bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predictability Associated with Nonlinear Regimes in an Atmospheric Model
Authors: Peters John M. , Kravtsov Sergey , Schwartz Nicholas T. 
Published: October 2011

Abstract
Atmospheric regimes are midlatitude flow patterns that persist for periods of time exceeding a few days. Here, the authors analyzed the output of an idealized atmospheric model (QG3) to examine the relationship between regimes and predictability.
The regimes were defined as the regions of the QG3 phase subspace characterized by excess persistence probability relative to a benchmark linear empirical model (EMR) for geographically two-dimensional and then zonally averaged flow patterns. The regimes identified correspond to the opposite phases of the Arctic Oscillation (AO+ and AO−) and to a more regional pattern reflecting the positive phase of the North Atlantic Oscillation (NAO+).
For all of these phase-space regime regions, the leading modes of the QG3 state vector decay to climatology at a slower rate than predicted by the EMR, which contributes to the maintenance of non-Gaussian regime anomalies. Predictable regimes are connected to “regime precursor” regions of the phase space, from which trajectories flow into regime regions following mean phase-space velocities. Packets of trajectories originating from these regions are characterized by anomalously low spreading rates due to a combination of low local stochastic diffusivity and convergence of the nonlinear component of mean phase-space velocities along the trajectory pathways. While unpredictable regimes do have precursor regions, trajectories emanating from these regions are characterized by relatively high spreading rates.
The predictable regimes AO+ and AO− are insensitive to the metric used to identify the regimes; however, the unpredictable regime NAO+ in the 2D space is not directly associated with its zonal-metric counterpart.
On the Relationship between Thermodynamic Structure and Cloud Top, and Its Climate Significance in the Arctic
Authors: Sedlar Joseph , Shupe Matthew D. , Tjernström Michael 
Published: October 2011

Abstract
Cloud and thermodynamic characteristics from three Arctic observation sites are investigated to understand the collocation between low-level clouds and temperature inversions. A regime where cloud top was 100–200 m above the inversion base [cloud inside inversion (CII)] was frequently observed at central Arctic Ocean sites, while observations from Barrow, Alaska, indicate that cloud tops were more frequently constrained to inversion base height [cloud capped by inversion (CCI)]. Cloud base and top heights were lower, and temperature inversions were also stronger and deeper, during CII cases. Both cloud regimes were often decoupled from the surface except for CCI over Barrow. In-cloud lapse rates differ and suggest increased cloud-mixing potential for CII cases.
Specific humidity inversions were collocated with temperature inversions for more than 60% of the CCI and more than 85% of the CII regimes. Horizontal advection of heat and moisture is hypothesized as an important process controlling thermodynamic structure and efficiency of cloud-generated motions. The portion of CII clouds above the inversion contains cloud radar signatures consistent with cloud droplets. The authors test the longwave radiative impact of cloud liquid above the inversion through hypothetical liquid water distributions. Optically thin CII clouds alter the effective cloud emission temperature and can lead to an increase in surface flux on the order of 1.5 W m−2 relative to the same cloud but whose top does not extend above the inversion base. The top of atmosphere impact is even larger, increasing outgoing longwave radiation up to 10 W m−2. These results suggest a potentially significant longwave radiative forcing via simple liquid redistributions for a distinctly dominant cloud regime over sea ice.
Using Genetic Algorithms to Optimize Bathymetric Sampling for Predictive Model Input
Authors: Manian Dinesh , Kaihatu James M. , Zechman Emily M. 
Published: October 2011

Abstract
This paper describes the use of an optimization method to effectively reduce the required bathymetric sampling for forcing a numerical forecast model by using the model’s sensitivity to this input. A genetic algorithm is developed to gradually evolve the survey path for a ship, autonomous underwater vehicle (AUV), or other measurement platform to an optimum, with the resulting effect of the corresponding measured bathymetry on the model used as a metric. Starting from an initial simulated set of possible random or heuristic sampling paths over the given bathymetry using certain constraints like limited length of track, the algorithm can be used to arrive at the path that would provide the best possible input to the model under those constraints. This suitability is tested by a comparison of the model results obtained by using these new simulated observations, with the results obtained using the most recent and complete bathymetric data available. Two test study areas were considered, and the algorithm was found to consistently converge to a sampling pattern that best captured the bathymetric variability critical to the model prediction.
Spatial Error Metrics for Oceanographic Model Verification
Authors: Ziegeler Sean B. , Dykes James D. , Shriver Jay F. 
Published: October 2011

Abstract
A common problem with modern numerical oceanographic models is spatial displacement, including misplacement and misshapenness of ocean circulation features. Traditional error metrics, such as least squares methods, are ineffective in many such cases; for example, only small errors in the location of a frontal pattern are translated to large differences in least squares of intensities. Such problems are common in meteorological forecast verification as well, so the application of spatial error metrics have been a recently popular topic there. Spatial error metrics separate model error into a displacement component and an intensity component, providing a more reliable assessment of model biases and a more descriptive portrayal of numerical model prediction skill. The application of spatial error metrics to oceanographic models has been sparse, and further advances for both meteorology and oceanography exist in the medical imaging field. These advances are presented, along with modifications necessary for oceanographic model output. Standard methods and options for those methods in the literature are explored, and where the best arrangements of options are unclear, comparison studies are conducted. These trials require the reproduction of synthetic displacements in conjunction with synthetic intensity perturbations across 480 Navy Coastal Ocean Model (NCOM) temperature fields from various regions of the globe throughout 2009. Study results revealed the success of certain approaches novel to both meteorology and oceanography, including B-spline transforms and mutual information. That, combined with other common methods, such as quasi-Newton optimization and land masking, could best recover the synthetic displacements under various synthetic intensity changes.
Direct Assimilation of AMSR-E Brightness Temperatures for Estimating Sea Ice Concentration
Authors: Scott K. Andrea , Buehner Mark , Caya Alain , Carrieres Tom 
Published: October 2011

Abstract
In this paper a method to directly assimilate brightness temperatures from the Advanced Microwave Scanning Radiometer for Earth Observing System (AMSR-E) to produce ice concentration analyses within a three-dimensional variational data assimilation system is investigated. To assimilate the brightness temperatures a simple radiative transfer model is used as the forward model that maps the state vector to the observation space. This allows brightness temperatures to be modeled for all channels as a function of the total ice concentration, surface wind speed, sea surface temperature, ice temperature, vertically integrated water vapor, and vertically integrated cloud liquid water. The brightness temperatures estimated by the radiative transfer model are sensitive to the specified values for the sea ice emissivity. In this paper, two methods of specifying the sea ice emissivity are compared. The first uses a constant value for each polarization and frequency, while the second uses a simple emissivity parameterization. The emissivity parameterization is found to significantly improve the fit to the observations, reducing both the bias and the standard deviation. Results from the assimilation of brightness temperatures are compared with those from assimilating a retrieved ice concentration in the context of initializing a coupled ice–ocean model for an area along the east coast of Canada. It is found that with the emissivity parameterization the assimilation of brightness temperatures produces ice concentration analyses that are in slightly better agreement with operational ice charts than when assimilating an ice concentration retrieval, with the most significant improvements during the melt season.
Nodulin 41, a novel late nodulin of common bean with peptidase activity
Authors: Olivares Juan Elías , Díaz-Camino Claudia , Estrada-Navarrete Georgina , Alvarado-Affantranger Xochitl , Rodríguez-Kessler Margarita , Zamudio Fernando Z , Olamendi-Portugal Timoteo , Márquez Yamile , Servín Luis Eduardo , Sánchez Federico 
Published: October 2011

Abstract

Background
The legume-rhizobium symbiosis requires the formation of root nodules, specialized organs where the nitrogen fixation process takes place. Nodule development is accompanied by the induction of specific plant genes, referred to as nodulin genes. Important roles in processes such as morphogenesis and metabolism have been assigned to nodulins during the legume-rhizobium symbiosis.

Results
Here we report the purification and biochemical characterization of a novel nodulin from common bean (Phaseolus vulgaris L.) root nodules. This protein, called nodulin 41 (PvNod41) was purified through affinity chromatography and was partially sequenced. A genomic clone was then isolated via PCR amplification. PvNod41 is an atypical aspartyl peptidase of the A1B subfamily with an optimal hydrolytic activity at pH 4.5. We demonstrate that PvNod41 has limited peptidase activity against casein and is partially inhibited by pepstatin A. A PvNod41-specific antiserum was used to assess the expression pattern of this protein in different plant organs and throughout root nodule development, revealing that PvNod41 is found only in bean root nodules and is confined to uninfected cells.

Conclusions
To date, only a small number of atypical aspartyl peptidases have been characterized in plants. Their particular spatial and temporal expression patterns along with their unique enzymatic properties imply a high degree of functional specialization. Indeed, PvNod41 is closely related to CDR1, an Arabidopsis thaliana extracellular aspartyl protease involved in defense against bacterial pathogens. PvNod41's biochemical properties and specific cell-type localization, in uninfected cells of the common bean root nodule, strongly suggest that this aspartyl peptidase has a key role in plant defense during the symbiotic interaction.
The time since last menstrual period is important as a clinical predictor for non-steroidal aromatase inhibitor-related arthralgia
Authors: Kanematsu Miyuki , Morimoto Masami , Honda Junko , Nagao Taeko , Nakagawa Misako , Takahashi Masako , Tangoku Akira , Sasa Mitsunori 
Published: October 2011

Abstract

Background
The clinical predictors of aromatase inhibitor-related arthralgia (AIA), a drug-related adverse reaction of aromatase inhibitors (AIs), remain unclear.

Methods
AIA was prospectively surveyed every 4 months in 328 postmenopausal breast cancer patients administered a non-steroidal AI (anastrozole). Various clinicopathological parameters were recorded and analyzed (chi-square test, Fisher's exact test and logistic regression analysis).

Results
The mean observation period was 39.9 months. AIA manifested in 114 patients (34.8%), with peaks of onset at 4 (33.7%) and 8 months (11.4%) after starting AI administration. Some cases manifested even after 13 months. AIA tended to occur in younger patients (incidences of 46.3%, 37.4% and 28.0% for ages of < 55, 55-65 and > 65 years, respectively (p = 0.063)) and decreased significantly with the age at menarche (53.3%, 35.3% and 15.4% for < 12, 12-15 and > 15 years, respectively (p = 0.036)). The incidences were 45.1%, 46.3 and 25.1% for the time since the last menstrual period (LMP) < 5 years, 5-10 years and > 10 years, being significantly lower at > 10 years (p < 0.001). In logistic regression analysis, the AIA incidence was significantly lower in the time since LMP > 10-year group versus the < 5-year group (odds ratio 0.44, p = 0.002), but the age at menarche showed no association. AIA manifested significantly earlier (≤ 6 months) as the time since LMP became shorter (< 5 years).

Conclusion
AIA tends to manifest early after starting AI, but some cases show delayed onset. The incidence was significantly lower in patients with a duration of > 10 years since LMP. When the time since LMP was short, the onset of AIA was significantly earlier after starting AI administration.
Pb(core)/ZnO(shell) nanowires obtained by microwave-assisted method
Authors: Solis-Pomar F , Meléndrez MF , Esparza R , Pérez-Tijerina E 
Published: October 2011

AbstractIn this study, Pb-filled ZnO nanowires [Pb(core)/ZnO(shell)] were synthesized by a simple and novel one-step vapor transport and condensation method by microwave-assisted decomposition of zinc ferrite. The synthesis was performed using a conventional oven at 1000 W and 5 min of treatment. After synthesis, a spongy white cotton-like material was obtained in the condensation zone of the reaction system. HRTEM analysis revealed that product consists of a Pb-(core) with (fcc) cubic structure that preferentially grows in the [111] direction and a hexagonal wurtzite ZnO-(Shell) that grows in the [001] direction. Nanowire length was more than 5 μm and a statistical analysis determined that the shell and core diameters were 21.00 ± 3.00 and 4.00 ± 1.00 nm, respectively. Experimental, structural details, and synthesis mechanism are discussed in this study.
Medicinal animals used in ethnoveterinary practices of the 'Cariri Paraibano', NE Brazil
Authors: Souto Wedson MS , Mourão José S , Barboza Raynner RD , Mendonça Lívia ET , Lucena Reinaldo FP , Confessor Maine VA , Vieira Washington LS , Montenegro Paulo FGP , Lopez Luiz CS , Alves Rômulo RN 
Published: October 2011

AbstractBackgroundZootherapy is important in various socio-cultural environments, and innumerous examples of the use of animal derived remedies can currently be found in many urban, semi-urban and more remote localities in all parts of the world, particularly in developing countries. However, although a number of ethnobiological inventories concerning the use of medicinal animals in human health care have been compiled in Brazil in recent years, zootherapeutic practices in ethnoveterinary medicine (EVM) are poorly described and neglected in favor of human ethnomedicine. In this sense, the purpose of this study was to describe the local zootherapeutic practices in ethnoveterinary medicine of semi-arid of NE Brazil (Caatinga biome) and to contribute to future research about the validation of the effects and side effects of these animal productsMethodsThe information obtained through semi-structured interviews was complemented by free interviews and informal conversations. A total of 67 people were interviewed (53 men and 14 women) about the use and commercialization of medicinal animals. To determine the relative importance of each local known species, their use-values (UV) were calculated. Diversity of species utilized was compared, between localities, using rarefaction curves and diversity estimate (Chao2)Results and ConclusionsA total of 44 animal species (37 vertebrates and 7 invertebrates), distributed among 6 taxonomic categories were found to be used to treat 30 different ailments in livestock and pets. The results of our surveys revealed a rich traditional knowledge of local residents about the use of animals in traditional veterinary medicine. Although it is gradually being discontinued, the perceived efficacy, economic and geographic accessibility were main reasons for popularity of zootherapy in studied areas.
A pair of new BAC and BIBAC vectors that facilitate BAC/BIBAC library construction and intact large genomic DNA insert exchange
Authors: Shi Xue , Zeng Haiyang , Xue Yadong , Luo Meizhong 
Published: October 2011

Abstract

Background
Large-insert BAC and BIBAC libraries are important tools for structural and functional genomics studies of eukaryotic genomes. To facilitate the construction of BAC and BIBAC libraries and the transfer of complete large BAC inserts into BIBAC vectors, which is desired in positional cloning, we developed a pair of new BAC and BIBAC vectors.

Results
The new BAC vector pIndigoBAC536-S and the new BIBAC vector BIBAC-S have the following features: 1) both contain two 18-bp non-palindromic I-Sce I sites in an inverted orientation at positions that flank an identical DNA fragment containing the lac Z selection marker and the cloning site. Large DNA inserts can be excised from the vectors as single fragments by cutting with I-Sce I, allowing the inserts to be easily sized. More importantly, because the two vectors contain different antibiotic resistance genes for transformant selection and produce the same non-complementary 3' protruding ATAA ends by I-Sce I that suppress self- and inter-ligations, the exchange of intact large genomic DNA inserts between the BAC and BIBAC vectors is straightforward; 2) both were constructed as high-copy composite vectors. Reliable linearized and dephosphorylated original low-copy pIndigoBAC536-S and BIBAC-S vectors that are ready for library construction can be prepared from the high-copy composite vectors pHZAUBAC1 and pHZAUBIBAC1, respectively, without the need for additional preparation steps or special reagents, thus simplifying the construction of BAC and BIBAC libraries. BIBAC clones constructed with the new BIBAC-S vector are stable in both E. coli and Agrobacterium. The vectors can be accessed through our website http://GResource.hzau.edu.cn.

Conclusions
The two new vectors and their respective high-copy composite vectors can largely facilitate the construction and characterization of BAC and BIBAC libraries. The transfer of complete large genomic DNA inserts from one vector to the other is made straightforward.
The promoting effect of byproducts from Irpex lacteus on subsequent enzymatic hydrolysis of bio-pretreated cornstalks
Authors: Du Wanqing , Yu Hongbo , Song Lili , Zhang Ji , Weng Changlong , Ma Fuying , Zhang Xiaoyu 
Published: October 2011

Abstract

Background

Irpex lacteus, a versatile lignin-degrading fungus with various extracellular enzymes, has been widely used for biological pretreatment. However, most studies have focused on the change of substrate structure after biological pretreatment, and the effect of these changes on the enzymatic hydrolysis, but the effect of byproducts from biological pretreatment process on subsequent enzymatic hydrolysis is not well understood.

Methods
We developed a biological pretreatment process with I. lacteus that can produce stimulatory byproducts that enhance the enzymatic hydrolysis of cornstalks.

Results
The maximum hydrolysis yield of glucan (82%) was obtained after pretreatment for 28 days. The maximum reducing sugar yield decreased from 313.5 to 200.1 mg/g raw cornstalks after water-soluble byproducts of biological pretreatment were removed from pretreated cornstalks. The effect of byproducts on enzymatic hydrolysis was also investigated. We found that the hydrolysis efficiency of commercial cellulase preparation on cornstalks could be improved by water extracts from bio-pretreated cornstalks with hydrolytic enzyme activity and iron-reducing activity.

Conclusion
The key finding suggested that byproducts from biological pretreatment play important roles in enhancing downstream hydrolysis, which might be attributable to hydrolytic enzymes and iron-reducing compounds produced by I. lacteus.
Development of a highly sensitive method for detection of JAK2V617F
Authors: Zhao Anna H , Gao Rufei , Zhao Zhizhuang J 
Published: October 2011

Abstract

Background
Ph- myeloproliferative neoplasms (MPNs) represent a heterogeneous group of chronic diseases characterized by increased expansion of hematopoietic cells of the myeloid lineage. JAK2V617F, an activation mutation form of tyrosine kinase JAK2, is found in the majority of patients with MPNs. Studies have demonstrated that JAK2V617F can cause MPNs, and various methods have been developed to detect JAK2V617F for diagnostic purposes. However, a highly sensitive method is still needed for the earliest possible detection and for disease prevention and treatment.

Methods
In the present study, we developed a method dubbed restriction fragment nested allele-specific PCR (RFN-AS-PCR). The method consists of three steps: 1) initial amplification of DNA samples with PCR primers surrounding the JAK2V617F mutation site, 2) digestion of the PCR products with restriction enzyme BsaXI which only cleaves the wild type allele, and 3) detection of JAK2V617F by allele-specific PCR with nested primers.

Results
We tested the sensitivity of the method by using purified plasmid DNAs and blood cell DNAs containing known proportions of JAK2V617F. We were able to detect JAK2V617F with a sensitivity of 0.001%. We further analyzed blood cell DNA samples from 105 healthy donors with normal blood cell counts and found three JAK2V617F-positive cases, which would have remained undetected using a less sensitive method.

Conclusions
We have developed a highly sensitive method that will allow for detection of JAK2V617F at a very early stage. This method may have major implications in diagnosis and prevention of MPNs and related diseases.
On the interpretation of alienable vs. inalienable possession: A psycholinguistic investigation
Authors: Lichtenberk Frantisek , Vaid Jyotsna , Chen Hsin-Chin 
Published: October 2011

AbstractOceanic languages typically make a grammatical contrast between expressions of alienable and inalienable possession. Moreover, further distinctions are made in the alienable category but not in the inalienable category. The present research tests the hypothesis that there is a good motivation for such a development in the former case. As English does not have a grammaticalized distinction between alienable and inalienable possession, it provides a good testing ground. Three studies were conducted. In Study 1, participants were asked to write down the first interpretation that came to mind for possessive phrases, some of which contained inherently relational possessums, while others contained possessums that are not inherently relational. Phrases with non-relational possessums elicited a broader range of interpretations and a lower consistency of a given interpretation across possessor modifiers than those with relational possessums. Study 2 demonstrated that users assign a default interpretation to a possessive phrase containing a relational possessum even when another reading is plausible. Study 3, a corpus-based analysis of possessive phrase use, showed that phrases with relational possessums have a narrower range of interpretations than those with other possessums. Taken together, the findings strongly suggest that grammatical distinctions between different types of alienable possession are motivated.