Mitochondrial NO and reactive nitrogen species production: Does mtNOS exist?

It is more than 10 years now that mitochondria are suspected to be sources of nitric oxide (NO). This hypothesis is intriguing since NO has multiple targets within the organelle and it is even suggested that mitochondria are the primary targets of NO in the cell. Most remarkably, nanomolar concentrations of NO can inhibit mitochondrial respiration, so even a small amount of NO in the mitochondrial matrix may regulate ATP synthesis. Therefore, the idea that mitochondria themselves are capable of NO production is an important concept in several physiological and pathological mechanisms. However, this field of research generates surprisingly few original papers and the published studies contain conflicting results. The reliability of the results is frequently questioned since they are seldom reproduced by independent investigators. Until 2003, all papers published in this field showed affirmative results but since then several studies directly challenged the existence of a mitochondrial nitric oxide synthase. The present review aims to summarize the most recent developments in mitochondrial NO production, highlights a few unsolved questions, and proposes new directions for future work in this research area.     

Will technology trample peer review in ecology? Ongoing issues and potential solutions

The classical view of peer review is that it is our primary process for assessing and judging whether research results should be published in a scholarly journal. However, the increased pressure to publish and technological developments are transforming peer review such that it is becoming a system that judges where work is published rather than whether the research is publishable (a ‘where rather than if’ process). Ecology is a field in which publication numbers puts a particular pressure on the review system. In this forum piece, I summarize the issues with the current publication system and discuss how technology is changing it, while suggesting solutions for important prior and ongoing issues with the peer review system. The view explored here is that technological developments (e.g. ease of creating journals, internet sites, storage, data generation, sharing of data and analytical code) will not eliminate peer review per se but will allow for a new set of parameters in which ethics and the optimal use of public funding will play a vital role in the evolution of the review process. Synthesis The number of papers and journals in Ecology has increased dramatically in the past decade. I present a critical overview of our review system and proposes that pressure to publish and technological developments have transformed peer review into a system that decides “where rather than if” papers are publishable. While reviewing the current pressures and factors playing a vital role in the evolution of the review and publication systems, I propose potential solutions to deal with current and future challenges to the peer review and publication systems.     

An introduction to metabolic networks and their structural analysis

There has been a renewed interest for metabolism in the computational biology community, leading to an avalanche of papers coming from methodological network analysis as well as experimental and theoretical biology. This paper is meant to serve as an initial guide for both the biologists interested in formal approaches and the mathematicians or computer scientists wishing to inject more realism into their models. The paper is focused on the structural aspects of metabolism only. The literature is vast enough already, and the thread through it difficult to follow even for the more experienced worker in the field. We explain methods for acquiring data and reconstructing metabolic networks, and review the various models that have been used for their structural analysis. Several concepts such as modularity are introduced, as are the controversies that have beset the field these past few years, for instance, on whether metabolic networks are small-world or scale-free, and on which model better explains the evolution of metabolism. Clarifying the work that has been done also helps in identifying open questions and in proposing relevant future directions in the field, which we do along the paper and in the conclusion.     

Issues in clinical ethics consultation: an introduction

Any area that surges ahead as rapidly as this one [clinical ethics] has over the last five years is virtually certain to find that there are many problems which will need to be addressed. There will also be a need for persons working in this field (or studying it) to take some time to reflect on where it is going, as well as to examine some of the possible pitfalls -- both the obvious and the not so obvious -- which lie ahead. The series of papers in this issue of Theoretical Medicine have been written by a group of ethicists who have had a longstanding interest in the field of clinical ethics, and most of whom have spent many years working in the area. While all of the papers focus on the field of clinical ethics, they are very diverse in the topics covered. Some may be viewed as controversial by readers....     

Role of carbon nanotubes (CNTs) in transgenic plant development

Carbon nanotubes (CNTs) are nanostructures, allotropes of carbon which are made up of graphene sheets wrapped around it forming cylindrical structures. CNTs have been regarded to have interesting and attractive physical and chemical properties and have been tremendously used in genetic engineering. Understanding the role of CNTs in development of transgenic plants, review of research papers in the field was done. CNTs are classified into two categories: the single-walled and multiwalled (MWCNTs) structures. They are valuable vectors in various biomedicine fields such as Gene delivery, Drug delivery, Immunotherapy, Tissue engineering, and Biomedical imaging and also, they deliver the DNA without damaging the cells. Based on recent studies, the functionalization of CNTs when combined with some other suitable molecules can drastically subside their toxic effects. Having unique properties such as small size, larger surface area is useful in delivering DNA into mammalian cells as well. Modifications in CNTs can make nucleic acids adhere to them even more efficiently. Also, MWCNTs are crucial in delivery DNA into the cytoplasm. Based on other methods, the CNTs-DNA are a preferred choice and the inclination toward double-stranded DNA is used over single-stranded DNA in gene delivery shows effective results. The only downside of CNTs is that they are hydrophobic and are difficult to form an aqueous solution, thus limiting their applicability. This review will aid you in comprehending useful knowledge related to a general overview of topics related to CNTs.     

Realist synthesis: illustrating the method for implementation research

ABSTRACT: BACKGROUND: Realist synthesis is an increasingly popular approach to the review and synthesis of evidence, which focuses on understanding the mechanisms by which an intervention works (or not). There are few published examples of realist synthesis. This paper therefore fills a gap by describing, in detail, the process used for a realist review and synthesis to answer the question 'what interventions and strategies are effective in enabling evidence-informed healthcare?' The strengths and challenges of conducting realist review are also considered. METHODS: The realist approach involves identifying underlying causal mechanisms and exploring how they work under what conditions. The stages of this review included: defining the scope of the review (concept mining and framework formulation); searching for and scrutinising the evidence; extracting and synthesising the evidence; and developing the narrative, including hypotheses. RESULTS: Based on key terms and concepts related to various interventions to promote evidenceinformed healthcare, we developed an outcome-focused theoretical framework. Questions were tailored for each of four theory/intervention areas within the theoretical framework and were used to guide development of a review and data extraction process. The search for literature within our first theory area, change agency, was executed and the screening procedure resulted in inclusion of 52 papers. Using the questions relevant to this theory area, data were extracted by one reviewer and validated by a second reviewer. Synthesis involved organisation of extracted data into evidence tables, theming and formulation of chains of inference, linking between the chains of inference, and hypothesis formulation. The narrative was developed around the hypotheses generated within the change agency theory area. CONCLUSIONS: Realist synthesis lends itself to the review of complex interventions because it accounts for context as well as outcomes in the process of systematically and transparently synthesising relevant literature. While realist synthesis demands flexible thinking and the ability to deal with complexity, the rewards include the potential for more pragmatic conclusions than alternative approaches to systematic reviewing. A separate publication will report the findings of the review.     

Post-translational carboxylation of preprothrombin

Summary In summary, in this review on the function of vitamin K in post-translational modification of precursor proteins by carboxylation of certain glutamyl residues, I have tried to cover in particular the recent work on the reaction, the enzymes involved and the mechanisms being considered.In doing this I have also considered vitamin K, its discovery, its functional form and the possible relation of its metabolism to the carboxylation reaction. Equally the various vitamin K-dependent gla-containing proteins currently known have been described. The carboxylation of synthetic small molecule exogenous substrates and the synthesis and metabolism of the products of carboxylation are of great help in studying the reaction.Structural specificity of vitamin K analogs in vivo and in vitro has been compared and the use of various antagonists in vivo and in vitro considered in attempts to gain an understanding of the overall reaction.The reactions subsequent to carboxylation, e.g., the activation of prothrombin to thrombin via serine proteases and the related activation of the other vitamin K-dependent proteins have not been considered in this review. The review has not covered prothrombin or other vitamin K-dependent protein isolation, nor the determination of these proteins.As the vitamin K-dependent protein carboxylation story has developed over the past six years, a number of reviews have been written which help in keeping up with the various aspects of the field as it has expanded. These reviews refer to many of the papers I have had to eliminate due to space limitations. They are referenced as 469–489.The review is in no sense comprehensive and many papers have been missed or only mentioned. I have tried to concentrate on the more recent work and, thus, much of the very fine work of the 1940's on vitamin K chemistry is hardly mentioned.Some redundancy has been built into the organization of the review so that a reader can obtain a reasonable view of any one section without having to search the whole review for all possible relevant information on any particular part of the field.     

Invited review: Big Data in precision dairy farming

Insight into current scientific applications of Big Data in the precision dairy farming area may help us to understand the inflated expectations around Big Data. The objective of this invited review paper is to give that scientific background and determine whether Big Data has overcome the peak of inflated expectations. A conceptual model was created, and a literature search in Scopus resulted in 1442 scientific peer reviewed papers. After thorough screening on relevance and classification by the authors, 142 papers remained for further analysis. The area of precision dairy farming (with classes in the primary chain (dairy farm, feed, breed, health, food, retail, consumer) and levels for object of interest (animal, farm, network)), the Big Data-V area (with categories on Volume, Velocity, Variety and other V’s) and the data analytics area (with categories in analysis methods (supervised learning, unsupervised learning, semi-supervised classification, reinforcement learning) and data characteristics (time-series, streaming, sequence, graph, spatial, multimedia)) were analysed. The animal sublevel, with 83% of the papers, exceeds the farm sublevel and network sublevel. Within the animal sublevel, topics within the dairy farm level prevailed with 58% over the health level (33%). Within the Big Data category, the Volume category was most favoured with 59% of the papers, followed by 37% of papers that included the Variety category. None of the papers included the Velocity category. Supervised learning, representing 87% of the papers, exceeds unsupervised learning (12%). Within supervised learning, 64% of the papers dealt with classification issues and exceeds the regression methods (36%). Time-series were used in 61% of the papers and were mostly dealing with animal-based farm data. Multimedia data appeared in a greater number of recent papers. Based on these results, it can be concluded that Big Data is a relevant topic of research within the precision dairy farming area, but that the full potential of Big Data in this precision dairy farming area is not utilised yet. However, the present authors expect the full potential of Big Data, within the precision dairy farming area, will be reached when multiple Big Data characteristics (Volume, Variety and other V’s) and sources (animal, groups, farms and chain parts) are used simultaneously, adding value to operational and strategic decision.     

基于文献计量的中国自然保护地监测研究

建立自然保护地是迄今为止世界上公认的最有效的保护自然生态系统、维护生物多样性的理想模式,对其进行监测是保护管理工作的重要一环。为了把握我国自然保护地的监测研究现状与发展趋势,基于CNKI和万方数据库检索并筛选出自然保护地监测文献698篇,基于文献计量法,对自然保护地的监测研究趋势、监测指标、监测方法和所属行政区域四个方面进行了分析。结果发现,我国自然保护地监测研究发文量在历经30多年的萌芽期与缓慢增长期后,当前正处于跳跃式增长期。其中,自然保护区的监测发文量最高,占比达67%;在监测内容方面,关注度由高到低依次为:生物多样性生态环境人类活动生态安全,其中,涉及鸟类监测的文献数量最多,占比20.75%。目前,人工实地调查方法仍然是主要的监测研究方法,但随着红外相机、卫星遥感和自动监测系统的发展,其占比已降到60%;在所属行政区域方面,各区不平衡现象十分显著,发文量在6—48篇不等。因此,今后科研监测应兼顾不同自然保护地类型,尽可能采用新的科技手段开展监测,并对两栖爬行类、鱼类、无脊椎动物以及人类活动和生态安全方面给予更高的关注度,最后本文还提出了相应的监测管理建议。     

Microwave and Optical Gas Discharges in Superstrong Pulsed Fields

A review is given of theoretical papers on gas breakdown in high-power pulsed microwave and optical fields under conditions such that the electron oscillatory energy in the wave field is much higher than the ionization energy of gas atoms. In microwave fields, which are much weaker than the atomic field, the ionization mechanism for gas atoms is governed by electron-impact avalanche ionization. In high-power optical fields that are comparable in strength to the atomic field, the gas atoms are ionized via the tunneling of the bound electrons. It is shown that, in both cases, the electrons obey similar, highly anisotropic distributions, thereby strongly affecting the stability of the discharge plasma.     

Do Scientific Advancements Lean on the Shoulders of Giants? A Bibliometric Investigation of the Ortega Hypothesis

Background

In contrast to Newton''s well-known aphorism that he had been able “to see further only by standing on the shoulders of giants,” one attributes to the Spanish philosopher Ortega y Gasset the hypothesis saying that top-level research cannot be successful without a mass of medium researchers on which the top rests comparable to an iceberg.

Methodology/Principal Findings

The Ortega hypothesis predicts that highly-cited papers and medium-cited (or lowly-cited) papers would equally refer to papers with a medium impact. The Newton hypothesis would be supported if the top-level research more frequently cites previously highly-cited work than that medium-level research cites highly-cited work. Our analysis is based on (i) all articles and proceedings papers which were published in 2003 in the life sciences, health sciences, physical sciences, and social sciences, and (ii) all articles and proceeding papers which were cited within these publications. The results show that highly-cited work in all scientific fields more frequently cites previously highly-cited papers than that medium-cited work cites highly-cited work.

Conclusions/Significance

We demonstrate that papers contributing to the scientific progress in a field lean to a larger extent on previously important contributions than papers contributing little. These findings support the Newton hypothesis and call into question the Ortega hypothesis (given our usage of citation counts as a proxy for impact).     

从文献计量角度分析中国生物多样性研究现状

以汤森路透科技集团的WEB OF KNOWLEDGE信息平台提供的Science Citation Index Expanded数据库为数据源,检索到从1997年至2009年期间国际生物多样性研究论文文献219773篇,其中11182篇来自于中国学者。利用NoteExpress软件,对这13a间生物多样性研究论文发表的国家分布、年度分布、研究机构、引用情况、期刊分布和学科分类等做的分析与比较表明:1)全球生物多样性研究的论文数量一直呈增长趋势,中国13年间每年发文量占当年全球生物多样性论文总量的百分率逐年增加;2)从论文总被引频次、篇均引用次数和h-index三项论文影响力特征参数分析,中国与国际其他国家相比有一定差距;3)从学科分类来看,与国际相比,中国在生物多样性保护领域、进化生物学和海洋与淡水生物学领域研究略显不足,昆虫学和真菌学研究领域活跃。     

Mammalian feeding and primate evolution: An overview

Most of the papers included in this volume are derived from presentations in a symposium on Mammalian Feeding at the 65th Annual Meetings of the American Association of Physical Anthropologists in North Carolina in 1996. The aims of this symposium were to gather together the preeminent researchers on mammalian mastication and document the state of research in that field. The symposium emphasized in vivo studies of mammalian feeding because of a paucity of recent reviews of this field, but included morphometric and modeling papers as well. Subsequently the papers were revised, and were submitted in spring 1998 for publication, pending the outcome of peer review. Copyright 2000 Wiley-Liss, Inc.     

Proteomics: general strategies and application to nutritionally relevant proteins

Proteomics as a subset of applied genomics technologies will be a key area of biology during the first decade or two of the new Millennium, and that it will have major impact, both directly and indirectly, on nutritional science. The aim of this review is to summarize information about general strategies of proteome and its application to important food proteins (plant, animal, and microbial). Methods are also described for protein separation, identification and determination. This article covers papers published within the last decade.     

Comparative analyses in aquatic microbial ecology: how far do they go?

Methodological developments in recent years have led to an increase in empirical databases on the abundance and functions of aquatic microbes, now allowing synthesis studies. Most of these studies have adopted a comparative approach, such that comparative analyses are now available for most aspects of aquatic microbial food webs (more than 50 papers published in the last 15 years). Some of these analyses apparently yield conflicting results, introducing confusion and unnecessary disputes in the field. We briefly review the comparative analyses so far produced and we highlight generalities, show that some of the perceived discrepancies largely derive from partial analyses of a general underlying trend and formulate predictions based on these general trends that provide new avenues for research.