bluuebunny/crossref_metadata_2025 huggingface dataset:
Systematic Identification of Functional Plant Modules through the Integration of Complementary Data Sources
Authors: Heyndrickx Ken S. , Vandepoele Klaas
Published: May 2012

A major challenge is to unravel how genes interact and are regulated to exert specific biological functions. The integration of genome-wide functional genomics data, followed by the construction of gene networks, provides a powerful approach to identify functional gene modules. Large-scale expression data, functional gene annotations, experimental protein-protein interactions, and transcription factor-target interactions were integrated to delineate modules in Arabidopsis (Arabidopsis thaliana). The different experimental input data sets showed little overlap, demonstrating the advantage of combining multiple data types to study gene function and regulation. In the set of 1,563 modules covering 13,142 genes, most modules displayed strong coexpression, but functional and cis-regulatory coherence was less prevalent. Highly connected hub genes showed a significant enrichment toward embryo lethality and evidence for cross talk between different biological processes. Comparative analysis revealed that 58% of the modules showed conserved coexpression across multiple plants. Using module-based functional predictions, 5,562 genes were annotated, and an evaluation experiment disclosed that, based on 197 recently experimentally characterized genes, 38.1% of these functions could be inferred through the module context. Examples of confirmed genes of unknown function related to cell wall biogenesis, xylem and phloem pattern formation, cell cycle, hormone stimulus, and circadian rhythm highlight the potential to identify new gene functions. The module-based predictions offer new biological hypotheses for functionally unknown genes in Arabidopsis (1,701 genes) and six other plant species (43,621 genes). Furthermore, the inferred modules provide new insights into the conservation of coexpression and coregulation as well as a starting point for comparative functional annotation.
Agrobacterium tumefaciensTumor Morphology Root Plastid Localization and Preferential Usage of Hydroxylated Prenyl Donor Is Important for Efficient Gall Formation
Authors: Ueda Nanae , Kojima Mikiko , Suzuki Katsunori , Sakakibara Hitoshi
Published: May 2012

Upon Agrobacterium tumefaciens infection of a host plant, Tumor morphology root (Tmr) a bacterial adenosine phosphate-isopentenyltransferase (IPT), creates a metabolic bypass in the plastid for direct synthesis of trans-zeatin (tZ) with 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate as the prenyl donor. To understand the biological importance of Tmr function for gall formation, we compared Tmr and Trans-zeatin secretion (Tzs) another agrobacterial IPT that functions within the bacterial cell. Although there is no significant difference in their substrate specificities in vitro, ectopic overexpression of Tzs in Arabidopsis (Arabidopsis thaliana) resulted in the accumulation of comparable amounts of tZ- and N  6-(∆2-isopentenyl)adenine (iP)-type cytokinins, whereas overexpression of Tmr resulted exclusively in the accumulation of tZ-type cytokinins. Ectopic expression of Tzs in plant cells yields only small amounts of the polypeptide in plastid-enriched fractions. Obligatory localization of Tzs into Arabidopsis plastid stroma by translational fusions with ferredoxin transit peptide (TP-Tzs) increased the accumulation of both tZ- and iP-type cytokinins. Replacement of tmr on the Ti plasmid with tzs, TP-tzs, or an Arabidopsis plastidic IPT induced the formation of smaller galls than wild-type A. tumefaciens, and they were accompanied by the accumulation of iP-type cytokinins. Tmr is thus specialized for plastid localization and preferential usage of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate in vivo and is important for efficient gall formation.
Aurora‐A activation, correlated with hypoxia‐inducible factor‐1α, promotes radiochemoresistance and predicts poor outcome for nasopharyngeal carcinoma
Authors: Wan Xiang‐Bo , Fan Xin‐Juan , Huang Pei‐Yu , Dong Dong , Zhang Yan , Chen Ming‐Yuan , Xiang Jin , Xu Jie , Liu Li , Zhou Wei‐Hua , Lv Yan‐Chun , Wu Xiang‐Yuan , Hong Ming‐Huang , Liu Quentin
Published: May 2012

Previously, we and others showed that hypoxia‐inducible factor‐1α (HIF‐1α) and transcriptionally upregulated Aurora‐A were required for disease progression in several tumors. Here, we address the clinicopathologic value of Aurora‐A and HIF‐1α in locally advanced nasopharyngeal carcinoma (NPC). Aurora‐A and HIF‐1α expression was semiquantitatively evaluated by immunohistochemistry staining in 144 cases from a randomized controlled trial. Of these patients, 69 received neoadjuvant chemotherapy plus concurrent chemoradiotherapy, and acted as the training set, and 75 cases treated with neoadjuvant chemotherapy plus radiotherapy were used as the testing set to validate the prognostic effect of Aurora‐A and HIF‐1α. We found that Aurora‐A and HIF‐1α were highly expressed in NPC, but were deficient in normal adjacent epithelia. In the testing set, Aurora‐A overexpression predicted a shortened 5‐year overall survival (59.1% vs 82.5%, P = 0.024), progression‐free survival (44.8% vs 79.8%, P = 0.004), and distant metastasis‐free survival (43.0% vs 17.3%, P = 0.016). Multivariate regression analysis confirmed that Aurora‐A was indeed an independent prognostic factor for death, recurrence, and distant metastasis both in the testing set and overall patients. Moreover, a positive correlation between Aurora‐A and HIF‐1α was detected (P = 0.037). Importantly, although HIF‐1α did not show any prognostic effect for patient outcome, the subset with Aurora‐A and HIF‐1α co‐overexpression had the poorest overall, progression‐free, and distant metastasis‐free survival (all P < 0.05). Our results confirmed that Aurora‐A was an independent prognostic factor for NPC. Aurora‐A combined with HIF‐1α refined the risk definition of the patient subset, thus potentially directing locally advanced NPC patients for more selective therapy. (Cancer Sci, doi: 10.1111/j.1349‐7006.2012.02332.x, 2012)
Phase I study of TAC‐101, an oral synthetic retinoid, in Japanese patients with advanced hepatocellular carcinoma
Authors: Okusaka Takuji , Ueno Hideki , Ikeda Masafumi , Takezako Yoriko , Morizane Chigusa
Published: May 2012

Preclinical models have shown that TAC‐101 (4‐[3,5‐bis(trimethylsilyl) benzamide] benzoic acid), an oral synthetic retinoid, has antitumor activity in hepatocellular carcinoma (HCC). We conducted a phase I study in Japanese patients with advanced HCC to examine the pharmacokinetics, recommended dose, safety, and efficacy of TAC‐101. The administered dose of TAC‐101 was 10 mg/day in four patients (level 1), 20 mg/day in six (level 2), and 30 mg/day in three (level 3). There was no dose‐limiting toxicity at level 1. Only one patient each had dose‐limiting toxicity at level 2 (grade 2 fatigue, recovery requiring eight or more consecutive days of rest) and at level 3 (grade 3 splenic vein thrombosis). Level 3 (30 mg/day) was considered the maximum tolerated dose and 20 mg/day the recommended dose by a panel of medical experts, placing maximum emphasis on safety. The most frequent adverse events were fatigue, headache, and dermal symptoms such as rash. Pharmacokinetic parameters in Japanese patients with HCC were similar to those in patients in the United States, most of whom were Caucasian. Although no patient had a complete or partial response, the disease control rate was 38.5%. In conclusion, the recommended dose of TAC‐101 for patients with HCC is 20 mg/day. TAC‐101 had an acceptable toxicity profile, warranting further evaluation in clinical trials. (Cancer Sci, doi: 10.1111/j.1349‐7006.2012.02334.x, 2012)
Timing of Xunhua and Guide basin development and growth of the northeastern Tibetan Plateau, China
Authors: Liu Shaofeng , Zhang Guowei , Pan Feng , Zhang Huiping , Wang Ping , Wang Kai , Wang Yan
Published: May 2012

The Xunhua, Guide and Tongren intermontane basin system in the NE Tibetan Plateau, situated near the Xining basin to the N and the Linxia basin to the E, is bounded by thrust fault‐controlled ranges. These include to the N, the Riyue Shan, Laji Shan and Jishi Shan ranges, and to the S the northern West Qinling Shan (NWQ). An integrated study of the structural geology, sedimentology and provenance of the Cenozoic Xunhua and Guide basins provides a detailed record of the growth of the NE Tibetan Plateau since the early Eocene. The Xining Group (ca. 52–21 Ma) is interpreted as consisting of unified foreland basin deposits which were controlled by the bounding thrust belt of the NWQ. The Xunhua, Guide and Xining subbasins were interconnected prior to later uplift and damming by the Laji Shan and Jishi Shan ranges. Their sediment source, the NWQ, is constrained by strong unidirectional paleocurrent trends towards the N, a northward fining lithology, distinct and recognizable clast types and detrital zircon ages. Collectively, formation of this mountain–basin system indicates that the Tibetan Plateau expanded into the NWQ at a time roughly coinciding with Eocene to earliest Miocene continental collision between India and Eurasia. The Guide Group (ca. 21–1.8 Ma) is inferred to have been deposited in the separate Xunhua, Guide and Tongren broken foreland basins. Each basin was filled by locally sourced alluvial fans, braided streams and deltaic‐lacustrine systems. Structural, paleogeographic, paleocurrent and provenance data indicate that thrust faulting in the NWQ stepped northward to the Laji Shan from ca. 21 to 16 Ma. This northward shift was accompanied by E–W shortening related to nearly N–S‐striking thrust faulting in Jishi Shan after 11–13 Ma. A lower Pleistocene conglomerate (1.8–1.7 Ma) was deposited by a through‐flowing river system in the overfilled and connected Guide and Xunhua basins following the termination of thrust activity. All of the basin–mountain zones developed along the Tibetan Plateau's NE margin since Indian–Tibetan continental collision may have been driven by collision‐induced basal drag of old slab remnants in the manner of N‐dipping and flat‐slab subduction, and their subsequent sinking into the deep mantle.
Novel dual inhibitors of vascular endothelial growth factor and VEGFR2 receptor
Authors: Nguyen Jennifer P. , Frost Chelsea D. , Lane Meghan L. , Skelton IV William P. , Skelton Michelle , Vesely David L.
Published: May 2012

Eur J Clin Invest 2012; 42 (10): 1061–1067

Background  Vascular endothelial growth factor (VEGF) helps control tumour growth via causing new capillaries growth in tumours. Four cardiac hormones [i.e. vessel dilator, long‐acting natriuretic peptide (LANP), kaliuretic peptide (KP) and atrial natriuretic peptide (ANP)] that eliminate up to up to 86% of human small‐cell lung cancers growing in mice were investigated for their effects on VEGF and the VEGFR2/KDR/Flk‐1 receptor. The VEGFR2 receptor is the main receptor mediating VEGF’s cancer‐enhancing effects.

Materials and Methods  Four cardiac hormones were evaluated for their ability to decrease VEGF/VEGFR2 measured by ELISAs in three human cancer cell lines.

Results  Vessel dilator, LANP, KP and ANP, over a concentration range of 100 pM to 10 μM, maximally decreased the VEGFR2 receptor in human pancreatic adenocarcinoma cells by 48%, 49%, 74% and 83%. Vessel dilator, LANP, KP and ANP decreased the VEGFR2 receptor by 77%, 89%, 88% and 67% in human small‐cell lung cancer cells and by 48%, 92%, 64% and 71% in human prostate cancer cells. These results were confirmed with the cardiac hormones also decreasing the VEGFR2 receptor measured by Western blots. VEGF itself in pancreatic carcinoma cells was decreased by 42%, 58%, 36% and 40% by vessel dilator, LANP, KP and ANP. VEGF levels were decreased 25%, 23%, 17% and 23% in small‐cell lung cancer cells and decreased by 24%, 20%, 23% and 24% in prostate cancer cells by vessel dilator, LANP, KP and ANP.

Conclusion  Four cardiac hormones are the first dual inhibitors of VEGF and the VEGFR2/KDR/Flk‐1 receptor.
Clinical information transfer and data capture in the acute myocardial infarction pathway: an observational study
Authors: Kesavan Sujatha , Kelay Tanika , Collins Ruth E. , Cox Benita , Bello Fernando , Kneebone Roger L. , Sevdalis Nick
Published: May 2012

Rationale, aims and objectives  Acute myocardial infarctions (MIs) or heart attacks are the result of a complete or an incomplete occlusion of the lumen of the coronary artery with a thrombus. Prompt diagnosis and early coronary intervention results in maximum myocardial salvage, hence time to treat is of the essence. Adequate, accurate and complete information is vital during the early stages of admission of an MI patient and can impact significantly on the quality and safety of patient care. This study aimed to record how clinical information between different clinical teams during the journey of a patient in the MI care pathway is captured and to review the flow of information within this care pathway.

Method  A prospective, descriptive, structured observational study to assess (i) current clinical information systems (CIS) utilization and (ii) real‐time information availability within an acute cardiac care setting was carried out. Completeness and availability of patient information capture across four key stages of the MI care pathway were assessed prospectively.

Results  Thirteen separate information systems were utilized during the four phases of the MI pathway. Observations revealed fragmented CIS utilization, with users accessing an average of six systems to gain a complete set of patient information. Data capture was found to vary between each pathway stage and in both patient cohort risk groupings. The highest level of information completeness (100%) was observed only in the discharge stage of the MI care pathway. The lowest level of information completeness (58%) was observed in the admission stage.

Conclusion  The study highlights fragmentation, CIS duplication, and discrepancies in the current clinical information capture and data transfer across the MI care pathway in an acute cardiac care setting. The development of an integrated and user‐friendly electronic data capture and transfer system would reduce duplication and would facilitate efficient and complete information provision at the point of care.
Study protocol for a pilot study to explore the determinants of knowledge use in a medical education context
Authors: Reeves Scott , Leslie Karen , Baker Lindsay , Egan‐Lee Eileen , Légaré France , Silver Ivan , Rosenfield Jay , Hodges Brian , Curran Vernon , Armson Heather , Kitto Simon
Published: May 2012

Rationale, aims and objectives  While the science of knowledge translation (KT) has been growing steadily for the past decade in relation to understanding processes and actions which are embedded within clinical practice settings, little is known about how empirical knowledge is used within the medical education system. Despite an increase of research in this domain, we know very little about the contribution of this evidence in the development of medical students into effective physicians. This pilot study aims to: provide a synthesis of the evidence for educational strategies within medical education; explore the perceptions and experiences of faculty in undergraduate (UG) medical education in relation to their use of evidence in their educational practices; and illuminate how medical education evidence is formally integrated into a UG medical curriculum.

Method  The study will involve three phases. First, a scoping review of the medical education research literature will be undertaken to generate insight into the evidence available for curriculum development, teaching and assessment activities within this domain. Second, a content analysis of undergraduate courses at the University of Toronto will be undertaken to generate an additional insight into the extent that medical education research has been formally integrated into the UG curriculum for medical students at the University. Finally, a purposeful sample of 30–40 medical education leaders from a single large university, selected as it aims to deliver a rigorous research‐oriented medical curriculum, will be interviewed to understand how they use the available evidence in their education practices.

Discussion  This study will lay the grounds to generate initial data into the determinants of knowledge use in a medical education context. In doing so, the findings will also inform the development of a larger, pan‐Canadian study at medical schools that will generate a comprehensive account of the processes and challenges related to KT within an educational context. This larger study will also begin to explore the relevance of the Knowledge‐to‐Action model to a medical education context.
Paediatric nutrition risk scores in clinical practice: children with inflammatory bowel disease
Authors: Wiskin A. E. , Owens D. R. , Cornelius V. R. , Wootton S. A. , Beattie R. M.
Published: May 2012

How to cite this article
 Wiskin A.E., Owens D.R., Cornelius V.R., Wootton S.A. & Beattie R.M. (2012) Paediatric nutrition risk scores in clinical practice: children with inflammatory bowel disease. J Hum Nutr Diet. 25, 319–322

Background:  There has been increasing interest in the use of nutrition risk assessment tools in paediatrics to identify those who need nutrition support. Four non‐disease specific screening tools have been developed, although there is a paucity of data on their application in clinical practice and the degree of inter‐tool agreement.

Methods:  The concurrent validity of four nutrition screening tools [Screening Tool for the Assessment of Malnutrition in Paediatrics (STAMP), Screening Tool for Risk On Nutritional status and Growth (STRONGkids), Paediatric Yorkhill Malnutrition Score (PYMS) and Simple Paediatric Nutrition Risk Score (PNRS)] was examined in 46 children with inflammatory bowel disease. Degree of malnutrition was determined by anthropometry alone using World Health Organization International Classification of Diseases (ICD‐10) criteria.

Results:  There was good agreement between STAMP, STRONGkids and PNRS (kappa > 0.6) but there was only modest agreement between PYMS and the other scores (kappa = 0.3). No children scored low risk with STAMP, STRONGkids or PNRS; however, 23 children scored low risk with PYMS. There was no agreement between the risk tools and the degree of malnutrition based on anthropometric data (kappa < 0.1). Three children had anthropometry consistent with malnutrition and these were all scored high risk. Four children had body mass index SD scores < −2, one of which was scored at low nutrition risk.

Conclusions:  The relevance of nutrition screening tools for children with chronic disease is unclear. In addition, there is the potential to under recognise nutritional impairment (and therefore nutritional risk) in children with inflammatory bowel disease.
Reconstruction of paternal genotypes over multiple breeding seasons reveals male green turtles do not breed annually
Authors: WRIGHT LUCY I. , FULLER WAYNE J. , GODLEY BRENDAN J. , McGOWAN ANDREW , TREGENZA TOM , BRODERICK ANNETTE C.
Published: May 2012

For species of conservation concern, knowledge of key life‐history and demographic components, such as the number and sex ratio of breeding adults, is essential for accurate assessments of population viability. Species with temperature‐dependent sex determination can produce heavily biased primary sex ratios, and there is concern that adult sex ratios may be similarly skewed or will become so as a result of climate warming. Prediction and mitigation of such impacts are difficult when life‐history information is lacking. In marine turtles, owing to the difficultly in observing males at sea, the breeding interval of males is unknown. It has been suggested that male breeding periodicity may be shorter than that of females, which could help to compensate for generally female‐biased sex ratios. Here we outline how the use of molecular‐based paternity analysis has allowed us, for the first time, to assess the breeding interval of male marine turtles across multiple breeding seasons. In our study rookery of green turtles (Chelonia mydas), 97% of males were assigned offspring in only one breeding season within the 3‐year study period, strongly suggesting that male breeding intervals are frequently longer than 1 year at this site. Our results also reveal a sex ratio of breeding adults of at least 1.3 males to each female. This study illustrates the utility of molecular‐based parentage inference using reconstruction of parental genotypes as a method for monitoring the number and sex ratio of breeders in species where direct observations or capture are difficult.
Voltage‐gated potassium channel (Kv1) autoantibodies in patients with chagasic gut dysmotility and distribution of Kv1 channels in human enteric neuromusculature (autoantibodies in GI dysmotility)
Authors: Hubball A. W. , Lang B. , Souza M. A. N. , Curran O. D. , Martin J. E. , Knowles C. H.
Published: May 2012

Background  Autoantibodies directed against specific neuronal antigens are found in a significant number of patients with gastrointestinal neuromuscular diseases (GINMDs) secondary to neoplasia. This study examined the presence of antineuronal antibodies in idiopathic GINMD and GINMD secondary to South American Trypanosomiasis. The GI distribution of voltage‐gated potassium channels (VGKCs) was also investigated.

Methods  Seventy‐three patients were included in the study with diagnoses of primary achalasia, enteric dysmotility, chronic intestinal pseudo‐obstruction, esophageal or colonic dysmotility secondary to Chagas’ disease. Sera were screened for specific antibodies to glutamic acid decarboxylase, voltage‐gated calcium channels (VGCCs; P/Q subtype), nicotinic acetylcholine receptors (nAChRs; α3 subtype), and voltage‐gated potassium channels (VGKCs, KV1 subtype) using validated immunoprecipitation assays. The distribution of six VGKC subunits (KV1.1–1.6), including those known to be antigenic targets of anti‐VGKC antibodies was immunohistochemically investigated in all main human GI tract regions.

Key Results  Three patients (14%) with chagasic GI dysmotility were found to have positive anti‐VGKC antibody titers. No antibodies were detected in patients with idiopathic GINMD. The VGKCs were found in enteric neurons at every level of the gut in unique yet overlapping distributions. The VGKC expression in GI smooth muscle was found to be limited to the esophagus.

Conclusions & Inferences  A small proportion of patients with GI dysfunction secondary to Chagas’ disease have antibodies against VGKCs. The presence of these channels in the human enteric nervous system may have pathological relevance to the growing number of GINMDs with which anti‐VGKC antibodies have been associated.
Rectal hypersensitivity as hallmark for irritable bowel syndrome: defining the optimal cutoff
Authors: Ludidi S. , Conchillo J. M. , Keszthelyi D. , Van Avesaat M. , Kruimel J. W. , Jonkers D. M. , Masclee A. A. M.
Published: May 2012

Background  Visceral hypersensitivity is a frequently observed hallmark of irritable bowel syndrome (IBS). Studies have reported differently about the presence of visceral hypersensitivity in IBS resulting from lack of standardization of the barostat procedure and due to different criteria used to assess hypersensitivity. We aimed to calculate the optimal cutoff to detect visceral hypersensitivity in IBS.

Methods  A total of 126 IBS patients and 30 healthy controls (HC) were included for assessment of visceroperception by barostat. Pain perception was assessed on a visual analogue scale (VAS). ROC‐curves were used to calculate optimal discriminative cutoff (pressure and VAS‐score) between IBS patients and HC to define hypersensitivity. Furthermore, pain perception to distension sequences below the pressure threshold for hypersensitivity was defined as allodynia.

Key Results  Irritable bowel syndrome patients showed increased visceroperception compared to HC. Thresholds for first sensation and first pain were lower in IBS patients VS HC (P < 0.01). ROC‐curves showed optimal discrimination between IBS patients and HC at 26 mmHg with a VAS cutoff ≥20 mm. Using this criterion, hypersensitivity percentages were 63.5% and 6.6% in IBS patients and HC, respectively. No significant differences were observed between IBS subtypes. Allodynia was found in a small number of patients (11%).

Conclusions & Inferences  Optimal cutoff for visceral hypersensitivity was found at pressure 26 mmHg with a VAS ≥20 mm, resulting in 63.5% of IBS patients being hypersensitive and 11% being allodynic. Standardization of barostat procedures and defining optimal cutoff values for hypersensitivity is warranted when employing rectal barostat measurements for research or clinical purposes.
Male quality, signal reliability and female choice: assessing the expectations of inter‐sexual selection
Authors: McLEAN M. J. , BISHOP P. J. , NAKAGAWA S.
Published: May 2012

Numerous models have attempted to explain the evolution of extravagant male ornaments found in many species. Inter‐sexual indicator models postulate that male ornaments evolved as signals of quality, and that females use these signals to select the highest quality males. These models involve three traits – male quality, male signals and female preferences – and have specific expectations about the relative strengths of the phenotypic relationships between these traits. Using data from anuran species, we assessed the relative strengths of the phenotypic relationships using meta‐analysis. The relative strengths of these phenotypic correlations were as expected by indicator models, providing support for indicator models of inter‐sexual selection. We also found much variation in our data, suggesting that additional, untested factors may mediate inter‐sexual interactions in this taxon, such as differences in the importance of quality signalling between species. These factors require investigation, in order to improve our understanding of inter‐sexual selection.
Molecular Detection and Comparative Sequence Analysis of Viruses Infecting Fig Trees in Turkey
Authors: Elçi Eminur , Serçe Ç iğdem Ulubaş , Gazel Mona , Ç ağlayan Kadriye
Published: May 2012

Several viruses infecting fig trees in Turkey have been identified recently. The samples were collected from the commonest fig cultivars showing typical mosaic symptoms and from symptomless plants from different fig growing regions of Turkey. They were tested for Fig leaf mottle‐associated virus 1‐2 (FLMaV1‐2), Fig mosaic virus (FMV), Fig latent virus‐1 (FLV‐1), Fig mild mottle‐associated virus (FMMaV), Arkansas fig closterovirus 1‐2 (AFCV1‐2), Fig badnavirus‐1 (FBV‐1) and Fig cryptic virus (FCV) by PCR and sequence analyses. One hundred fig trees were tested, and 83% of tested samples were found to be infected by at least one virus. Complex infections were detected in most of the samples, and the most common viruses were FBV‐1 and FMV with 82 and 79% infection ratios, respectively. The sequence analyses confirmed virus identity except for AFCV‐1 for which no sequence data are available in GenBank. Based on phylogenetic analysis, the sequences clustered into seven groups: FLV‐1, FMMaV, FBV‐1, FCV, FMV, AFCV‐1, FLMaV‐1, as expected, and no correlation was found between Turkish isolates depending on cultivars and provinces for these viruses.
Cigarette smoke augments the expression and responses of toll‐like receptor 3 in human macrophages
Authors: KOARAI AKIRA , YANAGISAWA SATORU , SUGIURA HISATOSHI , ICHIKAWA TOMOHIRO , AKAMATSU KEIICHIRO , HIRANO TSUNAHIKO , NAKANISHI MASANORI , MATSUNAGA KAZUTO , MINAKATA YOSHIAKI , ICHINOSE MASAKAZU
Published: May 2012

Background and objective:  Cigarette smoking is the main risk factor for the development of chronic obstructive pulmonary disease (COPD). Recently, toll‐like receptor 3 (TLR3) was shown to recognize pathogen‐associated molecular patterns, especially viral‐derived double‐stranded RNA, and to be involved in immune responses. However, the effects of cigarette smoke on TLR3 remain unclear. In this study, it was examined whether cigarette smoke affects the expression and responses of TLR3 in human macrophages.

Methods:  The expression of TLR3 in alveolar macrophages from human lung tissues was analysed by immunohistochemistry, and the correlation of TLR3 expression with smoking history and lung function was evaluated. In addition, the effect of cigarette smoke on the expression and responses of TLR3 in macrophage lineage cells was investigated.

Results:  TLR3‐positive alveolar macrophage numbers were significantly increased in smokers and COPD patients compared with non‐smoking control subjects, but there was no difference between smokers and COPD patients. TLR3‐positive macrophage numbers were positively correlated with smoking history and inversely correlated with corrected carbon monoxide diffusing capacity, but were not correlated with % predicted forced expiratory volume in 1 s. Furthermore, cigarette smoke extract potentiated the expression of TLR3 in monocyte‐derived macrophages and significantly augmented the release of interleukin‐8, as well as total matrix metalloproteinase‐9 activity, in cells treated with TLR3 ligand.

Conclusions:  These data suggest that cigarette smoke augments the expression and responses of TLR3 in human macrophages, and this may contribute to neutrophilic airway inflammation and parenchymal destruction in the lungs of smokers and patients with COPD.
A new genus of gall midge (Diptera: Cecidomyiidae) from Australian Acacia
Authors: Kolesik Peter , Adair Robin J
Published: May 2012

A new species of gall midge, Austroacacidiplosis botrycephalae Kolesik gen. et sp. n. induces conspicuous spherical, often red coloured, galls on leaves of Acacia deanei (R. T. Baker), Acacia decurrens Willd., Acacia baileyana F. Muell. and Acacia dealbata Link in south‐eastern Australia. A new genus is erected to contain the new species. Austroacacidiplosis belongs to the tribe Cecidomyiini and its closest relative is Acacidiplosis Gagné, an African genus containing species that induce galls on leaves and flower buds of acacias in Kenya.
Species distribution modelling in low‐interaction environments: Insights from a terrestrial Antarctic system
Authors: LEE JENNIFER E. , LE ROUX PETER C. , MEIKLEJOHN K. IAN , CHOWN STEVEN L.
Published: May 2012

It is widely acknowledged that in the terrestrial Antarctic, interspecific interactions are typically unimportant in determining species distributions and community structure. Therefore, correlative models should prove useful for predicting current and future spatial variation in species abundance patterns. However, this idea has not been formally tested, and the utility of such models, which have shown value for understanding the distribution of diversity elsewhere, for investigating biodiversity patterns in Antarctica remains unclear. Here we make a start at such tests by using generalized linear and simultaneous autoregressive models to demonstrate that simple environmental variables and information about the spatial structure of the environment can explain more than 90% of the variation in the abundance of Maudheimia wilsoni (Oribatida; Maudheimiidae), a representative of one of the most significant groups of Antarctic terrestrial arthropods, the mites. We show that a single environmental variable, maximum soil moisture content, can account for as much as 80% of the variance in the abundance of the mite, and that linear models with only a few environmental and spatial terms can be used to forecast the species abundance at the landscape scale. Given ongoing calls for better understanding of the distribution of Antarctic diversity and its likely future change, this initial test indicates that such modelling procedures, and more sophisticated versions thereof, hold much promise for the region and should be tested for other taxa with different life forms and habitat requirements.
Fungicide‐induced declines of freshwater biodiversity modify ecosystem functions and services
Authors: McMahon Taegan A. , Halstead Neal T. , Johnson Steven , Raffel Thomas R. , Romansic John M. , Crumrine Patrick W. , Rohr Jason R.
Published: May 2012

Although studies on biodiversity and ecosystem function are often framed within the context of anthropogenic change, a central question that remains is how important are direct vs. indirect (via changes in biodiversity) effects of anthropogenic stressors on ecosystem functions in multitrophic‐level communities. Here, we quantify the effects of the fungicide chlorothalonil on 34 species‐, 2 community‐ and 11 ecosystem‐level responses in a multitrophic‐level system. At ecologically relevant concentrations, chlorothalonil increased mortality of amphibians, gastropods, zooplankton, algae and a macrophyte (reducing taxonomic richness), reduced decomposition and water clarity and elevated dissolved oxygen and net primary productivity. These ecosystem effects were indirect and predictable based on changes in taxonomic richness. A path analysis suggests that chlorothalonil‐induced reductions in biodiversity and top‐down and bottom‐up effects facilitated algal blooms that shifted ecosystem functions. This work emphasises the need to re‐evaluate the safety of chlorothalonil and to further link anthropogenic‐induced changes in biodiversity to altered ecosystem functions.
Phylogeny and systematics of Melanesia’s most diverse gecko lineage (Cyrtodactylus, Gekkonidae, Squamata)
Authors: Oliver Paul M. , Richards Stephen J. , Sistrom Mark
Published: May 2012

Oliver, P.M., Richards, S.J. & Sistrom, M. (2012). Phylogeny and systematics of Melanesia’s most diverse gecko lineage (Cyrtodactylus, Gekkonidae, Squamata). —Zoologica Scripta, 41, 437–454.

The systematics and biogeographical history of the diverse fauna of New Guinea and surrounding islands (Melanesia) remain poorly known. We present a phylogeny for 16 of the 21 recognised Melanesian bent‐toed geckos in the genus Cyrtodactylus based on mitochondrial sequence data. These analyses reveal two divergent lineages of Cyrtodactylus within Melanesia. One includes a single recognised species with clear affinities to sampled taxa from Asia. The other comprises a relatively diverse radiation (likely 30+ species), not closely related to sampled extralimital taxa and centred on the Melanesian region (including Australia). Many taxa within this second lineage are endemic to islands surrounding New Guinea, and dispersal and speciation on peripheral islands appears to have played an important role in the accumulation of species diversity within this clade. In contrast, little diversity is centred upon montane areas, although we do identify at least one lineage closely associated with hill and lower montane forest that probably dates to at least the late Miocene. Our phylogenetic analyses also reveal numerous divergent lineages that require taxonomic attention, including at least two widespread taxa that are likely to be composite, additional specimens of Cyrtodactylus capreoloides (until recently known only from the holotype) and several divergent and completely novel lineages, two of which we introduce herein: Cyrtodactylus arcanus sp. n. and Cyrtodactylus medioclivus sp. n.
Ramadan Prospective Diabetes Study: the role of drug dosage and timing alteration, active glucose monitoring and patient education
Authors: Ahmedani M. Y. , Haque M. S. , Basit A. , Fawwad A. , Alvi S. F. D.
Published: May 2012

Diabet. Med. 29, 709–715 (2012)

Aims  To observe the effects of active glucose monitoring, alteration of drug dosage and timing, dietary counselling and patient education in the occurrence of acute diabetic complications in fasting individuals with diabetes during the month of Ramadan.

Methods  This prospective study was conducted at the outpatient department of the Baqai Institute of Diabetology and Endocrinology. Two educational sessions, one about drug dosage and timing alteration and glucose monitoring, and the other about dietary and lifestyle modifications, were given to the patients by a doctor and a dietician, respectively. Patients who had been recruited were advised to note their blood glucose readings on a chart for at least 15 fasting days, twice a day with at least one reading in the fasting state.

Results  A total of 3946 readings were obtained in 110 subjects; 82 readings were in the hypoglycaemic range, and there were 22 episodes of symptomatic hypoglycaemia and 60 episodes of biochemical hypoglycaemia observed in 27 patients. Seven patients experienced symptomatic hypoglycaemia, whereas 20 patients had biochemical hypoglycaemia. Symptomatic hypoglycaemic episodes showed a downward trend from weeks 1 to 4. The highest frequencies of hypo‐ and hyperglycaemic episodes were observed pre‐dawn. None of the patients developed diabetic ketoacidosis or hyperglycaemic hyperosmolar state.

Conclusion  We observed that, with active glucose monitoring, alteration of drug dosage and timing, dietary counselling and patient education, the majority of the patients did not have any serious acute complications of diabetes during Ramadan.
Trait anxiety and glucose metabolism in people without diabetes: vulnerabilities among black women
Authors: Tsenkova V. K. , Albert M. A. , Georgiades A , Ryff C. D.
Published: May 2012

Diabet. Med. 29, 803–806 (2012)

Aims  We examined whether the relationship between anxiety and indicators of glucose metabolism in people without diabetes varies by race and gender.

Methods  Participants were 914 adults (777 white, 137 black) without diabetes in the MIDUS (Midlife in the USA) II study. Glucose metabolism was characterized by fasting glucose, insulin, HOMA‐IR (homeostasis model of assessment – insulin resistance), and HbA1c. Hierarchical linear regressions stratified by race and gender examined whether anxiety was associated with glucose metabolism.

Results  After adjustment for potential confounders, positive relationships between anxiety and fasting glucose (P = 0.04), insulin (P = 0.01), and HOMA‐IR (P = 0.02) but not HbA1c, were observed in black women only.

Conclusions  Our findings extend previous evidence for the links between psychosocial vulnerabilities and impaired glucose metabolism in black women, by documenting significant associations between anxiety and clinical indicators of glycaemic control among black women without diabetes. Thus, anxiety might constitute an intervention target in black women, a subgroup disproportionately affected by Type 2 diabetes, its complications, and premature mortality.
Is it good or bad to fish with FADs? What are the real impacts of the use of drifting FADs on pelagic marine ecosystems?
Authors: Dagorn Laurent , Holland Kim N. , Restrepo Victor , Moreno Gala
Published: May 2012

The use of fish aggregating devices (FADs) by purse seine fisheries has come under increasing criticism for its potential deleterious impacts on tuna stocks, for high levels of by‐catch and threats to the biodiversity of tropical pelagic ecosystems. Here, we review the current state of scientific knowledge of this fishing technique and current management strategies. Our intent is to encourage objective discussion of the topic and highlight areas worthy of future research. We show that catching juvenile tuna around FADs does not necessarily result in overfishing of stocks, although more selective fishing techniques would likely help obtain higher yield. Levels of non‐tuna by‐catch are comparable to or less than in other commercial tuna fisheries and are primarily comprised of species that are not considered threatened. Accordingly, to minimize impacts on ecosystem balance, there is merit in considering that all species captured in purse seine fisheries (excluding vulnerable species such as turtles and sharks) should be retained, but the consequences of such a measure should be carefully examined before implementation. The take of vulnerable species could be further reduced by introduction of additional mitigation measures, but their potential benefits would be limited without parallel efforts with other gears. Finally, there is no unequivocal empirical evidence that FADs represent an ‘ecological trap’ that inherently disrupts tuna biology although further research should focus on this issue. We encourage RFMOs to expand and improve their FAD management plans. Under appropriate management regimes, FAD fishing could be an ecologically and economically sensible fishing method.
REGIONAL INNOVATION SYSTEMS WITHIN A TRANSITIONAL CONTEXT: EVOLUTIONARY COMPARISON OF THE ELECTRONICS INDUSTRY IN SHENZHEN AND DONGGUAN SINCE THE OPENING OF CHINA
Authors: Fu Wenying , Diez Javier Revilla , Schiller Daniel
Published: May 2012

Abstract This paper, which is positioned in the interface of innovation economics and economic geography, contributes to the debate about the path‐dependent evolution of regional innovation systems (RIS) in emerging and transitional economies. Drawing on an empirical study conducted in Shenzhen and Dongguan, China, a path‐dependent nature of governance modality for initiating industrialization within the transitional context has been uncovered. The paper shows that the dirigiste globalized production system in Shenzhen, where the government exerted strong directive influence in the 1980s, has gradually evolved and reached a higher form of interactive RIS than the grassroots globalized production system in Dongguan, where innovation activities are few and are still passively managed by global players. The review of the evolutionary path of the electronics industry in Shenzhen and Dongguan reveals that the locational first‐mover advantage in Shenzhen is further strengthened by the institutional first‐mover advantage, incubating competitive and diversified firms in the business sector, which facilitate the interactive learning mechanism in RIS. Finally, policy implication is discussed for the construction of RIS under different governance modalities in the initial industrialization phase.
THE TRANSATLANTIC PRODUCTIVITY GAP: A SURVEY OF THE MAIN CAUSES
Authors: Ortega‐Argilés Raquel
Published: May 2012

Abstract During the last 2 decades, Europe's economy experienced a productivity slowdown whereas the United States (US) economy exhibited a marked acceleration. The result is that since the early 1990s the relative productivity levels between the two regions have continuously diverged, leading to a transatlantic productivity gap. Much of the explanation for this is the strong performance of the US in the so‐called ‘new economy’ or ‘knowledge economy’ and in particular the underinvestment in R&D, and as a result, productivity and innovation has been at the forefront in the European Policy agenda. However, various explanations for the US–European Union transatlantic productivity gap suggest that the picture is rather more complex than simply the effects on, or the result of, particular technology‐driven sectors.
THEORIES OF ENTREPRENEURSHIP, INNOVATION AND THE BUSINESS CYCLE
Authors: Parker Simon C.
Published: May 2012

Abstract This paper discusses several prominent economic theories which link entrepreneurs and their innovations to the creation and magnitude of business cycles. I distinguish three broad classes of theories: models of creative destruction; models of innovation and implementation cycles; and models of production under asymmetric information. Key insights of the theories are identified, policy implications are drawn, and suggestions for future research are proposed.
The Relation Between Exposure to Sophisticated and Complex Language and Early‐Adolescent English‐Only and Language Minority Learners’ Vocabulary
Authors: Gámez Perla B. , Lesaux Nonie K.
Published: May 2012

This study investigated the relation between teachers’ (N = 22) use of sophisticated and complex language in urban middle‐school classrooms and their students’ (mean age at pretest = 11.51 years; N = 782; 568 language minority and 247 English only) vocabulary knowledge. Using videotaped classroom observations, teachers’ speech was transcribed and coded for their total amount of talk, vocabulary usage, and syntactic complexity. Students’ vocabulary skills were assessed at the beginning and end of the school year. Results showed variation in students’ vocabulary skills and teachers’ language use. Hierarchical linear modeling techniques revealed that after controlling for classroom and school composition and students’ beginning‐of‐the‐year scores, students’ end‐of‐the‐year vocabulary skills were positively related to teachers’ use of sophisticated vocabulary and complex syntax, but not teachers’ total amount of talk.
Phylogeographic patterns of Buthus scorpions (Scorpiones: Buthidae) in the Maghreb and South‐Western Europe based on CO1 mtDNA sequences
Authors: Sousa P. , Harris D. J. , Froufe E. , van der Meijden A.
Published: May 2012

The genus Buthus is a medium diverse scorpion genus, with 35 species distributed from Portugal and Morocco ranging eastward to Yemen in the Arabic Peninsula. The bulk of the genus' known species diversity occurs in the Western Mediterranean area. A recent molecular study started to elucidate the patterns of diversity of this genus in the Iberian Peninsula and the Maghreb. Since then, the taxonomy of the genus has changed substantially, with several new species having been described, and with the elevation of former subspecies to species‐level. In this study, we assessed the patterns of diversity of Buthus scorpions from across the Maghreb region of North Africa using CO1 DNA sequence data. Based on our dataset of 147 sequences, including 67 new sequences, we recovered four well‐supported deep clades within Buthus scorpions from the Maghreb and Southern Europe. This further strengthens the support for cryptic diversity in the Maghreb region. The broader sampling of the Maghreb permitted a better understanding of the phylogeographic structure in this area. Three clades were restricted to Morocco and appear to have originated at the Atlantic Coast of this country, while the fourth was found throughout the region. We propose a model with two colonizing events to explain the distribution patterns across the Strait of Gibraltar, with an initial colonization from North Africa to Iberia followed by a reinvasion of the Rif Mountains region in Morocco.