bluuebunny/crossref_metadata_2025 huggingface dataset:
Contrasting effects of ocean acidification on the microbial food web under different trophic conditions
Authors: Sala M. M. , Aparicio F. L. , Balagué V. , Boras J. A. , Borrull E. , Cardelús C. , Cros L. , Gomes A. , López-Sanz A. , Malits A. , Martínez R. A. , Mestre M. , Movilla J. , Sarmento H. , Vázquez-Domínguez E. , Vaqué D. , Pinhassi J. , Calbet A. , Calvo E. , Gasol J. M. , Pelejero C. , Marrasé C.
Published: August 2015

We investigated the effects of an increase in dissolved CO2 on the microbial communities of the Mediterranean Sea during two mesocosm experiments in two contrasting seasons: winter, at the peak of the annual phytoplankton bloom, and summer, under low nutrient conditions. The experiments included treatments with acidification and nutrient addition, and combinations of the two. We followed the effects of ocean acidification (OA) on the abundance of the main groups of microorganisms (diatoms, dinoflagellates, nanoeukaryotes, picoeukaryotes, cyanobacteria, and heterotrophic bacteria) and on bacterial activity, leucine incorporation, and extracellular enzyme activity. Our results showed a clear stimulation effect of OA on the abundance of small phytoplankton (pico- and nanoeukaryotes), independently of the season and nutrient availability. A large number of the measured variables showed significant positive effects of acidification in summer compared with winter, when the effects were sometimes negative. Effects of OA were more conspicuous when nutrient concentrations were low. Our results therefore suggest that microbial communities in oligotrophic waters are considerably affected by OA, whereas microbes in more productive waters are less affected. The overall enhancing effect of acidification on eukaryotic pico- and nanophytoplankton, in comparison with the non-significant or even negative response to nutrient-rich conditions of larger groups and autotrophic prokaryotes, suggests a shift towards medium-sized producers in a future acidified ocean.
The first four-color photometric investigation of the W UMa type contact binary V868 Monocerotis
Authors: Xiao Zhou , Shengbang Qian , Jiajia He , Jia Zhang , Linqiao Jiang
Published: August 2015

The first four-color light-curves of V868 Monocerotis in the B, V, Rc, and Ic bands are presented and analyzed by using the 2013 version of the Wilson–Devinney method. It is discovered that V868 Mon is an A-subtype contact binary (f = 58.9%), with a large temperature difference of 916 K between the two components. Using the eight new data of the times of light minimum determined by the authors together with those collected from literature, the authors found that the general trend of the observed−calculated (O − C) curve shows an upward parabolic variation that corresponds to a long-term increase in the orbital period at a rate of dP/dt = 9.38 × 10−7 d yr−1. The continuous increase may be caused by a mass transfer from the less massive component to the more massive one.
MicroRNA-21 Mediates Isoflurane-induced Cardioprotection against Ischemia–Reperfusion Injury via Akt/Nitric Oxide Synthase/Mitochondrial Permeability Transition Pore Pathway
Authors: Qiao Shigang , Olson Jessica M. , Paterson Mark , Yan Yasheng , Zaja Ivan , Liu Yanan , Riess Matthias L. , Kersten Judy R. , Liang Mingyu , Warltier David C. , Bosnjak Zeljko J. , Ge Zhi-Dong
Published: August 2015

AbstractAbstract

Isoflurane protects mouse hearts from myocardial ischemia/reperfusion injury by a microRNA-21-dependent mechanism. The results of this article open a new area of investigation into epigenetic mechanisms of volatile anesthetic-induced cardiac protection.

Background:

The role of microRNA-21 in isoflurane-induced cardioprotection is unknown. The authors addressed this issue by using microRNA-21 knockout mice and explored the underlying mechanisms.

Methods:

C57BL/6 and microRNA-21 knockout mice were echocardiographically examined. Mouse hearts underwent 30 min of ischemia followed by 2 h of reperfusion in vivo or ex vivo in the presence or absence of 1.0 minimum alveolar concentration of isoflurane administered before ischemia. Cardiac Akt, endothelial nitric oxide synthase (eNOS), and neuronal nitric oxide synthase (nNOS) proteins were determined by Western blot analysis. Opening of the mitochondrial permeability transition pore (mPTP) in cardiomyocytes was induced by photoexcitation-generated oxidative stress and detected by rapid dissipation of tetramethylrhodamine ethyl ester fluorescence using a confocal microscope.

Results:

Genetic disruption of miR-21 gene did not alter phenotype of the left ventricle, baseline cardiac function, area at risk, and the ratios of phosphorylated-Akt/Akt, phosphorylated-eNOS/eNOS, and phosphorylated-nNOS/nNOS. Isoflurane decreased infarct size from 54 ± 10% in control to 36 ± 10% (P < 0.05, n = 8 mice per group), improved cardiac function after reperfusion, and increased the ratios of phosphorylated-Akt/AKT, phosphorylated-eNOS/eNOS, and phosphorylated-nNOS/nNOS in C57BL/6 mice subjected to ischemia–reperfusion injury. These beneficial effects of isoflurane were lost in microRNA-21 knockout mice. There were no significant differences in time of the mPTP opening induced by photoexcitation-generated oxidative stress in cardiomyocytes isolated between C57BL/6 and microRNA-21 knockout mice. Isoflurane significantly delayed mPTP opening in cardiomyocytes from C57BL/6 but not from microRNA-21 knockout mice.

Conclusions:

Isoflurane protects mouse hearts from ischemia–reperfusion injury by a microRNA-21-dependent mechanism. The Akt/NOS/mPTP pathway is involved in the microRNA-21-mediated protective effect of isoflurane.
Influence of Tracheal Obstruction on the Efficacy of Superimposed High-frequency Jet Ventilation and Single-frequency Jet Ventilation
Authors: Sütterlin Robert , LoMauro Antonella , Gandolfi Stefano , Priori Rita , Aliverti Andrea , Frykholm Peter , Larsson Anders
Published: August 2015

AbstractAbstract

In a study of pigs with obstructed airway, superimposed high-frequency jet ventilation was superior over high-frequency jet ventilation in providing adequate oxygenation by increasing lung volume and carbon dioxide removal by increasing tidal volume even without increasing the risk of barotrauma.

Supplemental Digital Content is available in the text.

Background:

Both superimposed high-frequency jet ventilation (SHFJV) and single-frequency (high-frequency) jet ventilation (HFJV) have been used with success for airway surgery, but SHFJV has been found to provide higher lung volumes and better gas exchange than HFJV in unobstructed airways. The authors systematically compared the ventilation efficacy of SHFJV and HFJV at different ventilation frequencies in a model of tracheal obstruction and describe the frequency and obstruction dependence of SHFJV efficacy.

Methods:

Ten anesthetized animals (weight 25 to 31.5 kg) were alternately ventilated with SHFJV and HFJV at a set of different fHF from 50 to 600 min−1. Obstruction was created by insertion of interchangeable stents with ID 2 to 8 mm into the trachea. Chest wall volume was measured using optoelectronic plethysmography, airway pressures were recorded, and blood gases were analyzed repeatedly.

Results:

SHFJV provided greater than 1.6 times higher end-expiratory chest wall volume than HFJV, and tidal volume (VT) was always greater than 200 ml with SHFJV. Increase of fHF from 50 to 600 min−1 during HFJV resulted in a more than 30-fold VT decrease from 112 ml (97 to 130 ml) to negligible values and resulted in severe hypoxia and hypercapnia. During SHFJV, stent ID reduction from 8 to 2 mm increased end-expiratory chest wall volume by up to 3 times from approximately 100 to 300 ml and decreased VT by up to 4.2 times from approximately 470 to 110 ml. Oxygenation and ventilation were acceptable for 4 mm ID or more, but hypercapnia occurred with the 2 mm stent.

Conclusion:

In this in vivo porcine model of variable severe tracheal stenosis, SHFJV effectively increased lung volumes and maintained gas exchange and may be advantageous in severe airway obstruction.
Association between breastfeeding and risk of endometrial cancer: a meta-analysis of epidemiological studies
Authors: Ma Xiao , Zhao Long-Gang , Sun Jiang-Wei , Yang Yang , Zheng Jia-Li , Gao Jing , Xiang Yong-Bing
Published: August 2015

Epidemiological studies have yielded inconsistent findings on the relationship between breastfeeding and the risk of endometrial cancer. Pertinent studies were identified by searching PubMed, Embase, and Web of Knowledge through February 2015 and by reviewing the reference lists of retrieved articles. Study-specific estimates were pooled using a random-effects model. Dose–response analysis was carried out for every 6-month increase in the duration of breastfeeding in relation to the risk of endometrial cancer. Three prospective and 11 case–control studies were included in this meta-analysis. The pooled estimates for ever compared with never breastfeeding and the longest duration of breastfeeding compared with the shortest were 0.91 [95% confidence interval (CI): 0.75–1.09] and 0.76 (95% CI: 0.59–0.98). The risk of endometrial cancer decreased by 7% for every 6-month increase in the duration of breastfeeding (relative risk: 0.93; 95% CI: 0.88–0.97). This study provides evidence that ever breastfeeding, particularly a longer duration of breastfeeding, is associated with a lower risk of endometrial cancer.
Nursing home director of nursing leadership style and director of nursing-sensitive survey deficiencies
Authors: McKinney Selina H. , Corazzini Kirsten , Anderson Ruth A. , Sloane Richard , Castle Nicholas G.
Published: August 2015

Background:

Nursing homes are becoming increasingly complex clinical environments because of rising resident acuity and expansion of postacute services within a context of historically poor quality performance. Discrete quality markers have been linked to director of nursing (DON) leadership behaviors. However, the impact of DON leadership across all measured areas of DON jurisdiction has not been tested using comprehensive domains of quality deficiencies.

Purpose:

The aim of this study was to examine the effects of DON leadership style including behaviors that facilitate the exchange of information between diverse people on care quality domains through the lens of complexity science.

Methodology:

Three thousand six hundred nine DONs completed leadership and intent-to-quit surveys. Quality markers that were deemed DON sensitive included all facility survey deficiencies in the domains of resident behaviors/facility practices, quality of life, nursing services, and quality of care. Logistic regression procedures estimated associations between variables.

Findings:

The odds of deficiencies for all DON sensitive survey domains were lower in facilities where DONs practiced complexity leadership including more staff input and shared decisional authority. DON quit intentions were aligned with higher odds of facility deficiencies across all domains.

Practice Implications:

Results supported the hypotheses that DONs using complexity leadership approaches by interacting more freely with staff, discussing resident issues, and sharing decision making produced better care outcomes from every DON sensitive metric assessed by Centers for Medicare and Medicaid Services. The mechanism linking poor quality with high DON quit intentions is an area for future research. Encouraging DON use of complexity leadership approaches has the potential to improve a broad swath of quality outcomes.
Ki-67 Membranous Staining: Biologically Relevant or an Artifact of Multiplexed Immunofluorescent Staining
Authors: Wang Dan , Pang Zhengyu , Clarke Gina M. , Nofech-Mozes Sharon , Liu Kela , Cheung Alison M. Y. , Filkins Robert J. , Yaffe Martin J.
Published: August 2015

In the process of developing a multiplex of 8 common breast cancer biomarkers (Her2/neu, estrogen receptor, progesterone receptor, Ki-67, aldehyde dehydrogenase-1, Na+K+-ATPase, cytokeratin 8/18, and myosin smooth muscle) on a single formalin-fixed paraffin-embedded slide using a sequential staining, imaging, and dye bleaching technology developed by General Electric Company, membranous Ki-67 staining was observed and colocalized with Her2/neu staining. Using immunohistochemistry as gold standards, we discovered that membranous Ki-67 was an artifact caused by the binding of cyanine 5-conjugated rabbit polyclonal Ki-67 antibody to a secondary cyanine 3-conjugated donkey anti-rabbit antibody which was previously applied and bound to rabbit Her2/neu antibody in our multiplexing experiment. After blocking with rabbit serum, a successful protocol for 8 biomarker multiplexing without cross-reactivity of antibodies from the same species was developed.
Insulin-like Growth Factor II Messenger RNA-binding Protein 3 in Salivary Gland Tumors
Authors: Ismerim Adna B. , Ferreira Stephany V. , Lessa Anne M.G. , Pereira Júnior Aderbal S. , Gurgel Clarissa A. , Coutinho-Camillo Claudia M. , Soares Fernando A. , Vilas-Bôas Deise S. , Vidal Manuela T.A. , Santos Jean N.d.
Published: August 2015

Insulin-like growth factor II mRNA-binding protein 3 (IMP3) is strongly expressed in malignant tumors and has been associated with their aggressive behavior. The aim of this study was to evaluate the presence of IMP3 in a series of salivary gland tumors. The sample consisted of 9 pleomorphic adenomas (PA), 14 adenoid cystic carcinomas (ACC), and 13 mucoepidermoid carcinomas (MEC) that were investigated by immunohistochemical technique. All cases of PA and MEC were positive for IMP3 particularly in the cytoplasm. PA showed 4 cases as high expression and 6 as low expression. MEC showed 10 cases as low expression and 3 as high expression. For ACC, 4 cases were high expression, whereas 6 cases were low expression. No significant difference was observed between tumors (P>0.05, Fisher’s test) when both scores of IMP3 were compared. This study showed that MEC seems to be more sensitive to IMP3 than ACC and provided an insight into this protein in salivary gland tumors. Furthermore, although IMP3 is not a specific diagnostic marker to distinguish the tumors studied, it seems to mediate cell adhesion and migration in these tumors. Further studies should be performed to better understand the IMP3 biology in salivary gland tumors.
Novel Method Probe-based Real-Time PCR to Detect 2 Single-Nucleotide Polymorphisms Close to Each Other: HFE Hemochromatosis Gene Model
Authors: Malta Frederico S. V. , Reis Zilma N. , Cabral Antônio C. V.
Published: August 2015

Hereditary hemochromatosis is known as the most common genetic disorder among individuals of European genetic background. It is possible to find 2 mutations closely placed in the HFE gene (H63D and S65C) and this proximity can cause errors when genotyped by real-time polymerase chain reaction (PCR) genotyping assay. The aim of this study was to develop a hydrolysis probe-based PCR assay for detection of the H63D and S65C mutations without interference from on each other. Herein the study involved the standardization of an improvement of the real-time PCR 5′ nuclease assay to detect the desired mutations close placed using a same probe system. The assay analytical properties performances were tested, including the primers selectivity and detection limits. Also, the interexaminer reproducibility and repeatability of assay were estimated in 30 blood samples. Others 153 results of samples were compared with reference method (PCR_RFLP) and the accordance of the results evaluated by Fleiss’ κ method. The results of variation of interexaminer reproducibility and repeatability of assay were not statistically relevant (P<0.001). The comparison between the 2 methods by Fleiss’ κ analysis showed that 5′ nuclease assay identified the H63D and S65C haplotype as well as the reference method in all 153 tested samples. Our results showed that novel method probe-based real-time PCR were capable to detect 2 adjacent polymorphisms without errors in genotyping.
Rheb/mTOR/p70s6k Cascade and TFE3 Expression in Conventional and Sclerosing PEComas of the Urinary Tract
Authors: Planelles María , Macías Laura , Peiró Gloria , Bulimbasič Stela , Hes Ondrej , Robles Antonio , Michal Michal , Davidson Whitney , López José I.
Published: August 2015

Perivascular epithelioid cell tumors (PEComas) are rarely found in the urinary tract. The clinicopathologic characteristics of 10 cases, retrospectively collected from 5 medical institutions in 3 different European countries, are presented in this study. Male/female ratio was 3:7 and the average age at diagnosis was 62.7 years. Nine cases were sporadic and 1 showed germline mutation of the TSC2 gene. Eight cases were located in the kidney, 1 in the left adrenal and 1 in the right ureter. All of the patients were alive and free of disease at the time of last contact (mean follow-up, 14.1 mo). Four cases displayed a conventional morphology and 6 showed a prominent sclerotic stroma. By immunohistochemistry, melanocytic markers were consistently expressed, especially HMB-45 (10 cases), MiTF (9 cases), and Melan-A (6 cases). Desmin was expressed in 6 cases; 2 cases were positive for CD117; a single case showed TFE3 expression. pMAPK, mTOR, and pAKT demonstrated variable immunostaining with focal positivity in 7, 4, and 2 cases, respectively. Cytokeratins were repeatedly negative in all cases. PEComas in the urinary tract, especially in the renal region, may show a relatively high frequency of the sclerosing histologic subtype. Knowledge of the distinct histology and immunohistochemical profile is vital to correctly diagnose this rare entity.
Primary Intestinal Diffuse Large B-cell Lymphoma in Taiwan Showed a Relative Higher Rate of Perforation and EBV Association
Authors: Lu Yi-Hsuan , Chang Sheng-Tsung , Yang Sheau-Fang , Weng Shih-Feng , Huang Wan-Ting , Hsieh Pin-Pen , Hsu Jeng-Dong , Tsou Mei-Hua , Chuang Shih-Sung
Published: August 2015

We retrospectively investigated 59 surgically resected primary intestinal diffuse large B-cell lymphomas (PI-DLBCL) including 31 males and 28 females with a median age of 66. Eleven (19%) tumors were perforated at presentation; 8 (14%) were multicentric. Ileum (n=24; 43%) and ileocecum (n=17; 30%) were most frequently involved. Twenty-one (36%) patients did not receive chemotherapy or radiotherapy including 6 with perforation and died in 0.2 to 7 months. The 1-, 2-, and 5-year overall survival rates were 68.4%, 56.5%, and 50.0%, respectively. Seven (12%) of 59 cases were positive for Epstein-Barr virus (EBV) by in situ hybridization. IGH, BCL2, BCL6, and MYC foci were rearranged in 22%, 3%, 17%, and 7% cases, respectively, with 14% exhibiting gain/amplification at the MYC locus. Perforation (P=0.009), high ECOG PS (≥2) (P=0.018), and no adjuvant chemotherapy (P<0.001) were poor prognostic factors but not immunophenotype including co-expression of bcl-2 and myc, EBV status, or chromosomal aberrations. Perforation and chemotherapy remained significant by multivariate analysis. PI-DLBCL in Taiwan carried a relatively higher rate of perforation, lower frequency of germinal center B-cell phenotype, and higher EBV association as compared with studies from other geographic areas. Furthermore, perforation was a poor prognostic factor.
Richard Maitland Laws CBE. 23 April 1926 — 7 October 2014
Authors: Croxall John , Boyd Ian , Parker Ian , Cook Geoffrey
Published: August 2015

Dick Laws was the leading marine mammalogist of his generation, developing in the Antarctic new techniques and approaches to population studies, notably with elephant seals and great whales. He later pioneered similar approaches with large mammals, especially elephants, in Africa before returning to the UK as Head of Life Sciences, then Director, of the British Antarctic Survey (BAS). His inspirational and unequivocal leadership saw BAS and its science develop and flourish, both in difficult times and through the major reorganization and expansion to fulfil its enhanced role and responsibilities after the Falklands conflict. He was a staunch supporter and leading advocate of the Antarctic Treaty System and was hugely instrumental in the development of the Convention for the Conservation of Antarctic Seals and of the Convention on the Conservation of Antarctic Marine Living Resources. He led the Scientific Committee on Antarctic Research (eventually as its president) into ground-breaking collaborative programmes of research into the biological oceanography of the Southern Ocean in support of the sustainable management of its living resources. On retirement from BAS he became Master of St Edmund's College, Cambridge, presiding over its transition to an institution fully integrated into the collegiate system of the university. He also served with distinction in Cambridge University affairs generally. An imposing and charismatic individual of total probity and conviction, loyalty and dedication, greatly admired by friends and colleagues, respected by opponents, he leaves an unrivalled legacy to the population ecology and management of large mammals and to the science, conservation and management of the Antarctic.
Jacques Friedel. 11 February 1921 — 27 August 2014
Authors: Sutton Adrian P. , Duparc Olivier Hardouin
Published: August 2015

Jacques Friedel was the father of condensed matter and materials physics in France. He was an educator, researcher and leader who transformed physics in France after World War II. He was one of the most respected and influential scientists in Europe, a co-founder of the Laboratory of Solid State Physics at Orsay, President of the European Physical Society, and President of the Academy of Sciences in France.
Fast and efficient QTL mapper for thousands of molecular phenotypes
Authors: Ongen Halit , Buil Alfonso , Brown Andrew Anand , Dermitzakis Emmanouil T. , Delaneau Olivier
Published: August 2015

Motivation

In order to discover quantitative trait loci (QTLs), multi-dimensional genomic data sets combining DNA-seq and ChiP-/RNA-seq require methods that rapidly correlate tens of thousands of molecular phenotypes with millions of genetic variants while appropriately controlling for multiple testing.

Results

We have developed FastQTL, a method that implements a popular cis-QTL mapping strategy in a user- and cluster-friendly tool. FastQTL also proposes an efficient permutation procedure to control for multiple testing. The outcome of permutations is modeled using beta distributions trained from a few permutations and from which adjusted p-values can be estimated at any level of significance with little computational cost. The Geuvadis & GTEx pilot data sets can be now easily analyzed an order of magnitude faster than previous approaches.

Availability

Source code, binaries and comprehensive documentation of FastQTL are freely available to download athttp://fastqtl.sourceforge.net/.

Contact

olivier.delaneau@unige.ch
Integrative approaches for large-scale transcriptome-wide association studies
Authors: Gusev Alexander , Ko Arthur , Shi Huwenbo , Bhatia Gaurav , Chung Wonil , Penninx Brenda W J H , Jansen Rick , de Geus Eco JC , Boomsma Dorret I , Wright Fred A , Sullivan Patrick F , Nikkola Elina , Alvarez Marcus , Civelek Mete , Lusis Aldonis J. , Lehtimäki Terho , Raitoharju Emma , Kähönen Mika , Seppälä Ilkka , Raitakari Olli T. , Kuusisto Johanna , Laakso Markku , Price Alkes L. , Pajukanta Päivi , Pasaniuc Bogdan
Published: August 2015

Many genetic variants influence complex traits by modulating gene expression, thus altering the abundance levels of one or multiple proteins. In this work we introduce a powerful strategy that integrates gene expression measurements with large-scale genome-wide association data to identify genes whose cis-regulated expression is associated to complex traits. We use a relatively small reference panel of individuals for which both genetic variation and gene expression have been measured to impute gene expression into large cohorts of individuals and identify expression-trait associations. We extend our methods to allow for indirect imputation of the expression-trait association from summary association statistics of large-scale GWAS1-3. We applied our approaches to expression data from blood and adipose tissue measured in ∼3,000 individuals overall. We then imputed gene expression into GWAS data from over 900,000 phenotype measurements4-6to identify 69 novel genes significantly associated to obesity-related traits (BMI, lipids, and height). Many of the novel genes were associated with relevant phenotypes in the Hybrid Mouse Diversity Panel. Overall our results showcase the power of integrating genotype, gene expression and phenotype to gain insights into the genetic basis of complex traits.
Impact of the X chromosome and sex on regulatory variation
Authors: Kukurba Kimberly R. , Parsana Princy , Smith Kevin S. , Zappala Zachary , Knowles David A. , Favé Marie-Julie , Li Xin , Zhu Xiaowei , Potash James B. , Weissman Myrna M. , Shi Jianxin , Kundaje Anshul , Levinson Douglas F. , Awadalla Philip , Mostafavi Sara , Battle Alexis , Montgomery Stephen B.
Published: August 2015

The X chromosome, with its unique mode of inheritance, contributes to differences between the sexes at a molecular level, including sex-specific gene expression and sex-specific impact of genetic variation. We have conducted an analysis of the impact of both sex and the X chromosome on patterns of gene expression identified through transcriptome sequencing of whole blood from 922 individuals. We identified that genes on the X chromosome are more likely to have sex-specific expression compared to the autosomal genes. Furthermore, we identified a depletion of regulatory variants on the X chromosome, especially among genes under high selective constraint. In contrast, we discovered an enrichment of sex-specific regulatory variants on the X chromosome. To resolve the molecular mechanisms underlying such effects, we generated and connected sex-specific chromatin accessibility to sex-specific expression and regulatory variation. As sex-specific regulatory variants can inform sex differences in genetic disease prevalence, we have integrated our data with genome-wide association study data for multiple immune traits and to identify traits with significant sex biases. Together, our study provides genome-wide insight into how the X chromosome and sex shape human gene regulation and disease.
Isolation-By-Distance-and-Time in a Stepping-Stone model
Authors: Duforet-Frebourg Nicolas , Slatkin Montgomery
Published: August 2015

With the great advances in ancient DNA extraction, population genetics data are now made of geographically separated individuals from both present and ancient times. However, population genetics theory about the joint effect of space and time has not been thoroughly studied. Based on the classical stepping–stone model, we develop the theory of Isolation by Distance and Time. We derive the correlation of allele frequencies between demes in the case where ancient samples are present in the data, and investigate the impact of edge effects with forward–in–time simulations. We also derive results about coalescent times in circular/toroidal models. As one of the most common way to investigate population structure is to apply principal component analysis, we evaluate the impact of this theory on plots of principal components. Our results demonstrate that time between samples is a non-negligible factor that requires new attention in population genetics.
The use of exome capture RNA-seq for highly degraded RNA with application to clinical cancer sequencing
Authors: Cieslik Marcin , Chugh Rashmi , Wu Yi-Mi , Wu Ming , Brennan Christine , Lonigro Robert , Su Fengyun , Wang Rui , Siddiqui Javed , Mehra Rohit , Cao Xuhong , Lucas David , Chinnaiyan Arul M. , Robinson Dan
Published: August 2015

RNA-seq by poly(A) selection is currently the most common protocol for whole transcriptome sequencing as it provides a broad, detailed, and accurate view of the RNA landscape. Unfortunately, the utility of poly(A) libraries is greatly limited when the input RNA is degraded, which is the norm for research tissues and clinical samples, especially when specimens are formalin-fixed. To facilitate the use of RNA sequencing beyond cell lines and in the clinical setting, we developed an exome-capture transcriptome protocol with greatly improved performance on degraded RNA. Capture transcriptome libraries enable measuring absolute and differential gene expression, calling genetic variants, and detecting gene fusions. Through validation against gold-standard poly(A) and Ribo-Zero libraries from intact RNA, we show that capture RNA-seq provides accurate and unbiased estimates of RNA abundance, uniform transcript coverage, and broad dynamic range. Unlike poly(A) selection and Ribo-Zero depletion, capture libraries retain these qualities regardless of RNA quality and provide excellent data from clinical specimens including formalin-fixed paraffin-embedded (FFPE) blocks. Systematic improvements across key applications of RNA-seq are shown on a cohort of prostate cancer patients and a set of clinical FFPE samples. Further, we demonstrate the utility of capture RNA-seq libraries in a patient with a highly malignant solitary fibrous tumor (SFT) enrolled in our clinical sequencing program called MI-ONCOSEQ. Capture transcriptome profiling from FFPE revealed two oncogenic fusions: the pathognomonic NAB2-STAT6 inversion and a therapeutically actionable BRAF fusion, which may drive this specific cancer's aggressive phenotype.
Social Sciences and Urban Studies: Goodbye to Paradigms?
Authors: Duhau Emilio
Published: August 2015

The development of urban studies during the 1960s and 1970s was an offshoot of mainstream social sciences which, at least in Latin America, were formulated from a critical standpoint based largely on a renovated Marxism and the rise of the structuralisms. Now that this framework's apparently solid base has come under question in the so‐called ‘paradigm crisis', what is the outlook for urban studies and, in general, for the critical social sciences? This article poses a series of ideas which hopefully will contribute to a discussion on these and other aspects of a theoretical debate which cannot be ignored by urban researchers.
The Erratic Behavior of Lesions in Burnt Bone
Authors: Collini Federica , Amadasi Alberto , Mazzucchi Alessandra , Porta Davide , Regazzola Valeria Luisa , Garofalo Paola , Di Blasio Annalisa , Cattaneo Cristina
Published: August 2015

This study analyses depressed fractures (by blunt force trauma) and circular full‐thickness injuries (drill injuries and gunshot wounds) in charred bones. Fifty bovine ribs (total 104 lesions) were divided into three groups. The first group consisted in 20 depressed hammer‐produced fractures; in the second one, 60 round drill‐holes were produced (30 circular, 30 semicircular); in the third group, 12 fleshed and 12 skeletonized ribs were hit by 9‐mm bullets. Each specimen was carbonized in an electric oven up to 800°C. Morphological and metric analyses were performed before and after: morphological features were preserved, but depressed fractures showed an increase in their dimensions (p‐value < 0.05); the drilled holes shrunk (p‐value < 0.01); the charring cycle increased the number of fractures in samples with gunshot wounds differently in fleshed and defleshed ribs. This study showed the complex behavior of charred bone, for what concerns the interpretation of trauma and how caution should be applied.
The missing vitamin alphabet
Authors: Williams Peter
Published: August 2015

Aim

The aims of this paper were to catalogue a complete list of all the alphabetical names for vitamins that have appeared in the scientific literature, provide the citations of their first use and seek explanations for any apparent gaps in the naming system.

Methods

The names of known vitamins and pseudo‐vitamins were identified from standard nutrition textbooks, historical monographs and several review articles. If the first citation for the alphabetical vitamin name was not found in these sources, additional searches were conducted in the Scopus and Medline databases, in Google and Google Scholar, using the names of vitamins as search terms.

Results

Sixty‐seven different alphabet‐based vitamin names were tabulated, including where possible the scientific and alternative names, a description of the source substance, physiological roles and the first citation of the alphabetical name. The results show that all the letters of the alphabet have been used to describe putative vitamin compounds. The simple alphabetical naming system proposed by Drummond in 1920 lasted for less than a decade. A number of other systems have been used based on the name of the discoverer, the source of the material or its physiological function.

Conclusions

Using simplified alphabetical names may assist in nutrition communication and education of the general public, but dietitians need to be careful to maintain a clear understanding of the proper biochemical distinctions and nomenclatures of the known vitamins, especially when writing for academic publication.
Characterization and Comparison of the Pungent Components in Commercial Zanthoxylum bungeanum Oil and Zanthoxylum schinifolium Oil
Authors: Zhao Zhi‐Feng , Zhu Rui‐Xue , Zhong Kai , He Qiang , Luo Ai‐Min , Gao Hong
Published: August 2015

In the present study, the characterization and comparison of the pungent components in commercial Z. bungeanum oils and Z. schinifolium oils were investigated. By high‐performance liquid chromatography (HPLC)‐mass spectrometry (MS/MS) analysis, the major alkylamides in Z. bungeanum and Z. schinifolium oils were identified as hydroxy‐ε‐sanshool, hydroxy‐α‐sanshool, hydroxy‐β‐sanshool, hydroxy‐γ‐sanshool, hydroxy‐γ‐isosanshool, bungeanool, isobungeanool, and tetrahydrobungeanool, respectively. Hydroxy‐α‐sanshool was found to be the most abundant alkylamide in all oils. The levels of hydroxy‐ε‐sanshool and hydroxy‐β‐sanshool in Z. bungeanum oils were comparable to that in Z. schinifolium oils, whereas Z. bungeanum oils contained significantly (P less than 0.05) higher levels of hydroxy‐γ‐isosanshool, bungeanool, isobungeanool, and tetrahydrobungeanool, compared with Z. schinifolium oils. Furthermore, principal component analysis (PCA) indicated that Z. bungeanum oil and Z. schinifolium oil were clearly classified by HPLC fingerprinting profiles and concentrations of alkylamides. In addition, the results of PCA suggested that alkylamides, such as hydroxy‐γ‐sanshool and bungeanool, could be potential markers to distinguish Z. bungeanum oil and Z. schinifolium oil. The results from this study could be used to discriminate the different flavor characterization and control the quality of commercial Z. bungeanum oil and Z. schinifolium oil.
Challenges to Providing Fetal Anomaly Testing in a Cross‐Cultural Environment: Experiences of Practitioners Caring for Aboriginal Women
Authors: Rumbold Alice R. , Wild Kayli J. , Maypilama Elaine Lawurrpa , Kildea Sue V. , Barclay Lesley , Wallace Euan M. , Boyle Jacqueline A.
Published: August 2015

Background

Across Australia there are substantial disparities in uptake of antenatal testing for fetal anomalies, with very low uptake observed among Aboriginal women. The reasons behind these disparities are unclear, although poorer access to testing has been reported in some communities. We interviewed health care practitioners to explore the perceived barriers to providing fetal anomaly screening to Aboriginal women.

Methods

In 2009 and 2010, in‐depth interviews were undertaken with 59 practitioners in five urban and remote sites across the Northern Territory (NT) of Australia. Data were analyzed thematically. Maximum variation sampling, independent review of findings by multiple analysts, and participant feedback were undertaken to strengthen the validity of findings.

Results

Participants included midwives (47%), Aboriginal health practitioners (AHP) (32%), general practitioners (12%), and obstetricians (9%); almost all (95%) were female. Participants consistently reported difficulties counseling women. Explaining the concept of “risk” (of abnormalities and the screening test result) was identified as particularly challenging, because of a perceived lack of an equivalent concept in Aboriginal languages. While AHPs could assist with overcoming language barriers, they are underutilized. Participants also identified impediments to organizing testing including difficulties establishing gestational age, late presentation for care, and a lack of standardized information and training.

Discussion

The availability of fetal anomaly testing is challenged by communication difficulties, including a focus on culturally specific biomedical concepts, and organizational barriers to arranging testing. Developing educational activities that address the technical aspects of screening and communication skills will assist in improving access. These activities must include AHPs.
Provenance of Palaeo‐Rhine sediments from zircon thermochronology, geochemistry, U/Pb dating and heavy mineral assemblages
Authors: Tatzel Michael , Dunkl István , von Eynatten Hilmar
Published: August 2015

Sediments deposited in the Late Cenozoic basins of the Central European Rift System, including the Upper Rhine Graben (URG) and the Lower Rhine Embayment (LRE), document the drastic extension of the Rhine's catchment towards the Central Alps in the Late Pliocene by distinct heavy mineral assemblages. This outstanding change in principal sediment sources should be accompanied by a change towards distinctly younger (i.e. Tertiary) detrital mineral cooling ages. Therefore, it provides a particularly well‐suited framework to explore the thermochronological provenance record in relation to heavy mineral assemblages. In this multi‐proxy approach we (i) exploit and elaborate detrital zircon (U–Th)/He thermochronology (ZHe) for sediment provenance surveys, (ii) document shortcomings if only a single geochronological method is employed, and (iii) obtain tighter constraints on the sources of Paleo‐Rhine sediments. Our results are based on Pliocene and Pleistocene sediment samples from the northern URG (drill core Ludwigshafen P36) and the LRE (lignite mine Hambach). In a Late Pliocene URG sample, Variscan and Permo‐Triassic cooling ages dominate the age spectra of the ZHe and Zircon fission track (ZFT) thermochronometers. The youngest ages are Late Cretaceous and these zircons show rare earth element signatures that suggest derivation from hydrothermally affected basement rocks of the URG margins. In contrast, a Lower Pleistocene URG sample contains significant Tertiary age components that unequivocally indicate Alpine sources. This cardinal difference coincides well with a significant change in the heavy mineral assemblage. The extension of the catchment of the Rhine towards the Central Alps is considered to occur no earlier than the latest Pliocene (i.e. after ~3.0 Ma). Despite strongly contrasting heavy mineral compositions, the Pliocene and Pleistocene samples from the LRE show largely similar ZHe and ZFT age distributions dominated by Permo‐Triassic and Variscan ages. Admixture of zircon‐dominated, but overall heavy mineral‐poor sediment derived from local drainages of the Rhenish Massif likely explains this apparent contradiction in sediment provenance proxies. Tertiary cooling ages occur in both Pliocene and Pleistocene LRE samples. Zircon Th/U ratios and U/Pb ages reveal that the young age component in Late Pliocene sediments from the LRE is not derived from the Alps but from Oligocene trachytic members of the Central European volcanic centres of the Vogelsberg, Westerwald, and/or Siebengebirge. The integration of ZHe and ZFT techniques with zircon geochemistry and U/Pb geochronology adds the respective advantages of each method and allows for a very detailed picture of detrital zircon provenance.
Multi‐scale constraints of sediment source to sink systems in frontier basins: a forward stratigraphic modelling case study of the Levant region
Authors: Hawie Nicolas , Deschamps Remy , Granjeon Didier , Nader Fadi H. , Gorini Christian , Müller Carla , Montadert Lucien , Baudin François
Published: August 2015

Recent scientific work has highlighted the presence of an up to 12 km thick Cenozoic siliclastic and carbonate infill in the Levant Basin. Since the Late Eocene, several regional geodynamic events affecting Afro‐Arabia and Eurasia (collision and strike slip deformation) induced marginal uplifts. The initiation of local and long‐lived regional drainage systems in the Oligo‐Miocene period (e.g., Lebanon, Arabia and Nile) provoked a change in the depositional pattern along the Levant region from carbonate‐dominated to mixed clastic‐rich systems. Herein, we explore the importance of multi‐scale constraints (i.e., seismic, well and field data) in the quantification of subsidence history, sediment transport and deposition of a Middle to Upper Miocene “multi‐source” to sink system along the northern Levant frontier region. Through a comprehensive 4D forward stratigraphic modelling workflow, we suggest that the contribution to basin infill is split between proximal and more distal clastic sources as well asin situcarbonate and hemipelagic deposition. The results show that single‐source scenarios could not reasonably satisfy the basin‐scale constraints. The worldwide application of such new multi‐disciplinary workflows in frontier regions highlights the additional data constraints that are needed to de‐risk highly uncertain geological models in the hydrocarbon exploration phase.
Challenges and Prospects for Scaling‐up Ecological Restoration to Meet International Commitments: Colombia as a Case Study
Authors: Murcia Carolina , Guariguata Manuel R. , Andrade Ángela , Andrade Germán Ignacio , Aronson James , Escobar Elsa Matilde , Etter Andrés , Moreno Flavio H. , Ramírez Wilson , Montes Elena
Published: August 2015

The field of ecological restoration (ER) is now challenged by the need to achieve recovery at large spatial scales. Such scaling up requires technological expertise, inclusiveness and clarity of goals, and correct governance schemes and monitoring protocols, which are often absent from ER projects in most countries. We analyze the case of Colombia by assessing the planning, governance, and monitoring practices of 119 ER projects, and discuss them in the context of scaling up efforts to meet international commitments. In a top‐down approach, Colombia´s government is the biggest ER driver: setting up the necessary policy framework to promote ER, and initiating 64% and fully financing 78% of the projects in the country. However, projects lack depth in participatory governance and adequate planning and monitoring, limiting their potential for sustainability and knowledge sharing, both of which are necessary for scaling up. We propose three areas for improvement in order to scale‐up and meet international ER targets in Colombia, as well as in other Latin American countries, such as Mexico, Chile, and Argentina, which are also in the process of consolidating a large‐scale ER vision. The benefits of some of those improvements have already been demonstrated in Brazil.
A prospective analysis of factors associated with decreased physical activity in patients with cirrhosis undergoing transplant evaluation
Authors: Dela Cruz Anna Christina , Vilchez Valery , Kim Sooyeon , Barnes Benjamin , Ravinuthala Abhishek , Zanni Anthony , Galuppo Roberto , Sourianarayanane Achuthan , Patel Trushar , Maynard Erin , Shah Malay B. , Daily Michael F. , Uhl Timothy , Esser Karyn , Gedaly Roberto
Published: August 2015

Background

Physical activity (PA) has been associated with improved recovery time after transplantation. Handgrip strength has been related to post‐transplant outcomes.

Aim

To evaluate predictors of PA and grip strength in patients with cirrhosis undergoing liver transplant evaluation.

Methods

Single‐center, prospective analysis.

Results

One hundred patients were evaluated (54% male, mean age 53 ± 9). Common etiologies of liver disease were non‐alcoholic steatohepatitis (27%), hepatitis C (22%) and alcoholic liver disease (21%). Mean model of end‐stage liver disease (MELD) score was 13.5. Forty‐one percent had a history of smoking. Ninety‐three patients completed the International Physical Activity Questionnaire (IPAQ). The median total PA score was 33 metabolic equivalent (MET)‐min/wk. The mean total grip strength was 62.1 ± 22 lb. Total grip strength was found to be an independent predictor of low–moderate PA (OR 4.7, 95% CI 1.4–16.2, p = 0.038), and smoking was the only significant factor associated with reduced grip strength (OR 3.4, 95% CI 1.4–8, p = 0.005).

Conclusions

Patients with end‐stage liver disease undergoing liver transplant evaluation have reduced total PA by IPAQ. Total grip strength was found to be a significant predictor of low–moderate PA in patients with cirrhosis. Smoking is a risk factor for reduced grip strength, an important indicator of muscle wasting in cirrhotics.
Primitive follicular induction in molluscum contagiosum
Authors: Molina‐Ruiz Ana María , Bernárdez Claudia , Requena Luis , Schärer Leo
Published: August 2015

Background

Molluscum contagiosum (MC) is the commonest human poxvirus infection. Follicular induction has rarely been observed in the epidermis surrounding lesions of MC. A virus‐induced localized proliferation of germinative/stem cells of the folliculosebaceous‐apocrine unit has been suggested as the underlying cause, however few reports of this peculiar phenomenon exist in the literature and the mechanisms involved in this proliferation require further study.

Methods

We prospectively collected MC cases showing multifocal areas of primitive follicular induction involving the adjacent undersurface epidermis. Immunohistochemical expression of BerEP4, PHLDA1 and cytokeratin 20 (CK20) was evaluated in the basaloid germs surrounding the lesions. For PHLDA1, we used epidermal melanocytes as a positive internal control. For BerEP4, we employed a basal cell carcinoma (BCC) and for CK20, colon as positive external controls. An incubation without the primary antibody functioned as an external negative control.

Results

All the cases studied showed an intense positive staining of the basaloid buds with BerEP4 and weaker stain for PHLDA1. CK20 showed the presence of scattered Merkel cells within the induced epidermal basaloid proliferations favoring their reactive origin.

Discussion

The pathogenetic mechanisms behind the development of these microscopic features and the link between follicular induction and poxvirus infection are explored. Awareness of this unusual phenomenon by dermatopathologists will be helpful in avoiding a misdiagnosis of a superficial BCC in such cases.

Conclusions

BerEP4 and PHLDA1 were consistently expressed in the areas of primitive follicular induction surrounding lesions of MC. CK 20 stained the Merkel cells present in the basaloid buds. All these findings support the reactive origin of this phenomenon, which we believe is most probably viral‐induced.
Saline Contrast Echocardiography in the Era of Multimodality Imaging—Importance of “Bubbling It Right”
Authors: Gupta Saurabh K. , Shetkar Sudhir S. , Ramakrishnan Sivasubramanian , Kothari Shyam S.
Published: August 2015

Saline contrast echocardiography is an established imaging modality. Logical interpretation of a carefully performed study is vital to realize its diagnostic potential. In this review, we discuss utility of saline contrast echocardiography in evaluation of various pathologies within and outside the heart other than a patent foramen ovale.