bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association Between Extracellular Matrix Expansion Quantified by Cardiovascular Magnetic Resonance and Short-Term Mortality
Authors: Wong Timothy C. , Piehler Kayla , Meier Christopher G. , Testa Stephen M. , Klock Amanda M. , Aneizi Ali A. , Shakesprere Jonathan , Kellman Peter , Shroff Sanjeev G. , Schwartzman David S. , Mulukutla Suresh R. , Simon Marc A. , Schelbert Erik B. 
Published: August 2012

Background—
Extracellular matrix expansion may be a fundamental feature of adverse myocardial remodeling, it appears to be treatable, and its measurement may improve risk stratification. Yet, the relationship between mortality and extracellular matrix is not clear because of difficulties with its measurement. To assess its relationship with outcomes, we used novel, validated cardiovascular magnetic resonance techniques to quantify the full spectrum of extracellular matrix expansion not readily detectable by conventional cardiovascular magnetic resonance.

Methods and Results—
We recruited 793 consecutive patients at the time of cardiovascular magnetic resonance without amyloidosis or hypertrophic cardiomyopathy as well as 9 healthy volunteers (ages 20–50 years). We measured the extracellular volume fraction (ECV) to quantify the extracellular matrix expansion in myocardium without myocardial infarction. ECV uses gadolinium contrast as an extracellular space marker based on T1 measures of blood and myocardium pre— and post–gadolinium contrast and hematocrit measurement. In volunteers, ECV ranged from 21.7% to 26.2%, but in patients it ranged from 21.0% to 45.8%, indicating considerable burden. There were 39 deaths over a median follow-up of 0.8 years (interquartile range 0.5–1.2 years), and 43 individuals who experienced the composite end point of death/cardiac transplant/left ventricular assist device implantation. In Cox regression models, ECV related to all-cause mortality and the composite end point (hazard ratio, 1.55; 95% confidence interval, 1.27–1.88 and hazard ratio, 1.48; 95% confidence interval, 1.23–1.78, respectively, for every 3% increase in ECV), adjusting for age, left ventricular ejection fraction, and myocardial infarction size.

Conclusions—
ECV measures of extracellular matrix expansion may predict mortality as well as other composite end points (death/cardiac transplant/left ventricular assist device implantation).
The impact of spirituality on eating disorder symptomatology in ethnically diverse Canadian women
Authors: Boisvert Jennifer A , Harrell W Andrew 
Published: August 2012

Background: There is currently a gap in our knowledge of how eating disorder symptomatology is impacted by spirituality and religiosity. To date, studies examining the role of ethnicity in women’s self-reported levels of eating disorder symptomatology have neglected the roles of spirituality and religiosity. Aims: This study addresses this gap in the literature by investigating ethnicity, spirituality, religiosity, body shame, body mass index (BMI) and age in relation to eating disorder symptomatology in women. Methods: A representative non-clinical sample of ethnically diverse Canadian women (N = 591) was surveyed. Results: Younger women, particularly those with higher body shame, BMI and lower spirituality, reported more eating disorder symptomatology. Hispanic and Asian women had higher body shame and lower BMI compared to white women. Spirituality was more strongly related to eating disorder symptomatology than religiosity. Conclusions: This is the first study identifying interactive relationships between ethnicity, spirituality, body shame, BMI and age on eating disorder symptomatology in women. Particularly significant is that higher spirituality was related to a lower level of eating disorder symptomatology. These findings have important implications for treatment and women’s physical and psychological health and wellness.
Contesting Urban and Rural Space in Desakota Regions of Taiwan—A Case Study of I-Lan County
Authors: SHIH C.S. Stone , Chi Chang-Liang 
Published: July 2012

The article focuses on the analysis of the desakotasi (village-city process) in Taiwan’s local context of I-Lan County. Particular attention is paid to the manner in which political conflicts have shaped the urbanization process in I-Lan County over the last 20 years. Those conflict points include primarily the construction of Industrial Zones (IZs) and Taipei-I-Lan super highway promoted by the ruling Kuomintang Party (KMT), which were designed to increase Taiwan’s international competitiveness. But such measures were opposed by the Democratic Progressive Party (DPP) with an ideology of local first. Local magistrates issued a series of environmental protection policies against the developmental strategies of the central state, the ruling Kuomintang. In the following years, the continuing rotation of political parties created conflict that brought demonstration at the local level. These developments were affected by international and national developments that led to a restructuring of economic space in Taiwan particularly processes of urban expansion that led to a steady decline of agriculture. The significant push-and-pull effect of contesting spaces in political conflicts between KMT- and DPP-controlled periods could be evidenced by: (1) the decline or prosperity of the Industrial Zones and Suao township; (2) the enlargement of urban cores like I-Lan City and Luodong Township; and (3) the formation of a mixed space of urban–rural corridor. I-Lan County, which so long remained in the shadow of the Taipei metropolis, is now increasingly integrated into the Taipei metropolitan region. And its future relies upon the resolution of the political conflicts surrounding environmental protection and the spatial reconstruction of the region so that its desakota heritage may be preserved.
Looking at the Russian health care system: through the eyes of patients with diabetes and their physicians
Authors: Kühlbrandt Charlotte , Basu Sanjay , Mckee Martin , Stuckler David 
Published: August 2012

Aims People with diabetes are well placed to evaluate and to assess the performance of health systems. We take the perspective of people living with diabetes and those caring for them to gain insights into how the contemporary Russian health system works for them. Methods We conducted 15 semi-structured interviews with patients with diabetes and physicians in rural and urban settings, in public and private sectors. Interviewees were identified using snowball sampling. Results Patients worried about high and rising costs of care, while physicians noted concerns about lack of time to treat patients adequately. Although all specifically diabetes-related services are free of charge, patients requiring urgent surgery often face high user fees, either to bypass waiting lists in state facilities or to be treated immediately in a private institution. These ‘hidden’, out-of-pocket payments impact adversely on equity and act as a barrier to timely care. Conclusions Although reform of health services in Russia has led to improvements in quality of care for diabetes, many gaps remain, particularly for management of complications. This paper provides further evidence of how people with diabetes can shed light on the reality, as opposed to the rhetoric of health system reform, especially in middle-income countries.
Myeloid skewing in murine autoimmune arthritis occurs in hematopoietic stem and primitive progenitor cells
Authors: Oduro Kwadwo A. , Liu Fang , Tan Qing , Kim Chan-Kyu , Lubman Olga , Fremont Daved , Mills Jason C. , Choi Kyunghee 
Published: August 2012

Abstract
Skewing toward myeloid cell production is often observed in chronic inflammation and autoimmune diseases. Herein, we determined whether persistent myeloid activation and proinflammatory output occurring in pathologic conditions is at the level of hematopoietic stem and primitive progenitor cells (HSPPCs). By using a mouse arthritis model, we found that even though HSPPCs in arthritis still retained the capacity to differentiate into different lineages, they acquired enhanced in vitro and in vivo propensity in a disease-dependent manner to generate myeloid cells, the key perpetrators of tissue damage in arthritis. This myeloid skewing was cell intrinsic, as arthritic HSPPCs up-regulate myeloid-specific transcripts including S100a8. Exogenous S100a8 promoted myeloid cell output from wild-type HSPPCs, suggesting mechanistic involvement of this gene in the myeloid priming that occurs in arthritic HSPPCs. Therefore, our results indicate that in arthritic mice, HSPPCs adopt a pathologic state that favors disease persistence.
Genetic parameters of infectious bovine keratoconjunctivitis and its relationship with weight and parasite infestations in Australian tropical Bos taurus cattle
Authors: Ali Abdirahman A , O’Neill Christopher J , Thomson Peter C , Kadarmideen Haja N 
Published: July 2012

Abstract

Background
Infectious bovine keratoconjunctivitis (IBK) or ‘pinkeye’ is an economically important ocular disease that significantly impacts animal performance. Genetic parameters for IBK infection and its genetic and phenotypic correlations with cattle tick counts, number of helminth (unspecified species) eggs per gram of faeces and growth traits in Australian tropically adapted Bos taurus cattle were estimated.

Methods
Animals were clinically examined for the presence of IBK infection before and after weaning when the calves were 3 to 6 months and 15 to 18 months old, respectively and were also recorded for tick counts, helminth eggs counts as an indicator of intestinal parasites and live weights at several ages including 18 months.

Results
Negative genetic correlations were estimated between IBK incidence and weight traits for animals in pre-weaning and post-weaning datasets. Genetic correlations among weight measurements were positive, with moderate to high values. Genetic correlations of IBK incidence with tick counts were positive for the pre-weaning and negative for the post-weaning datasets but negative with helminth eggs counts for the pre-weaning dataset and slightly positive for the post-weaning dataset. Genetic correlations between tick and helminth eggs counts were moderate and positive for both datasets. Phenotypic correlations of IBK incidence with helminth eggs per gram of faeces were moderate and positive for both datasets, but were close to zero for both datasets with tick counts.

Conclusions
Our results suggest that genetic selection against IBK incidence in tropical cattle is feasible and that calves genetically prone to acquire IBK infection could also be genetically prone to have a slower growth. The positive genetic correlations among weight traits and between tick and helminth eggs counts suggest that they are controlled by common genes (with pleiotropic effects). Genetic correlations between IBK incidence and tick and helminth egg counts were moderate and opposite between pre-weaning and post-weaning datasets, suggesting that the environmental and (or) maternal effects differ between these two growth phases. This preliminary study provides estimated genetic parameters for IBK incidence, which could be used to design selection and breeding programs for tropical adaptation in beef cattle.
A Newfoundland cohort of familial and sporadic idiopathic pulmonary fibrosis patients: clinical and genetic features
Authors: Fernandez Bridget A , Fox George , Bhatia Rick , Sala Eric , Noble Barbara , Denic Nash , Fernandez Dzintra , Duguid Nigel , Dohey Amanda , Kamel Fady , Edwards Laura , Mahoney Krista , Stuckless Susan , Parfrey Patrick S , Woods Michael O 
Published: August 2012

Abstract

Background
Idiopathic pulmonary fibrosis (IPF) is an adult-onset Idiopathic Interstitial Pneumonia (IIP) usually diagnosed between age 50 to 70 years. Individuals with Familial Pulmonary Fibrosis (FPF) have at least one affected first or second-degree relative and account for 0.5-20% of cases.

Methods
We ascertained and collected DNA samples from a large population-based cohort of IPF patients from Newfoundland, Canada. For each proband, a family history was documented and medical records were reviewed. Each proband was classified as familial (28 patients) or sporadic (50 patients) and all 78 probands were screened for variants in four highly penetrant, adult-onset PF genes (SFTPC, SFTPA2, TERT,
TERC).

Results
Seventy-eight IPF probands were enrolled of whom 28 (35.9%) had a positive family history. These 28 familial patients led to the recruitment of an additional 49 affected relatives (total of 77 FPF patients). By age 60 years, 42% of the familial cohort had been diagnosed with PF compared with only 16% of the sporadic patient collection (χ2 = 8.77, p = 0.003). Mean age of diagnosis in the familial group was significantly younger than the sporadic group (61.4 years vs. 66.6 yrs, p = 0.012) with a wider age range of diagnosis (19–92 years compared with 47–82 years). Thirty-three of 77 (42.8%) FPF patients had a tissue diagnosis and all but five had usual interstitial pneumonia histology. Compared with other published case series, the familial IIP histologies were more homogeneous. Three of 28 familial probands (10.7%) and none of the 50 sporadic probands had pathogenic variants in the four genes tested. All three familial probands had mutations in TERT. Other phenotypes associated with telomerase deficiency were present in these families including cirrhosis, bone marrow hypoplasia and premature graying. Telomere length assays were performed on mutation carriers from two families and confirmed telomere-related deficiency.

Conclusion
The proportion of familial cases in our cohort is higher than any previously reported estimate and we suggest that this is due to the fact that Newfoundland cohort is ethnically homogeneous and drawn from a founder population. In our patient collection, diagnosis with IPF prior to age 45 years predicted familial disease. In two of the three TERT mutation families, the pedigree appearance is consistent with genetic anticipation. In the other 25 FPF families negative for mutations in known PF genes, we did not identify other telomerase associated medical problems (bone marrow dysfunction, cirrhosis) and we hypothesize that there are novel PF genes segregating in our population.
Estimation of sequencing error rates in short reads
Authors: Victoria Wang Xin , Blades Natalie , Ding Jie , Sultana Razvan , Parmigiani Giovanni 
Published: July 2012

Abstract

Background
Short-read data from next-generation sequencing technologies are now being generated across a range of research projects. The fidelity of this data can be affected by several factors and it is important to have simple and reliable approaches for monitoring it at the level of individual experiments.

Results
We developed a fast, scalable and accurate approach to estimating error rates in short reads, which has the added advantage of not requiring a reference genome. We build on the fundamental observation that there is a linear relationship between the copy number for a given read and the number of erroneous reads that differ from the read of interest by one or two bases. The slope of this relationship can be transformed to give an estimate of the error rate, both by read and by position. We present simulation studies as well as analyses of real data sets illustrating the precision and accuracy of this method, and we show that it is more accurate than alternatives that count the difference between the sample of interest and a reference genome. We show how this methodology led to the detection of mutations in the genome of the PhiX strain used for calibration of Illumina data. The proposed method is implemented in an R package, which can be downloaded from http://bcb.dfci.harvard.edu/∼vwang/shadowRegression.html.

Conclusions
The proposed method can be used to monitor the quality of sequencing pipelines at the level of individual experiments without the use of reference genomes. Furthermore, having an estimate of the error rates gives one the opportunity to improve analyses and inferences in many applications of next-generation sequencing data.
The ribonuclease Dis3 is an essential regulator of the developmental transcriptome
Authors: Hou Dezhi , Ruiz Miriam , Andrulis Erik D 
Published: August 2012

Abstract

Background
Dis3 is ribonuclease that acts directly in the processing, turnover, and surveillance of a large number of distinct RNA species. Evolutionarily conserved from eubacteria to eukaryotes and a crucial component of the RNA processing exosome, Dis3 has been shown to be essential in yeast and fly S2 cells. However, it is not known whether Dis3 has essential functions in a metazoan. This study inquires whether Dis3 is required for Drosophila development and viability and how Dis3 regulates the transcriptome in the developing fly.

Results
Using transgenic flies, we show that Dis3 knock down (Dis3KD) retards growth, induces melanotic tumor formation, and ultimately results in 2nd instar larval lethality. In order to determine whether Dis3KD fly phenotypes were a consequence of disrupting developmentally regulated RNA turnover, we performed RNA deep sequencing analysis on total RNA isolated from developmentally staged animals. Bioinformatic analysis of transcripts from Dis3KD flies reveals substantial transcriptomic changes, most notably down-regulation in early expressed RNAs. Finally, gene ontology analysis of this early stage shows that Dis3 regulates transcripts related to extracellular structure and remodelling, neurogenesis, and nucleotide metabolism.

Conclusions
We conclude that Dis3 is essential for early Drosophila melanogaster development and has specific and important stage-specific roles in regulating RNA metabolism. In showing for the first time that Dis3 is required for the development of a multicellular organism, our work provides mechanistic insight into how Dis3—either independent of or associated with the RNA processing exosome—participates in cell type-specific RNA turnover in metazoan development.
Transcriptomic and physiological responses to fishmeal substitution with plant proteins in formulated feed in farmed Atlantic salmon (Salmo salar)
Authors: Tacchi Luca , Secombes Christopher J , Bickerdike Ralph , Adler Michael A , Venegas Claudia , Takle Harald , Martin Samuel AM 
Published: August 2012

Abstract

Background
Aquaculture of piscivorous fish is in continual expansion resulting in a global requirement to reduce the dependence on wild caught fish for generation of fishmeal and fish oil. Plant proteins represent a suitable protein alternative to fish meal and are increasingly being used in fish feed. In this study, we examined the transcriptional response of Atlantic salmon (Salmo salar) to a high marine protein (MP) or low fishmeal, higher plant protein replacement diet (PP), formulated to the same nutritional specification within previously determined acceptable maximum levels of individual plant feed materials.

Results
After 77 days of feeding the fish in both groups doubled in weight, however neither growth performance, feed efficiency, condition factor nor organ indices were significantly different. Assessment of histopathological changes in the heart, intestine or liver did not reveal any negative effects of the PP diet. Transcriptomic analysis was performed in mid intestine, liver and skeletal muscle, using an Atlantic salmon oligonucleotide microarray (Salar_2, Agilent 4x44K). The dietary comparison revealed large alteration in gene expression in all the tissues studied between fish on the two diets. Gene ontology analysis showed, in the mid intestine of fish fed PP, higher expression of genes involved in enteritis, protein and energy metabolism, mitochondrial activity/kinases and transport, and a lower expression of genes involved in cell proliferation and apoptosis compared to fish fed MP. The liver of fish fed PP showed a lower expression of immune response genes but a higher expression of cell proliferation and apoptosis processes that may lead to cell reorganization in this tissue. The skeletal muscle of fish fed PP vs MP was characterized by a suppression of processes including immune response, energy and protein metabolism, cell proliferation and apoptosis which may reflect a more energy efficient tissue.

Conclusions
The PP diet resulted in significant effects on transcription in all the 3 tissues studied. Despite of these alterations, we demonstrated that high level of plant derived proteins in a salmon diet allowed fish to grow with equal efficiency as those on a high marine protein diet, and with no difference in biometric quality parameters.
Spontaneous splenic rupture in patient with metastatic melanoma treated with vemurafenib
Authors: Castellani Elisa , Covarelli Piero , Boselli Carlo , Cirocchi Roberto , Rulli Antonio , Barberini Francesco , Caracappa Daniela , Cini Carla , Desiderio Jacopo , Burini Gloria , Noya Giuseppe 
Published: July 2012

Abstract

Background
BRAF inhibitors such as vemurafenib are a new family of biological drugs, recently available to treat metastatic malignant melanoma.

Methods
We present the case of a 38-year-old man affected by metastatic melanoma who had been under treatment with vemurafenib for a few days. The patient suffered from sudden onset of abdominal pain due to intra-abdominal hemorrhage with profuse hemoperitoneum. An emergency abdominal sonography confirmed the clinical suspicion of a splenic rupture.

Results
The intraoperative finding was hemoperitoneum due to splenic two-step rupture and splenectomy was therefore performed. Histopathology confirmed splenic hematoma and capsule laceration, in the absence of metastasis.

Conclusions
This report describes the occurrence of a previously unreported adverse event in a patient with stage IV melanoma receiving vemurafenib.
A zoological catalogue of hunted reptiles in the semiarid region of Brazil
Authors: Nóbrega Alves Rômulo Romeu , Pereira Filho Gentil Alves , Silva Vieira Kleber , Silva Souto Wedson Medeiros , Mendonça Lívia Emanuelle Tavares , Montenegro Paulo Fernando Guedes Pereira , Almeida Waltécio de Oliveira , Silva Vieira Washington Luiz 
Published: July 2012

AbstractThe variety of interactions between human cultures and herpetofauna is the subject matter of Ethnoherpetology, a subdivision of Ethnozoology. In the semi-arid region of Brazil, many reptiles interact with human communities because of their utility or because of the risks they represent. These interactions have obvious implications for the conservation of reptiles from this region.In this context, ethnoherpetology studies are crucial because they serve as subsidies for guiding strategies for the handling and conservation of reptiles. This paper presents ethnozoological and taxonomic informations of hunted reptiles in the semiarid region of Brazil and analyse the implications on conservation that are related to the interactions between people and reptiles in this region. Taxonomic keys to identifying recorded reptiles are provided. Records of humans interacting with 38 reptile species that belong to 31 genuses and 16 families have been found. The groups with the largest numbers of recorded species were snakes (18 species), and this group was followed in number by lizards (13), chelonians (4), and crocodilians (3). The reptiles that were recorded may be used for the following purposes: medicinal purposes (24 species), food (13 species), ornamental or decorative purposes (11 species), in magical/religious practices (10 species), and as pets (10 species). Some species (n = 16) may have multiple uses. Furthermore, more than half of the species (n = 19) are commonly killed because they are considered potentially dangerous. Strategies for conserving the reptiles of the Brazilian semi-arid region must reconcile and integrate human and conservation needs.