bluuebunny/crossref_metadata_2025 huggingface dataset:
Detecting Temporal Trends in Freshwater Fisheries Surveys: Statistical Power and the Important Linkages between Management Questions and Monitoring Objectives
Authors: Wagner Tyler , Irwin Brian J , Bence James R , Hayes Daniel B
Published: July 2013

Monitoring to detect temporal trends in biological and habitat indices is a critical component of fisheries management. Thus, it is important that management objectives are linked to monitoring objectives. This linkage requires a definition of what constitutes a management-relevant “temporal trend.” It is also important to develop expectations for the amount of time required to detect a trend (i.e., statistical power) and for choosing an appropriate statistical model for analysis. We provide an overview of temporal trends commonly encountered in fisheries management, review published studies that evaluated statistical power of long-term trend detection, and illustrate dynamic linear models in a Bayesian context, as an additional analytical approach focused on shorter term change. We show that monitoring programs generally have low statistical power for detecting linear temporal trends and argue that often management should be focused on different definitions of trends, some of which can be better addressed by alternative analytical approaches.

RESUMEN

el monitoreo que se realiza para detectar tendencias en el tiempo de indices biológicos y de hábitat es un componente critico para el manejo de pesquerias. Por tanto, es crucial que los objetivos de manejo estén concertados con los objetivos de monitoreo. Estas relaciones requieren de la definición de los constituyentes de una “tendencia temporal” que sea relevante para el manejo. También es importante desarrollar expectativas acerca de la cantidad de tiempo necesaria para detectar una tendencia (i.e. poder estadistico) y elegir un modelo estadistico apropiado para el análisis. En este trabajo (1) se presenta un panorama de las tendencias temporales que comúnmente se encuentran en el manejo de pesquerias, (2) se revisa la literatura publicada sobre evaluación del poder estadistico en la detección de tendencias temporales y (3) se aplicaron modelos lineales dinámicos de contexto Bayesiano, como un enfoque analitico adicional enfocado en cambios de corto plazo. Se muestra que los programas de monitoreo generalmente tienen bajo poder estadistico para detectar tendencias lineales en el tiempo y se argumenta que el manejo debiera enfocarse en diferentes definiciones de tendencias, algunas de las cuales pudieran ser mejor estudiadas mediante enfoques analiticos alternativos.
Studies on the Salinity Tolerance of the Juvenile Dark Sleeper
Authors: Lu Genhai , Zhang Haiming , Shi Yonghai , Zhang Genyu , Liu Jianzhong
Published: July 2013

Acute and chronic experiments were conducted to evaluate the effect of salinity on survival and growth of the juvenile Dark Sleeper Odontobutis potamophila. For the acute experiment, half-lethal concentrations (LC50) of salinity for the juvenile Dark Sleeper after exposures for 12, 24, 48, 72 and 96 h were determined. Mean survival time (MST) and half-survival time (ST50) at salinity of 32‰ were also recorded. For the chronic experiment, a 22-day trial focused on comparing the effects of different salinity levels (0, 2, 4, 6, 8, and 10‰) on survival rate and growth of the juvenile Dark Sleeper. Results revealed that the 96-h LC50 was 13.79‰ salinity. MST and ST50 at 32‰ were 35.4 min and 37.0 min, respectively. In the 22-d trial, survival rate and specific growth rate (SGR) decreased with salinity. Survival rate of groups in 8‰ and 10‰ salinity were significantly lower than that of other groups. The SGR for body length and body weight of the 10‰ group was significantly lower than that of the other groups. This study indicates that the optimal salinity level for satisfactory survival and growth of juvenile Dark Sleeper in cultures should be below 6‰.
As if ‘relations’ mattered: how to subvert positional bias in social science with a lot of help from ‘others’…
Authors: Weber Martin
Published: July 2013

The study of international relations has, by and large, been the study of ‘international positions’. The article supplements this claim with the aim of recasting debates around orthodoxies and heterodoxies in the social and political sciences through an intermediary discussion of the limitations of what is criticized as ‘positionalism’. By drawing on examples, the juxtaposition of relational to positional analysis is supplemented with an account of the difference such orientations produce in practice.
A genomic random interval model for statistical analysis of genomic lesion data
Authors: Pounds Stan , Cheng Cheng , Li Shaoyu , Liu Zhifa , Zhang Jinghui , Mullighan Charles
Published: July 2013

Motivation: Tumors exhibit numerous genomic lesions such as copy number variations, structural variations and sequence variations. It is difficult to determine whether a specific constellation of lesions observed across a cohort of multiple tumors provides statistically significant evidence that the lesions target a set of genes that may be located across different chromosomes but yet are all involved in a single specific biological process or function.

Results: We introduce the genomic random interval (GRIN) statistical model and analysis method that evaluates the statistical significance of the abundance of genomic lesions that overlap a specific locus or a pre-defined set of biologically related loci. The GRIN model retains certain biologically important properties of genomic lesions that are ignored by other methods. In a simulation study and two example analyses of leukemia genomic lesion data, GRIN more effectively identified important loci as significant than did three methods based on a permutation-of-markers model. GRIN also identified biologically relevant pathways with a significant abundance of lesions in both examples.

Availability: An R package will be freely available at CRAN and www.stjuderesearch.org/site/depts/biostats/software.

Contact:  stanley.pounds@stjude.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
Topologically inferring risk-active pathways toward precise cancer classification by directed random walk
Authors: Liu Wei , Li Chunquan , Xu Yanjun , Yang Haixiu , Yao Qianlan , Han Junwei , Shang Desi , Zhang Chunlong , Su Fei , Li Xiaoxi , Xiao Yun , Zhang Fan , Dai Meng , Li Xia
Published: July 2013

Motivation: The accurate prediction of disease status is a central challenge in clinical cancer research. Microarray-based gene biomarkers have been identified to predict outcome and outperform traditional clinical parameters. However, the robustness of the individual gene biomarkers is questioned because of their little reproducibility between different cohorts of patients. Substantial progress in treatment requires advances in methods to identify robust biomarkers. Several methods incorporating pathway information have been proposed to identify robust pathway markers and build classifiers at the level of functional categories rather than of individual genes. However, current methods consider the pathways as simple gene sets but ignore the pathway topological information, which is essential to infer a more robust pathway activity.

Results: Here, we propose a directed random walk (DRW)-based method to infer the pathway activity. DRW evaluates the topological importance of each gene by capturing the structure information embedded in the directed pathway network. The strategy of weighting genes by their topological importance greatly improved the reproducibility of pathway activities. Experiments on 18 cancer datasets showed that the proposed method yielded a more accurate and robust overall performance compared with several existing gene-based and pathway-based classification methods. The resulting risk-active pathways are more reliable in guiding therapeutic selection and the development of pathway-specific therapeutic strategies.

Availability: DRW is freely available at http://210.46.85.180:8080/DRWPClass/

Contact:  lixia@hrbmu.edu.cn or dm42298@126.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Allosite: a method for predicting allosteric sites
Authors: Huang Wenkang , Lu Shaoyong , Huang Zhimin , Liu Xinyi , Mou Linkai , Luo Yu , Zhao Yanlong , Liu Yaqin , Chen Zhongjie , Hou Tingjun , Zhang Jian
Published: July 2013

Motivation: The use of allosteric modulators as preferred therapeutic agents against classic orthosteric ligands has colossal advantages, including higher specificity, fewer side effects and lower toxicity. Therefore, the computational prediction of allosteric sites in proteins is receiving increased attention in the field of drug discovery. Allosite is a newly developed automatic tool for the prediction of allosteric sites in proteins of interest and is now available through a web server.

Availability: The Allosite server and tutorials are freely available at http://mdl.shsmu.edu.cn/AST

Contact:  jian.zhang@sjtu.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
A computational method to preclude multistationarity in networks of interacting species
Authors: Feliu Elisenda , Wiuf Carsten
Published: July 2013

Motivation: Modeling and analysis of complex systems are important aspects of understanding systemic behavior. In the lack of detailed knowledge about a system, we often choose modeling equations out of convenience and search the (high-dimensional) parameter space randomly to learn about model properties. Qualitative modeling sidesteps the issue of choosing specific modeling equations and frees the inference from specific properties of the equations. We consider classes of ordinary differential equation (ODE) models arising from interactions of species/entities, such as (bio)chemical reaction networks or ecosystems. A class is defined by imposing mild assumptions on the interaction rates. In this framework, we investigate whether there can be multiple positive steady states in some ODE models in a given class.

Results: We have developed and implemented a method to decide whether any ODE model in a given class cannot have multiple steady states. The method runs efficiently on models of moderate size. We tested the method on a large set of models for gene silencing by sRNA interference and on two publicly available databases of biological models, KEGG and Biomodels. We recommend that this method is used as (i) a pre-screening step for selecting an appropriate model and (ii) for investigating the robustness of non-existence of multiple steady state for a given ODE model with respect to variation in interaction rates.

Availability and Implementation: Scripts and examples in Maple are available in the Supplementary Information.

Contact:  wiuf@math.ku.dk

Supplementary information:  Supplementary data are available at Bioinformatics online.
iLoops: a protein–protein interaction prediction server based on structural features
Authors: Planas-Iglesias Joan , Marin-Lopez Manuel A. , Bonet Jaume , Garcia-Garcia Javier , Oliva Baldo
Published: July 2013

Summary: Protein–protein interactions play a critical role in many biological processes. Despite that, the number of servers that provide an easy and comprehensive method to predict them is still limited. Here, we present iLoops, a web server that predicts whether a pair of proteins can interact using local structural features. The inputs of the server are as follows: (i) the sequences of the query proteins and (ii) the pairs to be tested. Structural features are assigned to the query proteins by sequence similarity. Pairs of structural features (formed by loops or domains) are classified according to their likelihood to favor or disfavor a protein–protein interaction, depending on their observation in known interacting and non-interacting pairs. The server evaluates the putative interaction using a random forest classifier.

Availability: iLoops is available at http://sbi.imim.es/iLoops.php

Contact:  baldo.oliva@upf.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
MIG: Multi-Image Genome viewer
Authors: McGowan Simon J. , Hughes Jim R. , Han Zong-Pei , Taylor Stephen
Published: July 2013

Summary: Multi-Image Genome (MIG) viewer is a web-based application for visualizing, querying and filtering many thousands of genome browser regions as well as for exporting the data in a variety of formats. This methodology has been used successfully to analyze ChIP-Seq data and RNA-Seq data and to detect somatic mutations in genome resequencing projects.

Availability: MIG is available at https://mig.molbiol.ox.ac.uk/mig/

Contact:  simon.mcgowan@imm.ox.ac.uk
Pathoscope: Species identification and strain attribution with unassembled sequencing data
Authors: Francis Owen E. , Bendall Matthew , Manimaran Solaiappan , Hong Changjin , Clement Nathan L. , Castro-Nallar Eduardo , Snell Quinn , Schaalje G. Bruce , Clement Mark J. , Crandall Keith A. , Johnson W. Evan
Published: July 2013

Emerging next-generation sequencing technologies have revolutionized the collection of genomic data for applications in bioforensics, biosurveillance, and for use in clinical settings. However, to make the most of these new data, new methodology needs to be developed that can accommodate large volumes of genetic data in a computationally efficient manner. We present a statistical framework to analyze raw next-generation sequence reads from purified or mixed environmental or targeted infected tissue samples for rapid species identification and strain attribution against a robust database of known biological agents. Our method,Pathoscope, capitalizes on a Bayesian statistical framework that accommodates information on sequence quality, mapping quality, and provides posterior probabilities of matches to a known database of target genomes. Importantly, our approach also incorporates the possibility that multiple species can be present in the sample and considers cases when the sample species/strain is not in the reference database. Furthermore, our approach can accurately discriminate between very closely related strains of the same species with very little coverage of the genome and without the need for multiple alignment steps, extensive homology searches, or genome assembly—which are time-consuming and labor-intensive steps. We demonstrate the utility of our approach on genomic data from purified and in silico “environmental” samples from known bacterial agents impacting human health for accuracy assessment and comparison with other approaches.
The Endocytosis of Cellulose Synthase in Arabidopsis Is Dependent on μ2, a Clathrin-Mediated Endocytosis Adaptin
Authors: Bashline Logan , Li Shundai , Anderson Charles T. , Lei Lei , Gu Ying
Published: July 2013

Clathrin-mediated endocytosis (CME) is the best-characterized type of endocytosis in eukaryotic cells. Plants appear to possess all of the molecular components necessary to carry out CME; however, functional characterization of the components is still in its infancy. A yeast two-hybrid screen identified μ2 as a putative interaction partner of CELLULOSE SYNTHASE6 (CESA6). Arabidopsis (Arabidopsis thaliana) μ2 is homologous to the medium subunit 2 of the mammalian ADAPTOR PROTEIN COMPLEX2 (AP2). In mammals, the AP2 complex acts as the central hub of CME by docking to the plasma membrane while concomitantly recruiting cargo proteins, clathrin triskelia, and accessory proteins to the sites of endocytosis. We confirmed that μ2 interacts with multiple CESA proteins through the μ-homology domain of μ2, which is involved in specific interactions with endocytic cargo proteins in mammals. Consistent with its role in mediating the endocytosis of cargos at the plasma membrane, μ2-YELLOW FLUORESCENT PROTEIN localized to transient foci at the plasma membrane, and loss of μ2 resulted in defects in bulk endocytosis. Furthermore, loss of μ2 led to increased accumulation of YELLOW FLUORESCENT PROTEIN-CESA6 particles at the plasma membrane. Our results suggest that CESA represents a new class of CME cargo proteins and that plant cells might regulate cellulose synthesis by controlling the abundance of active CESA complexes at the plasma membrane through CME.
Identification and Functional Analysis of Tomato BRI1 and BAK1 Receptor Kinase Phosphorylation Sites
Authors: Bajwa Vikramjit S. , Wang Xiaofeng , Blackburn R. Kevin , Goshe Michael B. , Mitra Srijeet K. , Williams Elisabeth L. , Bishop Gerard J. , Krasnyanski Sergei , Allen George , Huber Steven C. , Clouse Steven D.
Published: July 2013

Brassinosteroids (BRs) are plant hormones that are perceived at the cell surface by a membrane-bound receptor kinase, BRASSINOSTEROID INSENSITIVE1 (BRI1). BRI1 interacts with BRI1-ASSOCIATED RECEPTOR KINASE1 (BAK1) to initiate a signal transduction pathway in which autophosphorylation and transphosphorylation of BRI1 and BAK1, as well as phosphorylation of multiple downstream substrates, play critical roles. Detailed mechanisms of BR signaling have been examined in Arabidopsis (Arabidopsis thaliana), but the role of BRI1 and BAK1 phosphorylation in crop plants is unknown. As a foundation for understanding the mechanism of BR signaling in tomato (Solanum lycopersicum), we used liquid chromatography-tandem mass spectrometry to identify multiple in vitro phosphorylation sites of the tomato BRI1 and BAK1 cytoplasmic domains. Kinase assays showed that both tomato BRI1 and BAK1 are active in autophosphorylation as well as transphosphorylation of each other and specific peptide substrates with a defined sequence motif. Site-directed mutagenesis revealed that the highly conserved kinase domain activation loop residue threonine-1054 was essential for tomato BRI1 autophosphorylation and peptide substrate phosphorylation in vitro. Furthermore, analysis of transgenic lines expressing full-length tomato BRI1-Flag constructs in the weak tomato bri1 allele, curl3-abs1, demonstrated that threonine-1054 is also essential for normal BRI1 signaling and tomato growth in planta. Finally, we cloned the tomato ortholog of TGF-β Receptor Interacting Protein (TRIP1), which was previously shown to be a BRI1-interacting protein and kinase domain substrate in Arabidopsis, and found that tomato TRIP1 is a substrate of both tomato BRI1 and BAK1 kinases in vitro.
Effect of 1‐methyl‐D‐tryptophan and adoptive transfer of dendritic cells on polymicrobial sepsis induced by cecal content injection
Authors: Yim Hong Soon , Choi Kyung Min , Kim Byoungjae , Jung In Duk , Park Yeong‐Min , Kang Yoon Kyu , Lee Min‐Goo
Published: July 2013

A mouse model of polymicrobial sepsis induced by cecal content injection (CCI) was developed with the aim of gaining a better understanding of the mechanism of sepsis. This model has a similar survival pattern to the conventional model with the added benefits of ability to vary the severity of sepsis and greater consistency. Administration of 1‐methyl‐D‐tryptophan (1‐MT) to inhibit indoleamine 2,3‐dioxygenase (IDO) in mice with CCI‐induced sepsis increased the survival rate and tended to up‐regulate IL‐10/IL‐12 serum concentrations. The effectiveness of 1‐MT was confirmed by increases in IL‐10 over IL‐12 in bone marrow‐derived dendritic cells (BMDCs) treated with LPS and 1‐MT and a superior survival rate 24 hr after injection of these double treated BMDCs in the CCI‐induced sepsis model. Therefore, CCI is both a useful and reliable technique for investigating polymicrobial sepsis. The present findings using this newly developed model suggest that inhibition of IDO alleviates the severity of polymicrobial sepsis and modulates the immune response even in cases of severe systemic septic inflammation.
Why polar gigantism and Palaeozoic gigantism are not equivalent: effects of oxygen and temperature on the body size of ectotherms
Authors: Verberk Wilco C. E. P. , Atkinson David
Published: July 2013

Organisms of gigantic proportions inhabited the world at a time of a hyperoxic prehistoric atmosphere (Palaeozoic gigantism). Extant giants are found in cold polar waters, with large quantities of dissolved oxygen (polar gigantism). Oxygen is usually deemed central to explain such gigantism. Examples of one category of gigantism are often cited in support of the other, but novel insights into the bioavailability of oxygen imply that they cannot be taken as equivalent manifestations of the effect of oxygen on body size.

Recently, the availability of oxygen has been shown to be lower in cold waters, despite greater oxygen solubility. Consequently, gigantism in cold, oxygenated waters and gigantism in an oxygen‐pressurized world are fundamentally different: Palaeozoic gigantism likely arose because of greater oxygen availability, while polar gigantism arises in spite of lower oxygen availability.

The traditional view of respiration focuses on meeting the challenge of extracting sufficient amounts of oxygen, which essentially is a toxic gas. We present a broader perspective, which specifically includes risks of oxygen poisoning. We discuss how challenges pertaining to balancing oxygen uptake capacity and risks of oxygen poisoning are very different for animals breathing either air or water.

We propose a novel explanation for polar gigantism in aquatic ectotherms, arguing that their larger body size represents a respiratory advantage that helps to overcome the larger viscous forces in water. Being large helps organisms to balance the opposing risks of asphyxiation and poisoning, especially in colder, more viscous, water. This results in a selection for larger sizes, with polar gigantism as the extreme manifestation. Hence, a larger size provides respiratory benefits to water‐breathing ectotherms, but not terrestrial ectotherms. This can explain why clines in body size across temperature and latitude are stronger in aquatic ectotherms.
Differential effects of a gelatinase inhibitor on adipocyte differentiation and adipose tissue development
Authors: Van Hul Matthias , Bauters Dries , Lijnen Roger H
Published: July 2013

A potential role for the gelatinases in adipocyte differentiation in vitro and adipose tissue development in vivo was investigated using the gelatinase inhibitor tolylsam ((R)‐3‐methyl‐2‐[4‐(3‐p‐tolyl‐[1,2,4]oxadiazol‐5‐yl)‐benzenesulphonylamino]‐butyric acid).

Differentiation of murine 3T3‐F442A preadipocytes (12 days after reaching confluence) into mature adipocytes in vitro was promoted in the presence of tolylsam (10–100 μmol/L).

De novo development of fat tissue in nude mice injected with preadipocytes and kept on a high‐fat diet was significantly impaired following treatment with tolylsam (100 mg/kg per day for 4 weeks).

Adipose tissue development in matrix metalloproteinase (MMP)‐2 deficient mice, kept on a high‐fat diet, was significantly impaired following administration of tolylsam (100 mg/kg per day for 15 weeks). This was associated with markedly enhanced metabolic rate.

Treatment of MMP‐2‐deficient mice with tolylsam (100 mg/kg per day, 15 weeks) was associated with the preservation of collagen and a reduction in blood vessel size in adipose tissues in vivo.

Furthermore, plasma levels of triglycerides and free fatty acids were reduced by tolylsam treatment of MMP‐2‐deficient mice (100 mg/kg per day, 15 weeks), whereas nutrient adsorption in the intestine was not affected.

The results of the present study indicate that tolylsam promotes preadipocyte differentiation in vitro, but impairs adipose tissue development in vivo.
Beyond static assessment of children's receptive vocabulary: the dynamic assessment of word learning (DAWL)
Authors: Camilleri Bernard , Botting Nicola
Published: July 2013

Background

Children's low scores on vocabulary tests are often erroneously interpreted as reflecting poor cognitive and/or language skills. It may be necessary to incorporate the measurement of word‐learning ability in estimating children's lexical abilities.

Aims

To explore the reliability and validity of the Dynamic Assessment of Word Learning (DAWL), a new dynamic assessment of receptive vocabulary.

Methods & Procedures

A dynamic assessment (DA) of word learning ability was developed and adopted within a nursery school setting with 15 children aged between 3;07 and 4;03, ten of whom had been referred to speech and language therapy.

Outcomes & Results

A number of quantitative measures were derived from the DA procedure, including measures of children's ability to identify the targeted items and to generalize to a second exemplar, as well as measures of children's ability to retain the targeted items. Internal, inter‐rater and test–retest reliability of the DAWL was established as well as correlational measures of concurrent and predictive validity.

Conclusions & Implications

The DAWL was found to provide both quantitative and qualitative information which could be used to improve the accuracy of differential diagnosis and the understanding of processes underlying the child's performance. The latter can be used for the purpose of designing more individualized interventions.
Anthropometric protocols for the construction of new international fetal and newborn growth standards: the INTERGROWTH‐21st Project
Authors: Cheikh Ismail L , Knight HE , Bhutta Z , Chumlea WC ,   for the International Fetal and Newborn Growth Consortium for the 21 Century (INTERGROWTH‐21)
Published: July 2013

The primary aim of the INTERGROWTH‐21st Project is to construct new, prescriptive standards describing optimal fetal and preterm postnatal growth. The anthropometric measurements include the head circumference, recumbent length and weight of the infants, and the stature and weight of the parents. In such a large, international, multicentre project, it is critical that all study sites follow standardised protocols to ensure maximal validity of the growth and nutrition indicators used. This paper describes, in detail, the selection of anthropometric personnel, equipment, and measurement and calibration protocols used to construct the new standards. Implementing these protocols at each study site ensures that the anthropometric data are of the highest quality to construct the international standards.
Anthropometric standardisation and quality control protocols for the construction of new, international, fetal and newborn growth standards: the INTERGROWTH‐21st Project
Authors: Cheikh Ismail L , Knight HE , Ohuma EO , Hoch L , Chumlea WC ,   for the International Fetal and Newborn Growth Consortium for the 21 Century (INTERGROWTH‐21)
Published: July 2013

The primary aim of the INTERGROWTH‐21st Project is to construct new, prescriptive standards describing optimal fetal and preterm postnatal growth. The anthropometric measurements include the head circumference, recumbent length and weight of the infants, and the stature and weight of the parents. In such a large, international, multicentre project, it is critical that all study sites follow standardised protocols to ensure maximal validity of the growth and nutrition indicators used. This paper describes in detail the anthropometric training, standardisation and quality control procedures used to collect data for these new standards. The initial standardisation session was in Nairobi, Kenya, using newborns, which was followed by similar sessions in the eight participating study sites in Brazil, China, India, Italy, Kenya, Oman, UK and USA. The intraobserver and inter‐observer technical error of measurement values for head circumference range from 0.3 to 0.4 cm, and for recumbent length from 0.3 to 0.5 cm. These standardisation protocols implemented at each study site worldwide ensure that the anthropometric data collected are of the highest quality to construct international growth standards.
Ultrasound methodology used to construct the fetal growth standards in the INTERGROWTH‐21st Project
Authors: Papageorghiou AT , Sarris I , Ioannou C , Todros T , Carvalho M , Pilu G , Salomon LJ ,   for the International Fetal and Newborn Growth Consortium for the 21 Century (INTERGROWTH‐21)
Published: July 2013

A unified protocol is essential to ensure that fetal ultrasound measurements taken in multicentre research studies are accurate and reproducible. This paper describes the methodology used to take two‐dimensional, ultrasound measurements in the longitudinal, fetal growth component of the INTERGROWTH‐21st Project. These standardised methods should minimise the systematic errors associated with pooling data from different study sites. They represent a model for carrying out similar research studies in the future.
Molecular identification of a pancreatic lipase‐like gene involved in sex pheromone biosynthesis of Bombyx mori
Authors: Zhang Song‐Dou , Li Xun , Bin Zhu , Du Meng‐Fang , Yin Xin‐Ming , An Shi‐Heng
Published: July 2013

Cytoplasmic lipid droplet (LD) lipolysis is regulated by pheromone biosynthesis activating neuropeptide (PBAN) in Bombyx mori. To elucidate the molecular mechanism of cytoplasm LD lipolysis, the pancreatic lipase‐like gene in B. mori pheromone glands (PGs), designated as B. mori pancreatic lipase‐like gene (BmPLLG), was identified in this study. Spatial expression analysis revealed that BmPLLG is a ubiquitous gene present in all studied tissues, such as PGs, brain, epidermis, egg, midgut, flight muscle and fat body. Temporal expression analysis showed that the BmPLLG transcript begins to express 96 h before eclosion (−96 h), continues to increase, peaks in newly emerged females and steadily decreases after eclosion. Translational expression analysis of BmPLLG using a prepared antiserum demonstrated that BmPLLG was expressed in an age‐dependent pattern at different development stages in B. mori. This finding was similar to the transcript expression pattern. Further RNA interference‐mediated knockdown of BmPLLG significantly inhibited bombykol production. Overall, these results demonstrated that BmPLLG is involved in PBAN‐induced sex pheromone biosynthesis and release.
Macroeconomic Implications of the German Short‐time Work Policy during the Great Recession
Authors: Herzog‐Stein Alexander , Horn Gustav A. , Stein Ulrike
Published: July 2013

Despite a sharp fall in GDP, German employment in terms of employees stayed remarkably robust during the Great Recession. At the same time, hours worked per employee declined significantly. This is seen as the core of the German employment ‘miracle’. A general discussion arose about the reasons behind this astonishing labour market performance and the role of short‐time work (STW) as a kind of exportable panacea. In this article we look at the macroeconomic implications of STW and other measures of internal flexibility, in particular focusing on the quantification of safeguarded jobs during the crisis. We find that STW played an important role and helped to safeguard employment in Germany during the Great Recession. However, we show that other measures of internal flexibility (working time accounts, contractual arrangements on working time reductions, reduction of overtime) were equally important. Together with STW these instruments saved around 1 million jobs. To explain and understand the German success story, the features of the German core model – with a strong employer–employee relationship of mutual trust, strong employment protection, traditional standard working contracts and strong works councils at the firm level – are of key importance.
A comparison of the BURP and conventional and modified jaw thrust manoeuvres for orotracheal intubation using the Clarus Video System
Authors: Lee A. R. , Yang S. , Shin Y. H. , Kim J. A. , Chung I. S. , Cho H. S. , Lee J. J.
Published: July 2013

We evaluated the effects of three airway manipulation manoeuvres: (a) conventional (single‐handed chin lift); (b) backward, upward and right‐sided pressure (BURP) manoeuvre; and (c) modified jaw thrust manoeuvre (two‐handed aided by an assistant) on laryngeal view and intubation time using the Clarus Video System in 215 patients undergoing general anaesthesia with orotracheal intubation. In the first part of this study, the laryngeal view was recorded as a modified Cormack–Lehane grade with each manoeuvre. In the second part, intubation was performed using the assigned airway manipulation. The primary outcome was the time to intubation, and the secondary outcomes were the modified Cormack–Lehane grade, the number of attempts and the overall success rate. There were significant differences in modified Cormack–Lehane grade between the three airway manipulations (p < 0.0001). Post‐hoc analysis indicated that the modified jaw thrust improved the laryngeal view compared with the conventional (p < 0.0001) and the BURP manoeuvres (p < 0.0001). The BURP worsened the laryngeal view compared with the conventional manoeuvre (p = 0.0132). The time to intubation in the modified jaw thrust group was shorter than with the conventional manoeuvre (p = 0.0004) and the BURP group (p < 0.0001). We conclude that the modified jaw thrust is the most effective manoeuvre at improving the laryngeal view and shortening intubation time with the Clarus Video System.
Gallbladder bed pocket score as a preoperative measure for assessing the difficulty of laparoscopic cholecystectomy
Authors: Shinozaki Kenta , Ajiki Tetsuo , Okazaki Taro , Ueno Kimihiko , Matsumoto Taku , Ohtsubo Izuru , Murakami Sae , Yoshida Yuko , Matsumoto Ippei , Fukumoto Takumi , Sugimoto Takemi , Ohno Masakazu , Ku Yonson
Published: July 2013

Introduction

Laparoscopic cholecystectomy (Lap‐C) is a standard surgery for symptomatic gallbladder stones and acute or chronic cholecystitis. Resident surgeons often perform this operation early in their training, but they sometimes encounter difficulties for various technical reasons. Although encountering a gallbladder buried deep within the gallbladder bed is a common operative difficulty, literature on the subject scarcely exists.

Methods

Forty‐two patients underwent Lap‐C at our hospitals and were analyzed retrospectively. We defined the gallbladder bed pocket score (GBPS) as the maximum ratio between the height and width of the gallbladder bed measured based on multi‐detector computed tomography (MDCT) images. GBPS and clinical factors were assessed in terms of their correlation with the time required for gallbladder dissection from the gallbladder bed.

Results

Of the 42 patients, 20 had histories of acute or chronic cholecystitis. The mean gallbladder dissection time was 14.9 min, and the mean GBPS was 0.43 in the coronal MDCT section and 0.56 in the sagittal section. The correlation coefficient between the GBPS and gallbladder dissection time was 0.40 (P = 0.01) in the coronal section and 0.38 (P = 0.02) in the sagittal section of the MDCT images. There was no statistically significant correlation between gallbladder dissection time and the surgeon's experience, patient's history of cholecystitis, gallstone size, or blood loss. However, GBPS > 0.4 predicted more difficult and prolonged dissection.

Conclusion

GBPS is a useful tool for preoperatively predicting the time needed to dissect the gallbladder from the gallbladder bed during Lap‐C. Cases with GBPS < 0.4 seem more suitable for resident surgeons who are performing gallbladder dissection early in their Lap‐C training.
When Intuition is Not Enough. Why the Principle of Procreative Beneficence Must Work Much Harder to Justify Its Eugenic Vision
Authors: Bennett Rebecca
Published: July 2013

The Principle of Procreative Beneficence (PPB) claims that we have a moral obligation, where choice is possible, to choose to create the best child we can. The existence of this moral obligation has been proposed by John Harris and Julian Savulescu and has proved controversial on many levels, not least that it is eugenics, asking us to produce the best children we can, not for the sake of that child's welfare, but in order to make a better society. These are strong claims that require robust justification that can be open to scrutiny and debate.

This article argues that robust justifications are currently lacking in the work of Savulescu and Harris. The justifications provided for their conclusions about this obligation to have the best child possible rely heavily on Derek Parfit's Non‐Identity Problem and the intuitive response this provokes in many of us. Unfortunately Harris and Savulescu do not embrace the entirety of the Non‐Identity Problem and the puzzle that it presents. The Non‐Identity Problem actually provides a refutation of PPB. In order to establish PPB as a credible and defendable principle, Harris and Savulescu need to find what has eluded Parfit and many others: a solution to the Non‐Identity Problem and thus an overturning of the refutation it provides for PPB. While Harris and Savulescu do hint at possible but highly problematic solutions to the Non‐Identity Problem, these are not developed or defended. As a result their controversial is left supported by little more than intuition.
Shrinkage Empirical Likelihood Estimator in Longitudinal Analysis with Time‐Dependent Covariates—Application to Modeling the Health of Filipino Children
Authors: Leung Denis Heng‐Yan , Small Dylan S. , Qin Jing , Zhu Min
Published: July 2013

The method of generalized estimating equations (GEE) is a popular tool for analysing longitudinal (panel) data. Often, the covariates collected are time‐dependent in nature, for example, age, relapse status, monthly income. When using GEE to analyse longitudinal data with time‐dependent covariates, crucial assumptions about the covariates are necessary for valid inferences to be drawn. When those assumptions do not hold or cannot be verified, Pepe and Anderson (1994,Communications in Statistics, Simulations and Computation23, 939–951) advocated using an independence working correlation assumption in the GEE model as a robust approach. However, using GEE with the independence correlation assumption may lead to significant efficiency loss (Fitzmaurice, 1995,Biometrics51, 309–317). In this article, we propose a method that extracts additional information from the estimating equations that are excluded by the independence assumption. The method always includes the estimating equations under the independence assumption and the contribution from the remaining estimating equations is weighted according to the likelihood of each equation being a consistent estimating equation and the information it carries. We apply the method to a longitudinal study of the health of a group of Filipino children.
Correcting the Optimal Resampling‐Based Error Rate by Estimating the Error Rate of Wrapper Algorithms
Authors: Bernau Christoph , Augustin Thomas , Boulesteix Anne‐Laure
Published: July 2013

High‐dimensional binary classification tasks, for example, the classification of microarray samples into normal and cancer tissues, usually involve a tuning parameter. By reporting the performance of the best tuning parameter value only, over‐optimistic prediction errors are obtained. For correcting this tuning bias, we develop a new method which is based on a decomposition of the unconditional error rate involving the tuning procedure, that is, we estimate the error rate of wrapper algorithms as introduced in the context of internal cross‐validation (ICV) by Varma and Simon (2006, BMC Bioinformatics 7, 91). Our subsampling‐based estimator can be written as a weighted mean of the errors obtained using the different tuning parameter values, and thus can be interpreted as a smooth version of ICV, which is the standard approach for avoiding tuning bias. In contrast to ICV, our method guarantees intuitive bounds for the corrected error. Additionally, we suggest to use bias correction methods also to address the conceptually similar method selection bias that results from the optimal choice of the classification method itself when evaluating several methods successively. We demonstrate the performance of our method on microarray and simulated data and compare it to ICV. This study suggests that our approach yields competitive estimates at a much lower computational price.
Mark‐Recapture with Multiple, Non‐Invasive Marks
Authors: J Bonner Simon , Holmberg Jason
Published: July 2013

Non‐invasive marks, including pigmentation patterns, acquired scars, and genetic markers, are often used to identify individuals in mark‐recapture experiments. If animals in a population can be identified from multiple, non‐invasive marks then some individuals may be counted twice in the observed data. Analyzing the observed histories without accounting for these errors will provide incorrect inference about the population dynamics. Previous approaches to this problem include modeling data from only one mark and combining estimators obtained from each mark separately assuming that they are independent. Motivated by the analysis of data from the ECOCEAN online whale shark (Rhincodon typus) catalog, we describe a Bayesian method to analyze data from multiple, non‐invasive marks that is based on the latent‐multinomial model of Link et al. (2010, Biometrics 66, 178–185). Further to this, we describe a simplification of the Markov chain Monte Carlo algorithm of Link et al. (2010, Biometrics 66, 178–185) that leads to more efficient computation. We present results from the analysis of the ECOCEAN whale shark data and from simulation studies comparing our method with the previous approaches.
Bayesian Approach for Clinical Trial Safety Data Using an Ising Prior
Authors: McEvoy Bradley W. , Nandy Rajesh R. , Tiwari Ram C.
Published: July 2013

In drug safety, development of statistical methods for multiplicity adjustments has exploited potential relationships among adverse events (AEs) according to underlying medical features. Due to the coarseness of the biological features used to group AEs together, which serves as the basis for the adjustment, it is possible that a single adverse event can be simultaneously described by multiple biological features. However, existing methods are limited in that they are not structurally flexible enough to accurately exploit this multi‐dimensional characteristic of an adverse event. In order to preserve the complex dependencies present in clinical safety data, a Bayesian approach for modeling the risk differentials of the AEs between the treatment and comparator arms is proposed which provides a more appropriate clinical description of the drug's safety profile. The proposed procedure uses an Ising prior to unite medically related AEs. The proposed method and an existing Bayesian method are applied to a clinical dataset, and the signals from the two methods are presented. Results from a small simulation study are also presented.
Bayesian Quantile Regression for Censored Data
Authors: Reich Brian J. , Smith Luke B.
Published: July 2013

In this paper we propose a semiparametric quantile regression model for censored survival data. Quantile regression permits covariates to affect survival differently at different stages in the follow‐up period, thus providing a comprehensive study of the survival distribution. We take a semiparametric approach, representing the quantile process as a linear combination of basis functions. The basis functions are chosen so that the prior for the quantile process is centered on a simple location‐scale model, but flexible enough to accommodate a wide range of quantile processes. We show in a simulation study that this approach is competitive with existing methods. The method is illustrated using data from a drug treatment study, where we find that the Bayesian model often gives smaller measures of uncertainty than its competitors, and thus identifies more significant effects.
Decreased tissue factor pathway inhibitor (TFPI)‐dependent anticoagulant capacity in patients with cirrhosis who have decreased protein S but normal TFPI plasma levels
Authors: Potze Wilma , Arshad Freeha , Adelmeijer Jelle , Blokzijl Hans , van den Berg Arie P. , Meijers Joost C. M. , Porte Robert J. , Lisman Ton
Published: July 2013

Protein S acts as a cofactor for tissue factor pathway inhibitor (TFPI) in the down regulation of thrombin generation, and acquired and congenital protein S deficiencies are associated with a concomitant TFPI deficiency. In contrast, in patients with liver diseases, decreased protein S, but normal or increased levels of TFPI have been reported. We compared TFPI and protein S plasma levels between 26 patients with cirrhosis and 20 healthy controls and found that TFPI levels were comparable between patients (111 ± 38%) and controls (108 ± 27%), despite reduced protein S levels (74 ± 23% in patients vs. 98 ± 10% in controls). Subsequently, we quantified the activity of the TFPI‐protein S system by measuring thrombin generation in the absence and presence of neutralizing antibodies to protein S or TFPI. Ratios of peak thrombin generation in the absence and presence of these antibodies were calculated. Both the protein S and the TFPI ratios were increased in patients with cirrhosis compared to controls. Protein S ratios were (0·62 [0·08–0·93] in patients vs. 0·32 [0·20–0·54] in controls; TFPI ratios were 0·50 [0·05–0·90] in patients vs. 0·18 [0·11–0·49] in controls). Thus, although the acquired protein S deficiency in patients with cirrhosis is not associated with decreased TFPI levels, the TFPI/protein S anticoagulant system is functionally impaired.
Copper(I) (Pseudo)Halide Complexes with Neocuproine and Aminomethylphosphines Derived from Morpholine and Thiomorpholine – In Vitro Cytotoxic and Antimicrobial Activity and the Interactions with DNA and Serum Albumins
Authors: Starosta Radosław , Bykowska Aleksandra , Kyzioł Agnieszka , Płotek Michał , Florek Magdalena , Król Jarosław , Jeżowska‐Bojczuk Małgorzata
Published: July 2013

Herein, a series of CuI or CuNCS complexes with neocuproine (2,9‐dimethyl‐1,10‐phenanthroline: dmp) and two tris(aminomethyl)phosphines derived from morpholine (P(CH2N(CH2CH2)2O)3) or thiomorpholine (P(CH2N(CH2CH2)2S)3) were tested as cytotoxic agents in vitro towards mouse colon carcinoma (CT26) and human lung adenocarcinoma (A549). The studies showed that the complexes exhibit potential antitumor properties, displayed by IC50 values below 10 μm towards the tested cell lines, in the case of 4‐h incubation time with the examined compounds. Moreover, a high antimicrobial activity of all the complexes was observed against Staphylococcus aureus and Candida albicans with minimal inhibitory concentrations equal to 1–2 μg/mL. To gain insight into the molecular mechanism of biological activity of the complexes, we investigated also their interactions with plasmid DNA (pUC18) and the human and bovine serum albumins. Gel electrophoresis experiments demonstrated that all the compounds were comparably efficient in DNA degradation process; however, luminescence quenching showed surprising dependence on the interactions strength of the used compounds with the albumins. Apart from exceptionally effective [CuI(dmp)P(CH2N(CH2CH2)2O)3], the complexes with P(CH2N(CH2CH2)2O)3 quenched more strongly luminescence of bovine serum albumin, while the complexes with P(CH2N(CH2CH2)2S)3 were more active in the quenching of human serum albumin luminescence.
Alveolar macrophages in pulmonary host defence – the unrecognized role of apoptosis as a mechanism of intracellular bacterial killing
Authors: Aberdein J D , Cole J , Bewley M A , Marriott H M , Dockrell D H
Published: July 2013

Alveolar macrophages play an essential role in clearing bacteria from the lower airway, as the resident phagocyte alveolar macrophages must both phagocytose and kill bacteria, and if unable to do this completely must co-ordinate an inflammatory response. The decision to escalate the inflammatory response represents the transition between subclinical infection and the development of pneumonia. Alveolar macrophages are well equipped to phagocytose bacteria and have a large phagolysosomal capacity in which ingested bacteria are killed. The rate-limiting step in control of extracellular bacteria, such as Streptococcus pneumoniae, is the capacity of alveolar macrophages to kill ingested bacteria. Therefore, alveolar macrophages complement canonical microbicidal strategies with an additional level of apoptosis-associated killing to help kill ingested bacteria.