bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sedimentology and depositional architecture of tufas deposited in stepped fluvial systems of changing slope: Lessons from the Quaternary Añamaza valley (Iberian Range, Spain)
Authors: Arenas Concha , Vázquez‐Urbez Marta , Pardo Gonzalo , Sancho Carlos 
Published: April 2013

AbstractThe Pleistocene and Holocene tufas of the Añamaza valley (stepped build‐ups, up to 70 m thick, along the valley) consist of several depositional stages separated by erosional surfaces. Eight associations of tufa and related carbonate facies, plus minor polygenic detrital facies, represent the processes that occurred in different fluvial and related environments. The bedrock lithology and structure controlled the location of the knickpoints along the valley and allowed separation of two stepped stretches with distinct conceptual facies models. The moderate‐slope model includes extensive standing‐water areas dammed by barrage‐cascades. In the lakes, bioclastic silts, sands and limestones along with phytoclastic and marly, at places peaty, sediments formed. Abundant stem phytoherms account for extensive palustrine areas. The high‐slope model consists of smaller dammed areas between close‐up cascades and barrage‐cascades, which were composed primarily of moss phytoherms and phytoclastic tufas. An outstanding feature is the extensive steep reach with phytoclastic and polygenic detrital sediments, and stepped cascades consisting of stromatolitic and moss phytoherms. There, the steep slope limited the preservation of stem phytoherms and favoured erosion. The geometry and thickness of the sedimentary fill (wedge‐shaped units composed of cascade and barrage‐cascade deposits downstream, and dammed and gentle‐sloped channel deposits upstream) are therefore different for each model. Multi‐storey wedges are a distinctive feature of the high‐slope model. The initial knickpoint geometry and the tufa aggradation/progradation ratio on such steep surfaces (for example, related to changes in discharge) controlled the growth style of the cascades or barrage‐cascades and, hence, the extent, thickness and vertical evolution of the upstream deposits. The sedimentological attributes and stable‐isotope composition of the carbonate facies suggest a higher and more variable precipitation/evaporation ratio during the Pleistocene than during the Holocene, consistent with an overall decrease in the river discharge. This evolution was coupled with warm conditions, which prevailed during the stages of tufa formation. These results may help to assess architectural patterns in interpreting other basins, and underscore the significance of tufas as records of past hydrology and climate.
Foxp3 Expression and Nitric Oxide Production in Peripheral Blood Mononuclear Cells of Communicants with Pulmonary Tuberculosis
Authors: Cavalcanti Y. V. N. , de Almeida T. M. , de Almeida A. F. , Reis L. C. , Lucena‐Silva N. , Pereira V. R. A. 
Published: April 2013

AbstractThe understanding of the mechanisms involved in the immune response is of significant relevance to the control of tuberculosis (TB), especially in individuals living with patients with TB. To characterize the nitric oxide (NO) production and the Foxp3 marker expression in this population, peripheral blood mononuclear cells of intradomiciliary contacts of individuals with pulmonary tuberculosis with (CTb, susceptible) and without (STb, resistant) previous history of active infection were stimulated in vitro with Mycobacterium tuberculosis antigen (TbAg) and with the mitogen Concanavalin A for 24 and 48 h. The groups analysed did not present significant difference in the Foxp3 mRNA expression nor in the NO production. Negative correlation (P = 0.09) between NO and Foxp3 after a 48‐h stimulation with TbAg was observed in the STb group. In this group, after a 24‐h culture stimulated with TbAg (P = 0.03), this same correlation was observed. In comparison with the cytokines previously studied by our group (Cavalcanti et al., 2009), a positive correlation was observed between IL‐10 and Foxp3 after a 48‐h culture of cells from communicants susceptible to tuberculosis (STb) stimulated with TbAg (P = 0.04). Evaluating the entire population, a positive correlation was observed between the cytokine TNF‐α and the Foxp3 marker in the cultures stimulated for 24 (P = 0.03) and 48 (P = 0.02) hours with TbAg. Therefore, considering the similarity in the exposure and the individual capacity of responding to the contact with M. tuberculosis, the present study contributes to the comprehension of the immune regulation in individuals living with patients with TB.
Pharmacokinetics of micafungin in patients undergoing allogeneic hematopoietic stem cell transplantation
Authors: Oshima K. , Kanda Y. , Kako S. , Ohno K. , Kishino S. , Kurokawa M. 
Published: April 2013

AbstractObjectivesMicafungin (MCFG) is an antifungal agent that is widely used for the treatment of invasive fungal infection. Although the pharmacokinetics of MCFG is considered to depend on the hepatic metabolism, the impact of hepatic function on the pharmacokinetics of MCFG has been inconsistent among previous studies. The object of this study was to evaluate the relationship between plasma MCFG concentration and clinical and laboratory data.Patients and methodsWe examined the plasma concentration of MCFG in 10 patients who underwent allogeneic hematopoietic stem cell transplantation (HSCT). MCFG at 150 mg/day was administered intravenously a median of 58.5 days after HSCT. Trough and peak concentrations of MCFG (Cmin and Cmax) were measured at a median of 5.5 days after the first administration of MCFG.ResultsThe presence of graft‐versus‐host disease involving the liver at blood sampling was associated with significantly higher Cmin and Cmax of MCFG. Among the laboratory data, Cmin and Cmax were significantly higher in patients with severely impaired hepatic function defined as serum total bilirubin (TBi) level >5 mg/dL and/or serum gamma‐glutamyltransferase (γ‐GTP) level >500 IU/L, but the presence of mildly impaired hepatic function defined as serum TBi level >2 mg/dL and/or serum γ‐GTP level >200 IU/L did not affect Cmin and Cmax. Renal function did not show significant impact on Cmin and Cmax.ConclusionThese findings suggest that the pharmacokinetics of MCFG is affected only by severely impaired liver function.
Draft Genome Sequence for Desulfovibrio africanus Strain PCS
Authors: Brown Steven D. , Utturkar Sagar M. , Arkin Adam P. , Deutschbauer Adam M. , Elias Dwayne A. , Hazen Terry C. , Chakraborty Romy 
Published: April 2013

ABSTRACT

Desulfovibrio africanus
strain PCS is an anaerobic sulfate-reducing bacterium (SRB) isolated from sediment from Paleta Creek, San Diego, CA. Strain PCS is capable of reducing metals such as Fe(III) and Cr(VI), has a cell cycle, and is predicted to produce methylmercury. We present the
D. africanus
PCS genome sequence.
Genome Sequence of a Novel Reassortant H3N6 Avian Influenza Virus from Domestic Mallard Ducks in Eastern China
Authors: Li Qunhui , Zhong Lei , Zhao Qingqing , He Liang , Duan Zhiqiang , Chen Chaoyang , Chen Yuxin , Gu Min , Wang Xiaoquan , Liu Xiaowen , Liu Xiufan 
Published: April 2013

ABSTRACT
Here, we report the complete genome sequence of an H3N6 avian influenza virus (AIV) isolated from domestic ducks in Jiangsu province of eastern China in 2010. Phylogenetic analysis showed that the H3N6 virus is a natural recombinant virus whose genes were derived from H3N8, H4N6, H6N6, H7N7, and H11N2 AIVs. This analysis will help to understand the molecular characteristics and evolution of the H3N6 influenza virus in eastern China.
Use of simulation to assess electronic health record safety in the intensive care unit: a pilot study
Authors: March Christopher A , Steiger David , Scholl Gretchen , Mohan Vishnu , Hersh William R , Gold Jeffrey A 
Published: April 2013

ObjectiveTo establish the role of high-fidelity simulation training to test the efficacy and safety of the electronic health record (EHR)–user interface within the intensive care unit (ICU) environment.DesignProspective pilot study.SettingMedical ICU in an academic medical centre.ParticipantsPostgraduate medical trainees.InterventionsA 5-day-simulated ICU patient was developed in the EHR including labs, hourly vitals, medication administration, ventilator settings, nursing and notes. Fourteen medical issues requiring recognition and subsequent changes in management were included. Issues were chosen based on their frequency of occurrence within the ICU and their ability to test different aspects of the EHR–user interface. ICU residents, blinded to the presence of medical errors within the case, were provided a sign-out and given 10 min to review the case in the EHR. They then presented the case with their management suggestions to an attending physician. Participants were graded on the number of issues identified. All participants were provided with immediate feedback upon completion of the simulation.Primary and secondary outcomesTo determine the frequency of error recognition in an EHR simulation. To determine factors associated with improved performance in the simulation.Results38 participants including 9 interns, 10 residents and 19 fellows were tested. The average error recognition rate was 41% (range 6–73%), which increased slightly with the level of training (35%, 41% and 50% for interns, residents, and fellows, respectively). Over-sedation was the least-recognised error (16%); poor glycemic control was most often recognised (68%). Only 32% of the participants recognised inappropriate antibiotic dosing. Performance correlated with the total number of screens used (p=0.03).ConclusionsDespite development of comprehensive EHRs, there remain significant gaps in identifying dangerous medical management issues. This gap remains despite high levels of medical training, suggesting that EHR-specific training may be beneficial. Simulation provides a novel tool in order to both identify these gaps as well as foster EHR-specific training.
Homo Economicus and the Stories of Jacob: On the Methodological Relevance of Rational Choice Theory for Studying the Hebrew Bible
Authors: Wagner-Tsukamoto Sigmund A. 
Published: April 2013

Abstract
Economics is widely accused of being a portrayer of a dark and dismal image of human nature (i.e. its model of homo economicus as a self-interested, even selfish and opportunistic maximizer of its own gains). This article argues that the model of homo economicus is not an empirical or prescriptive image of human nature but a useful, “heuristic,” methodical instrument for economic theorizing (in our case, for the economic study of religion that connects to the Hebrew Bible). This article demonstrates that in generic, methodological perspective, the model of homo economicus compares well to similarly unrealistic, “dismal” models of human nature in other disciplines that study religion. I develop these arguments by focusing on selective stories from Genesis, especially the stories of Jacob. Implications are derived regarding the application of economic methods and concepts for research on the texts in the Hebrew Bible.
Researching the Dominant Religion: Anthropology at Home and Methodological Catholicism
Authors: Sekerdej Kinga , Pasieka Agnieszka 
Published: April 2013

Abstract
The article discusses methodological problems of researching the dominant religion by native anthropologists in a majority Catholic society. By presenting both ethnographic examples and scholarly publications on religion we point at a Catholic hegemonic frame in Poland, within which religion is interpreted. Such an approach results in treating Catholicism as the taken for granted denomination, and the Roman Catholic Church as a bearer of moral authority. Engaging critically with the existing scholarship we argue that in Poland one can speak of methodological Catholicism, connected to certain implicit assumptions: treating Catholic faith as a desirable norm, describing religiosity at large with Catholic vocabulary and measuring religiosity through the prism of the Church dogmas as opposed to inquiring about the ways Catholicism is lived as a religion.
Discursive Study of Religion: Approaches, Definitions, Implications
Authors: von Stuckrad Kocku 
Published: April 2013

Abstract
The article explores recent approaches to historical analysis of discourse that have been developed in disciplines such as the sociology of knowledge and historical epistemology. These approaches have only sporadically been taken seriously in the academic study of religion, although they have a great potential to establish a study of religion that is both academically rigorous and aware of its societal and historical contexts and limitations. The article defines the necessary concepts for a discursive study of religion as an hermeneutical discipline that scrutinizes and historicizes the societal organization of knowledge about religion. This discourse on religion—defined here as religion—generates, legitimizes, and maintains meaning structures and societal realities. The discourse-historical analysis of religion is not itself a method but a research perspective. Nevertheless, this perspective implies several steps in designing a research project that the article describes with concrete examples.
A Response to Kevin Schilbrack
Authors: Fitzgerald Timothy 
Published: April 2013

Abstract
Kevin Schilbrack has pointed out that in my publications over a period from 1994 to 2007 there are some discrepancies in my arguments about some categories, especially “politics” and “culture.” In some earlier research on Dalits and Buddhists in Maharashtra I could not locate “religion,” so I attempted, unsuccessfully, to develop a tripartite conceptual substitution for “religion”—ritual, politics and soteriology—for purposes of description and analysis. However, though this was repeated in Ideology, I have come to realize that it contradicts a more fundamental argument which is tacit all the way through Ideology, for example in the critique of constructions of “religion-and-society.” It has become progressively clearer to me that the religion-politics binary is one of a series which rhetorically invents both domains (fundamentally religion-nonreligion) as mutually parasitic, while simultaneously transforming the nonreligious secular domains into the common sense order of things. Religion acts as the arena of “faith” and “belief ” in contrast to the supposed objective secular knowledge of the “real” world. I have pursued this latter argument most recently in Religion and Politics in International Relations: the Modern Myth, which shows how writers in that discipline have transformed “religion” into a global agent of malice threatening the benignly rational secular state.
Water Mass Transformations in the Southern Ocean Diagnosed from Observations: Contrasting Effects of Air–Sea Fluxes and Diapycnal Mixing
Authors: Badin Gualtiero , Williams Richard G. , Jing Zhao , Wu Lixin 
Published: April 2013

Abstract
Transformation and formation rates of water masses in the Southern Ocean are estimated in a neutral-surface framework using air–sea fluxes of heat and freshwater together with in situ estimates of diapycnal mixing. The air–sea fluxes are taken from two different climatologies and a reanalysis dataset, while the diapycnal mixing is estimated from a mixing parameterization applied to five years of Argo float data. Air–sea fluxes lead to a large transformation directed toward lighter waters, typically from −45 to −63 Sv (1 Sv ≡ 106 m3 s−1) centered at γ = 27.2, while interior diapycnal mixing leads to two weaker peaks in transformation, directed toward denser waters, 8 Sv centered at γ = 27.8, and directed toward lighter waters, −16 Sv centered at γ = 28.3. Hence, air–sea fluxes and interior diapycnal mixing are important in transforming different water masses within the Southern Ocean. The transformation of dense to lighter waters by diapycnal mixing within the Southern Ocean is slightly larger, though comparable in magnitude, to the transformation of lighter to dense waters by air–sea fluxes in the North Atlantic. However, there are significant uncertainties in the authors' estimates with errors of at least ±5 W m−2 in air–sea fluxes, a factor 4 uncertainty in diapycnal mixing and limited coverage of air–sea fluxes in the high latitudes and Argo data in the Pacific. These water mass transformations partly relate to the circulation in density space: air–sea fluxes provide a general lightening along the core of the Antarctic Circumpolar Current and diapycnal diffusivity is enhanced at middepths along the current.
Logic and the Self: After Certain Crises in Western Thought
Authors: van Fraassen Bas C 
Published: April 2013

AbstractDelivered on the occasion of the 2009 “Giulio Preti Prize”, this lecture examines and questions the contrast between the sense of intellectual crisis in the scientific world of the first decades of the 20th century and the absence of any such sense of crisis in current philosophy. Starting in the 19the century, we were confronted with changes in perspective that affected our relation to the universe we live in as well as to our own language and logic. Not only how we see ourselves but the tools by means of which we think about ourselves came into question. How would it be possible to rationally assess conceptual change that affects the very form of reasoning by which we assesssuch changes? Such are the paradoxes to which philosophers and scientists, in the throes of crisis in the first half of the 20th century, tried to respond. Philosophers today may seemingly have overcome those aporias that vexed their recent predecessors, in denial of the existence of a crisis that should actually be a fecund source for reflection.
Long-term prevention of chronic allograft rejection by regulatory T-cell immunotherapy involves host Foxp3-expressing T cells
Authors: Pasquet Lise , Douet Jean-Yves , Sparwasser Tim , Romagnoli Paola , van Meerwijk Joost P. M. 
Published: April 2013

Key PointsAdministration of donor-specific regulatory T cells prevents chronic rejection of BM and skin allografts in the mouse. Injected regulatory T cells induce the emergence of host regulatory T cells with similar specificity thus ensuring persistence of tolerance.
Downregulation of FOXP1 is required during germinal center B-cell function
Authors: Sagardoy Ainara , Martinez-Ferrandis Jose I. , Roa Sergio , Bunting Karen L. , Aznar María Angela , Elemento Olivier , Shaknovich Rita , Fontán Lorena , Fresquet Vicente , Perez-Roger Ignacio , Robles Eloy F. , De Smedt Linde , Sagaert Xavier , Melnick Ari , Martinez-Climent Jose A. 
Published: April 2013

Key Points
FOXP1 is downregulated in germinal centers, inversely to BCL6, whereby it regulates a network of genes, half of which are also BCL6 targets. In transgenic mice, constitutive FOXP1 expression impairs GC formation and function, which might contribute to B-cell lymphomagenesis.
Identification and characterization of lysine-rich proteins and starch biosynthesis genes in the opaque2mutant by transcriptional and proteomic analysis
Authors: Jia Mo , Wu Hao , Clay Kasi L , Jung Rudolf , Larkins Brian A , Gibbon Bryan C 
Published: April 2013

AbstractBackgroundTheopaque2mutant is valuable for producing maize varieties with enhanced nutritional value. However, the exact mechanisms by which it improves protein quality and creates a soft endosperm texture are unclear. Given the importance of improving nutritional quality in grain crops, a better understanding of the physiological basis for these traits is necessary.ResultsIn this study, we combined transcript profiling and proteomic analysis to better understand which genes and proteins are altered byopaque2in the W64A inbred line. These analyses showed that the accumulation of some lysine-rich proteins, such as sorbitol dehydrogenase and glyceraldehyde3-phosphate dehydrogenase, was increased in mature kernels and may contribute substantially to the lysine content ofopaque2endosperm. Some defense proteins such as beta-glucosidase aggregating factor were strongly down regulated and may be regulated directly byopaque2. The mutant also had altered expression of a number of starch biosynthesis genes and this was associated with a more highly crystalline starch.ConclusionsThe results of these studies revealed specific target genes that can be investigated to further improve nutritional quality and agronomic performance of high lysine maize lines, particularly those based on the presence of theopaque2mutation. Alteration of amylopectin branching patterns inopaque2starch could contribute to generation of the soft, starchy endosperm.
Best proximity point theorems for rational proximal contractions
Authors: Nashine Hemant Kumar , Kumam Poom , Vetro Calogero 
Published: April 2013

Abstract
We provide sufficient conditions which warrant the existence and uniqueness of the best proximity point for two new types of contractions in the setting of metric spaces. The presented results extend, generalize and improve some known results from best proximity point theory and fixed-point theory. We also give some examples to illustrate and validate our definitions and results.

MSC:41A65, 46B20, 47H10.
Clinical and molecular characterization of 40 patients with classic Ehlers–Danlos syndrome: identification of 18 COL5A1 and 2 COL5A2 novel mutations
Authors: Ritelli Marco , Dordoni Chiara , Venturini Marina , Chiarelli Nicola , Quinzani Stefano , Traversa Michele , Zoppi Nicoletta , Vascellaro Annalisa , Wischmeijer Anita , Manfredini Emanuela , Garavelli Livia , Calzavara-Pinton Piergiacomo , Colombi Marina 
Published: April 2013

Abstract

Background
Classic Ehlers–Danlos syndrome (cEDS) is a rare autosomal dominant connective tissue disorder that is primarily characterized by skin hyperextensibility, abnormal wound healing/atrophic scars, and joint hypermobility. A recent study demonstrated that more than 90% of patients who satisfy all of these major criteria harbor a type V collagen (COLLV) defect.

Methods
This cohort included 40 patients with cEDS who were clinically diagnosed according to the Villefranche nosology. The flowchart that was adopted for mutation detection consisted of sequencing the COL5A1 gene and, if no mutation was detected, COL5A2 analysis. In the negative patients the presence of large genomic rearrangements in COL5A1 was investigated using MLPA, and positive results were confirmed via SNP-array analysis.

Results
We report the clinical and molecular characterization of 40 patients from 28 families, consisting of 14 pediatric patients and 26 adults. A family history of cEDS was present in 9 patients. The majority of the patients fulfilled all the major diagnostic criteria for cEDS; atrophic scars were absent in 2 females, skin hyperextensibility was not detected in a male and joint hypermobility was negative in 8 patients (20% of the entire cohort). Wide inter- and intra-familial phenotypic heterogeneity was observed. We identified causal mutations with a detection rate of approximately 93%. In 25/28 probands, COL5A1 or COL5A2 mutations were detected. Twenty-one mutations were in the COL5A1 gene, 18 of which were novel (2 recurrent). Of these, 16 mutations led to nonsense-mediated mRNA decay (NMD) and to COLLV haploinsufficiency and 5 mutations were structural. Two novel COL5A2 splice mutations were detected in patients with the most severe phenotypes. The known p. (Arg312Cys) mutation in the COL1A1 gene was identified in one patient with vascular-like cEDS.

Conclusions
Our findings highlight that the three major criteria for cEDS are useful and sufficient for cEDS clinical diagnosis in the large majority of the patients. The borderline patients for whom these criteria fail can be diagnosed when minor signs of connective tissue diseases and family history are present and when genetic testing reveals a defect in COLLV. Our data also confirm that COL5A1 and COL5A2 are the major, if not the only, genes involved in cEDS.