a Schaefer-like dichotomy theorem for conservative valued languages: if all cost functions in the language satisfy a certain condition (specified by a complementary combination ofSTP and MJN multimorphisms), then any instance can be solved in polynomial time (via a new algorithm developed in this article), otherwise the language is NP-hard. This is the first complete complexity classification ofgeneral-valued constraint languagesover non-Boolean domains. It is a common phenomenon that complexity classifications of problems over non-Boolean domains are significantly harder than the Boolean cases. The polynomial-time algorithm we present for the tractable cases is a generalization of the submodular minimization problem and a result of Cohen et al. [2008].Our results generalize previous results by Takhanov [2010a] and (a subset of results) by Cohen et al. [2006] and Deineko et al. [2008]. Moreover, our results do not rely on any computer-assisted search as in Deineko et al. [2008], and provide a powerful tool for proving hardness of finite-valued and general-valued languages.
A framework for partitioning and execution of data stream applications in mobile cloud computing
Authors: Yang Lei , Cao Jiannong , Yuan Yin , Li Tao , Han Andy , Chan Alvin 
Published: May 2013

The contribution of cloud computing and mobile computing technologies lead to the newly emerging mobile cloud computing paradigm. Three major approaches have been proposed for mobile cloud applications: 1) extending the access to cloud services to mobile devices; 2) enabling mobile devices to work collaboratively as cloud resource providers; 3) augmenting the execution of mobile applications on portable devices using cloud resources. In this paper, we focus on the third approach in supporting mobile data stream applications. More specifically, we study how to optimize the computation partitioning of a data stream application between mobile and cloud to achieve maximum speed/throughput in processing the streaming data.
To the best of our knowledge, it is the first work to study the partitioning problem for mobile data stream applications, where the optimization is placed on achieving high throughput of processing the streaming data rather than minimizing the makespan of executions as in other applications. We first propose a framework to provide runtime support for the dynamic computation partitioning and execution of the application. Different from existing works, the framework not only allows the dynamic partitioning for a single user but also supports the sharing of computation instances among multiple users in the cloud to achieve efficient utilization of the underlying cloud resources. Meanwhile, the framework has better scalability because it is designed on the elastic cloud fabrics. Based on the framework, we design a genetic algorithm for optimal computation partition. Both numerical evaluation and real world experiment have been performed, and the results show that the partitioned application can achieve at least two times better performance in terms of throughput than the application without partitioning.
An architecture for ethical and privacy-sensitive social network experiments
Authors: Hutton Luke , Henderson Tristan 
Published: May 2013

Social Network Sites (SNSs) are used for sharing personal data and delivering personalised services to hundreds of millions of users, and thus represent an important sector of the Digital Economy. Measuring and collecting data from SNSs is crucial for research and development of new services, but the sensitive and personal nature of these data means that great care must be taken by researchers when conducting SNS studies.
This paper presents a work-in-progress architecture for conducting experiments across multiple SNSs while acknowledging and preserving participant privacy. We evaluate the architecture by conducting an experiment using live SNS data, exploring willingness to share sensitive data with researchers. We also outline some outstanding challenges as we finalise the implementation of the architecture.
A forensic case study on as hijacking
Authors: Schlamp Johann , Carle Georg , Biersack Ernst W. 
Published: May 2013

The Border Gateway Protocol (BGP) was designed without security in mind. Until today, this fact makes the Internet vulnerable to hijacking attacks that intercept or blackhole Internet traffic. So far, significant effort has been put into the detection of IP prefix hijacking, while AS hijacking has received little attention. AS hijacking is more sophisticated than IP prefix hijacking, and is aimed at a long-term benefit such as over a duration of months.
In this paper, we study a malicious case of AS hijacking, carried out in order to send spam from the victim's network. We thoroughly investigate this AS hijacking incident using live data from both the control and the data plane. Our analysis yields insights into how an attacker proceeded in order to covertly hijack a whole autonomous system, how he misled an upstream provider, and how he used an unallocated address space. We further show that state of the art techniques to prevent hijacking are not fully capable of dealing with this kind of attack. We also derive guidelines on how to conduct future forensic studies of AS hijacking. Our findings show that there is a need for preventive measures that would allow to anticipate AS hijacking and we outline the design of an early warning system.
Latest trends in telecommunication standards
Authors: Costa-Pérez Xavier , Festag Andreas , Kolbe Hans-Joerg , Quittek Juergen , Schmid Stefan , Stiemerling Martin , Swetina Joerg , van der Veen Hans 
Published: May 2013

Standardization organizations play a major role in the telecommunications industry to guarantee interoperability between vendors and allow for a common ground where all players can voice their opinion regarding the direction the industry should follow. In this paper we review the current activities in some of the most relevant standardization bodies in the area of communication networks: 3GPP, IEEE 802.11, BBF, IETF, ONF, ETSI ISG NFV, oneM2M and ETSI TC ITS. Major innovations being developed in these bodies are summarized describing the most disruptive directions taken and expected to have a remarkable impact in future networks.
Finally, some trends common among different bodies are identified covering different dimensions: i) core technology enhancements, ii) inter-organizations cooperation for convergence, iii) consideration of raising disruptive technical concepts, and iv) expanding into emerging use cases aiming at an increase of future market size.
Myeloid Cell Receptor LRP1/CD91 Regulates Monocyte Recruitment and Angiogenesis in Tumors
Authors: Staudt Nicole D. , Jo Minji , Hu Jingjing , Bristow Jeanne M. , Pizzo Donald P. , Gaultier Alban , VandenBerg Scott R. , Gonias Steven L. 
Published: May 2013

Abstract
Recruitment of monocytes into sites of inflammation is essential in the immune response. In cancer, recruited monocytes promote invasion, metastasis, and possibly angiogenesis. LDL receptor-related protein (LRP1) is an endocytic and cell-signaling receptor that regulates cell migration. In this study, we isografted PanO2 pancreatic carcinoma cells into mice in which LRP1 was deleted in myeloid lineage cells. Recruitment of monocytes into orthotopic and subcutaneous tumors was significantly increased in these mice, compared with control mice. LRP1-deficient bone marrow–derived macrophages (BMDM) expressed higher levels of multiple chemokines, including, most prominently, macrophage inflammatory protein-1α/CCL3, which is known to amplify inflammation. Increased levels of CCL3 were detected in LRP1-deficient tumor-associated macrophages (TAM), isolated from PanO2 tumors, and in RAW 264.7 macrophage-like cells in which LRP1 was silenced. LRP1-deficient BMDMs migrated more rapidly than LRP1-expressing cells in vitro. The difference in migration was reversed by CCL3-neutralizing antibody, by CCR5-neutralizing antibody, and by inhibiting NF-κB with JSH-23. Inhibiting NF-κB reversed the increase in CCL3 expression associated with LRP1 gene silencing in RAW 264.7 cells. Tumors formed in mice with LRP1-deficient myeloid cells showed increased angiogenesis. Although VEGF mRNA expression was not increased in LRP1-deficient TAMs, at the single-cell level, the increase in TAM density in tumors with LRP1-deficient myeloid cells may have allowed these TAMs to contribute an increased amount of VEGF to the tumor microenvironment. Our results show that macrophage density in tumors is correlated with cancer angiogenesis in a novel model system. Myeloid cell LRP1 may be an important regulator of cancer progression. Cancer Res; 73(13); 3902–12. ©2013 AACR.
Disrupting Protein NEDDylation with MLN4924 Is a Novel Strategy to Target Cisplatin Resistance in Ovarian Cancer
Authors: Nawrocki Steffan T. , Kelly Kevin R. , Smith Peter G. , Espitia Claudia M. , Possemato Anthony , Beausoleil Sean A. , Milhollen Michael , Blakemore Stephen , Thomas Michael , Berger Allison , Carew Jennifer S. 
Published: May 2013

Abstract
Purpose: Ovarian cancer has the highest mortality rate of all female reproductive malignancies. Drug resistance is a major cause of treatment failure and novel therapeutic strategies are urgently needed. MLN4924 is a NEDDylation inhibitor currently under investigation in multiple phase I studies. We investigated its anticancer activity in cisplatin-sensitive and -resistant ovarian cancer models.
Experimental Design: Cellular sensitivity to MLN4924/cisplatin was determined by measuring viability, clonogenic survival, and apoptosis. The effects of drug treatment on global protein expression, DNA damage, and reactive oxygen species generation were determined. RNA interference established natural born killer/bcl-2–interacting killer (NBK/BIK) as a regulator of therapeutic sensitivity. The in vivo effects of MLN4924/cisplatin on tumor burden and key pharmacodynamics were assessed in cisplatin-sensitive and -resistant xenograft models.
Results: MLN4924 possessed significant activity against both cisplatin-sensitive and -resistant ovarian cancer cells and provoked the stabilization of key NEDD8 substrates and regulators of cellular redox status. Notably, MLN4924 significantly augmented the activity of cisplatin against cisplatin-resistant cells, suggesting that aberrant NEDDylation may contribute to drug resistance. MLN4924 and cisplatin cooperated to induce DNA damage, oxidative stress, and increased expression of the BH3-only protein NBK/BIK. Targeted NBK/BIK knockdown diminished the proapoptotic effects of the MLN4924/cisplatin combination. Administration of MLN4924 to mice bearing ovarian tumor xenografts significantly increased the efficacy of cisplatin against both cisplatin-sensitive and -resistant tumors.
Conclusions: Our collective data provide a rationale for the clinical investigation of NEDD8-activating enzyme (NAE) inhibition as a novel strategy to augment cisplatin efficacy in patients with ovarian cancer and other malignancies. Clin Cancer Res; 19(13); 3577–90. ©2013 AACR.
Nonequivalent Gene Expression and Copy Number Alterations in High-Grade Serous Ovarian Cancers with BRCA1 and BRCA2 Mutations
Authors: George Joshy , Alsop Kathryn , Etemadmoghadam Dariush , Hondow Heather , Mikeska Thomas , Dobrovic Alexander , deFazio Anna ,   for the Australian Ovarian Cancer Study Group, Smyth Gordon K. , Levine Douglas A. , Mitchell Gillian , Bowtell David D. 
Published: May 2013

Abstract
Purpose: High-grade serous carcinoma (HGSC) accounts for the majority of epithelial ovarian cancer deaths. Genomic and functional data suggest that approximately half of unselected HGSC have disruption of the BRCA pathway and defects in homologous recombination repair (HRR). Pathway disruption is regarded as imparting a BRCAness phenotype. We explored the molecular changes in HGSC arising in association with specific BRCA1/BRCA2 somatic or germline mutations and in those with BRCA1 DNA promoter methylation.
Experimental Design: We describe gene expression and copy number analysis of two large cohorts of HGSC in which both germline and somatic inactivation of HRR has been measured.
Results: BRCA1 disruptions were associated with the C2 (immunoreactive) molecular subtype of HGSC, characterized by intense intratumoral T-cell infiltration. We derived and validated a predictor of BRCA1 mutation or methylation status, but could not distinguish BRCA2 from wild-type tumors. DNA copy number analysis showed that cases with BRCA1 mutation were significantly associated with amplification both at 8q24 (frequencies: BRCA1 tumors 50%, BRCA2 tumors 32%, and wild-type tumors 9%) and regions of the X-chromosome specifically dysregulated in basal-like breast cancer (BLBC; BRCA1 62%, BRCA2 34%, and wild-type 35%). Tumors associated with BRCA1/BRCA2 mutations shared a negative association with amplification at 19p13 (BRCA1 0%, BRCA2 3%, and wild-type 20%) and 19q12 (BRCA1 6%, BRCA2 3%, and wild-type 29%).
Conclusion: The molecular differences between tumors associated with BRCA1 compared with BRCA2 mutations are in accord with emerging clinical and pathologic data and support a growing appreciation of the relationship between HGSC and BLBC. Clin Cancer Res; 19(13); 3474–84. ©2013 AACR.
Effects of a question prompt sheet on active patient behaviour: A randomized controlled trial with depressed outpatients
Authors: Hamann Johannes , Maris Nikolaos , Iosifidou Paraskevi , Mendel Rosmarie , Cohen Rudolf , Wolf Petra , Kissling Werner 
Published: May 2013

Background: A deeper engagement into medical decision-making is demanded by treatment guidelines for patients with affective disorders. There is to date little evidence on what facilitates active behaviour of patients with depression. In general medicine ‘question prompt sheets’ (QPSs) have been shown to change patients’ behaviour in the consultation and improve treatment satisfaction but there is no evidence for such interventions for mental health settings. Aims: To study the effects of a QPS on active patient behaviour in the consultation. Methods: Randomized controlled trial (involving N = 100 outpatients with depression) evaluating the effects of a QPS on patients’ behaviour in the consultation. Results: The QPS showed no influence on the number of topics raised by patients ( p = .13) nor on the external rater’s perception of ‘Who made the decisions in today’s consultation?’ ( p = .50). Conclusions: A QPS did not change depressed patients’ behaviour in the consultation. More complex interventions might be needed to change depressed patients’ behaviour within an established doctor–patient dyad. Patient seminars addressing behavioural aspects have been shown to be effective in other settings and may also be feasible for outpatients with affective disorders.