bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying Characteristics of Design Guidelines for Elderly Care Environments from the Holistic Health Perspective
Authors: Lee Yeunsook , Hwang Jihye , Lim Soohyun , Kim Jeong Tai
Published: December 2012

The purpose of this paper is to identify features of space planning guidelines for elderly care environments from a holistic health perspective. This was undertaken with the expected outcome of promoting a better understanding of elderly care environment as a health resource. The major method used was a content analysis technique that employed physical, psychological, and social health criteria. Data for analysis were collected through care facility administrators using a checklist of 114 items related to spatial planning, developed through analyzing design guidelines from Japan, the UK, Germany, and the USA. As a supplementary method, a literature review was conducted on the current status of Korean healthcare facilities and recent trends in design theories for elderly care facilities. To measure results, a matrix was developed in which each guideline item was matched to each of the three health dimensions, thereby delineating the relationship between them. The elderly care environment is a vital resource to provide and support holistic health, and it is. Thus, important to understand how these factors relate to and utilize one another in order to increase their congruence. The resulting matrix is expected to function as a foundation for providing better planning services, which could develop further into “elderly care facility design guidelines for holistic health”.
A diffractive and Deleuzian approach to analysing interview data
Authors: Taguchi Hillevi Lenz
Published: December 2012

This article explores the possibilities of considering how ‘matter and meaning are mutually constituted’ in the production of knowledge ( Barad, 2007 : 152) through presenting a diffractive analysis of a piece of interview data with a six-year-old boy in a preschool class. Inspired by Donna Haraway’s (1997) and Karen Barad’s (2007) theorising, I understand diffractive analysis as an embodied engagement with the materiality of research data: a becoming-with the data as researcher. Understanding the body as a space of transit, a series of open-ended systems in interaction with the material-discursive ‘environment’, diffractive analyses constitute transcorporeal engagements with data. Stacy Alaimo’s (2010) theorisation of the transcorporeal is put to work diffractively with Gilles Deleuze and Felix Guattari’s (1987) thinking on the process of becoming minor or minoritarian. This implies a reconceptualisation of the very act of thinking as a transcorporeal process of engagement, going beyond the idea of reflexivity and interpretation as inner mental activities taking place in the mind of the researcher understood as separated from the data. Through my example, I argue that diffractive analysis can make visible new kinds of material-discursive realities that can have transformative and political consequences.
Minding the body, sexing the brain: Hormonal truth and the post-feminist hermeneutics of adolescence
Authors: Pinto Pedro , Nogueira Conceição , Oliveira João
Published: December 2012

Drawing on feminist and queer epistemologies, this article is concerned with the post-feminist media’s construction of girls’ sexual subjecthood. Broadly defined as a biopolitical ideal, post-feminism is here related to a set of principles of the neoliberal art of government. It will be argued that these principles ethically sustain the exponential mainstreaming of a post-feminist hermeneutics of adolescence and its programme of governmentality. The article also links post-feminism to a particular methodology of subjectification, ultimately locating its hermeneutics of adolescence within the pornographic and pharmacological imperatives of contemporary capitalism. On the empirical level, the analysis explores how techno-scientific discourses and bodily figurations (namely brains and hormones) enter the discursive apparatus of a Portuguese girls’ magazine, giving ideological ground to a distinctive production of adolescent body-subjects. Post-feminist media markets are finally discussed as a significant segment of the capitalist industrialisation of sexual difference that frames the general problematic of this study.
Inconsistent Respondents and Sensitive Questions
Authors: Castro Rubén
Published: December 2012

This article focuses on respondents as the source of measurement error, regardless of the question being asked, interviewer effects, or other factors that influence survey quality. Some individuals simply provide poorer answers as a result of a behavior called satisficing. An especially troublesome case is that of sensitive questions, where misreporting is common. In the study reported here, a significant role was found for individual-level time consistency as a predictor for answers to sensitive questions related to children, sex, condoms, and HIV. Couples’ reports, where couple-level fixed effects (including the “true” answer) can be ruled out, confirm this result. Satisficing may have more of an impact on how individuals respond to sensitive questions than previously thought.
Use of accident precursor event investigations in the understanding of major hazard risk potential in the Norwegian offshore industry
Authors: Vinnem Jan-Erik
Published: December 2012

The recent offshore accidents at the Macondo and Montara fields in the US and Australia have demonstrated the importance of learning from major accident precursors in order to appraise the risk potential involved in critical offshore operations. This is fully realised by the Petroleum Safety Authority in Norway, which has a specific requirement for such learning in its regulations. However, an unfortunate practice has been developed by the major players in the Norwegian offshore industry, whereby potential is severely and systematically downplayed, probably to limit the negative exposure if the actual potential consequences were known. The present article analyses 45 major accident precursor investigations in order to demonstrate the effect of downplaying the potential of major accidents. It demonstrates how the risk potential classified in investigation reports has a random relationship to the more objective risk potential, as shown in the national risk indicator project conducted by the Petroleum Safety Authority. This is further demonstrated by comparing company investigations with authority investigations in four cases where parallel investigations were performed.
The war next door: Peace journalism in US local and distant newspapers’ coverage of Mexico
Authors: Lacasse Katherine , Forster Larissa
Published: December 2012

This study explores the relationship between proximity to a conflict and the tendency to use peace journalism rather than war journalism modes of reporting. In the context of the current drug war occurring in Mexico, articles from both local, border region US newspapers and distant US newspapers were coded according to their usage of war or peace journalism frames. Analyses revealed that local newspapers utilized more peace journalism frames overall, and presented a less pessimistic and negative view of the conflict and parties. Distant newspapers, however, were more likely to showcase complexity of the conflict and many parties and people involved.
Playing discreet war in the US: Negotiating subjecthood and sovereignty through Special Forces video games
Authors: Mantello Peter
Published: December 2012

This article examines the War on Terror and US response strategies of discreet war through the lens of the Special Forces video game as a site of contestation between the real and the imaginary world, the nation-state and market-state, the West and the Rest. While mainstream films and news media increasingly pay homage to discreet war, the author argues that the Special Forces shooter goes a step further, by providing a participatory middle ground that seeks to naturalize and legitimize covert force solutions as acceptable instruments of statecraft. Thus, the intention of this article is to analyze the various ways in which the aesthetics and politics of the Special Forces shooter organizes, structures, and legitimates frameworks of subjecthood and sovereignty.
Cerebral Oximetry During Prolonged Cardiac Arrest and Percutaneous Coronary Intervention
Authors: Wagner Henrik , Madsen-Hardig Bjarne , Rundgren Malin , Harnek Jan , Gotberg Matthias , Olivecrona Goran K.
Published: December 2012

Objective. To evaluate the feasibility of cerebral oximetry (SctO2) with arterial blood pressure (ABP), central venous pressure (CVP), end tidal carbon dioxide (ETCO2), pulse oximetry (SpO2), and arterial blood gases during resuscitation in the coronary catheterization laboratory (cath-lab) setting. Design. We have implemented SctO2 in our cath-lab when cardiac arrest patients are in the need of prolonged resuscitation efforts with mechanical chest compressions (MCC) during simultaneous percutaneous coronary intervention (PCI). Setting. An academic coronary catheterization laboratory. Patients. Five cardiac arrest patients required prolonged resuscitation efforts with MCC in the cath-lab during simultaneous PCI. Results. During MCC, median SctO2 (n = 5) was 47%, median systolic ABP (n = 5) was 88 mm Hg, mean ABP (n = 5) was 58 mm Hg, coronary perfusion pressure (n = 3) was 19 mm Hg, SpO2 (n = 4) was 81%, and ETCO2 (n = 4) was 18.8 torr (2.5 kPa). Four patients had a successful PCI, including 1 patient with a pericardial drainage for cardiac tamponade during MCC. Mean treatment time of MCC in the cath-lab was 50.8 ± 28.3 minutes (median = 45 minutes, range = 12-90 minutes). Two patients obtained return of spontaneous circulation (ROSC). They died in the ICU due to impaired circulation and multiorgan failure, after 32 and 60 hours, respectively. Conclusion. Cerebral oximetry seems to be a feasible noninvasive parameter in assessing the perfusion and oxygenation of the brain in cardiac arrest patients receiving chest compressions during simultaneous PCI. Further studies are needed to evaluate its use in resuscitation situations to predict ROSC, quality of cardiopulmonary resuscitation, and neurologic outcome.
Reflections on Communication and Sport
Authors: Pedersen Paul M.
Published: December 2012

In this essay, Paul M. Pedersen provides a personal reflection on communication and sport and examines the area of strategic communication and management. His assessment begins with an overview of the growth and significance of the sport industry and communication’s ubiquitous and influential roles within it. In tracing his scholarly journey, Pedersen comes to see communication as an essential element in the sport industry, whether viewed from individualistic, organizational, or sport-specific perspectives. The focus section in this essay examines research on the Strategic Sport Communication Model (SSCM) and its usefulness in categorizing and operationalizing the field from a strategic management perspective. Using the SSCM as the guide, this reflection provides examples of sport communication research focused on each of the model’s three components. The reflection concludes with an analysis of future research opportunities, particularly opportunities to explore strategic decisions and effectiveness in the sport industry’s use of new/social media. Pedersen concludes that a key to developing best communication practices will be a research agenda that more fully contextualizes strategic communication and management in the sport marketplace.
Functional relevance of dynamic properties of Dimeric NADP-dependent Isocitrate Dehydrogenases
Authors: Vinekar Rithvik , Verma Chandra , Ghosh Indira
Published: December 2012

Background

Isocitrate Dehydrogenases (IDHs) are important enzymes present in all living cells. Three subfamilies of functionally dimeric IDHs (subfamilies I, II, III) are known. Subfamily I are well-studied bacterial IDHs, like that of Escherischia coli. Subfamily II has predominantly eukaryotic members, but it also has several bacterial members, many being pathogens or endosymbionts. subfamily III IDHs are NAD-dependent.

The eukaryotic-like subfamily II IDH from pathogenic bacteria such as Mycobacterium tuberculosis IDH1 are expected to have regulation similar to that of bacteria which use the glyoxylate bypass to survive starvation. Yet they are structurally different from IDHs of subfamily I, such as the E. coli IDH.

Results

We have used phylogeny, structural comparisons and molecular dynamics simulations to highlight the similarity and differences between NADP-dependent dimeric IDHs with an emphasis on regulation. Our phylogenetic study indicates that an additional subfamily (IV) may also be present. Variation in sequence and structure in an aligned region may indicate functional importance concerning regulation in bacterial subfamily I IDHs.

Correlation in movement of prominent loops seen from molecular dynamics may explain the adaptability and diversity of the predominantly eukaryotic subfamily II IDHs.

Conclusion

This study discusses possible regulatory mechanisms operating in various IDHs and implications for regulation of eukaryotic-like bacterial IDHs such as that of M. tuberculosis, which may provide avenues for intervention in disease.
C-mii: a tool for plant miRNA and target identification
Authors: Numnark Somrak , Mhuantong Wuttichai , Ingsriswang Supawadee , Wichadakul Duangdao
Published: December 2012

Background

MicroRNAs (miRNAs) have been known to play an important role in several biological processes in both animals and plants. Although several tools for miRNA and target identification are available, the number of tools tailored towards plants is limited, and those that are available have specific functionality, lack graphical user interfaces, and restrict the number of input sequences. Large-scale computational identifications of miRNAs and/or targets of several plants have been also reported. Their methods, however, are only described as flow diagrams, which require programming skills and the understanding of input and output of the connected programs to reproduce.

Results

To overcome these limitations and programming complexities, we proposed C-mii as a ready-made software package for both plant miRNA and target identification. C-mii was designed and implemented based on established computational steps and criteria derived from previous literature with the following distinguishing features. First, software is easy to install with all-in-one programs and packaged databases. Second, it comes with graphical user interfaces (GUIs) for ease of use. Users can identify plant miRNAs and targets via step-by-step execution, explore the detailed results from each step, filter the results according to proposed constraints in plant miRNA and target biogenesis, and export sequences and structures of interest. Third, it supplies bird's eye views of the identification results with infographics and grouping information. Fourth, in terms of functionality, it extends the standard computational steps of miRNA target identification with miRNA-target folding and GO annotation. Fifth, it provides helper functions for the update of pre-installed databases and automatic recovery. Finally, it supports multi-project and multi-thread management.

Conclusions

C-mii constitutes the first complete software package with graphical user interfaces enabling computational identification of both plant miRNA genes and miRNA targets. With the provided functionalities, it can help accelerate the study of plant miRNAs and targets, especially for small and medium plant molecular labs without bioinformaticians. C-mii is freely available at http://www.biotec.or.th/isl/c-mii for both Windows and Ubuntu Linux platforms.
Whole-genome sequencing and identification of Morganella morganii KT pathogenicity-related genes
Authors: Chen Yu-Tin , Peng Hwei-Ling , Shia Wei-Chung , Hsu Fang-Rong , Ken Chuian-Fu , Tsao Yu-Ming , Chen Chang-Hua , Liu Chun-Eng , Hsieh Ming-Feng , Chen Huang-Chi , Tang Chuan-Yi , Ku Tien-Hsiung
Published: December 2012

Background

The opportunistic enterobacterium, Morganella morganii, which can cause bacteraemia, is the ninth most prevalent cause of clinical infections in patients at Changhua Christian Hospital, Taiwan. The KT strain of M. morganii was isolated during postoperative care of a cancer patient with a gallbladder stone who developed sepsis caused by bacteraemia. M. morganii is sometimes encountered in nosocomial settings and has been causally linked to catheter-associated bacteriuria, complex infections of the urinary and/or hepatobiliary tracts, wound infection, and septicaemia. M. morganii infection is associated with a high mortality rate, although most patients respond well to appropriate antibiotic therapy. To obtain insights into the genome biology of M. morganii and the mechanisms underlying its pathogenicity, we used Illumina technology to sequence the genome of the KT strain and compared its sequence with the genome sequences of related bacteria.

Results

The 3,826,919-bp sequence contained in 58 contigs has a GC content of 51.15% and includes 3,565 protein-coding sequences, 72 tRNA genes, and 10 rRNA genes. The pathogenicity-related genes encode determinants of drug resistance, fimbrial adhesins, an IgA protease, haemolysins, ureases, and insecticidal and apoptotic toxins as well as proteins found in flagellae, the iron acquisition system, a type-3 secretion system (T3SS), and several two-component systems. Comparison with 14 genome sequences from other members of Enterobacteriaceae revealed different degrees of similarity to several systems found in M. morganii. The most striking similarities were found in the IS4 family of transposases, insecticidal toxins, T3SS components, and proteins required for ethanolamine use (eut operon) and cobalamin (vitamin B12) biosynthesis. The eut operon and the gene cluster for cobalamin biosynthesis are not present in the other Proteeae genomes analysed. Moreover, organisation of the 19 genes of the eut operon differs from that found in the other non-Proteeae enterobacterial genomes.

Conclusions

This is the first genome sequence of M. morganii, which is a clinically relevant pathogen. Comparative genome analysis revealed several pathogenicity-related genes and novel genes not found in the genomes of other members of Proteeae. Thus, the genome sequence of M. morganii provides important information concerning virulence and determinants of fitness in this pathogen.
Maxillary nerve compression in cynomolgus monkey Macaca fascicularis: altered somatic sensation and peripheral nerve firing
Authors: Guo Ning , Gu Xiyao , Zhao Jun , Zhao Guoping , Jin Meilei , Zou Hong , Zhang Yuqiu , Zhao Zhiqi , Jin Gang Jason , Yu Lei
Published: December 2012

Background

Trigeminal nerve is a major source of the sensory input of the face, and trigeminal neuropathology models have been reported in rodents with injury to branches of the maxillary or mandibular division of the trigeminal nerve. Non-human primates are neuroanatomically more closely related to human than rodents; however, nerve injury studies in non-human primates are limited.

Results

We describe here a nerve injury model of maxillary nerve compression (MNC) in the cynomolgus macaque monkey, Macaca fascicularis, and the initial characterization of the consequences of damage to this trigeminal nerve branch. The nerve injury from the compression appeared to be mild, as we did not observe overt changes in home-cage behavior in the monkeys. When mechanical stimulation was applied to the facial area, monkeys with MNC displayed increased mechanical sensitivity, as the avoidance response scores were lower than those from the control animals. Such a change in mechanical sensitivity appeared to be somewhat bilateral, as the contralateral side also showed increased mechanical sensitivity, although the change on the ipsilateral side was more robust. Multiple-unit recording of the maxillary nerve showed a general pattern of increasing responsiveness to escalating force in mechanical stimulation on the contralateral side. Ipsilateral side of the maxillary nerve showed a lack of responsiveness to escalating force in mechanical stimulation, possibly reflecting a maximum stimulation threshold effect from sensitized nerve due to MNC injury.

Conclusions

These results suggest that MNC may produce increased sensitivity of the ipsilateral maxillary nerve, and that this model may serve as a non-human primate model to evaluate the effect of injury to trigeminal nerve branches.
Volunteering in the care of people with severe mental illness: a systematic review
Authors: Hallett Claudia , Klug Günter , Lauber Christoph , Priebe Stefan
Published: December 2012

Background

Much of the literature to date concerning public attitudes towards people with severe mental illness (SMI) has focused on negative stereotypes and discriminatory behaviour. However, there also exists a tradition of volunteering with these people, implying a more positive attitude. Groups with positive attitudes and behaviours towards people with SMI have received relatively little attention in research. They merit further attention, as evidence on characteristics and experiences of volunteers may help to promote volunteering. The present paper aims to systematically review the literature reporting characteristics, motivations, experiences, and benefits of volunteers in the care of people with SMI.

Methods

In November 2010, a systematic electronic search was carried out in BNI, CINAHL, Embase, Medline, PsycINFO, Cochrane Registers and Web of Science databases, using a combination of ‘volunteer’, ‘mental health’ and ‘outcome’ search terms. A secondary hand search was performed in relevant psychiatric journals, grey literature and references.

Results

14 papers met the inclusion criteria for the review, with data on a total of 540 volunteers. The results suggest that volunteers are a mostly female, but otherwise heterogeneous group. Motivations for volunteering are a combination of what they can ‘give’ to others and what they can ‘get’ for themselves. Overall volunteers report positive experiences. The main benefit to persons with a psychiatric illness is the gaining of a companion, who is non-stigmatizing and proactive in increasing their social-community involvement.

Conclusions

The evidence base for volunteers in care of people with SMI is small and inconsistent. However there are potential implications for both current and future volunteering programmes from the data. As the data suggests that there is no ‘typical’ volunteer, volunteering programmes should recruit individuals from a variety of backgrounds. The act of volunteering can not only benefit people with SMI, but also the volunteers. Further research may specify methods of recruiting, training, supervising and using volunteers to maximise the benefit for all involved.
The optimal duration of progesterone supplementation in pregnant women after IVF/ICSI: a meta-analysis
Authors: Liu Xi-Ru , Mu Hua-Qiao , Shi Qi , Xiao Xiao-Qiu , Qi Hong-Bo
Published: December 2012

Background

Progesterone supplementation after in vitro fertilisation/intracytoplasmic sperm injection (IVF/ICSI) can improve the rates of clinical pregnancy and live birth, but the optimal duration of treatment remains controversial. The objective of this meta-analysis was to investigate the effects of early progesterone cessation on pregnancy outcomes in women undergoing IVF/ICSI.

Methods

We searched MEDLINE, EMBASE, the Cochrane Central Register of Controlled Trials (CENTRAL), the Chinese biomedicine (CBM) literature database, and the Wanfang database. The final search was performed in July 2012. All available randomised trials that compared the effects of early progesterone cessation with progesterone continuation during early pregnancy after IVF/ICSI were included. The main outcome measures were live birth rate, miscarriage rate and ongoing pregnancy rate. Fixed or random-effects models were chosen to calculate the risk ratio (RR).

Results

Six eligible studies with a total of 1,201 randomised participants were included in the final analysis. No statistically significant differences were detected between patients who underwent early progesterone cessation and those who received progesterone continuation for luteal phase support in terms of live birth rate (RR: 0.95, 95% CI: 0.86–1.05), miscarriage rate (RR: 1.01, 95% CI: 0.74–1.38) or ongoing pregnancy rate (RR: 0.97, 95% CI: 0.90–1.05). These results did not change after a sensitivity analysis.

Conclusions

The currently available evidence suggests that progesterone supplementation beyond the first positive hCG test after IVF/ICSI might generally be unnecessary, although large-scale randomised controlled trials are needed to strengthen this conclusion.
The production of concentrated dispersions of few-layer graphene by the direct exfoliation of graphite in organosilanes
Authors: Nuvoli Daniele , Alzari Valeria , Sanna Roberta , Scognamillo Sergio , Piccinini Massimo , Peponi Laura , Kenny Josè Maria , Mariani Alberto
Published: December 2012

We report the formation and characterization of graphene dispersions in two organosilanes, 3-glycidoxypropyl trimethoxysilane (GPTMS) and phenyl triethoxysilane (PhTES) as new reactive solvents. The preparation method was mild and easy and does not produce any chemical modification. The dispersions, which exhibit the Tyndall effect, were characterized by TEM and Raman spectroscopy to confirm the presence of few-layer graphene. Concentrations as high as 0.66 and 8.00 mg/ml were found for PhTES and GPTMS, respectively. The latter is one of the highest values reported for a dispersion of graphene obtained by any method. This finding paves the way for the direct synthesis of polymer nanofiller-containing composites consisting of graphene and reactive silanes to be used in sol–gel synthesis, without any need for solvent removal, thus preventing graphene reaggregation to form graphite flakes.
A novel approach to mapping load transfer from the plantar surface of the foot to the walls of the total contact cast: a proof of concept study
Authors: Begg Lindy , McLaughlin Patrick , Manning Leon , Vicaretti Mauro , Fletcher John , Burns Joshua
Published: December 2012

Background

Total contact casting is regarded as the gold standard treatment for plantar foot ulcers. Load transfer from the plantar surface of the foot to the walls of the total contact cast has previously been assessed indirectly. The aim of this proof of concept study was to determine the feasibility of a new method to directly measure the load between the cast wall and the lower leg interface using capacitance sensors.

Methods

Plantar load was measured with pedar® sensor insoles and cast wall load with pliance® sensor strips as participants (n=2) walked along a 9 m walkway at 0.4±0.04 m/sec. The relative force (%) on the cast wall was calculated by dividing the mean cast wall force (N) per step by the mean plantar force (N) per step in the shoe‐cast condition.

Results

The combined average measured load per step upon the walls of the TCC equated to 23‐34% of the average plantar load on the opposite foot. The highest areas of load on the lower leg were located at the posterior margin of the lateral malleolus and at the anterior ankle/extensor retinaculum.

Conclusions

These direct measurements of cast wall load are similar to previous indirect assessment of load transfer (30‐36%) to the cast walls. This new methodology may provide a more comprehensive understanding of the mechanism of load transfer from the plantar surface of the foot to the cast walls of the total contact cast.
Current status and implications of microRNAs in ovarian cancer diagnosis and therapy
Authors: Zaman Mohd Saif , Maher Diane M , Khan Sheema , Jaggi Meena , Chauhan Subhash C
Published: December 2012

Ovarian cancer is the fifth most common cancer among women and causes more deaths than any other type of female reproductive cancer. Currently, treatment of ovarian cancer is based on the combination of surgery and chemotherapy. While recurrent ovarian cancer responds to additional chemotherapy treatments, the progression-free interval becomes shorter after each cycle, as chemo-resistance increases until the disease becomes incurable. There is, therefore, a strong need for prognostic and predictive markers to help optimize and personalize treatment in order to improve the outcome of ovarian cancer. An increasing number of studies indicate an essential role for microRNAs in ovarian cancer progression and chemo-resistance. MicroRNAs (miRNAs) are small endogenous non-coding RNAs (~22bp) which are frequently dysregulated in cancer. Typically, miRNAs are involved in crucial biological processes, including development, differentiation, apoptosis and proliferation. Two families of miRNAs, miR-200 and let-7, are frequently dysregulated in ovarian cancer and have been associated with poor prognosis. Both have been implicated in the regulation of epithelial-to-mesenchymal transition, a cellular transition associated with tumor aggressiveness, tumor invasion and chemo-resistance. Moreover, miRNAs also have possible implications for improving cancer diagnosis; for example miR-200 family, let-7 family, miR-21 and miR-214 may be useful in diagnostic tests to help detect ovarian cancer at an early stage. Additionally, the use of multiple target O-modified antagomirs (MTG-AMO) to inhibit oncogenic miRNAs and miRNA replacement therapy for tumor suppressor miRNAs are essential tools for miRNA based cancer therapeutics. In this review we describe the current status of the role miRNAs play in ovarian cancer and focus on the possibilities of microRNA-based therapies and the use of microRNAs as diagnostic tools.
Autoantibody-mediated arthritis in the absence of C3 and activating Fcγ receptors: C5 is activated by the coagulation cascade
Authors: Auger Jennifer L , Haasken Stefanie , Binstadt Bryce A
Published: December 2012

Introduction

The effector functions of immunoglobulin G (IgG) are mediated by interaction of its Fc region with Fc receptors (FcγRs) and/or the complement system. The three main pathways of complement activation converge at C3. However, C3-independent pathways can activate C5 and other downstream complement components during IgG-initiated inflammatory responses. These C3-independent pathways of C5 activation are triggered by activating FcγRs in some systems or can be activated by factors of the coagulation cascade such as thrombin. Here we studied the interplay of C3, C5, and activating FcγRs in a model of spontaneous autoantibody-driven arthritis.

Methods

We utilized the K/BxN TCR transgenic mouse model of arthritis. We bred K/BxN mice bearing targeted or naturally-occurring mutations in one or more of the genes encoding complement components C3, C5, and FcRγ, the cytoplasmic signaling chain shared by the activating FcγRs. We measured arthritis development, the production of arthritogenic autoantibodies, T cell activation status and cytokine synthesis. In addition, we treated mice with anti-C5 monoclonal antibodies or with the thrombin inhibitor argatroban.

Results

We have previously shown that genetic deficiency of C5 protects K/BxN mice from the development of arthritis. We found here that C3-deficient K/BxN mice developed arthritis equivalent in severity to C3-sufficient animals. Arthritis also developed normally in K/BxN mice lacking both C3 and FcRγ, but could be ameliorated in these animals by treatment with anti-C5 monoclonal antibody or by treatment with argatroban. Production of arthritogenic autoantibodies, T cell activation, and T cell cytokine production were not affected by the absence of C3, C5, and/or FcRγ.

Conclusions

In K/BxN mice, C5-dependent autoantibody-driven arthritis can occur in the genetic absence of both complement C3 and activating FcγRs. Our findings suggest that in this setting, thrombin activates C5 to provoke arthritis.
Whole-genome reconstruction and mutational signatures in gastric cancer
Authors: Nagarajan Niranjan , Bertrand Denis , Hillmer Axel M , Zang Zhi Jiang , Yao Fei , Jacques Pierre-Étienne , Teo Audrey SM , Cutcutache Ioana , Zhang Zhenshui , Lee Wah Heng , Sia Yee Yen , Gao Song , Ariyaratne Pramila N , Ho Andrea , Woo Xing Yi , Veeravali Lavanya , Ong Choon Kiat , Deng Niantao , Desai Kartiki V , Khor Chiea Chuen , Hibberd Martin L , Shahab Atif , Rao Jaideepraj , Wu Mengchu , Teh Ming , Zhu Feng , Chin Sze Yung , Pang Brendan , So Jimmy BY , Bourque Guillaume , Soong Richie , Sung Wing-Kin , Tean Teh Bin , Rozen Steven , Ruan Xiaoan , Yeoh Khay Guan , Tan Patrick BO , Ruan Yijun
Published: December 2012

Background

Gastric cancer is the second highest cause of global cancer mortality. To explore the complete repertoire of somatic alterations in gastric cancer, we combined massively parallel short read and DNA paired-end tag sequencing to present the first whole-genome analysis of two gastric adenocarcinomas, one with chromosomal instability and the other with microsatellite instability.

Results

Integrative analysis and de novo assemblies revealed the architecture of a wild-type KRAS amplification, a common driver event in gastric cancer. We discovered three distinct mutational signatures in gastric cancer - against a genome-wide backdrop of oxidative and microsatellite instability-related mutational signatures, we identified the first exome-specific mutational signature. Further characterization of the impact of these signatures by combining sequencing data from 40 complete gastric cancer exomes and targeted screening of an additional 94 independent gastric tumors uncovered ACVR2A, RPL22 and LMAN1 as recurrently mutated genes in microsatellite instability-positive gastric cancer and PAPPA as a recurrently mutated gene in TP53 wild-type gastric cancer.

Conclusions

These results highlight how whole-genome cancer sequencing can uncover information relevant to tissue-specific carcinogenesis that would otherwise be missed from exome-sequencing data.
FOCAL: an experimental design tool for systematizing metabolic discoveries and model development
Authors: Tervo Christopher J , Reed Jennifer L
Published: December 2012

Current computational tools can generate and improve genome-scale models based on existing data; however, for many organisms, the data needed to test and refine such models are not available. To facilitate model development, we created the forced coupling algorithm, FOCAL, to identify genetic and environmental conditions such that a reaction becomes essential for an experimentally measurable phenotype. This reaction's conditional essentiality can then be tested experimentally to evaluate whether network connections occur or to create strains with desirable phenotypes. FOCAL allows network connections to be queried, which improves our understanding of metabolism and accuracy of developed models.
Nonstretching NMO correction of prestack time-migrated gathers using a matching-pursuit algorithm
Authors: Zhang Bo , Zhang Kui , Guo Shiguang , Marfurt Kurt J.
Published: December 2012

Wide-azimuth, long-offset surveys are becoming increasingly common in unconventional exploration plays where one of the key routine processes is maintaining data fidelity at far offsets. The conventional NMO correction that processes the data sample-by-sample results in the well-known decrease of frequency content and amplitude distortion through stretch, which lowers the seismic resolution and hinders [Formula: see text] and amplitude variation with offset and azimuth (AVAz) analysis of the long-offset signal. To mitigate the stretch typically associated with large offsets, we use a matching-pursuit-based normal moveout correction (MPNMO) to reduce NMO-stretch effects in long-offset data. MPNMO corrects the data wavelet-by-wavelet rather than sample-by-sample, thereby avoiding stretch. We apply our technique (1) to a set of synthetic gathers and (2) as part of a residual velocity analysis workflow to a prestack time-migrated data volume acquired over the Northern Chicontepec Basin, Mexico. Test results show that MPNMO can produce relatively nonstretched events and generate higher temporal resolution prestack gathers.
Physical modeling of anisotropic domains: Ultrasonic imaging of laser-etched fractures in glass
Authors: Stewart Robert R. , Dyaur Nikolay , Omoboya Bode , de Figueiredo J. J. S. , Willis Mark , Sil Samik
Published: December 2012

Many regions of subsurface interest are, or will be, fractured. Seismically characterizing these zones is a complicated but essential task for resource development. Physical modeling, using ultrasonic sources and receivers over scaled exploration targets, can play a useful role as an analog for reservoir imaging and assessment. We explored the anisotropic response of glass blocks containing internal fractures created by a novel laser-etching technique. We compared transmitted and reflected signals for P- and S-waves from fractured and unfractured zones in a suite of ultrasonic (1–5 MHz) experiments. The unaltered glass velocities have averages of [Formula: see text] and [Formula: see text] for P- and S-waves, respectively (giving [Formula: see text]). The unfractured glass has a very high quality (Q) factor of over 500 for P-waves and S-waves. The fractured zones have a small (up to 1.5%) velocity decrease. Signals propagating through the fractured zone have diminished amplitudes and increased coda signatures. Reflection surveys (zero-offset and with variable polarizations) record significant scatter from the fractured zones. The fracture-scattered energy can be migrated to provide a sharper image. The glass specimens with laser-etched fractures display a rich anisotropic response, which can help inform field-scale imaging.
3D inversion of marine CSEM and MT data: An approach to shallow-water problem
Authors: Sasaki Yutaka
Published: December 2012

The application of the marine controlled-source electromagnetic (CSEM) technique for shallow-water hydrocarbon exploration is challenged by the effect of an airwave that masks the response from the reservoir at depth. We applied Gauss–Newton-based 3D inversion method to synthetic CSEM and magnetotelluric (MT) data to demonstrate the capability of 3D inversion to recover thin resistive targets in shallow-water environments. The experiment on the model with water depth of 300 m shows that the target signals at 0.25 Hz are significant enough to resolve the reservoir at a burial depth of 1 km for the given noise level (6% of the electric-field amplitude). For the 100-m water depth case, the high-resistivity zone recovered is located much deeper and thicker than the true reservoir, suggesting that the airwave component obscures the target signal more seriously. However, inverting inline and broadside data together or adding inline data at a different frequency (0.1 Hz) is quite effective in improving the resolution to the thin resistive target and more so than simultaneously inverting inline CSEM and MT data.
President's Page
Authors: Monk Dave
Published: December 2012

Recently we saw a number of geoscientists (the L'Aquila Seven) convicted in Italy for their failure to predict and issue adequate warnings prior to an earthquake. While we may decry such action, to some it was seen as a failure of the scientists, and perhaps even the science of geophysics. What I believe it says is that many people do not understand the basic tenets and limits of science itself. A refresher may be of value.
Seismic attribute expression of differential compaction
Authors: Chopra Satinder , Marfurt Kurt J.
Published: December 2012

In a marine environment, topographic features on the sea floor will usually be covered by a thick layer of shale with the rise of sea level, resulting in a uniform, nearly flat surface. Evaporating seas may bury sea-floor topography with a thick layer of salt. In a fluvial-deltaic environment, channels are cut and filled with a lithology that may be different from that through which it is cut, followed by subsequent burial with (perhaps) a more uniform sedimentary layer. With continued burial and overburden, pore sizes are reduced and water is squeezed out of the rocks, reducing the rock volume. Different lithologies have different original porosity, pore shapes, and mineral matrix composition, and thus different responses to burial. Lateral changes in lithology give rise to lateral changes in compaction, or simply “differential compaction.” For this reason, easily mapped flooding and other surfaces that were originally flat can exhibit measurable, and often significant structural relief. These maps give rise to lateral “structural” anomalies. Recognition of differential compaction forms a key component in modern seismic interpretation workflows based on geomorphology with excellent publications showing the expression of differential compaction on vertical slices. Mapping the 3D expression of compaction features takes considerable time and is thus less well reported while the use of 3D geometric attributes to map compaction features is underutilized. In this article, we illustrate the attribute expression of the more common differential compaction features over channels and carbonate reefs using examples from the Western Canadian Sedimentary Basin.
Introduction to this special section: Passive seismic and microseismic—Part 2
Authors: Shemeta Julie , Goodway Bill , Willis Mark , Heigl Werner
Published: December 2012

Welcome to the second half of TLE's two-part special section on passive seismic and microseismic. This month, we focus again on monitoring hydraulic fracturing with microseismic with five articles, but also expand beyond “micro” seismicity, to include unintended “induced” seismicity that may occur during injection. Five articles in this special section focus on induced-seismicity topics. In this introduction, we will highlight various issues related to undesired induced seismicity which may be caused by hydraulic fracturing and deep, underground salt water disposal.
Ongoing seismicity in the Dallas-Fort Worth area
Authors: Janská Eva , Eisner Leo
Published: December 2012

We report on and discuss the continuous seismic activity in the Dallas-Fort Worth (DFW) area. There was no reported seismic activity by USGS/NEIS until 31 October 2008, approximately seven weeks after the start of salt-water disposal at a nearby injection well in the southern part of the DFW airport. The salt-water disposal injection ceased in August 2009. The event detection based on crosscorrelation between several template events from DFW area and continuous seismic record shows that the seismic activity has been continuous for more than three years. Continuous monitoring at a local station allows us to complete the catalog down to a magnitude of zero, providing more detailed information on seismicity in the DFW area. This seismic activity migrated in space from a cluster southwest of the injection well to a cluster 2 km northeast of the injection well after May 2010. We show that the crosscorrelation detection at the WMOK regional station is not able to detect both south and northeast clusters of events without using multiple template events. Furthermore, we show magnitudes of the largest events increase since May 2010.
Can small events (M < 0) observed during hydraulic fracture stimulations initiate large events (M > 0)?
Authors: Baig Adam , Urbancic Ted , Viegas Gisela , Karimi Sepideh
Published: December 2012

It is becoming evident that under different circumstances, such as injection rates and geologic conditions, it might be possible to generate larger magnitude (M > 0) events during hydraulic fracture stimulations. By utilizing fully integrated passive seismic monitoring programs, we can examine the relationship between the occurrence of small magnitude events (M < 0) and the fracture and stress conditions that may lead to larger events. In our investigations, we identify that over all scales of observation the events follow a self-similar behavior; however, the small magnitude events are generally lower in stress release than observed for the larger events. These differences can be explained by the observed failure mechanisms where smaller events tend to be driven by shear-tensile failures of pre-existing discrete fractures (joints) whereas the larger events appear to be dominated by shear-driven failure processes associated with pre-existing faults. These observations suggest that there can be sufficient stress transfer and stress buildup resulting from the smaller events associated with hydraulic stimulation to allow for nearby pre-existing faults to slip in shear.
Checking up on the neighbors: Quantifying uncertainty in relative event location
Authors: Poliannikov Oleg V. , Malcolm Alison E. , Prange Michael , Djikpesse Hugues
Published: December 2012

With high-permeability hydrocarbon reservoirs exhausting their potential, developing low-permeability reservoirs is becoming of increasing importance. In order to be produced economically, these reservoirs need to be stimulated to increase their permeability. Hydraulic fracturing is a technique used to do this. A mixture of water, additives, and proppants is injected under high pressure into the subsurface; this fluid fractures the rock, creating additional pathways for the oil or gas. Understanding the nature of the resulting fracture system, including the geometry, size, and orientation of individual fractures, as well as the distance from one fracture to the next, is key to answering important practical questions such as: What is the affected reservoir volume? Where should we fracture next? What are the optimal locations for future production wells?
GEOPHYSICS BRIGHT SPOTS
Authors: Sun Yonghe
Published: December 2012

Below I mention two papers in the November-December issue of Geophysics. One paper is on using full-azimuth AVO inversion for HTI models to characterize fracture zones in reservoir cap and seal rocks for a Canadian CO2 storage site; the other demonstrates improved estimation of magnetic source location using normalized magnetic strength in the presence of remanent magnetization.
Yeast eIF4B binds to the head of the 40S ribosomal subunit and promotes mRNA recruitment through its N-terminal and internal repeat domains
Authors: Walker Sarah E. , Zhou Fujun , Mitchell Sarah F. , Larson Victoria S. , Valasek Leos , Hinnebusch Alan G. , Lorsch Jon R.
Published: December 2012

Eukaryotic translation initiation factor (eIF)4B stimulates recruitment of mRNA to the 43S ribosomal pre-initiation complex (PIC). Yeast eIF4B (yeIF4B), shown previously to bind single-stranded (ss) RNA, consists of an N-terminal domain (NTD), predicted to be unstructured in solution; an RNA-recognition motif (RRM); an unusual domain comprised of seven imperfect repeats of 26 amino acids; and a C-terminal domain. Although the mechanism of yeIF4B action has remained obscure, most models have suggested central roles for its RRM and ssRNA-binding activity. We have dissected the functions of yeIF4B’s domains and show that the RRM and its ssRNA-binding activity are dispensable in vitro and in vivo. Instead, our data indicate that the 7-repeats and NTD are the most critical domains, which mediate binding of yeIF4B to the head of the 40S ribosomal subunit via interaction with Rps20. This interaction induces structural changes in the ribosome’s mRNA entry channel that could facilitate mRNA loading. We also show that yeIF4B strongly promotes productive interaction of eIF4A with the 43S•mRNA PIC in a manner required for efficient mRNA recruitment.
The boronic acid Mannich reaction in alkaloid synthesis
Authors: Pyne Stephen G. , Davis Andrew S. , Ritthiwigrom Thunwadee , Au Christopher W. G. , Savaspun Kongdech , Wotherspoon Matthew
Published: December 2012

Our work on the application of the boronic acid Mannich reaction to the synthesis of pyrrolizidine alkaloids is described.