bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phenotyping for Abiotic Stress Tolerance in MaizeF
Authors: Masuka Benhilda , Araus Jose Luis , Das Biswanath , Sonder Kai , Cairns Jill E. 
Published: March 2012

Abstract
image
[ Jill E. Cairns ]The ability to quickly develop germplasm having tolerance to several complex polygenic inherited abiotic and biotic stresses combined is critical to the resilience of cropping systems in the face of climate change. Molecular breeding offers the tools to accelerate cereal breeding; however, suitable phenotyping protocols are essential to ensure that the much‐anticipated benefits of molecular breeding can be realized. To facilitate the full potential of molecular tools, greater emphasis needs to be given to reducing the within‐experimental site variability, application of stress and characterization of the environment and appropriate phenotyping tools. Yield is a function of many processes throughout the plant cycle, and thus integrative traits that encompass crop performance over time or organization level (i.e. canopy level) will provide a better alternative to instantaneous measurements which provide only a snapshot of a given plant process. Many new phenotyping tools based on remote sensing are now available including non‐destructive measurements of growth‐related parameters based on spectral reflectance and infrared thermometry to estimate plant water status. Here we describe key field phenotyping protocols for maize with emphasis on tolerance to drought and low nitrogen.
Financial Markets and Economic Growth*
Authors: Miller Merton H. 
Published: March 2012

In this reprinting of the Nobel Prize‐winning financial economist's classic statement about the origins of financial crises, the Southeast Asian crisis of the late 1990s is attributed “not to too much reliance on financial markets, but to too little.” Like the U.S. economy a century ago, the emerging Asian economies did not then—and do not now—have well‐developed capital markets and remain heavily dependent on their banking systems to finance growth. But for all its benefits, banking is not only basically 19th‐century technology, but disaster‐prone technology. And in the summer of 1997, a banking‐driven disaster struck in East Asia, just as it had struck so many times before in U.S. history.During the 20th century, the author argues, the U.S. economy reduced its dependence on banks by developing “dispersed and decentralized” financial markets. In so doing, it increased the efficiency of the capital allocation process and reduced the economy's vulnerability to the credit crunches that have recurred throughout U.S. history. By contrast, Japan has not reduced its economy's dependence on banks, and its efforts to deal with its banking problems during the crisis of the late'90s served only to destabilize itself as well as its neighbors. Developing countries in Asia and elsewhere are urged not to follow the Japanese example, but to take measures aimed at developing financial markets and institutions that will either substitute for or, in some cases, complement bank products and services.
CHEMOSTRATIGRAPHY OF CENOMANIAN–TURONIAN CARBONATES OF THE SARVAK FORMATION, SOUTHERN IRAN
Authors: Hajikazemi E. , Al‐Aasm I.S. , Coniglio M. 
Published: March 2012

Stable‐isotope and trace‐element analyses from five surface and subsurface sections of the mid‐Cretaceous Sarvak Formation in southern and offshore Iran confirm the presence of the regional‐scale Turonian unconformity and of a more local Cenomanian–Turonian unconformity. The geochemical results indicate the presence of previously unrecognized and/or undifferentiated subaerial exposure surfaces. Sarvak Formation carbonates at or near palaeo‐exposure surfaces show varying degrees of diagenetic modification, and more extensive alteration is associated with longer periods of exposure. The subaerial exposure and associated diagenetic processes greatly influenced reservoir quality and amplified karstification and evolution of porosity in the Upper Sarvak Formation.The palaeo‐exposure surfaces are identified by their negative δ13C values (as low as – 6.4%) and negative δ18O values (as low as –9.4%), together with low Sr concentrations and relatively high 87Sr/86Sr ratios. These geochemical characteristics are interpreted to be the result of the interaction of the Sarvak Formation carbonates with meteoric waters charged with atmospheric CO2. The meteoric waters also caused karstification and soil formation which in some places extends a few metres below the exposure surfaces. Depleted carbon values were not recorded in areas where palaeosols are not well developed or where the uppermost layers of the Sarvak Formation have been removed by erosion.
Comparative Echocardiographic and Clinical Features of Hypertrophic Cardiomyopathy in 5 Breeds of Cats: A Retrospective Analysis of 344 Cases (2001–2011)
Authors: Trehiou‐Sechi E. , Tissier R. , Gouni V. , Misbach C. , Petit A.M.P. , Balouka D. , Carlos Sampedrano C. , Castaignet M. , Pouchelon J.‐L. , Chetboul V. 
Published: March 2012

BackgroundPrimary hypertrophic cardiomyopathy (HCM) is the most common feline heart disease and has been demonstrated to be inherited in some breeds. However, few studies have comparedHCMphenotypes and survival according to breed.ObjectivesTo compare epidemiological characteristics, clinical findings, left ventricular (LV) geometric patterns, and survival in several breeds of cats withHCM.AnimalsThree hundred and forty‐four cats from 5 different breeds (Persian, Domestic Shorthair [DS], Sphynx, Maine coon [MC], and Chartreux) with primaryHCMdiagnosed by conventional echocardiography.MethodsRetrospective study. Cats were classified according to breed and clinical status.ResultsAge at the time of diagnosis was lower (P < .001) inMC(median age, 2.5 years) and Sphynx (3.5 years) than in other breeds (OB), ie, 8.0, 8.0, and 11.0 years forDS, Chartreux, and Persians, respectively. The prevalence ofLVoutflow tract obstruction was higher (P < .001) in Persians (23/41; 56%) than inOB(115/303; 38%). Age at the first cardiac event was lower (P < .01) inMC(median age, 2.5 years) than inOB(7.0 years). All cats surviving > 15 years of age wereDS, Persians, or Chartreux. Sudden death (representing 24% of all cardiac deaths) was observed only in 3 breeds (DS,MC, and Sphynx).Conclusion and Clinical ImportanceAs in humans, felineHCMis characterized by marked phenotypic variability with several breed‐dependent features regarding epidemiology,LVgeometric patterns, and clinical course (ie, age at diagnosis, 1st cardiac event, and cause of death).
Statistical evaluation of parameters estimating autocorrelation and individual heterogeneity in longitudinal studies
Authors: Hamel Sandra , Yoccoz Nigel G. , Gaillard Jean‐Michel 
Published: March 2012

Summary1. Autocorrelation and individual heterogeneity are now considered to reflect biological processes rather than simply being a nuisance requiring to be accounted for. Before using parameter estimates that represent autocorrelation and individual heterogeneity to infer biological processes, a statistical evaluation of their precision and accuracy is required to validate their use.2. Using simulated data, we evaluated accuracy and precision of temporal autocorrelation and individual heterogeneity estimates provided by different statistical models. We compared estimates across different intensity of individual variation and life histories, and sampling effort. We focused on recurrent binary variables because statistical evaluations of models describing binary processes have often been overlooked although several evolutionary and ecological processes are expressed as binary variables (e.g. probability of annual reproduction, plant annual flowering and detection, seasonal migration decision).3. Our results showed that autocorrelation and individual heterogeneity were generally better estimated using a ‘time series’ modelling approach, but that a ‘state dependence’ modelling approach also provided fair estimates in most cases. The latter method was even more robust when data sets included missing values. Data sets including missing values or consisting of very short times series resulted in important bias in some instances.4. Models ignoring either individual heterogeneity or autocorrelation performed poorly, illustrating the fundamental association between these two processes, and demonstrating that the complex structure of autocorrelation and individual heterogeneity patterns is difficult to tackle using simple models.5. Our work’s major finding is the demonstration that autocorrelation and individual heterogeneity need to be both accounted for to provide reliable estimates even in studies focusing on only one of these processes. Our study also offers a set of practical recommendations for helping researchers modelling these two processes depending on their scientific aims and the structure of their data. Finally, our results illustrate that more research is required for estimating individual heterogeneity when positive temporal autocorrelation is expected because none of the models evaluated provided suitable estimates.
New Range of Vectors with a Stringent 5-Fluoroorotic Acid-Based Counterselection System for Generating Mutants by Allelic Replacement in Staphylococcus aureus
Authors: Redder Peter , Linder Patrick 
Published: March 2012

ABSTRACT

We have developed a range of vectors for allelic replacements in
Staphylococcus aureus
to facilitate genetic work in this opportunistic pathogen. The central feature of the vector range is a selection/counterselection system that takes advantage of the 5-fluoroorotic acid (FOA) resistance and pyrimidine prototrophy caused by the loss and gain, respectively, of the
pyrF
and
pyrE
genes. This system allows for stringent counterselection of the vectors during the second homologous recombination of a classic allelic replacement. The basic vector pRLY2, which contains the
pyrFE
genes from
Bacillus subtilis
, was combined with chloramphenicol, erythromycin, and tetracycline resistance genes and four different versions of nonreplicative or conditionally replicative origins of replication. The choice between these 12 different pRLY vectors allows for high versatility and ensures that the vectors can be used in virtually any genetic background. Finally, as proof of concept, we present six deletions or modifications of components in the
S. aureus
degradosome as well as the operon containing the
cshB
DEAD box helicase.
Genetic Analysis of the Cronobacter sakazakii O4 to O7 O-Antigen Gene Clusters and Development of a PCR Assay for Identification of All C. sakazakii O Serotypes
Authors: Sun Yamin , Wang Min , Wang Quan , Cao Boyang , He Xin , Li Kun , Feng Lu , Wang Lei 
Published: March 2012

ABSTRACT

The Gram-negative bacterium
Cronobacter sakazakii
is an emerging food-borne pathogen that causes severe invasive infections in neonates. Variation in the O-antigen lipopolysaccharide in the outer membrane provides the basis for Gram-negative bacteria serotyping. The O-antigen serotyping scheme for
C. sakazakii
, which includes seven serotypes (O1 to O7), has been recently established, and the O-antigen gene clusters and specific primers for three
C. sakazakii
serotypes (O1, O2, and O3) have been characterized. In this study, the
C. sakazakii
O4, O5, O6, and O7 O-antigen gene clusters were sequenced, and gene functions were predicted on the basis of homology.
C. sakazakii
O4 shared a similar O-antigen gene cluster with
Escherichia coli
O103. The general features and anomalies of all seven
C. sakazakii
O-antigen gene clusters were evaluated and the relationship between O-antigen structures and their gene clusters were investigated. Serotype-specific genes for O4 to O7 were identified, and a molecular serotyping method for all
C. sakazakii
O serotypes, a multiplex PCR assay, was developed by screening against 136 strains of
C. sakazakii
and closely related species. The sensitivity of PCR-based serotyping method was determined to be 0.01 ng of genomic DNA and 10
3
CFU of each strain/ml. This study completes the elucidation of
C. sakazakii
O-antigen genetics and provides a molecular method suitable for the identification of
C. sakazakii
O1 to O7 strains.
Anaerobic Metabolism of Indoleacetate
Authors: Ebenau-Jehle Christa , Thomas Markus , Scharf Gernot , Kockelkorn Daniel , Knapp Bettina , Schühle Karola , Heider Johann , Fuchs Georg 
Published: March 2012

ABSTRACT

The anaerobic metabolism of indoleacetate (indole-3-acetic acid [IAA]) in the denitrifying betaproteobacterium
Azoarcus evansii
was studied. The strain oxidized IAA completely and grew with a generation time of 10 h. Enzyme activities that transformed IAA were present in the soluble cell fraction of IAA-grown cells but were 10-fold downregulated in cells grown on 2-aminobenzoate or benzoate. The transformation of IAA did not require molecular oxygen but required electron acceptors like NAD
+
or artificial dyes. The first products identified were the enol and keto forms of 2-oxo-IAA. Later, polar products were observed, which could not yet be identified. The first steps likely consist of the anaerobic hydroxylation of the N-heterocyclic pyrrole ring to the enol form of 2-oxo-IAA, which is catalyzed by a molybdenum cofactor-containing dehydrogenase. This step is probably followed by the hydrolytic ring opening of the keto form, which is catalyzed by a hydantoinase-like enzyme. A comparison of the proteome of IAA- and benzoate-grown cells identified IAA-induced proteins. Owing to the high similarity of
A. evansii
with strain EbN1, whose genome is known, we identified a cluster of 14 genes that code for IAA-induced proteins involved in the early steps of IAA metabolism. These genes include a molybdenum cofactor-dependent dehydrogenase of the xanthine oxidase/aldehyde dehydrogenase family, a hydantoinase, a coenzyme A (CoA) ligase, a CoA transferase, a coenzyme B
12
-dependent mutase, an acyl-CoA dehydrogenase, a fusion protein of an enoyl-CoA hydratase and a 3-hydroxyacyl-CoA dehydrogenase, a beta-ketothiolase, and a periplasmic substrate binding protein for ABC transport as well as a transcriptional regulator of the GntR family. Five predicted enzymes form or act on CoA thioesters, indicating that soon after the initial oxidation of IAA and possibly ring opening, CoA thioesters are formed, and the carbon skeleton is rearranged, followed by a CoA-dependent thiolytic release of another CoA thioester. We propose a scheme of an anaerobic IAA metabolic pathway that ultimately leads to 2-aminobenzoyl-CoA or benzoyl-CoA.
Organizational Requirements of the SaeR Binding Sites for a Functional P1 Promoter of the
sae
Operon in Staphylococcus aureus
Authors: Cho Hoonsik , Jeong Do-Won , Li Chunling , Bae Taeok 
Published: March 2012

ABSTRACT

In
Staphylococcus aureus
, the SaeRS two-component system controls the expression of multiple virulence factors. Of the two promoters in the
sae
operon, P1 is autoinduced and has two binding sites for the response regulator SaeR. In this study, we examined the organizational requirements of the SaeR binding sites in P1 for transcription activation. Mutational studies showed that both binding sites are essential for binding to phosphorylated SaeR (P-SaeR) and transcription activation. When the 21-bp distance between the centers of the two SaeR binding sites was altered to 26 bp, 31 bp, 36 bp, or 41 bp, only the 31-bp mutant retained approximately 40% of the original promoter activity. When the −1-bp spacing (i.e.,1-bp overlap) between the primary SaeR binding site and the −35 promoter region was altered, all mutant P1 promoters failed to initiate transcription; however, when the first nucleotide of the −35 region was changed from A to T, the mutants with 0-bp or 22-bp spacing showed detectable promoter activity. Although P-SaeR was essential for the binding of RNA polymerase to P1, it was not essential for the binding of the enzyme to the alpha-hemolysin promoter. When the nonoptimal spacing between promoter elements in P1 or the coagulase promoter was altered to the optimal spacing of 17 bp, both promoters failed to initiate transcription. These results suggest that SaeR binding sites are under rather strict organizational restrictions and provide clues for understanding the molecular mechanism of
sae
-mediated transcription activation.
Pop hole use by hens with different keel fracture status monitored throughout the laying period
Authors: Richards G. J. , Wilkins L. J. , Knowles T. G. , Booth F. , Toscano M. J. , Nicol C. J. , Brown S. N. 
Published: March 2012

The aim of this work was to study the effect of keel fractures on the extent to which free‐range hens access the range through pop holes. Over two consecutive laying periods (two production years) a total of 1100 individual birds from one half of a house, divided into four separated flocks, were caught at 25, 35, 45, 55 and 65 weeks, palpated to assess the prevalence and severity of keel fractures and tagged with RFID transponders. Their use of pop holes was subsequently monitored in some cases from week 25 to end of lay at 68 to 70 weeks. At regular intervals (every 10 weeks), the tagged birds were re‐caught to assess changes in keel fracture prevalence and severity. The average percentage of birds with fractured keels at 25, 35, 45, 55, 65 and at end of lay (68 to 70 weeks of age) was 5.5, 25.5, 49, 63, 66.5 and 78.5, respectively, across both production years. The effect of keel score on pop hole use was modelled statistically, adjusting for weather conditions and age of the birds. There were significant effects of most of the weather variables recorded, as well as age of the bird, on use of pop holes and also a significant effect of keel score. Higher keel scores resulted in a reduction in pop hole use. A significant statistical interaction between keel score and ambient temperature revealed an accelerated reduction in use as the temperature decreased and keel score increased. It is concluded that the occurrence of keel fractures may affect the birds' ability or willingness to utilise the outdoor range provided by free‐range housing systems, thereby reducing the potential welfare advantages of this type of housing.
Cyclin-Dependent Kinase 7/9 Inhibitor SNS-032 Abrogates FIP1-like-1 Platelet-Derived Growth Factor Receptor α and Bcr-Abl Oncogene Addiction in Malignant Hematologic Cells
Authors: Wu Yongbin , Chen Chun , Sun Xiaoyong , Shi Xianping , Jin Bei , Ding Ke , Yeung Sai-Ching Jim , Pan Jingxuan 
Published: March 2012

Abstract
Purpose: The “gate-keeper” mutations T674I platelet—derived growth factor receptor α (PDGFRα) in hypereosinophilic syndrome (HES) and T315I Bcr-Abl in chronic myeloid leukemia (CML) are resistant to imatinib and the second-generation small-molecule tyrosine kinase inhibitors (TKI). However, to combat acquired resistance to imatinib, an alternative approach is to decrease the expression of the addicted gene to efficiently kill resistant malignant hematologic cells. The purpose of this study was to evaluate the strategy of shutting down the transcription and expression of FIP1-like-1 (FIP1L1)–PDGFRα and Bcr-Abl with SNS-032, an inhibitor of cyclin-dependent kinase 7 (CDK7) and CDK9 in phase I clinical trials.
Experimental Design: The effects of SNS-032 on PDGFRα and Bcr-Abl signaling pathways, apoptosis, and cell cycling were analyzed in TKI-resistant cells of HES and CML. The in vivo antitumor activity of SNS-032 was assessed with xenografted BaF3-T674I FIP1L1-PDGFRα and KBM5-T315I Bcr-Abl cells in nude mouse models.
Results: SNS-032 inhibited the phosphorylation on Ser5 and Ser2 of RNA polymerase II. SNS-032 decreased both the mRNA and protein levels of FIP1L1-PDGFRα and Bcr-Abl and inhibited the proliferation of malignant cells expressing FIP1L1-PDGFRα or Bcr-Abl. It also decreased the phosphorylation of downstream molecules. It induced apoptosis by triggering both the mitochondrial pathway and the death receptor pathway.
Conclusions: This CDK7/9 inhibitor potently inhibits FIP1L1-PDGFRα–positive HES cells and Bcr-Abl–positive CML cells regardless of their sensitivity to imatinib. SNS-032 may have potential in treating hematologic malignancy by abrogating oncogene addiction. Clin Cancer Res; 18(7); 1966–78. ©2012 AACR.
Folic acid supplementation increases survival and modulates high risk HPV-induced phenotypes in oral squamous cell carcinoma cells and correlates with p53 mRNA transcriptional down-regulation
Authors: Moody Michael , Le Oanh , Rickert Megan , Manuele Jeremy , Chang Sarah , Robinson Gary , Hajibandeh Jeffrey , Silvaroli John , Keiserman Mark A , Bergman Christine J , Kingsley Karl 
Published: March 2012

Abstract

Background
Although the primary risk factors for developing oral cancers are well understood, less is known about the relationship among the secondary factors that may modulate the progression of oral cancers, such as high-risk human papillomavirus (HPV) infection and folic acid (FA) supplementation. This study examined high-risk HPV and FA supplementation effects, both singly and in combination, to modulate the proliferative phenotypes of the oral cancer cell lines CAL27, SCC25 and SCC15.

Results
Using a comprehensive series of integrated in vitro assays, distinct effects of HPV infection and FA supplementation were observed. Both high-risk HPV strains 16 and 18 induced robust growth-stimulating effects in CAL27 and normal HGF-1 cells, although strain-specific responses were observed in SCC25 and SCC15 cells. Differential effects were also observed with FA administration, which significantly altered the growth rate of the oral cancer cell lines CAL27, SCC15, and SCC25, but not HGF-1 cells. Unlike HPV, FA administration induced broad, general increases in cell viability among all cell lines that were associated with p53 mRNA transcriptional down-regulation. None of these cell lines were found to harbor the common C677T mutation in methylenetetrahydrofolate reductase (MTHFR), which can reduce FA availability and may increase oral cancer risk.

Conclusion
Increased FA utilization and DNA hypermethylation are common features of oral cancers, and in these cell lines, specifically. The results of this study provide further evidence that FA antimetabolites, such as Fluorouracil (f5U or 5-FU) and Raltitrexed, may be alternative therapies for tumors resistant to other therapies. Moreover, since the incidence of oral HPV infection has been increasing, and can influence oral cancer growth, the relationship between FA bioavailability and concomitant HPV infection must be elucidated. This study is among the first pre-clinical studies to evaluate FA- and HPV-induced effects in oral cancers, both separately and in combination, which provides additional rationale for clinical screening of HPV infection prior to treatment.
Shaping and Ultimate Loading of Space Trusses, Shaped by Post-Tensioning Technique
Authors: Karbaschi M. E. , Dehdashti G. 
Published: March 2012

By means of post-tensioning technique, planar space trusses, particularly the single chord space trusses can be formed into curved forms. This novel process of the shape formation results in the architecturally interesting forms with the sufficient structural stability and stiffness, and with the additional advantage of being economical due to eliminating the need to use scaffolding or heavy cranes for their construction. This paper deals with the shape formation and loading tests as well as analyses of the single chord space trusses shaped by post-tensioning technique. To validate analyses and investigate effect of curvature of the shaped models on the results, two models are included; a gently curved dome-shape and a sharply curved barrel-vault. First, shape formation analysis is carried out and next, buckling load of shaped models in loading analyses are determined and findings are compared with the experimental results. Also, effect of the residual stresses of shape formation step on the results of loading analysis is investigated.