bluuebunny/crossref_metadata_2025_split huggingface dataset:
MapView: visualization of short reads alignment on a desktop computer
Authors: Bao Hua , Guo Hui , Wang Jinwei , Zhou Renchao , Lu Xuemei , Shi Suhua 
Published: April 2009

Abstract
Summary: We introduce a new visual analytics tool named MapView to facilitate the representation of large-scale short reads alignment data and genetic variation analysis. MapView can handle hundreds of millions of short reads on a desktop computer with limited memory. It supports a compact alignment view for both single-end and paired end short reads, multiple navigation and zoom modes and multi-thread processing. Moreover, MapView offers automated genetic variation detection. MapView has been used in our lab and by over 10 research labs worldwide.
Availability: http://evolution.sysu.edu.cn/mapview/.
Contact: baohua100@hotmail.com; lssssh@mail.sysu.edu.cn
Supplementary information: Supplementary data are available at http://evolution.sysu.edu.cn/mapview/MVF.pdf
ProtVirDB: a database of protozoan virulent proteins
Authors: Ramana Jayashree , Gupta Dinesh 
Published: April 2009

Abstract
Summary: ProtVirDB is a comprehensive and user-friendly web-based knowledgebase of virulent proteins belonging to protozoan species. The database will facilitate research and provide an integrated platform for comparative studies of virulent proteins in different parasitic protozoans and organize them under a unifying classification schema with functional categories. Remarkably, one-third of the protein sequences in the database showed presence of either mono- or hetero-repeats, or both concomitantly—hence reiterating the importance of repeats in parasite virulence mechanisms. A number of useful bioinformatics tools including BLAST and tools for phylogenetic analysis are integrated with the database. With the rapidly burgeoning interest in the pathogenesis mechanisms of protozoans and ongoing genome sequencing projects, we anticipate that the database will be a useful tool for the research community.
Availability: http://bioinfo.icgeb.res.in/protvirdb
Contact: dinesh@icgeb.res.in
Supplementary information: Supplementary data are available at Bioinformatics online
Size-dependent frequency response of sandeel schools
Authors: Johnsen Espen , Pedersen Ronald , Ona Egil 
Published: April 2009

Abstract
Johnsen, E., Pedersen, R., and Ona, E. 2009. Size-dependent frequency response of sandeel schools. – ICES Journal of Marine Science, 66: 1100–1105. Annual Norwegian sandeel surveys have been conducted in the North Sea since 2005 to measure the stock of lesser sandeel (Ammodytes marinus). Target identification is often a major challenge in acoustic surveys, and discriminant analyses have been used to separate echoes accurately from schools of herring, mackerel, and sandeel based on their acoustic-frequency responses measured at 18, 38, 120, and 200 kHz. At two fishing grounds during the 2008 survey, 332 schools were identified as sandeel, based on the characteristics of the acoustic signal, and validated by trawl samples. The schools consisted almost entirely of 1-year-old sandeels on one of the grounds, and 2-year-olds on the other. In this study, the potential of acoustic-frequency responses is advanced to classify the sizes of fish in them. A discriminant analysis using frequency responses as independent variables was able to differentiate between sandeel schools comprising 1- and 2-year-old fish (p < 0.001). Approximately 83% of the 2-year-old fish and 77% of the 1-year-old fish were classified correctly. The frequency responses at 18 and 38 kHz were the most important independent variables. Sandeel landings in the North Sea are normally dominated by 1- and 2-year-old sandeels in the first half of the year. This study revealed that these two age classes could be identified acoustically; a finding that may be important for acoustic surveys of sandeels and for management of the commercial sandeel fishery.
Nursery grounds of the orange roughy around New Zealand
Authors: Dunn M. R. , Rickard G. J. , Sutton P. J. H. , Doonan I. J. 
Published: April 2009

Abstract
Dunn, M. R., Rickard, G. J., Sutton, P. J. H., and Doonan, I. J. 2009. Nursery grounds of the orange roughy around New Zealand. – ICES Journal of Marine Science, 66: 871–885. The orange roughy (Hoplostethus atlanticus) is a deep-sea species with a centenarian lifespan, a life-history feature that may enable the stocks to withstand prolonged periods of recruitment failure. Most stocks have been substantially depleted, however, so estimating recruitment has become a priority in setting catch quotas to ensure future sustainability of the fisheries. A description of the nursery grounds of the species off New Zealand is provided, using extensive research-survey data from 12 541 bottom trawls and 713 midwater trawls. The juveniles were initially caught on the seabed, near known spawning grounds, and towards the shallower end of the species' distribution, and not in midwater or the shallower or deeper bottom tows. Densities were greatest at 850-900 m. As juveniles grew, their spatial and depth distribution expanded, both shallower and deeper, with a skew towards deeper water, such that by the onset of maturation, densities were relatively high in 850–1300 m of water. The early nursery grounds were in relatively warm water, but on the south Chatham Rise, appeared to be bounded by the presence of a cold-water front.
A Specialized Outer Layer of the Primary Cell Wall Joins Elongating Cotton Fibers into Tissue-Like Bundles
Authors: Singh Bir , Avci Utku , Eichler Inwood Sarah E. , Grimson Mark J. , Landgraf Jeff , Mohnen Debra , Sørensen Iben , Wilkerson Curtis G. , Willats William G.T. , Haigler Candace H. 
Published: April 2009

Abstract
Cotton (Gossypium hirsutum) provides the world's dominant renewable textile fiber, and cotton fiber is valued as a research model because of its extensive elongation and secondary wall thickening. Previously, it was assumed that fibers elongated as individual cells. In contrast, observation by cryo-field emission-scanning electron microscopy of cotton fibers developing in situ within the boll demonstrated that fibers elongate within tissue-like bundles. These bundles were entrained by twisting fiber tips and consolidated by adhesion of a cotton fiber middle lamella (CFML). The fiber bundles consolidated via the CFML ultimately formed a packet of fiber around each seed, which helps explain how thousands of cotton fibers achieve their great length within a confined space. The cell wall nature of the CFML was characterized using transmission electron microscopy, including polymer epitope labeling. Toward the end of elongation, up-regulation occurred in gene expression and enzyme activities related to cell wall hydrolysis, and targeted breakdown of the CFML restored fiber individuality. At the same time, losses occurred in certain cell wall polymer epitopes (as revealed by comprehensive microarray polymer profiling) and sugars within noncellulosic matrix components (as revealed by gas chromatography-mass spectrometry analysis of derivatized neutral and acidic glycosyl residues). Broadly, these data show that adhesion modulated by an outer layer of the primary wall can coordinate the extensive growth of a large group of cells and illustrate dynamic changes in primary wall structure and composition occurring during the differentiation of one cell type that spends only part of its life as a tissue.
A Comparative Study of the Involvement of 17 Arabidopsis Myosin Family Members on the Motility of Golgi and Other Organelles
Authors: Avisar Dror , Abu-Abied Mohamad , Belausov Eduard , Sadot Einat , Hawes Chris , Sparkes Imogen A. 
Published: April 2009

Abstract
Gene families with multiple members are predicted to have individuals with overlapping functions. We examined all of the Arabidopsis (Arabidopsis thaliana) myosin family members for their involvement in Golgi and other organelle motility. Truncated fragments of all 17 annotated Arabidopsis myosins containing either the IQ tail or tail domains only were fused to fluorescent markers and coexpressed with a Golgi marker in two different plants. We tracked and calculated Golgi body displacement rate in the presence of all myosin truncations and found that tail fragments of myosins MYA1, MYA2, XI-C, XI-E, XI-I, and XI-K were the best inhibitors of Golgi body movement in the two plants. Tail fragments of myosins XI-B, XI-F, XI-H, and ATM1 had an inhibitory effect on Golgi bodies only in Nicotiana tabacum, while tail fragments of myosins XI-G and ATM2 had a slight effect on Golgi body motility only in Nicotiana benthamiana. The best myosin inhibitors of Golgi body motility were able to arrest mitochondrial movement too. No exclusive colocalization was found between these myosins and Golgi bodies in our system, although the excess of cytosolic signal observed could mask myosin molecules bound to the surface of the organelle. From the preserved actin filaments found in the presence of enhanced green fluorescent protein fusions of truncated myosins and the motility of myosin punctae, we conclude that global arrest of actomyosin-derived cytoplasmic streaming had not occurred. Taken together, our data suggest that the above myosins are involved, directly or indirectly, in the movement of Golgi and mitochondria in plant cells.
Faecal DNA and calprotectin as biomarkers of acute intestinal toxicity in patients undergoing pelvic radiotherapy
Authors: VARELA E. , ANTOLÍN M. , GUARNER F. , VERGES R. , GIRALT J. , MALAGELADA J.‐R. 
Published: April 2009

SummaryBackground  Acute intestinal toxicity is a frequent complication that may lead to interruption of treatment in patients undergoing pelvic radiotherapy. Reliable, non‐invasive biological markers to evidence their severity are not yet available.Aim  To test faecal DNA and calprotectin as potential biomarkers of intestinal toxicity caused by pelvic radiotherapy.Methods  Patients were categorized according to the location of the cancer as nonrectal (n = 25) and rectal (n = 27). Four stool samples were collected at weeks w0, w3, w5 (end of radiotherapy) and w7. Faecal DNA was determined by quantitative PCR and calprotectin by ELISA. Intestinal toxicity was scored according to the Common Toxicity Criteria.Results  In the nonrectal group, acute diarrhoea toxicity was present in 80% of patients, faecal DNA increased 10‐fold during radiotherapy (1.5 × 103 copies/mg dry weight, 9.5 × 102–8.8 × 103 at w0, median and interquartile range vs. 1.3 × 104, 1.9 × 103–3.9 × 104 at w5, P < 0.01), but was not recovered at w7 (3.4 × 103, 1.5 × 103–4.1 × 104) and calprotectin doubled during treatment at w3 and w5. No significant changes in faecal markers were found in the rectal group.Conclusion  Faecal excretion of human DNA and calprotectin increased during pelvic radiotherapy treatment, and may be a good objective biomarker of intestinal damage in nonrectal cancer patients.
Meta‐analysis: longitudinal studies of serum vitamin D and colorectal cancer risk
Authors: YIN L. , GRANDI N. , RAUM E. , HAUG U. , ARNDT V. , BRENNER H. 
Published: April 2009

SummaryBackground  In 1980, Garland hypothesized that lower levels of vitamin D resulting from much weaker UV‐B radiation at higher latitudes may account for the striking geographical pattern of cancer mortality. Further research has been conducted over the past 20 years.Aim  To perform a systematic review and meta‐analysis of longitudinal studies on the association between serum 25 hydroxyvitamin D (25(OH)D) and the risk of colorectal cancer (CRC).Methods  Relevant studies published until September 2008 were identified by systematically searching Ovid Medline, EMBASE, and ISI Web of Knowledge databases and by cross‐referencing. Due to the heterogeneity of studies in categorizing serum vitamin D levels, all results were recalculated for an increase of serum 25(OH)D by 20 ng/mL. Summary odds ratios (ORs) were calculated using meta‐analysis methods.Results  Overall, eight original articles reporting on the association between serum 25(OH) D and CRC risk were included. In meta‐analyses, summary ORs (95% confidence intervals) for the incidence of CRC, colon cancer and rectal cancer associated with an increase of 25(OH)D by 20 ng/mL were 0.57 (0.43–0.76), 0.78 (0.54–1.13) and 0.41 (0.11–1.49). No indication for publication bias was found.Conclusions  Our results support suggestions that serum 25(OH)D is inversely related to CRC risk.
Meta‐analysis: the efficacy of azathioprine and mercaptopurine in ulcerative colitis
Authors: GISBERT J. P. , LINARES P. M. , MCNICHOLL A. G. , MATÉ J. , GOMOLLÓN F. 
Published: April 2009

SummaryBackground  Debate exists regarding to whether thiopurine therapy is as effective in ulcerative colitis (UC) as it is in Crohn's disease.Aim  To review systematically the efficacy of azathioprine (AZA) and mercaptopurine (MP) in UC, and to conduct a meta‐analysis of randomized clinical trials evaluating the efficacy of AZA/MP for the induction or maintenance of UC clinical remission.Methods  Selection of studies: Evaluating AZA/MP for induction and/or maintenance of clinical remission of UC. Randomized‐controlled‐trials comparing AZA/MP with placebo/5‐aminosalicylates were included in the meta‐analysis. Search strategy: Electronic and manual. Study quality: Independently assessed by two reviewers. Data synthesis: By ‘intention‐to‐treat’.Results  Thirty noncontrolled studies (1632 patients) were included in the systematic review. Mean efficacy of AZA/MP was 65% for induction and 76% for maintenance of the remission. Seven controlled studies were included in the meta‐analysis. (i) Induction of remission: four studies (89 AZA/MP‐treated patients) showed mean efficacy of 73% vs. 64% in controls (OR = 1.59; 95% CI = 0.59–4.29). (ii) Maintenance of remission: six studies (124 AZA/MP‐treated patients) showed mean efficacy of 60% vs. 37% in controls (OR = 2.56; 95% CI = 1.51–4.34). When only studies comparing AZA/MP vs. placebo were considered, OR was 2.59 (95% CI = 1.26–5.3), absolute risk reduction was 23% and number‐needed‐to‐treat (NNT) to prevent one recurrence was 5.Conclusion  Thiopurine drugs (AZA/MP) are more effective than placebo for the prevention of relapse in UC, with an NNT of 5 and an absolute risk reduction of 23%.
Beta2‐microglobulin is a better predictor of treatment‐free survival in patients with chronic lymphocytic leukaemia if adjusted according to glomerular filtration rate
Authors: Delgado Julio , Pratt Guy , Phillips Neil , Briones Javier , Fegan Chris , Nomdedeu Josep , Pepper Chris , Aventin Anna , Ayats Ramon , Brunet Salut , Martino Rodrigo , Valcarcel David , Milligan Donald , Sierra Jorge 
Published: April 2009

SummaryEven in the era of newer and sophisticated prognostic markers, beta2‐microglobulin (B2M) remains a simple but very powerful predictor of treatment‐free survival (TFS) and overall survival (OS) in patients with chronic lymphocytic leukaemia (CLL). However, B2M levels are heavily influenced by the patient’s glomerular filtration rate (GFR) and this study aimed to evaluate whether GFR‐adjusted B2M (GFR‐B2M) had improved prognostic value compared to unadjusted B2M in a cohort of over 450 consecutive CLL patients from two separate institutions. Multivariate analysis identified a significantly shorter TFS in patients who were ZAP‐70 + (P < 0·001), with increased GFR‐B2M (P < 0·001), and del(11q) or del(17p) as detected by fluorescence in situ hybridization (FISH; P < 0·001). When OS was evaluated by multivariate analysis, age 65 years or older (P < 0·001) and poor risk FISH abnormalities (P < 0·001) had a confirmed adverse prognostic impact, but the predictive value of GFR‐B2M was lost in the validation analysis. In all survival models, B2M did not attain independent significance unless GFR‐B2M was eliminated from the analysis. In conclusion, GFR‐B2M is a better predictor of TFS than unadjusted B2M in CLL patients.
Serine protease activity of Per a 10 augments allergen‐induced airway inflammation in a mouse model
Authors: Sudha V. T. , Arora N. , Singh B. P. 
Published: April 2009

AbstractBackground We recently reported an immunodominant serine protease allergen (Per a 10) fromPeriplaneta americana.This study investigates the role of its proteolytic activity in driving the immune responses towards self and other allergens.Materials and methods Groups of Balb/c mice were sensitized intraperitoneally and subcutaneously with proteolytically active Per a 10 or inactivated Per a 10 (using aminoethyl benzenesulfonyl fluoride hydrochloride) or whole bodyP. americanaextract and subsequently challenged intranasally with the respective antigens. Mice were also sensitized and challenged with ovalbumin (OVA) alone or co‐administered with active or inactive Per a 10. The immune‐inflammatory responses were measured by airway hyperresponsiveness (AHR) and cellular infiltration of lungs i.e. eosinophil counts, eosinophil peroxidase (EPO) activity, myeloperoxidase activity (MPO), lung histopathology, serum levels of specific‐antibodies and levels of Th1/Th2 interleukins in bronchoalveolar lavage fluid (BALF) and in spleen cells culture supernatant.Results Mice challenged with active Per a 10/P. americanaextract showed a significant airway inflammation demonstrated by enhanced AHR and increased cellular infiltration of lungs as evidenced by high eosinophil counts, EPO activity, IL‐4 and IL‐5 in BALF. Active Per a 10 also induced a significant proliferation of spleen cells, increased secretion of IL‐4 and IL‐5 in the spleen cells culture supernatant and systemic production of specific‐IgE and IgG1. However, exposure with inactive Per a 10 elicited a low cellular infiltration and systemic antibody production. Exposure to OVA with active Per a 10 demonstrated a significantly high cellular infiltration and production of OVA‐specific IgE and IgG1, than exposure to OVA alone or with inactive Per a 10.Conclusions Proteolytic activity of Per a 10 plays an important role in driving the allergic immune response by providing an adjuvant effect, towards self and other potential allergens present in the same microenvironment.
Nutrient allocations and metabolism in two collembolans with contrasting reproduction and growth strategies
Authors: Larsen Thomas , Ventura Marc , Damgaard Christian , Hobbie Erik A. , Krogh Paul Henning 
Published: April 2009

Summary

Physiological mechanisms such as allocation and release of nutrients are keys to understanding an animal's adaptation to a particular habitat. This study investigated how two detrivores with contrasting life‐history traits allocated carbon (C) and nitrogen (N) to growth, reproduction and metabolism. As model organisms we used the collembolans, Proisotoma minuta (Tullberg 1871) and Protaphorura fimata (Gisin 1952).
To estimate allocations of C and N in tissue, we changed the isotopic composition of the animal's yeast diets when they became sexually mature and followed isotope turnover in tissue, growth and reproduction for 28 days. In addition, we measured the composition of C, N and phosphorus (P) to gain complementary information on the stoichiometry underlying life‐history traits and nutrient allocation.
For P. minuta, the smallest and most fecund of the two species, the tissue turnover of C and N were 13% and 11% day−1, respectively. For P. fimata, the equivalent rates were 5% and 4% d−1, respectively. Protaphorura fimata had the lowest metabolic rate relative to total body mass but the highest metabolic rates relative to reproductive investment. Adult P. fimata retained approximately 17% of the nutrient reserves acquired while a juvenile and adult P. minuta about 11%. N and P contents of total tissue were significantly higher in P. minuta than in P. fimata, suggesting that tissue turnover was correlated with high protein‐N and RNA‐P.
Our results suggest that the lower metabolism and nutritional requirements by P. fimata than P. minuta is an adaptation to the generally low availability and quality of food in its natural habitat.
The methodological approach we implemented tracking mass balance, isotope turnover and elemental composition is promising for linking nutrient budgets and life‐history traits in small invertebrates such as Collembola.
Impacts of climate change on the seasonal distribution of migratory caribou
Authors: SHARMA SAPNA , COUTURIER SERGE , CÔTÉ STEEVE D. 
Published: April 2009

AbstractArctic ecosystems are especially vulnerable to global climate change as temperature and precipitation regimes are altered. An ecologically and socially highly important northern terrestrial species that may be impacted by climate change is the caribou, Rangifer tarandus. We predicted the current and potential future occurrence of two migratory herds of caribou [Rivière George herd (RG) and Rivière‐aux‐Feuilles (RAF) herd] under a Canadian General Circulation Model climate change scenario, across all seasons in the Québec–Labrador peninsula, using climatic and habitat predictor variables. Argos satellite‐tracking collars have been deployed on 213 caribou between 1988 and 2003 with locations recorded every 4–5 days. In addition, we assembled a database of climate (temperature, precipitation, snowfall, timing and length of growing season) and habitat data obtained from the SPOT VEGETATION satellite sensor. Logistic regression models indicated that both climatic and physical habitat variables were significant predictors of current migratory caribou occurrence. Migratory caribou appeared to prefer regions with higher snowfall and lichen availability in the fall and winter. In the summer, caribou preferred cooler areas likely corresponding to a lower prevalence of insects, and they avoided disturbed and recently burnt areas. Climate change projections using climate data predicted an increased range for the RAF herd and decreased range for the RG herd during 2040–2069, limiting the herds to northeastern regions of the Québec–Labrador peninsula. Direct and indirect consequences of climate change on these migratory caribou herds possibly include alteration in habitat use, migration patterns, foraging behaviour, and demography, in addition to social and economic stress to arctic and subarctic native human populations.