bluuebunny/crossref_metadata_2025_split huggingface dataset:
ReplicationDomain: a visualization tool and comparative database for genome-wide replication timing data
Authors: Weddington Nodin , Stuy Alexander , Hiratani Ichiro , Ryba Tyrone , Yokochi Tomoki , Gilbert David M 
Published: December 2008

Abstract

Background
Eukaryotic DNA replication is regulated at the level of large chromosomal domains (0.5–5 megabases in mammals) within which replicons are activated relatively synchronously. These domains replicate in a specific temporal order during S-phase and our genome-wide analyses of replication timing have demonstrated that this temporal order of domain replication is a stable property of specific cell types.

Results
We have developed ReplicationDomain http://www.replicationdomain.org as a web-based database for analysis of genome-wide replication timing maps (replication profiles) from various cell lines and species. This database also provides comparative information of transcriptional expression and is configured to display any genome-wide property (for instance, ChIP-Chip or ChIP-Seq data) via an interactive web interface. Our published microarray data sets are publicly available. Users may graphically display these data sets for a selected genomic region and download the data displayed as text files, or alternatively, download complete genome-wide data sets. Furthermore, we have implemented a user registration system that allows registered users to upload their own data sets. Upon uploading, registered users may choose to: (1) view their data sets privately without sharing; (2) share with other registered users; or (3) make their published or "in press" data sets publicly available, which can fulfill journal and funding agencies' requirements for data sharing.

Conclusion
ReplicationDomain is a novel and powerful tool to facilitate the comparative visualization of replication timing in various cell types as well as other genome-wide chromatin features and is considerably faster and more convenient than existing browsers when viewing multi-megabase segments of chromosomes. Furthermore, the data upload function with the option of private viewing or sharing of data sets between registered users should be a valuable resource for the scientific community.
Valproic acid induces differentiation and inhibition of proliferation in neural progenitor cells via the beta-catenin-Ras-ERK-p21Cip/WAF1 pathway
Authors: Jung Gyung-Ah , Yoon Ju-Yong , Moon Byoung-San , Yang Dong-Hwa , Kim Hyun-Yi , Lee Sang-Hun , Bryja Vitezslav , Arenas Ernest , Choi Kang-Yell 
Published: December 2008

Abstract

Background
Valproic acid (VPA), a commonly used mood stabilizer that promotes neuronal differentiation, regulates multiple signaling pathways involving extracellular signal-regulated kinase (ERK) and glycogen synthase kinase3β (GSK3β). However, the mechanism by which VPA promotes differentiation is not understood.

Results
We report here that 1 mM VPA simultaneously induces differentiation and reduces proliferation of basic fibroblast growth factor (bFGF)-treated embryonic day 14 (E14) rat cerebral cortex neural progenitor cells (NPCs). The effects of VPA on the regulation of differentiation and inhibition of proliferation occur via the ERK-p21Cip/WAF1 pathway. These effects, however, are not mediated by the pathway involving the epidermal growth factor receptor (EGFR) but via the pathway which stabilizes Ras through β-catenin signaling. Stimulation of differentiation and inhibition of proliferation in NPCs by VPA occur independently and the β-catenin-Ras-ERK-p21Cip/WAF1 pathway is involved in both processes. The independent regulation of differentiation and proliferation in NPCs by VPA was also demonstrated in vivo in the cerebral cortex of developing rat embryos.

Conclusion
We propose that this mechanism of VPA action may contribute to an explanation of its anti-tumor and neuroprotective effects, as well as elucidate its role in the independent regulation of differentiation and inhibition of proliferation in the cerebral cortex of developing rat embryos.
Primate-specific spliced PMCHL RNAs are non-protein coding in human and macaque tissues
Authors: Schmieder Sandra , Darré-Toulemonde Fleur , Arguel Marie-Jeanne , Delerue-Audegond Audrey , Christen Richard , Nahon Jean-Louis 
Published: December 2008

Abstract

Background
Brain-expressed genes that were created in primate lineage represent obvious candidates to investigate molecular mechanisms that contributed to neural reorganization and emergence of new behavioural functions in Homo sapiens. PMCHL1 arose from retroposition of a pro-melanin-concentrating hormone (PMCH) antisense mRNA on the ancestral human chromosome 5p14 when platyrrhines and catarrhines diverged. Mutations before divergence of hylobatidae led to creation of new exons and finally PMCHL1 duplicated in an ancestor of hominids to generate PMCHL2 at the human chromosome 5q13. A complex pattern of spliced and unspliced PMCHL RNAs were found in human brain and testis.

Results
Several novel spliced PMCHL transcripts have been characterized in human testis and fetal brain, identifying an additional exon and novel splice sites. Sequencing of PMCHL genes in several non-human primates allowed to carry out phylogenetic analyses revealing that the initial retroposition event took place within an intron of the brain cadherin (CDH12) gene, soon after platyrrhine/catarrhine divergence, i.e. 30–35 Mya, and was concomitant with the insertion of an AluSg element. Sequence analysis of the spliced PMCHL transcripts identified only short ORFs of less than 300 bp, with low (VMCH-p8 and protein variants) or no evolutionary conservation. Western blot analyses of human and macaque tissues expressing PMCHL RNA failed to reveal any protein corresponding to VMCH-p8 and protein variants encoded by spliced transcripts.

Conclusion
Our present results improve our knowledge of the gene structure and the evolutionary history of the primate-specific chimeric PMCHL genes. These genes produce multiple spliced transcripts, bearing short, non-conserved and apparently non-translated ORFs that may function as mRNA-like non-coding RNAs.
High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families
Authors: Szittya Gyorgy , Moxon Simon , Santos Dulce M , Jing Runchun , Fevereiro Manuel PS , Moulton Vincent , Dalmay Tamas 
Published: December 2008

AbstractBackgroundHigh-throughput sequencing technology is capable to identify novel short RNAs in plant species. We used Solexa sequencing to find new microRNAs in one of the model legume species, barrel medic (Medicago truncatula).Results3,948,871 reads were obtained from two separate short RNA libraries generated from total RNA extracted fromM. truncatulaleaves, representing 1,563,959 distinct sequences. 2,168,937 reads were mapped to the availableM. truncatulagenome corresponding to 619,175 distinct sequences. 174,504 reads representing 25 conserved miRNA families showed perfect matches to known miRNAs. We also identified 26 novel miRNA candidates that were potentially generated from 32 loci. Nine of these loci produced eight distinct sequences, for which the miRNA* sequences were also sequenced. These sequences were not described in other plant species and accumulation of these eight novel miRNAs was confirmed by Northern blot analysis. Potential target genes were predicted for most conserved and novel miRNAs.ConclusionDeep sequencing of short RNAs fromM. truncatulaleaves identified eight new miRNAs indicating that specific miRNAs exist in legume species.
Evaluation of an in silico predicted specific and immunogenic antigen from the OmcB protein for the serodiagnosis of Chlamydia trachomatis infections
Authors: Frikha-Gargouri Olfa , Gdoura Radhouane , Znazen Abir , Gargouri Boutheina , Gargouri Jalel , Rebai Ahmed , Hammami Adnene 
Published: December 2008

AbstractBackgroundThe OmcB protein is one of the most immunogenic proteins inC. trachomatisandC. pneumoniaeinfections. This protein is highly conserved leading to serum cross reactivity between the various chlamydial species. Since previous studies based on recombinant proteins failed to identify a species specific immune response against the OmcB protein, this study evaluated anin silicopredicted specific and immunogenic antigen from the OmcB protein for the serodiagnosis ofC. trachomatisinfections.ResultsUsing the ClustalW and Antigenic programs, we have selected two predicted specific and immunogenic regions in the OmcB protein: the N-terminal (Nt) region containing three epitopes and the C-terminal (Ct) region containing two epitopes with high scores. These regions were cloned into the PinPoint Xa-1 and pGEX-6P-1 expression vectors, incorporating a biotin purification tag and a glutathione-S-transferase tag, respectively. These regions were then expressed inE. coli. Only the pGEX-6P-1 has been found suitable for serological studies as its tag showed less cross reactivity with human sera and was retained for the evaluation of the selected antigens. Only the Ct region of the protein has been found to be well expressed inE. coliand was evaluated for its ability to be recognized by human sera. 384 sera were tested for the presence of IgG antibodies toC. trachomatisby our in house microimmunofluorescence (MIF) and the developed ELISA test. Using the MIF as the reference method, the developed OmcB Ct ELISA has a high specificity (94.3%) but a low sensitivity (23.9). Our results indicate that the use of the sequence alignment tool might be useful for identifying specific regions in an immunodominant antigen. However, the two epitopes, located in the selected Ct region, of the 24 predicted in the full length OmcB protein account for approximately 25% of the serological response detected by MIF, which limits the use of the developed ELISA test when screeningC. trachomatisinfections.ConclusionThe developed ELISA test might be used as a confirmatory test to assess the specificity of serological results found by MIF.
Antioxidant and free radical scavenging activity of Spondias pinnata
Authors: Hazra Bibhabasu , Biswas Santanu , Mandal Nripendranath 
Published: December 2008

AbstractBackgroundMany diseases are associated with oxidative stress caused by free radicals. Current research is directed towards finding naturally-occurring antioxidants of plant origin. The aim of the present study was to evaluate thein vitroantioxidant activities ofSpondias pinnatastem bark extract.MethodsA 70% methanol extract ofSpondias pinnatastem bark was studiedin vitrofor total antioxidant activity, for scavenging of hydroxyl radicals, superoxide anions, nitric oxide, hydrogen peroxide, peroxynitrite, singlet oxygen and hypochlorous acid, and for iron chelating capacity, reducing power, and phenolic and flavonoid contents.ResultsThe extract showed total antioxidant activity with a trolox equivalent antioxidant concentration (TEAC) value of 0.78 ± 0.02. The IC50values for scavenging of free radicals were 112.18 ± 3.27 μg/ml, 13.46 ± 0.66 μg/ml and 24.48 ± 2.31 μg/ml for hydroxyl, superoxide and nitric oxide, respectively. The IC50for hydrogen peroxide scavenging was 44.74 ± 25.61 mg/ml. For the peroxynitrite, singlet oxygen and hypochlorous acid scavenging activities the IC50values were 716.32 ± 32.25 μg/ml, 58.07 ± 5.36 μg/ml and 127.99 ± 6.26 μg/ml, respectively. The extract was found to be a potent iron chelator with IC50= 66.54 ± 0.84 μg/ml. The reducing power was increased with increasing amounts of extract. The plant extract (100 mg) yielded 91.47 ± 0.004 mg/ml gallic acid-equivalent phenolic content and 350.5 ± 0.004 mg/ml quercetin-equivalent flavonoid content.ConclusionThe present study provides evidence that a 70% methanol extract ofSpondias pinnatastem bark is a potential source of natural antioxidants.
Identification of recruitment and retention strategies for rehabilitation professionals in Ontario, Canada: results from expert panels
Authors: Tran Diem , Hall Linda McGillis , Davis Aileen , Landry Michel D , Burnett Dawn , Berg Katherine , Jaglal Susan 
Published: December 2008

AbstractBackgroundDemand for rehabilitation services is expected to increase due to factors such as an aging population, workforce pressures, rise in chronic and complex multi-system disorders, advances in technology, and changes in interprofessional health service delivery models. However, health human resource (HHR) strategies for Canadian rehabilitation professionals are lagging behind other professional groups such as physicians and nurses. The objectives of this study were: 1) to identify recruitment and retention strategies of rehabilitation professionals including occupational therapists, physical therapists and speech language pathologists from the literature; and 2) to investigate both the importance and feasibility of the identified strategies using expert panels amongst HHR and education experts.MethodsA review of the literature was conducted to identify recruitment and retention strategies for rehabilitation professionals. Two expert panels, one onRecruitment and Retentionand the other onEducationwere convened to determine the importance and feasibility of the identified strategies. A modified-delphi process was used to gain consensus and to rate the identified strategies along these two dimensions.ResultsA total of 34 strategies were identified by theRecruitment and RetentionandEducationexpert panels as being important and feasible for the development of a HHR plan for recruitment and retention of rehabilitation professionals. Seven were categorized under theQuality of Worklife and Work Environmenttheme, another seven inFinancial Incentives and Marketing, two inWorkload and Skill Mix, thirteen inProfessional Developmentand five inEducation and Training.ConclusionBased on the results from the expert panels, the three major areas of focus for HHR planning in the rehabilitation sector should include strategies addressingQuality of Worklife and Work Environment,Financial Incentives and MarketingandProfessional Development.
Fat-to-glucose interconversion by hydrodynamic transfer of two glyoxylate cycle enzyme genes
Authors: Cordero P , Campion J , Milagro FI , Marzo F , Martinez JA 
Published: December 2008

Abstract
The glyoxylate cycle, which is well characterized in higher plants and some microorganisms but not in vertebrates, is able to bypass the citric acid cycle to achieve fat-to-carbohydrate interconversion. In this context, the hydrodynamic transfer of two glyoxylate cycle enzymes, such as isocytrate lyase (ICL) and malate synthase (MS), could accomplish the shift of using fat for the synthesis of glucose. Therefore, 20 mice weighing 23.37 ± 0.96 g were hydrodinamically gene transferred by administering into the tail vein a bolus with ICL and MS. After 36 hours, body weight, plasma glucose, respiratory quotient and energy expenditure were measured. The respiratory quotient was increased by gene transfer, which suggests that a higher carbohydrate/lipid ratio is oxidized in such animals. This application could help, if adequate protocols are designed, to induce fat utilization for glucose synthesis, which might be eventually useful to reduce body fat depots in situations of obesity and diabetes.
Protein expression profiling during chick retinal maturation: a proteomics-based approach
Authors: Finnegan Sorcha , Robson Joanne L , Wylie Mildred , Healy Adrienne , Stitt Alan W , Curry William J 
Published: December 2008

Abstract

Background
The underlying pathways that drive retinal neurogenesis and synaptogenesis are still relatively poorly understood. Protein expression analysis can provide direct insight into these complex developmental processes. The aim of this study was therefore to employ proteomic analysis to study the developing chick retina throughout embryonic (E) development commencing at day 12 through 13, 17, 19 and post-hatch (P) 1 and 33 days.

Results
2D proteomic and mass spectrometric analysis detected an average of 1514 spots per gel with 15 spots demonstrating either modulation or constitutive expression identified via MS. Proteins identified included alpha and beta-tubulin, alpha enolase, B-creatine kinase, gamma-actin, platelet-activating factor (PAF), PREDICTED: similar to TGF-beta interacting protein 1, capping protein (actin filament muscle Z line), nucleophosmin 1 (NPM1), dimethylarginine dimethylaminohydrolase, triosphoaphate isomerase, DJ1, stathmin, fatty acid binding protein 7 (FABP7/B-FABP), beta-synuclein and enhancer of rudimentary homologue.

Conclusion
This study builds upon previous proteomic investigations of retinal development and represents the addition of a unique data set to those previously reported. Based on reported bioactivity some of the identified proteins are most likely to be important to normal retinal development in the chick. Continued analysis of the dynamic protein populations present at the early stages and throughout retinal development will increase our understanding of the molecular events underpinning retinogenesis.
Origins, Actions and Dynamic Expression Patterns of the Neuropeptide VGF in Rat Peripheral and Central Sensory Neurones Following Peripheral Nerve Injury
Authors: Moss Andrew , Ingram Rachel , Koch Stephanie , Theodorou Andria , Low Lucie , Baccei Mark , Hathway Gareth J , Costigan Michael , Salton Stephen R , Fitzgerald Maria 
Published: December 2008

Background: The role of the neurotrophin regulated polypeptide, VGF, has been investigated in a rat spared injury model of neuropathic pain. This peptide has been shown to be associated with synaptic strengthening and learning in the hippocampus and while it is known that VGFmRNA is upregulated in dorsal root ganglia following peripheral nerve injury, the role of this VGF peptide in neuropathic pain has yet to be investigated. Results: Prolonged upregulation of VGF mRNA and protein was observed in injured dorsal root ganglion neurons, central terminals and their target dorsal horn neurons. Intrathecal application of TLQP-62, the C-terminal active portion of VGF (5–50 nmol) to naïve rats caused a long-lasting mechanical and cold behavioral allodynia. Direct actions of 50 nM TLQP-62 upon dorsal horn neuron excitability was demonstrated in whole cell patch recordings in spinal cord slices and in receptive field analysis in intact, anesthetized rats where significant actions of VGF were upon spontaneous activity and cold evoked responses. Conclusion: VGF expression is therefore highly modulated in nociceptive pathways following peripheral nerve injury and can cause dorsal horn cell excitation and behavioral hypersensitivity in naïve animals. Together the results point to a novel and powerful role for VGF in neuropathic pain.
Parasites of importance for human health in Nigerian dogs: high prevalence and limited knowledge of pet owners
Authors: Ugbomoiko Uade Samuel , Ariza Liana , Heukelbach Jorg 
Published: December 2008

AbstractBackgroundDogs are the most common pet animals worldwide. They may harbour a wide range of parasites with zoonotic potential, thus causing a health risk to humans. In Nigeria, epidemiological knowledge on these parasites is limited.MethodsIn a community-based study, we examined 396 dogs in urban and rural areas of Ilorin (Kwara State, Central Nigeria) for ectoparasites and intestinal helminths. In addition, a questionnaire regarding knowledge and practices was applied to pet owners.ResultsNine ectoparasite species belonging to four taxa and six intestinal helminth species were identified: fleas (Ctenocephalides canis, Pulex irritans, Tunga penetrans), mites (Demodex canis, Otodectessp.,Sarcoptes scabieivar.canis), ticks (Rhipicephalus sanguineus, Ixodessp.), and lice (Trichodectes canis); andToxocara canis, Ancylostomasp.,Trichuris vulpis, Dipylidium caninum, Taenidae andStrongyloidessp. Overall prevalence of ectoparasites was 60.4% and of intestinal helminths 68.4%. The occurrence ofC. canis, R. sanguineus, T. canis, Ancylostomasp. andT. vulpiswas most common (prevalence 14.4% to 41.7%). Prevalence patterns in helminths were age-dependent, withT. canisshowing a decreasing prevalence with age of host, and a reverse trend in other parasite species. Knowledge regarding zoonoses was very limited and the diseases not considered a major health problem. Treatment with antiparasitic drugs was more frequent in urban areas.ConclusionParasites of importance for human health were highly prevalent in Nigerian dogs. Interventions should include health education provided to dog owners and the establishment of a program focusing on zoonotic diseases.
Parotid gland sparing IMRT for head and neck cancer improves xerostomia related quality of life
Authors: van Rij CM , Oughlane-Heemsbergen WD , Ackerstaff AH , Lamers EA , Balm AJM , Rasch CRN 
Published: December 2008

Abstract

Background and purpose
To assess the impact of intensity modulated radiotherapy (IMRT) versus conventional radiation on late xerostomia and Quality of Life aspects in head and neck cancer patients.

Patients and nethods
Questionnaires on xerostomia in rest and during meals were sent to all patients treated between January 1999 and December 2003 with a T1-4, N0-2 M0 head and neck cancer, with parotid gland sparing IMRT or conventional bilateral neck irradiation to a dose of at least 60 Gy, who were progression free and had no disseminated disease (n = 192). Overall response was 85% (n = 163); 97% in the IMRT group (n = 75) and 77% in the control group (n = 88) the median follow-up was 2.6 years. The prevalence of complaints was compared between the two groups, correcting for all relevant factors at multivariate ordinal regression analysis.

Results
Patients treated with IMRT reported significantly less difficulty transporting and swallowing their food and needed less water for a dry mouth during day, night and meals. They also experienced fewer problems with speech and eating in public. Laryngeal cancer patients in general had fewer complaints than oropharynx cancer patients but both groups benefited from IMRT. Within the IMRT group the xerostomia scores were better for those patients with a mean parotid dose to the "spared" parotid below 26 Gy.

Conclusion
Parotid gland sparing IMRT for head and neck cancer patients improves xerostomia related quality of life compared to conventional radiation both in rest and during meals. Laryngeal cancer patients had fewer complaints but benefited equally compared to oropharyngeal cancer patients from IMRT.
Intraneural injection of corticosteroids to treat nerve damage in leprosy: a case report and review of literature
Authors: Nashed Sherine G , Rageh Tarek A , Attallah-Wasif Emad S , Abd-Elsayed Alaa A 
Published: December 2008

Abstract

Introduction
Nerve damage in leprosy patients leads to deformities and disabilities. Oral corticosteroids are given early to prevent permanent injury. We present a new approach to treat well-established nerve damage with local injection of corticosteroids.

Case presentation
A 60-year-old leprosy patient presented with right claw hand deformity secondary to right ulnar and median neuropathy. Monthly intraneural injection of corticosteroids resulted in improvement in sensory and motor function of his right hand over a 6-month period. Nerve conduction velocity testing documented the success of our therapy.

Conclusion
We report the first case of successful nerve regeneration in neglected neuropathy secondary to leprosy after local injection of corticosteroids. Intraneural extra-fascicular injection of corticosteroids improved the sensory and motor nerve function in our patient with borderline leprosy regardless of the duration of nerve function loss.
Orthodontic traction of impacted canine using magnet: a case report
Authors: Li Larry CF , Wong Ricky WK , King Nigel M 
Published: December 2008

Abstract
A 15 year and 1 month old Chinese female with palatally impacted upper left canine was successfully treated with an upper removable appliance with a magnet incorporated to provide orthodontic traction force. This case report indicates the possibility of using magnetic force as a safe, effective and comfortable way for orthodontic traction.