bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oncogenic human papillomaviruses
Authors: McBride Alison A. 
Published: September 2017

Human papillomaviruses (HPVs) are an ancient group of viruses with small, double-stranded DNA circular genomes. They are species-specific and have a strict tropism for mucosal and cutaneous stratified squamous epithelial surfaces of the host. A subset of these viruses has been demonstrated to be the causative agent of several human cancers. Here, we review the biology, natural history, evolution and cancer association of the oncogenic HPVs.
This article is part of the themed issue ‘Human oncogenic viruses’.
Kaposi sarcoma herpesvirus pathogenesis
Authors: Mariggiò Giuseppe , Koch Sandra , Schulz Thomas F. 
Published: September 2017

Kaposi sarcoma herpesvirus (KSHV), taxonomical name human gammaherpesvirus 8, is a phylogenetically old human virus that co-evolved with human populations, but is now only common (seroprevalence greater than 10%) in sub-Saharan Africa, around the Mediterranean Sea, parts of South America and in a few ethnic communities. KSHV causes three human malignancies, Kaposi sarcoma, primary effusion lymphoma, and many cases of the plasmablastic form of multicentric Castleman's disease (MCD) as well as occasional cases of plasmablastic lymphoma arising from MCD; it has also been linked to rare cases of bone marrow failure and hepatitis. As it has colonized humans physiologically for many thousand years, cofactors are needed to allow it to unfold its pathogenic potential. In most cases, these include immune defects of genetic, iatrogenic or infectious origin, and inflammation appears to play an important role in disease development. Our much improved understanding of its life cycle and its role in pathogenesis should now allow us to develop new therapeutic strategies directed against key viral proteins or intracellular pathways that are crucial for virus replication or persistence. Likewise, its limited (for a herpesvirus) distribution and transmission should offer an opportunity for the development and use of a vaccine to prevent transmission.
This article is part of the themed issue ‘Human oncogenic viruses’.
Merkel cell polyomavirus and Merkel cell carcinoma
Authors: DeCaprio James A. 
Published: September 2017

Merkel cell polyomavirus (MCPyV) causes the highly aggressive and relatively rare skin cancer known as Merkel cell carcinoma (MCC). MCPyV also causes a lifelong yet relatively innocuous infection and is one of 14 distinct human polyomaviruses species. Although polyomaviruses typically do not cause illness in healthy individuals, several can cause catastrophic diseases in immunocompromised hosts. MCPyV is the only polyomavirus clearly associated with human cancer. How MCPyV causes MCC and what oncogenic events must transpire to enable this virus to cause MCC is the focus of this essay.
This article is part of the themed issue ‘Human oncogenic viruses’.
Making a virtue of necessity: the pleiotropic role of human endogenous retroviruses in cancer
Authors: Kassiotis George , Stoye Jonathan P. 
Published: September 2017

Like all other mammals, humans harbour an astonishing number of endogenous retroviruses (ERVs), as well as other retroelements, embedded in their genome. These remnants of ancestral germline infection with distinct exogenous retroviruses display various degrees of open reading frame integrity and replication capability. Modern day exogenous retroviruses, as well as the infectious predecessors of ERVs, are demonstrably oncogenic. Further, replication-competent ERVs continue to cause cancers in many other species of mammal. Moreover, human cancers are characterized by transcriptional activation of human endogenous retroviruses (HERVs). These observations conspire to incriminate HERVs as causative agents of human cancer. However, exhaustive investigation of cancer genomes suggests that HERVs have entirely lost the ability for re-infection and thus the potential for insertional mutagenic activity. Although there may be non-insertional mechanisms by which HERVs contribute to cancer development, recent evidence also uncovers potent anti-tumour activities exerted by HERV replication intermediates or protein products. On balance, it appears that HERVs, despite their oncogenic past, now represent potential targets for immune-mediated anti-tumour mechanisms.This article is part of the themed issue ‘Human oncogenic viruses’.
APC/CFZR-1Controls SAS-5 Levels to Regulate Centrosome Duplication inCaenorhabditis elegans
Authors: Medley Jeffrey C. , DeMeyer Lauren E. , Kabara Megan M. , Song Mi Hye 
Published: September 2017

ABSTRACTAs the primary microtubule-organizing center, centrosomes play a key role in establishing mitotic bipolar spindles that secure correct transmission of genomic content. For the fidelity of cell division, centrosome number must be strictly controlled by duplicating only once per cell cycle. Proper levels of centrosome proteins are shown to be critical for normal centrosome number and function. Overexpressing core centrosome factors leads to extra centrosomes, while depleting these factors results in centrosome duplication failure. In this regard, protein turnover by the ubiquitin-proteasome system provides a vital mechanism for the regulation of centrosome protein levels. Here, we report that FZR-1, theCaenorhabditis eleganshomolog of Cdh1/Hct1/Fzr, a co-activator of the anaphase promoting complex/cyclosome (APC/C), an E3 ubiquitin ligase, functions as a negative regulator of centrosome duplication in theCaenorhabditis elegansembryo. During mitotic cell division in the early embryo, FZR-1 is associated with centrosomes and enriched at nuclei. Loss offzr-1function restores centrosome duplication and embryonic viability to the hypomorphiczyg-1(it25)mutant, in part, through elevated levels of SAS-5 at centrosomes. Our data suggest that the APC/CFZR-1regulates SAS-5 levels by directly recognizing the conserved KEN-box motif, contributing to proper centrosome duplication. Together, our work shows that FZR-1 plays a conserved role in regulating centrosome duplication inCaenorhabditis elegans.
Trans-omic analysis reveals fed and fasting insulin signal across phosphoproteome, transcriptome, and metabolome
Authors: Kawata Kentaro , Yugi Katsuyuki , Hatano Atsushi , Fujii Masashi , Tomizawa Yoko , Kokaji Toshiya , Sano Takanori , Tanaka Kaori Y. , Uda Shinsuke , Kubota Hiroyuki , Suzuki Yutaka , Matsumoto Masaki , Nakayama Keiichi I. , Saitoh Kaori , Kato Keiko , Ueno Ayano , Ohishi Maki , Soga Tomoyoshi , Kuroda Shinya 
Published: September 2017

SUMMARYThe concentration and temporal pattern of insulin selectively regulate multiple cellular functions. To understand how insulin dynamics are interpreted by cells, we constructed a trans-omic network of insulin action in FAO hepatoma cells from three networks—a phosphorylation-dependent cellular functions regulatory network using phosphoproteomic data, a transcriptional regulatory network using phosphoproteomic and transcriptomic data, and a metabolism regulatory network using phosphoproteomic and metabolomic data. With the trans-omic regulatory network, we identified selective regulatory networks that mediate differential responses to insulin. Akt and Erk, hub molecules of insulin signaling, encode information of a wide dynamic range of dose and time of insulin. Down-regulated genes and metabolites in glycolysis had high sensitivity to insulin (fasting insulin signal); up-regulated genes and dicarboxylic acids in the TCA cycle had low sensitivity (fed insulin signal). This integrated analysis enables molecular insight into how cells interpret physiologically fed and fasting insulin signals.HighlightsWe constructed a trans-omic network of insulin action using multi-omic data.The trans-omic network integrates phosphorylation, transcription, and metabolism.We classified signaling, transcriptome, and metabolome by sensitivity to insulin.We identified fed and fasting insulin signal flow across the trans-omic network.
A Metabolic Reaction Balancing Web Service for Computational Systems Biology
Authors: Dobson Paul D. , Mendes Pedro , Kell Douglas B. , Swainston Neil 
Published: September 2017

AbstractBackgroundIn metabolic network reconstruction the stoichiometric balancing of reactions is essential to create realistic constraint-based models. At the genome scale, balancing is a repetitive task that consumes valuable curator resource that could be deployed elsewhere. Automatic reaction balancing is possible and could be useful across computational systems biology, but widespread use of the appropriate code has been limited by the diversity of non-interoperable programming languages used in the field. RESTful web services offer a language-agnostic way of binding services together.ResultsReaction balancing can be posed as a mixed integer linear programming problem to identify stoichiometric coefficients and infer commonly missing components. This functionality has been exposed as a web service that consumes a list of reactions as JSON or SBML. The reaction balancing web service has been deployed athttp://www.nactem.ac.uk/balancer. Code is available via Github. By way of demonstration the service has been applied to a Chinese hamster ovary cell metabolic reconstruction to bring a further 219 reactions into balance.ConclusionsThe majority of systems biology software cannot access existing automatic reaction balancing tools due to a lack of language-specific bindings. Web services bridge different languages by using widely-spoken web communication protocols, meaning that one binding works for almost all languages. Automatic reaction balancing can now be consumed by any systems biology software via a RESTful web service.
Americans’ cross-cultural schemata of Iranians: an online survey
Authors: Ameli Saied Reza , Shahghasemi Ehsan 
Published: September 2017

Purpose
For about four decades, Iran and the USA have continued to be two most stubborn enemies and this has drawn much research on this subject. Yet, only a very small fraction of this body of research has been allocated to studying the perceptions that the people of the two countries have of each other. Using a mixed method survey, the purpose of this paper is to explore cross-cultural schemata US American people have of Iranians.

Design/methodology/approach
By way of an e-mail survey, the authors collected 1,752 responses from American citizens across 50 American states. The open ended responses were codified and categorized. Three out of six categories were further sub-categorized.

Findings
The outcomes showed that about 40 percent of Americans had negative cross-cultural schemata of Iranians with the media being the main source of negative cross-cultural schemata. Conversely, personal contact and communication with Iranians proved to be the source of positive cross-cultural schemata toward Iranians. Other results showed that US American exceptionalism and negative attitudes toward Iranians had a direct and positive relationship with having negative cross-cultural schemata of Iranians.

Originality/value
As the authors have explained in this paper, very few scholars have taken up the issue of cross-cultural schemata Iranian and American people have of each other. By doing this and several other works, the authors have tried to create a new research interest in academic circles.
Improved TOPSIS method for power distribution network investment decision-making based on benefit evaluation indicator system
Authors: Niu Dongxiao , Song Zongyun , Wang Meng , Xiao Xinli 
Published: September 2017

Purpose
The aim of this paper is to review the current situation and existing problem, establish investment benefits evaluation indicator system and introduce synthetic approach degree containing Hamming approach degree, Euclid approach degree and gray correlation degree to improve the shortage of Euclidean distance in traditional TOPSIS method, and the evaluation result is strengthened by multiplication rule. This paper aims to solve the distribution network investment decision-making problem and construct a comprehensive distribution network investment benefit indicator system, which is more suitable for China distribution network characteristics.

Design/methodology/approach
This study develops improved TOPSIS methods for decision maker in the power distribution network market and uses an example to prove its effectiveness and superiority in practice which can realize the combination of theory and practice.

Findings
The research shows that the investment evaluation indicator system built in present paper covers more investment benefit influencing factors (such as qualified rate of trunk cross-section, pass rate of N-1 lines), and the evaluation result obtained by improved TOPSIS method is more efficient and persuasive.

Originality/value
The study can help investors evaluate distribution network project more efficient, and make contribution to the choice of distribution cases with similar investment benefits.
Habitat restoration benefits wild bees: A meta‐analysis
Authors: Tonietto Rebecca K. , Larkin Daniel J. 
Published: September 2017

Abstract

Pollinator conservation is of increasing interest in the light of managed honeybee (Apis mellifera) declines, and declines in some species of wild bees. Much work has gone into understanding the effects of habitat enhancements in agricultural systems on wild bee abundance, richness and pollination services. However, the effects of ecological restoration targeting “natural” ecological endpoints (e.g. restoring former agricultural fields to historic vegetation types or improving degraded natural lands) on wild bees have received relatively little attention, despite their potential importance for countering habitat loss.

We conducted a meta‐analysis to evaluate the effects of ecological restoration on wild bee abundance and richness, focusing on unmanaged bee communities in lands restored and managed to increase habitat availability and quality. Specifically, we assessed bee abundance and/or richness across studies comparing restored vs. unrestored treatments and studies investigating effects of specific habitat restoration techniques, such as burning, grazing, invasive plant removal and seeding.

We analysed 28 studies that met our selection criteria: these represented 11 habitat types and 7 restoration techniques. Nearly all restorations associated with these studies were performed without explicit consideration of habitat needs for bees or other pollinators. The majority of restorations targeted plant community goals, which could potentially have ancillary benefits for bees.

Restoration had overall positive effects on wild bee abundance and richness across multiple habitat types. Specific restoration actions, tested independently, also tended to have positive effects on wild bee richness and abundance.

Synthesis and applications. We found strong evidence that ecological restoration advances wild bee conservation. This is important given that habitat loss is recognized as a leading factor in pollinator decline. Pollinator responses to land management are rarely evaluated in non‐agricultural settings and so support for wild bees may be an underappreciated benefit of botanically focused management. Future restoration projects that explicitly consider the needs of wild bees could be more effective at providing nesting, foraging and other habitat resources. We encourage land managers to design and evaluate restoration projects with the habitat needs of wild bee species in mind.
Crisis and Change: The Making of a French FDA
Authors: NATHANSON CONSTANCE A. , BERGERON HENRI 
Published: September 2017

Policy Points:Introducing a recent special issue ofThe Lanceton the health system in France, Horton and Ceschia observe that “the dominance of English as the language of science and, increasingly, global health too often closes the door on the history and experiences of others.”1In that spirit, this manuscript presents a detailed case study of public health policy transformation in France in the early 1990s. It casts light on processes of policy change in a political and cultural environment very different from that of the United States, showing how the public health policy process is shaped by multiple contingencies of history, ideology, and politics.More specifically, we describe the transformation of a disease catastrophe into a political crisis and the deployment of that crisis to precipitate reform of the French public health system.ContextUntil the last decade of the 20th century, France had no equivalent to the US Food and Drug Administration. In this paper we describe and interpret the complex series of events that led to the passage by the French Parliament in December 1992 of a law incorporating such an agency, the Agence du Médicament (literally, “medicines agency”). The broad aim of this project was to learn how public health policy change comes about by detailed analysis of a specific instance. More specifically, we aimed to better understand the circumstances under which public health crisis leads to significant public health policy reform.MethodsThis paper is based on detailed analysis of primary documents (eg, archived French health ministry papers, recorded parliamentary debates, government reports, newspaper articles) and oral history interviews covering a period from 1988 to 1993. Thematic analysis of these materials was initially grounded in theories of organizational change, moving to constructs that emerged from the data themselves.FindingsPolicy entrepreneurs positioned to frame adverse events and seize opportunities are key to public health policy reform. However, whether these entrepreneurs will have the requisite institutional power is contingent both on political structure and on the power of competing institutional actors. Health crisesmaycatalyze institutional reform, but our analysis suggests that whether reform occurs, or even whether adverse episodes are labeled as crises, is highly contingent on circumstances of history, political structure, and political ideology and is extremely difficult to predict or control.ConclusionsActors positioned to shape public health policy need to have a detailed understanding of the circumstances that facilitate or impede policy reform. Health crises are now more often global than not. Comparative, theoretically grounded, cross‐national research that looks in detail at how different countries respond to similar health crises would be extremely valuable in informing both policymakers and researchers.
Changing Trends in Therapeutic Plasmapheresis: An Indian Perspective
Authors: Tiwari Aseem K , Bhardwaj Gunjan , Aggarwal Geet , Arora Dinesh , Dara Ravi C , Acharya Devi P , Gayam Sangeetha , Choudhuri Jui 
Published: September 2017

AbstractIndications for therapeutic apheresis (TA) are dynamic; they keep changing and expanding because of introduction of newer treatment modalities and accumulating evidence in the form of case‐reports, case‐series and original articles. We evaluated our therapeutic plasmapheresis (TP) data and compared this data with an earlier published Indian report for indications, frequency, response rate and adverse reactions. We conducted a retrospective analysis of all TP procedures performed from January 2014 to June 2016 in department of Transfusion Medicine at a tertiary care hospital. All TP procedures performed for various clinical disorders including neurological, hematological, renal, hepatic and rheumatologic indications were included in the study. Analysis was performed with respect to demography, procedure details and response. 187 patients (118 Males and 69 females) underwent 683 TP procedures during study period. According to 2013 ASFA guidelines, 99, 59 and 29 patients belonged to category I, II and III respectively. In comparison with the earlier report, the number of patients and procedures have increased, indications have changed, response rate is comparable, and the frequency of adverse reactions have decreased. In the last decade there has been increase in number and spectrum of indications for therapeutic apheresis and frequency of procedures. The response rate and safety of these procedures have also improved.
Phenological behaviour of Parthenium hysterophorus in response to climatic variations according to the extended BBCH scale
Authors: Kaur A. , Batish D.R. , Kaur S. , Singh H.P. , Kohli R.K. 
Published: September 2017

AbstractConsidering the importance of ecological and biological traits in imparting invasive success to the alien species, the phenological behaviour of an alien invasive weed Parthenium hysterophorus was documented according to the extended BBCH scale in four different seasons. A phenological calendar was prepared using both two‐ and three‐ digit coding system, precisely describing the developmental stages of the weed. The phenological documentation is further supplemented with the dates corresponding to a particular growth stage, pictures of the representative growth stages and meteorological data of all the four seasons. Results revealed that the phenology of the weed altered in response to the changing temperature and humidity conditions but no apparent climatic condition could inhibit its germination or flowering. However, the emergence of inflorescence was highly sensitive to the temperature/photoperiodic conditions. Variations in the phenological traits of P. hysterophorus with changing environmental conditions explain the acclimatisation potential of the weed permitting its vast spread in the non‐native regions. Since the given phenological illustrations are accurate, unambiguous and coded as per an internationally recognised scale, they could be exploited for agronomic practices, weed management programmes, and research purposes.
Ancestry Informative Marker Panel to Estimate Population Stratification Using Genome‐wide Human Array
Authors: Barbosa Fernanda B. , Cagnin Natalia F. , Simioni Milena , Farias Allysson A. , Torres Fábio R. , Molck Miriam C. , Araujo Tânia K. , Gil‐Da‐Silva‐Lopes Vera L. , Donadi Eduardo A. , Simões Aguinaldo L. 
Published: September 2017

SummaryCase‐control studies are a powerful strategy to identify candidate genes in complex diseases. In admixed populations, association studies can be affected by population stratification, leading to spurious genetic associations. Ancestry informative markers (AIMs) can be used to minimise this effect. The aim of this work was to select a set of AIMs to estimate population stratification in a Brazilian case‐control study performed using a genome‐wide array. A total of 345 single nucleotide polymorphism (SNP) AIMs, selected from the Cytoscan HD array and based on previously reported panels, was used to discriminate between European, African, and Amerindian populations. These SNP‐AIMs were used to infer ancestry in systemic lupus erythematosus (SLE) patients (n  =  23) and in healthy subjects (n  =  110). Moderate population substructure was observed between SLE and control groups (Fst  =  0.0113). Although patients and controls have shown a major European genomic contribution, significant differences in the European (P  =  6.47 × 10−5) and African (P  =  1.14 × 10−3) ancestries were detected between the two groups. We performed a two‐step validation of the 345 SNP‐AIMs panel estimating the ancestral contributions using a panel of 12 AIMs and approximately 70K SNPs from the array. Evaluation of population substructure in case‐control studies, avoiding spurious genetic associations, can be performed using our panel of 345 SNP‐AIMs.