bluuebunny/crossref_metadata_2025 huggingface dataset:
Using Redd Attributes, Fry Density, and Otolith Microchemistry to Distinguish the Presence of Steelhead and Rainbow Trout in the Elwha River Dam Removal Project
Authors: McMillan John R. , Pess George R. , Liermann Martin , Morley Sarah A. , McHenry Michael L. , Campbell Lance A. , Quinn Thomas P.
Published: October 2015

The removal of impassable dams can affect stream fish communities in many ways, including allowing previously separated anadromous and resident life history types to intermingle. Recolonization of steelhead Oncorhynchus mykiss (anadromous Rainbow Trout) into areas that were previously occupied solely by resident conspecifics presents a challenge for monitoring because (1) staging or spawning adults may be difficult to directly observe; and (2) the offspring of the two life history forms are indistinguishable during early life. We evaluated the utility of using redd attributes, fry (age-0) size, and fry density to distinguish the presence of steelhead and Rainbow Trout in the Elwha River, Washington. Redd area and substrate size differed between forms: steelhead redds were significantly larger and had a greater median substrate particle size than Rainbow Trout redds. Fry density was significantly higher in steelhead spawning reaches than in Rainbow Trout reaches during both survey years (2010 and 2011). Steelhead fry tended to be slightly larger than Rainbow Trout fry but not significantly so in either year. Additionally, otolith microchemical analyses indicated that all fry collected from newly colonized habitat were of steelhead maternal origin, and these fish were intermediate in size to the steelhead and Rainbow Trout fry collected prior to dam removal. Thus, fry size may not effectively differentiate parental origin despite the tendency of anadromous parents to be larger and to spawn earlier than residents. Redd attributes and fry density may be useful for evaluating the spatial distributions and relative abundances of steelhead and Rainbow Trout after dam removal. Our results have implications for other dam removal projects and other monitored species.

Received April 13, 2015; accepted July 3, 2015
Identification of a characteristic antioxidant, anthrasesamone F, in black sesame seeds and its accumulation at different seed developmental stages
Authors: Furumoto Toshio , Nishimoto Kiyoshi
Published: October 2015

Assay-guided fractionation of the methanol extract from black seeds of sesame (Sesamum indicum L.) led to the isolation of an active compound that had a 1,1-diphenyl-2-picrylhydrazyl radical scavenging activity. This antioxidant was confirmed to be anthrasesamone F, an anthraquinone derivative previously isolated from different black sesame seeds and biogenetically related to other anthrasesamones in sesame roots. The radical scavenging assay showed that anthrasesamone F had more potent activity than Trolox. The content of anthrasesamone F in different parts and at different developmental stages of black sesame seeds was investigated to clarify the accumulation pattern of this antioxidant in the black seeds. Anthrasesamone F was localized in the seed coat of black seeds and accumulated after the seed coat color changed to black. The content of anthrasesamone F increased gradually with seed maturation and drastically on air-drying, the final stage in sesame cultivation.
Induced Spawning and Larval Culture of Golden Trevally
Authors: Broach Jason S , Ohs Cortney L , Palau Andrew , Danson Bryan , Elefante Daniel
Published: October 2015

The Golden Trevally Gnathanodon speciosus is a popular sport, food, and ornamental fish native to the tropical Indo-Pacific region, yet there is little information regarding aquaculture technologies. A group of Golden Trevally broodfish was acquired from a local public aquarium in an effort to attempt captive spawning and larval culture. Broodfish were held in 4,500-L recirculating aquaculture systems and conditioned on a mixed diet of squid, capelin, and krill. Once water temperatures were averaging 26°C, Ovaplant was administered to mature broodfish (six males, two females) in one of the systems. Broodfish spawned on three separate occasions after this hormone administration, releasing probably 35,000 eggs/female during each spawn. Fertile eggs from two of these spawns were used for larval culture attempts. Larvae were stocked into five 104-L tanks at densities up to 173 larvae/L. Throughout larval culture trials, larvae were fed a combination of copepod nauplii, enriched rotifers, Artemia nauplii, and a dry diet, and the tank water was inoculated with live Tahitian strain Isochrysis galbana up to 26 d posthatch (dph). Larvae achieved complete metamorphosis around 30 dph. By 45 dph, nearly 4.3% of the larvae initially stocked survived and reached about 3.7 cm in length. These successful spawning induction and larval culture trials are promising for future development of a commercial-level production industry for Golden Trevally.
Chordal Komatu-Loewner equation and Brownian motion with darning in multiply connected domains
Authors: Chen Zhen-Qing , Fukushima Masatoshi , Rohde Steffen
Published: October 2015

Let

D
=

H

∖

⋃

k
=
1

N

C
k

D={\mathbb H} \setminus \bigcup _{k=1}^N C_k

be a standard slit domain where

H

\mathbb H

is the upper half-plane and

C
k

C_k

,

1
≤
k
≤
N

1\leq k\leq N

, are mutually disjoint horizontal line segments in

H

\mathbb {H}

. Given a Jordan arc

γ
⊂
D

\gamma \subset D

starting at

∂

H

,

\partial {\mathbb H},

let

g
t

g_t

be the unique conformal map from

D
∖
γ
[
0
,
t
]

D\setminus \gamma [0,t]

onto a standard slit domain

D
t

D_t

satisfying the hydrodynamic normalization. We prove that

g
t

g_t

satisfies an ODE with the kernel on its right-hand side being the complex Poisson kernel of the Brownian motion with darning (BMD) for

D
t

D_t

, generalizing the chordal Loewner equation for the simply connected domain

D
=

H

.

D={\mathbb H}.

Such a generalization has been obtained by Y. Komatu in the case of circularly slit annuli and by R. O. Bauer and R. M. Friedrich in the present chordal case, but only in the sense of the left derivative in

t
t

. We establish the differentiability of

g
t

g_t

in

t
t

to make the equation a genuine ODE. To this end, we first derive the continuity of

g
t

(
z
)

g_t(z)

in

t
t

with a certain uniformity in

z
z

from a probabilistic expression of

ℑ

g
t

(
z
)

\Im g_t(z)

in terms of the BMD for

D
D

, which is then combined with a Lipschitz continuity of the complex Poisson kernel under the perturbation of standard slit domains to get the desired differentiability.
JEPEGMIX: gene-level joint analysis of functional SNPs in cosmopolitan cohorts
Authors: Lee Donghyung , Williamson Vernell S. , Bigdeli T. Bernard , Riley Brien P. , Webb Bradley T. , Fanous Ayman H. , Kendler Kenneth S. , Vladimirov Vladimir I. , Bacanu Silviu-Alin
Published: October 2015

Motivation: To increase detection power, gene level analysis methods are used to aggregate weak signals. To greatly increase computational efficiency, most methods use as input summary statistics from genome-wide association studies (GWAS). Subsequently, gene statistics are constructed using linkage disequilibrium (LD) patterns from a relevant reference panel. However, all methods, including our own Joint Effect on Phenotype of eQTL/functional single nucleotide polymorphisms (SNPs) associated with a Gene (JEPEG), assume homogeneous panels, e.g. European. However, this renders these tools unsuitable for the analysis of large cosmopolitan cohorts.

Results: We propose a JEPEG extension, JEPEGMIX, which similar to one of our software tools, Direct Imputation of summary STatistics of unmeasured SNPs from MIXed ethnicity cohorts, is capable of estimating accurate LD patterns for cosmopolitan cohorts. JEPEGMIX uses this accurate LD estimates to (i) impute the summary statistics at unmeasured functional variants and (ii) test for the joint effect of all measured and imputed functional variants which are associated with a gene. We illustrate the performance of our tool by analyzing the GWAS meta-analysis summary statistics from the multi-ethnic Psychiatric Genomics Consortium Schizophrenia stage 2 cohort. This practical application supports the immune system being one of the main drivers of the process leading to schizophrenia.

Availability and implementation: Software, annotation database and examples are available at http://dleelab.github.io/jepegmix/.

Contact:  donghyung.lee@vcuhealth.org

Supplementary information:  Supplementary material is available at Bioinformatics online.
Generalized empirical Bayesian methods for discovery of differential data in high-throughput biology
Authors: Hardcastle Thomas J.
Published: October 2015

Motivation: High-throughput data are now commonplace in biological research. Rapidly changing technologies and application mean that novel methods for detecting differential behaviour that account for a ‘large P, small n’ setting are required at an increasing rate. The development of such methods is, in general, being done on an ad hoc basis, requiring further development cycles and a lack of standardization between analyses.

Results: We present here a generalized method for identifying differential behaviour within high-throughput biological data through empirical Bayesian methods. This approach is based on our baySeq algorithm for identification of differential expression in RNA-seq data based on a negative binomial distribution, and in paired data based on a beta-binomial distribution. Here we show how the same empirical Bayesian approach can be applied to any parametric distribution, removing the need for lengthy development of novel methods for differently distributed data. Comparisons with existing methods developed to address specific problems in high-throughput biological data show that these generic methods can achieve equivalent or better performance. A number of enhancements to the basic algorithm are also presented to increase flexibility and reduce computational costs.

Availability and implementation: The methods are implemented in the R baySeq (v2) package, available on Bioconductor http://www.bioconductor.org/packages/release/bioc/html/baySeq.html.

Contact:  tjh48@cam.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Cell line name recognition in support of the identification of synthetic lethality in cancer from text
Authors: Kaewphan Suwisa , Van Landeghem Sofie , Ohta Tomoko , Van de Peer Yves , Ginter Filip , Pyysalo Sampo
Published: October 2015

Motivation: The recognition and normalization of cell line names in text is an important task in biomedical text mining research, facilitating for instance the identification of synthetically lethal genes from the literature. While several tools have previously been developed to address cell line recognition, it is unclear whether available systems can perform sufficiently well in realistic and broad-coverage applications such as extracting synthetically lethal genes from the cancer literature. In this study, we revisit the cell line name recognition task, evaluating both available systems and newly introduced methods on various resources to obtain a reliable tagger not tied to any specific subdomain. In support of this task, we introduce two text collections manually annotated for cell line names: the broad-coverage corpus Gellus and CLL, a focused target domain corpus.

Results: We find that the best performance is achieved using NERsuite, a machine learning system based on Conditional Random Fields, trained on the Gellus corpus and supported with a dictionary of cell line names. The system achieves an F-score of 88.46% on the test set of Gellus and 85.98% on the independently annotated CLL corpus. It was further applied at large scale to 24 302 102 unannotated articles, resulting in the identification of 5 181 342 cell line mentions, normalized to 11 755 unique cell line database identifiers.

Availability and implementation: The manually annotated datasets, the cell line dictionary, derived corpora, NERsuite models and the results of the large-scale run on unannotated texts are available under open licenses at http://turkunlp.github.io/Cell-line-recognition/.

Contact:  sukaew@utu.fi
Pseudoknots in RNA folding landscapes
Authors: Kucharík Marcel , Hofacker Ivo L. , Stadler Peter F. , Qin Jing
Published: October 2015

Motivation: The function of an RNA molecule is not only linked to its native structure, which is usually taken to be the ground state of its folding landscape, but also in many cases crucially depends on the details of the folding pathways such as stable folding intermediates or the timing of the folding process itself. To model and understand these processes, it is necessary to go beyond ground state structures. The study of rugged RNA folding landscapes holds the key to answer these questions. Efficient coarse-graining methods are required to reduce the intractably vast energy landscapes into condensed representations such as barrier trees or basin hopping graphs (BHG) that convey an approximate but comprehensive picture of the folding kinetics. So far, exact and heuristic coarse-graining methods have been mostly restricted to the pseudoknot-free secondary structures. Pseudoknots, which are common motifs and have been repeatedly hypothesized to play an important role in guiding folding trajectories, were usually excluded.

Results: We generalize the BHG framework to include pseudoknotted RNA structures and systematically study the differences in predicted folding behavior depending on whether pseudoknotted structures are allowed to occur as folding intermediates or not. We observe that RNAs with pseudoknotted ground state structures tend to have more pseudoknotted folding intermediates than RNAs with pseudoknot-free ground state structures. The occurrence and influence of pseudoknotted intermediates on the folding pathway, however, appear to depend very strongly on the individual RNAs so that no general rule can be inferred.

Availability and implementation: The algorithms described here are implemented in C++ as standalone programs. Its source code and Supplemental material can be freely downloaded from http://www.tbi.univie.ac.at/bhg.html.

Contact:  qin@bioinf.uni-leipzig.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
ALP & FALP: C++ libraries for pairwise local alignment E-values
Authors: Sheetlin Sergey , Park Yonil , Frith Martin C. , Spouge John L.
Published: October 2015

Motivation: Pairwise local alignment is an indispensable tool for molecular biologists. In real time (i.e. in about 1 s), ALP (Ascending Ladder Program) calculates the E-values for protein–protein or DNA–DNA local alignments of random sequences, for arbitrary substitution score matrix, gap costs and letter abundances; and FALP (Frameshift Ascending Ladder Program) performs a similar task, although more slowly, for frameshifting DNA-protein alignments.

Availability and implementation: To permit other C++ programmers to implement the computational efficiencies in ALP and FALP directly within their own programs, C++ source codes are available in the public domain at http://go.usa.gov/3GTSW under ‘ALP’ and ‘FALP’, along with the standalone programs ALP and FALP.

Contact:  spouge@nih.gov

Supplementary information:  Supplementary data are available at Bioinformatics online.
A method of spherical harmonic analysis in the geosciences via hierarchical Bayesian inference
Authors: Muir J.B. , Tkalčić H.
Published: October 2015

The problem of decomposing irregular data on the sphere into a set of spherical harmonics is common in many fields of geosciences where it is necessary to build a quantitative understanding of a globally varying field. For example, in global seismology, a compressional or shear wave speed that emerges from tomographic images is used to interpret current state and composition of the mantle, and in geomagnetism, secular variation of magnetic field intensity measured at the surface is studied to better understand the changes in the Earth's core. Optimization methods are widely used for spherical harmonic analysis of irregular data, but they typically do not treat the dependence of the uncertainty estimates on the imposed regularization. This can cause significant difficulties in interpretation, especially when the best-fit model requires more variables as a result of underestimating data noise. Here, with the above limitations in mind, the problem of spherical harmonic expansion of irregular data is treated within the hierarchical Bayesian framework. The hierarchical approach significantly simplifies the problem by removing the need for regularization terms and user-supplied noise estimates. The use of the corrected Akaike Information Criterion for picking the optimal maximum degree of spherical harmonic expansion and the resulting spherical harmonic analyses are first illustrated on a noisy synthetic data set. Subsequently, the method is applied to two global data sets sensitive to the Earth's inner core and lowermost mantle, consisting of PKPab-df and PcP-P differential traveltime residuals relative to a spherically symmetric Earth model. The posterior probability distributions for each spherical harmonic coefficient are calculated via Markov Chain Monte Carlo sampling; the uncertainty obtained for the coefficients thus reflects the noise present in the real data and the imperfections in the spherical harmonic expansion.
Repurposing existing agents as adjunct therapies for glioblastoma
Authors: Purow Benjamin
Published: October 2015

Numerous non-oncologic medications have been found in the last decade to have anti-cancer properties. While the focus in oncology research should clearly remain on deriving new therapeutic strategies, repurposing these existing medications may offer the potential to rapidly enhance the effectiveness of treatment for resistant cancers. Glioblastoma, the most common and lethal brain cancer, is highly resistant to standard therapies and would benefit from even minor improvements in treatment. Numerous agents already in the clinic for non-cancer applications have been found to also possess potential against cancer or specifically against glioblastoma. These include agents with activities affecting oxidative stress, the immune reponse, epigenetic modifiers, cancer cell metabolism, and angiogenesis and invasiveness. This review serves as a guide for potential ways to repurpose individual drugs alongside standard glioblastoma therapies.
Link for Injured Kids
Authors: Ramirez Marizen , Toussaint Maisha , Woods-Jaeger Briana , Harland Karisa , Wetjen Kristel , Wilgenbusch Tammy , Pitcher Graeme , Jennissen Charles
Published: October 2015

Objective

Injury, the most common type of pediatric trauma, can lead to a number of adverse psychosocial outcomes, including posttraumatic stress disorder. Currently, few evidence-based parent programs exist to support children hospitalized after a traumatic injury. Using methods in evaluation and intervention research, we completed a formative research study to develop a new program of psychological first aid, Link for Injured Kids, aimed to educate parents in supporting their children after a severe traumatic injury.

Methods

Using qualitative methods, we held focus groups with parents and pediatric trauma providers of children hospitalized at a Level I Children's Hospital because of an injury in 2012. We asked focus group participants to describe reactions to trauma and review drafts of our intervention materials.

Results

Health professionals and caregivers reported a broad spectrum of emotional responses by their children or patients; however, difficulties were experienced during recovery at home and upon returning to school. All parents and health professionals recommended that interventions be offered to parents either in the emergency department or close to discharge among admissions.

Conclusions

Results from this study strongly indicate a need for posttrauma interventions, particularly in rural settings, to support families of children to address the psychosocial outcomes in the aftermath of an injury. Findings presented here describe the process of intervention development that responds to the needs of an affected population.
Current Concepts on Diagnosis and Prognosis of Arrhythmogenic Right Ventricular Cardiomyopathy/Dysplasia
Authors: Castaños Gutiérrez Sandra L. , Kamel Ihab R. , Zimmerman Stefan L.
Published: October 2015

Arrhythmogenic right ventricular cardiomyopathy/dysplasia (ARVC/D) is an uncommon cardiac disease characterized by progressive right ventricular dysfunction due to fibrofatty replacement of myocytes and risk of sudden cardiac death from malignant arrhythmias. ARVC/D is a disease of the cardiac desmosome, with genetic mutations in genes encoding proteins critical to this structure found in the majority of patients. The diagnosis of ARVC/D is based on fulfilling a combination of clinical, imaging, pathologic, and/or genetic criteria set forth by the 2010 modified Task Force Criteria. Cardiac magnetic resonance (CMR) is included in these criteria and plays an important role in the management of ARVC/D, demonstrating pathologic structural changes in the right and left ventricles that provide both diagnostic and prognostic information. The purpose of this article is to provide a background on the pathophysiology and genetics of ARVC/D and focus on the role of CMR in management of ARVC/D including diagnosis, prognosis, and treatment decisions. Common CMR pitfalls that can lead to misdiagnosis will also be reviewed.
Gibbsiella papilionis Kim et al. 2013 is a later heterotypic synonym of Gibbsiella dentisursi Saito et al. 2013
Authors: Brady Carrie , Irisawa Tomohiro , Iino Takao , Ohkuma Moriya , Arnold Dawn , Denman Sandra
Published: October 2015

Synonymy of Gibbsiella dentisursi DSM 23818T ( = NUM 1720T) and Gibbsiella papilionis JCM 18389T ( = LEN33T) was suspected following multilocus sequence analysis (MLSA) of both type strains in a previous classification study, where they were found to share >99.6 % gene sequence similarity. The taxonomic relationship between these two strains was re-examined here using a polyphasic approach. A DNA–DNA hybridization value of 98 % confirmed that the two type strains belong to a single taxon, while the phenotypic profiles were found to be nearly identical. Therefore we propose Gibbsiella papilionis as a later heterotypic synonym of Gibbsiella dentisursi, with the type strain as NUM 1720T ( = DSM 23818T = JCM 17201T).
Halomonas salicampi sp. nov., a halotolerant and alkalitolerant bacterium isolated from a saltern soil
Authors: Lee Jae-Chan , Kim Young-Sook , Yun Bong-Sik , Whang Kyung-Sook
Published: October 2015

A Gram-stain-negative, halotolerant and alkalitolerant bacterium, designated strain BH103T, was isolated from saltern soil in Gomso, Korea. Cells of strain BH103T were strictly aerobic, motile, straight rods and grew at pH 7.0–10.8 (optimum, pH 8.5), at 10–55 °C (optimum, 28 °C) and at salinities of 0–23 % (w/v) NaCl (optimum, 14 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain BH103T belongs to the genus Halomonas, showing highest sequence similarity to Halomonas boliviensis LC1T (97.7 %), Halomonas neptunia Eplume1T (97.7 %), Halomonas variabilis IIIT (97.7 %), Halomonas alkaliantarctica CRSST (97.7 %), Halomonas olivaria TYRC17T (97.5 %), Halomonas titanicae BH1T (97.2 %) and Halomonas sulfidaeris Esulfide1T (96.2 %). The predominant ubiquinone was Q-9. The major fatty acids were C18 : 1ω7c, C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C12 : 0 3-OH. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, aminophospholipid and an unknown phospholipid. The DNA G+C content of this novel isolate was 54.7 mol%. DNA–DNA relatedness between strain BH103T and H. boliviensis KACC 16615T, H. neptunia KCTC 2888T, H. variabilis KCTC 2889T, H. alkaliantarctica KCTC 22844T, H. olivaria DSM 19074T, H. titanicae JCM 16411T and H. sulfidaeris DSM 15722T was 45, 41, 39, 32, 38, 45 and 35 %, respectively. On the basis of polyphasic analysis from this study, strain BH103T represents a novel species of the genus Halomonas, for which the name Halomonas salicampi sp. nov. is proposed. The type strain is BH103T ( = KACC 17609T = NBRC 109914T = NCAIM B 02528T).
Physicochemical properties of powdered, soft and hard type rice flour by different milling methods
Authors: Choi Ok Ja , Jung Hee Nam , Shim Ki Hoon
Published: October 2015

This study investigated the physicochemical properties of three different types of rice flour prepared via dry and wet milling. The powder, soft, and hard-types of rice flour were Suwon No. 542, Suwon No. 541, and Unbong No. 30, respectively. The analysis of the proximate compositions of the different types of rice flour showed that their moisture content was 7.03~7.99%, their crude protein was 7.94~8.35%, their crude lipid was 0.71~1.49% and their crude ash was 0.25~0.82%. For the Hunter’s color values, the L value was highest in the wet-milled rice flour, the a value was highest in the dry-milled rice flour, and the b value was highest in the dry-milled rice flour. All the samples showed distinctive rice starch particles in the particle analysis using scanning electron microscope. The dry-milled rice flour showed the greatest amount of irregular particles and the coarsest texture. The water absorption and water solubility indices were higher in the wet-milled soft- and hard-type rice flour. The crystallinities of the samples by X-ray diffractography were all A-type, but the crystallinity of the dry-milled hard-type rice flour was higher in diffraction degree. For the amylogram properties, the wet-milled soft-type rice flour showed the highest maximum viscosity, breakdown and setback. In the meanwhile, the dry-milled soft-type rice flour showed the highest initial pasting temperature, onset, peak, and end temperatures despite of the reverse enthalpy.
Neuronal actin dynamics, spine density and neuronal dendritic complexity are regulated by CAP2
Authors: Kumar Atul , Paeger Lars , Kosmas Kosmas , Kloppenburg Peter , Noegel Angelika A. , Peche Vivek
Published: October 2015

Actin remodeling is indispensable for dendritic spine development, morphology and density which signify learning, memory and motor skills. CAP2 is a regulator of actin dynamics through sequestering G-actin and severing F-actin. In a mouse model, ablation of CAP2 leads to cardiovascular defects and delayed wound healing. This report investigates the role of CAP2 in the brain usingCap2gt/gtmice. Dendritic spine density and neuronal dendritic length were altered inCap2gt/gt. This was accompanied by increased F-actin content and F-actin accumulation in culturedCap2gt/gtneurons. In membrane depolarization assays,Cap2gt/gtsynaptosomes exhibit an impaired F/G actin ratio, indicating altered actin dynamics. We show an interaction between CAP2 and n-cofilin, presumably mediated through the C-terminal domain of CAP2 and is cofilin ser3 phosphorylation dependent. In vivo, the consequences of this interaction were altered phosphorylated cofilin levels and formation of cofilin aggregates in the neurons. Thus, our studies identify a novel role of CAP2 in neuronal development and neuronal actin dynamics.
Detecting and quantifying changing selection intensities from time-sampled polymorphism data
Authors: Shim Hyunjin , Laurent Stefan , Foll Matthieu , Jensen Jeffrey D.
Published: October 2015

During his well-known debate with Fisher regarding the phenotypic dataset ofPanaxia dominula, Wright (1948) suggested fluctuating selection as a potential explanation for the observed change in frequency. This model has since been invoked in a number of analyses, with the focus of discussion centering mainly on random or oscillatory fluctuations of selection intensities. Here, we present a novel method to consider non-random changes in selection intensities using Wright-Fisher approximate Bayesian (ABC)-based approaches, in order to detect and evaluate a change in selection strength from time-sampled data. This novel method jointly estimates the position of a change point as well as the strength of both corresponding selection coefficients (and dominance for diploid cases) from the allele trajectory. The simulation studies of CP-WFABC reveal the combinations of parameter ranges and input values that optimize performance, thus indicating optimal experimental design strategies. We apply this approach to both the historical dataset ofPanaxia dominulain order to shed light on this historical debate, as well as to whole-genome time-serial data from influenza virus in order to identify sites with changing selection intensities in response to drug treatment
Stochastic Analysis Of An Incoherent Feedforward Genetic Motif
Authors: Platini Thierry , Soltani Mohammad , Singh Abhyudai
Published: October 2015

Gene products (RNAs, proteins) often occur at low molecular counts inside individual cells, and hence are subject to considerable random fluctuations (noise) in copy number over time. Not surprisingly, cells encode diverse regulatory mechanisms to buffer noise. One such mechanism is the incoherent feedforward circuit. We analyze a simplistic version of this circuit, where an upstream regulatorXaffects both the production and degradation of a proteinY. Thus, any random increase inX’s copy numbers would increase both production and degradation, keepingYlevels unchanged. To study its stochastic dynamics, we formulate this network into a mathematical model using the Chemical Master Equation formulation. We prove that if the functional dependence ofY’s production and degradation onXis similar, then the steady-distribution ofY’s copy numbers is independent ofX. To investigate how fluctuations inYpropagate downstream, a proteinZwhose production rate only depend onYis introduced. Intriguingly, results show that the extent of noise inZincreases with noise inX, in spite of the fact that the magnitude of noise inYis invariant ofX. Such counter intuitive results arise becauseXenhances the time-scale of fluctuations inY, which amplifies fluctuations in downstream processes. In summary, while feedforward systems can buffer a protein from noise in its upstream regulators, noise can propagate downstream due to changes in the time-scale of fluctuations.
Indel variant analysis of short-read sequencing data with Scalpel
Authors: Fang Han , Grabowska Ewa A. , Arora Kanika , Vacic Vladimir , Zody Michael C. , Iossifov Ivan , O’Rawe Jason A. , Wu Yiyang , Barron Laura T Jimenez , Rosenbaum Julie , Ronemus Michael , Lee Yoon-ha , Wang Zihua , Lyon Gholson J. , Wigler Michael , Schatz Michael C. , Narzisi Giuseppe
Published: October 2015

As the second most common type of variations in the human genome, insertions and deletions (indels) have been linked to many diseases, but indels of more than a few bases are still challenging to discover from short-read sequencing data. Scalpel (http://scalpel.sourceforge.net) is open-source software for reliable indel detection based on the micro-assembly technique. To date, it has been successfully used to discover mutations in novel candidate genes for autism, and is extensively used in other large-scale studies of human diseases. This protocol gives an overview of the algorithm and describes how to use Scalpel to perform highly accurate indel calling from whole genome and exome sequencing data. We provide detailed instructions for an exemplary family-basedde novostudy, but we also characterize the other two supported modes of operation for single sample and somatic analysis. Indel normalization, visualization, and annotation of the mutations are also illustrated. Using a standard server, indel discovery and characterization in the exonic regions of the example sequencing data can be finished in ~6 hours after read mapping.
Crystal structure of tris[μ2-bis(diphenylphosphanyl)methane-κ2P:P′]di-μ3-iodido-trisilver(I) iodide–N-phenylthiourea (1/1)
Authors: Wattanakanjana Yupa , Nimthong-Roldán Arunpatcha , Palavat Suthida , Puetpaiboon Walailak
Published: October 2015

The title complex, [Ag3I2(C25H22P2)3]I·C7H8N2S, comprises a trinuclear [Ag3I2(C25H22P2)3]+unit, an I−anion and oneN,N′-phenylthiourea molecule (ptu). Two μ3-bridging I−anions are linked by three AgIions, leading to the formation of a dicapped triangular motif with Ag...Ag separations in the range 3.0823 (5)–3.2999 (5) Å. Each AgIatom exhibits a distorted tetrahedral geometry, with coordination to two I atoms and two P atoms from bis(diphenylphosphanyl)methane ligands. In the crystal, the I−anion is linked to the ptu molecule through two N—H...I hydrogen bonds [graph-set motifR21(6)]. These N—H...I hydrogen bonds, in addition to weak C—H...S and C—H...I hydrogen bonds, form zigzag chains along [010]. Two of the phenyl rings of two dppm ligands are disordered over two sets of sites with refined occupancies of 0.557 (16) and 0.443 (16).
Crystal structure of benzene-1,3,5-tricarboxylic acid–4-pyridone (1/3)
Authors: Staun Selena L. , Oliver Allen G.
Published: October 2015

Slow co-crystallization of a solution of benzene-1,3,5-tricarboxylic acid with a large excess of 4-hydroxypyridine produces an interpenetrating, three-dimensional, hydrogen-bonded framework consisting of three 4-pyridone and one benzene-1,3,5-tricarboxylic acid molecules, C9H6O6·3C5H5NO. This structure represents an orthorhombic polymorph of the previously reportedC-centered, monoclinic structure [Campos-Gaxiolaet al.(2014).Acta Cryst.E70, o453–o454].
Crystal structure of 2-bromo-4,6-dinitroaniline
Authors: Kang Gihaeng , Kim Tae Ho , Lee Eui-Jae , Kang Chang Ho
Published: October 2015

In the title compound, C6H4BrN3O4, the dihedral angles between the nitro groups and the aniline ring are 2.04 (3) and 1.18 (4)°, respectively. In the crystal, N—H...O and C—H...O hydrogen bonds and weak side-on C—Br...π interactions [3.5024 (12) Å] link adjacent molecules, forming a three-dimensional network. A close O...Br contact [3.259 (2) Å] may also add additional stability.
The crystal structure of 1-(2-hydroxy-5-methoxyphenyl)ethanone 4,4-dimethylthiosemicarbazone
Authors: Anderson Brian J. , Freedman Michael B. , Smolenski Victoria A. , Jasinski Jerry P.
Published: October 2015

The asymmetric unit of the title compound, C12H17N3O2S, contains two independent molecules,AandB. Both molecules are nearly planar with the dihedral angle between the mean planes of the thioamide group and benzene ring being 7.5 (1)° inAand 4.3 (2)° inB. In each molecule, the hydroxy group participates in intramolecular O—H...N hydrogen bonding, while the amino H atom is not involved in hydrogen bonding because of the steric hinderence caused by two neighboring methyl groups. In the crystal, the individual molecules are linked by weak C—H...O hydrogen bonds, formingA–AandB–Binversion dimers. The dimers are linkedviaC—H...π interactions which help stabilize the packing.
A conceptual review of risk communication network for protecting immigrant knowledge workers
Authors: Oh Namkyung , Beckett Julia
Published: October 2015

Purpose

– The purpose of this paper is to define immigrant knowledge workers (IKWs) as a vulnerable population in the urban emergency management context, and explored how to provide public safety services to IKWs. Due to nomadic features such as high mobility, spatio-temporality, and preferred autonomy, IKWs have difficulties in building required social ties with long-term residents in the urban emergency management system (UEMS). As such, IKWs are easily isolated and become vulnerable to disasters.

Design/methodology/approach

– This study introduced possible types of network structure, compared each structure’s weaknesses and strengths in terms of risk communication, and suggested the strategic use of brokers for effective risk communication with application of network analysis perspective.

Findings

– This study argued that the current space-based model causes tension in protecting NKWs and suggested the strategic use of brokers for the facilitated risk communication and for the protection of UKWs in more effective ways. The brokers in UEMS should pursue the core values of partnership, participation, and consultation in building mutual supportive channels within UEMS and the brokers should have sufficient cognitive capacity to avoid system fragmentation and collapse.

Research limitations/implications

– Due to the limitations as conceptual paper, sometimes it lacks empirical data to support the main arguments of this paper. To address this, the authors put that part as a suggestion for future studies.

Originality/value

– With the strategic use of brokers, UEMS would be more resilient and accountable in providing public safety services to its citizens.
A review of wildland fire smartphone applications
Authors: Kulemeka Owen
Published: October 2015

Purpose

– Fire management professionals are using smartphone applications to communicate information about wildland fires. The purpose of this paper is to examine English language wildland fire apps available to the general public to learn what information these apps contain and whether they match what are considered characteristics of well-designed apps.

Design/methodology/approach

– Content analysis of global app markets and other directories revealed ten relevant apps. Two coders installed the apps on identical smartphones and proceeded to review the apps’ content, features, and design characteristics.

Findings

– Results reveal that the ten English language wildland fire apps on the global app markets fall into three groups: apps that show nearby fires, emergency plan creation apps, and apps that inform on preparedness, response, and recovery. Strengths of these apps include that most load quickly on devices, they offer real-time contextual information, they can be used even when a device is offline, are easy to navigate, and do not utilize processor-intensive animation. Weaknesses include the fact that many lack a search engine, they do not explain how they protect sensitive user data, and they fail to reveal who authors of content are as well as when content was created or modified.

Originality/value

– Few studies have classified, analyzed content, or assessed the design of wildland fire apps. This study reveals that critical issues app designers should address include ensuring that apps contain privacy policies and disclaimers that app information is not supposed to replace live human advice.
Communication, dialogue and project management
Authors: Ziek Paul , Anderson J. Dwight
Published: October 2015

Purpose

– Project communication is overwhelmingly viewed as the proper and timely delivery of pertinent project information. The view of communication in this way misses the constitutive nature of communication. Communication is more than message exchange but a way that project managers generate the grounds for a project. The purpose of this paper is to explore how the communicative practices of project managers creates a dialogue with stakeholders that ultimately impacts the content, direction and outcome of a project.

Design/methodology/approach

– Semi-structured interviews were performed with project managers from the Project Management Office of a large international bank. The project managers were responsible for their own projects of varying size with scopes that included everything from marketing initiatives to heavily oriented technology projects.

Findings

– Overall, the project managers interviewed for the current project do not subscribe to the belief that communication is part of a constitutive dialogue. Instead, when discussing their overall views of communication, 82 percent of the interviewees took a transmission approach to the action. To that end, they believe that the goal of communication is to send clear, unambiguous and complete information.

Originality/value

– Unlike other studies about communication within the field of project management, the current study looks to uncover how communication is part of a constitutive dialogue between a project manager and project stakeholders. The researchers did not look just to understand the micro-level exchanges between project managers and stakeholders but how those exchanges enabled a sustained dialogue that shapes the scope and trajectory of a project.
Redefining governance: from confusion to certainty and clarity
Authors: McGrath Stephen Keith , Whitty Stephen Jonathan
Published: October 2015

Purpose

– The purpose of this paper is to resolve and remove from the governance arena in general and the project arena in particular, conflict which occurs when parties do not realise they have different meanings for common governance terms.

Design/methodology/approach

– Review literature on definitional confusion in general and on governance in particular and develop a method for defining an internally consistent group of terms, then apply this to a group of terms in the governance arena.

Findings

– Several important subjects commonly arranged under the governance banner do not actually constitute governance (strategy, behaviour, decision making).

Research limitations/implications

– Further work is necessary to remove similar confusion in other closely related areas, including power itself and authority as well as project and general management terms such as responsibility and accountability.

Practical implications

– Projects and business alike can potentially achieve significant improvements in efficiency and effectiveness through gaining consistency across current models, frameworks, policies and procedures thus reducing cross-boundary conflict.

Social implications

– Creation of a unifying feature within the project and management literature, shifting the understanding of the boundaries and limitations of governance. These definitions will help progress governance from complexity to simplicity, from an art to an understandable practice, from a concept that has been hijacked for partisan and political gain to a lean social tool which can be put to use for the benefit of organisations, whether public, charitable or private.

Originality/value

– The value is clarity – resulting in the avoidance of confusion and misunderstanding together with their consequent waste of time, resources and money.
Creativity and management control – the diversity of festival budgets
Authors: Knardal Per Ståle , Pettersen Inger Johanne
Published: October 2015

Purpose

– The purpose of this paper is to investigate how the budget, when split into a network of projects, can act as a management tool to balance control with creativity.

Design/methodology/approach

– A case study is used to discuss the budget in a large Norwegian festival. Simons’ (1995) concept of interactive use of budgets is applied for the analysis of empirical findings. Especially, the authors focus on the design and use of the budget and how it is aligned with the specific characteristics of festivals as economic organizations.

Findings

– The findings support earlier research which focusses on the need to balance between control and dynamic changes to successfully manage festivals. This study gives a detailed knowledge on how managers use budgets to combine management control with creativity and dynamic adaptions.

Originality/value

– This study contributes to a detailed understanding of how managers can use budgets as tools to stabilize between uncertainty, creativity and control.
Managing competing logics through situational irony
Authors: Wikberg Erik , Bomark Niklas
Published: October 2015

Purpose

– The purpose of this paper is to extend the literature on how actors manage competing logics in an organizational field. The authors do so by introducing the concept of organizational irony to the literature on how to manage competing logics, and analyze a collaborative cultural project encompassing actors subjected to competing institutional logics.

Design/methodology/approach

– The case study is built on qualitative data from in-depth interviews, newspaper articles and observations.

Findings

– The authors describe and analyze a cultural project encompassing actors subjected to competing institutional logics and show how they responded to institutional pressures in their environment with the use of organizational irony. Thereby, the actors could collaborate with actors subjected to a competing institutional logic and still maintain adherence to their respective institutional logic.

Research limitations/implications

– Most studies of how to manage competing logics asserts that one logic will prevail over a competing one, either through “battles” or gradual dominance (Reay and Hinings, 2009). This study supports and adds to Reay and Hinings’ (2009) finding that actors also can collaborate and maintain adherence to their respective logic under such circumstances. In particular, it supports two identified mechanisms of how this can be achieved, namely, to separate decisions and to jointly innovate in experimental sites. It also adds to these mechanisms by showing that this can be done through the use of organizational irony. The authors only study one cultural project in one organizational field. It remains unclear if these findings are common in other cultural projects or in other organizational field, and the authors therefore encourage other researchers to extend or challenge the findings of this study.

Practical implications

– The authors believe that the analysis and findings can be useful for politicians to take into account and address either to minimize the risk of organizational irony or on the contrary encourage it as a source of reflexive critique of society and cultural politics. The authors also believe that the response of organizational irony to institutional pressures broadens the acting space of cultural actors, provide media and critics with an analytical tool to analyze and deconstruct practices that otherwise would risk to be silenced or neglected. Finally, the authors believe that an analysis of organizational irony has the potential to make people attend to contradictions and multiple meanings in the artworks under study in a novel way.

Originality/value

– The paper provides an intriguing and complex empirical case to demonstrate how actors manage competing logics in an organizational field through the production of organizational irony. The authors believe that its theoretical contributions and practical implications can inspire future research on how paradoxes can be managed through the use of organizational irony in other projects and organizational fields.
Poverty and earning compulsions for the family have pushed children out of schools
Authors: Banik Arindam , Neogi Debasis
Published: October 2015

Purpose

– The purpose of this paper is to examine factors that explain dropout of children from primary schools in Lohit district of Arunachal Pradesh, India.

Design/methodology/approach

– The field survey was carried out in two phases, one, during January to April of 2010 and two, between August and November of 2011. The entire research work is based on stratified random sampling. The population in Lohit district is a set of tribal and non-tribal (mostly general) people. The district has two major tribes – Mishmi and Khamti.

Findings

– The authors find that children dropout of school is affected by number of factors such as earning compulsions, household work, access to school, school time not suitable and parental unawareness.

Research limitations/implications

– It is imperative to mention here that “earning compulsion” can be described only as a derivative of the major problem of abject poverty.

Practical implications

– By highlighting the role of appropriate intervention as well as incapacitation, the authors believe that the findings presented above shed light on some important factors that explain dropouts.

Social implications

– The evidence provided in this paper underscores the importance of social interactions in analysing individual outcomes.

Originality/value

– The findings may have significant bearings in reducing dropout rates in India.