bluuebunny/crossref_metadata_2025_split huggingface dataset:
A visual framework for sequence analysis using n-grams and spectral rearrangement
Authors: Maetschke Stefan R. , Kassahn Karin S. , Dunn Jasmyn A. , Han Siew-Ping , Curley Eva Z. , Stacey Katryn J. , Ragan Mark A. 
Published: February 2010

Abstract
Motivation: Protein sequences are often composed of regions that have distinct evolutionary histories as a consequence of domain shuffling, recombination or gene conversion. New approaches are required to discover, visualize and analyze these sequence regions and thus enable a better understanding of protein evolution.
Results: Here, we have developed an alignment-free and visual approach to analyze sequence relationships. We use the number of shared n-grams between sequences as a measure of sequence similarity and rearrange the resulting affinity matrix applying a spectral technique. Heat maps of the affinity matrix are employed to identify and visualize clusters of related sequences or outliers, while n-gram-based dot plots and conservation profiles allow detailed analysis of similarities among selected sequences. Using this approach, we have identified signatures of domain shuffling in an otherwise poorly characterized family, and homology clusters in another. We conclude that this approach may be generally useful as a framework to analyze related, but highly divergent protein sequences. It is particularly useful as a fast method to study sequence relationships prior to much more time-consuming multiple sequence alignment and phylogenetic analysis.
Availability: A software implementation (MOSAIC) of the framework described here can be downloaded from http://bioinformatics.org.au/mosaic/
Contact: m.ragan@uq.edu.au
Supplementary information: Supplementary data are available at Bioinformatics online.
Cascleave: towards more accurate prediction of caspase substrate cleavage sites
Authors: Song Jiangning , Tan Hao , Shen Hongbin , Mahmood Khalid , Boyd Sarah E. , Webb Geoffrey I. , Akutsu Tatsuya , Whisstock James C. 
Published: February 2010

Abstract
Motivation: The caspase family of cysteine proteases play essential roles in key biological processes such as programmed cell death, differentiation, proliferation, necrosis and inflammation. The complete repertoire of caspase substrates remains to be fully characterized. Accordingly, systematic computational screening studies of caspase substrate cleavage sites may provide insight into the substrate specificity of caspases and further facilitating the discovery of putative novel substrates.
Results: In this article we develop an approach (termed Cascleave) to predict both classical (i.e. following a P1 Asp) and non-typical caspase cleavage sites. When using local sequence-derived profiles, Cascleave successfully predicted 82.2% of the known substrate cleavage sites, with a Matthews correlation coefficient (MCC) of 0.667. We found that prediction performance could be further improved by incorporating information such as predicted solvent accessibility and whether a cleavage sequence lies in a region that is most likely natively unstructured. Novel bi-profile Bayesian signatures were found to significantly improve the prediction performance and yielded the best performance with an overall accuracy of 87.6% and a MCC of 0.747, which is higher accuracy than published methods that essentially rely on amino acid sequence alone. It is anticipated that Cascleave will be a powerful tool for predicting novel substrate cleavage sites of caspases and shedding new insights on the unknown caspase-substrate interactivity relationship.
Availability: http://sunflower.kuicr.kyoto-u.ac.jp/∼sjn/Cascleave/
Contact: jiangning.song@med.monash.edu.au; takutsu@kuicr.kyoto-u.ac.jp; james; whisstock@med.monash.edu.au
Supplementary information: Supplementary data are available at Bioinformatics online.
The allergen Bet v 1 in fractions of ambient air deviates from birch pollen counts
Authors: Buters J. T. M. , Weichenmeier I. , Ochs S. , Pusch G. , Kreyling W. , Boere A. J. F. , Schober W. , Behrendt H. 
Published: February 2010

To cite this article: Buters JTM, Weichenmeier I, Ochs S, Pusch G, Kreyling W, Boere AJF, Schober W, Behrendt H. The allergen Bet v 1 in fractions of ambient air deviates from birch pollen counts. Allergy 2010; 65: 850–858.AbstractBackground:  Proof is lacking that pollen count is representative for allergen exposure, also because allergens were found in nonpollen‐bearing fractions of ambient air.Objective:  We monitored simultaneously birch pollen and the major birch pollen allergen Bet v 1 in different size fractions of ambient air from 2004 till 2007 in Munich, Germany.Methods:  Air was sampled with a ChemVol® high‐volume cascade impactor equipped with stages for particulate matter (PM)>10 μm, 10 μm>PM>2.5 μm, and 2.5 μm>PM>0.12 μm. Allergen was determined with a Bet v 1‐specific ELISA. Pollen count was assessed with a Burkard pollen trap. We also measured the development of allergen in pollen during ripening.Results:  About 93 ± 3% of Bet v 1 was found in the PM > 10 μm fraction, the fraction containing birch pollen. We did not measure any Bet v 1 in 2.5 μm > PM > 0.12 μm. Either in Munich no allergen was in this fraction or the allergen was absorbed to diesel soot particles that also deposit in this fraction. Pollen released 115% more Bet v 1 in 2007 than in 2004. Also within 1 year, the release of allergen from the same amount of pollen varied more than 10‐fold between different days. This difference was explained by a rapidly increasing expression of Bet v 1 in pollen in the week just before pollination. Depending on the day the pollen is released during ripening, its potency varies.Conclusion:  In general, pollen count and allergen in ambient air follow the same temporal trends. However, because a 10‐fold difference can exist in allergen potency of birch pollen, symptoms might be difficult to correlate with pollen counts, but perhaps better with allergen exposure.
Risk factors of new‐onset asthma in adults: a population‐based international cohort study
Authors: Antó J. M. , Sunyer J. , Basagaña X. , Garcia‐Esteban R. , Cerveri I. , De Marco R. , Heinrich J. , Janson C. , Jarvis D. , Kogevinas M. , Kuenzli N. , Leynaert B. , Svanes C. , Wjst M. , Gislason T. , Burney P. 
Published: February 2010

To cite this article: Antó JM, Sunyer J, Basagaña X, Garcia‐Esteban R, Cerveri I, de Marco R, Heinrich J, Janson C, Jarvis D, Kogevinas M, Kuenzli N, Leynaert B, Svanes C, Wjst M, Gislason T, Burney P. Risk factors of new‐onset asthma in adults: a population‐based international cohort study. Allergy 2010; 65: 1021–1030AbstractBackground:  The occurrence of new‐onset asthma during adulthood is common, but there is insufficient understanding of its determinants including the role of atopy.Objective:  To assess the risk factors for the development of new‐onset asthma in middle‐aged adults and to compare them according to atopy.Methods:  A longitudinal analysis of 9175 young adults who participated in two surveys of the European Community Respiratory Health Survey (ECRHS) conducted 9 years apart.Findings:  We observed 179 cases of new‐onset asthma among 4588 participants who were free of asthma and reported at the beginning of the follow‐up that they had never had asthma (4.5 per 1000 person‐years). In a logistic regression, the following risk factors were found to increase the risk of new‐onset asthma: female gender (OR: 1.97; 95% confidence interval (CI): 1.38,2.81), bronchial hyperresponsiveness (3.25; 2.19,4.83), atopy (1.55;1.08,2.21), FEV1 < 100 % predicted (1.87;1.34,2.62), nasal allergy (1.98;1.39,2.84) and maternal asthma (1.91;1.13;3.21). Obesity, respiratory infections in early life and high‐risk occupations increased the risk of new‐onset asthma although we had limited power to confirm their role. Among the atopics, total IgE and sensitization to cat were independently related to the risk of new‐onset asthma. The proportion of new‐onset asthma attributable to atopy varied from 12% to 21%.Conclusion:  Adults reporting that they had never had asthma were at a substantial risk of new‐onset asthma as a result of multiple independent risk factors including lung function. Atopy explains a small proportion of new‐onset adult asthma.
Novel exon nucleotide substitution at the splice junction causes a neonatal Marfan syndrome
Authors: Chao S‐C , Chen J‐S , Tsai C‐H , Lin JY‐M , Lin Y‐J , Sun HS 
Published: February 2010

Chao S‐C, Chen J‐S, Tsai C‐H, Lin JY‐M, Lin Y‐J, Sun HS. Novel exon nucleotide substitution at the splice junction causes a neonatal Marfan syndrome.The fibrillin‐1 gene (FBN1) mutations are associated with a broad spectrum of disorders including Marfan syndrome (MFS) and show great clinical heterogeneity. An underrepresentation for mutations leading to premature termination codon (PTC) in FBN1 exons 24–32 was found in neonatal or severe MFS but the underlying cause was unclear. This study thoroughly examined two FBN1 mutations on exons 24–32 region to illustrate the molecular mechanisms underlying these FBN1 mutations on MFS etiology. Two nucleotide substitutions, c.3208G> C, the last nucleotide of exon 26, and c.3209A>G, the first nucleotide of exon 27, affecting the same amino acid, p.D1070H and p.D1070G, respectively, gave very different phenotypes. We demonstrate that c.3208G>C generates two alternatively spliced transcripts, while c.3209A>G does not affect the splicing. We further demonstrate that the aberrantly spliced transcripts do not go through nonsense‐mediated decay, but rather produce unstable, premature protein peptides that are degraded by endoplasmic reticulum associated degradation. The molecular mechanism outlined here defines a model for the pathogenesis of PTC‐containing mutation within the exons 24–32 of FBN1 in MFS. Furthermore, our data suggest that PTC mutation within this region may lead to early lethality in neonatal MFS.
Variable hearing impairment in a DFNB2 family with a novel MYO7A missense mutation
Authors: Hildebrand MS , Thorne NP , Bromhead CJ , Kahrizi K , Webster JA , Fattahi Z , Bataejad M , Kimberling WJ , Stephan D , Najmabadi H , Bahlo M , Smith RJH 
Published: February 2010

Hildebrand MS, Thorne NP, Bromhead CJ, Kahrizi K, Webster JA, Fattahi Z, Bataejad M, Kimberling WJ, Stephan D, Najmabadi H, Bahlo M, Smith RJH. Variable hearing impairment in a DFNB2 family with a novel MYO7A missense mutation.Myosin VIIA mutations have been associated with non‐syndromic hearing loss (DFNB2; DFNA11) and Usher syndrome type 1B (USH1B). We report clinical and genetic analyses of a consanguineous Iranian family segregating autosomal recessive non‐syndromic hearing loss (ARNSHL). The hearing impairment was mapped to the DFNB2 locus using Affymetrix 50K GeneChips; direct sequencing of the MYO7A gene was completed. The Iranian family (L‐1419) was shown to segregate a novel homozygous missense mutation (c.1184G>A) that results in a p.R395H amino acid substitution in the motor domain of the myosin VIIA protein. As one affected family member had significantly less severe hearing loss, we used a candidate approach to search for a genetic modifier. This novel MYO7A mutation is the first reported to cause DFNB2 in the Iranian population and this DFNB2 family is the first to be associated with a potential modifier. The absence of vestibular and retinal defects, and less severe low frequency hearing loss, is consistent with the phenotype of a recently reported Pakistani DFNB2 family. Thus, we conclude this family has non‐syndromic hearing loss (DFNB2) rather than USH1B, providing further evidence that these two diseases represent discrete disorders.
Radical prostatectomy: a systematic review of the impact of hospital and surgeon volume on patient outcome
Authors: Wilson Ailsa , Marlow Nicholas E. , Maddern Guy J. , Barraclough Bruce , Collier Neil A. , Dickinson Ian C. , Fawcett Jonathon , Graham John C. 
Published: February 2010

AbstractBackground:  To assess the impact of hospital and surgeon volume on mortality, morbidity, length of hospital stay and costs of radical prostatectomy (RP).Methods:  This systematic review identified relevant studies published between 1997 and June 2007. Inclusion of papers was established through application of a predetermined protocol, independent assessment by two reviewers, and a final consensus decision.Results:  Compared with low volume hospitals, the included studies showed high volume hospitals demonstrated lower rates of mortality, postoperative complications and readmissions, and lower overall hospital costs. High volume surgeons similarly showed lower rates of postoperative complications and shorter length of stay compared with low volume surgeons, but no difference in mortality.Conclusions:  From the literature obtained, patients undergoing RP performed by high volume providers may have better outcomes compared to low volume providers; however, any move to centralize RP must be further evaluated.
Nonsteroidal anti‐inflammatory drugs‐associated colopathy
Authors: Masannat Yazan A. , Harron Michael , Harinath Gandra 
Published: February 2010

AbstractBackground:  Nonsteroidal anti‐inflammatory drugs (NSAIDs) are commonly used worldwide, and their complications in the upper gastrointestinal tract are well described in the literature and well known to clinicians. However, complications in the large bowel are being increasingly recognized and reported. This review aims to address the different aspects of NSAIDs‐associated colopathy.Methods:  This is a review article addressing NSAIDs colopathy. A Medline‐based search was performed for articles published between 1950 and 2008 on this condition. Keywords detailed were colonic disease, ulcers, strictures and/or diaphragm strictures. Only articles in the English language were considered.Results:  The articles identified included letters to the editors, case reports, case series, review articles and few original research papers. The review was structured in a narrative style in different sections addressing pathophysiology, clinical presentation and management.Conclusions:  NSAIDs colopathy is a rare benign condition. Current evidence only suggests an association with prolonged use of the NSAIDs, however, there are no studies to support the direct causation. The presentation is non‐specific, and the commonest findings on endoscopy are ulceration and diaphragm‐like strictures. The importance of identifying this condition is to prevent complications and also to be able to differentiate it from other conditions such as inflammatory bowel disease (IBD) and malignancy.
Brief screening tool for mild cognitive impairment in older Japanese: Validation of the Japanese version of the Montreal Cognitive Assessment
Authors: Fujiwara Yoshinori , Suzuki Hiroyuki , Yasunaga Masashi , Sugiyama Mika , Ijuin Mutsuo , Sakuma Naoko , Inagaki Hiroki , Iwasa Hajime , Ura Chiaki , Yatomi Naomi , Ishii Kenji , Tokumaru Aya M , Homma Akira , Nasreddine Ziad , Shinkai Shoji 
Published: February 2010

Aim:  The Montreal Cognitive Assessment (MoCA), developed by Dr Nasreddine (Nasreddine et al. 2005), is a brief cognitive screening tool for detecting older people with mild cognitive impairment (MCI). We examined the reliability and validity of the Japanese version of the MoCA (MoCA‐J) in older Japanese subjects.Methods:  Subjects were recruited from the outpatient memory clinic of Tokyo Metropolitan Geriatric Hospital or community‐based medical health check‐ups in 2008. The MoCA‐J, the Mini‐Mental State Examination (MMSE), the revised version of Hasegawa's Dementia Scale (HDS‐R), Clinical Dementia Rating (CDR) scale, and routine neuropsychological batteries were conducted on 96 older subjects. Mild Alzheimer's disease (AD) was found in 30 subjects and MCI in 30, with 36 normal controls.Results:  The Cronbach's alpha of MoCA‐J as an index of internal consistency was 0.74. The test–retest reliability of MoCA, using intraclass correlation coefficient between the scores at baseline survey and follow‐up survey 8 weeks later was 0.88 (P < 0.001). MoCA‐J score was highly correlated with MMSE (r = 0.83, P < 0.001), HDS‐R (r = 0.79, P < 0.001) and CDR (r = −0.79, P < 0.001) scores. The areas under receiver–operator curves (AUC) for predicting MCI and AD groups by the MoCA‐J were 0.95 (95% confidence interval [CI] = 0.90–1.00) and 0.99 (95% CI = 0.00–1.00), respectively. The corresponding values for MMSE and HDS‐R were 0.85 (95% CI = 0.75–0.95) and 0.97 (95% CI = 0.00–1.00), and 0.86 (95% CI = 0.76–0.95) and 0.97 (95% CI = 0.00–1.00), respectively. Using a cut‐off point of 25/26, the MoCA‐J demonstrated a sensitivity of 93.0% and a specificity of 87.0% in screening MCI.Conclusion:  The MoCA‐J could be a useful cognitive test for screening MCI, and could be recommended in a primary clinical setting and for geriatric health screening in the community. Geriatr Gerontol Int 2010; 10: 225–232.
Molecular characterization of inorganic sulfur‐compound metabolism in the deep‐sea epsilonproteobacterium Sulfurovum sp. NBC37‐1
Authors: Yamamoto Masahiro , Nakagawa Satoshi , Shimamura Shigeru , Takai Ken , Horikoshi Koki 
Published: February 2010

SummaryThe molecular components involved in energy metabolism of deep‐sea Epsilonproteobacteria were characterized in the mesophilic hydrogen‐ and sulfur‐oxidizing chemolithoautotroph Sulfurovum sp. NBC37‐1. Previous whole‐genome analysis of strain NBC37‐1 identified key genes likely to be associated with both sulfur reduction (psr gene families) and oxidation (two sox gene clusters). However, the sox gene clusters showed unique organizations and low homologies to those in other bacteria. Therefore, the biochemical mechanism of inorganic sulfur metabolism has been uncertain. Enzymatic activity measurements and partial protein purification indicated that the Sox enzyme system was constitutively expressed, whereas the expression of sulfur‐reduction enzymes varied depending on the culture conditions. The operative Sox system in strain NBC37‐1 required membrane components. The molecular basis of energy metabolism reported in this study provides important insight into how deep‐sea Epsilonproteobacteria change their energy metabolism in response to variable physical and chemical conditions in mixing zones between hydrothermal fluid and ambient seawater.
Tantalizing evidence for caspase‐like protein expression and activity in the cellular stress response of Archaea
Authors: Bidle Kelly A. , Haramaty Liti , Baggett Natalie , Nannen Jennifer , Bidle Kay D. 
Published: February 2010

SummaryAn enigmatic feature of microbial evolution is the emergence of programmed cell death (PCD), a genetically controlled form of cell suicide triggered by environmental stimuli. Archaea, the second major prokaryotic domain of life, have been notably absent from the PCD inheritance discussion, due to a lack of genetic homologues. Using the model haloarchaeon Haloferax volcanii, we document extremely high caspase‐specific activity and expression of immunoreactive proteins to human caspase 8 antisera, both of which were induced by salt stress and death and were abolished by in vivo addition of a broad‐spectrum caspase inhibitor. Caspase inhibition severely impaired cell growth under low and high salt stress, demonstrating a critical role in the cellular stress response. In silico analysis of the H. volcanii proteome identified a subset of 18 potential target proteins containing a signature tetrapeptide caspase cleavage motif (IETD), some with putative roles in allosteric regulation, signal transduction, osmotic stress and cell communication. Detection of similarly high activity and expression in other haloarchaea (Halorubrum and Haloarcula) and in diverse members of Euryarchaeota (the methanogen Methanosarcina acetivorans and the hyperthermophile Pyrococcus furiosus) and Crenarchaeota (the acidophile Sulfolobus solfataricus) argue for a broad representation within the archaeal domain. By playing a role in normal cell function, caspase‐like proteases in Archaea appear to have co‐evolved with other metabolic pathways, broadening their biological roles beyond apoptosis and cell death.
Characterization of halotolerant Bicosoecida and Placididea (Stramenopila) that are distinct from marine forms, and the phylogenetic pattern of salinity preference in heterotrophic stramenopiles
Authors: Park Jong Soo , Simpson Alastair G. B. 
Published: February 2010

SummaryRecent culture‐based studies demonstrate the distinctiveness of the microbial eukaryote biota of very hypersaline environments. In contrast, microscopy‐based faunistic studies suggest that the biota of habitats of more moderate hypersalinity (60–150‰) overlaps substantially with that of marine environments, but this has barely been studied with modern techniques. To investigate the diversity and salinity tolerance range of these organisms, eight cultures of heterotrophic stramenopiles were established from (or from nearby) moderately hypersaline locations. These isolates represent five independent groups; Groups A, B and C are bicosoecids; Groups D and E belong to Placididea. One isolate (Group A) is a strain of the widespread marine species Cafeteria roenbergensis, and cannot grow above 100‰ salinity. The other isolates – Groups B–E – can all grow at 150–175‰ salinities and are probably moderate halophiles. Groups B–E all represent previously unsequenced species or even genera, although Group B is the sister group of the borderline extreme halophile Halocafeteria. The high level of novelty en countered suggests that moderately hypersaline environments may harbour a heterotrophic stramenopile biota distinct from that of marine environments. Interestingly, our new isolates are all most closely related to marine or halophilic forms, and our phylogenies show large clades defined by saline/non‐saline habitats within bicosoecids, placidomonads and related lineages. In particular, most freshwater/soil bicosoecids form one well‐supported clade. The sole major exception is Bicosoeca, which is intermixed with marine environmental sequences originally referred to as ‘MAST‐13’, which are from brackish water, not typical seawater. It seems that the freshwater/marine barrier has been crossed very few times in the evolutionary history of these heterotrophic stramenopile flagellates.
Nitrogen fixation by a marine non‐heterocystous cyanobacterium requires a heterotrophic bacterial consort
Authors: Li Zhongkui , Yu Jingjie , Kim Kyoung‐Rae , Brand Jerry 
Published: February 2010

SummaryCultures of the non‐heterocystous cyanobacterium, Leptolyngbya nodulosa, could be grown indefinitely in media devoid of combined nitrogen. Acetylene reduction assays showed that these cultures fixed nitrogen in the dark period of a diurnal cycle under micro‐oxygenic or anaerobic conditions. Addition of DCMU to cultures induced much higher rates of nitrogenase activity, most of which occurred in the light. Measurements of activity in the presence of chloramphenicol indicated that nitrogenase is synthesized in darkness and probably destroyed in the subsequent light period. Neither the dark‐mediated nitrogenase in the absence of DCMU nor light‐mediated activity in the presence of DCMU could be sustained for more than 3 days without a photoperiodic light/dark cycle. Axenic cultures could not be grown in the absence of combined nitrogen and did not demonstrate any acetylene reduction activity. An identical nifH gene sequence was found in axenic and non‐axenic cultures of L. nodulosa. RT‐PCR demonstrated that this gene was expressed only in non‐axenic cultures. Western blotting showed that the Fe‐protein of nitrogenase is absent in cultures that are incapable of acetylene reduction, indicating that the lack of nitrogenase activity is likely due to the absence of the enzyme. These observations strongly indicate that L. nodulosa contains a functional nitrogenase which is not expressed in the absence of heterotrophic bacteria.