bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of regression confidence intervals and Bayesian credible intervals for uncertainty quantification
Authors: Lu Dan , Ye Ming , Hill Mary C.
Published: July 2012

Confidence intervals based on classical regression theories augmented to include prior information and credible intervals based on Bayesian theories are conceptually different ways to quantify parametric and predictive uncertainties. Because both confidence and credible intervals are used in environmental modeling, we seek to understand their differences and similarities. This is of interest in part because calculating confidence intervals typically requires tens to thousands of model runs, while Bayesian credible intervals typically require tens of thousands to millions of model runs. Given multi‐Gaussian distributed observation errors, our theoretical analysis shows that, for linear or linearized‐nonlinear models, confidence and credible intervals are always numerically identical when consistent prior information is used. For nonlinear models, nonlinear confidence and credible intervals can be numerically identical if parameter confidence regions defined using the approximate likelihood method and parameter credible regions estimated using Markov chain Monte Carlo realizations are numerically identical and predictions are a smooth, monotonic function of the parameters. Both occur if intrinsic model nonlinearity is small. While the conditions of Gaussian errors and small intrinsic model nonlinearity are violated by many environmental models, heuristic tests using analytical and numerical models suggest that linear and nonlinear confidence intervals can be useful approximations of uncertainty even under significantly nonideal conditions. In the context of epistemic model error for a complex synthetic nonlinear groundwater problem, the linear and nonlinear confidence and credible intervals for individual models performed similarly enough to indicate that the computationally frugal confidence intervals can be useful in many circumstances. Experiences with these groundwater models are expected to be broadly applicable to many environmental models. We suggest that for environmental problems with lengthy execution times that make credible intervals inconvenient or prohibitive, confidence intervals can provide important insight. During model development when frequent calculation of uncertainty intervals is important to understanding the consequences of various model construction alternatives and data collection strategies, strategic use of both confidence and credible intervals can be critical.
Climate‐driven variability in lake and wetland distribution across the Prairie Pothole Region: From modern observations to long‐term reconstructions with space‐for‐time substitution
Authors: Liu Ganming , Schwartz Franklin W.
Published: July 2012

This study was designed (1) to explore the links between climate variability and the population dynamics of closed‐basin surface water bodies of the Prairie Pothole Region (PPR) in North America, and (2) to test the validity of space‐for‐time (SFT) substitution approach for the analysis of hydrologic systems. Observational results from 1981 to 2000 show that the climate with respect to annual residual moisture (ε, i.e., precipitation minus potential evaporation or evapotranspiration) of the PPR changed across space (over 0.6 m) and time (over 0.3 m in central North Dakota), causing spatiotemporal variability in water areas and water body numbers. Spatial analysis of a suite of surface water complexes along a spatial ε gradient in the Missouri Coteau shows that a four parameter Boltzmann function quantitatively describes how the number of water bodies (N) varied as a function of 5‐year average annualε (R2 = 0.76). Temporal analysis of monthly N data (1931–2005) reconstructed by a hydrologic model also demonstrates that values of temporally varying N were highly correlated with εand yielded a nearly identical Boltzmann function. This result confirms the validity of SFT substitution and suggests that detailed modern spatial data can be used to interpret hydrologic system behaviors under past or future climate conditions. This study also has important regional‐scale implications for water resources management by providing a complete picture of the spatiotemporal water body distribution across the entire PPR and the potential for rapidly converting climate predictions into surface water assessments.
Pyrrhotite as a tracer for denudation of the Taiwan orogen
Authors: Horng Chorng‐Shern , Huh Chih‐An , Chen Kuo‐Hang , Lin Chun‐Hung , Shea Kai‐Shuan , Hsiung Kan‐Hsi
Published: July 2012

The use of pyrrhotite as an index mineral to delineate metamorphic isograds has long been proposed. However, details of the occurrence of pyrrhotite in different metamorphic facies and its implications have rarely been explored. Here, by simple characterization of magnetic properties and mineral identification, we demonstrate that pyrrhotite is widely distributed in low‐grade metamorphic terranes of Taiwan's Central Range and in sediments derived therefrom. By coupling the distribution of pyrrhotite in rocks with that in dated sediment strata, we have studied the denudation history of Taiwan's orogen from a source‐to‐sink perspective. We suggest that pyrrhotite is a potential tracer for studying surface processes in orogens with high denudation rates similar to that in Taiwan.
Nonlinear climate response to regional brightening of tropical marine stratocumulus
Authors: Hill Spencer , Ming Yi
Published: July 2012

To counteract global warming, there have been suggestions to increase the albedo of low‐level marine clouds through the aerosol indirect effects by injecting them with sea salt. However, the full climate response to this geoengineering scheme is currently poorly understood. We simulate cloud seeding in a coupled mixed‐layer ocean‐atmosphere general circulation model in order to identify the specific physical mechanisms through which seeding could perturb the climate system's radiative balance, and cause temperature and precipitation changes. Seeding stratocumulus decks over three tropical maritime regions in the North Pacific, South Pacific and South Atlantic produces strong local reductions in solar absorption. Over half of the radiative cooling is due to direct scattering of solar radiation by the added sea salt aerosols, while the rest comes from enhancement of the local cloud albedo. The oceanic cooling due to the seeding over the southeastern equatorial Pacific induces a La Niña‐like response, with tropical precipitation changes resembling La Niña anomalies and teleconnections occurring in the mid‐latitude North Pacific and North America. Additionally, model runs in which only one of the three regions is seeded indicate nonlinearity in the climate response. We identify dynamical and thermodynamical constraints respectively on the temperature and hydrological cycle responses to cloud seeding, but the full response to such geoengineering remains poorly constrained.
The role of shortwave radiation in the 2007 Arctic sea ice anomaly
Authors: Nussbaumer Eric A. , Pinker Rachel T.
Published: July 2012

Recent satellite and re‐analysis model results on downwelling surface shortwave (DSSW) radiation allow the investigation of its role in the Arctic sea ice anomalies. Using satellite based information we revisit claims that reduced cloudiness and enhanced DSSW are associated with the significant loss of sea ice during 2007. We account for the fact that the Arctic Ocean is not homogenous in terms of the characteristics of the sea ice anomalies. We separate the Arctic Ocean region according to the spatial distribution of the sea ice anomalies and investigate the impact of DSSW on the ice conditions accordingly. The region which exhibits the strongest signal during the unprecedented 2007 reduction in sea ice is identified as 120°E to 210°E. Our analysis shows that the lowest cloud amount and the highest accumulated amount of DSSW prior to the ice melt season (June) occur in 2005. For 2007, areas showing the largest accumulation of DSSW do not correspond with negative sea ice concentration anomalies.
Particle acceleration and generation of diffuse superthermal ions at a quasi‐parallel collisionless shock: Hybrid simulations
Authors: Su Yanqing , Lu Quanming , Huang Can , Wu Mingyu , Gao Xinliang , Wang Shui
Published: July 2012

A large scale one‐dimensional hybrid simulation is performed to investigate the generation mechanism of diffuse superthermal ions at a high Mach number quasi‐parallel collisionless shock. The shock exhibits a cyclic behavior and reforms periodically. The generation of the diffuse ions is associated with the reformation of the shock. At the beginning of the reformation cycle, a part of ions are reflected by the shock due to the existence of the cross shock potential. At the same time, an upstream wave is brought back by the upstream plasma and interacts with the shock. The upstream wave begins to steepen as it approaches the shock, and then a new shock front is formed. The reflected ions are trapped between the new and old shock fronts. They are accelerated every time they are reflected by the new shock front until the reformation cycle of the shock is finished and the particles escape from the shock. In this way, diffuse superthermal ions are generated in the quasi‐parallel shock, which may be further accelerated to higher energy due to shock diffusive acceleration.
Pathways of shelf water export from the Hatteras shelf and slope
Authors: Churchill James H. , Gawarkiewicz Glen G.
Published: July 2012

It has long been recognized that a massive flow of Middle Atlantic Bight (MAB) shelf water is exported to the deep ocean in the region near Cape Hatteras, North Carolina. We examine the details of this export using data from an extensive array of 26 moorings, deployed over the shelf and slope between Cape Hatteras and the Chesapeake Bay mouth (from 35° 27′ to 36° 40′ N) as part of the U.S. Department of Energy's Ocean Margins Program. Our analysis indicates that the flow of the MAB shelf‐edge frontal jet, which typically extends over the MAB slope, falls victim to export over the length of the mooring array, essentially vanishing by the southern extreme of the array. By contrast, the flow of MAB shelf water entering the study region over the inner and middle shelf (to roughly the 40‐m isobath) tends to experience very little loss over the extent of the OMP array. Based on our findings and those of previous studies, we hypothesize that this inner and middle shelf flow is diverted seaward upon encountering the Hatteras Front, which separates MAB and South Atlantic Bight shelf waters. Some fraction of this flow appears to return to the OMP array, moving northeastward over the upper slope en route to the deep ocean. Our analysis also suggests that the export of MAB shelf water is enhanced as the Gulf Stream approaches the shelf‐edge near Diamond Shoals, a process we deem to be a high priority for future study.
On the validation effort of the Coupled Thermosphere Ionosphere Plasmasphere Electrodynamics model
Authors: Negrea C. , Codrescu M. V. , Fuller‐Rowell T. J.
Published: July 2012

The Coupled Thermosphere Ionosphere Plasmasphere electrodynamics model (CTIPe) has proven to be a valuable ionospheric research tool. Improving our knowledge of systematic and seasonal model biases is necessary if further improvements are to be made. This paper presents the next step in our verification and validation effort and in developing a standardized analysis methodology. A semi‐automated software part of the near‐real‐time‐run of CTIPe is described and results derived from its usage are presented. Model limitations and biases are detailed for the electron density profile peak (NmF2) and its corresponding height (hmF2). Model performance for hmF2 is constant throughout the whole year, with an average 10% deviation from observed values. There is a strong seasonal variation for NmF2, with greater deviations from the observed trends during summer. This effect seems to have latitude dependence, although the gaps in the available data do not allow for an exact determination of its nature.
A half‐century after the molecular clock: new dimensions of molecular evolution
Authors: Koonin Eugene V
Published: July 2012

The EMBO workshop on ‘Evolution in the Time of Genomics’ took place in May 2012 in the magnificent sixteenth century Palazzo Franchetti near Ponte dell'Accademia in Venice. The meeting focused on phenomena that are not part of the traditional narrative of molecular evolution and which might signal a paradigm shift in the field.
Involvement of the renin–angiotensin system in abdominal and thoracic aortic aneurysms
Authors: Lu Hong , Rateri Debra L. , Bruemmer Dennis , Cassis Lisa A. , Daugherty Alan
Published: July 2012

Aortic aneurysms are relatively common maladies that may lead to the devastating consequence of aortic rupture. AAAs (abdominal aortic aneurysms) and TAAs (thoracic aortic aneurysms) are two common forms of aneurysmal diseases in humans that appear to have distinct pathologies and mechanisms. Despite this divergence, there are numerous and consistent demonstrations that overactivation of the RAS (renin–angiotensin system) promotes both AAAs and TAAs in animal models. For example, in mice, both AAAs and TAAs are formed during infusion of AngII (angiotensin II), the major bioactive peptide in the RAS. There are many proposed mechanisms by which the RAS initiates and perpetuates aortic aneurysms, including effects of AngII on a diverse array of cell types and mediators. These experimental findings are complemented in humans by genetic association studies and retrospective analyses of clinical data that generally support a role of the RAS in both AAAs and TAAs. Given the lack of a validated pharmacological therapy for any form of aortic aneurysm, there is a pressing need to determine whether the consistent findings on the role of the RAS in animal models are translatable to humans afflicted with these diseases. The present review compiles the recent literature that has shown the RAS as a critical component in the pathogenesis of aortic aneurysms.
Eine Orthopädin forscht mit dem Klavier
Authors: Pancur Sarah
Published: July 2012

Die Leiterin des Integrationszentrums für Cerebralparesen in München, Professor Reneé Lampe, erforscht mit einem Klavierprojekt die Neuroplastizität des Gehirns bei Kindern mit Gehirnschädigung.
The Causes of Iran's 1953 Coup: A Critique of Darioush Bayandor's Iran and the CIA
Authors: Gasiorowski Mark J.
Published: July 2012

This article presents a detailed criticism of Darioush Bayandor's book Iran and the CIA. Bayandor argues that certain Shi'a clerics, rather than the US Central Intelligence Agency, were the main actors responsible for overthrowing Iranian Prime Minister Mohammad Mosaddeq in August 1953. Bayandor presents no major new evidence to support this claim. He gives too much weight to certain statements, draws unwarranted inferences from others, and discounts or disregards a wealth of evidence that conflicts with his account. He overemphasizes the role of civilian crowds in the overthrow of Mosaddeq and underemphasizes the role of Iranian military units organized by the CIA. And he fails to acknowledge the importance of US and especially British efforts to foment opposition to Mosaddeq before the coup.
Interactive Field Site Visits Can Help Students Translate Scientific Studies into Contextual Understanding
Authors: Burt J M , Donaldson M R , Hruska K A , Hinch S G , Richardson J S
Published: July 2012

This article describes how the interactive learning methods employed during a short (1.5 h) class visit to a nearby stream engaged undergraduate students in their own exploration of riparian ecology. We describe how the use of a published field study conducted at this stream site served as an effective learning tool to help students contextualize ecological research-based findings. During the outing, students worked in groups using a “stream station worksheet” and participated in facilitated discussions to relate their observations to the findings of the published field study. An anonymous survey of students Opinions after the site visit revealed positive responses, reflecting success in achieving the desired learning objectives. We discuss how the site visit has been enhanced from previous years to increase effective student learning and how this type of activity could be applied to other ecology or fisheries courses by utilizing appropriately chosen local research.

RESUMEN

En este artículo se describe cómo la aplicación de métodos interactivos de aprendizaje, durante visitas guiadas en clase (1.5 h de duración) a un arroyo natural, capta la atención de los estudiantes de licenciatura en cuanto a su capacidad de exploración de la ecología ripariana. Se describe también cómo una publicación sobre un estudio realizado en el sitio visitado, sirve como una herramienta efectiva de aprendizaje para ayudar a los estudiantes a poner en contexto los resultados del estudio ecológico. Durante la excursión, los estudiantes trabajaron en grupos usando hojas de referencia con estaciones de muestreo y participaron a través de discusiones en las que relacionaban sus observaciones con los resultados encontrados en el estudio. Un sondeo de opiniones anónimas aplicado a los estudiantes después de la salida de campo, reveló que las respuestas reflejaron el cumplimiento exitoso de los objetivos de aprendizaje. Se discute cómo las salidas de campo han ido mejorando en el tiempo en cuanto a la efectividad en el aprendizaje de los estudiantes, y cómo este tipo de actividades pudieran aplicarse a otros cursos de ecología y pesquerías, utilizando investigaciones locales.
Cofinality and measurability of the first three uncountable cardinals
Authors: Apter Arthur , Jackson Stephen , Löwe Benedikt
Published: July 2012

This paper discusses models of set theory without the Axiom of Choice. We investigate all possible patterns of the cofinality function and the distribution of measurability on the first three uncountable cardinals. The result relies heavily on a strengthening of an unpublished result of Kechris: we prove (under

A
D

\mathsf {AD}

) that there is a cardinal

κ
\kappa

such that the triple

(
κ
,

κ
+

,

κ

+
+

)

(\kappa ,\kappa ^+,\kappa ^{++})

satisfies the strong polarized partition property.
CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis
Authors: Li Pei , Ji Guoli , Dong Min , Schmidt Emily , Lenox Douglas , Chen Liangliang , Liu Qi , Liu Lin , Zhang Jie , Liang Chun
Published: July 2012

Summary: To address the impending need for exploring rapidly increased transcriptomics data generated for non-model organisms, we developed CBrowse, an AJAX-based web browser for visualizing and analyzing transcriptome assemblies and contigs. Designed in a standard three-tier architecture with a data pre-processing pipeline, CBrowse is essentially a Rich Internet Application that offers many seamlessly integrated web interfaces and allows users to navigate, sort, filter, search and visualize data smoothly. The pre-processing pipeline takes the contig sequence file in FASTA format and its relevant SAM/BAM file as the input; detects putative polymorphisms, simple sequence repeats and sequencing errors in contigs and generates image, JSON and database-compatible CSV text files that are directly utilized by different web interfaces. CBowse is a generic visualization and analysis tool that facilitates close examination of assembly quality, genetic polymorphisms, sequence repeats and/or sequencing errors in transcriptome sequencing projects.

Availability: CBrowse is distributed under the GNU General Public License, available at http://bioinfolab.muohio.edu/CBrowse/

Contact:  liangc@muohio.edu or liangc.mu@gmail.com; glji@xmu.edu.cn

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Association of QRS duration with left ventricular structure and function and risk of heart failure in middle‐aged and older adults: the Multi‐Ethnic Study of Atherosclerosis (MESA)
Authors: Ilkhanoff Leonard , Liu Kiang , Ning Hongyan , Nazarian Saman , Bluemke David A. , Soliman Elsayed Z. , Lloyd‐Jones Donald M.
Published: July 2012

Aims

Prolonged QRS duration (QRSd) on the electrocardiogram (ECG) has been associated with cardiac structural and functional abnormalities by echocardiography and an increased risk of heart failure (HF). Data are sparse on these relationships in middle‐aged and elderly individuals free of baseline cardiovascular disease with respect to cardiac magnetic resonance imaging (MRI). We sought to determine whether QRSd is associated with incident HF and measures of cardiac structure and function by cardiac MRI.

Methods and results

We analysed baseline ECGs in the Multi‐Ethnic Study of Atherosclerosis (MESA) to determine whether QRSd >100 ms was associated with incident HF. We adjusted for demographic and clinical risk factors, as well as MRI measures of left ventricular (LV) structure and function. Among 4591 eligible participants (51% women; 39% white; mean age 61 years), 75 developed incident HF over a mean follow‐up of 7.1 years. QRSd >100 ms was significantly associated with MRI measures of cardiac structure and function, as well as incident HF, even after adjustment for demographic covariates [hazard ratio (HR) 2.10, 95% confidence interval (CI) 1.29–3.42; P = 0.003] and clinical risk factors (HR 1.86, 95% CI 1.14–3.03; P = 0.01). With further adjustment for individual LV structural measures, findings were attenuated to non‐significance. Separate adjustment for LV functional measures yielded only mild attenuation.

Conclusion

In middle‐aged and older adults without cardiovascular disease, a QRSd >100 ms was significantly associated with incident HF. After adjustment for LV structural measures, the association was attenuated to non‐significance, suggesting that prolonged QRSd is potentially a useful marker of LV structure that may predispose to HF risk.
Expression of the chloroplast thioredoxins f and m is linked to short-term changes in the sugar and thiol status in leaves of Pisum sativum
Authors: Barajas-López Juan de Dios , Tezycka Justyna , Travaglia Claudia N , Serrato Antonio Jesús , Chueca Ana , Thormählen Ina , Geigenberger Peter , Sahrawy Mariam
Published: July 2012

Thioredoxins (TRXs) f and m are key components in the light regulation of photosynthetic metabolism via thiol–dithiol modulation in chloroplasts of leaves; however, little is known about the factors modulating the expression of these proteins. To investigate the effect of sugars as photosynthetic products on the expression of PsTRX f and m1 genes, sucrose and glucose were externally supplied to pea plants during the day. There was an increase in the mRNA levels of PsTRX f and m1 genes in response mainly to glucose. When leaf discs were incubated for up to 4h in the dark, glucose also led to an increase in both mRNA and protein levels of TRXs f and m, while sucrose had no substantial effect. Expression of PsDOF7, a carbon metabolism-related transcription factor gene, was also induced by glucose. Protein–DNA interaction showed that PsDOF7 binds specifically to the DOF core located in PsTRX f and m1 gene promoters. Transient expression in agroinfiltrated pea leaves demonstrated that PsDOF7 activated transcription of both promoters. The incubation of leaf discs in dithiotreitol (DTT) to increase the redox status led to a marked increase in the mRNA and protein levels of both TRXs within 4h. The increase in TRX protein levels occurred after 1h DTT feeding, implying a rapid effect of the thiol status on TRX f and m1 protein turnover rates, while transcriptional regulation took 3h to proceed. These results show that the protein levels of both TRXs are under short-term control of the sugar and thiol status in plants.
A Mixture Model for Middle Category Inflation in Ordered Survey Responses
Authors: Bagozzi Benjamin E. , Mukherjee Bumba
Published: July 2012

Recent research finds that, for social desirability reasons, uninformed individuals disproportionately give “neither agree nor disagree” type responses to survey attitude questions, even when a “do not know” option is available. Such “face-saving” responses inflate the indifference (i.e., middle) categories of ordered attitude variables with nonordered responses. When such inflation occurs within the middle category of one's ordered dependent variable, estimates from ordered probit (and ordered logit) models are likely to be unreliable and inefficient. This article develops a set of mixture models that estimate and account for the presence of “face-saving” responses in middle categories of ordered survey response variables, and applies these models to (1) simulated data and (2) a commonly studied survey question measuring attitudes toward European Union (EU) membership among individuals in EU-candidate countries. Results from the survey data set and the Monte Carlo experiments suggest that, when middle category inflation is present in one's ordered dependent variable, the estimates obtained from middle category mixture models are less biased than—and in some cases substantively distinct from—the estimates obtained from “naive” ordered probit models.
Effect of Perioperative Oxygen Supplementation on 30-day Surgical Site Infection Rate in Abdominal, Gynecologic, and Breast Surgery
Authors: Thibon Pascal , Borgey France , Boutreux Sébastien , Hanouz Jean-Luc , Le Coutour Xavier , Parienti Jean-Jacques
Published: July 2012

Background

Benefits and limitations of supplementation with 80% fraction of inspired oxygen for preventing surgical site infections have not yet been clearly defined. Some studies have reported benefits in colorectal surgery, whereas trials in abdominal and gynecologic surgery have reported either no effect or a deleterious effect.

Methods

Controlled, randomized, assessor-blind multicenter trial, the ISO2 study, comparing the effects of hyperoxygenation (fraction of inspired oxygen, 80%) with those of 30% oxygen on the frequency of surgical site infections in routine abdominal, gynecologic, and breast surgery on 434 patients. Patients not seen in consultation after discharge were contacted.

Results

In total, 208 patients received 30% perioperative oxygen and 226 received 80%. There was no difference between the two groups for baseline, intraoperative, and postoperative characteristics, except for oxygen saturation at closure, higher in the 80% group (P=0.01). The frequency of 30-day surgical site infections was 7.2% (15/208) in the 30% group and 6.6% (15/226) in the 80% group (relative risk, 0.92; 95% CI [0.46-1.84], P=0.81). Frequency of adverse events (nausea and vomiting, sternal pain, cough, hypotension) was similar in the two groups. Desaturation and bradycardia were more frequent in the 30% group. In an updated meta-analysis including the result of this trial and those of eight published randomized trials, the overall relative risk was 0.97; 95% CI (0.68-1.40), I2 (inconsistency degree)=73%, (P=0.88).

Conclusions

The routine use of hyperoxygenation throughout abdominal, gynecologic, and breast surgery had no effect on the frequency of 30-day surgical site infections and was not accompanied by more frequent adverse effects.
Isolation of Hokkaido virus, genus Hantavirus, using a newly established cell line derived from the kidney of the grey red-backed vole (Myodes rufocanus bedfordiae)
Authors: Sanada Takahiro , Seto Takahiro , Ozaki Yuka , Saasa Ngonda , Yoshimatsu Kumiko , Arikawa Jiro , Yoshii Kentaro , Kariwa Hiroaki
Published: July 2012

Hantaviruses belong to the family Bunyaviridae and are maintained in wild rodents. Although Vero E6 cells, which originate from African green monkey kidney, are used widely in hantavirus research, isolation of hantaviruses from this cell line is difficult. To develop an efficient method of propagation and isolation of hantaviruses we established a novel cell line, MRK101, derived from the kidney of the grey red-backed vole (Myodes rufocanus bedfordiae), the natural host of Hokkaido virus (HOKV). The MRK101 cells showed a significantly higher susceptibility to Puumala virus (PUUV) hosted by Myodes glareolus than Vero E6 cells. Viral nucleocapsid protein in PUUV-infected MRK101 cells was detected earlier than in Vero E6 cells, and the viral titre in the culture fluid of MRK101 cells was higher than that of Vero E6 cells during the early phase of infection. In contrast, MRK101 cells showed no susceptibility to Hantaan virus. HOKV, which has not been isolated to date, was isolated successfully using MRK101 cells. Moreover, the newly isolated HOKV was successfully propagated in MRK101, but not Vero E6, cells. Phylogenic analyses of the S (small), M (medium) and L (large) segment sequences revealed that HOKV is related most closely to PUUV, but is distinct from other hantaviruses. These data suggest that the MRK101 cell line is a useful tool for the isolation and propagation of hantaviruses. Moreover, this is (to our knowledge) the first report of hantavirus isolation in a cell line that originated from the natural host.
Toward Stable Genetic Engineering of Human O-Glycosylation in Plants
Authors: Yang Zhang , Bennett Eric P. , Jørgensen Bodil , Drew Damian P. , Arigi Emma , Mandel Ulla , Ulvskov Peter , Levery Steven B. , Clausen Henrik , Petersen Bent L.
Published: July 2012

Glycosylation is the most abundant and complex posttranslational modification to be considered for recombinant production of therapeutic proteins. Mucin-type (N-acetylgalactosamine [GalNAc]-type) O-glycosylation is found in eumetazoan cells but absent in plants and yeast, making these cell types an obvious choice for de novo engineering of this O-glycosylation pathway. We previously showed that transient implementation of O-glycosylation capacity in plants requires introduction of the synthesis of the donor substrate UDP-GalNAc and one or more polypeptide GalNAc-transferases for incorporating GalNAc residues into proteins. Here, we have stably engineered O-glycosylation capacity in two plant cell systems, soil-grown Arabidopsis (Arabidopsis thaliana) and tobacco (Nicotiana tabacum) Bright Yellow-2 suspension culture cells. Efficient GalNAc O-glycosylation of two stably coexpressed substrate O-glycoproteins was obtained, but a high degree of proline hydroxylation and hydroxyproline-linked arabinosides, on a mucin (MUC1)-derived substrate, was also observed. Addition of the prolyl 4-hydroxylase inhibitor 2,2-dipyridyl, however, effectively suppressed proline hydroxylation and arabinosylation of MUC1 in Bright Yellow-2 cells. In summary, stably engineered mammalian type O-glycosylation was established in transgenic plants, demonstrating that plants may serve as host cells for the production of recombinant O-glycoproteins. However, the present stable implementation further strengthens the notion that elimination of endogenous posttranslational modifications may be needed for the production of protein therapeutics.
Characterization of SOC1’s Central Role in Flowering by the Identification of Its Upstream and Downstream Regulators
Authors: Immink Richard G.H. , Posé David , Ferrario Silvia , Ott Felix , Kaufmann Kerstin , Valentim Felipe Leal , de Folter Stefan , van der Wal Froukje , van Dijk Aalt D.J. , Schmid Markus , Angenent Gerco C.
Published: July 2012

The transition from vegetative to reproductive development is one of the most important phase changes in the plant life cycle. This step is controlled by various environmental signals that are integrated at the molecular level by so-called floral integrators. One such floral integrator in Arabidopsis (Arabidopsis thaliana) is the MADS domain transcription factor SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1). Despite extensive genetic studies, little is known about the transcriptional control of SOC1, and we are just starting to explore the network of genes under the direct control of SOC1 transcription factor complexes. Here, we show that several MADS domain proteins, including SOC1 heterodimers, are able to bind SOC1 regulatory sequences. Genome-wide target gene analysis by ChIP-seq confirmed the binding of SOC1 to its own locus and shows that it also binds to a plethora of flowering-time regulatory and floral homeotic genes. In turn, the encoded floral homeotic MADS domain proteins appear to bind SOC1 regulatory sequences. Subsequent in planta analyses revealed SOC1 repression by several floral homeotic MADS domain proteins, and we show that, mechanistically, this depends on the presence of the SOC1 protein. Together, our data show that SOC1 constitutes a major hub in the regulatory networks underlying floral timing and flower development and that these networks are composed of many positive and negative autoregulatory and feedback loops. The latter seems to be crucial for the generation of a robust flower-inducing signal, followed shortly after by repression of the SOC1 floral integrator.
A fast methodology to determine the characteristics of thousands of grains using three-dimensional X-ray diffraction. I. Overlapping diffraction peaks and parameters of the experimental setup
Authors: Sharma Hemant , Huizenga Richard M. , Offerman S. Erik
Published: July 2012

A data-analysis methodology is presented for the characterization of three-dimensional microstructures of polycrystalline materials from data acquired using three-dimensional X-ray diffraction (3DXRD). The method is developed for 3DXRD microscopy using a far-field detector and yields information about the centre-of-mass position, crystallographic orientation, volume and strain state for thousands of grains. This first part deals with pre-processing of the diffraction data for input into the algorithms presented in the second part [Sharma, Huizenga & Offerman (2012).J. Appl. Cryst.45, 705–718] for determination of the grain characteristics. An algorithm is presented for accurate identification of overlapping diffraction peaks from X-ray diffraction images, which has been an issue limiting the accuracy of experiments of this type. The algorithm works in two stages, namely the identification of overlapping peaks using a seeded watershed algorithm, and then the fitting of the peaks with a pseudo-Voigt shape function to yield an accurate centre-of-mass position and integrated intensity for the peaks. Regions consisting of up to six overlapping peaks can be successfully fitted. Two simulations and an experiment are used to verify the results of the algorithms. An example of the processing of diffraction images acquired in a 3DXRD experiment with a sample consisting of more than 1600 grains is shown. Furthermore, a procedure for the determination of the parameters of the experimental setup (global parameters) without the need for a calibration sample is presented and validated using simulations. This is immensely beneficial for simplifying experiments and the subsequent data analysis.
QPCED2.0: a computer program for the processing and quantification of polycrystalline electron diffraction patterns
Authors: Li Xing-Zhong
Published: July 2012

The processing and quantification of electron diffraction patterns have become vital in advanced electron crystallographic analysis work. A computer program,QPCED2.0, has been developed for the handling of selected-area electron diffraction patterns for polycrystalline materials.QPCED2.0can be used to enhance the visibility of electron diffraction patterns, to convert electron diffraction patterns into intensity profiles, and to retrieve precisely the latticedspacings and the integral intensities of the diffraction rings. The design and implementation ofQPCED2.0are elucidated and application examples are given.
1,3-Phenylene bis{3-[2-chloro-4-(trifluoromethyl)phenoxy]benzoate}
Authors: Peng Hao , He Hongwu
Published: July 2012

In the title compound, C34H18Cl2F6O6, one terminal trifluoromethyl and one entire 2-chloro-4-(trifluoromethyl)phenyl group are disordered with refined occupancy ratios of 0.715 (11):0.285 (11) and 0.517 (5):0.429 (5), respectively. In the crystal, weak intermolecular C—H...O hydrogen bonds link the molecules into ribbons propagating along thea-axis direction.
(2E,6E)-2,6-Bis(ferrocenylmethylidene)cyclohexanone dichloromethane monosolvate
Authors: Long Shi-Jia , Yang Wu , Liu Yong-Hong
Published: July 2012

In the title compound, [Fe2(C5H5)2(C18H16O)]·CH2Cl2, the C=C bonds both adoptEconformations. In one ferrocenyl group, the five-membered rings are in a near-eclipsed conformation, whereas in the other they are mutually rotated byca21.5°. The central cyclohexanone ring adopts a sofa conformation. In the crystal, the dichloromethane solvent moleucle forms C—H...O hydrogen bonds to the organometallic molecules to generate [010] chains of alternating solvent and organometallic species.
P,P′-Diphenylethylenediphosphinic acid dihydrate
Authors: Swor Charles D. , Nell Bryan P. , Zakharov Lev N. , Tyler David R.
Published: July 2012

The title compound, C14H16O4P2·2H2O, possesses a crystallographic inversion center where two –P(=O)(OH)(C6H5) groups are joined togetherviatwo –CH2groups. In the crystal, the acid molecules are linked by the water moleculesviaO—H...O hydrogen bonds, leading to the formation of a two-dimensional network lying parallel to (101).
3-Isopropyl-2,6-bis(4-methoxyphenyl)piperidin-4-one
Authors: Ravichandran K. , Sethuvasan S. , Thirunavukarasu K. , Ponnuswamy S. , Ponnuswamy M. N.
Published: July 2012

In the title compound, C22H27NO3, the piperidine ring adopts a slightly distorted chair conformation. The dihedral angle between the two aromatic rings is 60.4 (1)°. In the crystal, the amino group forms a rather long N—H...O contact to a methoxy O atom. There are also C—H...O interactions present.
1,8-Dibenzoylnaphthalene-2,7-diyl dibenzoate
Authors: Sakamoto Rei , Sasagawa Kosuke , Hijikata Daichi , Okamoto Akiko , Yonezawa Noriyuki
Published: July 2012

In the title compound, C38H24O6, the phenyl rings of the benzoyl and benzoyloxy groups make dihedral angles of 67.12 (5), 85.15 (5), 76.41 (5) and 71.47 (5)° with the naphthalene ring system. In the crystal, C—H...O hydrogen bonds link molecules into chains parallel to thebaxis. The structure also features C—H...π and π–π stacking interactions, with centroid–centroid distances in the range 3.6441 (7)–3.9197 (8) Å.
Diiodido[methyl 2-(quinolin-8-yloxy)acetate-κN]mercury(II)
Authors: Wang Yu-Hong , Zhong Qin , Song Rui-Feng
Published: July 2012

In the title mononuclear complex, [HgI2(C12H11NO3)], the HgIIion has a distorted trigonal–planar coordination sphere defined by two I−anions and the N atom of a methyl 2-(quinolin-8-yloxy)acetate ligand. In the crystal, face-to-face π–π stacking interactions, with a centroid–centroid distance of 3.563 (9) Å, are observed.
2-[(4-Methoxy-2-nitrophenyl)iminomethyl]phenol
Authors: Khalaji Aliakbar Dehno , Nikookar Mahsa , Fejfarová Karla , Dušek Michal
Published: July 2012

The crystal structure of the title compound, C14H12N2O4, contains four crystallographically independent molecules in the asymmetric unit. All the molecules have similar conformations; the dihedral angles between the aromatic rings are 33.1 (1), 33.76 (9), 31.41 (9) and 32.56 (10)°. Intramolecular O—H...N hydrogen bonds formS(6) ring motifs in each molecule. In the crystal, there are two pairs of pseudo-inversion-related molecules. Along thecaxis, molecules are stacked with π–π interactions between the 2-hydroxyphenyl and 4-methoxy-2-nitrophenyl rings [centroid–centroid distances = 3.5441 (12)–3.7698 (12) Å].
6-Aminonicotinamide
Authors: Ntsala Lerato P. , Lemmerer Andreas
Published: July 2012

In the title compound, C6H7N3O, the amide group is rotated such that the carbonyl O atom issynto the pyridine N atom, with an O—C—C—C torsion angle of −23.55 (18)°. The crystal packing involves four hydrogen bonds of the types N—H...N and N—H...O. Two separate centrosymmetric rings are formed using N—H...N and N—H...O hydrogen bonds that result in a ribbon of 6-aminonicotinamide molecules, joined by the amide and amine functional groups. The remaining two hydrogen bonds are used to generate a three-dimensional packing arrangement.
Poly[[aqua(μ2-4,4′-bipyridine-κ2N:N′)[μ3-3-bromo-2-(carboxylatomethyl)benzoato-κ3O1:O1′:O2]cadmium] monohydrate]
Authors: Liu Yangmei , Cao Kai , Wang Fenglin
Published: July 2012

In the title compound, {[Cd(C9H5BrO4)(C10H8N2)(H2O)]·H2O}n, the CdIIatom has a distorted octahedral coordination geometry. Two N atoms from two 4,4′-bipyridine (bipy) ligands occupy the axial positions, while the equatorial positions are furnished by three carboxylate O atoms from three 3-bromo-2-(carboxylatomethyl)benzoate (bcb) ligands and one O atom from a water molecule. The bipy and bcb ligands link the CdIIatoms into a three-dimensional network. O—H...O hydrogen bonds and π–π interactions between the pyridine and benzene rings [centroid–centroid distance = 3.736 (4) Å] are present in the crystal.
N-(2,4,6-Trimethylphenyl)-1,3-thiazol-2-amine
Authors: Babar Ayesha , Munawar Munawar Ali , Tahir M. Nawaz , Khan Ather Farooq , Tariq Muhammad Ilyas
Published: July 2012

In the title compound, C12H14N2S, the dihedral angle between the 1,3,5-trimethylbenzene and 1,3-thiazol-2-amine groups is 73.15 (4)°. In the crystal, inversion dimers linked by pairs of N—H...N hydrogen bonds generateR22(8) loops.
Bis(μ3-pyrimidine-4-carboxylato)bis(μ2-pyrimidine-4-carboxylato)tetrakis(aqualithium)
Authors: Starosta Wojciech , Leciejewicz Janusz
Published: July 2012

The asymmetric unit of the title compound, [Li4(C5H3N2O2)4(H2O)4], contains two symmetry-independent LiIions, two symmetry-independent ligands and two symmetry-independent coordinated water molecules. They form a dinuclear unit in which the two LiIions are bridged by two carboxylate O atoms from the two ligands. Two dinuclear units related by an inversion centre form the tetrameric molecule. One of the LiIions shows a distorted tetrahedral coordination geometry, the other a distorted trigonal–bipyramidal environment. The tetramers are held together by hydrogen bonds in which coordinated water molecules act as donors, and the carboxylate O atoms act as acceptors. A hydrogen bond between coordinated water molecule as donor and a ring N atom as acceptor is also observed.
Contribution of a harpin protein fromXanthomonas axonopodispv.citrito pathogen virulence
Authors: Sgro Germán G. , Ficarra Florencia A. , Dunger Germán , Scarpeci Telma E. , Valle Estela M. , Cortadi Adriana , Orellano Elena G. , Gottig Natalia , Ottado Jorgelina
Published: July 2012

Xanthomonas axonopodispv.citri(Xac), the bacterium that causes citrus canker, contains a gene in thehrp[for hypersensitive response (HR) and pathogenicity] cluster that encodes a harpin protein calledHpa1.Hpa1 producedHRin the nonhost plants tobacco, pepper andArabidopsis, whereas, in the host plant citrus, it elicited a weak defence response with no visible phenotype. Co‐infiltrations ofXac with or without the recombinantHpa1 protein in citrus leaves produced a larger number of cankers in the presence of the protein. To characterize the effect ofHpa1 during the disease, anXacΔhpa1 mutant was constructed, and infiltration of this mutant caused a smaller number of cankers. In addition, the lack ofHpa1 hindered bacterial aggregation both in solution andin planta. Analysis of citrus leaves infiltrated withHpa1 revealed alterations in mesophyll morphology caused by the presence of cavitations and crystal idioblasts, suggesting the binding of the harpin to plant membranes and the elicitation of signalling cascades. Overall, these results suggest that, even thoughHpa1 elicits the defence response in nonhost plants and, to a lesser extent, in host plants, its main roles in citrus canker are to alter leaf mesophyll structure and to aggregate bacterial cells, and thus increase virulence and pathogen fitness. We expressed theN‐terminal andC‐terminal regions and found that, although both regions elicitedHRin nonhost plants, only theN‐terminal region showed increased virulence and bacterial aggregation, supporting the role of this region of the protein as the main active domain.
‘He didn't mean to hit mom, I think’: positioning, agency and point in adolescents' narratives about domestic violence
Authors: Øverlien Carolina
Published: July 2012

This paper analyses the narratives of adolescents who have experienced domestic violence. It focuses on what we can learn about being an adolescent who experiences domestic violence, using a narrative approach. Attentive to both form and content, the paper sheds light on why the narrative is being told, who the actors in the narratives are, who are positioned in the forefront/background and what the point of the narrative is. The analysis shows that through the storytelling, the father's position as the reluctant/dangerous/weak aggressor is negotiated, the mother is positioned both in the background as a victim and in the forefront as an actor resisting his violent behaviour. The children position themselves as actors with power to alter the progress, to protect and stop the violence. The point of the narratives is to describe the father as the aggressor, and to describe the important role of the children. This picture of the father, mother and child questions the traditional understanding of the father as the aggressor, the mother as the victim and the child as a powerless bystander being exposed to the violence, and underlines the complexities of the dynamics in families living with domestic violence.
Type I interferon induces CX3CL1 (fractalkine) and CCL5 (RANTES) production in human pulmonary vascular endothelial cells
Authors: Nakano M , Fujii T , Hashimoto M , Yukawa N , Yoshifuji H , Ohmura K , Nakaizumi A , Mimori T
Published: July 2012

Type I interferon (IFN) medications cause various adverse reactions, including vascular diseases. Although an association between chemokines and vascular diseases has also been reported, the relationship between type I IFN and chemokines in vascular endothelial cells (VEC) remains unclear. To provide clues to pathogenesis of the diseases, we analysed the effects of type I IFN on chemokine production in human VEC. Type I IFN induced higher CX3CL1 (fractalkine) mRNA expression and protein secretion in pulmonary arterial VEC than in umbilical vein VEC. Type I IFN also induced CCL5 [regulated upon activation normal T cell expressed and secreted (RANTES)] production in VEC, especially in lung micro-VEC. IFN-β induced much higher chemokine production than IFN-α, and Janus protein tyrosine kinase (JAK) inhibitor I prevented type I IFN-induced chemokine secretion. Type I IFN-induced chemokines may be involved in the pathophysiology of pulmonary vascular diseases, and the JAK inhibitor may serve as a therapeutic option for these diseases.
Impact of spring upwelling variability off southern‐central Chile on common sardine (Strangomera bentincki) recruitment
Authors: GOMEZ FABIAN , MONTECINOS ALDO , HORMAZABAL SAMUEL , CUBILLOS LUIS A. , CORREA‐RAMIREZ MARCO , CHAVEZ FRANCISCO P.
Published: July 2012

Off southern‐central Chile, the impact of spring upwelling variability on common sardine (Strangomera bentincki) recruitment was examined by analyzing satellite and coastal station winds, satellite chlorophyll, and common sardine recruitment from a stock assessment model. In austral spring, the intensity of wind‐driven upwelling is related to sea surface temperature (SST) from the Niño 3.4 region, being weak during warm periods (El Niño) and strong during cold periods (La Niña). Interannual changes in both spring upwelling intensity and SST from the Niño 3.4 region are related to changes in remotely sensed chlorophyll over the continental shelf. In turn, year‐to‐year changes in coastal chlorophyll are tightly coupled to common sardine recruitment. We propose that, in the period 1991–2004, interannual changes in the intensity of spring upwelling affected the abundance and availability of planktonic food for common sardine, and consequently determined pre‐recruit survival and recruitment strength. However, the importance of density‐dependent factors on the reproductive dynamic cannot be neglected, as a negative association exists between spawning biomass and recruitment‐per‐spawning biomass. Coastal chlorophyll, upwelling intensity, and SST anomalies from the Niño 3.4 region could potentially help to predict common sardine recruitment scenarios under strong spring upwelling and El Niño Southern Oscillation (ENSO)‐related anomalies.