bluuebunny/crossref_metadata_2025 huggingface dataset:
Carers’ experiences of being exposed to challenging behaviour in services for autism spectrum disorders
Authors: Butrimaviciute Rasa , Grieve Alan
Published: October 2013

Previous studies have demonstrated that being exposed to challenging behaviour in services of care can have a negative impact on staff. Recently, challenging behaviour has been linked to people with autism spectrum disorders; however, little research has been aimed at exploring staff’s experiences of facing such behaviour in services for autism spectrum disorders in particular. A qualitative study using interpretative phenomenological analysis was conducted. This method involves thorough exploration of experiences revealed by individuals. A purposive sample (N = 10) was used. Participants were involved in semi-structured interviews which were later analysed according to the guidelines by Smith and Osborn. Four themes were discovered: intense mental and physical engagement, importance of adaptive coping, ambiguous experience of failure and achievement and destructive emotional reactions. Being exposed to challenging behaviour in services for autism spectrum disorders is a complex multi-component experience. The present results allow some insight into personal worlds of staff and might be useful for improving their working environment as well as ensuring a higher quality of care for service users.
The micro-movie wave in a globalising China: Adaptation, formalisation and commercialisation
Authors: Zhao Elaine Jing
Published: October 2013

While user-generated short online videos have existed since the emergence of video sharing sites in China, they have undergone a process of formalisation and commercialisation, culminating in the wave of micro-movies in recent years. By addressing the wider context of globalisation alongside relevant state policies and shifting viewing habits, this article analyses the local and global causes of this wave. It offers evidence that illustrates how online video service providers in China have adapted in a changing industry landscape as they negotiate state policies, advertiser interests and user preference. It then examines the production and distribution dynamics, where professional producers draw on social media, grassroots creativity and creative talents in regional markets. Finally, it discusses the cultural implications of this process in terms of both the nature and flow of creativity. Based on these analyses, the article also sheds light on the interplay between the state and the market in the context of globalisation and marketisation of media sectors, which becomes more complicated when the state-owned or controlled media enter the emerging market sectors.
Social distribution: K-pop fan practices in Indonesia and the ‘Gangnam Style’ phenomenon
Authors: Jung Sun , Shim Doobo
Published: October 2013

Global consumers are increasingly enjoying popular cultural products such as music, film, television and other audiovisual media content through online social media community networks. Recently, Korean pop music, or K-pop, has become one of the most dynamically distributed forms of pop culture in the global pop market through these ‘social distribution’ networks. This article explores the ways that this new mode of social distribution is characterised by bottom-up grassroots aspects as well as corporate-controlled top-down aspects by analysing the recent dynamics and practices of K-pop consumption and circulation on social media, using a case study of K-pop fandom in Indonesia and the ‘Gangnam Style’ phenomenon.
Rewind and recollect: Activating dormant memories and politics in Teresa Teng’s music videos uploaded on YouTube
Authors: Khiun Liew Kai
Published: October 2013

Posted mostly by consumers rather than industry players, music videos on video-sharing websites like YouTube have been instrumental in expanding the circulation of audio-visual materials in cyberspace. In transnational Chinese pop music, with shared memories engendered by viewers’ nostalgic comments on clips, particularly the older ones, uploads promise the possibilities of transcending existing geopolitical divides between Mainland China, Taiwan, Hong Kong and the Chinese diaspora. However, as evinced in this case study of video clips featuring prominent Taiwanese female singer Teresa Teng, the uploaders are divided between advocates for a ‘Greater China’ and detractors seeking a more indigenised Taiwanese identity. Analysis of some of Teng’s more politically contentious music videos in the highly networked and circulatory media context, this article advocates looking beyond the immediate sensory audio-projections of the music videos to better understand them as historical and ideological texts. To engage with the posted texts, a set of cultural literacies, including prior historical awareness of the posted music video as well as the geo-cultural contexts of the multilingual and gendered responses in the viewers’ comments, is needed. Placed on the seemingly more open platform of YouTube, Teng’s music videos have become part of the broader attempts of her viewers to re-appropriate and re-territorialise her legacy according to new cultural imaginations and desires.
Rhizomatic behaviours in social media: V-logging and the independent film industry in Malaysia
Authors: Lim Joanne B.Y.
Published: October 2013

Amidst highly ambiguous policies governing the creative industry in Malaysia, discourses concerning censorship, funding and distribution continue to implicate popular content within the independent film industry. While independent filmmakers are increasingly looking to the possibilities of online distribution of their work, there is a new generation of filmmakers or v-loggers who are actively using social media to confront a range of national, social and cultural issues within their texts. By drawing upon examples of independent film productions and v-logs made popular through online portals ranging from YouTube to more activist-centred sites, this article considers the ways in which creative products that would have been banned or removed from local screens by the state have in fact garnered millions of online views, and are discussed, referenced and widely shared by the public via social networking platforms. Through the rhizomatic capacities of v-logging, I argue that the emergence of new cultural distribution strategies challenges us to rethink notions of social practice and action. In addition to understanding social media as an alternative platform for public discourse in Malaysia, there is a further need to engage with the idea of the ‘prosumer’, and to consider the changing dynamics of the independent film industry.
Tension pneumoperitoneum caused by blunt thoracic trauma
Authors: Webman Rachel , Rosenzweig Matthew , Bholat Omar , Bernstein Mark , Todd S Rob , Frangos Spiros G
Published: October 2013

Tension pneumoperitoneum is a rare entity that occurs when free air under pressure accumulates in the abdominal cavity compromising visceral function and blood flow. The case of a 23-year-old man whose chest was run over by the wheels of a truck is presented. He arrived with a severely distended abdomen, significant thoracic trauma, hypoxemia, and elevated airway pressures following intubation. Imaging studies revealed massive intraperitoneal free air. He was treated with a decompressive laparotomy but was not found to have a hollow viscus nor diaphragmatic injury. We hypothesize a possible, as yet unpublished, mechanism: secondary to the patient’s rib fractures and significant torso soft tissue shearing, a defect in the parietal pleura allowed air to track from the thorax inferiorly along subcutaneous and fascial planes, eventually entering into the peritoneal cavity through a violated parietal peritoneum. We present a review of the literature on tension pneumoperitoneum.
The effects of micropayments on online news story selection and engagement
Authors: Geidner Nick , D’Arcy Denae
Published: October 2013

This study examines the effects of micropayments on individuals’ selection and engagement with online journalism. Micropayment represent a means of monetizing online content in which the user pays a small amount of money (i.e., pennies to a few dollars) for each story purchased. Realistically, micropayments have not been a viable option until recently. With the introduction of Google Wallet and other payment infrastructures, micropayments are on the tipping point of mainstream acceptance and use. This study utilizes an experimental design ( N = 156) in which motivation (low versus high) and cost (no pay versus pay) were manipulated. The findings demonstrate that while individuals are willing to purchase news via micropayment, they become less likely to select news from opinion-challenging sources. In light of the results, the implications discussed include suggestions for media producers on how to create effective micropayment systems.
Investigation of friction stir welding tool parameters using FEM and neural network
Authors: Shojaeefard Mohammad Hasan , Khalkhali Abolfazl , Akbari Mostafa , Asadi Parviz
Published: October 2013

The welding tool geometry plays a critical role in acquiring desired microstructures and the heat-affected zones, and consequently improving the strength of the joint in friction stir welding. In this study, a friction stir welding process with different tool pin and shoulder diameter was numerically modeled. A thermomechanically coupled, 3D FEM analysis was used to investigate the effect of tool pin and shoulder diameter on welding force, material flow, thermal, and strain distributions in AA5083 aluminum alloy. Then, an artificial neural network model was employed to model the correlation between the tool parameters (pin and shoulder diameter) and heat-affected zone, thermal, and strain value in the weld zone.
Emerging news non-profits: A case study for rebuilding community trust?
Authors: Konieczna Magda , Robinson Sue
Published: October 2013

A new news disseminator has emerged to revitalize the profession of information gathering – the non-profit news organization. Adopting a framework of community trust, this article begins a scholarly response to the questions: Who are these non-profit journalists and what do they aim to accomplish? A rhetorical analysis of nearly 50 mission statements and ethnographic work on two case studies revealed a commitment to rebuilding public trust, to reclaiming community journalism, to re-emphasizing the “ordinary” citizen, and to pioneering collaborative news work by means of digital technologies. Our analysis demonstrated that many of these organizations, in considering news as a public good, work to re-conceptualize the industry for citizens, but depend upon a level of funding that might not be viable in the long term. However, this research posits that little in the way of true community trust can be achieved until these organizations discover a sustainable business model.
Experiences of using a memory aid to structure and support daily activities in a small-scale group accommodation for people with dementia
Authors: Kerkhof Yvonne JF , Rabiee Fatemeh , Willems Charles G
Published: October 2013

Background

Use of technology to structure and support the daily activities of the residents in a small-scale group accommodation (SSGA) for dementia is a new innovation in the Netherlands. This paper presents the process of development of this new way of structuring activities and the findings of a pilot study looking at the experiences of using this device in people with dementia.

Method

A qualitative method was chosen, data were collected using individual interviews with the residents ( n = 6), focus groups interviews with informal carers ( n = 5) and members of staff ( n = 6). Data were analysed using Ritchie & Spencer’s framework (1994) .

Findings

Three main themes emerged: issues regarding the implementation, needs for further development and the learning experiences acquired during the development. The majority of the residents were happy with the use and function of the memory aid. However, the occurrence of installation errors, limited ease of use and a lack of knowledge regarding the function and use of the memory aid were issues that prevented a successful implementation. Findings highlighted shared views about ways of improving through adaptation of the software program and additional technological applications; internet connectivity, improving its accessibility by using a remote control and adding videos and photos.

Conclusion

Lessons are learned about the use and transferability of this innovation in people with dementia and other vulnerable target groups including those with learning disabilities as well as its limitation and the needs for further development.
The impact of dementia on length of stay in acute hospitals in Ireland
Authors: Connolly Sheelah , O’Shea Eamon
Published: October 2013

The outcomes for those with dementia admitted to acute hospitals are often poor, with higher mortality, increased risk of institutionalisation and longer length of stay. The aim of this study was to examine the impact of dementia on length of stay and the associated cost of care in acute hospitals in Ireland. People with a recorded diagnosis of dementia were found to have a significantly longer length of stay than those with no recorded dementia. Multiplying the excess length of stay by the number of dementia-related admissions gave an estimate of 246,908 additional hospital days per annum due to dementia at an associated additional annual cost of over €199 million. Improving the experience of those with dementia in acute hospitals will likely lead to cost savings for the health service; however, it will require a number of measures including: earlier diagnosis, training for medical professionals and improvements in the built environment.
Couples with dementia: Positioning the ‘we'
Authors: Hydén Lars-Christer , Nilsson Elin
Published: October 2013

The aim of this article is to investigate how spouses in couples with dementia position themselves in relation to each other by analysing their use of pronouns, especially the we. The study uses joint interviews with 11 couples. Based on a quantitative analysis of pronoun use, it is argued that the pronoun we is used by all the spouses; however, it is used less frequently by the spouses with dementia in comparison with healthy spouses. A qualitative analysis of the use of the pronoun we shows that the spouses position, experience and consider themselves as a couple and that they position and experience themselves as individuals in relation to the couple. One of the challenges for couples with dementia is to be able to retain a we in face of the progression of the dementia disease. By positioning themselves in various ways, the spouses establish and negotiate quite a complex and emotionally charged web of relationships.
Engaging publics: writing as praxis
Authors: Kitchin Rob
Published: October 2013

Geographers have long debated for whom and for what ends academics should research and publish, how geographical knowledge is produced, and the use and value of such knowledges. This paper contributes to these debates through a discussion of an on-going project concerning the financial crisis in Ireland and its legacy of ‘ghost estates’. The analysis is framed with respect to Michael Burawoy’s taxonomy of forms of scholarly knowledge production and details the use of 10 forms of writing praxis, aimed at engaging a variety of audiences. The paper demonstrates that the classes in Burawoy’s taxonomy are far from mutually exclusive, and illustrates how geographical scholarship can make an impact in a variety of registers.
Geographies of poetry/poetries of geography
Authors: Cresswell Tim
Published: October 2013

This contribution is a reflection on the process of becoming a poet as a geographer. It charts my journey into the world of poetry and reflects on the cross-overs between academic geography and poetic practice in the past. It considers the way in which geography and poetry can inform each other in the practice of writing creatively, and tentatively suggests how this engagement might influence my on-going writing practice now and in the future.
‘Afters’: 26 authors and a ‘workshop imagination geared to writing’
Authors: Cook et al Ian
Published: October 2013

As academics, research participants and readers can now write more together online, this paper reflects on the way that a review article on the Geographies of Food was written out of online conversations between 26 authors. This process began as an emailed invitation, moved online into blogged conversations, and produced a paper that aimed to stretch the journal format to capture and continue that conversation. This was an experiment in creative collaborative writing, writing that was intended to be evocative and engaging, writing that imagined its readers not as recipients of its expertise, but as participants in its creative process.
The Equalizer? Crime, Vulnerability, and Gender in Pro-Gun Discourse
Authors: Carlson Jennifer
Published: October 2013

Alongside literature on how crime and crime control reproduce racial inequality, less attention has been paid to how the social construction of crime reproduces masculine privilege. To address this gap, I examine 71 interviews with gun carriers. While gun carriers actively promote guns to women, they tend to assume a masculine perspective on crime by emphasizing fast, warlike violence perpetrated by strangers—the kinds of crime men, as opposed to women, are likely to face. Extending theories of vulnerability to gun politics, I argue that the social construction of crime is a key vehicle through which gender is reproduced.
What drives media attention for climate change? Explaining issue attention in Australian, German and Indian print media from 1996 to 2010
Authors: Schäfer Mike S , Ivanova Ana , Schmidt Andreas
Published: October 2013

The article identifies the drivers of media attention for climate change in three countries: Australia, Germany and India. It calculates the monthly amount of climate change-related coverage in two leading newspapers for each country in relation to all articles published in the respective newspapers over a 15-year time span (1996–2010). Based on an explanatory model derived from agenda setting theory, punctuated equilibrium theory and multiple streams theory, it uses time series regression analysis to assess the influence of weather and climate characteristics as well as various social events and feedbacks on issue attention. The results show that weather and climate characteristics are no important drivers for issue attention in two of the three countries, and that societal activity, particularly international climate summits and the agenda building efforts from international non-governmental organizations, has stronger impacts on issue attention.
The darkest hour: diagnosing and managing insomnia
Authors: Aung Damian , Chandalia Prakhar
Published: October 2013

Insomnia is categorised by difficulties in initiating sleep or maintaining sleep, and/or early awakenings. It is a common and significant problem that impacts on the physical, mental and social well-being of sufferers as well as their families and carers. Around 25% of the general population experiences insomnia at some point and 20–50% will seek help from their GP. This article aims to provide an overview of the common causes of insomnia and how best to manage them in primary care.
The influence and changes in the dosages of concomitantly used psychotropic drugs associated with the discontinuation of donepezil in severe Alzheimer’s disease with behavioral and psychological symptoms on dementia: a preliminary open-label trial
Authors: Suzuki Hidenobu , Inoue Yuichi , Mikami Katsunaka , Gen Keishi
Published: October 2013

Objective:

We investigated the influence on behavioral and psychological symptoms on dementia (BPSD) and the changes in the dosages of concomitant psychotropic drugs associated with the discontinuation of donepezil in patients with severe Alzheimer’s disease (AD) who developed BPSD during donepezil therapy.

Methods:

The subjects were 44 inpatients who had been diagnosed with AD according to the Diagnostic and Statistical Manual of Mental Disorders IV (DSM-IV). The outcome measures assessed were BPSD and cognitive function. BPSD was assessed using the Neuropsychiatric Inventory (NPI) and cognitive function was assessed using the Mini Mental Examination (MMSE). The changes in the dosages of concomitant psychotropic drugs were also assessed.

Results:

Significant decreases were found in the donepezil treatment discontinuation group in the following NPI total score and two NPI subscales (agitation and irritability), but no significant differences were seen between the donepezil treatment discontinuation group and the control group. Furthermore, the mean changes from baseline in the risperidone equivalent dose and the diazepam equivalent dose were hardly changed in the donepezil treatment discontinuation group.

Conclusion:

The results of this study suggest that the discontinuation of donepezil treatment in patients with AD with BPSD may afford superior efficacy and may make it possible to not increase the dosage of other psychotropic drugs.
African American Primary Care Physicians’ Prostate Cancer Screening Practices
Authors: Ross Louie E. , Hall Ingrid J.
Published: October 2013

Introduction: Prostate cancer is the most common cancer and the second leading cause of cancer death among men in the United States. African American (AA) men have greater prostate cancer burden than other men. Little is known about AA primary care physicians’ (PCPs) practices regarding prostate cancer screening. Methods: We analyzed data from the 2007-2008 National Survey of Primary Care Physicians’ Practices Regarding Prostate Cancer Screening. The current study included 604 AA PCPs. Outcomes assessed were ( a) offering screening using the prostate-specific antigen (PSA) test, ( b) use of screening discussions to involve patients in the decision to screen, and ( c) having a discussion policy to try to talk the patient into getting the screening tests. Results: Most AA PCPs were male (52%), younger than 50 years (61%), and had 21% to 100% AA patients in their practices (74%). The majority (94%) of AA PCPs offered prostate cancer screening using PSA, discussed the tests with their male patients to involve them in the decision to screen (83%), and had a policy to try to talk the patient into getting the screening tests (77%). Multivariate analysis showed that offering screening, use of discussions, and a usual policy to encourage taking the screening tests varied mainly by practice-related factors, including practice type, practice location, and percentage of AA patients in the practice. Conclusion: Data from this study indicate that most AA PCPs reported high proscreening behaviors for all 3 outcomes. Additionally, practice- and screening-related factors may be important when examining AA PCP screening behaviors.
Impact of allele-level HLA matching on outcomes after myeloablative single unit umbilical cord blood transplantation for hematologic malignancy
Authors: Eapen Mary , Klein John P. , Ruggeri Annalisa , Spellman Stephen , Lee Stephanie J. , Anasetti Claudio , Arcese William , Barker Juliet N. , Baxter-Lowe Lee Ann , Brown Maria , Fernandez-Vina Marcelo A. , Freeman John , He Wensheng , Iori Anna Paola , Horowitz Mary M. , Locatelli Franco , Marino Susana , Maiers Martin , Michel Gerard , Sanz Guillermo F. , Gluckman Eliane , Rocha Vanderson
Published: October 2013

Key Points

Efficacy of transplanting allele-level HLA-matched cord blood units.
Clinical and laboratory predictive markers for acute dengue infection
Authors: Ho Tzong-Shiann , Wang Shih-Min , Lin Yee-Shin , Liu Ching-Chuan
Published: October 2013

Background

Early diagnosis of dengue virus infection during the febrile stage is essential for adjusting appropriate management. This study is to identify the predictive markers of clinical and laboratory findings in the acute stage of dengue infection during a major outbreak of dengue virus type 1 that occurred in southern Taiwan during 2007. A retrospective, hospital-based study was conducted at a university hospital in southern Taiwan from January to December, 2007. Patient who was reported for clinically suspected dengue infection was enrolled. Laboratory-positive dengue cases are confirmed by enzyme-linked immunosorbent assay of specific dengue IgM, fourfold increase of dengue-specific IgG titers in convalescent serum, or by reverse transcription-polymerase chain reaction (RT-PCR) of dengue virus.

Results

The suspected dengue cases consist of 100 children (≤ 18 years) and 481 adults. Among the 581 patients, 67 (67%) children and 309 (64.2%) adults were laboratory-confirmed. Patients who had laboratory indeterminate were excluded. Most cases were uncomplicated and 3.8% of children and 2.9% of adults developed dengue hemorrhagic fever or dengue shock syndrome (DHF/DSS). The overall mortality rate in those with DHF/DSS was 7.1%, and the average duration of hospitalization was 20 days. The most common symptoms/signs at admission were myalgia (46.8%), petechiae (36.9%) and nausea/vomiting (33.5%). The most notable laboratory findings included leukopenia (2966 ± 1896/cmm), thrombocytopenia (102 ± 45 × 103/cmm), prolonged activated partial thromboplastin time (aPTT) (45 ± 10 s), and elevated serum levels of aminotransferase (AST, 166 ± 208 U/L; ALT, 82 ± 103 U/L) and low C - reactive protein (CRP) (6 ± 11 mg/L). Based on the clinical features for predicting laboratory-confirmed dengue infection, the sensitivities of typical rash, myalgia, and positive tourniquet test are 59.2%, 46.8%, and 34.2%, while the specificities for above features are 75.4%, 53.5% and 100%, respectively. The positive predictive value (PPV) for combination of leukopenia, thrombocytopenia (< 150 × 103/cmm), elevated aminotransferase (AST/ALT > 1.5) and low CRP (< 20 mg/L) is 89.5%, while the negative predictive value is 37.4%. Furthermore, the PPV of the combination was increased to 93.1% by adding prolonged aPTT (>38 secs).

Conclusions

Leukopenia, thrombocytopenia, elevated aminotransferases, low CRP and prolonged aPTT, were useful predictive markers for early diagnosis of dengue infection during a large outbreak in southern Taiwan.
A new model for the biodegradation kinetics of oil droplets: application to the Deepwater Horizon oil spill in the Gulf of Mexico
Authors: Vilcáez Javier , Li Li , Hubbard Susan S
Published: October 2013

Oil biodegradation by native bacteria is one of the most important natural processes that can attenuate the environmental impacts of marine oil spills. Existing models for oil biodegradation kinetics are mostly for dissolved oil. This work developed a new mathematical model for the biodegradation of oil droplets and applied the model to estimate the time scale for oil biodegradation under conditions relevant to the Deepwater Horizon oil spill in the Gulf of Mexico. In the model, oil is composed of droplets of various sizes following the gamma function distribution. Each oil droplet shrinks during the microbe-mediated degradation at the oil-water interface. Using our developed model, we find that the degradation of oil droplets typically goes through two stages. The first stage is characterized by microbial activity unlimited by oil-water interface with higher biodegradation rates than that of the dissolved oil. The second stage is governed by the availability of the oil-water interface, which results in much slower rates than that of soluble oil. As a result, compared to that of the dissolved oil, the degradation of oil droplets typically starts faster and then quickly slows down, ultimately reaching a smaller percentage of degraded oil in longer time. The availability of the water-oil interface plays a key role in determining the rates and extent of degradation. We find that several parameters control biodegradation rates, including size distribution of oil droplets, initial microbial concentrations, initial oil concentration and composition. Under conditions relevant to the Deepwater Horizon spill, we find that the size distribution of oil droplets (mean and coefficient of variance) is the most important parameter because it determines the availability of the oil-water interface. Smaller oil droplets with larger variance leads to faster and larger extent of degradation. The developed model will be useful for evaluating transport and fate of spilled oil, different remediation strategies, and risk assessment.
Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicumATCC 13032
Authors: Mentz Almut , Neshat Armin , Pfeifer-Sancar Katharina , Pühler Alfred , Rückert Christian , Kalinowski Jörn
Published: October 2013

Background

Recent discoveries on bacterial transcriptomes gave evidence that small RNAs (sRNAs) have important regulatory roles in prokaryotic cells. Modern high-throughput sequencing approaches (RNA-Seq) enable the most detailed view on transcriptomes offering an unmatched comprehensiveness and single-base resolution. Whole transcriptome data obtained by RNA-Seq can be used to detect and characterize all transcript species, including small RNAs. Here, we describe an RNA-Seq approach for comprehensive detection and characterization of small RNAs from Corynebacterium glutamicum, an actinobacterium of high industrial relevance and model organism for medically important Corynebacterianeae, such as C. diphtheriae and Mycobacterium tuberculosis.

Results

In our RNA-Seq approach, total RNA from C. glutamicum ATCC 13032 was prepared from cultures grown in minimal medium at exponential growth or challenged by physical (heat shock, cold shock) or by chemical stresses (diamide, H2O2, NaCl) at this time point. Total RNA samples were pooled and sequencing libraries were prepared from the isolated small RNA fraction. High throughput short read sequencing and mapping yielded over 800 sRNA genes. By determining their 5′- and 3′-ends and inspection of their locations, these potential sRNA genes were classified into UTRs of mRNAs (316), cis-antisense sRNAs (543), and trans-encoded sRNAs (262). For 77 of trans-encoded sRNAs significant sequence and secondary structure conservation was found by a computational approach using a whole genome alignment with the closely related species C. efficiens YS-314 and C. diphtheriae NCTC 13129. Three selected trans-encoded sRNAs were characterized by Northern blot analysis and stress-specific transcript patterns were found.

Conclusions

The study showed comparable numbers of sRNAs known from genome-wide surveys in other bacteria. In detail, our results give deep insight into the comprehensive equipment of sRNAs in C. glutamicum and provide a sound basis for further studies concerning the functions of these sRNAs.
Global regulatory architecture of human, mouse and rat tissue transcriptomes
Authors: Prasad Ajay , Kumar Suchitra Suresh , Dessimoz Christophe , Bleuler Stefan , Laule Oliver , Hruz Tomas , Gruissem Wilhelm , Zimmermann Philip
Published: October 2013

Background

Predicting molecular responses in human by extrapolating results from model organisms requires a precise understanding of the architecture and regulation of biological mechanisms across species.

Results

Here, we present a large-scale comparative analysis of organ and tissue transcriptomes involving the three mammalian species human, mouse and rat. To this end, we created a unique, highly standardized compendium of tissue expression. Representative tissue specific datasets were aggregated from more than 33,900 Affymetrix expression microarrays. For each organism, we created two expression datasets covering over 55 distinct tissue types with curated data from two independent microarray platforms. Principal component analysis (PCA) revealed that the tissue-specific architecture of transcriptomes is highly conserved between human, mouse and rat. Moreover, tissues with related biological function clustered tightly together, even if the underlying data originated from different labs and experimental settings. Overall, the expression variance caused by tissue type was approximately 10 times higher than the variance caused by perturbations or diseases, except for a subset of cancers and chemicals. Pairs of gene orthologs exhibited higher expression correlation between mouse and rat than with human. Finally, we show evidence that tissue expression profiles, if combined with sequence similarity, can improve the correct assignment of functionally related homologs across species.

Conclusion

The results demonstrate that tissue-specific regulation is the main determinant of transcriptome composition and is highly conserved across mammalian species.
Genomic diversity and adaptation of Salmonella enterica serovar Typhimurium from analysis of six genomes of different phage types
Authors: Pang Stanley , Octavia Sophie , Feng Lu , Liu Bin , Reeves Peter R , Lan Ruiting , Wang Lei
Published: October 2013

Background

Salmonella enterica serovar Typhimurium (or simply Typhimurium) is the most common serovar in both human infections and farm animals in Australia and many other countries. Typhimurium is a broad host range serovar but has also evolved into host-adapted variants (i.e. isolated from a particular host such as pigeons). Six Typhimurium strains of different phage types (defined by patterns of susceptibility to lysis by a set of bacteriophages) were analysed using Illumina high-throughput genome sequencing.

Results

Variations between strains were mainly due to single nucleotide polymorphisms (SNPs) with an average of 611 SNPs per strain, ranging from 391 SNPs to 922 SNPs. There were seven insertions/deletions (indels) involving whole or partial gene deletions, four inactivation events due to IS200 insertion and 15 pseudogenes due to early termination. Four of these inactivated or deleted genes may be virulence related. Nine prophage or prophage remnants were identified in the six strains. Gifsy-1, Gifsy-2 and the sopE2 and sspH2 phage remnants were present in all six genomes while Fels-1, Fels-2, ST64B, ST104 and CP4-57 were variably present. Four strains carried the 90-kb plasmid pSLT which contains several known virulence genes. However, two strains were found to lack the plasmid. In addition, one strain had a novel plasmid similar to Typhi strain CT18 plasmid pHCM2.

Conclusion

The genome data suggest that variations between strains were mainly due to accumulation of SNPs, some of which resulted in gene inactivation. Unique genetic elements that were common between host-adapted phage types were not found. This study advanced our understanding on the evolution and adaptation of Typhimurium at genomic level.
Accurate measurement of gene copy number for human alpha-defensin DEFA1A3
Authors: Khan Fayeza F , Carpenter Danielle , Mitchell Laura , Mansouri Omniah , Black Holly A , Tyson Jess , Armour John AL
Published: October 2013

Background

Multi-allelic copy number variants include examples of extensive variation between individuals in the copy number of important genes, most notably genes involved in immune function. The definition of this variation, and analysis of its impact on function, has been hampered by the technical difficulty of large-scale but accurate typing of genomic copy number. The copy-variable alpha-defensin locus DEFA1A3 on human chromosome 8 commonly varies between 4 and 10 copies per diploid genome, and presents considerable challenges for accurate high-throughput typing.

Results

In this study, we developed two paralogue ratio tests and three allelic ratio measurements that, in combination, provide an accurate and scalable method for measurement of DEFA1A3 gene number. We combined information from different measurements in a maximum-likelihood framework which suggests that most samples can be assigned to an integer copy number with high confidence, and applied it to typing 589 unrelated European DNA samples. Typing the members of three-generation pedigrees provided further reassurance that correct integer copy numbers had been assigned. Our results have allowed us to discover that the SNP rs4300027 is strongly associated with DEFA1A3 gene copy number in European samples.

Conclusions

We have developed an accurate and robust method for measurement of DEFA1A3 copy number. Interrogation of rs4300027 and associated SNPs in Genome-Wide Association Study SNP data provides no evidence that alpha-defensin copy number is a strong risk factor for phenotypes such as Crohn’s disease, type I diabetes, HIV progression and multiple sclerosis.
Surveillance of ischemic heart disease should include physician billing claims: population-based evidence from administrative health data across seven Canadian provinces
Authors: Robitaille Cynthia , Bancej Christina , Dai Sulan , Tu Karen , Rasali Drona , Blais Claudia , Plante Céline , Smith Mark , Svenson Lawrence W , Reimer Kim , Casey Jill , Puchtinger Rolf , Johansen Helen , Gurevich Yana , Waters Chris , Lix Lisa M , Quan Hude
Published: October 2013

Background

Canadian provinces and territories routinely collect health information for administrative purposes. This study used Canadian medical and hospital administrative data for population-based surveillance of diagnosed ischemic heart disease (IHD).

Methods

Hospital discharge abstracts and physician billing claims data from seven provinces were analyzed to estimate prevalence and incidence of IHD using three validated algorithms: a) one hospital discharge abstract with an IHD diagnosis or procedure code (1H); b) 1H or at least three physician claims within a one-year period (1H3P) and c) 1H or at least two physician claims within a one-year period (1H2P). Crude and age-standardized prevalence and incidence rates were calculated for Canadian adults aged 20 +.

Results

IHD prevalence and incidence varied by province, were consistently higher among males than females, and increased with age. Prevalence and incidence were lower using the 1H method compared to using the 1H2P or 1H3P methods in all provinces studied for all age groups. For instance, in 2006/07, crude prevalence by province ranged from 3.4%-5.5% (1H), from 4.9%-7.7% (1H3P) and from 6.0%-9.2% (1H2P). Similarly, crude incidence by province ranged from 3.7-5.9 per 1,000 (1H), from 5.0-6.9 per 1,000 (1H3P) and from 6.1-7.9 per 1,000 (1H2P).

Conclusions

Study findings show that incidence and prevalence of diagnosed IHD will be underestimated by as much as 50% using inpatient data alone. The addition of physician claims data are needed to better assess the burden of IHD in Canada.
The protective effect of VSL#3 on intestinal permeability in a rat model of alcoholic intestinal injury
Authors: Chang Bing , Sang Lixuan , wang Ying , Tong Jing , Zhang Dai , Wang Bingyuan
Published: October 2013

Background

This study aimed to investigate the mechanism of the probiotic VSL#3 in acute alcoholic intestinal injury, and evaluate the effect of VSL#3, glutamine,VSL#3+glutamine and heat-killed VSL#3 therapy in a rat model.

Methods

Six- to eight-week-old male wild-type rats were divided into seven groups. To establish the acute alcohol liver disease model, rats received three doses of corn starch dissolved in PBS/40% alcohol administered intra-gastrically every 12 hours. Treatment groups received an intra-gastric dose of VSL#3, Glutamine, heat-killed VSL#3, or VSL#3+Glutamine 30 minutes prior to alcohol administration. The placebo group was treated with PBS prior to alcohol administration. TNFα and endotoxin in plasma was measured by ELISA and Tachypleus Ameboctye Lysate assays, and electron microscopy, Western blotting, and reverse transcription polymerase chain reaction were used to identify the mechanisms of VSL#3 in the regulation of epithelial permeability.

Results

First, compared with control group, endotoxin and TNFα in alcohol group was obviously high. At the same time, in VSL#3 group,the expression of endotoxin and TNFα obviously lower than the alcohol group. And the trends of the expression of tight junction proteins in these groups were reversed with the change of endotoxin and TNFα. Second, compared the groups of VSL#3 with glutamine,VSL#3+glutamine and heat-killed VSL#3,we found that both VSL#3 and heat-killed VSL#3, glutamine were as effective as VSL#3+glutamine in the treatment of acute alcohol liver disease, the expression of endotoxin and TNFα were lower than the alcohol group, and tight junction proteins were higher than the alcohol group whereas the expression of tight junction proteins were higher in VSL#3 + glutamine group than either agent alone, but have no significant difference.

Conclusion

We conclude that VSL#3 treatment can regulate the ecological balance of the gut microflora, preventing passage of endotoxin and other bacterial products from the gut lumen into the portal circulation and down-regulating the expression of TNFα, which could otherwise down-regulate the expression of tight junction proteins and increase epithelial permeability.
Time to blood culture positivity as a predictor of clinical outcome in patients with Candida albicansbloodstream infection
Authors: Nunes Cintia Zoya , Marra Alexandre R , Edmond Michael B , da Silva Victor Elivane , Pereira Carlos Alberto Pires
Published: October 2013

Background

Few studies have assessed the time to blood culture positivity as a predictor of clinical outcome in fungal bloodstream infections (BSIs). The purpose of this study was to evaluate the time to positivity (TTP) of blood cultures in patients with Candida albicans BSIs and to assess its impact on clinical outcome.

Methods

A historical cohort study with 89 adults patients with C. albicans BSIs. TTP was defined as the time between the start of incubation and the time that the automated alert signal indicating growth in the culture bottle sounded.

Results

Patients with BSIs and TTPs of culture of ≤36 h (n=39) and >36 h (n=50) were compared. Septic shock occurred in 46.2% of patients with TTPs of ≤36 h and in 40.0% of patients with TTP of >36 h (p=0.56). A central venous catheter source was more common with a BSI TTP of ≤36 h (p=0.04). Univariate analyis revealed that APACHE II score≥20 at BSI onset, the development of at least one organ system failure (respiratory, cardiovascular, renal, hematologic, or hepatic), SOFA at BSI onset, SAPS II at BSI onset, and time to positivity were associated with death. By using logistic regression analysis, the only independent predictor of death was time to positivity (1.04; 95% CI, 1.0-1.1, p=0.035), with the chance of the patient with C. albicans BSI dying increasing 4.0% every hour prior to culture positivity.

Conclusion

A longer time to positivity was associated with a higher mortality for Candida albicans BSIs; therefore, initiating empiric treatment with antifungals may improve outcomes.
Computer-assisted counting of retinal cells by automatic segmentation after TV denoising
Authors: Bredies Kristian , Wagner Marcus , Schubert Christian , Ahnelt Peter
Published: October 2013

Background

Quantitative evaluation of mosaics of photoreceptors and neurons is essential in studies on development, aging and degeneration of the retina. Manual counting of samples is a time consuming procedure while attempts to automatization are subject to various restrictions from biological and preparation variability leading to both over- and underestimation of cell numbers. Here we present an adaptive algorithm to overcome many of these problems.

Digital micrographs were obtained from cone photoreceptor mosaics visualized by anti-opsin immuno-cytochemistry in retinal wholemounts from a variety of mammalian species including primates. Segmentation of photoreceptors (from background, debris, blood vessels, other cell types) was performed by a procedure based on Rudin-Osher-Fatemi total variation (TV) denoising. Once 3 parameters are manually adjusted based on a sample, similarly structured images can be batch processed. The module is implemented in MATLAB and fully documented online.

Results

The object recognition procedure was tested on samples with a typical range of signal and background variations. We obtained results with error ratios of less than 10% in 16 of 18 samples and a mean error of less than 6% compared to manual counts.

Conclusions

The presented method provides a traceable module for automated acquisition of retinal cell density data. Remaining errors, including addition of background items, splitting or merging of objects might be further reduced by introduction of additional parameters. The module may be integrated into extended environments with features such as 3D-acquisition and recognition.
The risk of childhood autism among second-generation migrants in Finland: a case–control study
Authors: Lehti Venla , Hinkka-Yli-Salomäki Susanna , Cheslack-Postava Keely , Gissler Mika , Brown Alan S , Sourander Andre
Published: October 2013

Background

Studying second-generation immigrants can help in identifying genetic or environmental risk factors for childhood autism. Most previous studies have focused on maternal region of birth and showed inconsistent results. No previous study has been conducted in Finland.

Methods

The study was a nested case–control study based on a national birth cohort. Children born in 1987–2005 and diagnosed with childhood autism by the year 2007 were identified from the Finnish Hospital Discharge Register. Controls were selected from the Finnish Medical Birth Register. Information on maternal and paternal country of birth and mother tongue was collected from the Finnish Central Population Register. There were 1132 cases and 4515 matched controls. The statistical test used was conditional logistic regression analysis.

Results

Compared with children with two Finnish parents, the risk of childhood autism was increased for those whose parents are both immigrants (adjusted odds ratio [aOR] 1.8, 95% confidence interval [CI] 1.2–2.7) and for those with only an immigrant mother (aOR 1.8, 95% CI 1.2–2.7), but not for those with only an immigrant father. The risk was increased for those with a mother born in the former Soviet Union or Yugoslavia and for those with a mother or a father born in Asia. Specific parental countries of birth associated with an increased risk were the former Soviet Union, the former Yugoslavia and Vietnam.

Conclusions

In Finland, children who are born to immigrant mothers with or without an immigrant partner, have an increased risk of childhood autism. The risk varies with immigrant parents’ region of birth. The findings may help in identifying possible risk factors, which can be examined in future studies.