bluuebunny/crossref_metadata_2025 huggingface dataset:
Planning and production in computer-mediated communication (CMC) writing
Authors: Adams Rebecca , Amani Sara , Newton Jonathan , Nik Mohd Alwi Nik Aloesnita
Published: October 2014

A growing body of research has documented the effect of pre-task and online planning on second language task-based production (e.g. Ellis 2005; Ortega 1999; Yuan & Ellis 2003). However, relatively little research has addressed the effects of planning time on written communication and none to date has considered the role of planning in computer-mediated task-based writing. The current study investigates the effect of planning on the task-based writing of 45 Malaysian civil engineering majors studying at a technical university and enrolled in courses focusing on English for professional communication. The students were divided into teams of three and linked via networked computers. Each team member was provided with information on a civil engineering scenario and asked to write a proposal via a wiki for the best type of equipment to use. The text from the wiki pages formed the data for the current study. The teams were grouped into three experimental conditions: pre-task planning, online planning, and no planning. Multiple measures of fluency, accuracy, and complexity of their language production were analyzed. The results showed that different types of planning promoted different aspects of written production and therefore different learning opportunities. Overall, this study contributes to the aims of the book of expanding the research base on the connection between TBLT and language development by providing evidence for how task implementation options influence the language learning opportunities available in CMC-based writing tasks.
Task complexity and linguistic performance in advanced college-level foreign language writing
Authors: Ruiz-Funes Marcela
Published: October 2014

This study contributes to our understanding of the potential of tasks in the domain of writing for second/foreign language (L2/FL) development by exploring task complexity in academic writing and its effect on the linguistic performance of advanced college-level learners of Spanish. It focuses on essay-type writing tasks of different levels of complexity in terms of topic, discourse genre, task type, and cognitive processing and their relationship to syntactic complexity, accuracy, and fluency (CAF). It adds to the emerging research on task complexity in L2/FL writing in terms of two models: Skehan and Foster’s Limited Attentional Capacity Model (Skehan 1998a, 2001, 2003; Skehan & Foster 1999, 2001) and Robinson’s Cognition Hypothesis (Robinson 2001a, 2001b, 2003, 2005, 2007). Findings suggest a tendency towards an emerging tension between syntactic complexity and accuracy and fluency in relation to task complexity and, at the same time, a positive association between task complexity and some measures of syntactic complexity, accuracy, and fluency depending on the writing abilities of the students based on the quality of the essays they produced. The chapter calls for future research that provides a classificatory system of task complexity in L2/FL writing to help explain the effect of task variables on attentional resources and the role played by long-term and working memory capacity in the composing processes. In addition, further research is needed that considers writing ability in relation to levels of L2/FL language proficiency in order to understand better the interaction between tasks, L2/FL composing skills, and language production.
Differences across modalities of performance
Authors: Kormos Judit
Published: October 2014

This study investigated the linguistic and discourse differences between oral and written narrative performance on two tasks of different degrees of cognitive complexity. The participants of the study were 44 secondary school students in their second academic year of an English-Hungarian bilingual educational program in Hungary. Two narrative tasks were administered in speech and in writing. Three global linguistic aspects of students’ performance were assessed: lexical diversity and variety, accuracy, and grammatical complexity. Task specific measures included the ratio of correctly used relative clauses and past-tense verbs as well as the ratio of relative clauses compared to the total number of clauses. The frequency of positive and negative additive, temporal, causal, and logical connectives was measured using the Coh-Metrix 2.0 program. Spatial, temporal, intentional, and causal cohesion indices were also calculated with the help of Coh-Metrix 2.0. My findings indicate that, in writing, the participants were more accurate and used more varied vocabulary than in speech, but their performance was similar in terms of syntactic complexity. The analysis of cohesion revealed that students used significantly more positive and negative additive and causal connectives in speech than in writing in both types of tasks. The research presented in this chapter provides new insights into the nature of task complexity and complexity of performance in the field of L2 writing and elucidates potentials of writing tasks in furthering language development.
Storyline complexity and syntactic complexity in writing and speaking tasks
Authors: Tavakoli Parvaneh
Published: October 2014

Task-based Language Teaching (TBLT) research has provided ample evidence that cognitive complexity is an important aspect of task design that influences learner performance in terms of fluency, accuracy, and syntactic and lexical complexity. Task features such as the degree of structure and storyline complexity contribute to task complexity and affect different aspects of L2 performance. Two of the current models of task complexity (i.e. Skehan 1998, and Robinson 2001), have further encapsulated different dimensions of task complexity and have provided both a framework for evaluating and predicting task complexity and a detailed discussion of the factors that may affect cognitive complexity. These models by principle are assumed to be pertinent to all tasks regardless of their purpose, type, or mode. However, little is known about whether cognitive complexity affects writing and speaking tasks in similar ways, or whether it has similar influences on L2 oral and written performance. By replicating previous research in oral task performance (Tavakoli & Foster 2008), the current study investigates the effects of storyline complexity on L2 learners writing in narrative tasks. The findings indicate that, although cognitive complexity affects both written and spoken performances, the way it affects the syntactic complexity of writing and speaking differs to some extent. In addition to presenting empirical data that provides insights into the effects of cognitive complexity on L2 learners’ writing and speaking, the main contribution of the chapter is to help extend our understanding of how task complexity plays out with the syntactic complexity of L2 performance in the two different modes, and to allow for a more in-depth understanding of the ways in which task complexity contributes to L2 writing. In that fashion, the findings of the current study can also begin to answer the question of whether or not a single model of task complexity can account for both writing and speaking tasks.
Enhanced in vitro caulogenesis and quantitative estimation of aloin through HPLC in Aloe vera
Authors: Sharma V. , Guleria M. , Chaudhary P.
Published: October 2014

Aloe vera(Liliaceae) is well known for its medicinal properties. It contains flavonoids, saponins, tannins, alkaloids and other compounds which exhibit medicinal, cosmetic and pharmacological properties. There is a lack of production of aloe leaf to meet the industry demand and therefore the means to facilitate large-scale aloe cultivation schemes need to be developed. Because sexual reproduction by seeds is almost ineffective inAloe veradue to male sterility and vegetative propagation by offshoots is only possible during the growing seasons, there is a need to develop a propagation method to facilitate large-scale cultivation.In vitroregeneration of medicinal plants is important and there is the potential for the production of high-quality plant-based medicine. In the present study, an attempt has been made to enhancein vitrocaulogenesis and aloin content in plants in the presence of a precursor (tryptophan) in the nutrient media. Forin vitroculture establishment and shoot bud multiplication, MS basal media were used supplemented with different concentrations and different combinations of growth regulators such as BAP (6-benzylaminopurine) and IAA (3-indole acetic acid). Shoot proliferation was optimal in MS medium containing 2.0 mg l−1BAP. For evaluation ofin vitroenhancement of aloin production the precursor tryptophan was added to the nutrient media at different levels (5, 10, 15 and 20 mg l−1). Addition of 20 mg l−1tryptophan induced a 2.43-fold increase in aloin content in multiple shoots cultures ofAloe barbadensis.
Enhanced butanol production by eukaryotic Saccharomyces cerevisiae engineered to contain an improved pathway
Authors: Sakuragi Hiroshi , Morisaka Hironobu , Kuroda Kouichi , Ueda Mitsuyoshi
Published: October 2014

Compared with ethanol, butanol has more advantageous physical properties as a fuel, and biobutanol is thus considered a promising biofuel material. Biobutanol has often been produced by Clostridium species; however, because they are strictly anaerobic microorganisms, these species are challenging to work with. We attempted to introduce the butanol production pathway into yeast Saccharomyces cerevisiae, which is a well-known microorganism that is tolerant to organic solvents. 1-Butanol was found to be produced at very low levels when the butanol production pathway of Clostridium acetobutylicum was simply introduced into S. cerevisiae. The elimination of glycerol production pathway in the yeast contributed to the enhancement of 1-butanol production. In addition, by the use of trans-enoyl-CoA reductase in the engineered pathway, 1-butanol production was markedly enhanced to yield 14.1 mg/L after 48 h of cultivation.
Roles of Ala-149 in the catalytic activity of diadenosine tetraphosphate phosphorylase from Mycobacterium tuberculosis H37Rv
Authors: Mori Shigetarou , Kim Hyun , Rimbara Emiko , Arakawa Yoshichika , Shibayama Keigo
Published: October 2014

Diadenosine 5′,5′′′-P1,P4-tetraphosphate (Ap4A) phosphorylase from Mycobacterium tuberculosis H37Rv (MtAPA) belongs to the histidine triad motif (HIT) superfamily, but is the only member with an alanine residue at position 149 (Ala-149). Enzymatic analysis revealed that the Ala-149 deletion mutant displayed substrate specificity for diadenosine 5′,5′′′-P1,P5-pentaphosphate and was inactive on Ap4A and other substrates that are utilized by the wild-type enzyme.
Vertical and Horizontal Movements of Yellowfin Tuna in the Gulf of Mexico
Authors: Hoolihan J. P. , Wells R. J. D. , Luo J. , Falterman B. , Prince E. D. , Rooker J. R.
Published: October 2014

Pop up satellite archival tags (n = 31) were deployed on Yellowfin Tuna Thunnus albacares in the Gulf of Mexico for periods ranging from 14 to 95 d. Differences in diel vertical behavior were assessed by comparing time spent at temperature relative to the surface temperature (ΔT). Pooled samples revealed that 31% of darkness hours, 20% of twilight hours, and 12% of daylight hours were spent in the uniform temperature surface layer (i.e., ΔT = 0). Total time spent above 100 m was less during daylight (90.0%) than during darkness (99.8%), suggesting greater exploration of deeper depths during daylight hours. Maximum depth visited ranged from 208 to 984 m, and minimum temperature visited ranged from 5.4°C to 11.8°C. Only a small proportion of total time was spent at temperatures colder than 8°C below the surface temperature. Horizontal excursions for the majority of individuals were less than 100 km from the point of release; however, three individuals moved distances of 411–1,124 km, suggesting that this species has the capability to move relatively long distances within the Gulf of Mexico. The ΔT values are provided in tabular format and serve as direct input variables for use in habitat standardization models.

Received January 7, 2014; accepted June 8, 2014
Impaired Exercise Capacity following Atrial Septal Defect Closure: An Invasive Study of the Right Heart and Pulmonary Circulation
Authors: Santos Mário , Systrom David , Epstein Stephen E. , John Anitha , Ruiz George , Landzberg Michael J. , Opotowsky Alexander R.
Published: October 2014

Patients with early repair of an isolated atrial septal defect (ASD) are expected to have unremarkable right ventricular (RV) and pulmonary circulation physiology. Some studies, however, suggest persistent functional impairment. We aimed to examine the role of abnormal RV and pulmonary vascular response to exercise in patients who had undergone ASD closure. Using a previously published data set, we reviewed invasive exercise cardiopulmonary testing with right‐sided hemodynamic data for 12 asymptomatic patients who had undergone ASD closure. The 5 (42%) patients with impaired maximal oxygen uptake (o2max) were older and exhibited a lower peak cardiac index (5.6 ± 0.8 vs. 9.0 ± 1.2 L/min/m2; P =. 005) because of abnormal stroke volume augmentation (+3.2 ± 3.9 vs. +17.4 ± 10.2 mL/m2; P =. 02). While all resting hemodynamic variables were similar, patients with low o2max tended to have abnormal total pulmonary vascular resistance change during exercise (+11% ± 41% vs. ?28% ± 26%; P =. 06) and had a steeper relation between mean pulmonary arterial pressure and cardiac index (5.8 ± 0.6 vs. 2.2 ± 0.1 L/min/m2; P =. 02). The increase in peak mean RV power during exercise was also significantly lower in the impaired‐o2max patients (4.7 ± 1.6 vs. 7.6 ± 2.1 J/s; P =. 04). As described in the original study, despite normal resting hemodynamics, a subset of asymptomatic patients with repaired ASD had diminished exercise capacity. Our analysis allows us to conclude that this is due to a combination of abnormal pulmonary vascular response to exercise and impaired RV function.
Inefficiency of Male and Female Labor Supply in Agricultural Households: Evidence from Uganda
Authors: Andrews Martyn J. , Golan Jennifer , Lay Jann
Published: October 2014

This article analyzes the efficiency of the intra‐household allocation of female and male labor inputs in agricultural production. In a collective household model, spouses’ optimal on‐farm labor supply is such that the marginal rate of technical substitution between male and female labor is equated over different crops. Using the Uganda National Household Survey 2005/06, we test whether this condition holds by estimating production functions and controlling for endogeneity using a method proposed by Gandhi, Navarro, and Rivers (2009). We find that women are less productive than men, that there is more female labor input on low productivity parcels, and that men are relatively more productive on female‐controlled plots compared with male‐controlled plots. Total farm output could be higher and Pareto improvements could be possible if male labor was reallocated to female‐controlled plots and/or female labor was reallocated to male‐controlled plots.
DIANA—algorithmic improvements for analysis of data-independent acquisition MS data
Authors: Teleman Johan , Röst Hannes L , Rosenberger George , Schmitt Uwe , Malmström Lars , Malmström Johan , Levander Fredrik
Published: October 2014

Motivation: Data independent acquisition mass spectrometry has emerged as a reproducible and sensitive alternative in quantitative proteomics, where parsing the highly complex tandem mass spectra requires dedicated algorithms. Recently, targeted data extraction was proposed as a novel analysis strategy for this type of data, but it is important to further develop these concepts to provide quality-controlled, interference-adjusted and sensitive peptide quantification.

Results: We here present the algorithm DIANA and the classifier PyProphet, which are based on new probabilistic sub-scores to classify the chromatographic peaks in targeted data-independent acquisition data analysis. The algorithm is capable of providing accurate quantitative values and increased recall at a controlled false discovery rate, in a complex gold standard dataset. Importantly, we further demonstrate increased confidence gained by the use of two complementary data-independent acquisition targeted analysis algorithms, as well as increased numbers of quantified peptide precursors in complex biological samples.

Availability and implementation: DIANA is implemented in scala and python and available as open source (Apache 2.0 license) or pre-compiled binaries from http://quantitativeproteomics.org/diana. PyProphet can be installed from PyPi (https://pypi.python.org/pypi/pyprophet).

Supplementary information:  Supplementary data are available at Bioinformatics online.
MetMSLine: an automated and fully integrated pipeline for rapid processing of high-resolution LC–MS metabolomic datasets
Authors: Edmands William M. B. , Barupal Dinesh K. , Scalbert Augustin
Published: October 2014

Summary: MetMSLine represents a complete collection of functions in the R programming language as an accessible GUI for biomarker discovery in large-scale liquid-chromatography high-resolution mass spectral datasets from acquisition through to final metabolite identification forming a backend to output from any peak-picking software such as XCMS. MetMSLine automatically creates subdirectories, data tables and relevant figures at the following steps: (i) signal smoothing, normalization, filtration and noise transformation (PreProc.QC.LSC.R); (ii) PCA and automatic outlier removal (Auto.PCA.R); (iii) automatic regression, biomarker selection, hierarchical clustering and cluster ion/artefact identification (Auto.MV.Regress.R); (iv) Biomarker—MS/MS fragmentation spectra matching and fragment/neutral loss annotation (Auto.MS.MS.match.R) and (v) semi-targeted metabolite identification based on a list of theoretical masses obtained from public databases (DBAnnotate.R).

Availability and implementation: All source code and suggested parameters are available in an un-encapsulated layout on http://wmbedmands.github.io/MetMSLine/. Readme files and a synthetic dataset of both X-variables (simulated LC–MS data), Y-variables (simulated continuous variables) and metabolite theoretical masses are also available on our GitHub repository.

Contact:  ScalbertA@iarc.fr
PPDMs—a resource for mapping small molecule bioactivities from ChEMBL to Pfam-A protein domains
Authors: Kruger Felix A. , Gaulton Anna , Nowotka Michal , Overington John P.
Published: October 2014

Summary: PPDMs is a resource that maps small molecule bioactivities to protein domains from the Pfam-A collection of protein families. Small molecule bioactivities mapped to protein domains add important precision to approaches that use protein sequence searches alignments to assist applications in computational drug discovery and systems and chemical biology. We have previously proposed a mapping heuristic for a subset of bioactivities stored in ChEMBL with the Pfam-A domain most likely to mediate small molecule binding. We have since refined this mapping using a manual procedure. Here, we present a resource that provides up-to-date mappings and the possibility to review assigned mappings as well as to participate in their assignment and curation. We also describe how mappings provided through the PPDMs resource are made accessible through the main schema of the ChEMBL database.

Availability and implementation: The PPDMs resource and curation interface is available at https://www.ebi.ac.uk/chembl/research/ppdms/pfam_maps. The source-code for PPDMs is available under the Apache license at https://github.com/chembl/pfam_maps. Source code is available at https://github.com/chembl/pfam_map_loader to demonstrate the integration process with the main schema of ChEMBL.

Contact:  jpo@ebi.ac.uk
Navigating protected genomics data with UCSC Genome Browser in a Box
Authors: Haeussler Maximilian , Raney Brian J. , Hinrichs Angie S. , Clawson Hiram , Zweig Ann S. , Karolchik Donna , Casper Jonathan , Speir Matthew L. , Haussler David , Kent W. James
Published: October 2014

Summary: Genome Browser in a Box (GBiB) is a small virtual machine version of the popular University of California Santa Cruz (UCSC) Genome Browser that can be run on a researcher's own computer. Once GBiB is installed, a standard web browser is used to access the virtual server and add personal data files from the local hard disk. Annotation data are loaded on demand through the Internet from UCSC or can be downloaded to the local computer for faster access.

Availability and implementation: Software downloads and installation instructions are freely available for non-commercial use at https://genome-store.ucsc.edu/. GBiB requires the installation of open-source software VirtualBox, available for all major operating systems, and the UCSC Genome Browser, which is open source and free for non-commercial use. Commercial use of GBiB and the Genome Browser requires a license (http://genome.ucsc.edu/license/).

Contact:  genome@soe.ucsc.edu
Huntington’s Disease in a Historical Context
Authors: Harper Peter S.
Published: October 2014

Huntington’s disease (HD) provides a paradigm for advancement of our understanding of numerous inherited brain degenerations. The classic 1872 description by George Huntington led to its recognition worldwide. HD was one of the first clearly Mendelian disorders recognized, but also one closely linked to abuses of eugenics. It has provided a model for analyzing unusual genetic features, notably genetic anticipation, and for positional cloning of disease genes. The finding that its molecular basis is an unstable trinucleotide repeat expansion coding for polyglutamine has led to an increasing understanding of its pathogenesis and possibilities for therapy. HD has been a prototype for the wise use of genetic testing and for recognition of the ethical issues that can arise, especially in presymptomatic testing. It has provided a model for international research collaborations, for development of lay associations to support patients and families, and for the close ties between these associations and research workers.
Neuropsychiatry and Neuropsychology
Authors: Craufurd David , Snowden Julie S.
Published: October 2014

Huntington’s disease (HD) causes a combination of motor, cognitive, and psychiatric changes; of these, the behavioral and cognitive aspects cause the greatest disability and have the highest impact on quality of life. The most common and troublesome behavioral problems are depression, suicidal thinking, irritability, apathy, and perseveration. Apathy and perseveration become more common as the disease progresses and correlate with other markers of disease progression, including cognitive impairment, whereas mood changes do not. The most prominent cognitive changes are psychomotor slowing and problems in executive skills and memory. Emotional processing and odor recognition difficulties also occur early. Simple psychomotor measures provide sensitive markers of change, even in premanifest HD, and therefore are crucial in evaluating efficacy of therapeutic interventions. The causes of problem behaviors in HD are complex and reflect an interaction of biologic, social, and environmental factors.
Juvenile Huntington’s Disease
Authors: Quarrell Oliver W. J.
Published: October 2014

In approximately 5% of cases of Huntington’s disease, onset is before 20 years of age, and these cases are defined as juvenile Huntington’s disease (JHD). The clinical and pathologic features of JHD overlap with those of typical adult-onset disease, so it is not a distinct entity. As a generalization, however, dystonia and bradykinesia are more likely to occur earlier in the disease process, epilepsy is more frequent, the average CAG repeat length is longer, and the pathology within the brain is more widespread. There are conflicting reports in the literature regarding both disease duration and disease progression. Management of JHD patients, and their families, requires a multidisciplinary, symptomatic, and supportive approach. Despite the lack of an evidence base for pharmacologic management and other interventions, helpful reviews and suggestions are available.
Neuropathology in the Human Brain
Authors: Waldvogel Henry J. , Kim Eric H. , Tippett Lynette J. , Vonsattel Jean-Paul G. , Faull Richard L. M.
Published: October 2014

The neuropathology of Huntington’s disease (HD) has been studied for many years, but it is only now becoming clear that despite the disease being caused by dysfunction of a single gene, expressed as an expanded polyglutamine in the huntingtin protein, there is a major variability in the pathology throughout different brain regions, especially the basal ganglia and cerebral cortex. Also, the symptoms present as varying degrees of involuntary movements, mood, personality changes, cognitive changes, and dementia, which can vary throughout the course of the disease and vary greatly between cases. Recent extensive clinicopathologic studies suggest that the variable degeneration of the striatum and cerebral cortex correlates with the variable symptom profiles that characterize HD. These overall results suggest that despite the single-gene etiology of HD, there are multiple pathways of degeneration in the forebrain in HD that reflect the symptom diversity.
Normal Function of Huntingtin
Authors: Zuccato Chiara , Cattaneo Elena
Published: October 2014

Huntingtin (HTT) is the 3,144–amino acid protein product of the Huntington’s disease gene (HTT), which can be traced back through 800 million years of evolution. It carries a trinucleotide CAG repeat that encodes polyglutamine (polyQ) at an evolutionarily conserved NH2-terminal position in exon 1. This chapter discusses the discoveries that have mapped the evolutionary history of HTT and the CAG repeat and the critical role of the protein in development as well as its activities in the adult brain. During embryogenesis, HTT is critical for gastrulation, neurulation, and neurogenesis. In the adult brain, HTT acts as an antiapoptotic protein and promotes transcription of neuronal genes and vesicle transport. Subversion or exacerbation of HTT brain function by an abnormally expanded polyQ repeat contributes to neuronal vulnerability in HD and suggests that loss of normal HTT function may be implicated in the disease.
Pathogenic Mechanisms
Authors: Hughes Alis , Jones Lesley
Published: October 2014

Huntington’s disease (HD) pathogenesis is complex. In the two decades since the gene and its mutation were discovered, there has been extensive exploration of how the expanded CAG repeat in HTT leads to neurodegeneration in HD. This chapter focuses on the mechanisms that potentially contribute to the dysfunction and death of cells in HD. These include repeat instability and RNA toxicity and the production, processing, modification, and degradation of mutant huntingtin. The effects of mutant HTT on cellular processes such as transcription, transport, neurotransmission, and protein clearance are also described. The interdependence and individual importance of these mechanisms in disease etiology remains to be clarified; however, consideration of each could be important for the development of therapeutic interventions in HD.
Peripheral Pathology
Authors: van der Burg Jorien M. M. , Aziz N. Ahmad , Björkqvist Maria
Published: October 2014

Clinicians and researchers have previously focused on the neurologic and psychiatric aspects of Huntington’s disease (HD). However, it is becoming evident that many neurodegenerative disorders are also complicated by pathology in tissues outside the brain. Although many clinical features of HD can be ascribed to neuronal loss and dysfunction, there is accumulating evidence indicating a role for the pathology of non-neuronal tissues in the disease process. Mutant huntingtin is expressed throughout the body and may induce pathology in parallel in both the brain and other organs. Insights into peripheral pathology in HD have the potential of improving knowledge of key pathogenic mechanisms. This chapter describes peripheral manifestations of HD, including weight loss, muscle wasting, and cardiac dysfunction, and discusses how these might constitute targets for drug treatment as well as offering disease modeling systems and potential sources of biomarkers.
Disseminated Cutaneous Mycobacterium chelonae Infection in a Patient With Acute Myeloid Leukemia
Authors: Roukens Anna Helena , Mendels Elodie J. , Verbeet Nicolette L. , von dem Borne Peter A. , Nicolae-Cristea Alina R. , Bentvelsen Robbert G. , van Doorn Remco , de Boer Mark G.
Published: October 2014

We report a case of disseminated cutaneous Mycobacterium chelonae infection in a patient who was treated with chemotherapy for acute myeloid leukemia. We discuss the clinical manifestations, diagnosis, and treatment of this unusual infection in neutropenic patients.
Effects of Adjuvant Radiotherapy in Patients With Synovial Sarcoma
Authors: Song Sanghyuk , Park Junghwan , Kim Hak Jae , Kim Il Han , Han Ilkyu , Kim Han-Soo , Kim Suzy
Published: October 2014

Objectives:

To analyze the treatment outcomes and the effects of adjuvant radiotherapy (RT) in patients with synovial sarcoma (SS).

Materials and Methods:

The medical records of 103 patients treated with definitive surgery for SS, with/without RT, from August 1982 to July 2013 were reviewed retrospectively. The median age of the patients was 33 years (range, 5 to 72 y). The most frequent tumor location was the extremities (79 patients, 77%). Seventy-five patients (73%) received adjuvant RT and 26 (25%) did not. The median dose of adjuvant RT was 61.2 Gy (range, 45 to 66.6 Gy).

Results:

The median follow-up period was 5.4 years (range, 0.2 to 31.0 y). The 5- and 10-year overall survival rates were 77 % and 65%, respectively. The progression-free survival (PFS) rates at 5 and 10 years were 52% and 43%, respectively. The most common site of initial failure was the lung (24 patients), followed by local recurrence (14 patients). The 5-year local-recurrence-free survival (LRFS) and distant-metastasis-free survival (DMFS) rates were 80% and 63%, respectively. On multivariate analysis, a mitosis count of <10 per 10 high-power fields (HPF) was a significant predictor of better overall survival, PFS, LRFS, and DMFS (P=0.004, <0.001, 0.025, and <0.001, respectively). Adjuvant RT was an additional prognostic factor for better PFS and LRFS (P=0.006 and 0.028, respectively). A positive/uncheckable resection margin was associated with poor prognosis for DMFS (P=0.011). There was no significant difference in LRFS between the higher and lower RT dose groups (<63 Gy group, 89%; ≥63 Gy group, 88%;P=0.772).

Conclusions:

The lung and primary site were frequent sites of failure in patients treated with definitive surgery for SS. Adjuvant RT improved LRFS and PFS. Frequent mitotic figures (≥10 mitoses per 10 HPF) were the worst prognostic factor for these patients.
Origin of cellular asymmetries in the pre-implantation mouse embryo: a hypothesis
Authors: Takaoka Katsuyoshi , Hamada Hiroshi
Published: October 2014

The first cell fate decision during mouse development concerns whether a blastomere will contribute to the inner cell mass (ICM; which gives rise to the embryo proper) or to trophectoderm (TE; which gives rise to the placenta). The position of a cell within an 8- to 16-cell-stage embryo correlates with its future fate, with outer cells contributing to TE and inner cells to the ICM. It remains unknown, however, whether an earlier pre-pattern exists. Here, we propose a hypothesis that could account for generation of such a pre-pattern and which is based on epigenetic asymmetry (such as in histone or DNA methylation) between maternal and paternal genomes in the zygote.
From blastocyst to gastrula: gene regulatory networks of embryonic stem cells and early mouse embryogenesis
Authors: Parfitt David-Emlyn , Shen Michael M.
Published: October 2014

To date, many regulatory genes and signalling events coordinating mammalian development from blastocyst to gastrulation stages have been identified by mutational analyses and reverse-genetic approaches, typically on a gene-by-gene basis. More recent studies have applied bioinformatic approaches to generate regulatory network models of gene interactions on a genome-wide scale. Such models have provided insights into the gene networks regulating pluripotency in embryonic and epiblast stem cells, as well as cell-lineage determinationin vivo. Here, we review how regulatory networks constructed for different stem cell types relate to corresponding networksin vivoand provide insights into understanding the molecular regulation of the blastocyst–gastrula transition.
Heading forwards: anterior visceral endoderm migration in patterning the mouse embryo
Authors: Stower Matthew J. , Srinivas Shankar
Published: October 2014

The elaboration of anterior–posterior (A–P) pattern is one of the earliest events during development and requires the precisely coordinated action of several players at the level of molecules, cells and tissues. In mammals, it is controlled by a specialized population of migratory extraembryonic epithelial cells, the anterior visceral endoderm (AVE). The AVE is a signalling centre that is responsible for several important patterning events during early development, including specifying the orientation of the A–P axis and the position of the heart with respect to the brain. AVE cells undergo a characteristic stereotypical migration which is crucial to their functions.
Elucidation of the bicarbonate binding site and insights into the carboxylation mechanism of (N5)-carboxyaminoimidazole ribonucleotide synthase (PurK) fromBacillus anthracis
Authors: Tuntland Micheal L. , Santarsiero Bernard D. , Johnson Michael E. , Fung Leslie W.-M.
Published: October 2014

Structures of (N5)-carboxyaminoimidazole ribonucleotide synthase (PurK) fromBacillus anthraciswith various combinations of ATP, ADP, Mg2+, bicarbonate and aminoimidazole ribonucleotide (AIR) in the active site are presented. The binding site of bicarbonate has only been speculated upon previously, but is shown here for the first time. The binding involves interactions with the conserved residues Arg272, His274 and Lys348. These structures provide insights into each ligand in the active site and allow a possible mechanism to be proposed for the reaction that converts bicarbonate and AIR, in the presence of ATP, to produce (N5)-carboxyaminoimidazole ribonucleotide. The formation of a carboxyphosphate intermediate through ATP phosphoryl transfer is proposed, followed by carboxylation of AIR to give the product, facilitated by a cluster of conserved residues and an active-site water network.
Structure of the OsSERK2 leucine-rich repeat extracellular domain
Authors: McAndrew Ryan , Pruitt Rory N. , Kamita Shizuo G. , Pereira Jose Henrique , Majumdar Dipali , Hammock Bruce D. , Adams Paul D. , Ronald Pamela C.
Published: October 2014

Somatic embryogenesis receptor kinases (SERKs) are leucine-rich repeat (LRR)-containing integral membrane receptors that are involved in the regulation of development and immune responses in plants. It has recently been shown that rice SERK2 (OsSERK2) is essential for XA21-mediated resistance to the pathogenXanthomonas oryzaepv.oryzae. OsSERK2 is also required for the BRI1-mediated, FLS2-mediated and EFR-mediated responses to brassinosteroids, flagellin and elongation factor Tu (EF-Tu), respectively. Here, crystal structures of the LRR domains of OsSERK2 and a D128N OsSERK2 mutant, expressed as hagfish variable lymphocyte receptor (VLR) fusions, are reported. These structures suggest that the aspartate mutation does not generate any significant conformational change in the protein, but instead leads to an altered interaction with partner receptors.
Structure of the gas vesicle protein GvpF from the cyanobacteriumMicrocystis aeruginosa
Authors: Xu Bo-Ying , Dai Ya-Nan , Zhou Kang , Liu Yun-Tao , Sun Qianqian , Ren Yan-Min , Chen Yuxing , Zhou Cong-Zhao
Published: October 2014

Gas vesicles are gas-filled proteinaceous organelles that provide buoyancy for bacteria and archaea. A gene cluster that is highly conserved in various species encodes about 8–14 proteins (Gvp proteins) that are involved in the formation of gas vesicles. Here, the first crystal structure of the gas vesicle protein GvpF fromMicrocystis aeruginosaPCC 7806 is reported at 2.7 Å resolution. GvpF is composed of two structurally distinct domains (the N-domain and C-domain), both of which display an α+β class overall structure. The N-domain adopts a novel fold, whereas the C-domain has a modified ferredoxin fold with an apparent variation owing to an extension region consisting of three sequential helices. The two domains pack against each otherviainteractions with a C-terminal tail that is conserved among cyanobacteria. Taken together, it is concluded that the overall architecture of GvpF presents a novel fold. Moreover, it is shown that GvpF is most likely to be a structural protein that is localized at the gas-facing surface of the gas vesicle by immunoblotting and immunogold labelling-based tomography.
Crystal structure of 2-{[2-(3-phenylallylidene)hydrazin-1-yl]thiocarbonylsulfanylmethyl}pyridinium chloride
Authors: Low May Lee , Ravoof Thahira Begum S. A. , Tahir Mohamed Ibrahim Mohamed , Crouse Karen A. , Tiekink Edward R. T.
Published: October 2014

In the title salt of anS-substituted dithiocarbazate, C16H16N3S2+·Cl−, the dihedral angles between the almost planar (r.m.s deviation = 0.005 Å) central CN2S2residue and the terminal pyridinium and phenyl rings are 80.09 (11) and 3.82 (11)°, respectively, indicating the cation has an L-shape; the amine H and thione S atoms aresyn. The conformation about each of the imine [1.376 (3) Å] and ethene [1.333 (4) Å] bonds isE. The shortened C—C bond [1.444 (4) Å] linking the double bonds is consistent with conjugation in this part of the molecule. In the crystal, supramolecular layers with a jagged topology are formed by charged-assisted amine-H...Cl−and pyridinium-N+—H...Cl−hydrogen bonds. The layers stack along theaaxis with no specific directional interactions between them.
Crystal structure of (2E)-3-(3-ethoxy-4-hydroxyphenyl)-1-(4-hydroxyphenyl)prop-2-en-1-one
Authors: Vasanthi R. , Reuben Jonathan D. , Elizhlarasi K. S. , Revathi B. K. , Usha G.
Published: October 2014

In the title compound, C17H16O4, the dihedral angle between the benzene rings is 21.22 (1)° and the mean plane of the prop-2-en-1-one group makes dihedral angles of 10.60 (1) and 11.28 (1)°, respectively, with those of the hydroxyphenyl and ethoxyphenyl rings. The ethoxy substituent forms a dihedral angle of 88.79 (2)° with the the prop-2-en-1-one group, which is found to be slightly twisted. In the crystal, phenolic O—H...O hydrogen bonds to the carbonyl O atom form a two-dimensional supramolecular network structure lying parallel to (010).
Crystal structure ofN-(2-hydroxyethyl)-5-nitroisophthalamic acid monohydrate
Authors: Zou Pei , Wang Hong-Yong , Luo Shi-Neng , Liu Ya-Ling , Shen Yong-Jia
Published: October 2014

In the title compound, C10H10N2O6·H2O, the carboxylic acid group and the nitro group are essentially coplanar with the benzene ring [maximum deviation = 0.0264 (9) Å], while the amide group is oriented at a dihedral angle of 9.22 (5)° with respect to the benzene ring. In the crystal, classical O—H...O and N—H...O hydrogen bonds and weak C—H...O interactions link the organic molecules and water molecules of crystallization into a three-dimensional supramolecular architecture.
Crystal structure of μ-1κC:2(η2)-carbonyl-carbonyl-1κC-chlorido-2κCl-μ-chloridoborylene-1:2κ2B:B-[1(η5)-pentamethylcyclopentadienyl](tricyclohexylphosphane-2κP)iron(II)platinum(II) benzene monosolvate
Authors: Braunschweig Holger , Kramer Thomas
Published: October 2014

In the molecular structure of the dinuclear title compound [η5-(C5(CH3)5)(CO)Fe{(μ-BCl)(μ-CO)}PtCl(P(C6H11)3)]·C6H6, the two metal atoms, iron(II) and platinum(II), are bridged by one carbonyl (μ-CO) and one chloridoborylene ligand (μ-BCl). The PtIIatom is additionally bound to a chloride ligand situatedtransto the bridging borylene, and a tricyclohexylphosphane ligand (PCy3)transto the carbonyl ligand, forming a distorted square-planar structural motif at the PtIIatom. The FeIIatom is bound to a pentamethylcyclopentadienyl ligand [η5-C5(CH3)5] and one carbonyl ligand (CO), forming a piano-stool structure. Additionally, one benzene solvent molecule is incorporated into the crystal structure, positioned staggered relative to the pentamethylcyclopentadienyl ligand at the FeIIatom, with a centroid–centroid separation of 3.630 (2) Å.
Capability of X-ray diffraction for the study of microstructure of metastable thin films
Authors: Rafaja David , Wüstefeld Christina , Dopita Milan , Motylenko Mykhaylo , Baehtz Carsten
Published: October 2014

Metastable phases are often used to design materials with outstanding properties, which cannot be achieved with thermodynamically stable compounds. In many cases, the metastable phases are employed as precursors for controlled formation of nanocomposites. This contribution shows how the microstructure of crystalline metastable phases and the formation of nanocomposites can be concluded from X-ray diffraction experiments by taking advantage of the high sensitivity of X-ray diffraction to macroscopic and microscopic lattice deformations and to the dependence of the lattice deformations on the crystallographic direction. The lattice deformations were determined from the positions and from the widths of the diffraction lines, the dependence of the lattice deformations on the crystallographic direction from the anisotropy of the line shift and the line broadening. As an example of the metastable system, the supersaturated solid solution of titanium nitride and aluminium nitride was investigated, which was prepared in the form of thin films by using cathodic arc evaporation of titanium and aluminium in a nitrogen atmosphere. The microstructure of the (Ti,Al)N samples under study was tailored by modifying the [Al]/[Ti] ratio in the thin films and the surface mobility of the deposited species.
New capabilities for `colouring in' the chemistry of crystal defects atom-by-atom
Authors: Haigh Sarah J.
Published: October 2014

The latest generation of scanning transmission electron microscopes equipped with high-efficiency energy-dispersive X-ray detectors are breaking new ground with respect to high-resolution elemental imaging of materials. In this issue, Paulauskaset al.[Acta Cryst.(2014), A70, 524–531] demonstrate impressive results when applying this technique to improve understanding of CdTe dislocation structures.
Do online communities support research collaboration?
Authors: R. Jamali Hamid , Russell Bill , Nicholas David , Watkinson Anthony
Published: October 2014

Purpose

– The purpose of this paper is to explore the extent to which academics are engaged with online communities for research purposes, and the research activities, platforms and tools associated with these communities. In addition, the paper aims to discover the benefits, disadvantages and barriers involved in the use of online communities, and especially in regard to the trust and authority issues, so important in scholarly communications.

Design/methodology/approach

– A layered, mixed-methods approach was used for this complex research topic. Interviews were undertaken with social science and humanities researchers, followed up with focus groups in both the USA and UK. This qualitative work was then followed up with an online questionnaire that generated over 1,000 responses.

Findings

– Over half the sample had experience of an online research community and a majority of researchers are making at least occasional use of one or more Web 2.0 services for communicating their research activity; for developing and sustaining networks and collaboration; or for finding out what others are doing. Big differences exist in membership rates according to subject, but not really by age or other demographic factors. The biggest benefit to joining an online community is the ability to seek information in one’s own specialism. Younger researchers are more engaged with online communities.

Research limitations/implications

– The qualitative research was limited to the UK and USA. While use of online communities is now accepted by both established and younger researchers, the main ways of communicating research remain scholarly journals and books.

Practical implications

– The implications for learned societies and publishers are not clear. Journals are confirmed as the primary way of disseminating research. However, it would be easy for these stakeholders to miss how younger researchers expect to connect in digital communities.

Social implications

– With researchers of all ages accepting the existing and importance of online communities and connections, there are few technical or social barriers to using mainstream digital tools to connect professionally.

Originality/value

– There is little published research considering the role of online research communities, so the study is highly original. It is valuable to discover that researchers still prefer to share research findings primarily through journals, rather than through social technologies.
Information needs and information sources of family caregivers of cancer patients
Authors: Chen Shih-chuan
Published: October 2014

Purpose

– The purpose of this paper is to analyse the information needs of family caregivers of cancer patients. Information sources used by the caregivers were also examined.

Design/methodology/approach

– We interviewed 15 family caregivers (nine females, six males) in Taiwan for this study. The participants were aged from 23 to 67 years, and all except two had attained college or higher degrees. Their relationships with patients included spousal, parental, and that of son or daughter.

Findings

– Family caregivers’ information needs varied along the cancer journey, and they used various information sources to satisfy these needs. Demographic variables affected the information-seeking behaviour of the family caregivers.

Originality/value

– The majority of studies on this topic have been based in western countries. This paper reveals the importance of considering cultural factors. The findings can assist researchers in gaining a greater understanding of the information-seeking behaviour of family caregivers of cancer patients worldwide.