bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of Havana and communities in the manual curation of unfinished vertebrate genomes
Authors: Carvalho-Silva Denise , Chen Chao-Kung , Frankish Adam , Gilbert James , Gordon Leo , Hunt Toby , Larbaoui Mustapha , Loveland Jane , Mudge Jonathan , Sehra Harminder , Snow Catherine , Steward Charlie , Suner Marie Marthe , Thomas Mark , Wilming Laurens , Harrow Jennifer 
Published: April 2009

AbstractManual annotation‭ (‬the‭ "‬museum‭" ‬model of annotation‭) ‬relies on a small group of specialized curators to catalogue and classify genes according to their functional roles.‭ This‬ is both costly and time consuming and therefore is used only for model organisms with sufficient funding.‭ ‬Smaller research communities often have to rely on other models of annotation,‭ ‬mainly automated annotation‭ (‬the‭ "‬factory‭" ‬model,‭ ‬e.g.‭ ‬Ensembl‭)‬,‭ ‬and the‭ "‬jamboree‭" ‬model‭ (‬in which a group of leading biologists from the community and bioinformaticians come together for a short intensive annotation workshop‭)‬.‭ ‬At the Wellcome Trust Sanger Institute‭ (‬WTSI‭)‬,‭ ‬the Havana team provides high quality manual annotation of finished vertebrate genome sequences,‭ ‬namely human,‭ ‬mouse and zebrafish.‭ ‬We also perform the curation of specific finished regions such as the MHC in dog,‭ ‬cow and pig,‭ ‬whose whole genomes have been‭ ‬assembled from unfinished BACs or from whole genome shotgun sequences.‭ ‬In addition,‭ ‬we at Havana have also hosted annotation jamborees for the cow‭ (‬Bos taurus‭) ‬and pig‭ (‬Sus scrofa‭) ‬genomes.‭ ‬During those sessions,‭ ‬the research community had the opportunity to annotate their genes of interest under expert guidance using the custom written publicly available Otterlace annotation system,‭ ‬and the unified manual annotation guidelines.‭ ‬By making use of the tools and skills acquired during the cow and pig jamborees,‭ ‬the delegates can continue annotating their genomes remotely.‭ ‬For the pig genome,‭ ‬a highly contiguous physical map has been generated by an international effort of four laboratories (available in Pre!Ensembl) and‭ ‬is being used as a substrate for the swine genome sequencing project.‭ ‬Upcoming vertebrate genomes will be sequenced to a high depth coverage with the next generation sequencing technologies‭ (‬e.g.‭ ‬Illumina,‭ ‬454,‭ ‬SOLiD‭) ‬but will have the drawback of not being manually finished.‭ ‬Manual annotation will be more accurate than the automated predictions at coping with any assembly problems derived from these high coverage but unfinished‭ (‬or automatic pre-finished‭) ‬genomes.‭ ‬Once these inherent assembly errors are corrected and the gene structures are accurately identified with manual annotation,‭ ‬the curated genes will be incorporated and merged with the predicted gene models in Ensembl to provide a unified view of the landscape of vertebrate genomes.‭ ‬I will present an introduction to our manual annotation system and our experience using it for annotation jamborees at the WTSI.
Inhibition of myeloperoxidase-mediated hypochlorous acid production by nitroxides
Authors: Rees Martin D. , Bottle Steven E. , Fairfull-Smith Kathryn E. , Malle Ernst , Whitelock John M. , Davies Michael J. 
Published: April 2009

Tissue damage resulting from the extracellular production of HOCl (hypochlorous acid) by the MPO (myeloperoxidase)-hydrogen peroxide-chloride system of activated phagocytes is implicated as a key event in the progression of a number of human inflammatory diseases. Consequently, there is considerable interest in the development of therapeutically useful MPO inhibitors. Nitroxides are well established antioxidant compounds of low toxicity that can attenuate oxidative damage in animal models of inflammatory disease. They are believed to exert protective effects principally by acting as superoxide dismutase mimetics or radical scavengers. However, we show here that nitroxides can also potently inhibit MPO-mediated HOCl production, with the nitroxide 4-aminoTEMPO inhibiting HOCl production by MPO and by neutrophils with IC50 values of approx. 1 and 6 μM respectively. Structure–activity relationships were determined for a range of aliphatic and aromatic nitroxides, and inhibition of oxidative damage to two biologically-important protein targets (albumin and perlecan) are demonstrated. Inhibition was shown to involve one-electron oxidation of the nitroxides by the compound I form of MPO and accumulation of compound II. Haem destruction was also observed with some nitroxides. Inhibition of neutrophil HOCl production by nitroxides was antagonized by neutrophil-derived superoxide, with this attributed to superoxide-mediated reduction of compound II. This effect was marginal with 4-aminoTEMPO, probably due to the efficient superoxide dismutase-mimetic activity of this nitroxide. Overall, these data indicate that nitroxides have considerable promise as therapeutic agents for the inhibition of MPO-mediated damage in inflammatory diseases.
Angiotensin-(1–7), an alternative metabolite of the renin–angiotensin system, is up-regulated in human liver disease and has antifibrotic activity in the bile-duct-ligated rat
Authors: Lubel John S. , Herath Chandana B. , Tchongue Jorge , Grace Josephine , Jia Zhiyuan , Spencer Karen , Casley David , Crowley Peter , Sievert William , Burrell Louise M. , Angus Peter W. 
Published: April 2009

Ang-(1–7) (angiotensin-1–7), a peptide product of the recently described ACE (angiotensin-converting enzyme) homologue ACE2, opposes the harmful actions of AngII (angiotensin II) in cardiovascular tissues, but its role in liver disease is unknown. The aim of the present study was to assess plasma levels of Ang-(1–7) in human liver disease and determine its effects in experimental liver fibrosis. Angiotensin peptide levels were measured in cirrhotic and non-cirrhotic patients with hepatitis C. The effects of Ang-(1–7) on experimental fibrosis were determined using the rat BDL (bile-duct ligation) model. Liver histology, hydroxyproline quantification and expression of fibrosis-related genes were assessed. Expression of RAS (renin–angiotensin system) components and the effects of Ang-(1–7) were examined in rat HSCs (hepatic stellate cells). In human patients with cirrhosis, both plasma Ang-(1–7) and AngII concentrations were markedly elevated (P&lt;0.001). Non-cirrhotic patients with hepatitis C had elevated Ang-(1–7) levels compared with controls (P&lt;0.05), but AngII concentrations were not increased. In BDL rats, Ang-(1–7) improved fibrosis stage and collagen Picrosirius Red staining, and reduced hydroxyproline content, together with decreased gene expression of collagen 1A1, α-SMA (smooth muscle actin), VEGF (vascular endothelial growth factor), CTGF (connective tissue growth factor), ACE and mas [the Ang-(1–7) receptor]. Cultured HSCs expressed AT1Rs (AngII type 1 receptors) and mas receptors and, when treated with Ang-(1–7) or the mas receptor agonist AVE 0991, produced less α-SMA and hydroxyproline, an effect reversed by the mas receptor antagonist A779. In conclusion, Ang-(1–7) is up-regulated in human liver disease and has antifibrotic actions in a rat model of cirrhosis. The ACE2/Ang-(1–7)/mas receptor axis represents a potential target for antifibrotic therapy in humans.
Comparison of the Efficacy of a Hydrogen Peroxide Dry-Mist Disinfection System and Sodium Hypochlorite Solution for Eradication ofClostridium difficileSpores
Authors: Barbut F. , Menuet D. , Verachten M. , Girou E. 
Published: April 2009

Objective.To compare a hydrogen peroxide dry-mist system and a 0.5% hypochlorite solution with respect to their ability to disinfectClostridiumdifficile-contaminated surfaces in vitro and in situ.Design.Prospective, randomized, before-after trial.Setting.Two French hospitals affected byC. difficile.Intervention.In situ efficacy of disinfectants was assessed in rooms that had housed patients withC. difficileinfection. A prospective study was performed at 2 hospitals that involved randomization of disinfection processes. When a patient withC. difficileinfection was discharged, environmental contamination in the patient's room was evaluated before and after disinfection. Environmental surfaces were sampled forC. difficileby use of moistened swabs; swab samples were cultured on selective plates and in broth. Both disinfectants were tested in vitro with a spore-carrier test; in this test, 2 types of material, vinyl polychloride (representative of the room's floor) and laminate (representative of the room's furniture), were experimentally contaminated with spores from 3C. difficilestrains, including the epidemic clone ribotype 027-North American pulsed-field gel electrophoresis type 1.Results.There were 748 surface samples collected (360 from rooms treated with hydrogen peroxide and 388 from rooms treated with hypochlorite). Before disinfection, 46 (24%) of 194 samples obtained in the rooms randomized to hypochlorite treatment and 34 (19%) of 180 samples obtained in the rooms randomized to hydrogen peroxide treatment showed environmental contamination. After disinfection, 23 (12%) of 194 samples from hypochlorite-treated rooms and 4 (2%) of 180 samples from hydrogen peroxide treated rooms showed environmental contamination, a decrease in contamination of 50% after hypochlorite decontamination and 91% after hydrogen peroxide decontamination (P< .005). The in vitro activity of 0.5% hypochlorite was time dependent. The mean (±SD) reduction in initial log10 bacterial count was 4.32 ± 0.35 log10 colony-forming units after 10 minutes of exposure to hypochlorite and 4.18 ± 0.8 logl0 colony-forming units after 1 cycle of hydrogen peroxide decontamination.Conclusion.In situ experiments indicate that the hydrogen peroxide dry-mist disinfection system is significantly more effective than 0.5% sodium hypochlorite solution at eradicating Сdifficilespores and might represent a new alternative for disinfecting the rooms of patients withC. difficileinfection.
Outbreak of Pseudomonas aeruginosa Infection Associated With Contamination of a Flexible Bronchoscope
Authors: DiazGranados Carlos A. , Jones Marolyn Y. , Kongphet-Tran Thiphasone , White Nancy , Shapiro Mark , Wang Yun F. , Ray Susan M. , Blumberg Henry M. 
Published: April 2009

Background.A cluster of patients with respiratory cultures positive for Pseudomonas aeruginosa with a unique antibiogram was observed during June and July 2007 at a 1,000-bed urban teaching hospital in Atlanta, Georgia. These P. aeruginosa isolates were recovered from bronchoscopically obtained specimens.Methods.A cross-sectional study was performed to assess whether the cluster was associated with exposure to a particular bronchoscope (B1); cultures from specimens from the bronchoscopes and the environment were obtained, and the P. aeruginosa isolate type was determined using pulsed-field gel electrophoresis (PFGE). Records of patients exposed to B1 during the cluster period were reviewed.Results.Twelve patients with a culture positive for P. aeruginosa with the unique susceptibility pattern were identified in June-July 2007. No cases were documented from March 1 through May 31, 2007. Culture specimens obtained from B1 after high-level disinfection revealed P. aeruginosa, prompting removal of B1 from service on July 23, 2007. No cases occurred after that date. Eleven (55%) of 20 patients who were exposed to Bl during the cluster period had a culture positive for P. aeruginosa, compared with 1 (2%) of 53 patients who were exposed to other bronchoscopes (P < .001). PFGE patterns for P. aeruginosa isolates obtained from case patients and from B1 were identical. An engineering evaluation of B1 documented several internal damages. Two (10.5%) of 19 patients exposed to Bl during the cluster period may have developed P. aeruginosa infection following exposure to B1.Conclusions.An outbreak or pseudo-outbreak of P. aeruginosa infection occurred in association with use of a damaged bronchoscope. Periodic engineering maintenance may be needed to prevent bronchoscope contamination that is resistant to high-level disinfection.
BEsTRF: a tool for optimal resolution of terminal-restriction fragment length polymorphism analysis based on user-defined primer–enzyme–sequence databases
Authors: Stres Blaž , Tiedje James M. , Murovec Boštjan 
Published: April 2009

Abstract
Summary: BEsTRF (Best Estimated T-RF) provides a standalone environment for analyzing primers-enzymes-gene section combinations used in terminal-restriction fragment length polymorphism (T-RFLP) for its optimal resolution. User-defined sequence databases of several hundred thousand DNA sequences can be explored and the resolution of user-specified sets of primers and restriction endonucleases can be analyzed on either forward or reverse terminal fragments. Sequence quality, primer mismatches, insertions and deletions can be controlled and each primer pair-specific sequence collections can be exported for downstream analyses. The configuration for a novel T-RFLP population profiling using rpoB gene (DNA-directed RNA polymerase, beta subunit) on forward fluorescently labeled primer are presented.
Availability: BEsTRF is freely available at http://lie.fe.uni-lj.si/bestrf and can be downloaded from the same site. The online protocol, numerous primer and enzyme dictionaries, sequence collections and results generated during this work for various genes are available at our website http://lie.fe.uni-lj.si/bestrf.
Contact: blaz.stres@bfro.uni-lj.si
Variations in the target strength of Atlantic cod during vertical migration
Authors: Rose George A. 
Published: April 2009

Abstract
Rose, G. A. 2009. Variations in the target strength of Atlantic cod during vertical migration. – ICES Journal of Marine Science, 66: 1205–1211. Experiments conducted at sea in June 1999 and January 2000 indicated that the mean target strength (TS) of Atlantic cod (Gadus morhua) varies not just with length, but also with pressure (depth) and fish orientation, particularly during vertical migration. In June, when fish were migrating and spawning, vertical migration was pronounced, extending up to 150 m off the seabed, and the associated TS declined by as much as 5 dB. In January, when the fish were located nearer the seabed, mean TS was more stable and matched a conventional model of TS vs. length [L, cm; i.e. TS = 20 log(L) − 66] based on measurements of ex situ fish orientated horizontally and positioned at close range. This paper demonstrates that mean TS is inversely related (p < 0.05) to the range off the seabed (r, m), which includes 90% of fish. Based on this finding, a new multivariate TS model is proposed: TS = 20 log(L) − 65 − 0.05 r. In this model, r is a proxy for swimbladder volume and fish orientation. A survey in May 2007 found that cod (mean L = 63 cm) dispersed in such a way that single targets could be resolved up to 100 m from the seabed. Measurements of TS of in situ individual fish (TSindividual) and mean TS inferred from a comparison of area-backscattering coefficients (sa) and count-based densities (TSindirect) were positively correlated with a slope not different from unity. Means of these TS estimates were −32.4 and −32.2 dB, respectively, or ∼2.3 dB less than that predicted by the conventional model. In contrast, the new multivariate model predicts TS = −32.5 dB, which is nearly identical with the means of TSindividual and TSindirect.
The acoustic quantification of fish in the presence of methane bubbles in the stratified Lake Kinneret, Israel
Authors: Ostrovsky Ilia 
Published: April 2009

Abstract
Ostrovsky, I. 2009. The acoustic quantification of fish in the presence of methane bubbles in the stratified Lake Kinneret, Israel. – ICES Journal of Marine Science, 66: 1043–1047. Methane ebullition from bottom sediments is common in many productive bodies of water. During acoustic surveys, the methane bubbles can be mistaken as fish. In the stratified Lake Kinneret, the densities and target-strength (TS) values of acoustic targets were measured with a 120-kHz, dual-beam echosounder at night, when the fish schools were dispersed and single targets could be detected. The density and TS of methane bubbles were estimated in the anoxic hypolimnion, where there were no fish. A discrete-bubble model was applied in combination with a TS vs. methane bubble-size relationship to estimate the methane bubble TS at different depths. This information was used to quantify the densities of methane bubbles and fish, and the fish TS in the epilimnion where both types of target were found. During periods of rapid decrease in water level, methane bubbles could be the principal acoustic targets in the epilimnion, and their TS strongly overlapped that of fish. In some strata, they contributed up to 90–95% of all targets. The amount of methane bubbles in the water column depends on the type of sediment, bottom depth, and the history of sediment degassing. Their presence could be a serious obstacle to the accurate assessment of fish abundance in lakes and reservoirs with varying water levels, where intensive gas emission is a common feature. For such situations, backscattering by methane bubbles must be taken into account to avoid the erroneous quantification of fish abundance.
Changes of psychiatric parameters and their relationships by oral isotretinoin in acne patients
Authors: HAHM Bong Jin , MIN Seong Uk , YOON Mi Young , SHIN Yong Wook , KIM Jin Sook , JUNG Jae Yoon , SUH Dae Hun 
Published: April 2009

ABSTRACTOral isotretinoin is a highly effective agent for the treatment of moderate to severe acne, but ever since oral isotretinoin was introduced as a modality for acne, the relationship between oral isotretinoin therapy and psychiatric problems, especially depression, has been controversial. The purposes of this study were to know the acute effects of oral isotretinoin therapy on psychiatric symptoms and to investigate the relationships among them, which have not been reported in the published work. This cohort study included 38 acne patients who started oral isotretinoin therapy. Individual patients were examined before administering oral isotretinoin and 2 and 8 weeks after commencement. Acne severity was graded using the Leeds revised acne grading system. Acute psychiatric effects of oral isotretinoin were assessed using a questionnaire authorized by two psychiatrists. This questionnaire included assessments of acne‐related quality of life (Assessment of the Psychological and Social Effects of Acne [APSEA]), depression (Beck's depression inventory [BDI]), anxiety (Beck's anxiety inventory [BAI]) and psychopathology (Symptomchecklist‐90‐revised [SCL‐90‐R]). Acne grading and APSEA showed similar change patterns. Both improved after 8 weeks of oral isotretinoin treatment. On the other hand, the severity of depression decreased after 2 weeks of treatment. A significant correlation was found between BDI and APSEA, but no correlation was found between BDI and acne grade. These results indicate that oral isotretinoin therapy alleviates depressive symptoms. Improvements in depression are directly related to acne‐related life quality improvements rather than to improvement in acne grade.
Ocular alterations in patients of alopecia areata
Authors: PANDHI Deepika , SINGAL Archana , GUPTA Ritika , DAS Gopal 
Published: April 2009

ABSTRACTThere is paucity of published work on ocular alterations in patients of alopecia areata (AA), especially from the Asian continent. We studied the clinical profile of 83 patients of AA and 80 sex‐ and age‐matched controls to assess and compare the ocular changes, namely punctate opacities, cataract, intraocular tension and retinal changes. The outcome was analyzed with respect to prevalence of atopy, concomitant personal or family history of autoimmune diseases and nail changes in both the groups. The prevalence of atopy and family history of autoimmune diseases was significantly higher in the patient group. Lenticular changes were observed in 40.9% patients (including cataract in 16.9%) and 11.2% controls (P < 0.005). Within the patient group, lenticular involvement occurred with increased frequency in atopics (P = 0.034) and in the presence of family history of autoimmune diseases (P < 0.05). Retinal changes in the form of degenerative changes, pigmentary clumping and abnormal vascular changes were more prevalent (P < 0.001) in the study group. As the ocular changes were not found to correlate with the age, severity or extent of the disease, an initial ophthalmological screening of all patients is suggested.
Evaluation of polymerase chain reaction‐based detection of Mycobacterium leprae for the diagnosis of leprosy
Authors: BANG Pham Dang , SUZUKI Koichi , PHUONG Le Thi , CHU Tran Man , ISHII Norihisa , KHANG Tran Hau 
Published: April 2009

ABSTRACTBecause Mycobacterium leprae cannot be cultivated in vitro, laboratory diagnosis of leprosy is generally made by microscopic and histopathological examination. The objective of the present study was to evaluate the sensitivity and utility of polymerase chain reaction (PCR) to detect M. leprae in comparison with other conventional methods for diagnosis such as split skin smears, histopathology and serodiagnosis. PCR amplification of the M. leprae‐specific 16S ribosomal RNA was compared to other methods. Samples included 37 multibacillary (MB) patients with a positive bacteriological index (BI), 32 newly diagnosed paucibacillary (PB) patients whose BI were negative and 30 plaque psoriasis patients not residing in leprosy endemic areas as controls. The sensitivity of PCR was 30 fg of M. leprae DNA, which is equivalent to the DNA from 8.3 bacilli. The detection rate in MB and PB were 100% and 50%, respectively; the specificity was 100%. Semiquantitative evaluation of PCR correlated well with BI, but not with the morphological index (MI) nor with the serum antibody against phenolic glycolipid‐1 (PGL‐1). PCR detection of M. leprae targeting 16S ribosomal RNA was specific and more sensitive than conventional methods, and can contribute to early and accurate diagnosis of leprosy.
Severity factors of Mamushi (Agkistrodon blomhoffii) bite
Authors: OKAMOTO Osamu , OISHI Masaki , HATANO Yutaka , KAI Yoshitaka , GOTO Mizuki , KATO Aiko , SHIMIZU Fumiaki , KATAGIRI Kazumoto , FUJIWARA Sakuhei 
Published: April 2009

ABSTRACTThe factors determining the severity of a Mamushi (Agkistrodon blomhoffii) bite were analyzed based on the findings of our 34 cases and those appearing in the published work. It was not possible to forecast the final severity at the time of the patient's arrival and by the initial blood examination data. The maximal creatinine kinase (CK) values elevated proportionally with the time from the bite, and the relation approximated the equation of y = 300χ, where y represents the maximal CK value and χ indicates the time from the bite to the peak of CK level. In the severe cases which required intensive care, the level of the CK deviated remarkably from this line, and could be grossly distinguished from the non‐severe cases. The maximal white blood cell (WBC) count also gradually increased in concordance with the time from the bite, and in addition, the WBC count of most of the severe cases exceeded 20 000/µL. This evidence suggests that the rate of the CK value elevation in relation to the time from the bite can be a useful indicator of the severity of a Mamushi bite, and the WBC count also reflects the severity.
Rituximab‐induced vasculitis: A case report and review of the medical published work
Authors: KIM Min Joo , KIM Hyung Ok , KIM Ho Yeon , PARK Young Min 
Published: April 2009

ABSTRACTRituximab is an anti‐CD20 chimeric murine/human monoclonal antibody mainly used in the treatment of patients with a cutaneous lymphoid malignancy. Among the side‐effects associated with rituximab administration, vasculitis has been rarely reported. There are two reported cases in the English language medical published work. We describe a 38‐year‐old Korean man with cutaneous vasculitis occurring 1 day after rituximab administration.