bluuebunny/crossref_metadata_2025_split huggingface dataset:
Higher Resolution in an Operational Ensemble Kalman Filter
Authors: Houtekamer P. L. , Deng Xingxiu , Mitchell Herschel L. , Baek Seung-Jong , Gagnon Normand 
Published: September 2013

Abstract
Recently, the computing facilities available to the Meteorological Service of Canada were significantly upgraded. This provided an opportunity to improve the resolution of the global ensemble Kalman filter (EnKF) and the medium-range Global Ensemble Prediction System (GEPS). In the EnKF, the main upgrades include improved horizontal, vertical, and temporal resolution. With the introduction of the higher horizontal resolution, it was decided to use a filtered topography in order to address an occasional instability problem. At the same time, the number of assimilated radiance observations was increased via a relaxation of the data-thinning procedures. In the medium-range GEPS, which already used the higher horizontal resolution, the filtered topography was also adopted. Likewise, the temporal resolution was increased to be the same as in the short-range integrations of the EnKF. With these changes, the grid used by the Canadian EnKF has 600 × 300 points in the horizontal and 74 vertical levels. The forecast model uses a 20-min time step and, for time interpolation of the model trajectories, model states are stored every hour. The EnKF uses an ensemble having 192 members. This paper sequentially examines the impact of these implemented changes. The upgraded EnKF became operational at the Canadian Meteorological Centre in mid-February 2013.
The interrelationships between moral attitudes, posttraumatic stress disorder symptoms and mixed lateral preference in Israeli reserve combat troops
Authors: Ritov Gilad , Barnetz Zion 
Published: September 2013

Background: Combat soldiers often encounter moral dilemmas during operational deployment, especially when an armed engagement is situated within a civilian setting. The study of moral dilemmas and posttraumatic stress disorder (PTSD) has mostly focused on the impact of war atrocities and moral injury. However, the relationship between moral attitudes and different combat-related pathologies has not been thoroughly addressed by quantitative studies. Aims: We aimed to assess the relationship between combatant’s moral attitudes, severity of PTSD symptoms and mixed lateral preference. Methods: Data on moral objection, PTSD severity and lateral preference were collected in a right-handed non-pathologic sample ( n = 147) of reserve combat troops in the Israel Defense Forces (IDF). Results: Nearly one-fifth (19.7%) of the reserve personnel who served in the occupied territories have reported high moral objection to the commands they were expected to act upon. This group of participants exhibited more PTSD symptoms and higher levels of mixed lateral preference. Multiple linear regression analyses revealed a mediating role of moral objection in the relationship between PTSD symptoms severity and lateral preference. Conclusions: Our findings suggest that moral objection has significant implications on combatant’s psychological and organic well-being. The findings highlight the need to include moral attitudes in research and clinical practice among combat personnel and veterans.
Comparison of patient comfort between iodixanol and iopamidol in contrast-enhanced computed tomography of the abdomen and pelvis: a randomized trial
Authors: Weiland Frederick L , Marti-Bonmati Luis , Lim Lauren , Becker Hans-Christoph 
Published: September 2013

Background Previous clinical studies have shown that iso-osmolar iodixanol (Visipaque®) causes less patient discomfort than low-osmolar contrast media (LOCM) when administered via intra-arterial injection. No data are available comparing these agents for patient discomfort when administered intravenously (i.v.) using power injectors. Purpose To compare the frequency and intensity of patient discomfort between iodixanol and iopamidol (Isovue®) administered i.v. using a power injector in contrast-enhanced computed tomography (CECT) of the abdomen and pelvis. Material and Methods This was a prospective, randomized, double-blind, multicenter study of iodixanol 320 mg I/mL or iopamidol 370 mg I/mL on patient discomfort. The presence of discomfort (heat, pain, coldness) and intensity was verbally rated by patients on a 0–10 scale and converted into four categories (0, none; 1–3, mild; 4–7, moderate; 8–10, severe). Image quality was evaluated. Results Of the 299 evaluable patients enrolled at nine centers, 151 received iodixanol and 148 received iopamidol. The average age was 58 years. Iodixanol patients experienced significantly less moderate/severe discomfort (35.1% vs. 67.3%; P < 0.0001) or heat (29.8% vs. 63.9%; P < 0.0001), and severe discomfort (2.6% vs. 16.3%; P = 0.0004) or heat (2.6% vs. 15%; P = 0.0008), but three times more no discomfort (21.2% vs. 7.5%; P = 0.0008) than iopamidol patients. Excellent image quality was in 95.4% of iodixanol vs. 89.9% of iopamidol patients ( P = 0.0508). Overall, adverse event (AE) rate excluding patient discomfort was 19.9% in the iodixanol group and 14.9% in the iopamidol group ( P = 0.2870), but contrast-related AEs were comparable: 11.3% vs. 10.1% ( P = 0.8522). Delayed skin reactions occurred in 2.6% of patients in the iodixanol group and in no patient in the iopamidol group ( P = 0.1226). Conclusion Patients receiving iodixanol had significantly lower moderate-to-severe or severe discomfort than patients receiving iopamidol, with heat being the major contributor. Iodixanol use trended towards better image quality but the difference was not statistically significant. No significant differences in incidences of overall or contrast-related AEs or delayed skin reactions were seen between the two groups. These data support that CM osmolality may be a key determinant of patient discomfort.
Numerical investigation on effect of inlet nozzle size on efficiency and flow pattern in squirrel cage fans
Authors: Gholamian Mojtaba , Rao Gurram K Mohan , Bhramara Panitapu 
Published: September 2013

Squirrel cage fan is a special type of turbo machines commonly used in industries and buildings (as a part of heating, ventilation and air conditioning (HVAC) systems). There are lots of important parameters that can affect the performance and efficiency (energy consuming). Experiments have shown that there are some turbulent areas in volute and impeller, and also in few cases, the relationships between the fan parameters, geometry and nondimensional parameters, and turbulent areas or performances were defined. In this paper, the effect of inlet-nozzle diameter on performance and flow pattern is considered. Three inlet nozzle sizes with respect to impeller size were chosen (smaller, nearly same, and bigger than inner impeller diameter), and numerical simulations with different turbulence models were performed to find the effect of inlet size on flow pattern, performance, and efficiency. For the validation of numerical results, some experiments were done, and all the performance parameters were compared to that of numerical results. These results showed good matching between experimental and numerical results. From each case study, flow pattern and its mechanism and the reasons of low efficiency are studied and presented.
Subjective well-being, social work, and the environment: The impact of the socio-political context of practice on social worker happiness
Authors: Shier Micheal L , Graham John R 
Published: September 2013

Summary The environmental context of direct social work practice has been found to impact social worker subjective well-being. Most research focus on the geographic and cultural characteristics of that practice environment. To expand this knowledge domain a qualitative inquiry has been undertaken to understand what aspects of the socio-political environment impacted social worker well-being. Findings This qualitative study, with a sample of social workers ( n = 19), found three themes related to the socio-political environment that can contribute to practitioner well-being. Respondents identified that their subjective well-being is impacted by: (1) perceptions of practitioners by community members, (2) conflict with social work program mandates, and (3) changes with the social welfare system. Applications Possible methods of addressing these issues to improve workplace functioning for social workers are discussed along with areas of future research.
Cochrane corner: local corticosteroid injection for carpal tunnel syndrome
Authors: Stark H. , Amirfeyz R. 
Published: September 2013

Background: Carpal tunnel syndrome is a clinical syndrome manifested by signs and symptoms of irritation of the median nerve at the carpal tunnel in the wrist. Local corticosteroid injection for carpal tunnel syndrome has been studied but its effectiveness is unknown. Objectives: To evaluate the effectiveness of local corticosteroid injection for carpal tunnel syndrome versus placebo injection or other non-surgical interventions. Search methods: We searched the Cochrane Neuromuscular Disease Group Trials register (searched May 2006), MEDLINE (searched January 1966 to May 2006), EMBASE (searched January 1980 to May 2006) and CINAHL (searched January 1982 to May 2006). Selection criteria: Randomized or quasi-randomized studies. Data collection and analysis: Three authors independently selected the trials and rated their overall quality. Relative risks and 95% confidence intervals were calculated for each trial and summary relative risks and 95% confidence intervals were also calculated.
Integrating in vitro sensitivity and dose-response slope is predictive of clinical response to ABL kinase inhibitors in chronic myeloid leukemia
Authors: Vainstein Vladimir , Eide Christopher A. , O’Hare Thomas , Shukron Ofir , Druker Brian J. 
Published: September 2013

Key Points
Decreased in vitro dose-response slope tracks with resistance BCR-ABL mutants to ABL tyrosine kinase inhibitors. Integrating in vitro dose-response slope, the IC50 of various BCR-ABL mutants, and clinical PK data can predict CML patients’ response to TKIs.
Riemann-Liouville fractional Hermite-Hadamard inequalities. Part I: for once differentiable geometric-arithmetically s-convex functions
Authors: Liao YuMei , Deng JianHua , Wang JinRong 
Published: September 2013

Abstract
By using the definition of geometric-arithmetically s-convex functions in (Analysis 33:197-208, 2013) and first-order fractional integral identities in (Math. Comput. Model. 57:2403-2407, 2013; J. Appl. Math. Stat. Inform. 8:21-28, 2012; Comput. Math. Appl. 63:1147-1154, 2012), we present some interesting Riemann-Liouville fractional Hermite-Hadamard inequalities for differentiable geometric-arithmetically s-convex functions. Both beta function and incomplete beta function are used in the desired estimations.

MSC:26A33, 26A51, 26D15.
Peak Finder Metaserver - a novel application for finding peaks in ChIP-seq data
Authors: Kruczyk Marcin , Umer Husen M , Enroth Stefan , Komorowski Jan 
Published: September 2013

Abstract

Background
Finding peaks in ChIP-seq is an important process in biological inference. In some cases, such as positioning nucleosomes with specific histone modifications or finding transcription factor binding specificities, the precision of the detected peak plays a significant role. There are several applications for finding peaks (called peak finders) based on different algorithms (e.g. MACS, Erange and HPeak). Benchmark studies have shown that the existing peak finders identify different peaks for the same dataset and it is not known which one is the most accurate. We present the first meta-server called Peak Finder MetaServer (PFMS) that collects results from several peak finders and produces consensus peaks. Our application accepts three standard ChIP-seq data formats: BED, BAM, and SAM.

Results
Sensitivity and specificity of seven widely used peak finders were examined. For the experiments we used three previously studied Transcription Factors (TF) ChIP-seq datasets and identified three of the selected peak finders that returned results with high specificity and very good sensitivity compared to the remaining four. We also ran PFMS using the three selected peak finders on the same TF datasets and achieved higher specificity and sensitivity than the peak finders individually.

Conclusions
We show that combining outputs from up to seven peak finders yields better results than individual peak finders. In addition, three of the seven peak finders outperform the remaining four, and running PFMS with these three returns even more accurate results. Another added value of PFMS is a separate report of the peaks returned by each of the included peak finders.
Australian and Pacific contributions to the genetic diversity of Norfolk Island feral chickens
Authors: Langford S Shannan M , Kraitsek Spiridoula , Baskerville Bruce , Ho Simon YW , Gongora Jaime 
Published: September 2013

Abstract

Background
Norfolk Island has a population of feral chickens which could be the result of domestic stock introduced onto the island by British settlers in 1788. However, there is ongoing debate about their origins because multiple human arrivals to the island may have brought chickens with them. Here we investigate the genetic origins of these feral chickens by sequencing their mitochondrial control region. We infer their phylogenetic relationships using a large dataset of novel sequences from Australian mainland domestic chickens and published sequences from around the world.

Results
Eleven control region haplotypes were found among the Norfolk Island feral and Australian mainland domestic chickens. Six of the Norfolk Island haplotypes fall within haplogroup E, but given the worldwide distribution of this haplogroup, the putative European origin of these chickens requires further investigation. One haplotype common among Norfolk Island and Australian samples belonged to a subgroup of haplogroup D, which appears to be restricted to chickens from Indonesia, Vanuatu and Guam.

Conclusions
Our data show that at least two mitochondrial DNA haplogroups (D and E) have contributed to the genetic make-up of Norfolk Island feral chickens. In addition, we have provided insights into the discrete geographical distribution and diversity of the chicken haplogroup D. In view of the worldwide interest in the characterisation of poultry resources, further assessment of chicken populations of Island Southeast Asia and the Pacific region is warranted.
Comparative methylomics between domesticated and wild silkworms implies possible epigenetic influences on silkworm domestication
Authors: Xiang Hui , Li Xin , Dai Fangyin , Xu Xun , Tan Anjiang , Chen Lei , Zhang Guojie , Ding Yun , Li Qiye , Lian Jinmin , Willden Andrew , Guo Qiuhong , Xia Qingyou , Wang Jun , Wang Wen 
Published: September 2013

Abstract

Background
In contrast to wild species, which have typically evolved phenotypes over long periods of natural selection, domesticates rapidly gained human-preferred agronomic traits in a relatively short-time frame via artificial selection. Under domesticated conditions, many traits can be observed that cannot only be due to environmental alteration. In the case of silkworms, aside from genetic divergence, whether epigenetic divergence played a role in domestication is an unanswered question. The silkworm is still an enigma in that it has two DNA methyltransferases (DNMT1 and DNMT2) but their functionality is unknown. Even in particular the functionality of the widely distributed DNMT1 remains unknown in insects in general.

Results
By embryonic RNA interference, we reveal that knockdown of silkworm Dnmt1 caused decreased hatchability, providing the first direct experimental evidence of functional significance of insect Dnmt1. In the light of this fact and those that DNA methylation is correlated with gene expression in silkworms and some agronomic traits in domesticated organisms are not stable, we comprehensively compare silk gland methylomes of 3 domesticated (Bombyx mori) and 4 wild (Bombyx mandarina) silkworms to identify differentially methylated genes between the two. We observed 2-fold more differentiated methylated cytosinces (mCs) in domesticated silkworms as compared to their wild counterparts, suggesting a trend of increasing DNA methylation during domestication. Further study of more domesticated and wild silkworms narrowed down the domesticates’ epimutations, and we were able to identify a number of differential genes. One such gene showing demethyaltion in domesticates correspondently displays lower gene expression, and more interestingly, has experienced selective sweep. A methylation-increased gene seems to result in higher expression in domesticates and the function of its Drosophila homolog was previously found to be essential for cell volume regulation, indicating a possible correlation with the enlargement of silk glands in domesticated silkworms.

Conclusions
Our results imply epigenetic influences at work during domestication, which gives insight into long time historical controversies regarding acquired inheritance.
Comprehensive transcriptomic study on horse gram (Macrotyloma uniflorum): De novo assembly, functional characterization and comparative analysis in relation to drought stress
Authors: Bhardwaj Jyoti , Chauhan Rohit , Swarnkar Mohit Kumar , Chahota Rakesh Kumar , Singh Anil Kumar , Shankar Ravi , Yadav Sudesh Kumar 
Published: September 2013

Abstract

Background
Drought tolerance is an attribute maintained in plants by cross-talk between multiple and cascading metabolic pathways. Without a sequenced genome available for horse gram, it is difficult to comprehend such complex networks and intercalated genes associated with drought tolerance of horse gram (Macrotyloma uniflorum). Therefore, de novo transcriptome discovery and associated analyses was done for this highly drought tolerant yet under exploited legume to decipher its genetic makeup.

Results
Eight samples comprising of shoot and root tissues of two horse gram genotypes (drought-sensitive; M-191 and drought-tolerant; M-249) were used for comparison under control and polyethylene glycol-induced drought stress conditions. Using Illumina sequencing technology, a total of 229,297,896 paired end read pairs were generated and utilized for de novo assembly of horse gram. Significant BLAST hits were obtained for 26,045 transcripts while, 3,558 transcripts had no hits but contained important conserved domains. A total of 21,887 unigenes were identified. SSRs containing sequences covered 16.25% of the transcriptome with predominant tri- and mono-nucleotides (43%). The total GC content of the transcriptome was found to be 43.44%. Under Gene Ontology response to stimulus, DNA binding and catalytic activity was highly expressed during drought stress conditions. Serine/threonine protein kinase was found to dominate in Enzyme Classification while pathways belonging to ribosome metabolism followed by plant pathogen interaction and plant hormone signal transduction were predominant in Kyoto Encyclopedia of Genes and Genomes analysis. Independent search on plant metabolic network pathways suggested valine degradation, gluconeogenesis and purine nucleotide degradation to be highly influenced under drought stress in horse gram. Transcription factors belonging to NAC, MYB-related, and WRKY families were found highly represented under drought stress. qRT-PCR validated the expression profile for 9 out of 10 genes analyzed in response to drought stress.

Conclusions

De novo transcriptome discovery and analysis has generated enormous information over horse gram genomics. The genes and pathways identified suggest efficient regulation leading to active adaptation as a basal defense response against drought stress by horse gram. The knowledge generated can be further utilized for exploring other underexploited plants for stress responsive genes and improving plant tolerance.
Estradiol prevents olfactory dysfunction induced by A-β 25–35 injection in hippocampus
Authors: Bernal-Mondragón Carlos , Rivas-Arancibia Selva , Kendrick Keith M , Guevara-Guzmán Rosalinda 
Published: September 2013

Abstract

Background
Some neurodegenerative diseases, such as Alzheimer and Parkinson, present an olfactory impairment in early stages, and sometimes even before the clinical symptoms begin. In this study, we assess the role of CA1 hippocampus (structure highly affected in Alzheimer disease) subfield in the rats’ olfactory behavior, and the neuroprotective effect of 17 beta estradiol (E2) against the oxidative stress produced by the injection of amyloid beta 25–35.

Results
162 Wistar rats were ovariectomized and two weeks after injected with 2 μl of amyloid beta 25–35 (A-β25–35) in CA1 subfield. Olfactory behavior was evaluated with a social recognition test, odor discrimination, and search tests. Oxidative stress was evaluated with FOX assay and Western Blot against 4-HNE, Fluoro Jade staining was made to quantify degenerated neurons; all these evaluations were performed 24 h, 8 or 15 days after A-β25–35 injection. Three additional groups treated with 17 beta estradiol (E2) were also evaluated. The injection of A-β25–35 produced an olfactory impairment 24 h and 8 days after, whereas a partial recovery of the olfactory behavior was observed at 15 days. A complete prevention of the olfactory impairment was observed with the administration of E2 two weeks before the amyloid injection (A-β25–35 24 h + E2) and one or two weeks after (groups 8 A-β +E2 and 15 A-β +E2 days, respectively); a decrease of the oxidative stress and neurodegeneration were also observed.

Conclusions
Our finding shows that CA1 hippocampus subfield plays an important role in the olfactory behavior of the rat. The oxidative stress generated by the administration of A-β25–35 is enough to produce an olfactory impairment. This can be prevented with the administration of E2 before and after amyloid injection. This suggests a possible therapeutic use of estradiol in Alzheimer’s disease.
Development-associated microRNAs in grains of wheat (Triticum aestivumL.)
Authors: Meng Fanrong , Liu Hao , Wang Ketao , Liu Lulu , Wang Shaohui , Zhao Yanhong , Yin Jun , Li Yongchun 
Published: September 2013

Abstract

Background
MicroRNAs (miRNAs) are a class of regulatory small RNAs (sRNAs) that down-regulate target genes by mRNA degradation or translational repression. Numerous plant miRNAs have been identified. Evidence is increasing for their crucial roles during plant development. In the globally important crop of wheat (Triticum aestivum L.), the process by which grains are formed determines yield and end-use quality. However, little is known about miRNA-mediated developmental regulation of grain production. Here, we applied high-throughput sRNA sequencing and genome-wide mining to identify miRNAs potentially involved in the developmental regulation of wheat grains.

Results
Four sRNA libraries were generated and sequenced from developing grains sampled at 5, 15, 25, and 30 days after pollination (DAP). Through integrative analysis, we identified 605 miRNAs (representing 540 families) and found that 86 are possibly involved in the control of grain-filling. Additionally, 268 novel miRNAs (182 families) were identified, with 18 of them also potentially related to that maturation process. Our target predictions indicated that the 104 grain filling-associated miRNAs might target a set of wheat genes involved in various biological processes, including the metabolism of carbohydrates and proteins, transcription, cellular transport, cell organization and biogenesis, stress responses, signal transduction, and phytohormone signaling. Together, these results demonstrate that the developmental steps by which wheat grains are filled is correlated with miRNA-mediated gene regulatory networks.

Conclusions
We identified 605 conserved and 268 novel miRNAs from wheat grains. Of these, 104 are potentially involved in the regulation of grain-filling. Our dataset provides a useful resource for investigating miRNA-mediated regulatory mechanisms in cereal grains, and our results suggest that miRNAs contribute to this regulation during a crucial phase in determining grain yield and flour quality.