Novel prognostic factors in chronic kidney disease

Chronic kidney disease (CKD) is a prevalent condition and is associated with an increased risk of serious adverse outcomes, including kidney failure and death. The identification of prognostic factors that improve our ability to predict an individual’s risk of these adverse outcomes and identify potential targets for new treatments could bring significant benefits to the care of patients with CKD. In this work, data and samples from prospective cohort studies of participants with CKD were used to examine four potential prognostic factors: serum free light chains (FLC), urine FLC, monoclonal gammopathy, and serum endotrophin. Serum FLC and endotrophin concentrations were both associated with the risk of death in patients with CKD after adjustment for established prognostic factors, and serum FLC concentration was also independently associated with the risk of kidney failure. Urine FLC and monoclonal gammopathy were not associated with the risk of adverse outcomes. Possible explanations for the identified associations are discussed, as are suggestions for the next steps needed to assess the potential use of these prognostic factors in clinical practice with a view to improving the care of patients with CKD

Chromosomal duplications and cointegrates generated by the bacteriophage lamdba Red system in Escherichia coli K-12

BACKGROUND: An Escherichia coli strain in which RecBCD has been genetically replaced by the bacteriophage λ Red system engages in efficient recombination between its chromosome and linear double-stranded DNA species sharing sequences with the chromosome. Previous studies of this experimental system have focused on a gene replacement-type event, in which a 3.5 kbp dsDNA consisting of the cat gene and flanking lac operon sequences recombines with the E. coli chromosome to generate a chloramphenicol-resistant Lac- recombinant. The dsDNA was delivered into the cell as part of the chromosome of a non-replicating λ vector, from which it was released by the action of a restriction endonuclease in the infected cell. This study characterizes the genetic requirements and outcomes of a variety of additional Red-promoted homologous recombination events producing Lac+ recombinants. RESULTS: A number of observations concerning recombination events between the chromosome and linear DNAs were made: (1) Formation of Lac+ and Lac- recombinants depended upon the same recombination functions. (2) High multiplicity and high chromosome copy number favored Lac+ recombinant formation. (3) The Lac+ recombinants were unstable, segregating Lac- progeny. (4) A tetracycline-resistance marker in a site of the phage chromosome distant from cat was not frequently co-inherited with cat. (5) Recombination between phage sequences in the linear DNA and cryptic prophages in the chromosome was responsible for most of the observed Lac+ recombinants. In addition, observations were made concerning recombination events between the chromosome and circular DNAs: (6) Formation of recombinants depended upon both RecA and, to a lesser extent, Red. (7) The linked tetracycline-resistance marker was frequently co-inherited in this case. CONCLUSIONS: The Lac+ recombinants arise from events in which homologous recombination between the incoming linear DNA and both lac and cryptic prophage sequences in the chromosome generates a partial duplication of the bacterial chromosome. When the incoming DNA species is circular rather than linear, cointegrates are the most frequent type of recombinant

A Study of Learner Attitudes and Perspectives in Japanese Communicative Language Teaching EFL Contexts

アジア諸国(台湾,タイ,韓国,日本),そして最近では中国の英語教育の現況として,コミュニカティブ・アプローチ(コミュニケーション能力上達に重点をおく教授法)の採用に,より一層,取り組む傾向が挙げられる。そしてその傾向は,各国それぞれの省庁により推進されている英語教育カリキュラムの変更により確認出来る。これらの教育改革の影響は,最終的に学習環境それ自体を分析することにより,その正当性を判断しなければならない。何故なら,EFL(外国語としての英語)教育に於いて,CLT(コミュニケーションに関する言語教授法)の導入に際し,様々な障壁を示す数多くの研究結果が存在するからである。CLTの導入に関して,教師の認識を評価する研究は幾つもあるが,実際の授業内容に対する生徒の考え方や認識まで考慮したものは,残念ながら限られている。従って,この研究では,EFLを学習する日本人学生の授業内容に対する考え方や認識を,主として\u27meaning-based\u27(CLT,コミュニケーションに関する言語教授法)と\u27form-focused\u27(文法訳読式教授法)に分類して調査して行くこととする。この論文は,生徒が必要,又は要求しているものと,今まで体験して来た授業内容との問の不整合を浮き彫りにしている。しかし,生徒がCLTに対し,切望しているとは言えないまでも,純粋に興味を示していることも明らかになる。よって,CLTは,その内容が正確に解釈され適切に統合されれば,現在のアジア文化圏にとって他の文化圏同様に,近年導入されている英語教育カリキュラムの変更を単に後押しするだけのものに止まらず,最適で有効なものだと言えるであろう。これらを視野に入れ,改革の局面にあるアジア諸国のEFL教育は,(学習環境において成功をもたらすよう)授業での教授法と生徒の考え方との間の建設的な橋渡しに向けで慎重に邁進していく必要がある。There is a challenged movement toward the adoption of a more communicative approach to English language learning in Asian contexts, in particular, Taiwan, Thailand, Korea, Japan, and more recently-China. Such is evidenced with the curricular changes undertaken by the respective ministries within the region. The impaction of these policy reforms must eventually be validated through analysis in the learning environment itself, as there is in existence considerable research findings demonstrative of the various barriers related to the implementation of communicative language teaching (CLT) in EFL contexts. Although there are a number of studies that assess teachers\u27 perceptions in adopting communicative language teaching practices, only a limited number have taken account of learner attitudes and perceptions with regard to classroom practice. This paper investigates Japanese EFL learners\u27 attitudes and perceptions with respect to classroom practices identified as primarily meaning-based and form-focused. my research reveals a mismatch between learner preferences, as well as their reported experience of classroom instruction. There is clear evidence of a genuine interest in, if not desire for, communicative language teaching, which should not only proffer support for the curricular changes recently implemented, but also to the idea that CLT, if correctly interpreted and adequately integrated, is no less appropriate for modernizing Asian cultures than it is in the context of so many others. With a view to such, Asian EFL contexts-in-reform need to work toward a constructive bridging of classroom practice with the attitudes of young learners-that is, if the stakeholders are to realize successful change in the learners\u27 environment

Paradigm Lost? A Belated Response to Jarvis and Atselarat from Japan

今回の発表は,2部編制の研究論文の前半(第1部)である。第1部,第2部共に,アジア諸国に顕在するEFL(外国語としての英語教育)を担う講師陣の先入観や,重要事項が周知されていない状況下での認識,見解を検証し,課題として調査をしている。今回の研究は,多分にアジアにおけるCLT(コミュニケーションに関する言語教育)方法論の適合性にAsian EFL Journalで異議を唱えたJARVIS, ATSILARAT両氏による最新の論文に起因していると思われる。我々がこれから実証して行くのは,既存のパラダイムや理論,理論体系,又それらに付随する方法論等を否認するものではあるが,単に否認することに止まらず,準備不足の手段で見出された曖昧な所見に基づくそれらを完全に退ける全く別のものである。論文の第1部は,広義でヒューリスティック・パラダイム(発見的探索法)に含まれる一連の理論と関連原則,論考等,我々の拠り所は,正確に解釈され的確に統合されれば,他地域同様に,現代のアジア諸国の文化的環境下でも,やはりCLT(コミュニケーションに関する言語教育)が適切なものであると信憑性を与え得る数々の文献の詳細総括となっている。次回のジャーナルで発表予定の論文後半(第2部)では,JARVIS, ATSILARAT氏の研究(タイ・2004),SAVIGNON, WANG氏の研究(台湾・2003)と,我々が日本で行った調査研究詳細の比較分析をし,その特徴の総覧と共に結論を導き出す。結果,それがアジア諸国でEFL(外国語としての英語教育)に携わる各位の心を和ませ,奮起させるものとはならなくとも,教育的状況の適度な調整で,CLT(コミュニケーションに関する言語教育)方法論の採用が,より容易なものとなるという見識を助長するものとはなるはずである。This submission is the first of two papers, both of which examine and challenge the preconceived and often ill-informed notions held by instructors of English as a Foreign Language (EFL) in many Asian settings. It was Jarvis and Atsilarat\u27s recent publication in Asian EFL Journal, which takes issue with the suitability of Communicative Language Teaching (CLT) methodology for the Asian context that prompted us to undertake a reflective review of the literature and undertake our own research. While it is one matter to disavow any paradigm, theory or set of theories, and corresponding methodology; it is indeed quite another to outright dismiss such on the basis of some vague findings with an ill-equipped instrument. This initial paper provides a detailed review of the literature which takes stock of a range of theory and related topic discussion, situated in the broader heuristic paradigm, that lends credence to the position being that, CLT-if correctly interpreted and adequately integrated-is no less appropriate for modernizing Asian cultural settings, than it is in so many others. The second follow-on paper will provide a comparative analysis of the research from Jarvis and Atsilarat\u27s (2004) study on the Thailand context; Savignon and Wang\u27s (2003) examination of that in Taiwan; and, our own detailed survey research of the Japanese setting. The second paper will conclude with an overview of the comparative features of the said studies. Such should offer some added insight as to how, with some educational contextual adjustments, adoption of CLT methodology could prove less problematic, if not more endearing to its stakeholders in the Asian EFL context

How to model mutually exclusive events based on independent causal pathways in Bayesian network models

This is supported by ERC project ERC-2013-AdG339182-BAYES_KNOWLEDGE

Dated Plant Phylogenies Resolve Neogene Climate and Landscape Evolution in the Cape Floristic Region

In the context of molecularly-dated phylogenies, inferences informed by ancestral habitat reconstruction can yield valuable insights into the origins of biomes, palaeoenvironments and landforms. In this paper, we use dated phylogenies of 12 plant clades from the Cape Floristic Region (CFR) in southern Africa to test hypotheses of Neogene climatic and geomorphic evolution. Our combined dataset for the CFR strengthens and refines previous palaeoenvironmental reconstructions based on a sparse, mostly offshore fossil record. Our reconstructions show remarkable consistency across all 12 clades with regard to both the types of environments identified as ancestral, and the timing of shifts to alternative conditions. They reveal that Early Miocene land surfaces of the CFR were wetter than at present and were dominated by quartzitic substrata. These conditions continue to characterize the higher-elevation settings of the Cape Fold Belt, where they have fostered the persistence of ancient fynbos lineages. The Middle Miocene (13-17 Ma) saw the development of perennial to weakly-seasonal arid conditions, with the strongly seasonal rainfall regime of the west coast arising ~6.5-8 Ma. Although the Late Miocene may have seen some exposure of the underlying shale substrata, the present-day substrate diversity of the CFR lowlands was shaped by Pliocene-Pleistocene events. Particularly important was renewed erosion, following the post-African II uplift episode, and the reworking of sediments on the coastal platform as a consequence of marine transgressions and tectonic uplift. These changes facilitated adaptive radiations in some, but not all, lineages studied

Breaking beta: deconstructing the parasite transmission function

Transmission is a fundamental step in the life cycle of every parasite but it is also one of the most challenging processes to model and quantify. In most host–parasite models, the transmission process is encapsulated by a single parameterβ. Many different biological processes and interactions, acting on both hosts and infectious organisms, are subsumed in this single term. There are, however, at least two undesirable consequences of this high level of abstraction. First, nonlinearities and heterogeneities that can be critical to the dynamic behaviour of infections are poorly represented; second, estimating the transmission coefficientβfrom field data is often very difficult. In this paper, we present a conceptual model, which breaks the transmission process into its component parts. This deconstruction enables us to identify circumstances that generate nonlinearities in transmission, with potential implications for emergent transmission behaviour at individual and population scales. Such behaviour cannot be explained by the traditional linear transmission frameworks. The deconstruction also provides a clearer link to the empirical estimation of key components of transmission and enables the construction of flexible models that produce a unified understanding of the spread of both micro- and macro-parasite infectious disease agents