bluuebunny/crossref_metadata_2025_split huggingface dataset:
Precipitation Sensitivity to Surface Heat Fluxes over North America in Reanalysis and Model Data
Authors: Berg Alexis , Findell Kirsten , Lintner Benjamin R. , Gentine Pierre , Kerr Christopher 
Published: January 2013

AbstractA new methodology for assessing the impact of surface heat fluxes on precipitation is applied to data from the North American Regional Reanalysis (NARR) and to output from the Geophysical Fluid Dynamics Laboratory’s Atmospheric Model 2.1 (AM2.1). The method assesses the sensitivity of afternoon convective rainfall frequency and intensity to the late-morning partitioning of latent and sensible heating, quantified in terms of evaporative fraction (EF). Over North America, both NARR and AM2.1 indicate sensitivity of convective rainfall triggering to EF but no appreciable influence of EF on convective rainfall amounts. Functional relationships between the triggering feedback strength (TFS) metric and mean EF demonstrate the occurrence of stronger coupling for mean EF in the range of 0.6 to 0.8. To leading order, AM2.1 exhibits spatial distributions and seasonality of the EF impact on triggering resembling those seen in NARR: rainfall probability increases with higher EF over the eastern United States and Mexico and peaks in Northern Hemisphere summer. Over those regions, the impact of EF variability on afternoon rainfall triggering in summer can explain up to 50% of seasonal rainfall variability. However, the AM2.1 metrics also exhibit some features not present in NARR, for example, strong coupling extending northwestward from the central Great Plains into Canada. Sources of disagreement may include model hydroclimatic biases that affect the mean patterns and variability of surface flux partitioning, with EF variability typically much lower in NARR. Finally, the authors also discuss the consistency of their results with other assessments of land–precipitation coupling obtained from different methodologies.
Influence of Filter Band Function on Retrieval of Aerosol Optical Depth from Sunphotometer Data
Authors: Zhang Hao , Zhang Bing , Chen Dongmei , Li Junsheng , Zhao Guangning 
Published: January 2013

Abstract
Beer’s attenuation law is the basis for the retrieval of aerosol optical depth (AOD) from sunphotometer data. However, the filter band function causes uncertainty during the retrieval of AOD from sunphotometer data, particularly for channels covering spectral regions of strong gas absorption. In this work, the uncertainty in AOD retrieval due to the filter band function is systematically analyzed by employing fine spectral absorption cross sections obtained from the Molecular Spectroscopy and Chemical Kinetics Group and the line-by-line radiative transfer model (LBLRTM). The uncertainty in AOD retrieval includes the uncertainty due to the wings of the filter band function in the ultraviolet (UV) region and errors in the optical depth calculation for Rayleigh scattering and absorption of O3, NO2, H2O, CH4, and CO2. The results showed that 1) the uncertainty of AOD retrieval by this method, which is called the approximate AOD retrieval method, might become large when the filter band function is not well designed, particularly in the UV region; 2) in the case of a large zenith observation condition, the errors will be nonnegligible if the Rayleigh scattering optical depth is calculated at a central wavelength without including filter band function; 3) the band-weighted absorption coefficients of O3 and NO2 remain nearly constant when the gas amounts change, except in the case of questionably designed band filters; and 4) these weak-absorption optical depths for H2O, CH4, and CO2 cannot be ignored in the 1020- or 1640-nm channels, where an optical depth error of 0.01−0.02 may be introduced.
Bayesian Inference of Drag Parameters Using AXBT Data from Typhoon Fanapi
Authors: Sraj Ihab , Iskandarani Mohamed , Srinivasan Ashwanth , Thacker W. Carlisle , Winokur Justin , Alexanderian Alen , Lee Chia-Ying , Chen Shuyi S. , Knio Omar M. 
Published: January 2013

Abstract
The authors introduce a three-parameter characterization of the wind speed dependence of the drag coefficient and apply a Bayesian formalism to infer values for these parameters from airborne expendable bathythermograph (AXBT) temperature data obtained during Typhoon Fanapi. One parameter is a multiplicative factor that amplifies or attenuates the drag coefficient for all wind speeds, the second is the maximum wind speed at which drag coefficient saturation occurs, and the third is the drag coefficient's rate of change with increasing wind speed after saturation. Bayesian inference provides optimal estimates of the parameters as well as a non-Gaussian probability distribution characterizing the uncertainty of these estimates. The efficiency of this approach stems from the use of adaptive polynomial expansions to build an inexpensive surrogate for the high-resolution numerical model that couples simulated winds to the oceanic temperature data, dramatically reducing the computational burden of the Markov chain Monte Carlo sampling. These results indicate that the most likely values for the drag coefficient saturation and the corresponding wind speed are about 2.3 × 10−3 and 34 m s−1, respectively; the data were not informative regarding the drag coefficient behavior at higher wind speeds.
Spatial, Temporal and Spatio-Temporal Patterns of Maritime Piracy
Authors: Marchione Elio , Johnson Shane D. 
Published: January 2013

Objectives: To examine patterns in the timing and location of incidents of maritime piracy to see whether, like many urban crimes, attacks cluster in space and time. Methods: Data for all incidents of maritime piracy worldwide recorded by the National Geospatial Intelligence Agency are analyzed using time-series models and methods originally developed to detect disease contagion. Results: At the macro level, analyses suggest that incidents of pirate attacks are concentrated in five subregions of the earth’s oceans and that the time series for these different subregions differ. At the micro level, analyses suggest that for the last 16 years (or more), pirate attacks appear to cluster in space and time suggesting that patterns are not static but are also not random. Conclusions: Much like other types of crime, pirate attacks cluster in space, and following an attack at one location the risk of others at the same location or nearby is temporarily elevated. The identification of such regularities has implications for the understanding of maritime piracy and for predicting the future locations of attacks.
Renal deterioration in multiple sclerosis patients with neurovesical dysfunction
Authors: Fletcher Sophie G , Dillon Benjamin E , Gilchrist Alienor S , Haverkorn Rashel M , Yan Jingsheng , Frohman Elliot M , Lemack Gary E 
Published: January 2013

Objectives: Our aims were to determine the prevalence of renal ultrasound (RUS) abnormalities over time in multiple sclerosis (MS) patients with lower urinary tract symptoms (LUTS). Methods: Data were examined retrospectively from MS patients with LUTS, from 2000–2009. Study inclusion requirements were both baseline urodynamics (UD) and RUS data, with followup RUS at ≥ 12 months. Age, time since diagnosis (TSD), MS subtype and the UD/RUS results were evaluated for associations. Results: At presentation, 173 subjects underwent UD and RUS, but only 89 had a repeat RUS at ≥ 12 months. Median followup was 61 months. Initial RUS abnormalities were found in 10 (5.8%) subjects. At followup, upper urinary tract (UUT) abnormalities were seen in 11 (12.4%) subjects. Patients > 49 years old were more likely to have an abnormality (OR 0.181, 95% CI 0.037–0.892, p = 0.04). Patients with abnormal compliance were also more likely to have an abnormal followup RUS (OR 0.185, 95% CI 0.037–0.924, p = 0.04). No other demographic or UD factor was associated with RUS abnormalities. Conclusions: The development of structural UUT changes is low in MS patients. Urodynamic studies are useful for LUTS treatment strategies in complicated patients, but UD does not appear to have much impact with regard to upper tract changes.
No Increased Risk of Spinal Cord Ischemia in Delayed AAA Repair Following Thoracic Aortic Surgery
Authors: Ullery Brant W. , Wang Grace J. , Woo Edward Y. , Cheung Albert T. , McGarvey Michael L. , Carpenter Jeffrey P. , Fairman Ronald M. , Jackson Benjamin M. 
Published: January 2013

Objective: To examine the results of open or endovascular abdominal aortic aneurysm (AAA) repair following prior open or endovascular thoracic aortic surgery. Methods: A retrospective review of all patients who underwent AAA repair in a delayed fashion following prior thoracic aortic surgery at a single university hospital between 1999 and 2011 was performed. Results: Thirteen patients underwent AAA repair following prior thoracic aortic repair. Mean age was 68.9 ± 6.9 years and 77% (n = 10) were male. Three patients experienced transient delayed-onset spinal cord ischemia (SCI) following initial thoracic surgery. Mean time interval between initial thoracic aortic surgery and subsequent AAA repair was 2.0 ± 1.8 years. Overall rate of SCI and 30-day mortality after delayed AAA repair was 0%. Conclusions: This series does not demonstrate any evidence of increased risk of perioperative mortality or SCI in patients undergoing delayed AAA repair after prior thoracic aortic surgery.
Clinical trial in the treatment of 80 Iranian patients with major depression disorder by the combination of omega 3 fatty acid and a selective serotonin reuptake inhibitor
Authors: Safa Mitra , Fallah Tafti Saeed , Ghassem Boroujerdi Fatemeh , Talischi Firouzeh 
Published: January 2013

Objectives: Bipolar disorder type I is a disturbing psychiatric syndrome, which is treated by mood-stabilizing medications, psychosocial intervention and electroconvulsive therapy. As supplementation with omega 3 has been considered effective in the treatment of many diseases especially mental disorders, this study aimed at evaluating the effect of omega 3 with fluvoxamine compared with fluvoxamine alone in the treatment of the deep depression phase in bipolar patients type I. Methods: A total of 80 patients in this clinical trial study were selected using a randomized controlled trial in two case and control groups by a psychiatrist. The case group took fluvoxamine and omega 3 tablets and the control group took only fluvoxamine. Patients completed the Hamilton Depression Rating Scale and demographic questionnaire at the beginning of the study and after 2, 4, 8 and 12 weeks. Results: The mean scores in the Hamilton Depression Rating Scale in both groups under study after 2, 4, 8, 12 weeks decreased. Statistics showed a significant difference in scores in both groups before the treatment and after mentioned weeks. Conclusions: Since research findings showed the effectiveness of omega 3 and its harmlessness, it is suggested that omega 3 can be prescribed with other antidepressant medications.
Mitochondrial DNA and Y-chromosomal diversity in ancient populations of domestic sheep (Ovis aries) in Finland: comparison with contemporary sheep breeds
Authors: Niemi Marianna , Bläuer Auli , Iso-Touru Terhi , Nyström Veronica , Harjula Janne , Taavitsainen Jussi-Pekka , Storå Jan , Lidén Kerstin , Kantanen Juha 
Published: January 2013

Abstract

Background
Several molecular and population genetic studies have focused on the native sheep breeds of Finland. In this work, we investigated their ancestral sheep populations from Iron Age, Medieval and Post-Medieval periods by sequencing a partial mitochondrial DNA D-loop and the 5’-promoter region of the SRY gene. We compared the maternal (mitochondrial DNA haplotypes) and paternal (SNP oY 1) genetic diversity of ancient sheep in Finland with modern domestic sheep populations in Europe and Asia to study temporal changes in genetic variation and affinities between ancient and modern populations.

Results
A 523-bp mitochondrial DNA sequence was successfully amplified for 26 of 36 sheep ancient samples i.e. five, seven and 14 samples representative of Iron Age, Medieval and Post-Medieval sheep, respectively. Genetic diversity was analyzed within the cohorts. This ancient dataset was compared with present-day data consisting of 94 animals from 10 contemporary European breeds and with GenBank DNA sequence data to carry out a haplotype sharing analysis. Among the 18 ancient mitochondrial DNA haplotypes identified, 14 were present in the modern breeds. Ancient haplotypes were assigned to the highly divergent ovine haplogroups A and B, haplogroup B being the major lineage within the cohorts. Only two haplotypes were detected in the Iron Age samples, while the genetic diversity of the Medieval and Post-Medieval cohorts was higher. For three of the ancient DNA samples, Y-chromosome SRY gene sequences were amplified indicating that they originated from rams. The SRY gene of these three ancient ram samples contained SNP G-oY 1, which is frequent in modern north-European sheep breeds.

Conclusions
Our study did not reveal any sign of major population replacement of native sheep in Finland since the Iron Age. Variations in the availability of archaeological remains may explain differences in genetic diversity estimates and patterns within the cohorts rather than demographic events that occurred in the past. Our ancient DNA results fit well with the genetic context of domestic sheep as determined by analyses of modern north-European sheep breeds.
In silico mining of putative microsatellite markers from whole genome sequence of water buffalo (Bubalus bubalis) and development of first BuffSatDB
Authors: Sarika  , Arora Vasu , Iquebal Mir Asif , Rai Anil , Kumar Dinesh 
Published: January 2013

Abstract

Background
Though India has sequenced water buffalo genome but its draft assembly is based on cattle genome BTau 4.0, thus de novo chromosome wise assembly is a major pending issue for global community. The existing radiation hybrid of buffalo and these reported STR can be used further in final gap plugging and “finishing” expected in de novo genome assembly. QTL and gene mapping needs mining of putative STR from buffalo genome at equal interval on each and every chromosome. Such markers have potential role in improvement of desirable characteristics, such as high milk yields, resistance to diseases, high growth rate. The STR mining from whole genome and development of user friendly database is yet to be done to reap the benefit of whole genome sequence.

Description
By in silico microsatellite mining of whole genome, we have developed first STR database of water buffalo, BuffSatDb (Buffalo MicroSatellite Database (http://cabindb.iasri.res.in/buffsatdb/) which is a web based relational database of 910529 microsatellite markers, developed using PHP and MySQL database. Microsatellite markers have been generated using MIcroSAtellite tool. It is simple and systematic web based search for customised retrieval of chromosome wise and genome-wide microsatellites. Search has been enabled based on chromosomes, motif type (mono-hexa), repeat motif and repeat kind (simple and composite). The search may be customised by limiting location of STR on chromosome as well as number of markers in that range. This is a novel approach and not been implemented in any of the existing marker database. This database has been further appended with Primer3 for primer designing of the selected markers enabling researcher to select markers of choice at desired interval over the chromosome. The unique add-on of degenerate bases further helps in resolving presence of degenerate bases in current buffalo assembly.

Conclusion
Being first buffalo STR database in the world , this would not only pave the way in resolving current assembly problem but shall be of immense use for global community in QTL/gene mapping critically required to increase knowledge in the endeavour to increase buffalo productivity, especially for third world country where rural economy is significantly dependent on buffalo productivity.
Functional characterization and gene expression profiling of Drosophila melanogastershort dADA2b isoform-containing dSAGA complexes
Authors: Pankotai Tibor , Zsindely Nóra , Vamos Edith E , Komonyi Orbán , Bodai László , Boros Imre M 
Published: January 2013

Abstract

Background
ADA2 proteins, together with ADA3, SGF29 and GCN5 form the acetyltransferase module of GNAT-type histone acetyltransferase complexes. ADA2b is present in the SAGA complex, which plays roles in various chromatin-related processes via histone H3 modifications and by other mechanisms.

Results
In this report we present findings showing that during Drosophila melanogaster development two dADA2b isoforms (dADA2bS and dADA2bL) - which differ in their C-terminal domains - are expressed at various levels. Genetic complementation experiments indicate that dADA2bS alone can support development but cannot fully complement dAda2b mutations. In the presence of dADA2bS, the SAGA-specific histone H3 acetylation level is partially restored in dAda2b mutants. Comparison of whole transcriptome profiles of dAda2b null and dAda2bS transgene-carrier dAda2b null larvae indicates partial overlap between affected genes. mRNA levels corresponding to selected genes which are either up- or down-regulated in dAda2b mutants are altered by dADA2bS expression to different extents, ranging from complete restoration to wild type levels to no restoration at all. The short (dADA2bS) isoform of dADA2b seems to be more capable of restoring lost dSAGA functions that cause mRNA level up-regulation than those that lead to decreased mRNA levels.

Conclusions
The data presented here are in accord with results of genetic complementation experiments, and support the hypothesis that different isoforms of dADA2b contribute to the functional variations of dSAGA multiprotein HAT complexes.
Differential gene expression in the endometrium on gestation day 12 provides insight into sow prolificacy
Authors: Zhang Hao , Wang Shouqi , Liu Manqing , Zhang Ailing , Wu Zhenfang , Zhang Zhe , Li Jiaqi 
Published: January 2013

Abstract

Background
Erhualian pigs, one of Chinese Taihu pig breeds, are known to have the largest recorded litter size in the world. A lower prenatal death rate is the major contributing factor to the prolificacy of Taihu pigs. Cross-breeding experiments have demonstrated that Taihu sows exhibit a strong maternal effect and that their large litter sizes are mainly caused by maternal genes. The growth and development of porcine embryos on gestation day (GD) 12 are dependent on histotroph secreted by endometrium. Embryonic loss of Taihu pigs on GD12 is lower than that of Western pigs. Here, endometrial samples were collected from pregnant Erhualian sows (parity 3) and Landrace × Large White (LL) sows (parity 3) on GD12. Digital gene expression profiling (DGE) was used to measure the gene expression in the endometrium of the two breeds.

Results
A total of 13,612 genes were differentially expressed between the two breeds (P < 0.001, FDR < 0.001). Gene Ontology (GO) analysis showed that the differential genes involved in reproduction and growth. Pathway analysis revealed that the differentially expressed genes significantly enriched in 24 KEGG pathways. Quantitative real-time RT-PCR confirmed the differential expression of eight genes. Analyses of the differentially expressed genes suggested possible reasons for the difference in embryonic survival ratio between the two breeds. Specifically, these findings point to a higher ratio of PGE2:PGF2α in the endometrium of Erhualian pigs, which facilitates the establishment and maintenance of pregnancy. We also suggest that the differences in the uterine environment lead to higher uterine capacity in Erhualian pigs.

Conclusions
The DGE expression profiles of Erhualian and LL endometrium demonstrated differential expression of genes. Our results will increase understanding of the molecular mechanisms of the low rate of embryonic loss in Chinese Taihu pigs, facilitate the identification of major genes that affect litter size, and be valuable for porcine transcriptomic studies.
Reassessment of the Listeria monocytogenespan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome
Authors: Kuenne Carsten , Billion André , Mraheil Mobarak Abu , Strittmatter Axel , Daniel Rolf , Goesmann Alexander , Barbuddhe Sukhadeo , Hain Torsten , Chakraborty Trinad 
Published: January 2013

AbstractBackgroundListeria monocytogenesis an important food-borne pathogen and model organism for host-pathogen interaction, thus representing an invaluable target considering research on the forces governing the evolution of such microbes. The diversity of this species has not been exhaustively explored yet, as previous efforts have focused on analyses of serotypes primarily implicated in human listeriosis. We conducted complete genome sequencing of 11 strains employing 454 GS FLX technology, thereby achieving full coverage of all serotypes including the first complete strains of serotypes 1/2b, 3c, 3b, 4c, 4d, and 4e. These were comparatively analyzed in conjunction with publicly available data and assessed for pathogenicity in theGalleria mellonellainsect model.ResultsThe species pan-genome ofL. monocytogenesis highly stable but open, suggesting an ability to adapt to new niches by generating or including new genetic information. The majority of gene-scale differences represented by the accessory genome resulted from nine hyper variable hotspots, a similar number of different prophages, three transposons (Tn916, Tn554, IS3-like), and two mobilizable islands. Only a subset of strains showed CRISPR/Cas bacteriophage resistance systems of different subtypes, suggesting a supplementary function in maintenance of chromosomal stability. Multiple phylogenetic branches of the genusListeriaimply long common histories of strains of each lineage as revealed by a SNP-based core genome tree highlighting the impact of small mutations for the evolution of speciesL. monocytogenes. Frequent loss or truncation of genes described to be vital for virulence or pathogenicity was confirmed as a recurring pattern, especially for strains belonging to lineages III and II. New candidate genes implicated in virulence function were predicted based on functional domains and phylogenetic distribution. A comparative analysis of small regulatory RNA candidates supports observations of a differential distribution oftrans-encoded RNA, hinting at a diverse range of adaptations and regulatory impact.ConclusionsThis study determined commonly occurring hyper variable hotspots and mobile elements as primary effectors of quantitative gene-scale evolution of speciesL. monocytogenes, while gene decay and SNPs seem to represent major factors influencing long-term evolution. The discovery of common and disparately distributed genes considering lineages, serogroups, serotypes and strains of speciesL. monocytogeneswill assist in diagnostic, phylogenetic and functional research, supported by the comparative genomic GECO-LisDB analysis server (http://bioinfo.mikrobio.med.uni-giessen.de/geco2lisdb).