bluuebunny/crossref_metadata_2025_split huggingface dataset:
cSSMD: assessing collective activity for addressing off-target effects in genome-scale RNA interference screens
Authors: Zhang Xiaohua Douglas , Santini Francesca , Lacson Raul , Marine Shane D. , Wu Qian , Benetti Luca , Yang Ruojing , McCampbell Alex , Berger Joel P. , Toolan Dawn M. , Stec Erica M. , Holder Daniel J. , Soper Keith A. , Heyse Joseph F. , Ferrer Marc 
Published: August 2011

Abstract
Motivation: Off-target activity commonly exists in RNA interference (RNAi) screens and often generates false positives. Existing analytic methods for addressing the off-target effects are demonstrably inadequate in RNAi confirmatory screens.
Results: Here, we present an analytic method assessing the collective activity of multiple short interfering RNAs (siRNAs) targeting a gene. Using this method, we can not only reduce the impact of off-target activities, but also evaluate the specific effect of an siRNA, thus providing information about potential off-target effects. Using in-house RNAi screens, we demonstrate that our method obtains more reasonable and sensible results than current methods such as the redundant siRNA activity (RSA) method, the RNAi gene enrichment ranking (RIGER) method, the frequency approach and the t-test.
Contact: xiaohua_zhang@merck.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Myocardial collagen turnover after surgical ventricular restoration in heart failure patients
Authors: ten Brinke Ellen A. , Witkowski Tomasz G. , Delgado Victoria , Klein Patrick , Klok Margreet , Marsan Nina A. , Klautz Robert J. , van der Wall Ernst E. , Bax Jeroen J. , van der Laarse Arnoud , Steendijk Paul 
Published: August 2011

AimsSurgical ventricular restoration (SVR) aims to normalize left ventricular (LV) volume and shape in patients with ischaemic cardiomyopathy and anterior wall scar. The chronic effects on LV function may depend on alterations in myocardial collagen metabolism. The present study evaluated myocardial collagen synthesis and degradation rates at baseline and at 6 months follow‐up after SVR. We hypothesize that the chronic effects of SVR on LV function and clinical outcome depend on alterations in myocardial collagen metabolism.Methods and resultsSerum levels of aminoterminal propeptides of type I and III collagen (PINP, PIIINP), carboxyterminal telopeptide of type I collagen (ICTP), and tenascin‐C (TNC) were measured at baseline and 6 months after SVR in 24 patients. In addition, New York Heart Association (NYHA) functional class, LV volumes and function were evaluated. At follow‐up, a significant improvement in NYHA class (from 3.2 ± 0.8 to 1.4 ± 0.6, P< 0.001) and LV ejection fraction (from 28 ± 9 to 35 ± 7%, P< 0.001) was found, whereas E/A ratio tended to increase (from 1.4 ± 1.1 to 1.9 ± 1.1, P= 0.064). Serum levels of PINP, PIIINP, ICTP, and TNC increased significantly (PINP: from 37 ± 15 to 67 ± 26 μg/L, P< 0.001; PIIINP: from 4.9 ± 1.7 to 7.9 ± 4.0 μg/L, P< 0.001; ICTP: from 5.9 ± 3.7 to 10.0 ± 5.3 μg/L, P< 0.001; TNC: from 30 ± 20 to 44 ± 23 μg/L, P= 0.020). At follow‐up, an LV ejection fraction <34% and E/A ratio ≥2.0 were significantly associated with increased serum levels of PIIINP and ICTP.ConclusionIn patients who underwent SVR, myocardial collagen metabolism was significantly enhanced 6 months after surgery. Serum levels of myocardial collagen turnover biomarkers were related to post‐surgical LV systolic and diastolic function.
Kidney injury molecule‐1 and N‐acetyl‐ß‐d‐glucosaminidase in chronic heart failure: possible biomarkers of cardiorenal syndrome
Authors: Jungbauer Carsten G. , Birner Christoph , Jung Bettina , Buchner Stefan , Lubnow Matthias , von Bary Christian , Endemann Dierk , Banas Bernhard , Mack Matthias , Böger Carsten A. , Riegger Günter , Luchner Andreas 
Published: August 2011

AimsPatients with chronic heart failure are often characterized by impaired renal function, also referred to as cardiorenal syndrome (CRS). The aim of this study was to assess whether novel markers of kidney injury are elevated in chronic heart failure and CRS.Methods and resultsThe new renal biomarkers kidney injury molecule‐1 (KIM‐1), N‐acetyl‐ß‐d‐glucosaminidase (NAG) and neutrophil gelatinase‐associated lipocalin (NGAL) were assessed from urine samples of 173 individuals. Patients with chronic heart failure (n= 150) were characterized by decreased ejection fraction (32 ± 9% vs. controls 62 ± 4%, P < 0.001) and increased plasma N‐terminal pro‐brain natriuretic peptide (median 1460 pg/mL, interquartile range (IQR) 630–3000 pg/mL vs. controls 56, IQR 25–64l pg/mL, P < 0.001). Urinary analysis showed that KIM‐1 was significantly elevated in heart failure patients compared with healthy controls (1100, IQR 620–1920 vs. 550, IQR 320–740 ng/g urinary creatinine, P < 0.001). Further, KIM‐1 increased significantly with decreasing left ventricular function (r = −0.37, P < 0.001) and severity of New York Heart Association (NYHA)‐class (r = 0.5, P < 0.001). N‐acetyl‐ß‐d‐glucosaminidase showed a weaker response but correlated significantly with left ventricular dysfunction (r = −0.18, P= 0.015) and more severe clinical condition (r = 0.22, P= 0.04). In contrast, NGAL showed no significant correlation. Kidney injury molecule‐1 and NAG were also predictors of all‐cause mortality and the composite of all‐cause mortality and rehospitalization for heart failure (all P < 0.05).ConclusionsKidney injury molecule‐1 and NAG are elevated in symptomatic heart failure. This finding may be present in patients with apparently normal kidney function and indicates tubular injury in chronic heart failure. Kidney injury molecule‐1 and NAG are potential markers of CRS with additional prognostic value.
Biogeographic patterns of reef fish community structure in the northeastern Arabian Peninsula
Authors: Burt John A. , Feary David A. , Bauman Andrew G. , Usseglio Paolo , Cavalcante Georgenes H. , Sale Peter F. 
Published: August 2011

AbstractBurt, J. A., Feary, D. A., Bauman, A. G., Usseglio, P., Cavalcante, G. H., and Sale, P. F. 2011. Biogeographic patterns of reef fish community structure in the northeastern Arabian Peninsula. – ICES Journal of Marine Science, 68: 1875–1883. This study provides the first large-scale comparison of reef-associated fish communities in the northeastern Arabian Peninsula, with 24 sites spanning >3000 km of coastline in the southern Persian Gulf, the western Gulf of Oman, and the northwestern Arabian Sea, each with its own unique environmental conditions. Multivariate analyses revealed three distinct community types that were represented mainly by sites within each major water body, with >70% dissimilarity in community structure between each. Persian Gulf communities had low species richness, abundance, and biomass of reef fish compared with the other subregions, with communities dominated by herbivores and generalist predators that had little association with live coral. Reef fish biomass in the Gulf of Oman and Arabian Sea was comparable, and communities were dominated by fish with moderate coral association. However, there were relatively more herbivores and larger fish in the Arabian Sea than in the Gulf of Oman, where communities were dominated by planktivores. Species richness was highest in the Arabian Sea when differences in abundance among regions were accounted for. The influence of distinct environmental and oceanographic conditions on reef fish community structure in each of these areas is discussed.
Age determination in merobenthic octopuses using stylet increment analysis: assessing future challenges using Macroctopus maorum as a model
Authors: Doubleday Zoë A. , White Jimmy , Pecl Gretta T. , Semmens Jayson M. 
Published: August 2011

Abstract
Doubleday, Z. A., White, J., Pecl, G. T., and Semmens, J. M. 2011. Age determination in merobenthic octopuses using stylet increment analysis: assessing future challenges using Macroctopus maorum as a model. – ICES Journal of Marine Science, 68: 2059–2063. Stylet increment analysis (SIA) is a method recently developed to age octopuses; it involves the enumeration of daily growth increments within stylets (an internal shell). To examine the potential of SIA in a merobenthic octopus species, SIA was applied to Macroctopus maorum collected from southeast Australia and New Zealand (n = 147). The stylets had clear concentric growth increments and a core-like region. However, low increment counts (≤224 d) produced non-feasibly high (≤21.7% body weight per day) instantaneous growth rates, based on the assumption that increment number relates to age (d). In the light of these results, the issues surrounding the application of SIA to merobenthic octopuses is discussed, particularly in relation to the lack of understanding in regard to stylet development in the early life history stages and the importance of validating age at first increment formation.
Copepod reproductive success in spring-bloom communities with modified diatom and dinoflagellate dominance
Authors: Vehmaa Anu , Kremp Anke , Tamminen Timo , Hogfors Hedvig , Spilling Kristian , Engström-Öst Jonna 
Published: August 2011

Abstract
Vehmaa, A., Kremp, A., Tamminen, T., Hogfors, H., Spilling, K., and Engström-Öst, J. 2012. Copepod reproductive success in spring-bloom communities with modified diatom and dinoflagellate dominance. – ICES Journal of Marine Science, 69: 351–357. Dinoflagellates have increased and diatoms decreased in the Baltic Sea in recent decades, possibly because of changes in the climate and altered patterns of stratification. The hypothesis that grazing copepods would benefit from the change in species composition was tested experimentally by studying the reproductive output of the crustacean copepod Eurytemora affinis in five Baltic Sea phytoplankton spring communities dominated by different dinoflagellates (Biecheleria baltica, Gymnodinium corollarium) and diatoms (Chaetoceros cf. wighamii, Skeletonema marinoi, and Thalassiosira baltica). After a 5-d acclimation and a 4-d incubation, egg production, egg hatching success, and the RNA:DNA ratio of E. affinis were measured. Egg production was highest on a G. corollarium-dominated diet and lowest on a S. marinoi-dominated diet and on a B. baltica-dominated natural spring bloom, but there were no differences in hatching success. The results demonstrate strong species-specific effects unconstrained by the dominating group. Hence, the hypothesis of specific effects derived from a diatom or dinoflagellate diet is too simplistic, and there is a need to explore phytoplankton taxa at a species level to reveal the reasons for copepod reproductive success.
First Report of Puccinia graminis f. sp. tritici Races with Virulence to Wheat Stem Rust Resistance Genes Sr31 and Sr24 in Eritrea
Authors: Wolday A. , Fetch T. , Hodson D. P. , Cao W. , Briere S. 
Published: August 2011

Wheat stem rust, caused by Puccinia graminis f. sp. tritici, has historically been a major limiting factor in wheat production. Identification of isolate Ug99 in Uganda in 1999 highlighted the vulnerability of a large proportion of the global wheat crop and raised international concerns. Since initial detection, seven races have been identified in the Ug99 lineage and occurrence has been confirmed in nine countries (4). During rust surveys of Eritrea undertaken in October 2010, stem rust was found to be widespread throughout the highland wheat-growing areas. Presence of P. graminis f. sp. tritici was recorded in 95% of the 92 cereal fields surveyed, with high disease severity (>40%) recorded at 50 sites. Collected stem rust samples were analyzed for race identity in a level 3 biocontainment laboratory in Canada. Nine collections yielded viable spores for infection studies. Virulence analysis with 20 differentials in the letter-code nomenclature system (1) identified two races from repeated experiments; TTKST (four confirmed isolates) and PTKST (five confirmed isolates). Both races belong to the Ug99 lineage and both exhibit combined Sr31 and Sr24 virulence. TTKST and PTKST differ only in their virulence or avirulence to Sr21, respectively. This first confirmation of TTKST and PTKST in Eritrea is important because it represents further geographical spread of Ug99-related races. Since first detection of a Sr24 variant of Ug99 (race TTKST) in Kenya in 2006 (1), these variants have become the predominant P. graminis f. sp. tritici pathotypes in most of eastern Africa. Race TTKST caused epidemics in Kenya in 2007, and race PTKST was first detected in Ethiopia the same year (T. Fetch, unpublished data). Recent detection of race PTKST in three additional southern Africa countries (South Africa, Zimbabwe, and Mozambique [2,3]) indicates on-going range expansion within the African continent. Sr24-virulent variants of Ug99 are a cause for concern since a high frequency of cultivars from South America, Australia, the United States, and the CIMMYT are known to possess the Sr24 resistance gene. On the basis of observed occurrence and postulated migration routes of the original Ug99 (race TTKSK), the confirmed presence of TTKST and PTKST in Eritrea increases the possibility for range expansion out of Africa by crossing the Red Sea and into the Arabian Peninsula. Future spread of TTKST and PTKST to western Asia is considered highly likely. References: (1) Y. Jin et al. Plant Dis. 92:923, 2008. (2) F. Mukoyi et al. Plant Dis. 95:1188, 2011. (3) Z. A. Pretorius et al. Plant Dis. 94:784, 2010. (4) R. P. Singh et al. Annu. Rev. Phytopathol. 49:465, 2011.
Origin, Fate, and Function of Epicardium-Derived Cells (EPDCs) in Normal and Abnormal Cardiac Development
Authors: Lie-Venema Heleen , van den Akker Nynke M. S. , Bax Noortje A. M. , Winter Elizabeth M. , Maas Saskia , Kekarainen Tuija , Hoeben Rob C. , deRuiter Marco C. , Poelmann Robert E. , Gittenberger-de Groot Adriana C. 
Published: August 2011

During heart development, cells of the primary and secondary heart field give rise to the myocardial component of the heart. The neural crest and epicardium provide the heart with a considerable amount of nonmyocardial cells that are indispensable for correct heart development. During the past 2 decades, the importance of epicardium-derived cells (EPDCs) in heart formation became increasingly clear. The epicardium is embryologically formed by the outgrowth of proepicardial cells over the naked heart tube. Following epithelial-mesenchymal transformation, EPDCs form the subepicardial mesenchyme and subsequently migrate into the myocardium, and differentiate into smooth muscle cells and fibroblasts. They contribute to the media of the coronary arteries, to the atrioventricular valves, and the fibrous heart skeleton. Furthermore, they are important for the myocardial architecture of the ventricular walls and for the induction of Purkinje fiber formation.Whereas the exact signaling cascades in EPDC migration and function still need to be elucidated, recent research has revealed several factors that are involved in EPDC migration and specialization, and in the cross-talk between EPDCs and other cells during heart development. Among these factors are the Ets transcription factors Ets-1 and Ets-2. New data obtained with lentiviral antisense constructs targeting Ets-1 and Ets-2 specifically in the epicardium indicate that both factors are independently involved in the migratory behavior of EPDCs. Ets-2 seems to be especially important for the migration of EPDCs into the myocardial wall, and to subendocardial positions in the atrioventricular cushions and the trabeculae.With respect to the clinical importance of correct EPDC development, the relation with coronary arteriogenesis has been noted well before. In this review, we also propose a role for EPDCs in cardiac looping, and emphasize their contribution to the development of the valves and myocardial architecture. Lastly, we focus on the congenital heart anomalies that might be caused primarily by an epicardial developmental defect.
Thermoelastic properties and crystal structure of CaPtO3post-perovskite from 0 to 9 GPa and from 2 to 973 K
Authors: Lindsay-Scott Alex , Wood Ian G. , Dobson David P. , Vočadlo Lidunka , Brodholt John P. , Knight Kevin S. , Tucker Matthew G. , Taniguchi Takashi 
Published: August 2011

ABX3post-perovskite (PPV) phases that are stable (or strongly metastable) at ambient pressure are important as analogues of PPV-MgSiO3, a deep-Earth phase stable only at very high pressure. The thermoelastic and structural properties of orthorhombic PPV-structured CaPtO3have been determined to 9.27 GPa at ambient temperature and from 2 to 973 K at ambient pressure by time-of-flight neutron powder diffraction. The equation-of-state from this high-pressure study is consistent with that found by Lindsay-Scott, Wood, Dobson, Vočadlo, Brodholt, Crichton, Hanfland & Taniguchi [(2010).Phys. Earth Planet. Inter.182, 113–118] using X-ray powder diffraction to 40 GPa. However, the neutron data have also enabled the determination of the crystal structure. Thebaxis is the most compressible and thecaxis the least, with theaandcaxes shortening under pressure by a similar amount. Above 300 K, the volumetric coefficient of thermal expansion, α(T), of CaPtO3can be represented by α(T) =a0+a1(T), witha0= 2.37 (3) × 10−5 K−1anda1= 5.1 (5) × 10−9 K−2. Over the full range of temperature investigated, the unit-cell volume of CaPtO3can be described by a second-order Grüneisen approximation to the zero-pressure equation of state, with the internal energy calculatedviaa Debye model and parameters θD(Debye temperature) = 615 (8) K,V0(unit-cell colume at 0 K) = 227.186 (3) Å3,K′0(first derivative with respect to pressure of the isothermal incompressibilityK0) = 7.9 (8) and (V0K0/γ′) = 3.16 (3) × 10−17 J, where γ′ is a Grüneisen parameter. Combining the present measurements with heat-capacity data gives a thermodynamic Grüneisen parameter γ = 1.16 (1) at 291 K. PPV-CaPtO3, PPV-MgSiO3and PPV-CaIrO3have the same axial incompressibility sequence, κc > κa > κb. However, when heated, CaPtO3shows axial expansion in the form αc > αb > αa, a sequence which is not simply the inverse of the axial incompressibilities. In this respect, CaPtO3differs from both MgSiO3(where the sequence αb > αa > αcis the same as 1/κi) and CaIrO3(where αb > αc > αa). Thus, PPV-CaPtO3and PPV-CaIrO3are better analogues for PPV-MgSiO3in compression than on heating. The behaviour of the unit-cell axes of all three compounds was analysed using a model based on nearest-neighbourB—XandA—Xdistances and angles specifying the geometry and orientation of theBX6octahedra. Under pressure, all contract mainly by reduction in theB—XandA—Xdistances. On heating, MgSiO3expands (at high pressure) mainly by lengthening of the Si—O and Mg—O bonds. In contrast, the expansion of CaPtO3(and possibly also CaIrO3), at atmospheric pressure, arises more from changes in angles than from increased bond distances.
Inflammatory activation and carbohydrate antigen‐125 levels in subjects with atrial fibrillation
Authors: De Gennaro Luisa , Brunetti Natale Daniele , Montrone Deodata , De Rosa Fiorella , Cuculo Andrea , Di Biase Matteo 
Published: August 2011

Eur J Clin Invest 2012; 42 (4): 371–375AbstractBackground  Atrial fibrillation (AF) might be associated with an inflammatory activation and reduced left ventricular (LV) function. Less is known with regard to newly introduced markers of LV dysfunction such as carbohydrate antigen‐125 (CA‐125) in subjects with AF. The aim of this study was therefore to assess possible associations between AF, inflammatory markers and CA‐125.Methods and results  Forty‐eight consecutive patients with AF and 58 control patients in sinus rhythm were enrolled in this study. Patients with acute heart failure, chronic inflammatory or neoplastic disease were excluded from the study. Circulating levels of hs‐C‐reactive protein (CRP), interleukin‐8 (IL‐8), IL‐6, soluble IL‐2 receptor (sIL‐2r), TNF‐α and CA‐125 were assessed; all patients underwent clinical examination with NYHA class assessment and echocardiography. Patients with AF were characterised by higher levels of IL‐8 (180 ± 266 vs. 39 ± 43 pg/mL, P < 0·001), sIL‐2r (987 ± 1045 vs. 680 ± 336 U/mL, P < 0·05) and TNF‐α (26 ± 25 vs. 9 ± 4 pg/mL, P < 0·001). Patients with AF duration < 6 months had higher levels of CRP (54 ± 73 vs. 12 ± 14 mg/dL, P < 0·05) and IL‐8 (251 ± 225 vs. 99 ± 123 pg/mL, P < 0·05) when compared with AF duration > 6 months. CA‐125 levels were not statistically different if comparing subjects with AF with controls and AF > 6 months with AF < 6 months. Among patients with AF, CA‐125 levels were significantly related to NYHA class, (r = 0·33, P < 0·05) as well as IL‐6 levels (r = 0·31, P < 0·05). Results remained statistically significant even after multivariable correction for age, gender and LV ejection fraction.Results and conclusion  AF is characterised by an inflammatory activation. Impaired functional class in AF subjects might be associated with increased CA‐125 levels and higher inflammatory markers.
Metacommunity analysis of Mexican bats: environmentally mediated structure in an area of high geographic and environmental complexity
Authors: López‐González Celia , Presley Steven J. , Lozano Abraham , Stevens Richard D. , Higgins Christopher L. 
Published: August 2011

AbstractAim  We tested the hypothesis that distributions of Mexican bats are defined by shared responses to environmental gradients for the entire Mexican bat metacommunity and for each of four metaensembles (frugivores, nectarivores, gleaning insectivores, and aerial insectivores). Further, we identified the main environmental factors to which bats respond for multiple spatial extents.Location  Mexico.Methods  Using bat presence–absence data, as well as vegetation composition for each of 31 sites, we analysed metacommunity structure via a comprehensive, hierarchical approach that uses reciprocal averaging (RA) to detect latent environmental gradients corresponding to each metacommunity structure (e.g. Clementsian, Gleasonian, nested, random). Canonical correspondence analysis (CCA) was used to relate such gradients to variation in vegetation composition.Results  For all bat species and for each ensemble, the primary gradient of ordination from RA, which is based on species data only, recovered an axis of humidity that matched that obtained for the first axis of the CCA ordination, which is based both on vegetation attributes and on species composition of sites. For the complete assemblage as well as for aerial and gleaning insectivores, analyses revealed Clementsian or quasi‐Clementsian structures with discrete compartments (distinctive groups of species along portions of an environmental gradient) coincident with the humidity gradient and with the Nearctic–Neotropical divide. Within‐compartment analysis further revealed Clementsian or quasi‐Clementsian structures corresponding to a gradient of elevational complexity that matched the second ordination axis in CCA. Frugivores had quasi‐nested structure, whereas nectarivores had Gleasonian structure.Main conclusions  Our hierarchical approach to metacommunity analysis detected complex metacommunity structures associated with multiple environmental gradients at different spatial extents. More importantly, the resulting structures and their extent along environmental gradients are determined by ensemble‐specific characteristics and not by arbitrarily circumscribed study areas. This property renders compartment‐level analyses particularly useful for large‐scale ecological analyses in areas where more than one gradient may exist and species sorting may occur at multiple scales.