bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcriptome Differences between Alternative Sex Determining Genotypes in the House Fly,Musca domestica
Authors: Meisel Richard P , Scott Jeffrey G , Clark Andrew G
Published: March 2015

Sex determination evolves rapidly, often because of turnover of the genes at the top of the pathway. The house fly,Musca domestica, has a multifactorial sex determination system, allowing us to identify the selective forces responsible for the evolutionary turnover of sex determination in action. There is a male determining factor,M, on the Y chromosome (YM), which is probably the ancestral state. AnMfactor on the third chromosome (IIIM) has reached high frequencies in multiple populations across the world, but the evolutionary forces responsible for the invasion of IIIMare not resolved. To test if the IIIMchromosome invaded because of sex-specific selection pressures, we used mRNA sequencing to determine if isogenic males that differ only in the presence of the YMor IIIMchromosome have different gene expression profiles. We find that more genes are differentially expressed between YMand IIIMmales in testis than head, and that genes with male-biased expression are most likely to be differentially expressed between YMand IIIMmales. We additionally find that IIIMmales have a "masculinized" gene expression profile, suggesting that the IIIMchromosome has accumulated an excess of male-beneficial alleles because of its male-limited transmission. These results are consistent with the hypothesis that sex-specific selection acts on alleles linked to the male-determining locus driving evolutionary turnover in the sex determination pathway.
Repeatability of evolution on epistatic landscapes
Authors: Bauer Benedikt , Gokhale Chaitanya S.
Published: March 2015

Evolution is a dynamic process. The two classical forces of evolution are mutation and selection. Assuming small mutation rates, evolution can be predicted based solely on the fitness differences between phenotypes. Predicting an evolutionary process under varying mutation rates as well as varying fitness is still an open question. Experimental procedures, however, do include these complexities along with fluctuating population sizes and stochastic events such as extinctions. We investigate the mutational path probabilities of systems having epistatic effects on both fitness and mutation rates using a theoretical and computational framework. In contrast to previous models, we do not limit ourselves to the typicalstrong selection, weak mutation (SSWM)-regime or to fixed population sizes. Rather we allow epistatic interactions to also affect mutation rates. This can lead to qualitatively non-trivial dynamics. Pathways, that are negligible in the SSWM-regime, can overcome fitness valleys and become accessible. This finding has the potential to extend the traditional predictions based on the SSWM foundation and bring us closer to what is observed in experimental systems.
Breaking through evolutionary constraint by environmental fluctuations
Authors: de Vos Marjon GJ , Dawid Alexandre , Sunderlikova Vanda , Tans Sander J
Published: March 2015

Epistatic interactions can frustrate and shape evolutionary change1, 23–7. Indeed, phenotypes may fail to evolve because essential mutations can only be selected positively if fixed simultaneously5,8,9. How environmental variability affects such constraints is poorly understood. Here we studied genetic constraints in fixed and fluctuating environments, using theEscherichia coli lacoperon as a model system for genotype-environment interactions. The data indicated an apparent paradox: in different fixed environments, mutational trajectories became trapped at sub-optima where no further improvements were possible, while repeated switching between these same environments allowed unconstrained adaptation by continuous improvements. Pervasive cross-environmental trade-offs transformed peaks into valleys upon environmental change, thus enabling escape from entrapment. This study shows that environmental variability can lift genetic constraint, and that trade-offs not only impede but can also facilitate adaptive evolution.
CSN and CAVA: variant annotation tools for rapid, robust next-generation sequencing analysis in the clinic
Authors: Münz Márton , Ruark Elise , Renwick Anthony , Ramsay Emma , Clarke Matthew , Mahamdallie Shazia , Cloke Victoria , Seal Sheila , Strydom Ann , Lunter Gerton , Rahman Nazneen
Published: March 2015

Background

Next-generation sequencing (NGS) offers unprecedented opportunities to expand clinical genomics. It also presents challenges with respect to integration with data from other sequencing methods and historical data. Provision of consistent, clinically applicable variant annotation of NGS data has proved difficult, particularly of indels, an important variant class in clinical genomics. Annotation in relation to a reference genome sequence, the DNA strand of coding transcripts and potential alternative variant representations has not been well addressed. Here we present tools that address these challenges to provide rapid, standardized, clinically appropriate annotation of NGS data in line with existing clinical standards.

Methods

We developed a clinical sequencing nomenclature (CSN), a fixed variant annotation consistent with the principles of the Human Genome Variation Society (HGVS) guidelines, optimized for automated variant annotation of NGS data. To deliver high-throughput CSN annotation we created CAVA (Clinical Annotation of VAriants), a fast, lightweight tool designed for easy incorporation into NGS pipelines. CAVA allows transcript specification, appropriately accommodates the strand of a gene transcript and flags variants with alternative annotations to facilitate clinical interpretation and comparison with other datasets. We evaluated CAVA in exome data and a clinicalBRCA1/BRCA2gene testing pipeline.

Results

CAVA generated CSN calls for 10,313,034 variants in the ExAC database in 13.44 hours, and annotated the ICR1000 exome series in 6.5 hours. Evaluation of 731 different indels from a single individual revealed 92% had alternative representations in left aligned and right aligned data. Annotation of left aligned data, as performed by many annotation tools, would thus give clinically discrepant annotation for the 339 (46%) indels in genes transcribed from the forward DNA strand. By contrast, CAVA provides the correct clinical annotation for all indels. CAVA also flagged the 370 indels with alternative representations of a different functional class, which may profoundly influence clinical interpretation. CAVA annotation of 50BRCA1/BRCA2gene mutations from a clinical pipeline gave 100% concordance with Sanger data; only 8/25BRCA2mutations were correctly clinically annotated by other tools.

Conclusions

CAVA is a freely available tool that provides rapid, robust, high-throughput clinical annotation of NGS data, using a standardized Clinical Sequencing Nomenclature.
Effect of Coenzyme Q10 on Th1/Th2 Paradigm in Females with Idiopathic Recurrent Pregnancy Loss
Authors: Talukdar Ayantika , Sharma Kandala Aparna , Rai Reeta , Deka Dipika , Rao Donthamsetty Nageshwara
Published: March 2015

Problem

Recurrent pregnancy loss is characterized by predominant Th1‐type immunity and increased reactive oxygen species. Low levels of Coenzyme Q10 are found in the plasma of RPL as compared to healthy pregnant females. Our aim was to investigate whether in vitro supplementation of PBMCs from such females with CoQ10 could change the observed Th1 bias.

Method of study

PBMCs were isolated from 20 RPL pregnant and non‐pregnant females and 16 healthy pregnant females and incubated with CoQ10 in in vitro conditions. Phenotyping of Th1, Th2, and Th17 cells was performed by flow cytometry. Cytokine levels were determined by ELISA.

Results

PBMCs treated with CoQ10 showed significantly decreased percentage of Th1 cells (P < 0.005) in pregnant females with history of RPL than in the untreated ones. Also, levels of IFN‐γ and TNF‐α were significantly decreased in the culture supernatant of treated PBMCs from RPL. DCFDA staining showed significantly reduced production of ROS in the treated PBMCs in RPL females.

Conclusion

CoQ10 was effective in maintaining the immune homeostasis by reducing the proportion of IFN‐γ‐producing T cells and proinflammatory cytokine levels in the RPL pregnant females. This property could be attributed to the capability of CoQ10 in reducing oxidative stress by decreasing ROS production.
Primary synovial epithelioid sarcoma of the knee: distinctly unusual location leading to its confusion with pigmented villonodular synovitis
Authors: Chow Louis Tsun Cheung
Published: March 2015

Epithelioid sarcoma (ES) is a rare malignant soft tissue tumor occurring in the distal extremities of young adults and is characterized histologically by nodules of epithelioid cells showing central necrosis. Intra‐articular ES is extremely rare; only four cases have been reported, but their radiologic and histologic documentation of intra‐articular origin have been imprecise. We report the first radiologically and histologically well‐documented case of primary synovial ES. A 59‐year‐old woman presented with pain followed by swelling of her right knee for 6 months. MRI revealed an entirely intra‐articular nodular synovial mass in the lateral part of the right knee joint in a background of diffusely thickened synovium. Synovectomy was performed under the clinical impression of pigmented villonodular synovitis (PVNS), a diagnosis erroneously confirmed by the reporting pathologist. The tumor rapidly recurred 3 months afterward and the diagnosis of primary synovial ES was made. Despite above‐knee amputation, the tumor continued to spread proximally to the retroperitoneum. She developed multiple lung metastases and died 20 months after initial presentation. The nodular aggregates of tumor cells with central necrosis resulted in diffuse polypoid synovial thickening mimicking tuberculous synovitis and PVNS. The tumor cells showed positive staining for EMA, CK19, CD34, and complete loss of INI1 staining, establishing the diagnosis of primary synovial ES. The ES spread from the synovium to and along the joint capsule, and then extra‐articularly into the soft tissue surrounding the knee joint, with lymphovascular permeation. Such pattern of spread calls for radical surgical excision as the treatment of choice.
Peripheral blood monocyte and T‐lymphocyte activation levels at diagnosis predict long‐term survival in head and neck squamous cell carcinoma patients
Authors: Aarstad Hans Jørgen , Vintermyr Olav K. , Ulvestad Elling , Aarstad Helene H. , Kross Kenneth W. , Heimdal John. H.
Published: March 2015

This study was performed to determine whether peripheral blood (PB) monocyte and/or lymphocyte activation at diagnosis were associated with long‐term prognosis in patients with head and neck squamous cell carcinoma (HNSCC), and to what extent such prognostic properties relate to human papilloma virus (HPV)‐associated tumor infection of the included patients. This was a long‐term prospective study describing patient survival in relation to PB T lymphocyte and monocyte activation in patients observed for up to 14 years following diagnosis. Sixty‐four patients from a consecutive cohort of newly diagnosed HNSCC patients along with 16 non‐cancer control patients were included over a period of almost 2 years. Monocyte responsiveness was assessed at diagnosis (N = 56 HNSCC/16 non‐cancer controls) by measuring net levels of spontaneous vs lipopolysaccharide‐induced monocyte chemotactic protein (MCP)‐1 secretion in vitro. PB T lymphocyte activation was determined (N = 58 HNSCC/16 controls) by measuring the percentage of T cells expressing CD69 by flow cytometry. Whether HPV infection or not was determined by PCR analysis on formalin fixed paraffin‐embedded tumor tissue. Tumor HPV‐positive patients had better prognosis than HPV‐negative patients. A low net MCP‐1 response in monocytes predicted increased survival (Relative risk (RR) = 2.1; Confidence interval (CI): 1.1–4.0; p < 0.05). A low percentage of CD69 positive T lymphocytes also predicted better prognosis (RR = 2.6; CI: 1.3–5.0; p = 0.005). The predictive power of MCP‐1 monocyte and CD69 T lymphocyte measures were retained when adjusted for age and gender of the patients and shown to be independent of each other (N = 50 HNSCC/16 controls). The results were similar in HPV tumor‐positive and ‐negative patients. Patients with high monocyte‐ and/or T lymphocyte activation status had low survival with 8% 5 year overall survival (OS) compared to 65% 5 year OS for patients with dual low activation levels (RR = 0.27; CI: 0.14–0.56; p < 0.001), mostly secondary to disease‐specific survival. Both tumor HPV‐positive and ‐negative HNSCC patients with high percentage of CD69 positive T lymphocytes and/or high monocyte MCP‐1 secretion had low long‐term survival. The data suggest that the general inflammatory and adaptive immune systems are independently linked to the clinical aggressiveness of both tumor HPV‐negative and ‐positive HNSCC patients.
Japanese Society of Medical Oncology Clinical Guidelines: RAS (KRAS/NRAS) mutation testing in colorectal cancer patients
Authors: Taniguchi Hiroya , Yamazaki Kentaro , Yoshino Takayuki , Muro Kei , Yatabe Yasushi , Watanabe Toshiaki , Ebi Hiromichi , Ochiai Atsushi , Baba Eishi , Tsuchihara Katsuya
Published: March 2015

The Japanese guidelines for the testing of KRAS mutations in colorectal cancer have been used for the past 5 years. However, new findings of RAS (KRAS/NRAS) mutations that can further predict the therapeutic effects of anti‐epidermal growth factor receptor (EGFR) antibody therapy necessitated a revision of the guidelines. The revised guidelines included the following five basic requirements for RAS mutation testing to highlight a patient group in which anti‐EGFR antibody therapy may be ineffective: First, anti‐EGFR antibody therapy may not offer survival benefit and/or tumor shrinkage to patients with expanded RAS mutations. Thus, current methods to detect KRAS exon 2 (codons 12 and 13) mutations are insufficient for selecting appropriate candidates for this therapy. Additional testing of extended KRAS/NRAS mutations is recommended. Second, repeated tests are not required for the detection; tissue materials of either primary or metastatic lesions are applicable for RAS mutation testing. Evaluating RAS mutations prior to anti‐EGFR antibody therapy is recommended. Third, direct sequencing with manual dissection or allele‐specific PCR‐based methods is currently applicable for RAS mutation testing. Fourth, thinly sliced sections of formalin‐fixed, paraffin‐embedded tissue blocks are applicable for RAS mutation testing. One section stained with H&E should be provided to histologically determine whether the tissue contains sufficient amount of tumor cells for testing. Finally, RAS mutation testing must be performed in laboratories with appropriate testing procedures and specimen management practices.
801. CYPRIPEDIUM CALCEOLUS
Authors: Fay Michael F. , Taylor Ian
Published: March 2015

Cypripedium calceolus L., the lady's slipper orchid, is described and illustrated. Details of its distribution, relationships, pollination, patterns of hybridization and its history and conservation in England are provided. Notes on propagation and cultivation are also included.
802. DACTYLORHIZA VIRIDIS
Authors: Fay Michael F. , Sayers Brendan , Taylor Ian
Published: March 2015

Dactylorhiza viridis(L.)R.M.Bateman,Pridgeon &M.W.Chase, the frog orchid, is described and illustrated. Details of its distribution, relationships, pollination, patterns of hybridization and its conservation status inBritain andIreland are provided. Notes on propagation and cultivation are also included.
803. OPHRYS FUCIFLORA
Authors: Fay Michael F. , Taylor Ian
Published: March 2015

Ophrys fuciflora (F.W.Schmidt) Moench, late spider orchid, is described and illustrated. Details of its relationships, pollination biology, distribution and conservation status are presented. Possible reasons for its rarity in Britain are suggested. Cultivation and propagation are discussed.
804. OPHRYS INSECTIFERA
Authors: Fay Michael F. , Taylor Ian , Sayers Brendan
Published: March 2015

Ophrys insectifera L., fly orchid is described and illustrated. Details of its relationships, pollination biology, distribution and conservation status are presented. Possible reasons for its ongoing decline in the UK are suggested. Cultivation and propagation are discussed.
806. ORCHIS PURPUREA
Authors: Fay Michael F. , Taylor Ian
Published: March 2015

Orchis purpurea Huds., lady orchid, is described and illustrated. Details of its relationships, pollination biology, distribution and conservation status are presented. Cultivation and propagation are discussed.
Insights into Frizzled evolution and new perspectives
Authors: Schenkelaars Quentin , Fierro‐Constain Laura , Renard Emmanuelle , Hill April L. , Borchiellini Carole
Published: March 2015

The Frizzled proteins (FZDs) are a family of trans‐membrane receptors that play pivotal roles in Wnt pathways and thus in animal development. Based on evaluation of the Amphimedon queenslandica genome, it has been proposed that two Fzd genes may have been present before the split between demosponges and other animals. The major purpose of this study is to go deeper into the evolution of this family of proteins by evaluating an extended set of available data from bilaterians, cnidarians, and different basally branching animal lineages (Ctenophora, Placozoa, Porifera). The present study provides evidence that the last common ancestor of metazoans did possess two Fzd genes, and that the last common ancestor of cnidarians and bilaterians may have possessed four Fzd. Furthermore, amino acid analyses revealed an accurate diagnostic motif for these four FZD subfamilies facilitating the assignation of Frizzled paralogs to each subfamily. By highlighting conserved amino acids for each FZD subfamily, our study could also provide a framework for further research on the precise mechanisms that have driven FZD neo‐functionalization.
Patterning of mammalian heterodont dentition within the upper and lower jaws
Authors: Yamanaka Atsushi , Iwai Haruki , Uemura Masanori , Goto Tetsuya
Published: March 2015

Mammalian heterodont dentition is differentiated into incisors, canines, premolars, and molars in the mesial–distal direction, in both the upper and lower jaws. Although all the lower teeth are rooted in the mandible, the upper incisors are rooted in the premaxilla and the upper canine and the teeth behind it are in the maxilla. The present study uncovers ontogenetic backgrounds to these shared and differing mesiodistal patterns of the upper and lower dentition. To this end, we examined the dentition development of the house shrew, Suncus murinus, instead of the rodent model animals because the dentition of this primitive eutherian species includes all the tooth classes, and no toothless diastema region. In the shrew, the upper incisor‐forming region extended over the medial nasal prominence and the mesial part of the maxillary prominence. Consequently, the maxillary and mandibular prominences were in a mirror‐image relationship in terms of the mesiodistally differentiated tooth‐forming regions and of the complementary gene expression pattern, with Bmp4 in the mesial and Fgf8 in the distal regions. This suggests shared molecular mechanisms regulating tooth class differentiation between the upper and lower jaws. However, the premaxillary bone appeared within the mesenchyme of the medial nasal prominence, but grew distally beyond the former epithelial boundary with the maxillary prominence to form, finally, the incisive (premaxillary–maxillary) suture just mesial to the canine. Therefore, the developmental locations of the upper incisors are not inconsistent with the classical osteological criterion of the upper canine by comparative odontologists.
A combination of developmental plasticity, parental effects, and genetic differentiation mediates divergences in life history traits between dung beetle populations
Authors: Beckers Oliver M. , Anderson Wendy , Moczek Armin P.
Published: March 2015

The dung beetle, Onthophagus taurus, was introduced <50 years ago from its native Mediterranean range into Western Australia (WA) and the Eastern United States (EUS). The intensity of intra‐ and interspecific competition for dung as a breeding resource is substantially higher in WA. First, we tested whether differential resource competition in the two exotic ranges is associated with divergences in life history traits, which impact on resource use. We predicted that high levels of resource competition in WA should favor females that produce brood balls more efficiently and of altered size, and produce offspring more readily when a breeding opportunity arises. Furthermore, we predicted that larvae from WA populations may have evolved more efficient development and thus exhibit higher eclosion success, shorter development time, and altered body size under standardized conditions. Second, we examined the likely developmental mechanisms underlying these divergences, that is, genetic differentiation, developmental plasticity, or parental effects in a common garden experiment. Field‐collected EUS and WA populations significantly differed, as predicted, in most of the traits examined. However, these differences are facilitated by a complex combination of proximate mechanisms. Developmental plasticity and (grand) parental effects mediated differences related to reproductive performance, whereas genetic differentiation mediated differences in the duration of larval development. Our study highlights that population divergences can be the product of a patchwork of proximate mechanisms, with each mechanism adjusting different traits in a way that the resulting composite phenotype may be better suited to its competitive environment.
Expression patterns of Eph genes in the “dual visual development” of the lamprey and their significance in the evolution of vision in vertebrates
Authors: Suzuki Daichi G. , Murakami Yasunori , Yamazaki Yuji , Wada Hiroshi
Published: March 2015

Image‐forming vision is crucial to animals for recognizing objects in their environment. In vertebrates, this type of vision is achieved with paired camera eyes and topographic projection of the optic nerve. Topographic projection is established by an orthogonal gradient of axon guidance molecules, such as Ephs. To explore the evolution of image‐forming vision in vertebrates, lampreys, which belong to the basal lineage of vertebrates, are key animals because they show unique “dual visual development.” In the embryonic and pre‐ammocoete larval stage (the “primary” phase), photoreceptive “ocellus‐like” eyes develop, but there is no retinotectal optic nerve projection. In the late ammocoete larval stage (the “secondary” phase), the eyes grow and form into camera eyes, and retinotectal projection is newly formed. After metamorphosis, this retinotectal projection in adult lampreys is topographic, similar to that of gnathostomes. In this study, we explored the involvement of Ephs in lamprey “dual visual development” and establishment of the image‐form vision. We found that gnathostome‐like orthogonal gradient expression was present in the retina during the “secondary” phase; i.e., EphB showed a gradient of expression along the dorsoventral axis, while EphC was expressed along the anteroposterior axis. However, no orthogonal gradient expression was observed during the “primary” phase. These observations suggest that Ephs are likely recruited de novo for the guidance of topographical “second” optic nerve projection. Transformations during lamprey “dual visual development” may represent “recapitulation” from a protochordate‐like ancestor to a gnathostome‐like vertebrate ancestor.
Young People, Community Radio and Urban Life
Authors: Wilkinson Catherine
Published: March 2015

Young people are living in an era where their daily routines are saturated with different media platforms, competing for their attention. One such platform is community radio. However, community radio has not gained as significant scholarly attention as other media outputs. Although there is not a wealth of extant literature on the topic of young people and community radio, much of the available literature provides colourful accounts of young people, community radio and urban life – typically through detailed case studies. Collating these case studies, my discussion is organised around two central themes: first, community radio as a platform for youth voice; and second, social inclusion of young people through youth media participation. I situate these lively exchanges and debates within the wider literature of youth media, the arts and creative industries. I suggest that community radio stations, both traditional FM and online community stations, are crucial spaces of development for young people's identities, and a space of creative learning outside of a more formal environment of school. However, I wish this to be more than a whistle‐stop tour of key literature; usefully, this paper critically assesses key conversations and highlights areas for urban geographers to devote future research interest.
Geographies of Caribbean Vulnerability in a Changing Climate: Issues and Trends
Authors: Rhiney Kevon
Published: March 2015

While it is generally recognized that the projected changes in the global climate will have serious negative consequences for the Caribbean as a whole, it is becoming more and more evident that the impacts of climate change will not be uniformly felt across the region. The primary aim of this paper is to provide a review of the Caribbean climate change literature. The paper begins with a brief discussion on the shifting nature of Caribbean vulnerability within the context of the region's longstanding and continued exposure to forces of global economic and environmental change. Particular attention is paid to both the practical and discursive dimensions of vulnerability, and the specific ways the term has been understood and framed in relation to other crosscutting themes such as adaptation and resilience in the broader academic literature. In addition to providing an overview of the regional climate change science literature, the paper offers a critical review of the existing climate change impacts literature for the Caribbean. By drawing on, and taking stock of this growing body of impact studies, the paper seeks to shed light on the differential and multi‐scalar drivers of social and economic vulnerabilities to climate variability and change in the Caribbean as well as highlight some of the existing knowledge gaps that need to be addressed. The paper ends by providing some brief reflections on the emerging themes arising from the discussion and highlights a few key areas for future academic research for the Caribbean in light of existing knowledge gaps observed in the regional climate change impact literature.
Everyday Ethics of Consumption in the Austere City
Authors: Hall Sarah Marie
Published: March 2015

This paper provides a first critical overview of literature within and beyond geography regarding the everyday ethics of consumption in times of austerity, with a focus on urban spaces. How consumers balance their ethical imperatives in a time of austerity has significant, multi‐scalar social and economic impacts, and yet there is a limited literature that addresses the everyday ethics of consuming in austere conditions. By teasing out the differences between the ‘ethics of consumption’ and ‘ethical consumption’, and reflecting on research regarding consumption in contemporary and historical periods of austerity, I highlight the need for greater geographical insight into the impacts of economic and political change on everyday urban life. I demonstrate that geographers might begin to tackle this emerging research agenda by attending to issues that impact on people's everyday lives, using the examples of ordinary mobilities, including home spaces and tourism, and food consumption in the case of food banks.
Transient bullous dermolysis of the newborn: a novel de novo mutation in the COL7A1 gene
Authors: Shi Bing‐Jun , Zhu Xiao‐Juan , Liu Yi , Hao Jin , Yan Guo‐Fu , Wang Su‐Ping , Wang Xiu‐Yong , Diao Qing‐Chun
Published: March 2015

Background

Bullous dermolysis of the newborn (BDN), an extremely rare clinical type of dystrophic epidermolysis bullosa (DEB), is characterized by subepidermal blistering at birth or shortly thereafter, followed by rapid improvement with minimal scarring or pigmentation. A total of 38 cases have been reported in the literature since the disease was initially described in 1985, but only 14 mutations in COL7A1, the gene responsible for the disease, have been detected in families with BDN.

Objectives

We report a Chinese male infant with BDN and indirect inguinal hernia, in whom a novel de novo mutation in COL7A1 was demonstrated.

Methods

DNA was obtained from the blood of the patient and his parents. The coding exon and flanking regions of COL7A1 gene were amplified by polymerase chain reaction and subjected to sequence analysis.

Results

Sequencing showed a heterozygous substitution of guanine by adenine at nucleotide position 6136 of exon 73 in the triple helical domain of type VII collagen, which predicts a change of glycine by serine at position p.G2046S. The mutation was considered to be a pathogenic and de novo mutation.

Conclusions

The coexistence of BDN and indirect inguinal hernia may simply be coincidental. These data contribute to the expanding database of COL7A1 mutations in DEB and should be useful for genetic counseling and prenatal diagnosis in affected families.
BIOMARKER CHARACTERISTICS OF POTENTIAL SOURCE ROCKS IN THE JABAL NAFUSAH AREA, NW LIBYA: PETROLEUM SYSTEMS SIGNIFICANCE
Authors: Abohajar A. , Littke R. , Schwarzbauer J. , Weniger P. , Boote D. R. D.
Published: March 2015

The Jifarah Arch of NW Libya is a structurally prominent feature at the eastern end of the regional Talemzane Arch, separating the Ghadamis hydrocarbon province to the south from the offshore Pelagian province to the north. The Arch has experienced a complex structural history with repeated episodes of uplift, exhumation and burial. This paper provides a provisional assessment of its hydrocarbon habitat based on detailed geochemical analyses of potential Triassic, Silurian and Ordovician source rocks encountered by wells drilled in the area.

Twenty‐seven core and cuttings samples of marine shales were collected from eight widely‐ dispersed wells and analyzed using standard Rock‐Eval pyrolysis techniques. Kerogen types II‐III were identified in the majority of Triassic samples analysed, indicating a low hydrocarbon generation potential, but oil‐prone Type II kerogen was found in the basal Silurian Tanezzuft Formation and Ordovician Memouniat Formation. The presence of steranes and acyclic isoprenoids suggested variable inputs of algal, bacterial and terrestrial organic matter, while biomarkers including C30‐gammacerane and β–carotene and selected biomarker ratios (Pr/Ph ratio and homohopane index) were used to assess their depositional environment. Results indicate that extended zones with periodic (if not continuous) oxygen‐deficient conditions existed throughout the basin during Late Ordovician and Early Silurian time, favouring the preservation of organic matter.

The thermal maturity of the samples was assessed by Rock‐Eval pyrolysis, zooclast reflectance, molecular ratios including C32‐22S/(22S+22R)‐homohopanes, Ts/(Ts+Tm), C29‐steranes and parameters based on the relative abundance of methylphenanthrene, methyldibenzothiophene and methylnaphthalene isomers. The results indicate significant variability in thermal maturity, with Ordovician and Silurian source rocks ranging from 0.6% to 0.7% VRo equivalent increasing to 1.0% locally. These values represent palaeo‐maturities achieved at different times in the past and are considered too low to have generated significant volumes of hydrocarbons directly. However the downdip equivalents of these source rocks in the adjacent Ghadamis Basin contributed to prolific petroleum systems. The absence of large petroleum accumulations on the Jifarah Arch contrasts with the western part of the geologically similar Talemzane Arch, which harbours several giant and supergiant oil and gas fields. This difference is attributed both to the complex structural history of the Jifarah Arch, which permitted post‐charge leakage of palaeo‐accumulations, and stratigraphic migration barriers which restricted migration between Tanezzuft source rocks and Ordovician and Triassic reservoirs.
DETERMINING HYDRAULIC FLOW UNITS USING A HYBRID NEURAL NETWORK AND MULTI‐RESOLUTION GRAPH‐BASED CLUSTERING METHOD: CASE STUDY FROM SOUTH PARS GASFIELD, IRAN
Authors: Nouri‐Taleghani M. , Kadkhodaie‐llkhchi A. , Karimi‐Khaledi M.
Published: March 2015

Hydraulic flow units are defined as reservoir units with lateral continuity whose geological properties controlling fluid flow are consistent and different from those of other flow units. Because pore‐throat size is the ultimate control on fluid flow, each flow unit has a relatively similar pore‐throat size distribution resulting in consistent flow behaviour. The relations between porosity and permeability in terms of hydraulic flow units can be used to characterize heterogeneous carbonate reservoirs.

In this study, a quantitative correlation is made between hydraulic flow units and well logs in South Pars gasfield, offshore southern Iran, by integrating intelligent and clustering methods of data analysis. For this purpose, a supervised artificial neural network model was integrated with multi‐resolution graph‐based clustering (MRGC) to identify hydraulic flow units from well log data. The hybrid model provides a more precise definition of flow units compared to definitions based only on a neural network. There is a good agreement between the results of well log analyses and core‐derived flow units. The synthesized flow units derived from the well log data are sufficiently reliable to be considered as inputs in the construction of a 3D reservoir model of the South Pars field.
CRUDE OIL GEOCHEMISTRY AND SOURCE ROCK POTENTIAL OF THE UPPER CRETACEOUS – EOCENE SUCCESSION IN THE BELAYIM OILFIELDS, CENTRAL GULF OF SUEZ, EGYPT
Authors: Diasty W. Sh. El , Beialy S. Y. El , Mostafa A. R. , Ghonaim A. A. Abo , Peters K. E.
Published: March 2015

This study evaluates the petroleum potential of source rocks in the pre‐rift Upper Cretaceous – Eocene succession at the Belayim oilfields in the central Gulf of Suez Basin. Organic geochemical and palynofacies investigations were carried out on 65 cuttings samples collected from the Thebes, Brown Limestone and Matulla Formations. Analytical methods included Rock‐Eval pyrolysis, Liquid Chromatography, Gas Chromatography and Gas Chromatography – Mass Spectrometry. Four crude oil samples from producing wells were characterised using C7 light hydrocarbons, stable carbon isotopes and biomarker characteristics. The results showed that the studied source rocks are composed of marine carbonates with organic matter dominated by algae and bacteria with minimal terrigenous input, deposited under reducing conditions. This conclusion was supported by n‐alkane distributions, pristane/ phytane ratios, homohopane and gammacerane indices, high concentrations of cholestane, the presence of C30 n‐propylcholestanes, and low diasterane ratios. The source rocks ranged from immature to marginally mature based on the Rock‐Eval Tmax together with biomarker maturity parameters. The analysed crude oil samples are interpreted to have been derived from source rock intervals within the Eocene Thebes Formation and the Upper Cretaceous Brown Limestone. The similarity in the geochemical characteristics of the crude oils suggests that there was little variation in the organofacies of the source rocks from which they were derived.
Learning to labour: an evaluation of internships and employability in theICTsector
Authors: Chillas Shiona , Marks Abigail , Galloway Laura
Published: March 2015

The employability of graduates is often reduced to lists of de‐contextualised skills that graduates may or may not have and which may or may not translate to prized graduate positions. Recently, internships have become the way in which graduates acquire and demonstrate work‐readiness to potential employers. This article examines a particular type of internship in theICTsector, namely placements incorporated in degree education. The findings suggest that while internships can enhance employability and indeed be a mechanism for accessing permanent jobs, more often, instead of ‘learning to labour’, interns are expected to be productive workers. A mini labour market operates at the undergraduate level that advantages those already possessed of the required soft skills. The emphasis on soft skills signals a shift in the nature ofICTwork with attendant implications for education of workers in this sector, revealed by anchoring employability to particular labour process(es).
It's all about games: enterprise and entrepreneurialism in digital games
Authors: Wright Adrian
Published: March 2015

This article aims to contrast benign notions of ‘free’ and ‘creative’ work in the context of labour market conditions and employment relationships. Empirical research reveals the exploitative and precarious nature of work in the experiences of self‐employed digital game developers and charts the responses of developers to unstable and insecure working conditions. Building on work by Pongratz and Voß, Haunschild and Eikhof, and Bergvall‐Kåreborn and Howcroft, this study finds that a typical response to increasing instability in the labour market is to adopt more enterprising and entrepreneurial behaviour in order to find work. This article illustrates the consequences for developers by highlighting examples of self‐exploitation, which is fuelled by a passion for work and is where entrepreneurial practices lead to long working hours, unpaid work and a blurring of work–life boundaries.
Crowdsourcing and work: individual factors and circumstances influencing employability
Authors: Barnes Sally‐Anne , Green Anne , de Hoyos Maria
Published: March 2015

The development of a fast and reliable Internet, new technologies online payment systems, and changes in work structure that enable and demand flexible working patterns have driven a move to a new form of Internet‐enabled labour exchange called crowdsourcing. Evidence from an in‐depth qualitative study is presented, focusing on selected users' interactions and experiences of working on two UK‐based crowdsourcing platforms. The paper shows that workers engaged in this form of labour exchange need to deploy existing employability skills and networks to effectively meet the challenges, and take advantage of the opportunities, that crowdsourcing presents. Individual factors and circumstances emerge as paramount for workers' continued engagement in this form of employment. Using selected components from an employability framework, the findings suggest that crowdsourcing can offer new pathways to practising skills and enhancing employability for some workers.
European Peace Advocates and the Great War: Prevention, Protest, Resignation, and Resistance
Authors: Cooper Sandi E.
Published: March 2015

This article presents an overview of pre‐1914 efforts to avoid what was expected to be a huge conflagration that would destroy Europe, with particular focus on the development of differing gender approaches to preventing Armageddon.
History, Memory, and Peace Education: History's Hardest Questions in the Classroom
Authors: Duckworth Cheryl Lynn
Published: March 2015

Many peace educators wish to be able to do more than foster enhanced communication or cultural skills, but further wish to interrupt macro‐historical causes of violence. Peace education can be usefully advanced by drawing on the literature on what is often called historical or collective memory. An important area of interest in peace studies, scholars working in this area seek to understand the role of the “heavy hand of history” in conflict. This article explores the nexus between peace education and historical memory, filling a current gap in the literature by addressing the question of what classroom teachers might actually be able to do in their settings to interrupt transgenerational cycles of violent conflict. I explore two possible ways forward for implementing such an audacious goal in the classroom: oral histories and “futures visioning,” inspired by Elise Boulding's notion of the 200‐year present.
The Wartime Political Thought of the Pan‐Netherlander Van Es and the Flemish Activist Van Genechten
Authors: Guldentops Kurt
Published: March 2015

Flemish nationalists willing to collaborate with German initiatives in occupied Belgium as well as their Dutch supporters worked under the expectation of a compromise peace to the Great War, in which they hoped to gain a say. How did these nationalists understand the nation at this moment when the anticipation of a general settlement demanded a comprehensive outlook? This contribution looks at two advocates of the Flemish cause. First, the Dutch Pan‐Netherlander Willem Van Es (1886‐1943) who proposed a New European order in September 1915. His vision is compared to the ideas of the Flemish Activist Robert Van Genechten (1895‐1945), a student at Ghent University, reopened in 1916 under German auspices.
The Great War, the Collapse of Civilization, and Chinese Visions of World Order
Authors: Kim Sungshin
Published: March 2015

This contribution discusses the impact of the Great War on China in terms of the collapse of the nineteenth century imperial order constructed around the concept of "civilization," in which China had been subordinated. Conceptions to strengthen China, from reformist to revolutionary, that had developed under this old order were now put to the test through this period of geopolitical change. Particular examples covered range from the diplomat Wu Tingfang, the public intellectual and politician Liang Qichao, to the nationalist revolutionary Sun Yat‐sen.
Experimental Study of Ingestion in the Rotor–Stator Disk Cavity of a Subscale Axial Turbine Stage
Authors: Balasubramanian J. , Pathak P. S. , Thiagarajan J. K. , Singh P. , Roy R. P. , Mirzamoghadam A. V.
Published: March 2015

This paper describes experiments in a subscale axial turbine stage equipped with an axially overlapping radial-clearance seal at the disk cavity rim and a labyrinth seal radially inboard which divides the disk cavity into a rim cavity and an inner cavity. An orifice model of the rim seal is presented; values of ingestion and egress discharge coefficients based on the model and experimental data are reported for a range of cavity purge flow rate. In the experiments, time-averaged pressure distribution was measured in the main gas annulus and in the disk cavity; also measured was the time-averaged ingestion into the cavity. The pressure and ingestion data were combined to obtain the discharge coefficients. Locations on the vane platform 1 mm upstream of its lip over two vane pitches circumferentially defined the main gas annulus pressure; in the rim cavity, locations at the stator surface in the radially inner part of the “seal region” over one vane pitch defined the cavity pressure. For the sealing effectiveness, two locations in the rim cavity at the stator surface, one in the “mixing region” and the other radially further inward at the beginning of the stator boundary layer were considered. Two corresponding sets of ingestion and egress discharge coefficients are reported. The ingestion discharge coefficient was found to decrease in magnitude as the purge flow rate increased; the egress discharge coefficient increased with purge flow rate. The discharge coefficients embody fluid-mechanical effects in the ingestion and egress flows. Additionally, the minimum purge flow rate required to prevent ingestion was estimated for each experiment set and is reported. It is suggested that the experiments were in the combined ingestion (CI) region with externally induced (EI) ingestion being the dominant contributor.
Controlled SSCI With Moderate End-Gas Auto-Ignition for Fuel Economy Improvement and Knock Suppression
Authors: Liu Hui , Wang Zhi , Wang Jianxin , Wang Mengke , Yang Wanli
Published: March 2015

Hybrid combustion mode including flame propagation induced by spark ignition (SI) and auto-ignition could be an effective method to improve fuel economy and suppress engine knock simultaneously. An experimental research on controlled spark-assisted stratified compression ignition (SSCI) for this purpose was conducted in a gasoline direct injection (GDI) engine with high compression ratio. At wide open throttle (WOT) and minimum spark advance for best torque (MBT) condition without turbocharging, direct injection was used to form desired stoichiometric stratified mixture while 20% cooled external exhaust gas recirculation (e-EGR) was sucked into the cylinder. The combustion characteristics of controlled SSCI show two-stage heat release, where the first stage is caused by SI and the second stage is due to moderate auto-ignition. Compared with engine knock, the second stage heat release of controlled SSCI shows smooth pressure curve without pressure oscillation. This is due to the low energy density mixture around the cylinder wall caused by cooled e-EGR. The stratified mixture could suppress knock. Fuel economy and combustion characteristics of the baseline and the controlled SSCI combustion were compared. The baseline GDI engine reaches a maximum of 8.9 bar brake mean effective pressure (BMEP) with brake specific fuel consumption (BSFC) of 291 g/(kWh), and the controlled SSCI combustion achieves a maximum of 8.3 bar BMEP with BSFC of 256 g/(kWh), improving the fuel economy over 12% while maintaining approximately the same power. The results show that controlled SSCI with two-stage heat releases is a potential combustion strategy to suppress engine knock while achieving high efficiency of the high compression ratio gasoline engine.
Hydrodynamics and Heat Transfer Characteristics of a Miniature Plate Pin-Fin Heat Sink Utilizing Al2O3–Water and TiO2–Water Nanofluids
Authors: Roshani Majid , Ziaeddin Miry Seyed , Hanafizadeh Pedram , Ashjaee Mehdi
Published: March 2015

In this paper, the hydrodynamic and thermal performance of a miniature plate pin-finned heat sink is investigated experimentally by utilizing two widely used nanofluids, Al2O3–water and TiO2–water. The heat sink base plate, which is used in the cooling process of electronic devices, has the dimensions of 42 mm (L) × 42 mm (W) × 14 mm (H) and is made of aluminum and placed in a plexiglass case which is isolated from the environment using an insulator foam. The thermal performance of the heat sink is investigated by passing the nanofluid at constant inlet temperature while applying a constant heat flux of 124.8 kW/m2 to the bottom surface of the heat sink. The nanofluids are prepared in volume concentrations of 0.5, 1, 1.5, and 2% and their performances are measured considering water as the base fluid. Measuring the pressure difference between the entrance and exit of the heat sink made it possible to study the hydrodynamic performance of the heat sink. Although the measurements showed 15% and 30% increase in the pumping power for the volume concentration of 2% of Al2O3–water and TiO2–water nanofluids, respectively, the average heat transfer coefficients increased by 16% and 14% and the thermal resistance decreased by 17% and 14% for each nanofluid.
An Experimental Investigation of Wavy and Straight Minichannel Heat Sinks Using Water and Nanofluids
Authors: Dominic A. , Sarangan J. , Suresh S. , Devah Dhanush V. S.
Published: March 2015

An experimental investigation on the heat transfer performance and pressure drop characteristics of thermally developing and hydrodynamically developed laminar flow of de-ionized (DI) water and 0.1%, 0.5%, and 0.8% concentrations of Al2O3/water nanofluid in wavy and straight minichannels was conducted. Reynolds number was varied from 700 to 1900 and two different heat fluxes of 45 kW/m2 and 65 kW/m2 were applied. The performance factor (PF) of water in wavy minichannels over their straight counterparts was higher than the nanofluids. Temperature distributions and general correlations of these minichannels are also presented.