bluuebunny/crossref_metadata_2025_split huggingface dataset:
A combined strategy involving Sanger and 454 pyrosequencing increases genomic resources to aid in the management of reproduction, disease control and genetic selection in the turbot (Scophthalmus maximus)
Authors: Ribas Laia , Pardo Belén G , Fernández Carlos , Álvarez-Diós José Antonio , Gómez-Tato Antonio , Quiroga María Isabel , Planas Josep V , Sitjà-Bobadilla Ariadna , Martínez Paulino , Piferrer Francesc 
Published: March 2013

AbstractBackgroundGenomic resources for plant and animal species that are under exploitation primarily for human consumption are increasingly important, among other things, for understanding physiological processes and for establishing adequate genetic selection programs. Current available techniques for high-throughput sequencing have been implemented in a number of species, including fish, to obtain a proper description of the transcriptome. The objective of this study was to generate a comprehensive transcriptomic database in turbot, a highly priced farmed fish species in Europe, with potential expansion to other areas of the world, for which there are unsolved production bottlenecks, to understand better reproductive- and immune-related functions. This information is essential to implement marker assisted selection programs useful for the turbot industry.ResultsExpressed sequence tags were generated by Sanger sequencing of cDNA libraries from different immune-related tissues after several parasitic challenges. The resulting database (“Turbot 2 database”) was enlarged with sequences generated from a 454 sequencing run of brain-hypophysis-gonadal axis-derived RNA obtained from turbot at different development stages. The assembly of Sanger and 454 sequences generated 52,427 consensus sequences (“Turbot 3 database”), of which 23,661 were successfully annotated. A total of 1,410 sequences were confirmed to be related to reproduction and key genes involved in sex differentiation and maturation were identified for the first time in turbot (AR,AMH,SRY-related genes,CYP19A,ZPGs,STAR FSHR,etc.). Similarly, 2,241 sequences were related to the immune system and several novel key immune genes were identified (BCL,TRAF,NCK,CD28andTOLLIP,among others). The number of genes of many relevant reproduction- and immune-related pathways present in the database was 50–90% of the total gene count of each pathway. In addition, 1,237 microsatellites and 7,362 single nucleotide polymorphisms (SNPs) were also compiled. Further, 2,976 putative natural antisense transcripts (NATs) including microRNAs were also identified.ConclusionsThe combined sequencing strategies employed here significantly increased the turbot genomic resources available, including 34,400 novel sequences. The generated database contains a larger number of genes relevant for reproduction- and immune-associated studies, with an excellent coverage of most genes present in many relevant physiological pathways. This database also allowed the identification of many microsatellites and SNP markers that will be very useful for population and genome screening and a valuable aid in marker assisted selection programs.
Comparative genomics of parasitic silkworm microsporidia reveal an association between genome expansion and host adaptation
Authors: Pan Guoqing , Xu Jinshan , Li Tian , Xia Qingyou , Liu Shao-Lun , Zhang Guojie , Li Songgang , Li Chunfeng , Liu Handeng , Yang Liu , Liu Tie , Zhang Xi , Wu Zhengli , Fan Wei , Dang Xiaoqun , Xiang Heng , Tao Meilin , Li Yanhong , Hu Junhua , Li Zhi , Lin Lipeng , Luo Jie , Geng Lina , Wang LinLing , Long Mengxian , Wan Yongji , He Ningjia , Zhang Ze , Lu Cheng , Keeling Patrick J , Wang Jun , Xiang Zhonghuai , Zhou Zeyang 
Published: March 2013

Abstract

Background
Microsporidian Nosema bombycis has received much attention because the pébrine disease of domesticated silkworms results in great economic losses in the silkworm industry. So far, no effective treatment could be found for pébrine. Compared to other known Nosema parasites, N. bombycis can unusually parasitize a broad range of hosts. To gain some insights into the underlying genetic mechanism of pathological ability and host range expansion in this parasite, a comparative genomic approach is conducted. The genome of two Nosema parasites, N. bombycis and N. antheraeae (an obligatory parasite to undomesticated silkworms Antheraea pernyi), were sequenced and compared with their distantly related species, N. ceranae (an obligatory parasite to honey bees).

Results
Our comparative genomics analysis show that the N. bombycis genome has greatly expanded due to the following three molecular mechanisms: 1) the proliferation of host-derived transposable elements, 2) the acquisition of many horizontally transferred genes from bacteria, and 3) the production of abundnant gene duplications. To our knowledge, duplicated genes derived not only from small-scale events (e.g., tandem duplications) but also from large-scale events (e.g., segmental duplications) have never been seen so abundant in any reported microsporidia genomes. Our relative dating analysis further indicated that these duplication events have arisen recently over very short evolutionary time. Furthermore, several duplicated genes involving in the cytotoxic metabolic pathway were found to undergo positive selection, suggestive of the role of duplicated genes on the adaptive evolution of pathogenic ability.

Conclusions
Genome expansion is rarely considered as the evolutionary outcome acting on those highly reduced and compact parasitic microsporidian genomes. This study, for the first time, demonstrates that the parasitic genomes can expand, instead of shrink, through several common molecular mechanisms such as gene duplication, horizontal gene transfer, and transposable element expansion. We also showed that the duplicated genes can serve as raw materials for evolutionary innovations possibly contributing to the increase of pathologenic ability. Based on our research, we propose that duplicated genes of N. bombycis should be treated as primary targets for treatment designs against pébrine.
Etanercept attenuates traumatic brain injury in rats by reducing early microglial expression of tumor necrosis factor-α
Authors: Chio Chung-Ching , Chang Chin-Hong , Wang Che-Chuan , Cheong Chong-Un , Chao Chien-Ming , Cheng Bor-Chih , Yang Chung-Zhing , Chang Ching-Ping 
Published: March 2013

Abstract

Background
Tumor necrosis factor-alpha (TNF-α) is elevated early in injured brain after traumatic brain injury (TBI), in humans and in animals. Etanercept (a TNF-α antagonist with anti-inflammatory effects) attenuates TBI in rats by reducing both microglial and astrocytic activation and increased serum levels of TNF-α. However, it is not known whether etanercept improves outcomes of TBI by attenuating microglia-associated, astrocytes-associated, and/or neurons-associated TNF-α expression in ischemic brain. A well clinically relevant rat model, where a lateral fluid percussion is combined with systemic administration of etanercept immediately after TBI, was used. The neurological severity score and motor function was measured on all rats preinjury and on day 3 after etanercept administration. At the same time, the neuronal and glial production of TNF-α was measured by Immunofluorescence staining. In addition, TNFα contents of ischemic cerebral homogenates was measured using commercial enzyme-linked immunosorbent assay kits.

Results
In addition to inducing brain ischemia as well as neurological and motor deficits, TBI caused significantly higher numbers of microglia-TNF-α double positive cells, but not neurons-TNF-α or astrocytes-TNF-α double positive cells in the injured brain areas than did the sham operated controls, when evaluated 3 days after TBI. The TBI-induced cerebral ischemia, neurological motor deficits, and increased numbers of microglia-TNF-α double positive cells and increased TNF-α levels in the injured brain were all significantly attenuated by etanercept therapy.

Conclusion
This finding indicates that early microglia overproduction of TNF-α in the injured brain region after TBI contributes to cerebral ischemia and neurological motor deficits, which can be attenuated by etanercept therapy. Studies in this model could provide insight into the mechanisms underlying neurological motor disturbance in brain-injured patients.
Comparative proteomic and metabolomic profiling of citrus fruit with enhancement of disease resistance by postharvest heat treatment
Authors: Yun Ze , Gao Huijun , Liu Ping , Liu Shuzhen , Luo Tao , Jin Shuai , Xu Qiang , Xu Juan , Cheng Yunjiang , Deng Xiuxin 
Published: March 2013

Abstract

Background
From field harvest to the consumer’s table, fresh citrus fruit spends a considerable amount of time in shipment and storage. During these processes, physiological disorders and pathological diseases are the main causes of fruit loss. Heat treatment (HT) has been widely used to maintain fruit quality during postharvest storage; however, limited molecular information related to this treatment is currently available at a systemic biological level.

Results
Mature ‘Kamei’ Satsuma mandarin (Citrus unshiu Marc.) fruits were selected for exploring the disease resistance mechanisms induced by HT during postharvest storage. Proteomic analyses based on two-dimensional gel electrophoresis (2-DE), and metabolomic research based on gas chromatography coupled to mass spectrometry (GC-MS), and liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QToF-MS) were conducted. The results show resistance associated proteins were up-regulated in heat treated pericarp, such as beta-1, 3-glucanase, Class III chitinase, 17.7 kDa heat shock protein and low molecular weight heat-shock protein. Also, redox metabolism enzymes were down-regulated in heat treated pericarp, including isoflavone reductase, oxidoreductase and superoxide dismutase. Primary metabolic profiling revealed organic acids and amino acids were down-regulated in heat treated pericarp; but significant accumulation of metabolites, including tetradecanoic acid, oleic acid, ornithine, 2-keto-d-gluconic acid, succinic acid, turanose, sucrose, galactose, myo-inositol, glucose and fructose were detected. Noticeably, H2O2 content decreased, while, lignin content increased in heat treated pericarp compared to the control, which might increase fruit resistibility in response to external stress. Also, flavonoids, substances which are well-known to be effective in reducing external stress, were up-regulated in heat treated pericarp.

Conclusions
This study provides a broad picture of differential accumulation of proteins and metabolites in postharvest citrus fruit, and gives new insights into HT improved fruit disease resistance during subsequent storage of ‘Kamei’ Satsuma mandarin. Interpretation of the data for the proteins and metabolites revealed reactive oxygen species (ROS) and lignin play important roles in heat treatment induced fruit resistance to pathogens and physiological disorders.
Weight patterns and perceptions among female university students of Karachi: a cross sectional study
Authors: Sirang Zubaida , Bashir Hassaan Hasan , Jalil Bilal , Khan Sarah Haroon , Hussain Samia Altaf , Baig Aneeqa , Taufeeq Maryam , Samad Kashif , Kadir Muhammad Masood 
Published: March 2013

Abstract

Background
Body weight and its perception play an important role in the physical and mental well-being of a person. Weight perception is found to be a better predictor of weight management behaviour as compared to actual weight. In Pakistan, studies have been done on the prevalence of weight status but weight perception is still unexplored. The study was done to examine relationships between body weight perception, actual weight status, and weight control behaviour among the female university students of Karachi.

Methods
A cross sectional study was carried out during Sep-Nov 2009 on female students in four universities of Karachi, Pakistan. Our final sample size included 338 female university students. Height and weight were measured on calibrated scales. A modified BMI criterion for Asian populations was used.

Results
Based on measured BMI; the prevalence of underweight, normal weight and overweight females was 27.2%, 51.5% and 21.3% respectively. As a whole, just over one third (33.73%) of the sample misclassified their weight status. Among underweight (n=92), 45.70% thought they were of normal weight. No one who was truly underweight perceived them self as overweight. Among the normal weight (n= 174), 9.8% thought they were underweight and 23.6% considered themselves overweight. Among the overweight (n=72); 18.3% considered themselves normal. Only one female student thought she was underweight despite being truly overweight.

Conclusions
Our study shows that among female university students in Karachi, the prevalence of being underweight is comparatively high. There is a significant misperception of weight, with one third of students misclassifying themselves. Underweight females are likely to perceive themselves as normal and be most satisfied with their weight. Health policy makers should implement these findings in future development of health interventions and prevention of depression, social anxiety and eating disorders associated with incorrect weight perception among young females. Studies that employ a longitudinal approach are needed to validate our findings.
The use of DNA from archival dried blood spots with the Infinium HumanMethylation450 array
Authors: Joo JiHoon E , Wong Ee Ming , Baglietto Laura , Jung Chol-Hee , Tsimiklis Helen , Park Daniel J , Wong Nicholas C , English Dallas R , Hopper John L , Severi Gianluca , Giles Graham G , Southey Melissa C 
Published: March 2013

Abstract

Background
Dried blood (Guthrie card) spots provide an efficient way to collect and store blood specimens. DNA from this source has been utilised for a number of molecular analyses including genome-wide association studies, but only few studies have tested the feasibility of using it for epigenetic applications, particularly at a genome-wide level.

Results
In this study, we demonstrate the successful use of DNA isolated from archived dried blood spots for the Infinium HumanMethylation450 Beadchip, along with DNA from matched frozen buffy coats. We obtained high quality and reproducible genome-wide DNA methylation profiles using both sample types. We also report high correlations (r > 0.9907) between DNA obtained from matched dried blood spots and frozen buffy coats, sufficient to distinguish between unrelated individuals.

Conclusions
We, thus, demonstrate that DNA from archived dried blood spots is suitable for genome-wide DNA methylation profiling.
The role of Cysteine 6.47 in class A GPCRs
Authors: Olivella Mireia , Caltabiano Gianluigi , Cordomí Arnau 
Published: March 2013

Abstract

Background
The CWxP motif of transmembrane helix 6 (x: any residue) is highly conserved in class A GPCRs. Within this motif, W6.48 is a big star in the theory of the global “toggle switch” because of its key role in the activation mechanism of GPCRs upon ligand binding. With all footlights focused on W6.48, the reason why the preceding residue, C6.47, is largely conserved is still unknown. The present study is aimed to fill up this lack of knowledge by characterizing the role of C6.47 of the CWxP motif.

Results
A complete analysis of available crystal structures has been made alongside with molecular dynamics simulations of model peptides to explore a possible structural role for C6.47.

Conclusions
We conclude that C6.47 does not modulate the conformation of the TM6 proline kink and propose that C6.47 participates in the rearrangement of the TM6 and TM7 interface accompanying activation.
Ferromagnetism in freestanding MoS2 nanosheets
Authors: Gao Daqiang , Si Mingsu , Li Jinyun , Zhang Jing , Zhang Zhipeng , Yang Zhaolong , Xue Desheng 
Published: March 2013

Abstract
Freestanding MoS2 nanosheets with different sizes were prepared through a simple exfoliated method by tuning the ultrasonic time in the organic solvent. Magnetic measurement results reveal the clear room-temperature ferromagnetism for all the MoS2 nanosheets, in contrast to the pristine MoS2 in its bulk form which shows diamagnetism only. Furthermore, results indicate that the saturation magnetizations of the nanosheets increase as the size decreases. Combining the X-ray photoelectron spectroscopy, transmission electron microscopy, and electron spin resonance results, it is suggested that the observed magnetization is related to the presence of edge spins on the edges of the nanosheets. These MoS2 nanosheets may find applications in nanodevices and spintronics by controlling the edge structures.
Two-stage decoding algorithm for unmodulated parallel combinatory high-compaction multicarrier modulation signals
Authors: Hayashi Ryuji , Li Yingsong , Hamamura Masanori 
Published: March 2013

Abstract
A new decoding algorithm that consists of two decoding stages to reduce the computational complexity of maximum likelihood decoding for parallel combinatory high-compaction multicarrier modulation is proposed. The first decoding stage is responsible for a preliminary decision that serves to roughly find candidate messages using the QRD-M algorithm, and the second decoding stage is responsible for the final decision that reduces the error contained in the candidate and determines the message using the minimum value of the Hamming distances between the candidate and the replicas of the message. The complexity is considerably reduced by the proposed two-stage decoding algorithm at a cost of approximately 1.5 dB or less in E

b
/N
0 with respect to the bit-error rate of 10-3 under the given parameter settings.
Experimental infection with a Thai reassortant swine influenza virus of pandemic H1N1 origin induced disease
Authors: Charoenvisal Nataya , Keawcharoen Juthatip , Sreta Donruethai , Tantawet Siriporn , Jittimanee Suphattra , Arunorat Jirapat , Amonsin Alongkorn , Thanawongnuwech Roongroje 
Published: March 2013

Abstract

Background
Following the emergence of the pandemic H1N1 influenza A virus in 2009 in humans, this novel virus spread into the swine population. Pigs represent a potential host for this virus and can serve as a mixing vessel for genetic mutations of the influenza virus. Reassortant viruses eventually emerged from the 2009 pandemic and were reported in swine populations worldwide including Thailand. As a result of the discovery of this emergent disease, pathogenesis studies of this novel virus were conducted in order that future disease protection and control measures in swine and human populations could be enacted.

Methods
The pandemic H1N1 2009 virus (pH1N1) and its reassortant virus (rH1N1) isolated from pigs in Thailand were inoculated into 2 separate cohorts of 9, 3-week-old pigs. Cohorts were consisted of one group experimentally infected with pH1N1 and one group with rH1N1. A negative control group consisting of 3 pigs was also included. Clinical signs, viral shedding and pathological lesions were investigated and compared. Later, 3 pigs from viral inoculated groups and 1 pig from the control group were necropsied at 2, 4, and 12 days post inoculation (DPI).

Results
The results indicated that pigs infected with both viruses demonstrated typical flu-like clinical signs and histopathological lesions of varying severity. Influenza infected-pigs of both groups had mild to moderate pulmonary signs on 1-4 DPI. Interestingly, pigs in both groups demonstrated viral RNA detection in the nasal swabs until the end of the experiment (12 DPI).

Conclusion
The present study demonstrated that both the pH1N1 and rH1N1 influenza viruses, isolated from naturally infected pigs, induced acute respiratory disease in experimentally inoculated nursery pigs. Although animals in the rH1N1-infected cohort demonstrated more severe clinical signs, had higher numbers of pigs shedding the virus, were noted to have increased histopathological severity of lung lesions and increased viral antigen in lung tissue, the findings were not statistically significant in comparison with the pH1N1-infected group. Interestingly, viral genetic material of both viruses could be detected from the nasal swabs until the end of the experiment. Similar to other swine influenza viruses, the clinical signs and pathological lesions in both rH1N1 and pH1N1 were limited to the respiratory tract.
Metabolic markers in Ossabaw pigs fed high fat diets enriched in regular or low α-linolenic acid soy oil
Authors: Potu Ramesh B , Lu Hang , Adeola Olayiwola , Ajuwon Kolapo M 
Published: March 2013

Abstract

Background
Soy oil is a major vegetable oil consumed in the US. A recently developed soybean variety produces oil with a lower concentration of α-linolenic acid, hence a higher (n-6)/(n-3) ratio, than regular soy oil. The study was conducted to determine the metabolic impact of the low α-linolenic acid containing soy oil.

Methods
Ossabaw pigs were fed diets supplemented with either 13% regular soybean oil (SBO), or 13% of the low α-linolenic soybean oil (LLO) or a control diet (CON) without extra oil supplementation, for 8 weeks.

Results
Serum and adipose tissue α-linolenic acid concentration was higher in pigs fed the SBO diet than those on the CON and LLO diets. In the serum, the concentration of saturated fatty acids (SFA) was lower in the LLO group than in CON and SBO groups polyunsaturated fatty acid (PUFA) concentration was higher in the LLO group compared to CON and SBO groups. Glucose, insulin, triglycerides and LDL-cholesterol were higher in pigs fed the SBO diet than those fed the CON and LLO diets. HDL-cholesterol was lower in pigs on the SBO diet than those on the CON and LLO diets. Pigs fed SBO and LLO diets had lower CRP concentration than those on the CON diet. Adipose tissue expression of Interleukin 6 (IL-6) was higher in the SBO and LLO diets than the CON. Expression of ECM genes, COLVIA and fibronectin, was significantly reduced in the SBO diet relative to the CON and LLO diets whereas expression of inflammation-related genes, cluster of differentiation 68 (CD68) and monocyte chemoattractant protein 1 (MCP-1), was not different across treatments.

Conclusions
Results suggest that lowering the content of α-linolenic acid in the context of a high fat diet could lead to mitigation of development of hyperinsulinemia and dyslipidemia without significant effects on adipose tissue inflammation.