bluuebunny/crossref_metadata_2025_split huggingface dataset:
Look@NanoSIMS – a tool for the analysis of nanoSIMS data in environmental microbiology
Authors: Polerecky Lubos , Adam Birgit , Milucka Jana , Musat Niculina , Vagner Tomas , Kuypers Marcel M. M. 
Published: January 2012

SummaryWe describe an open‐source freeware programme for high throughput analysis of nanoSIMS (nanometre‐scale secondary ion mass spectrometry) data. The programme implements basic data processing and analytical functions, including display and drift‐corrected accumulation of scanned planes, interactive and semi‐automated definition of regions of interest (ROIs), and export of the ROIs' elemental and isotopic composition in graphical and text‐based formats. Additionally, the programme offers new functions that were custom‐designed to address the needs of environmental microbiologists. Specifically, it allows manual and automated classification of ROIs based on the information that is derived either from the nanoSIMS dataset itself (e.g. from labelling achieved by halogen in situ hybridization) or is provided externally (e.g. as a fluorescence in situ hybridization image). Moreover, by implementing post‐processing routines coupled to built‐in statistical tools, the programme allows rapid synthesis and comparative analysis of results from many different datasets. After validation of the programme, we illustrate how these new processing and analytical functions increase flexibility, efficiency and depth of the nanoSIMS data analysis. Through its custom‐made and open‐source design, the programme provides an efficient, reliable and easily expandable tool that can help a growing community of environmental microbiologists and researchers from other disciplines process and analyse their nanoSIMS data.
Morphology of the female genital ducts of the blue land crab Cardisoma guanhumi (Crustacea: Brachyura: Gecarcinidae)
Authors: de Souza Leonardo P. , Silva José R.F. , Araujo Andréa M. , Camargo‐Mathias Maria I. 
Published: January 2012

AbstractThis is a histological and histochemical analysis of the terminal portion of the female reproductive system and genital ducts of the blue land crab (Cardisoma guanhumi). Animals were collected in the Jaguaribe estuary (Ceará, Brazil) and dissected. Genital duct fragments were fixed and submitted to different staining techniques. The female reproductive system consists of a pair of ovaries and a pair of genital ducts. In the mid‐posterior portion of each lobe, the ovaries communicate with the genital ducts, which are subdivided into oviduct, spermatheca, vagina, and gonopore. Histologically, the spermatheca of C. guanhumi is composed of columnar secretory epithelium and is divided into a dorsal zone and a ventral zone, the latter covered internally by a cuticle layer. Both zones are enveloped by a thin layer of loose connective tissue. Histological cross sections revealed the vagina to be concave, a pattern considered phylogenetically more advanced than the simple, tubular form. Our findings suggest fertilization is internal, favoring sperm from the most recent copulation.
Partial nephrectomy for renal masses ≥7 cm: technical, oncological and functional outcomes
Authors: Long Christopher J. , Canter Daniel J. , Kutikov Alexander , Li Tianyu , Simhan Jay , Smaldone Marc , Teper Ervin , Viterbo Rosalia , Boorjian Stephen A. , Chen David Y.T. , Greenberg Richard E. , Uzzo Robert G. 
Published: January 2012

What's known on the subject? and What does the study add?Partial nephrectomy for the pT1 renal mass has demonstrated acceptable oncological outcomes in addition to improved overall long‐term survival when compared with radical nephrectomy. Previous reports for lesions ≥7 cm have shown mixed data concerning oncological outcomes and technological success.We demonstrate that partial nephrectomy for renal masses ≥7 cm has acceptable oncological, technical, and functional outcomes. As such, partial nephrectomy should be a surgical option when feasible regardless of tumour size.Study Type – Therapy (case series)Level of Evidence 4OBJECTIVE
To present outcomes for patients with renal masses ≥7 cm in size who are treated with partial nephrectomy (PN) at our institution and to summarize the cumulative published experience.
PATIENTS AND METHODS
We reviewed our prospectively maintained institutional kidney cancer database and identified patients undergoing PN for tumours >7 cm in size.
Technical, oncological and renal functional data were analyzed and compared with the existing published experience of PNs for tumours >7 cm in size.
RESULTS
In total, 46 patients with 49 renal tumours >7 cm in size who underwent PN were identified.
With a median (range) follow‐up of 13.1 (0.2–170.0) months, there were 16 complications, including four (8.2%) blood transfusions and six (12.2%) urinary fistulae.
The 5‐ and 10‐year overall and renal cell carcinoma (RCC)‐specific survivals were 94.5% and 70.9%. There were five (10.9%) patients who had an upward migration in their chronic kidney disease status after PN.
There were six previous series totalling 280 tumours encompassing the published experience of PN for tumours >7 cm in size. The incidence of urinary fistulae and postoperative haemorrhage, respectively, was in the range 3.3–18.8% and 0–3%.
Although oncological outcomes showed cancer‐specific survival in the range 66–97.0%, series matching PN and RN in patients with T2 RCC show equivalency in RCC‐specific and overall survivals. When reported, PN for tumours >7 cm in size was associated with better renal functional preservation.
CONCLUSION
The findings of the present study show that PN can safely be performed in tumours ≥7 cm in size with acceptable technical, oncological and functional outcomes. Further studies are warranted.
What determines the profitability of banks? Evidence from Spain
Authors: Trujillo‐Ponce Antonio 
Published: January 2012

AbstractThis paper empirically analyses the factors that determine the profitability of Spanish banks for the period of 1999–2009. We conclude that the high bank profitability during these years is associated with a large percentage of loans in total assets, a high proportion of customer deposits, good efficiency and a low doubtful assets ratio. In addition, higher capital ratios also increase the bank’s return, but only when return on assets (ROA) is used as the profitability measure. We find no evidence of either economies or diseconomies of scale or scope in the Spanish banking sector. Finally, our study reveals differences in the performance of commercial and savings banks.
Bedlam or Parnassus: The Verse Idea
Authors: Jarvis Simon 
Published: January 2012

AbstractThis essay considers some problems in philosophical approaches to poetry. Philosophers’ accounts of what poetry is are often ill informed. They tend to select, as essential, features that can also characterize prose works: conspicuous metaphoricity, imagination, fictionality, and so on. This essay considers instead a humbler term: verse. It argues that the constraints on language implied by composing in verse are not only a handicap but can also be an engine for thinking. Even philosophy has sometimes been thought in verse, rather than thought first in prose and versified later. This argument is explored through a brief consideration of Alexander Pope's Essay on Man. The essay concludes by questioning a further way of distinguishing between poetry and philosophy, Peter Lamarque's claim that paraphrasability is essential to philosophy but fatal to poetry.
Philosophy, Early Modern Intellectual History, and the History of Philosophy
Authors: Edwards Michael 
Published: January 2012

AbstractHistorians of philosophy are increasingly likely to emphasize the extent to which their work offers a pay‐off for philosophers of un‐historical or anti‐historical inclinations; but this defence is less familiar, and often seems less than self‐evident, to intellectual historians. This article examines this tendency, arguing that such arguments for the instrumental value of historical scholarship in philosophy are often more problematic than they at first appear. Using the relatively familiar case study of René Descartes' reading of his scholastic and Aristotelian contemporaries, the article attempts to problematize this notion of pay‐off from an historian's perspective.
Forms of Reflection, Imagination, and the Love of Wisdom
Authors: Hedley Douglas 
Published: January 2012

AbstractThis article reflects upon the relationship between philosophy and theology. It further considers the persisting relevance of the specifically Hellenic inheritance of philosophy as contemplation and the Delphic exhortation, “Know thyself!” It concludes with reflections upon the role of imagination in relation to the philosophical idea of God as the supreme and transcendent causal principle of the physical cosmos.
Allometric covariation: a hallmark behavior of plants and leaves
Authors: Price Charles A. , Weitz Joshua S. 
Published: January 2012

SummarySize is one of the most important axes of variation among plants. As such, plant biologists have long searched for unifying principles that can explain how matter and energy flux and organ partitioning scale with plant size. Several recent models have proposed a universal biophysical basis for numerous scaling phenomena in plants based on vascular network geometry. Here, we review statistical analyses of several large‐scale plant datasets that demonstrate that a true hallmark of plant form variability is systematic covariation among traits. This covariation is constrained by allometries that combine and trade off with one another, rather than any single universal allometric scaling exponent for a trait or suite of traits. Further, we show that covariation can be successfully modeled using network approaches that allow for species‐specific designs in plants and geometric approaches that constrain relationships among economic traits in leaves. Finally, we report large‐scale efforts utilizing semi‐automated software tools that quantify physical networks and can inform our attempts to link vascular network structure to plant form and function. Collectively, this work highlights how the linking of morphology, biomass partitioning and the structure of physical distribution networks can improve our empirical and theoretical understanding of important drivers of plant functional diversity.
The Role of Matched Controls in Building an Evidence Base for Hospital‐Avoidance Schemes: A Retrospective Evaluation
Authors: Steventon Adam , Bardsley Martin , Billings John , Georghiou Theo , Lewis Geraint Hywel 
Published: January 2012

ObjectiveTo test whether two hospital‐avoidance interventions altered rates of hospital use: “intermediate care” and “integrated care teams.”Data Sources/Study SettingLinked administrative data for England covering the period 2004 to 2009.Study DesignThis study was commissioned after the interventions had been in place for several years. We developed a method based on retrospective analysis of person‐level data comparing health care use of participants with that of prognostically matched controls.Data Collection/Extraction MethodsIndividuals were linked to administrative datasets through a trusted intermediary and a unique patient identifier.Principal FindingsParticipants who received the intermediate care intervention showed higher rates of unscheduled hospital admission than matched controls, whereas recipients of the integrated care team intervention showed no difference. Both intervention groups showed higher rates of mortality than did their matched controls.ConclusionsThese are potentially powerful techniques for assessing impacts on hospital activity. Neither intervention reduced admission rates. Although our analysis of hospital utilization controlled for a wide range of observable characteristics, the difference in mortality rates suggests that some residual confounding is likely. Evaluation is constrained when performed retrospectively, and careful interpretation is needed.
Early progress in epigenetic regulation of endothelin pathway genes
Authors: Welch AK , Jacobs ME , Wingo CS , Cain BD 
Published: January 2012

Control of gene transcription is a major regulatory determinant for function of the endothelin pathway. Epigenetic mechanisms act on tissue‐specific gene expression during development and in response to physiological stimuli. Most of the limited evidence available on epigenetic regulation of the endothelin pathway focuses on the EDN1 and EDNRB genes. Examination of whole genome databases suggests that both genes are influenced by histone modifications and DNA methylation. This interpretation is supported by studies directed at detecting epigenetic action on the two genes. The clearest illustration of epigenetic factors altering endothelin signalling is DNA methylation‐associated EDNRB silencing during tumourigenesis. This review summarizes our current understanding of epigenetic regulation of the endothelin pathway genes.LINKED ARTICLES This article is part of a themed section on Endothelin. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2013.168.issue-2
Renin activates PI3K‐Akt‐eNOS signalling through the angiotensin AT1 and Mas receptors to modulate central blood pressure control in the nucleus tractus solitarii
Authors: Cheng Wen‐Han , Lu Pei‐Jung , Hsiao Michael , Hsiao Chun‐Hui , Ho Wen‐Yu , Cheng Pei‐Wen , Lin Chia‐Te , Hong Ling‐Zong , Tseng Ching‐Jiunn 
Published: January 2012

BACKGROUND AND PURPOSEThe renin‐angiotensin system (RAS) is critical for the control of blood pressure by the CNS. Recently, direct renin inhibitors were approved as antihypertensive agents. However, the signalling mechanism of renin, which regulates blood pressure in the nucleus tractus solitarii (NTS) remains unclear. Here we have investigated the signalling pathways involved in renin‐mediated blood pressure regulation, at the NTS.EXPERIMENTAL APPROACHDepressor responses to renin microinjected into the NTS of Wistar‐Kyoto rats were elicited in the absence and presence of the endothelial nitric oxide synthase (eNOS)‐specific inhibitor, N(5)‐(‐iminoethyl)‐L‐ornithine, Akt inhibitor IV and LY294002, a PI3K inhibitor and GP antagonist‐2A [Gq inhibitor]. Lisinopril (angiotensin converting enzyme inhibitor), losartan, valsartan (angiotensin AT1 receptor antagonists), D‐Ala7‐Ang‐(1‐7) (angiotensin‐(1‐7) receptor antagonist) were used to study the involvement of RAS on renin‐induced depressor effects.KEY RESULTSMicroinjection of renin into the NTS produced a prominent depressor effect and increased NO production. Pretreatment with Gq‐PI3K‐Akt‐eNOS pathway‐specific inhibitors significantly attenuated the depressor response evoked by renin. Immunoblotting and immunohistochemical studies further showed that inhibition of PI3K significantly blocked renin‐induced eNOS‐Ser117 and Akt‐Ser473 phosphorylation in situ. In addition, pre‐treatment of the NTS with RAS inhibitors attenuated the vasodepressor effects evoked by renin. Microinjection of renin also increased Ras activation in the NTS.CONCLUSIONS AND IMPLICATIONSTaken together, these results suggest renin modulated blood pressure at the NTS by AT1 and Mas receptor‐mediated activation of Gq and Ras to evoke PI3K‐Akt‐eNOS signalling.
Genomic Expression Patterns in Menstrual‐Related Migraine in Adolescents
Authors: Hershey Andrew , Horn Paul , Kabbouche Marielle , O'Brien Hope , Powers Scott 
Published: January 2012

Background.— Exacerbation of migraine with menses is common in adolescent girls and women with migraine, occurring in up to 60% of females with migraine. These migraines are oftentimes longer and more disabling and may be related to estrogen levels and hormonal fluctuations.Objective.— This study identifies the unique genomic expression pattern of menstrual‐related migraine (MRM) in comparison to migraine occurring outside the menstrual period and headache‐free controls.Methods.— Whole blood samples were obtained from female subjects having an acute migraine during their menstrual period (MRM) or outside of their menstrual period (non‐MRM) and controls (C) – females having a menstrual period without any history of headache. The messenger RNA was isolated from these samples, and genomic profile was assessed. Affymetrix Human Exon ST 1.0 (Affymetrix, Santa Clara, CA, USA) arrays were used to examine the genomic expression pattern differences between these3 groups.Results.— Blood genomic expression patterns were obtained on 56 subjects (MRM =  18, non‐MRM =  18, and controls =  20). Unique genomic expression patterns were observed for both MRM and non‐MRM. For MRM, 77 genes were identified that were unique to MRM, while 61 genes were commonly expressed for MRM and non‐MRM, and 127 genes appeared to have a unique expression pattern for non‐MRM. In addition, there were 279 genes that differentially expressed for MRM compared to non‐MRM that were not differentially expressed for non‐MRM. Gene ontology of these samples indicated many of these groups of genes were functionally related and included categories of immunomodulation/inflammation, mitochondrial function, and DNA homeostasis.Conclusions.— Blood genomic patterns can accurately differentiate MRM from non‐MRM. These results indicate that MRM involves a unique molecular biology pathway that can be identified with a specific biomarker and suggest that individuals with MRM have a different underlying genetic etiology.
Epilepsy is associated with unmet health care needs compared to the general population despite higher health resource utilization—A Canadian population‐based study
Authors: Reid Aylin Y. , Metcalfe Amy , Patten Scott B. , Wiebe Samuel , Macrodimitris Sophie , Jetté Nathalie 
Published: January 2012

SummaryPurpose:  (1) To determine whether health resource utilization (HRU) and unmet health care needs differ for individuals with epilepsy compared to the general population or to those with another chronic condition (asthma, diabetes, migraine); and (2) to assess the association among epilepsy status, sociodemographic variables and HRU.Methods:  Data on HRU were assessed using the 2001–2005 Canadian Community Health Surveys, a nationally representative population‐based survey. Weighted estimates of association were produced as adjusted odds ratio with 95% confidence intervals, and logistic regression was used to explore the association between sociodemographic variables and HRU in those with epilepsy. All data on disease status, HRU, and unmet health care needs were self‐reported.Key Findings:  Individuals with epilepsy had the highest rate of hospitalizations and the highest mean number of consultations with physicians. Despite higher rates of consultation with psychologists and social workers compared to the general population, those with epilepsy were significantly more likely to say they had unmet mental health care needs. People with epilepsy were also less likely to use dental services compared to the general population. Epilepsy was a significant predictor of HRU in logistic regression models.Significance:  Given the prevalence of psychiatric comorbidities in those with epilepsy, it is concerning that this group perceives unmet mental health care needs. It is also troublesome that there was decreased utilization of dental health care resources in those with epilepsy considering that these patients are more likely to have poor oral health. Although individuals with epilepsy use more health care services than the general population, this increase appears to be insufficient to address their health care needs.
Dose‐dependent functional benefit of human cardiosphere transplantation in mice with acute myocardial infarction
Authors: Shen Deliang , Cheng Ke , Marbán Eduardo 
Published: January 2012

AbstractDespite mounting pre‐clinical and clinical evidence of the beneficial effects of cell‐based therapy, optimal cell dosing and delivery approaches have not been identified. Cardiospheres are self‐assembling three‐dimensional (3D) microtissues formed by cardiac stem cells and supporting cell types. The ability of cardiospheres to augment cardiac function has been demonstrated in animal models of ischemic cardiomyopathy. In this study, we studied the dose dependence of the benefits of human cardiospheres, delivered via intramyocardial injection, upon cardiac function and ventricular remodelling in SCID mice with acute myocardial infarction. Four doses of cardiospheres were used: 1 × 104, 5 × 104, 1 × 105 and 5 × 105 (expressed as number of plated cardiosphere‐forming cells). Acute (24 hr) cell retention rates in all groups were similar. Functional assessment and quantitative heart morphometry indicated benefit from higher cell doses (≥5 × 104) in terms of ejection fraction, infarct size and capillary density. Histological analysis indicated that the dose‐dependent benefit was primarily because of indirect effects of transplanted cells. The results provide scalable data on cardiosphere dosing for intramyocardial injection.
Raf‐1 levels determine the migration rate of primary endometrial stromal cells of patients with endometriosis
Authors: Yotova Iveta , Quan Ping , Gaba Aulona , Leditznig Nadja , Pateisky Petra , Kurz Christine , Tschugguel Walter 
Published: January 2012

AbstractEndometriosis is a disease characterized by the localization of endometrial tissue outside the uterine cavity. The differences observed in migration of human endometrial stromal cells (hESC) obtained from patients with endometriosis versus healthy controls were proposed to correlate with the abnormal activation of Raf‐1/ROCKII signalling pathway. To evaluate the mechanism by which Raf‐1 regulates cytoskeleton reorganization and motility, we used primary eutopic (Eu‐, n = 16) and ectopic (Ec‐, n = 8; isolated from ovarian cysts) hESC of patients with endometriosis and endometriosis‐free controls (Co‐hESC, n = 14). Raf‐1 siRNA knockdown in Co‐ and Eu‐hESC resulted in contraction and decreased migration versus siRNA controls. This phenotype was reversed following the re‐expression of Raf‐1 in these cells. Lowest Raf‐1 levels in Ec‐hESC were associated with hyperactivated ROCKII and ezrin/radixin/moesin (E/R/M), impaired migration and a contracted phenotype similar to Raf‐1 knockdown in Co‐ and Eu‐hESC. We further show that the mechanism by which Raf‐1 mediates migration in hESC includes direct myosin light chain phosphatase (MYPT1) phosphorylation and regulation of the levels of E/R/M, paxillin, MYPT1 and myosin light chain (MLC) phosphorylation indirectly via the hyperactivation of ROCKII kinase. Furthermore, we suggest that in contrast to Co‐and Eu‐hESC, where the cellular Raf‐1 levels regulate the rate of migration, the low cellular Raf‐1 content in Ec‐hESC, might ensure their restricted migration by preserving the contracted cellular phenotype. In conclusion, our findings suggest that cellular levels of Raf‐1 adjust the threshold of hESC migration in endometriosis.