bluuebunny/crossref_metadata_2025 huggingface dataset:
Traversing the basement membrane in vivo: A diversity of strategies
Authors: Kelley Laura C. , Lohmer Lauren L. , Hagedorn Elliott J. , Sherwood David R.
Published: February 2014

The basement membrane is a dense, highly cross-linked, sheet-like extracellular matrix that underlies all epithelia and endothelia in multicellular animals. During development, leukocyte trafficking, and metastatic disease, cells cross the basement membrane to disperse and enter new tissues. Based largely on in vitro studies, cells have been thought to use proteases to dissolve and traverse this formidable obstacle. Surprisingly, recent in vivo studies have uncovered a remarkably diverse range of cellular- and tissue-level strategies beyond proteolysis that cells use to navigate through the basement membrane. These fascinating and unexpected mechanisms have increased our understanding of how cells cross this matrix barrier in physiological and disease settings.
Long-Term Effects of Hospital Water Network Disinfection onLegionellaand Other Waterborne Bacteria in an Italian University Hospital
Authors: Casini Beatrice , Buzzigoli Andrea , Cristina Maria Luisa , Spagnolo Anna Maria , Giudice Pietro Del , Brusaferro Silvio , Poscia Andrea , Moscato Umberto , Valentini Paola , Baggiani Angelo , Privitera Gaetano
Published: February 2014

Objective and Design.

Legionellacontrol still remains a critical issue in healthcare settings where the preferred approach to health risk assessment and management is to develop a water safety plan. We report the experience of a university hospital, where a water safety plan has been applied since 2002, and the results obtained with the application of different methods for disinfecting hot water distribution systems in order to provide guidance for the management of water risk.

Interventions.

The disinfection procedures included continuous chlorination with chlorine dioxide (0.4–0.6 mg/L in recirculation loops) reinforced by endpoint filtration in critical areas and a water treatment based on monochloramine (2-3 mg/L). Real-time polymerase chain reaction and a new immunoseparation and adenosine triphosphate bioluminescence analysis were applied in environmental monitoring.

Results.

After 9 years, the integrated disinfection-filtration strategy significantly reduced positive sites by 55% and the mean count by 78% (P< .05); however, the high costs and the occurrence of a chlorine-tolerant clone belonging toLegionella pneumophilaST269 prompted us to test a new disinfectant. The shift to monochloramine allowed us to eliminate planktonicLegionellaand did not require additional endpoint filtration; however, nontuberculous mycobacteria were isolated more frequently as long as the monochloramine concentration was 2 mg/L; their cultivability was never regained by increasing the concentration up to 3 mg/L.

Conclusions.

Any disinfection method needs to be adjusted/fine-tuned in individual hospitals in order to maintain satisfactory results over time, and only a locally adapted evidence-based approach allows assessment of the efficacy and disadvantages of the control measures.
Variability of Contact Precaution Policies in US Emergency Departments
Authors: Pallin Daniel J. , Camargo Carlos A. , Yokoe Deborah S. , Espinola Janice A. , Schuur Jeremiah D.
Published: February 2014

Contact precautions policies in US emergency departments have not been studied. We surveyed a structured random sample and found wide variation; for example, 45% required contact precautions for stool incontinence or diarrhea, 84% for suspected Clostridium difficile, and 79% for suspected methicillin-resistant Staphylococcus aureus infection. Emergency medicine departments and organizations should enact policies.
Parallel, non-iterative, multi-physics domain decomposition methods for time-dependent Stokes-Darcy systems
Authors: Cao Yanzhao , Gunzburger Max , He Xiaoming , Wang Xiaoming
Published: February 2014

Two parallel, non-iterative, multi-physics, domain decomposition methods are proposed to solve a coupled time-dependent Stokes-Darcy system with the Beavers-Joseph-Saffman-Jones interface condition. For both methods, spatial discretization is effected using finite element methods. The backward Euler method and a three-step backward differentiation method are used for the temporal discretization. Results obtained at previous time steps are used to approximate the coupling information on the interface between the Darcy and Stokes subdomains at the current time step. Hence, at each time step, only a single Stokes and a single Darcy problem need be solved; as these are uncoupled, they can be solved in parallel. The unconditional stability and convergence of the first method is proved and also illustrated through numerical experiments. The improved temporal convergence and unconditional stability of the second method is also illustrated through numerical experiments.
Mobyle SNAP Workbench: a web-based analysis portal for population genetics and evolutionary genomics
Authors: Monacell James T. , Carbone Ignazio
Published: February 2014

Summary: Previously we developed the stand-alone SNAP Workbench toolkit that integrated a wide array of bioinformatics tools for phylogenetic and population genetic analyses. We have now developed a web-based portal front-end, using the Mobyle portal framework, which executes all of the programs available in the stand-alone SNAP Workbench toolkit on a high-performance Linux cluster. Additionally, we have expanded the selection of programs to over 189 tools, including population genetic, genome assembly and analysis tools, as well as metagenomic and large-scale phylogenetic analyses. The Mobyle SNAP Workbench web portal allows end users to (i) execute and manage otherwise complex command-line programs, (ii) launch multiple exploratory analyses of parameter-rich and computationally intensive methods and (iii) track the sequence of steps and parameters that were used to perform a specific analysis. Analysis pipelines or workflows for population genetic, metagenomic and genome assembly provide automation of data conversion, analysis and graphical visualization for biological inference.

Availability: The Mobyle SNAP Workbench portal is freely available online at http://snap.hpc.ncsu.edu/. The XMLs can be downloaded at http://carbonelab.org/system/files/snap_xmls.tgz. Each XML provides links to help files, online documentation and sample data.

Supplementary information:  Supplementary data are available at Bioinformatics online.
Adaption of the global test idea to proteomics data with missing values
Authors: Jung Klaus , Dihazi Hassan , Bibi Asima , Dihazi Gry H. , Beißbarth Tim
Published: February 2014

Motivation: Global test procedures are frequently used in gene expression analysis to study the relationship between a functional subset of RNA transcripts and an experimental group factor. However, these procedures have been rarely used for the analysis of high-throughput data from other sources, such as proteome expression data. The main difficulties in transferring global test procedures from genomics to proteomics data are the more complicated way of obtaining functional annotations and the handling of missing values in some types of proteomics data.

Results: We propose a simple mixed linear model in combination with a permutation procedure and missing values imputation to conduct global tests in proteomics experiments. This new approach is motivated by protein expression data obtained by means of 2-D gel electrophoresis within a mouse experiment of our current research. A simulation study yielded that power and testing level of the mixed model alone can be affected by missing values in the dataset. Imputation of missing values was able to correct for a bias in some simulation settings. Our new approach provides the possibility to rank Gene Ontology (GO) terms associated with protein sets. It is also helpful in the case in which a specific protein is represented by multiple spots on a 2-D gel by considering these spots also as a protein set. Analysis of our data points at correlations between the deficiency of the protein ‘calreticulin’ and protein sets related to biological processes in the heart muscle.

Availability and implementation: Our proposed approach is included in the R-package ‘RepeatedHighDim’, which already contains a global test procedure for gene expression data. The package can be retrieved from http://cran.r-project.org/.

Contact: klaus.jung@ams.med.uni-goettingen.de
Bayesian joint analysis of heterogeneous genomics data
Authors: Ray Priyadip , Zheng Lingling , Lucas Joseph , Carin Lawrence
Published: February 2014

Summary: A non-parametric Bayesian factor model is proposed for joint analysis of multi-platform genomics data. The approach is based on factorizing the latent space (feature space) into a shared component and a data-specific component with the dimensionality of these components (spaces) inferred via a beta-Bernoulli process. The proposed approach is demonstrated by jointly analyzing gene expression/copy number variations and gene expression/methylation data for ovarian cancer patients, showing that the proposed model can potentially uncover key drivers related to cancer.

Availability and implementation: The source code for this model is written in MATLAB and has been made publicly available at https://sites.google.com/site/jointgenomics/

Contact:  catherine.ll.zheng@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Antibiotic stress-induced modulation of the endoribonucleolytic activity of RNase III and RNase G confers resistance to aminoglycoside antibiotics in Escherichia coli
Authors: Song Wooseok , Kim Yong-Hak , Sim Se-Hoon , Hwang Soonhye , Lee Jung-Hyun , Lee Younghoon , Bae Jeehyeon , Hwang Jihwan , Lee Kangseok
Published: February 2014

Here, we report a resistance mechanism that is induced through the modulation of 16S ribosomal RNA (rRNA) processing on the exposure of Escherichia coli cells to aminoglycoside antibiotics. We observed decreased expression levels of RNase G associated with increased RNase III activity on rng mRNA in a subgroup of E. coli isolates that transiently acquired resistance to low levels of kanamycin or streptomycin. Analyses of 16S rRNA from the aminoglycoside-resistant E. coli cells, in addition to mutagenesis studies, demonstrated that the accumulation of 16S rRNA precursors containing 3–8 extra nucleotides at the 5’ terminus, which results from incomplete processing by RNase G, is responsible for the observed aminoglycoside resistance. Chemical protection, mass spectrometry analysis and cell-free translation assays revealed that the ribosomes from rng-deleted E. coli have decreased binding capacity for, and diminished sensitivity to, streptomycin and neomycin, compared with wild-type cells. It was observed that the deletion of rng had similar effects in Salmonella enterica serovar Typhimurium strain SL1344. Our findings suggest that modulation of the endoribonucleolytic activity of RNase III and RNase G constitutes a previously uncharacterized regulatory pathway for adaptive resistance in E. coli and related gram-negative bacteria to aminoglycoside antibiotics.
Deletions in the highly polymorphic region (HPR) of infectious salmon anaemia virus HPR0 haemagglutinin–esterase enhance viral fusion and influence the interaction with the fusion protein
Authors: Fourrier Mickael , Lester Katherine , Thoen Even , Mikalsen Aase , Evensen Øystein , Falk Knut , Collet Bertrand , McBeath Alastair
Published: February 2014

Since the discovery of a non-virulent infectious salmon anaemia virus (ISAV) HPR0 variant, many studies have speculated on the functional role of deletions within the highly polymorphic region (HPR) of genomic segment 6, which codes for the haemagglutinin–esterase (HE) protein. To address this issue, mutant HE proteins with deletions in their HPR were generated from the Scottish HPR0 template (NWM10) and fusion-inducing activity was measured using lipid (octadecyl rhodamine B) and content mixing assays (firefly luciferase). Segment six HPR was found to have a strong influence on ISAV fusion, and deletions in this near-membrane region predominantly increased the fusion-inducing ability of the resulting HE proteins. The position and length of the HPR deletions were not significant factors, suggesting that they may affect fusion non-specifically. In comparison, the amino acid composition of the associated fusion (F) protein was a more crucial criterion. Antibody co-patching and confocal fluorescence demonstrated that the HE and F proteins were highly co-localized, forming defined clusters on the cell surface post-transfection. The binding of erythrocyte ghosts on the attachment protein caused a reduction in the percentage of co-localization, suggesting that ISAV fusion might be triggered through physical separation of the F and HE proteins. In this process, HPR deletion appeared to modulate and reduce the strength of interaction between the two glycoproteins, causing more F protein to be released and activated. This work provides a first insight into the mechanism of virulence acquisition through HPR deletion, with fusion enhancement acting as a major contributing factor.
Whole-genome analysis of bovine rotavirus species C isolates obtained in Yamagata, Japan, 2003–2010
Authors: Mawatari Takahiro , Hirano Kaori , Tsunemitsu Hiroshi , Suzuki Tohru
Published: February 2014

An epidemic of diarrhoea in adult cows occurred at a total of 105 dairy farms in Yamagata Prefecture, Japan, between 2003 and 2010. Reverse transcription-PCR diagnostic tests revealed the presence of bovine rotavirus species C (RVCs) in samples from each of six farms (5.7 %). In this study, we determined the full-length nucleotide sequences of 11 RNA segments from six bovine RVC strains and investigated genetic diversity among them, including two bovine RVC strains identified in a previous study. Comparisons of all segmental nucleotide and the deduced amino acid sequences among bovine RVCs indicated high identities across all genes except for the VP4 gene. Phylogenetic analysis of each gene revealed that the six bovine RVCs belonged to a bovine cluster distinct from human and porcine RVCs. Bovine RVC strains could be clearly divided into two lineages of the VP4 genes. The nucleotide sequence identity for VP4 genes between lineage I and II was 83.7–84.8 %. Moreover, bovine RVC strains belonging to lineage I exhibited one amino acid deletion and three amino acid insertions, which differed for those strains belonging to lineage II. Our data suggest that multiple bovine RVCs originated from a common ancestor, but had different genetic backgrounds, not only in Yamagata Prefecture but also in the rest of Japan.
Activation of MAPK overrides the termination of myelin growth and replaces Nrg1/ErbB3 signals during Schwann cell development and myelination
Authors: Sheean Maria E. , McShane Erik , Cheret Cyril , Walcher Jan , Müller Thomas , Wulf-Goldenberg Annika , Hoelper Soraya , Garratt Alistair N. , Krüger Markus , Rajewsky Klaus , Meijer Dies , Birchmeier Walter , Lewin Gary R. , Selbach Matthias , Birchmeier Carmen
Published: February 2014

Myelination depends on the synthesis of large amounts of myelin transcripts and proteins and is controlled by Nrg1/ErbB/Shp2 signaling. We developed a novel pulse labeling strategy based on stable isotope labeling with amino acids in cell culture (SILAC) to measure the dynamics of myelin protein production in mice. We found that protein synthesis is dampened in the maturing postnatal peripheral nervous system, and myelination then slows down. Remarkably, sustained activation of MAPK signaling by expression of the Mek1DD allele in mice overcomes the signals that end myelination, resulting in continuous myelin growth. MAPK activation leads to minor changes in transcript levels but massively up-regulates protein production. Pharmacological interference in vivo demonstrates that the effects of activated MAPK signaling on translation are mediated by mTOR-independent mechanisms but in part also by mTOR-dependent mechanisms. Previous work demonstrated that loss of ErbB3/Shp2 signaling impairs Schwann cell development and disrupts the myelination program. We found that activated MAPK signaling strikingly compensates for the absence of ErbB3 or Shp2 during Schwann cell development and myelination.
Assay of Ca2+ Transport by VDAC1 Reconstituted into Liposomes
Authors: Ben-Hail Danya , Shoshan-Barmatz Varda
Published: February 2014

Ca2+ permeability mediated by voltage-dependent anion-selective channel protein 1 (VDAC1) can be tested by reconstitution of purified VDAC1 into liposomes. Here, we describe a setup for this membranal system, which has been used to study the transport activity of various transporters, including VDAC1, and allows detection of the passage of molecules across the lipid bilayer. Despite the disadvantage of needing radiolabeled molecules, this system is highly desirable when the transport properties of noncharged molecules and/or active transporters are studied.
Assays of Mitochondrial Ca2+ Transport and Ca2+ Efflux via the MPTP
Authors: Ben-Hail Danya , Shoshan-Barmatz Varda
Published: February 2014

Studying Ca2+ transport in mitochondria in connection with energy production, as well as cell death, is of great importance. Ca2+ activates several key enzymes in the mitochondrial matrix to enhance ATP production. This provides an important mechanism for synchronizing energy production with the energy demands of Ca2+-activated processes, such as contraction, allowing important feedback effects to help shape cytosolic Ca2+ signals. A rise in mitochondrial Ca2+ can convey both apoptotic and necrotic death signals by inducing opening of the mitochondrial permeability transition pore (MPTP). Here, we present a protocol for measuring Ca2+ transport and release in isolated mitochondria.
Scanning Microarray Slides
Authors: Ares Manuel
Published: February 2014

Here we describe some practical concerns surrounding the scanning of microarray slides that have been hybridized with fluorescent dyes. We use a laser scanner that has two lasers, each set to excite a different fluor, and separate detectors to capture emission from each fluor. The laser passes over an address (position on the scanned surface) and the detectors capture photons emitted from each address. Two superimposed image files are written that carry intensities for each channel for each pixel of the image scan. These are the raw data. Image analysis software is used to identify and summarize the intensities of the pixels that make up each spot. After comparison to background pixels, the processed intensity levels representing the gene expression measurements are associated with the identity of each spot.
Tips on Hybridizing, Washing, and Scanning Affymetrix Microarrays
Authors: Ares Manuel
Published: February 2014

Starting in the late 1990s, Affymetrix, Inc. produced a commercial system for hybridizing, washing, and scanning microarrays that was designed to be easy to operate and reproducible. The system used arrays packaged in a plastic cassette or chamber in which the prefabricated array was mounted and could be filled with fluid through resealable membrane ports either by hand or by an automated “fluidics station” specially designed to handle the arrays. A special rotating hybridization oven and a specially designed scanner were also required. Primarily because of automation and standardization the Affymetrix system was and still remains popular. Here, we provide a skeleton protocol with the potential pitfalls identified. It is designed to augment the protocols provided by Affymetrix.
Methods for Processing Microarray Data
Authors: Ares Manuel
Published: February 2014

Quality control must be maintained at every step of a microarray experiment, from RNA isolation through statistical evaluation. Here we provide suggestions for analyzing microarray data. Because the utility of the results depends directly on the design of the experiment, the first critical step is to ensure that the experiment can be properly analyzed and interpreted. What is the biological question? What is the best way to perform the experiment? How many replicates will be required to obtain the desired statistical resolution? Next, the samples must be prepared, pass quality controls for integrity and representation, and be hybridized and scanned. Also, slides with defects, missing data, high background, or weak signal must be rejected. Data from individual slides must be normalized and combined so that the data are as free of systematic bias as possible. The third phase is to apply statistical filters and tests to the data to determine genes (1) expressed above background, (2) whose expression level changes in different samples, and (3) whose RNA-processing patterns or protein associations change. Next, a subset of the data should be validated by an alternative method, such as reverse transcription–polymerase chain reaction (RT–PCR). Provided that this endorses the general conclusions of the array analysis, gene sets whose expression, splicing, polyadenylation, protein binding, etc. change in different samples can be classified with respect to function, sequence motif properties, as well as other categories to extract hypotheses for their biological roles and regulatory logic.
Differential Methylation during Maize Leaf Growth Targets Developmentally Regulated Genes
Authors: Candaele Jasper , Demuynck Kirin , Mosoti Douglas , Beemster Gerrit T.S. , Inzé Dirk , Nelissen Hilde
Published: February 2014

DNA methylation is an important and widespread epigenetic modification in plant genomes, mediated by DNA methyltransferases (DMTs). DNA methylation is known to play a role in genome protection, regulation of gene expression, and splicing and was previously associated with major developmental reprogramming in plants, such as vernalization and transition to flowering. Here, we show that DNA methylation also controls the growth processes of cell division and cell expansion within a growing organ. The maize (Zea mays) leaf offers a great tool to study growth processes, as the cells progressively move through the spatial gradient encompassing the division zone, transition zone, elongation zone, and mature zone. Opposite to de novo DMTs, the maintenance DMTs were transcriptionally regulated throughout the growth zone of the maize leaf, concomitant with differential CCGG methylation levels in the four zones. Surprisingly, the majority of differentially methylated sequences mapped on or close to gene bodies and not to repeat-rich loci. Moreover, especially the 5′ and 3′ regions of genes, which show overall low methylation levels, underwent differential methylation in a developmental context. Genes involved in processes such as chromatin remodeling, cell cycle progression, and growth regulation, were differentially methylated. The presence of differential methylation located upstream of the gene anticorrelated with transcript expression, while gene body differential methylation was unrelated to the expression level. These data indicate that DNA methylation is correlated with the decision to exit mitotic cell division and to enter cell expansion, which adds a new epigenetic level to the regulation of growth processes.
Insights into the Maize Pan-Genome and Pan-Transcriptome
Authors: Hirsch Candice N. , Foerster Jillian M. , Johnson James M. , Sekhon Rajandeep S. , Muttoni German , Vaillancourt Brieanne , Peñagaricano Francisco , Lindquist Erika , Pedraza Mary Ann , Barry Kerrie , de Leon Natalia , Kaeppler Shawn M. , Buell C. Robin
Published: February 2014

Genomes at the species level are dynamic, with genes present in every individual (core) and genes in a subset of individuals (dispensable) that collectively constitute the pan-genome. Using transcriptome sequencing of seedling RNA from 503 maize (Zea mays) inbred lines to characterize the maize pan-genome, we identified 8681 representative transcript assemblies (RTAs) with 16.4% expressed in all lines and 82.7% expressed in subsets of the lines. Interestingly, with linkage disequilibrium mapping, 76.7% of the RTAs with at least one single nucleotide polymorphism (SNP) could be mapped to a single genetic position, distributed primarily throughout the nonpericentromeric portion of the genome. Stepwise iterative clustering of RTAs suggests, within the context of the genotypes used in this study, that the maize genome is restricted and further sampling of seedling RNA within this germplasm base will result in minimal discovery. Genome-wide association studies based on SNPs and transcript abundance in the pan-genome revealed loci associated with the timing of the juvenile-to-adult vegetative and vegetative-to-reproductive developmental transitions, two traits important for fitness and adaptation. This study revealed the dynamic nature of the maize pan-genome and demonstrated that a substantial portion of variation may lie outside the single reference genome for a species.
GLUTELIN PRECURSOR ACCUMULATION3Encodes a Regulator of Post-Golgi Vesicular Traffic Essential for Vacuolar Protein Sorting in Rice Endosperm
Authors: Ren Yulong , Wang Yihua , Liu Feng , Zhou Kunneng , Ding Yu , Zhou Feng , Wang Ying , Liu Kai , Gan Lu , Ma Weiwei , Han Xiaohua , Zhang Xin , Guo Xiuping , Wu Fuqing , Cheng Zhijun , Wang Jiulin , Lei Cailin , Lin Qibing , Jiang Ling , Wu Chuanyin , Bao Yiqun , Wang Haiyang , Wan Jianmin
Published: February 2014

In seed plants, a major pathway for sorting of storage proteins to the protein storage vacuole (PSV) depends on the Golgi-derived dense vesicles (DVs). However, the molecular mechanisms regulating the directional trafficking of DVs to PSVs remain largely elusive. Here, we report the functional characterization of the rice (Oryza sativa) glutelin precursor accumulation3 (gpa3) mutant, which exhibits a floury endosperm phenotype and accumulates excess proglutelins in dry seeds. Cytological and immunocytochemistry studies revealed that in the gpa3 mutant, numerous proglutelin-containing DVs are misrouted to the plasma membrane and, via membrane fusion, release their contents into the apoplast to form a new structure named the paramural body. Positional cloning of GPA3 revealed that it encodes a plant-specific kelch-repeat protein that is localized to the trans-Golgi networks, DVs, and PSVs in the developing endosperm. In vitro and in vivo experiments verified that GPA3 directly interacts with the rice Rab5a-guanine exchange factor VPS9a and forms a regulatory complex with Rab5a via VPS9a. Furthermore, our genetic data support the notion that GPA3 acts synergistically with Rab5a and VPS9a to regulate DV-mediated post-Golgi traffic in rice. Our findings provide insights into the molecular mechanisms regulating the plant-specific PSV pathway and expand our knowledge of vesicular trafficking in eukaryotes.
Asherman syndrome in a Danish population
Authors: Kjer Jens J.
Published: February 2014

Intrauterine adhesions (Asherman syndrome) are rare and mainly seen after delivery or abortion in the presence of retained placental tissue. This descriptive study aimed to identify common risk factors for intrauterine adhesions. In a 10‐year period 61 women were identified with intrauterine adhesions. The pathology was suspected from symptoms, ultrasonography or on hysterosalpingography, but a final diagnosis could only be given after hysteroscopy. There was no definite evidence regarding methods for prevention and treatment of the disorder. It seems, however, that a conservative approach to curettage, hysteroscopic removal of retained tissue, and the use of distending media are important, together with gentle tissue handling when such procedures are required.
Antisecretory factor effectively and safely stops childhood diarrhoea: a placebo‐controlled, randomised study
Authors: Zaman Shakila , Aamir Khalida , Lange Stefan , Jennische Eva , Silfverdal Sven‐Arne , Hanson Lars Å
Published: February 2014

Aim

We studied the response to high doses of egg yolk containing antisecretory factor (B221®, Salovum®) in young children with acute diarrhoea, presenting to the Children's Hospital, Lahore, Pakistan.

Methods

In a randomised, placebo‐controlled trial, 36 children aged 7 to 60 months with acute diarrhoea of unknown aetiology, with mild‐to‐moderate dehydration, were randomised to the Salovum® or placebo groups. Initially, 16 grams of Salovum® or ordinary egg yolk (placebo) mixed in oral rehydration salts was given, followed by 8 g every 5 h until recovery. The number and consistency of stools were recorded.

Results

The two groups were comparable in age, gender, duration of diarrhoea, hydration and nutritional status, although the proportion with watery stools was higher in the Salovum® group (p = 0.04). Reduction in the frequency of stools was seen at 7 versus 18 h (p < 0.0001) and normalising of stool consistency was 10 versus 18 h, p < 0.03) in the Salovum® and placebo groups. The overall effect was 35 versus 70 h in the two groups (p = 0.001). No side effects were reported.

Conclusion

High doses of AF in the form of Salovum® effectively and safely reduce childhood diarrhoea of a likely broad aetiology.
Effectiveness of Local Governance: Interactions Between Social Capital and Institutional Structures
Authors: Udayaadithya Avadhanam , Gurtoo Anjula
Published: February 2014

This paper critically evaluates the debate on what makes local governments more effective, higher social capital (such as trust, reciprocity, and informal social networks) or stronger institutional structures (such as democratic processes, ombudsman, and social audits). Empirical analysis of a decentralized welfare scheme in India, the Andhra Pradesh Rural Employment Guarantee Scheme (APREGS), using the latent variable path analysis modeling approach reveals that creation of formal democratic institutional channels in itself does not impact governance performance. Rather, it is mediated by complex institutional and social capital issues. For example, formal information dissemination activates social capital, leading to effective local governance. However, this (higher social capital and better institutions) does not automatically lead to empowerment or trust in the local government. The influence of the economically and politically powerful mediates this relationship. These and other results, cumulatively, highlight the complexity involved in the effectiveness of government empowerment initiatives. The paper calls for a fresh and wider debate on decision‐making dynamics in rural India, especially the interaction between government institutions, social capital, and the historical societal dynamics.
Fitting direct covariance structures by the MSTRUCT modeling language of the CALIS procedure
Authors: Yung Yiu‐Fai , Browne Michael W. , Zhang Wei
Published: February 2014

This paper demonstrates the usefulness and flexibility of the general structural equation modelling (SEM) approach to fitting direct covariance patterns or structures (as opposed to fitting implied covariance structures from functional relationships among variables). In particular, the MSTRUCT modelling language (or syntax) of the CALIS procedure (SAS/STAT version 9.22 or later: SAS Institute, 2010) is used to illustrate the SEM approach. The MSTRUCT modelling language supports a direct covariance pattern specification of each covariance element. It also supports the input of additional independent and dependent parameters. Model tests, fit statistics, estimates, and their standard errors are then produced under the general SEM framework. By using numerical and computational examples, the following tests of basic covariance patterns are illustrated: sphericity, compound symmetry, and multiple‐group covariance patterns. Specification and testing of two complex correlation structures, the circumplex pattern and the composite direct product models with or without composite errors and scales, are also illustrated by the MSTRUCT syntax. It is concluded that the SEM approach offers a general and flexible modelling of direct covariance and correlation patterns. In conjunction with the use of SAS macros, the MSTRUCT syntax provides an easy‐to‐use interface for specifying and fitting complex covariance and correlation structures, even when the number of variables or parameters becomes large.
Feeling Good, Happy, and Proud: A Meta‐Analysis of Positive Ethnic–Racial Affect and Adjustment
Authors: Rivas‐Drake Deborah , Syed Moin , Umaña‐Taylor Adriana , Markstrom Carol , French Sabine , Schwartz Seth J. , Lee Richard ,   Ethnic and Racial Identity in the 21st Century Study Group
Published: February 2014

One point of intersection in ethnic and racial identity research is the conceptual attention paid to how positively youth feel about their ethnicity or race, or positive ethnic–racial affect. This article reports results of a series of meta‐analyses based on 46 studies of this dimension and psychosocial, academic, and health risk outcomes among ethnic and racial minority youth. The overall pattern of results suggests that positive ethnic–racial affect exhibited small to medium associations (r range = |.11| to |.37|) with depressive symptoms, positive social functioning, self‐esteem, well‐being, internalizing, externalizing, academic achievement, academic attitudes, and health risk outcomes. Implications for theory and research about the role of positive ethnic–racial affect among youth growing up in an increasingly diverse society are discussed.
Methodological Issues in Ethnic and Racial Identity Research With Ethnic Minority Populations: Theoretical Precision, Measurement Issues, and Research Designs
Authors: Schwartz Seth J. , Syed Moin , Yip Tiffany , Knight George P. , Umaña‐Taylor Adriana J. , Rivas‐Drake Deborah , Lee Richard M.
Published: February 2014

This article takes stock of research methods employed in the study of racial and ethnic identity with ethnic minority populations. The article is presented in three parts. The first section reviews theories, conceptualizations, and measurement of ethnic and racial identity (ERI) development. The second section reviews theories, conceptualizations, and measurement of ERI content. The final section reviews key methodological and analytic principles that are important to consider for both ERI development and content. The article concludes with suggestions for future research addressing key methodological limitations when studying ERI.
Developmental States in Africa? A Review of Ongoing Debates and Buzzwords
Authors: Routley Laura
Published: February 2014

This article reviews the literature concerning the emergence of developmental states in Africa and gives an overview of debates on the usefulness of the ‘East Asian model’ for sub‐Saharan Africa. The conclusion highlights how historic developmental states were often the product of trial and error rather than a grand plan; the concept of a developmental state therefore often works less as a model and more as a ‘buzzword’ with its own uses and effects.
Brazil and the Shifting Consensus on Development Co‐operation: Salutary Diversions from the ‘Aid‐effectiveness’ Trail?
Authors: Cabral Lídia , Russo Giuliano , Weinstock Julia
Published: February 2014

Emerging economies emphasise horizontality and mutual opportunity in their relationship with developing countries, promising an alternative to the failings of traditional North‐South co‐operation. This article draws on research on Brazil's technical co‐operation and its health dimension to compare the Brazilian model with established aid‐effectiveness' principles and to discuss the appropriateness of the latter as standards against which to appraise emerging donors' co‐operation. The analysis shows that, despite progress towards greater dialogue between traditional and emerging donors, the ‘aid‐effectiveness’ framework still falls short of capturing the idiosyncrasies of South‐South co‐operation and therefore offers an incomplete international standard on how best to conduct development co‐operation.
Bringing the Citizen Back In: Supporting Decentralisation in Fragile States ‐ A View from Burundi
Authors: Gaynor Niamh
Published: February 2014

While, in theory, decentralisation offers many benefits, empirical evidence of these benefits remains limited. Drawing on fieldwork conducted in Burundi in 2011, this article argues that the current donor emphasis on institution‐building alone proves insufficient. Evidence is presented to show that current support, while consolidating the authority of local political elites, reinforces political and horizontal inequalities, thereby paving the way for further disaffection and conflict. Reflecting back to the initial aims of the process, a re‐orientation is proposed, moving the focus of support beyond elite state actors and institutions and bringing citizens back into the process of state building and transformation.
Improving the Measurement of the Relationship between Opportunities and Income: Evidence from Longitudinal Data from Chile
Authors: Contreras Dante , Larrañaga Osvaldo , Puentes Esteban , Rau Tomás
Published: February 2014

The relationship between exogenous circumstances faced in early childhood (opportunities) and earnings has been increasingly studied in the past decade. In this article we assess the sensitivity of this relationship to different income measures. Typically the empirical evidence is based on short‐term income measures that suffer from variability and measurement error. Using longitudinal data from Chile, we find that when four‐ and seven‐year earnings are used, the relationship between inequality of opportunity and income inequality is significantly higher than that obtained with yearly measures. Monte Carlo simulations with several data‐generating processes confirm this result. This supports policies targeted to reduce long‐term income inequality via providing equal opportunity to individuals at early stages in life.
Validating a script concordance test for assessing neurological localization and emergencies
Authors: Tan K. , Tan N. C. K. , Kandiah N. , Samarasekera D. , Ponnamperuma G.
Published: February 2014

Background and purpose

Clinical judgment is the ability to weigh clinical information and make decisions under conditions of uncertainty. Although neurological localization (NL) and neurological emergencies (NE) present such uncertainties, no validated method is reported to assess these decision‐making skills. A script concordance test (SCT) was designed and validated to assess clinical judgment in NL and NE.

Methods

Our SCT comprised 14 clinical scenarios (53 questions). Candidates picked the response they considered the best for the questions in each scenario. Undergraduates and internal medicine residents completed the SCT; their responses were scored against the scoring key derived from an expert panel of accredited neurologists. Scores were expressed as a percentage of the maximum score.

Results

Mean total scores for undergraduates (n = 52), residents (n = 37) and experts (n = 15) were 61.0 ± 0.9, 68.3 ± 1.1 and 76.6 ± 1.1 (mean ± standard error of the mean, P < 0.001). Mean scores for undergraduates, residents and experts were 59.3 ± 1.1, 66.4 ± 1.4 and 76.1 ± 1.8 (P < 0.001) for NL, and 62.9 ± 1.3, 70.4 ± 1.3 and 77.2 ± 1.6 (P < 0.001) for NE. Senior residents scored higher than junior residents (postgraduate years 2–5 versus postgraduate year 1, 69.7 ± 1.4 vs. 65.3 ± 1.1, P = 0.035). The higher scores with increasing clinical experience supports the construct validity of the SCT. The SCT showed acceptable reliability (G coefficient 0.74 ± 0.05).

Conclusions

Our SCT is validated to reliably assess NL and NE in undergraduate and postgraduate learners; it is generalizable and feasible. It has potential as a valuable adjunct assessment tool for clinical judgment. Future plans to design SCTs to evaluate other topics in clinical neurology, as a multi‐center study, are under way.
Ending overfishing while catching more fish
Authors: Zhou Shijie , Smith Anthony DM , Knudsen E Eric
Published: February 2014

The world's seas and oceans are a vital source of animal protein from fishing and a major contributor to global food security. It has been argued that global wild‐catch production has reached its limit, and there is concern that many species are overfished. Concerns are also mounting about the state of marine ecosystems and the ecological impacts of fishing on them, with increasing efforts to protect marine biodiversity. Fisheries appear to be at an impasse – demand for seafood is rising but so is concern about the impacts of fishing. However, through a simple analysis, we show that global exploitation rates are well below long‐term sustainable levels at a whole ecosystem level. The oceans can support considerably higher sustainable catch than currently harvested. Overfishing has happened but only to a small fraction of species as a result of intensive and selective fishing. Shifting fishing effort away from highly targeted stocks towards currently underutilized species would reduce pressure on overfished species, result in fewer adverse ecosystem effects of fishing and increase overall fisheries production. This shift requires significant changes to our views about seafood, particularly in the developed world. We suggest ways in which this paradigm shift could happen and the range of expertise that would be required to achieve higher global yields with less ecological impact.
Global warming will reshuffle the areas of high prevalence and richness of three genera of avian blood parasites
Authors: Pérez‐Rodríguez Antón , de la Hera Iván , Fernández‐González Sofía , Pérez‐Tris Javier
Published: February 2014

The importance of parasitism for host populations depends on local parasite richness and prevalence: usually host individuals face higher infection risk in areas where parasites are most diverse, and host dispersal to or from these areas may have fitness consequences. Knowing how parasites are and will be distributed in space and time (in a context of global change) is thus crucial from both an ecological and a biological conservation perspective. Nevertheless, most research articles focus just on elaborating models of parasite distribution instead of parasite diversity. We produced distribution models of the areas where haemosporidian parasites are currently highly diverse (both at community and at within‐host levels) and prevalent among Iberian populations of a model passerine host: the blackcapSylvia atricapilla; and how these areas are expected to vary according to three scenarios of climate change. On the basis of these models, we analysed whether variation among populations in parasite richness or prevalence are expected to remain the same or change in the future, thereby reshuffling the geographic mosaic of host‐parasite interactions as we observe it today. Our models predict a rearrangement of areas of high prevalence and richness of parasites in the future, withHaemoproteusandLeucocytozoonparasites (today the most diverse genera in blackcaps) losing areas of high diversity andPlasmodiumparasites (the most virulent ones) gaining them. Likewise, the prevalence of multiple infections and parasite infracommunity richness would be reduced. Importantly, differences among populations in the prevalence and richness of parasites are expected to decrease in the future, creating a more homogeneous parasitic landscape. This predicts an altered geographic mosaic of host‐parasite relationships, which will modify the interaction arena in which parasite virulence evolves.
A commentary on ‘Mineral soil carbon fluxes in forests and implications for carbon balance assessments’: a deeper look at the data
Authors: Hoover Coeli M. , Heath Linda S.
Published: February 2014

Forestry practitioners contacted us with their concerns about a recent review article by Buchholz T, Friedland AJ, Hornig CE, Keeton WS, Zanchi G, Nunery J (2013) GCB Bioenergy who questioned the way soil carbon is treated in many models and protocols, and indicated that an increasing number of research studies showed meaningful soil organic carbon (SOC) loss as a result of forest management. We revisit the major studies cited in the review and present a more complete look at the results, consistently treat forest floor carbon as a separate pool, discuss differences in interpretation, and suggest opportunities to advance the state of knowledge regarding SOC and forest carbon accounting. Overall, we conclude that the literature continues to support the current default assumption of little or no change in mineral SOC when sound forest management practices are followed.
Taxonomic identity of Musa cheesmanii (Musaceae) in northeast India
Authors: Gogoi Rajib , Häkkinen Markku , Borah Souravjyoti , Satyanarayana P.
Published: February 2014

The taxonomic identity of Musa cheesmanii N. W. Simmonds (1956a) has been uncertain to most botanists and the species has commonly been wrongly identified as M. nagensium Prain. The aim of this study is to settle the true identity of the species and provide a revised description and colored photo illustrations. Colored photo illustrations of two varieties of M. nagensium are also included to avoid misidentifications with M. cheesmanii. A key to closely related species is provided. The study is based on morphological characters observed in the field in northeast India, in various herbaria and supported by relevant literature.
Artificial Sinks: Opportunities and Challenges for Managing Offsite Nitrogen Losses
Authors: Gold Arthur J. , Addy Kelly , David Mark B. , Schipper Louis A. , Needelman Brian A.
Published: February 2014

Advanced control measures are needed after nitrogen (N) leaves agricultural fields and begins to flow through a catchment. Bioreactors – simple, wood‐chip filled trenches – and constructed wetlands afford additional treatment to reduce N from agricultural lands, but their success requires informed adoption and placement. Rates of N removal in field studies of bioreactors vary based on carbon substrate, hydrologic setting, temperature, N loading and hydraulic residence time. From limited measures in constructed wetlands, N removal can be substantial and influenced by seasonality. Additional research is needed to understand uncertainty and variability associated with these systems. Further synthesis of data from research and demonstration sites combined with geospatial tools will help guide the design and siting of these systems at regional and local scales. Professional and student training and web‐based data information exchange will advance the adoption and strategic placement of appropriate bioreactor and constructed wetland designs to remove edge‐of‐field N contributions.
Texas High Plains Initiative for Strategic and Innovative Irrigation Management and Conservation
Authors: Weinheimer Justin , Johnson Phillip , Mitchell Donna , Johnson Jeff , Kellison Rick
Published: February 2014

The strategic management of irrigation applications to improve water‐use efficiency and meet economic objectives has been identified as a key factor in the conservation of water resources in the Texas High Plains region. Two field level demonstration projects have been ongoing in the Texas High Plains to evaluate advantages and disadvantages of irrigation water conservation methods. Since 2010, the North Plains Groundwater Conservation District has evaluated corn production using 12 acre‐inches or less of applied irrigation water with a goal to produce 200 bushels per acre. In the South Plains, the Texas Alliance for Water Conservation (TAWC) has worked directly with 24 producers in Hale and Floyd Counties on 29 sites over the past seven years to monitor water use, soil moisture, crop productivity and economic returns on various cropping systems on over 4,000 acres. Both of these demonstration projects take an innovative approach to strategic irrigation management that uses new technologies with an overall goal to practice water conservation while maintaining economic profitability.