bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outlier detection at the transcriptome-proteome interface
Authors: Gunawardana Yawwani , Fujiwara Shuhei , Takeda Akiko , Woo Jeongmin , Woelk Christopher , Niranjan Mahesan 
Published: March 2015

AbstractBackground: In high-throughput experimental biology, it is widely acknowledged that while expression levels measured at the levels of transcriptome and the corresponding proteome do not, in general, correlate well, messenger RNA levels are used as convenient proxies for protein levels. Our interest is in developing data-driven computational models that can bridge the gap between these two levels of measurement at which different mechanisms of regulation may act on different molecular species causing any observed lack of correlations. To this end, we build data-driven predictors of protein levels using mRNA levels and known proxies of translation efficiencies as covariates. Previous work showed that in such a setting, outliers with respect to the model are reliable candidates for post-translational regulation.Results: Here, we present and compare two novel formulations of deriving a protein concentration predictor from which outliers may be extracted in a systematic manner. The first approach, outlier rejecting regression, allows explicit specification of a certain fraction of the data as outliers. In a regression setting, this is a non-convex optimization problem which we solve by deriving a difference of convex functions algorithm (DCA). With post-translationally regulated proteins, one expects their concentrations to be affected primarily by disruption of protein stability. Our second algorithm exploits this observation by minimizing an asymmetric loss using quantile regression and extracts outlier proteins whose measured concentrations are lower than what a genome-wide regression would predict. We validate the two approaches on a dataset of yeast transcriptome and proteome. Functional annotation check on detected outliers demonstrate that the methods are able to identify post-translationally regulated genes with high statistical confidence.Contact: mn@ecs.soton.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.
Long live the alien: is high genetic diversity a pivotal aspect of crested porcupine (Hystrix cristata) long-lasting and successful invasion?
Authors: Trucchi Emiliano , Facon Benoit , Gratton Paolo , Mori Emiliano , Stenseth Nils Chr. , Jentoft Sissel 
Published: March 2015

AbstractStudying the evolutionary dynamics of an alien species surviving and continuing to expand after several generations can provide fundamental information on the relevant features of clearly successful invasions. Here, we tackle this task by investigating the dynamics of the genetic diversity in invasive crested porcupine (Hystrix cristata) populations, introduced to Italy about 1500 years ago, which are still growing in size, distribution range and ecological niche. Using genome-wide RAD markers, we describe the structure of the genetic diversity and the demographic dynamics of theH. cristatainvasive populations and compare their genetic diversity with that of native African populations of bothH. cristataand its sister species,H. africaeaustralis. First, we demonstrate that genetic diversity is lower in both the invasive Italian and the North Africa source range relative to other native populations from Sub-Saharan and South Africa. Second, we find evidence of multiple introduction events in the invasive range followed by very limited gene flow. Through coalescence-based demographic reconstructions, we also show that the bottleneck at introduction was mild and did not affect the introduced genetic diversity. Finally, we reveal that the current spatial expansion at the northern boundary of the range is following a leading-edge model characterized by a general reduction of genetic diversity towards the edge of the expanding range. We conclude that the level of genome-wide diversity ofH. cristatainvasive populations is less important in explaining its successful invasion than species-specific life-history traits or the phylogeographic history in the native source range.
Using heterogeneity in the population structure of U.S. swine farms to compare transmission models for porcine epidemic diarrhoea
Authors: O’Dea Eamon B. , Snelson Harry , Bansal Shweta 
Published: March 2015

ABSTRACTIn 2013, U.S. swine producers were confronted with the disruptive emergence of porcine epidemic diarrhoea (PED). Movement of animals among farms is hypothesised to have played a role in the spread of PED among farms. Via this or other mechanisms, the rate of spread may also depend on the geographic density of farms and climate. To evaluate such effects on a large scale, we analyse state-level counts of outbreaks with variables describing the distribution of farm sizes and types, aggregate flows of animals among farms, and an index of climate. Our first main finding is that it is possible for a correlation analysis to be sensitive to transmission model parameters. This finding is based on a global sensitivity analysis of correlations on simulated data that included a biased and noisy observation model based on the available PED data. Our second main finding is that flows are significantly associated with the reports of PED outbreaks. This finding is based on correlations of pairwise relationships and regression modeling of total and weekly outbreak counts. These findings illustrate how variation in population structure may be employed along with observational data to improve understanding of disease spread.
Using targeted re-sequencing for identification of candidate genes and SNPs for a QTL affecting the pH value of chicken meat
Authors: Li Xidan , Liu Xiaodong , Nadaf Javad , Le Bihan-Duval Elisabeth , Berri Cécile , Dunn Ian C. , Talbot Richard , de Koning Dirk-Jan 
Published: March 2015

AbstractUsing targeted genetical genomics, a QTL affecting the initial post-mortem pH value of chicken breast muscle (Pectoralis major) on chromosome 1 (GGA1) was recently fine-mapped. Thirteen genes were present in the QTL region of about 1 Mb.In this study, ten birds that were inferred to be homozygous for either the high (QQ) or low (qq) QTL allele were selected for re-sequencing. After enrichment for 1 Mb around the QTL region, > 200 x coverage for the QTL region in each of the ten birds was obtained. We used custom tools to identify putative causal mutations in the mapped QTL region from next generation sequence data. Four non-synonymous SNPs differentiating the two QTL genotype groups were identified within four local genes (PRDX4, EIF2S3, PCYT1B and E1BTD2). These were defined to be most likely candidate SNPs to explain the QTL effect. Moreover, 29 consensus SNPs were detected within gene-related regions (UTR regions and splicing sites) for the QQ birds and 26 for the qq birds. These could also play a role explaining the observed QTL effect.The results provide an important step for prioritizing among a large amount of candidate mutations and significantly contribute to the understanding of the genetic mechanisms affecting the initial post-mortem pH value of chicken muscle.
Regional and global production networks: the case of China
Authors: Fung K.C. 
Published: March 2015

Purpose
– The purpose of this paper is to examine various aspects of regional and global production networks, with a special focus on China.

Design/methodology/approach
– The author studies four different approaches to measure production networks and discuss their strengths and weaknesses. The author presents some of the results associated with some of these measurements.

Findings
– The author finds that using trade data alone is simple but incomplete. Bringing in input–output tables is useful but much more data would be needed. In addition, for the case of China, electronic goods and telecommunication goods tend to have a higher foreign value added.

Research limitations/implications
– Data with good quality can be a problem. The authors also have difficulty getting input–output tables for many years.

Practical implications
– The results can guide policymakers as to which industries can create more domestic value added. The results can also lead to betting of an understanding of trade balances measured in the value added.

Social implications
– The results can generate further understanding among citizens of many different countries, including China, about the importance of different sectors in generating the value added.

Originality/value
– The value of this paper is to focus on alternative ways to measure the value added in exports from China. The paper is the first to discuss the strengths and weaknesses of different approaches and present some of these results.
The usefulness of derivative disclosures for investment decision-making
Authors: Huang Zhen , Gao Simon 
Published: March 2015

Purpose
– The purpose of this study is to examine the usefulness of derivative disclosures from the perspective of Chinese institutional investors in relation to their investment decision-making.

Design/methodology/approach
– This study uses semi-structured interviews with 21 institutional investors based in China including 10 funds managers and 11 professional analysts.

Findings
– This study finds that the information on the use of derivatives disclosed by listed companies in China is generally perceived to be useful to Chinese institutional investors (e.g. funds managers and professional analysts) in facilitating their investment decisions, although such information is generally thought to be less significant compared to other fundamental financial information such as assets, liabilities and profits/losses. It also finds that the current provisions of derivatives-related information by Chinese listed companies are largely unsatisfied primarily because of insufficient information and the lack of timely disclosures. Furthermore, it finds that the accounting and reporting policies currently imposed in China appear to be little understood by Chinese investors.

Research limitations/implications
– This study has its own limitations due to the approach of interviews with a relatively small sample from only two investment firms in China.

Practical implications
– The findings from the study provide a number of policy implications for derivatives regulators and accounting standards setters.

Originality/value
– This study is the first study of its kind to investigate the perceptions of Chinese institutional investors on the usefulness of derivatives reporting and disclosures with the use of interview research method.
Exploring family reading practices in non-Kuwaiti nannies
Authors: Fenimore Linda 
Published: March 2015

Purpose
– The purpose of this paper is to explore how home reading practices can impact what teachers assume to be the optimum practice in preparing students for school may not be supported by the local culture. In Kuwait, I have heard teachers repeatedly complain that students do not read at home or seem to value reading. Kuwaiti adults relate that they rarely engage in reading for pleasure. Students here are challenged with learning English, but also seem to take a greater amount of time to understand the use of reading in their lives and learning. These factors led me to consider that what teachers assume to be the optimum practice in preparing students for school may not be supported by the local culture.

Design/methodology/approach
– In this case study, five nannies were interviewed focusing on participants’ reading practices in their homes of origin and those practiced with Kuwaiti children. Observational notes were taken to record nonverbal communication. Data were analyzed to uncover references to home reading practices such as storytelling, recreational reading and verbal interaction based on the reading. References were color coded and a database was constructed of references the nannies made to reading practices both in their homes of origin and in the Kuwaiti homes in which they work. The references to reading practices were then categorized according to activities reported.

Findings
– As a result, it was found that the nannies perceived the purpose of reading to be for education only, storytelling is used for different purposes in different cultures, print material were rarely found in the homes of the nannies due to lack of economic means, and the fathers of most of the nannies were critical in their reading development.

Research limitations/implications
– Further exploration of the home reading practices of the Kuwaitis is needed to fully support the effective inclusion of their cultural reading traditions into school practice. Parent and student surveys, parent interviews and possibly home visits would assist researchers in more fully defining home reading practices. Partnering with Arabic-speaking or Kuwaiti teachers would benefit researchers in being able to efficiently translate for the interviews and then discuss their observations, giving the researchers a more nuanced perspective of the findings.

Originality/value
– This paper offers an original view on a particular aspect of international education, namely, reading habits, and discusses the promotion of multicultural reading instruction in a more culturally responsive manner.
A hierarchical model of social marketing
Authors: French Jeff , Russell-Bennett Rebekah 
Published: March 2015

Purpose– This paper aims to set out a new hierarchical and differentiated model of social marketing principles, concepts and techniques that builds on, but supersedes, the existing lists of non-equivalent and undifferentiated benchmark criteria.Design/methodology/approach– This is a conceptual paper that proposes a hierarchical model of social marketing principles, concepts and techniques.Findings– This new delineation of the social marketing principle, its four core concepts and five techniques, represents a new way to conceptualize and recognize the different elements that constitute social marketing. This new model will help add to and further the development of the theoretical basis of social marketing, building on the definitional work led by the International Social Marketing Association (iSMA), Australian Association of Social Marketing (AASM) and European Social Marketing Association (ESMA).Research limitations/implications– This proposed model offers a foundation for future research to expand upon. Further research is recommended to empirically test the proposed model.Originality/value– This paper seeks to advance the theoretical base of social marketing by making a reasoned case for the need to differentiate between principles, concepts and techniques when seeking to describe social marketing.
A 13‐year retrospective study evaluating the efficacy of using air‐fluidised beds for toxic epidermal necrolysis patients
Authors: Xia Weidong , Mao Cong , Luo Xu , Xu Jianjun , Chen Xiaofeng , Lin Cai 
Published: March 2015

AbstractObjectivesToxic epidermal necrolysis (TEN) is a potentially life‐threatening dermatological disease involving large areas of skin loss with systemic symptoms. This study evaluated the efficacy of air‐fluidised bed therapy for TEN patients.MethodsOf 27 people with TEN, 11 used air‐fluidised beds (the air‐fluidised group) and 16 used standard beds (the control group). Days to complete re‐epithelialisation, re‐epithelialisation rate, incidence of complications, mortality, pain measured by visual analogue score and the incidence of cutaneous infection were compared in these groups.ResultsThe mean body surface area of involvement was 77.0 ± 11.8% and baseline mean severity‐of‐illness score for TEN (SCORTEN) was 2.81 ± 1.08. The re‐epithelialisation rate in the air‐fluidised group was 100% but was only 56.3% in the control group (P < 0.05). There was a significant difference in the time taken to complete re‐epithelialisation between the air‐fluidised group (13 days [95% CI: 9.0–17.0]) and the control group (21 days [16.5–25.5], P < 0.05). Furthermore, the incidence of complications was 18% in the air‐fluidised group versus 75% in the control group, including fewer cutaneous infections (P < 0.05). There was a significant reduction in pain among the air‐fluidised group compared with the control group (P < 0.05). There were no deaths in the air‐fluidised group while 19% of the control group died.ConclusionAir‐fluidised beds can reduce the time to complete re‐epithelialisation, relieve pain and increase the re‐epithelialisation rate of TEN patients, but there was no significant difference between them in mortality rate in our study.
The applicability of the WHO classification in paediatric AML. A NOPHO‐AML study
Authors: Sandahl Julie D. , Kjeldsen Eigil , Abrahamsson Jonas , Ha Shau‐Yin , Heldrup Jesper , Jahnukainen Kirsi , Jónsson Ólafur G. , Lausen Birgitte , Palle Josefine , Zeller Bernward , Forestier Erik , Hasle Henrik 
Published: March 2015

SummaryThe World Health Organization (WHO) classification of myeloid leukaemia was revised in 2008. It incorporates newly recognized entities and emphasizes the pivotal role of cytogenetic abnormalities. The aim of this study was to evaluate the usability of the WHO classification when applied to a large population‐based paediatric acute myeloid leukaemia (AML) cohort. We included children diagnosed with de novo AML, 0–18 years of age from the Nordic countries and Hong Kong from 1993 to 2012. Data were retrieved from the Nordic Society for Paediatric Haematology and Oncology AML database and patients classified according to the WHO 2008 classification. A successful karyotype was available in 97% of the cases. AML with recurrent genetic abnormalities were present in 262 (41%) and 94 (15%) were classified as AML with myelodysplasia‐related changes (AML‐MDS). WHO classifies patients with monosomy 7 and del(7q) into one group. We found that −7 (n = 14) had significantly poorer outcome than del(7q) (n = 11); 5‐year event‐free survival 26% vs. 67%, (P = 0·02), and 5‐year overall survival 51% vs. 90%, (P = 0·04). The largest group was the highly heterogeneous AML not otherwise specified (NOS) (n = 280) (44%). In conclusion, the WHO classification allocated 15% to AML‐MDS, 44% to NOS and grouped together entities with clearly different outcome, therefore limiting the applicability of the current WHO classification in children with AML.
The iron chelator deferasirox affects redox signalling in haematopoietic stem/progenitor cells
Authors: Tataranni Tiziana , Agriesti Francesca , Mazzoccoli Carmela , Ruggieri Vitalba , Scrima Rosella , Laurenzana Ilaria , D'Auria Fiorella , Falzetti Franca , Di Ianni Mauro , Musto Pellegrino , Capitanio Nazzareno , Piccoli Claudia 
Published: March 2015

SummaryThe iron chelator deferasirox (DFX) prevents complications related to transfusional iron overload in several haematological disorders characterized by marrow failure. It is also able to induce haematological responses in a percentage of treated patients, particularly in those affected by myelodysplastic syndromes. The underlying mechanisms responsible for this feature, however, are still poorly understood. In this study, we investigated the effect of DFX‐treatment in human haematopoietic/progenitor stem cells, focussing on its impact on the redox balance, which proved to control the interplay between stemness maintenance, self‐renewal and differentiation priming. Here we show, for the first time, that DFX treatment induces a significant diphenyleneiodonium‐sensitive reactive oxygen species (ROS) production that leads to the activation of POU5F1 (OCT4), SOX2 and SOX17 gene expression, relevant in reprogramming processes, and the reduction of the haematopoietic regulatory proteins CTNNB1 (β‐Catenin) and BMI1. These DFX‐mediated events were accompanied by decreased CD34 expression, increased mitochondrial mass and up‐regulation of the erythropoietic marker CD71 (TFRC) and were compound‐specific, dissimilar to deferoxamine. Our findings would suggest a novel mechanism by which DFX, probably independently on its iron‐chelating property but through ROS signalling activation, may influence key factors involved in self‐renewal/differentiation of haematopoietic stem cells.
Response‐adapted therapy for aggressive non‐Hodgkin's lymphomas based on early [18F] FDG‐PET scanning: ECOG‐ACRIN Cancer Research Group study (E3404)
Authors: Swinnen Lode J. , Li Hailun , Quon Andrew , Gascoyne Randy , Hong Fangxin , Ranheim Erik A. , Habermann Thomas M. , Kahl Brad S. , Horning Sandra J. , Advani Ranjana H. 
Published: March 2015

SummaryA persistently positive positron emission tomography (PET) scan during therapy for diffuse large B‐cell lymphoma (DLBCL) is predictive of treatment failure. A response‐adapted strategy consisting of an early treatment change to four cycles of R‐ICE (rituximab, ifosfamide, carboplatin, etoposide) was studied in the Eastern Cooperative Oncology Group E3404 trial. Previously untreated patients with DLBCL stage III, IV, or bulky II, were eligible. PET scan was performed after three cycles of R‐CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine, prednisone) and scored as positive or negative by central review during the fourth cycle. PET‐positive patients received four cycles of R‐ICE, PET‐negative patients received two more cycles of R‐CHOP. A ≥45% 2‐year progression‐free survival (PFS) for mid‐treatment PET‐positive patients was viewed as promising. Of 74 patients, 16% were PET positive, 79% negative. The PET positivity rate was much lower than the 33% expected. Two‐year PFS was 70%; 42% [90% confidence interval (CI), 19–63%] for PET‐positives and 76% (90% CI 65–84%) for PET‐negatives. Three‐year overall survival (OS) was 69% (90% CI 43–85%) and 93% (90% CI 86–97%) for PET‐positive and ‐negative cases, respectively. The 2‐year PFS for mid‐treatment PET‐positive patients intensified to R‐ICE was 42%, with a wide confidence interval due to the low proportion of positive mid‐treatment PET scans. Treatment modification based on early PET scanning should remain confined to clinical trials.