bluuebunny/crossref_metadata_2025 huggingface dataset:
Information quality problems in Farsi web-based learning resources: how do teachers assure of the content quality for classroom use?
Authors: Mohammadi Faegheh , Abrizah A.
Published: December 2013

Although the Web has been seen as a critical source of information in K–12 education, Iranian educators’ acceptance for the web technology to become mainstream in the classroom remains a big challenge. Quality of information might be taken into account towards successful use of web-based learning resources. This study identifies the perceived information quality problems of Farsi web resources to be used in classroom instruction. This qualitative study employs focus group and interviews as the data collection technique, involving 10 secondary school teachers in Iran. It analyzed the information quality problems and information quality assurance applied or suggested by the participants in the context of web resources used in classroom instruction. Eleven dimensions of information quality problems emerged from the focus group discussion, seven of which are associated with content quality. Educators’ perceptions about the quality of web resources might be considered as critical in terms of usage of web resources in the Iranian school context. Not only the information quality dimensions highlighted in this study may help them, but also increased theoretical understanding can translate into practical insights that will benefit professionals who seek to design educational websites for credibility.
Investigations for the effect of parameters on the weld performance of AA 5083-H111 joined by friction stir welding
Authors: Kasman Şefika , Kahraman Fatih
Published: December 2013

In this article, friction stir welding experiments were performed on AA 5083-H111 aluminum alloy using a tool with a triangular pin to study the effect of tool rotational speed and welding speed on the ultimate tensile strength, percentage of elongation (ε), hardness and microstructure. The investigations were done with the optical microscopy, stereomicroscopy, scanning electron microscope and energy dispersive spectroscopy. In the visual inspection, it was observed that some of nugget zones have an onion ring like features and a basin-shaped profile. The ultimate tensile strength and percentage of elongation (ε) of the welds decrease with decreasing the welding speed for the 800 r/min. On the other hand, as the welding speed increases, the UTS and ε decrease for the 1250 rpm/min, the ultimate tensile strength and percentage of elongation (ε) decrease. The main factor, which affects the reduction in both ultimate tensile strength and percentage of elongation (ε), is defects in the welds. A comparison of ultimate tensile strength and percentage of elongation (ε) as a function of tool rotational speed for the 100 mm/min showed that both ultimate tensile strength and percentage of elongation (ε) decrease with the increase in the tool rotational speed. The weld efficiency varied between 88.3% and 92% in the defect-free welds. The hardness distribution of the zones on the welds revealed that no remarkable differences exist between them. Hence, the variance on the grain sizes of zones is small.
Caveat Emptor Under Prudentialism
Authors: Frauley Jon
Published: December 2013

Residential home (that is, housing) inspection has been a growth industry in Canada and the United States since its emergence in the 1970s. Within a legal context where the purchase of used housing is governed by the doctrine of caveat emptor, and a political and economic context characterized by prudentialism, home inspection appears to offer a means by which consumers can discharge their legal and political duty to be prudent. However, in Canada, because home inspection is largely unregulated and market driven, consumers of pre-owned housing are placed at a structural disadvantage relative to home inspectors. This article argues that we should be cautious of embracing private residential home inspection as an adequate consumer protection mechanism or form of risk consulting because there are fundamental and irreconcilable differences between a public service that strives to meet the objective of the public good and home inspection as a private service offered for public consumption that strives to meet the objectives of private interests.
Book Review: Start-up Sutra
Authors: Batra Annurag
Published: December 2013

Rohit Prasad, Start-up Sutra, 2013, New Delhi: Hachette India, pp. 168, ₹199 (Paperback).
Mortality in Cambodia
Authors: Goyet Sophie , Rammaert Blandine , McCarron Margaret , Khieu Virak , Fournier Isabelle , Kitsutani Paul , Ly Sowath , Mounts Anthony , Letson William G. , Buchy Philippe , Vong Sirenda
Published: December 2013

To estimate the 2009-2010 death rates, causes, and patterns of mortality in rural Cambodia, we conducted active, population-based death surveillance in 25 rural villages of Cambodia from March 2009 to August 2010. Among the population of 28 053 under surveillance, 280 deaths were reported and explored by physician-certified verbal autopsies, using the International Classification of Diseases 10, yielding an overall mortality rate (MR) of 6.7/1000 persons-year (95% CI 5.74-7.68). The MR was 39.1/1000 live births for those younger than 5 years old. Infants accounted for 5.4% of all deaths. In children younger than 5 years, infectious and parasitic diseases were the leading causes of death. In children 5 to 14 years, 3 out of 4 deaths were due to injuries. Adult deaths were mainly attributed to noncommunicable diseases (52%). We conclude that this rural population is facing a substantial burden of noncommunicable diseases while still struggling with infectious diseases, respiratory diseases in particular.
Diagnostic laparoscopy in the cat
Authors: Robertson Elise , Twedt David , Webb Craig
Published: December 2013

Practical relevance:

The integration of minimally invasive techniques into feline practice seems to be an intuitive step forward, especially for those cases where the owner may be reluctant to subject their cat to major surgery ‘just for a biopsy’. Although ultrasound is frequently employed as a diagnostic tool in similar cases, this modality can only provide information on gross abnormalities in organ size and shape, echogenicity and internal architecture; even with ultrasound-guided fine-needle aspiration a definitive diagnosis is rarely achieved. So the clinician and owner are left with unanswered questions that are central to the diagnosis, the most appropriate treatment to pursue and the prognosis for the cat. Laparoscopy does require anesthesia and is more expensive than ultrasound; however, when performed correctly, it is only marginally more invasive and vastly more informative, with a proven track record of minimal morbidity.

Audience:

This article is aimed at all feline practitioners, from first opinion through to the referral setting. It is intended to encourage practitioners untrained in minimally invasive procedures to seek formalized training, especially those who want to expand their diagnostic capabilities. For those already performing minimally invasive surgery, it describes how laparoscopic techniques can be applied to many feline gastrointestinal cases.

Evidence base:

Information provided in this article is based on published literature, comprising original studies, case review series and textbook chapters, and the authors’ own clinical experience.
Diagnostic laparoscopy in the cat
Authors: Robertson Elise , Webb Craig , Twedt David
Published: December 2013

Practical relevance:

Minimally invasive techniques are becoming increasingly available in both first opinion and referral veterinary surgeries. Clients may be reluctant to pursue open surgery for the collection of biopsy samples in a sick cat but may be more open to a laparoscopic approach. Furthermore, a laparoscopic approach provides excellent visualization of the abdominal organs and enables high quality biopsies to be taken that are invariably more diagnostic than percutaneous needle biopsies. Although the feline patient is small in size, its distensible abdomen allows more room for surgical manipulation than afforded by a similar sized canine patient.

Clinical challenges:

Clinical challenges for the most part relate to mastering laparoscopic technique. Familiarity with the use of long instrumentation viewed on a two-dimensional screen is essential. Hemostasis is an important consideration and suitable instrumentation for achieving hemostasis should be available at all times. Insufflation of the abdomen carries its own challenges with regard to anesthesia and this is covered in an accompanying article in this Special Issue series.

Aim:

This article introduces the feline practitioner to basic techniques required to effectively utilize diagnostic laparoscopy within feline medical investigations. It focuses on the common procedures of liver biopsy, cholecystocentesis, pancreatic biopsy, kidney biopsy and laparoscopic-assisted intestinal biopsy.

Evidence base:

Information provided in this article is drawn from the published literature and the authors’ own clinical experience.
Phonological skills and ability to perceive auditorily the structure of a word at the level of a single phoneme at ages 2–6
Authors: Suortti Outi , Lipponen Lasse
Published: December 2013

The present study is the first part of a longitudinal research project investigating whether children become more aware of phonemes or rhyming when they learn letters or letter sounds or even begin to read, and if so how. For the present paper, the phonological awareness of young children aged 2–6 years was analyzed, particularly their auditory knowledge of the phonemic structure of words as well as their knowledge of rhyme. Altogether, 110 children from Finnish day-care centres performed seven phonological tasks and a vocabulary size test. The results showed a clear age-dependent improvement in phonological awareness. Blending words of phonemes, separating rhyming words from each other and correcting words by substituting the wrong phoneme with the right one were found to be easier tasks for 2- to 5-year-old children than producing rhymes, twisting words or detecting an initial letter.
Stability of Clinical Etiologic Diagnosis in Dementia and Mild Cognitive Impairment
Authors: Koepsell Thomas D. , Gill Dawn P. , Chen Baojiang
Published: December 2013

Many new therapies for dementia target a specific pathologic process and must be applied early. Selection of specific therapy is based on the clinical etiologic diagnosis. We sought to determine the stability of the clinical etiologic diagnosis over time and to identify factors associated with instability. We identified 4141 patients with dementia or mild cognitive impairment who made at least 2 visits approximately a year apart to a dementia research center, receiving a clinical etiologic diagnosis on each visit. We assessed concordance of etiologic diagnoses across visits, κ-statistics, and transition probabilities among diagnoses. The primary clinical etiologic diagnosis remained stable for 91% of patients but with a net shift toward dementia with Lewy bodies and Alzheimer’s disease. Lower diagnostic stability was significantly associated with older age, nonwhite race, milder disease at presentation, more underlying conditions contributing to cognitive decline, lack of a consistent spouse/partner informant, and being evaluated by different clinicians on different visits. Multistate Markov modeling generally confirmed these associations. Clinical etiologic diagnoses were generally stable. However, several readily ascertained characteristics were associated with higher instability. These associations may be useful to clinicians for anticipating when an etiologic diagnosis may be more prone to future change.
Human Resource Development in Service Firms Across Cultures
Authors: Galperin Bella L. , Lituchy Terri R.
Published: December 2013

Due to the continued growth of the global services sector, it is essential that service firms have a greater understanding of the implementation of human resource development (HRD) in different cultures and how HRD relates to service quality. The purpose of this article is to develop a theoretical model that stresses the importance of HRD alignment with national and organizational culture in increasing perceptions of service quality. In this article, we present a model that integrates the role of national culture, organizational culture, and HRD into a conceptual framework and develops several propositions. This article suggests that the overall effectiveness in service quality will likely increase when HRD interventions are aligned with the national culture and organizational culture. HRD managers in service firms should understand the role of national culture and organizational culture when implementing HRD. Managers who fail to consider national values and their relationship with organizational culture will be less successful at implementing HRD.
Patterns of Caribbean Masculinities and Condom Compliance Among Males in Grenada
Authors: Hegamin-Younger Cecilia , Jeremiah Rohan , Bilbro Nicole
Published: December 2013

The construction of Caribbean male identities based on ideas of masculinity has raised widespread concerns across the island states, and in a region with such high rates of teenage pregnancy (18%), stigmatizing safe sex, contraception, and HIV/AIDS prevalence can only exacerbate the problem. The purpose of this study was to examine the extent to which males use condoms and to explore the association of condom use with their concern with acquiring and transmission of sexually transmitted infections.
Evaluation of pharmacist counseling in improving knowledge, attitude, and practice in chronic kidney disease patients
Authors: Ghimirey Anurodh , Sapkota Binaya , Shrestha Sweta , Basnet Nabin , Shankar P Ravi , Sapkota Sujata
Published: December 2013

Background:

Chronic kidney disease is a public health problem with an increasing incidence and prevalence, poor outcomes, and high cost. Patient involvement forms the keystone in the management of chronic kidney disease. This study evaluated effects of pharmacist-provided counseling in dialysis patients in terms of their knowledge, attitude, and practice outcomes.

Methods:

A total of 64 patients with chronic kidney disease were enrolled into the prospective, pre–post study based on the inclusion and exclusion criteria. The knowledge, attitude, and practice of patients regarding chronic kidney disease were assessed and recorded via baseline questionnaire. Case group patients were counseled regarding chronic kidney disease, their medication, diet, and lifestyle, and they were also provided with informative leaflet, whereas in the control group patients, the pharmacist did not intervene. After 1-month intervention, knowledge, attitude, and practice scores of patients of both groups were measured using the same knowledge, attitude, and practice questionnaire. Effectiveness of counseling on case group patients was evaluated by comparing the mean knowledge, attitude, and practice scores before and after counseling by paired t-test.

Results:

Mean knowledge, attitude, and practice scores before intervention were 8.16 ± 4.378, 38.19 ± 3.217, and 6.69 ± 0.896, respectively, and these scores were changed to 13.75 ± 3.510, 38.78 ± 3.035, and 6.91 ± 0.777, respectively, after the intervention ( p < 0.05).

Conclusions:

The pharmacist-provided counseling is effective in improving knowledge, attitude, and practice of patients toward the disease management.
The 2013 Karnataka Assembly Outcome: Government Performance and Party Organization Matters
Authors: Shastri Sandeep
Published: December 2013

This article assesses the outcome of state assembly elections in Karnataka held in 2013. Extensively using the Lokniti- Centre for the Study of Developing Societies (CSDS), Delhi Pre-Poll Survey data, the article concludes that the verdict was more an unequivocal indictment of the state government rather than a pro-Congress vote. A Congress victory in the state was essentially the channelizing of an anti-incumbency vote. The article also makes out the case that the vote for a party is often a function of the voter’s perception of the organizational strength of the party. Mapping electoral developments in the state, the article concludes that a phase of authentic multi-party competition is clearly ushered in by the 2013 electoral verdict.
Book Review: Corruption and Reform in India: Public Services in the Digital Age
Authors: Nooruddin Irfan
Published: December 2013

Jennifer Bussell, Corruption and Reform in India: Public Services in the Digital Age. New York: Cambridge University Press. 2012. 306 pages. ₹ 895.
Book Review: More than Maoism: Politics and Policies of Insurgency in South Asia and Ordinary People, Extraordinary Violence
Authors: Sen Rumela
Published: December 2013

Robin Jeffrey, Ronojoy Sen and Pratima Sen, eds, More than Maoism: Politics and Policies of Insurgency in South Asia. New Delhi: Manohar. 2012. 470 pages. ₹ 1,250.

Chitralekha, Ordinary People, Extraordinary Violence. New Delhi: Routledge. 2012. 348 pages. ₹ 795.
Book Review: Mobilizing Restraint: Democracy and Industrial Conflict in Post-reform South Asia
Authors: Wood Jolie M.F.
Published: December 2013

Emmanuel Teitelbaum, Mobilizing Restraint: Democracy and Industrial Conflict in Post-reform South Asia. New Delhi: Cambridge University Press India Pvt. Ltd. 2011. 244 pages. ₹ 795.
VTCdb: a gene co-expression database for the crop species Vitis vinifera (grapevine)
Authors: Wong Darren CJ , Sweetman Crystal , Drew Damian P , Ford Christopher M
Published: December 2013

Background

Gene expression datasets in model plants such asArabidopsishave contributed to our understanding of gene function and how a single underlying biological process can be governed by a diverse network of genes. The accumulation of publicly available microarray data encompassing a wide range of biological and environmental conditions has enabled the development of additional capabilities including gene co-expression analysis (GCA). GCA is based on the understanding that genes encoding proteins involved in similar and/or related biological processes may exhibit comparable expression patterns over a range of experimental conditions, developmental stages and tissues. We present an open access database for the investigation of gene co-expression networks within the cultivated grapevine,Vitis vinifera.

Description

The new gene co-expression database, VTCdb (http://vtcdb.adelaide.edu.au/Home.aspx), offers an online platform for transcriptional regulatory inference in the cultivated grapevine. Using condition-independent and condition-dependent approaches, grapevine co-expression networks were constructed using the latest publicly available microarray datasets from diverse experimental series, utilising the AffymetrixVitis viniferaGeneChip (16 K) and the NimbleGen Grape Whole-genome microarray chip (29 K), thus making it possible to profile approximately 29,000 genes (95% of the predicted grapevine transcriptome). Applications available with the online platform include the use of gene names, probesets, modules or biological processes to query the co-expression networks, with the option to choose between Affymetrix or Nimblegen datasets and between multiple co-expression measures. Alternatively, the user can browse existing network modules using interactive network visualisation and analysis via CytoscapeWeb. To demonstrate the utility of the database, we present examples from three fundamental biological processes (berry development, photosynthesis and flavonoid biosynthesis) whereby the recovered sub-networks reconfirm established plant gene functions and also identify novel associations.

Conclusions

Together, we present valuable insights into grapevine transcriptional regulation by developing network models applicable to researchers in their prioritisation of gene candidates, for on-going study of biological processes related to grapevine development, metabolism and stress responses.
Characterization of cytokinin signaling and homeostasis gene families in two hardwood tree species: Populus trichocarpa and Prunus persica
Authors: Immanen Juha , Nieminen Kaisa , Duchens Silva Héctor , Rodríguez Rojas Fernanda , Meisel Lee A , Silva Herman , Albert Victor A , Hvidsten Torgeir R , Helariutta Ykä
Published: December 2013

Background

Through the diversity of cytokinin regulated processes, this phytohormone has a profound impact on plant growth and development. Cytokinin signaling is involved in the control of apical and lateral meristem activity, branching pattern of the shoot, and leaf senescence. These processes influence several traits, including the stem diameter, shoot architecture, and perennial life cycle, which define the development of woody plants. To facilitate research about the role of cytokinin in regulation of woody plant development, we have identified genes associated with cytokinin signaling and homeostasis pathways from two hardwood tree species.

Results

Taking advantage of the sequenced black cottonwood (Populus trichocarpa) and peach (Prunus persica) genomes, we have compiled a comprehensive list of genes involved in these pathways. We identified genes belonging to the six families of cytokinin oxidases (CKXs), isopentenyl transferases (IPTs), LONELY GUY genes (LOGs), two-component receptors, histidine containing phosphotransmitters (HPts), and response regulators (RRs). All together 85Populusand 45Prunusgenes were identified, and compared to their Arabidopsis orthologs through phylogenetic analyses.

Conclusions

In general, when compared to Arabidopsis, differences in gene family structure were often seen in only one of the two tree species. However, one class of genes associated with cytokinin signal transduction, the CKI1-like family of two-component histidine kinases, was larger in bothPopulusandPrunusthan in Arabidopsis.
Escherichia coli challenge and one type of smectite alter intestinal barrier of pigs
Authors: Almeida Juliana Abranches Soares , Liu Yanhong , Song Minho , Lee Jeong Jae , Gaskins H Rex , Maddox Carol Wolfgang , Osuna Orlando , Pettigrew James Eugene
Published: December 2013

An experiment was conducted to determine how anE. colichallenge and dietary clays affect the intestinal barrier of pigs. Two groups of 32 pigs (initial BW: 6.9 ± 1.0 kg) were distributed in a 2 × 4 factorial arrangement of a randomized complete block design (2 challenge treatments: sham orE. coli, and 4 dietary treatments: control, 0.3% smectite A, 0.3% smectite B and 0.3% zeolite), with 8 replicates total. Diarrhea score, growth performance, goblet cell size and number, bacterial translocation from intestinal lumen to lymph nodes, intestinal morphology, and relative amounts of sulfo and sialo mucins were measured. TheE. colichallenge reduced performance, increased goblet cell size and number in the ileum, increased bacterial translocation from the intestinal lumen to the lymph nodes, and increased ileal crypt depth. One of the clays (smectite A) tended to increase goblet cell size in ileum, which may indicate enhanced protection. In conclusion,E. coliinfection degrades intestinal barrier integrity but smectite A may enhance it.
G protein-coupled receptors: computer-aided ligand discovery and computational structural analyses in the 2010s
Authors: Costanzi Stefano
Published: December 2013

G protein-coupled receptors, or GPCRs, are a large superfamily of proteins found on the plasma membrane of cells. They are involved in most physiological and pathophysiological functions and constitute the target of the majority of marketed drugs. Although these receptors have been historically elusive to attempts of structural determination, GPCR crystallography is now in full blossom, opening the way to structure-based drug discovery and enabling homology modeling. This thematic issue of the journal In Silico Pharmacology, which illustrates how the expanding body of structural knowledge is fostering complex computational analyses of the structure-function relationships of the receptors and their interactions with their ligands, stems from the 31st Camerino-Cyprus-Noordwijkerhout Symposium held in Italy, in May 2013, at the University of Camerino. Specifically, it originates from a session of the symposium entitled “Structure-Based Discovery of Ligands of G Protein-Coupled Receptors: Finally a Reality”, and features a mix of research articles and reviews on the application of computational modeling to the analysis of the structure of GPCRs and the interactions of the receptors with their ligands.
High end GPCR design: crafted ligand design and druggability analysis using protein structure, lipophilic hotspots and explicit water networks
Authors: Mason Jonathan S , Bortolato Andrea , Weiss Dahlia R , Deflorian Francesca , Tehan Benjamin , Marshall Fiona H
Published: December 2013

Purpose

G Protein-Coupled Receptors (GPCRs) are a large family of therapeutically important proteins and as diverse X-ray structures become available it is increasingly possible to leverage structural information for rational drug design.

We present herein approaches that use explicit water networks combined with energetic surveys of the binding site (GRID), providing an enhanced druggability and ligand design approach, with structural understanding of ligand binding, including a ‘magic’ methyl and binding site mutations, and a fast new approach to generate and score waters.

Methods

The GRID program was used to identify lipophilic and hydrogen bonding hotspots. Explicit full water networks were generated and scored for (pseudo)apo structures and ligand-protein complexes using a new approach, WaterFLAP (Molecular Discovery), together with WaterMap (Schrödinger) for (pseudo)apo structures. A scoring function (MetaScore) was developed using a fast computational protocol based on several short adiabatic biased MD simulations followed by multiple short well-tempered metadynamics runs.

Results

Analysis of diverse ligands binding to the adenosine A2A receptor together with new structures for the δ/κ/μ opioid and CCR5 receptors confirmed the key role of lipophilic hotspots in driving ligand binding and thus design; the displacement of ‘unhappy’ waters generally found in these regions provides a key binding energy component. Complete explicit water networks could be robustly generated for protein-ligand complexes using a WaterFLAP based approach. They provide a structural understanding of structure-activity relationships such as a ‘magic methyl’ effect and with the metadynamics approach a useful estimation of the binding energy changes resulting from active site mutations.

Conclusions

The promise of full structure-based drug design (SBDD) for GPCRs is now possible using a combination of advanced experimental and computational data. The conformational thermostabilisation of StaR® proteins provide the ability to easily generate biophysical screening data (binding including fragments, kinetics) and to get crystal structures with both potent and weak ligands. Explicit water networks for apo and ligand-complex structures are a critical ‘third dimension’ for SBDD and are key for understanding ligand binding energies and kinetics. GRID lipophilic hotspots are found to be key drivers for binding. In this context ‘high end’ GPCR ligand design is now enabled.
Deficient spontaneous in vitro apoptosis and increased tmTNF reverse signaling-induced apoptosis of monocytes predict suboptimal therapeutic response of rheumatoid arthritis to TNF inhibition
Authors: Meusch Undine , Klingner Maria , Baerwald Christoph , Rossol Manuela , Wagner Ulf
Published: December 2013

Introduction

In vitro apoptosis of peripheral monocytes in rheumatoid arthritis (RA) is disturbed and influenced by cytokine production and transmembrane TNF (tmTNF) reverse signaling. The goal of the study was the analysis of the predictive value of the rate of in vitro apoptosis for the therapeutic response to anti-TNF treatment.

Methods

Spontaneous and tmTNF reverse signaling-induced apoptosis were determined in vitro in monocytes from 20 RA patients prior to initiation of therapeutic TNF inhibition with etanercept, and the subsequent clinical response was monitored.

Results

Spontaneous in vitro apoptosis was significantly reduced in RA patients compared to controls. Deficiency in spontaneous apoptosis was associated with an insufficient therapeutic response according to the European League Against Rheumatism (EULAR) response criteria and less reduction of the disease activity determined by disease activity score (DAS) 28. High susceptibility to reverse signaling-induced apoptosis was also associated with less efficient reduction in the DAS28. Of note, a strong negative correlation between the two apoptotic parameters was discernible, possibly indicative of two pathogenetically relevant processes counter-regulating each other.

tmTNF reverse signaling induced in vitro production of soluble IL1-RI and IL-1RII only in monocytes not deficient in spontaneous apoptosis, and the levels of soluble IL1-RII were found to be predictive of a good clinical response to Etanercept.

Conclusion

Although tmTNF reverse signaling is able to induce apoptosis of RA monocytes in vitro, this process appears to occur in vitro preferentially in patients with suboptimal therapeutic response. Resistance to spontaneous in vitro apoptosis, in contrast, is a predictor of insufficient response to treatment.
The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution
Authors: Raats Dina , Frenkel Zeev , Krugman Tamar , Dodek Itay , Sela Hanan , Šimková Hana , Magni Federica , Cattonaro Federica , Vautrin Sonia , Bergès Hélène , Wicker Thomas , Keller Beat , Leroy Philippe , Philippe Romain , Paux Etienne , Doležel Jaroslav , Feuillet Catherine , Korol Abraham , Fahima Tzion
Published: December 2013

Background

The wheat genome sequence is an essential tool for advanced genomic research and improvements. The generation of a high-quality wheat genome sequence is challenging due to its complex 17 Gb polyploid genome. To overcome these difficulties, sequencing through the construction of BAC-based physical maps of individual chromosomes is employed by the wheat genomics community. Here, we present the construction of the first comprehensive physical map of chromosome 1BS, and illustrate its unique gene space organization and evolution.

Results

Fingerprinted BAC clones were assembled into 57 long scaffolds, anchored and ordered with 2,438 markers, covering 83% of chromosome 1BS. The BAC-based chromosome 1BS physical map and gene order of the orthologous regions of model grass species were consistent, providing strong support for the reliability of the chromosome 1BS assembly. The gene space for chromosome 1BS spans the entire length of the chromosome arm, with 76% of the genes organized in small gene islands, accompanied by a two-fold increase in gene density from the centromere to the telomere.

Conclusions

This study provides new evidence on common and chromosome-specific features in the organization and evolution of the wheat genome, including a non-uniform distribution of gene density along the centromere-telomere axis, abundance of non-syntenic genes, the degree of colinearity with other grass genomes and a non-uniform size expansion along the centromere-telomere axis compared with other model cereal genomes. The high-quality physical map constructed in this study provides a solid basis for the assembly of a reference sequence of chromosome 1BS and for breeding applications.
Obligate mutualism within a host drives the extreme specialization of a fig wasp genome
Authors: Xiao Jin-Hua , Yue Zhen , Jia Ling-Yi , Yang Xin-Hua , Niu Li-Hua , Wang Zhuo , Zhang Peng , Sun Bao-Fa , He Shun-Min , Li Zi , Xiong Tuan-Lin , Xin Wen , Gu Hai-Feng , Wang Bo , Werren John H , Murphy Robert W , Wheeler David , Niu Li-Ming , Ma Guang-Chang , Tang Ting , Bian Sheng-Nan , Wang Ning-Xin , Yang Chun-Yan , Wang Nan , Fu Yue-Guan , Li Wen-Zhu , Yi Soojin V , Yang Xing-Yu , Zhou Qing , Lu Chang-Xin , Xu Chun-Yan , He Li-Juan , Yu Li-Li , Chen Ming , Zheng Yuan , Wang Shao-Wei , Zhao Shuang , Li Yan-Hong , Yu Yang-Yang , Qian Xiao-Ju , Cai Yue , Bian Lian-Le , Zhang Shu , Wang Jun-Yi , Yin Ye , Xiao Hui , Wang Guan-Hong , Yu Hui , Wu Wen-Shan , Cook James M , Wang Jun , Huang Da-Wei
Published: December 2013

Background

Fig pollinating wasps form obligate symbioses with their fig hosts. This mutualism arose approximately 75 million years ago. Unlike many other intimate symbioses, which involve vertical transmission of symbionts to host offspring, female fig wasps fly great distances to transfer horizontally between hosts. In contrast, male wasps are wingless and cannot disperse. Symbionts that keep intimate contact with their hosts often show genome reduction, but it is not clear if the wide dispersal of female fig wasps will counteract this general tendency. We sequenced the genome of the fig wasp Ceratosolen solmsi to address this question.

Results

The genome size of the fig wasp C. solmsi is typical of insects, but has undergone dramatic reductions of gene families involved in environmental sensing and detoxification. The streamlined chemosensory ability reflects the overwhelming importance of females finding trees of their only host species, Ficus hispida, during their fleeting adult lives. Despite long-distance dispersal, little need exists for detoxification or environmental protection because fig wasps spend nearly all of their lives inside a largely benign host. Analyses of transcriptomes in females and males at four key life stages reveal that the extreme anatomical sexual dimorphism of fig wasps may result from a strong bias in sex-differential gene expression.

Conclusions

Our comparison of the C. solmsi genome with other insects provides new insights into the evolution of obligate mutualism. The draft genome of the fig wasp, and transcriptomic comparisons between both sexes at four different life stages, provide insights into the molecular basis for the extreme anatomical sexual dimorphism of this species.
Combination of seismic reflection and constrained resistivity inversion with an application to 4D imaging of the CO2 storage site, Ketzin, Germany
Authors: Bergmann P. , Ivandic M. , Norden B. , Rücker C. , Kiessling D. , Lüth S. , Schmidt-Hattenberger C. , Juhlin C.
Published: December 2013

A combination of seismic and geoelectric processing was studied by means of a structurally constrained inversion approach. Structural constraints were interpreted from the seismic data and integrated into the geoelectric inversion through a local regularization, which allowed inverted resistivities to behave discontinuously across defined boundaries. This arranged seismic processing and constrained resistivity inversion in a sequential workflow, making the generic assumption that the petrophysical parameters of both methods change across common lithostructural boundaries. We evaluated the approach using a numerical example and a real data example from the Ketzin [Formula: see text] pilot storage site, Germany. The latter demonstrated the efficiency of this approach for combining 4D seismic and surface-downhole geoelectric data. In consistence with the synthetic example, the constrained resistivity inversions produced clearer delineated images along the boundary between caprock and reservoir formation. Near the [Formula: see text]-flooded reservoir, the seismic and geoelectric time-lapse anomalies correlated well. At some distance to the downhole electrodes, however, the geoelectric images conveyed a notably lower resolution in comparison to the corresponding seismic images. Both methods confirm a northwesterly trend for the [Formula: see text] migration at the Ketzin site, although a rather northerly direction was initially expected. The results demonstrate the relevance of the presented approach for the combination of both methods for integrated geophysical [Formula: see text] storage monitoring.
Lessons from the Behavior of a Monitored 11-Story Building during the 2011 Tohoku Earthquake for Robustness against Design Uncertainties
Authors: Qu Zhe , Sakata Hiroyasu , Midorikawa Saburoh , Wada Akira
Published: December 2013

Specifically detailed pin-supported walls with steel dampers have been used to seismically strengthen an 11-story steel reinforced concrete building. By looking at the observed damage and monitored motions of the building during the M9.0 Tohoku earthquake in 2011, it is demonstrated that nonstructural reinforced concrete partition walls have had a major effect on its seismic behavior during the earthquake, the neglect of which constitutes a major design uncertainty. A finite element model used to assist the retrofit design is calibrated, taking advantage of the accelerograms obtained during the earthquake. The results of nonlinear time-history analysis investigations with the modified model identify both the positive and negative effects of the nonstructural walls at various ground motion intensities, and suggest that the pin-supported wall-frame system exhibits higher robustness against both record-to-record and modeling uncertainties than its bare-frame counterpart does.
Does Division Multiply Desert?
Authors: Pummer Theron
Published: December 2013

It seems plausible that (i) how much punishment a person deserves cannot be affected by the mere existence or nonexistence of another person. We might have also thought that (ii) how much punishment is deserved cannot increase merely in virtue of personal division. I argue that (i) and (ii) are inconsistent with the popular belief that, other things being equal, when people culpably do very wrong or bad acts, they ought to be punished for this—even if they have repented, are now virtuous, and punishing them would benefit no one. Insofar as we cannot deny (i), we are either forced to abandon the popular belief in desert, or else allow that personal division could, as I put it, “multiply desert.” Some may not find the latter, considered by itself, troubling. But I argue that the thesis that division multiplies desert faces a potentially serious problem, which arises in the context of personal fusion. It is difficult to see how to maintain a particular family of desert views in light of the cases here presented.
Agreement Matters: Critical Notice of Derek Parfit, On What Matters
Authors: Darwall Stephen
Published: December 2013

Derek Parfit's Reasons and Persons (1984) mounted a striking defense of Act Consequentialism against a Rawls-inspired Kantian orthodoxy in moral philosophy. On What Matters (2011) is notable for its serious engagement with Kant's ethics and for its arguments in support of the “Triple Theory,” which allies Rule Consequentialism with Kantian and Scanlonian Contractualism against Act Consequentialism as a theory of moral right. This critical notice argues that what underlies this change is a view of the deontic concept of moral rightness that ties it closely to blameworthiness and accountability in a way that effectively concedes a Rawlsian publicity condition. It is also argued that Parfit's arguments that Kantian and Scanlonian Contractualism entail Rule Consequentialism can be resisted. Two elements of Parfit's metaethics are critically discussed. First, concerning Parfit's arguments against subjectivist theories of practical reason, it is argued that a form of subjectivist theory exists that is not only consistent with Parfit's claim that all reasons for acting are object rather than state given, but that can support that claim. Second, it is argued that Parfit's arguments against identifying normative with natural statements and facts do not transfer seamlessly to identifying normative with natural properties.
Is “Region” Still Good to Think?
Authors: Sinha Mrinalini
Published: December 2013

This essay responds to the mission statement of Comparative Studies of South Asia, Africa and the Middle East and considers the place of region in the contemporary postnational and post-area studies moment of scholarship. In particular, it examines the possibilities of leveraging further the opening that the journal created between area studies scholarship and the traditional academic disciplines.
Ethics or Social Sciences?
Authors: V. Sanil
Published: December 2013

As a response to Gopal Guru and Sundar Sarukkai’s book The Cracked Mirror, Sanil’s essay explores the relation between ethics and the social sciences. The essay engages the work of Kant, Aristotle, Martin Heidegger, and Michel Foucault, among others, to make its argument. The Cracked Mirror, Sanil claims, makes a strong plea to take Indian philosophy and theory seriously, and it comes closest to an ethics of theory when it asserts that the task of theory is not merely to explain or interpret but to intensify experience.
Insulin signaling regulates neurite growth during metamorphic neuronal remodeling
Authors: Gu Tingting , Zhao Tao , Hewes Randall S.
Published: December 2013

Although the growth capacity of mature neurons is often limited, some neurons can shift through largely unknown mechanisms from stable maintenance growth to dynamic, organizational growth (e.g. to repair injury, or during development transitions). During insect metamorphosis, many terminally differentiated larval neurons undergo extensive remodeling, involving elimination of larval neurites and outgrowth and elaboration of adult-specific projections. Here, we show in the fruit fly, Drosophila melanogaster (Meigen), that a metamorphosis-specific increase in insulin signaling promotes neuronal growth and axon branching after prolonged stability during the larval stages. FOXO, a negative effector in the insulin signaling pathway, blocked metamorphic growth of peptidergic neurons that secrete the neuropeptides CCAP and bursicon. RNA interference and CCAP/bursicon cell-targeted expression of dominant-negative constructs for other components of the insulin signaling pathway (InR, Pi3K92E, Akt1, S6K) also partially suppressed the growth of the CCAP/bursicon neuron somata and neurite arbor. In contrast, expression of wild-type or constitutively active forms of InR, Pi3K92E, Akt1, Rheb, and TOR, as well as RNA interference for negative regulators of insulin signaling (PTEN, FOXO), stimulated overgrowth. Interestingly, InR displayed little effect on larval CCAP/bursicon neuron growth, in contrast to its strong effects during metamorphosis. Manipulations of insulin signaling in many other peptidergic neurons revealed generalized growth stimulation during metamorphosis, but not during larval development. These findings reveal a fundamental shift in growth control mechanisms when mature, differentiated neurons enter a new phase of organizational growth. Moreover, they highlight strong evolutionarily conservation of insulin signaling in neuronal growth regulation.
Mesomere-derived glutamate decarboxylase-expressing blastocoelar mesenchyme cells of sea urchin larvae
Authors: Katow Hideki , Katow Tomoko , Abe Kouki , Ooka Shioh , Kiyomoto Masato , Hamanaka Gen
Published: December 2013

The ontogenetic origin of blastocoelar glutamate decarboxylase (GAD)-expressing cells (GADCs) in larvae of the sea urchin Hemicentrotus pulcherrimus was elucidated. Whole-mount in situ hybridisation (WISH) detected transcription of the gene that encodes GAD in H. pulcherrimus (Hp-gad) in unfertilised eggs and all blastomeres in morulae. However, at and after the swimming blastula stage, the transcript accumulation was particularly prominent in clumps of ectodermal cells throughout the embryonic surface. During the gastrula stage, the transcripts also accumulated in the endomesoderm and certain blastocoelar cells. Consistent with the increasing number of Hp-gad transcribing cells, immunoblot analysis indicated that the relative abundance of Hp-Gad increased considerably from the early gastrula stage until the prism stage. The expression pattern of GADCs determined by immunohistochemistry was identical to the pattern of Hp-gad transcript accumulation determined using WISH. In early gastrulae, GADCs formed blastocoelar cell aggregates around the blastopore with primary mesenchyme cells. The increase in the number of blastocoelar GADCs was inversely proportional to the number of ectodermal GADCs ranging from a few percent of total GADCs in early gastrulae to 80% in late prism larvae; this depended on ingression of ectodermal GADCs into the blastocoel. Some of the blastocoelar GADCs were fluorescein-positive in the larvae that developed from the 16-cell stage chimeric embryos; these comprised fluorescein-labeled mesomeres and unlabelled macromeres and micromeres. Our finding indicates that some of the blastocoelar GADCs are derived from the mesomeres and thus they are the new group of mesenchyme cells, the tertiary mesenchyme cells.
Histone chaperone FACT regulates homologous recombination by chromatin remodeling through interaction with RNF20
Authors: Oliveira Douglas V , Kato Akihiro , Nakamura Kyosuke , Ikura Tsuyoshi , Okada Masahiro , Kobayashi Junya , Yanagihara Hiromi , Saito Yuichiro , Tauchi Hiroshi , Komatsu Kenshi
Published: December 2013

The E3 ubiquitin ligase RNF20 regulates chromatin structure through ubiquitination of histone H2B, so that early homologous recombination repair (HRR) proteins can access the DNA in eukaryotes during repair. However, it remains unresolved how RNF20 itself approaches the DNA in the presence of chromatin structure. Here, we identified the histone chaperone FACT as a key protein in the early step of HRR. Depletion of SUPT16H, a component of FACT, caused pronounced defects in accumulations of repair proteins, consequently decreased HRR activity. This led to enhanced sensitivity to ionizing radiation (IR) and mitomycin-C in a fashion similar to RNF20-deficient cells, indicating that SUPT16H is essential for RNF20-mediated pathway. Indeed, SUPT16H directly bound to RNF20 in vivo, and mutation at the RNF20's RING-finger domain abolished its interaction and accumulation, as well as RAD51 and BRCA1 at sites of DSBs, whereas the localization of SUPT16H remained intact. Interestingly, PAF1, implicated in transcription as a mediator of FACT and RNF20 association, was dispensable for DNA damage-induced interaction of RNF20 with SUPT16H. Furthermore, depletion of SUPT16H caused pronounced defects in RNF20-mediated H2B ubiquitination and thereby, impaired accumulation of the chromatin remodeling factor SNF2h. Consistent with this observation, the defective phenotypes of SUPT16H were effectively counteracted by enforced nucleosome relaxation. Taken together, present results indicate a primary role of FACT in RNF20 recruitment and the resulting chromatin remodeling for initiation of HRR.
Sharp-1 regulates TGF-β signaling and skeletal muscle regeneration
Authors: Acharjee Sujata , Chung Teng-Kai , Gopinadhan Suma , Shankar Shilpa Rani , Wang Yaju , Li Li , Vercherat Cecile , Gulbagci Neriman Tuba , Rossner Moritz , Taneja Reshma
Published: December 2013

Sharp-1 is a basic helix-loop-helix (bHLH) transcriptional repressor which is involved in a number of cellular processes. Our previous studies have demonstrated that Sharp-1 is a negative regulator of skeletal myogenesis and blocks differentiation of muscle precursor cells by modulating MyoD activity. In order to understand its role in pre- and post-natal myogenesis, we assessed skeletal muscle development, and freeze-injury induced regeneration in Sharp-1 deficient mice. We show that embryonic skeletal muscle development is not impaired in the absence of Sharp-1, but post-natally, the regenerative capacity is compromised. Although the initial phases of injury induced regeneration proceed normally in Sharp-1-/- mice, during late stages, the mutant muscle exhibits necrotic fibers, calcium deposits, and fibrosis. TGF-β expression, as well as pSmad 2/3 levels are sustained in the mutant tissue, and treatment with decorin, a TGF-β blocker improves histo-pathology of Sharp-1-/- injured muscles. In vitro, Sharp-1 associates with Smad3, and its overexpression inhibits TGF-β and Smad3-mediated expression of extracellular matrix genes in myofibroblasts. These results demonstrate that Sharp-1 regulates muscle regenerative capacity, at least in part, by modulation of TGF-β signaling.