bluuebunny/crossref_metadata_2025_split huggingface dataset:
Escape mortality of cod, saithe, and haddock in a Barents Sea trawl fishery
Authors: Ingólfsson Ólafur Arnar , Soldal Aud Vold , Huse Irene , Breen Mike 
Published: October 2007

Abstract
Ingólfsson, Ó. A., Soldal, A. V., Huse, I., and Breen, M. 2007. Escape mortality of cod, saithe, and haddock in a Barents Sea trawl fishery. – ICES Journal of Marine Science, 64: 000–000. We investigated the survival of gadoid fish in the Barents Sea escaping from a demersal trawl during commercial fishing conditions, with and without a sorting grid, at high and low levels of fishing intensity. The mortality of cod and saithe was negligible and unrelated to experimental conditions. Haddock mortality was generally greater than observed in earlier experiments and inversely related to fish length. Any possible effects of experimental conditions were hidden by large variability in the observed rates of mortality. We conclude that the observed mortality of haddock is confounded by methodological problems, particularly the instability of the observation cages, and does not reflect the true escape mortality. Cod and saithe are capable of surviving the stress of passage through, and escape from, the trawl, whereas haddock are more vulnerable, despite being a closely related species.
CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes
Authors: Huang Yi , Lau Susanna K. P. , Woo Patrick C. Y. , Yuen Kwok-yung 
Published: October 2007

Abstract
The recent SARS epidemic has boosted interest in the discovery of novel human and animal coronaviruses. By July 2007, more than 3000 coronavirus sequence records, including 264 complete genomes, are available in GenBank. The number of coronavirus species with complete genomes available has increased from 9 in 2003 to 25 in 2007, of which six, including coronavirus HKU1, bat SARS coronavirus, group 1 bat coronavirus HKU2, groups 2c and 2d coronaviruses, were sequenced by our laboratory. To overcome the problems we encountered in the existing databases during comparative sequence analysis, we built a comprehensive database, CoVDB (http://covdb.microbiology.hku.hk), of annotated coronavirus genes and genomes. CoVDB provides a convenient platform for rapid and accurate batch sequence retrieval, the cornerstone and bottleneck for comparative gene or genome analysis. Sequences can be directly downloaded from the website in FASTA format. CoVDB also provides detailed annotation of all coronavirus sequences using a standardized nomenclature system, and overcomes the problems of duplicated and identical sequences in other databases. For complete genomes, a single representative sequence for each species is available for comparative analysis such as phylogenetic studies. With the annotated sequences in CoVDB, more specific blast search results can be generated for efficient downstream analysis.
Relationship between menthol cigarettes and smoking cessation among African American light smokers
Authors: Okuyemi Kolawole S. , Faseru Babalola , Sanderson Cox Lisa , Bronars Carrie A. , Ahluwalia Jasjit S. 
Published: October 2007

ABSTRACTAims  To determine whether African American light smokers who smoked menthol cigarettes had lower cessation when treated with nicotine replacement therapy and counseling.Design  Data were derived from a clinical trial that assessed the efficacy of 2 mg nicotine gum (versus placebo) and counseling (motivational interviewing counseling versus Health Education) for smoking cessation among African American light smokers (smoked ≤ 10 cigarettes per day).Participants  The sample consisted of 755 African American light smokers.Measurements  The primary outcome variable was verified 7‐day point‐prevalence smoking cessation at 26 weeks follow‐up. Verification was by salivary cotinine.Findings  Compared to non‐menthol smokers, menthol smokers were younger and less confident to quit smoking (P = 0.023). At 26 weeks post‐randomization, 7‐day verified abstinence rate was significantly lower for menthol smokers (11.2% versus 18.8% for non‐menthol, P = 0.015).Conclusions  Among African American light smokers, use of menthol cigarettes is associated with lower smoking cessation rates. Because the majority of African American smokers use menthol cigarettes, a better understanding of the mechanism for this lower quit rate is needed.
Does early onset of non‐medical use of prescription drugs predict subsequent prescription drug abuse and dependence? Results from a national study
Authors: McCabe Sean E. , West Brady T. , Morales Michele , Cranford James A. , Boyd Carol J. 
Published: October 2007

ABSTRACTAims  The present study examined the associations between early onset of non‐medical use of prescription drugs (NMUPD) (i.e. sedatives, tranquilizers, opioids, stimulants) and the development of prescription drug abuse and dependence in the United States.Design  Data were collected from structured diagnostic interviews using the National Institute on Alcohol Abuse and Alcoholism (NIAAA) Alcohol Use Disorder and Associated Disabilities Interview Schedule: Diagnostic and Statistical Manual version IV (DSM‐IV).Setting  National prevalence estimates were derived from the 2001–2002 National Epidemiologic Survey on Alcohol and Related Conditions (NESARC, n = 43 093).Participants  A nationally representative cross‐sectional sample of civilian non‐institutionalized adults aged 18 years or older in the United States, of whom 52% were women, 71% white, 12% Hispanic, 11% African American, 4% Asian and 2% Native American or of other racial background.Findings  A higher percentage of individuals who began using prescription drugs non‐medically at or before 13 years of age were found to have developed prescription drug abuse and dependence versus those individuals who began using at or after 21 years of age. Multivariate logistic regression analyses indicated that the odds of developing any life‐time prescription drug abuse among non‐medical users was reduced by approximately 5% with each year non‐medical use was delayed [adjusted odds ratio (AOR) = 0.95, 95% CI = 0.94, 0.97], and that the odds of developing any life‐time prescription drug dependence were reduced by about 2% with each year onset was delayed (AOR = 0.98, 95% CI = 0.96, 1.00) when controlling for relevant covariates.Conclusions  The results of this study indicate that early onset of NMUPD was a significant predictor of prescription drug abuse and dependence. These findings reinforce the importance of developing prevention efforts to reduce NMUPD and diversion of prescription drugs among children and adolescents.
Correlates with the distribution and abundance of endangered Sclater’s monkeys (Cercopithecus sclateri) in southern Nigeria
Authors: Baker Lynne R. , Olubode Oluseun S. 
Published: October 2007

AbstractA distribution survey of the endangered Sclater’s monkey (Cercopithecus sclateri) was conducted over a wide area in southern Nigeria using forest surveys and hunter interviews. Sclater’s monkey, Nigeria’s only endemic primate species, is restricted to a land area of about 28,500 km2 in the densely human‐populated, oil‐producing region of southern Nigeria. Results indicate that this species is not as rare as previously thought; we confirmed its presence in 27 formerly unknown sites. Based on encounter‐rate and distribution data, Sclater’s monkey is one of the two most abundant diurnal primate taxa across its range. However, the species primarily occupies isolated and degraded forest fragments. Although hunting is widespread, selective hunting of larger‐bodied primate taxa offers some respite for the smaller Sclater’s monkey. We encountered this species more frequently in forests with relatively high hunting pressure, possibly indicating competitive release in the heavily hunted forests of southern Nigeria. Long‐term persistence of Sclater’s monkey, which has no official protection throughout its range, depends on the willingness of hunters to target smaller‐bodied wildlife (effort‐profit trade‐off), local bushmeat demand and protection of key forest fragments and the few larger forests in the region.
The utility of fine needle aspiration in HIV positive children
Authors: Michelow P. , Meyers T. , Dubb M. , Wright C. 
Published: October 2007

Objective:  To determine the spectrum of disease, diagnostic accuracy and adequacy of fine needle aspirates (FNA) in human immunodeficiency virus (HIV) positive children who present with mass lesions.Methods:  Between January 1997 and December 2002, 95 FNAs were performed in 91 children aged 15 years and younger who were known to be infected with the human immunodeficiency virus (HIV).Results:  Head and neck masses including salivary gland swellings were the most common presentation (58.9%) followed by axillary masses (25.3%). Groin masses were aspirated in six children, flank and abdominal masses in four children, buttock masses in three children, a chest wall mass in one child and a sonar guided FNA of a lung mass in one child. Eight FNAs (8.4%) proved inadequate. Reactive lymphadenopathy was diagnosed in 42 cases, mycobacterial infection in 22, four children were diagnosed with abscess, one child had a fungal infection and five were found to have non‐Hodgkin’s lymphoma. There were four cases each of lymphoepithelial lesion and Kaposi sarcoma. There was one case each of nephroblastoma, rhabdomyosarcoma, myeloma, melanotic progonoma and spindle cells, not otherwise specified.Conclusion:  Fine needle aspiration in HIV positive children is a worthwhile procedure and in most instances allows a rapid diagnosis obviating the need for surgery and enabling swift treatment to be undertaken where necessary. Ancillary studies form an important diagnostic component. Universal safety precautions must be strictly adhered to.
Fine needle aspiration cytology of the testis as the first‐line diagnostic modality in azoospermia: a comparative study of cytology and histology
Authors: Mehrotra R. , Chaurasia D. 
Published: October 2007

Objectives:  Male factors are responsible for about half of all infertility cases. Until recently, testicular biopsy was the standard method to ascertain the aetiology of azoospermia. Fine needle aspiration cytology has gained increasing popularity as a simple and minimally invasive procedure that can help in assessing testicular function accurately. This study was aimed at addressing the question whether testicular fine needle aspiration (FNA) may be used as a first‐line diagnostic modality in azoospermia and to assess its usefulness in the diagnostic protocol.Methods:  The FNA was performed in 78 consecutive azoospermic patients. To obviate sampling errors both testes were aspirated, except when contraindicated. Routine haematoxylin and eosin as well as Romanowsky staining was performed on the smears.Results:  The smears were categorized on cytological examination into normal spermatogenesis in 35 (50%) patients, Sertoli cells only syndrome in 22 (31.4%) and maturation arrest at the spermatocyte/spermatid level was seen in 13 (18.4%) patients. There were eight (10.2%) cases with scant smears where cytological diagnosis could not be made. A good correlation between cytological smears and histological sections was found in 54 of 58 testes (93.1%) in which histopathological confirmation was available.Conclusions:  Testicular FNA may be utilized as a first‐line investigative modality in patients with azoospermia, provided the procedure is performed and interpreted by experts.
Cytological criteria of endometrial lesions with emphasis on stromal and epithelial cell clusters: result of 8 years of experience with intrauterine sampling
Authors: Kobayashi H. , Otsuki Y. , Simizu S. , Yamada M. , Mukai R. , Sawaki Y. , Nakayama S. , Torii Y. 
Published: October 2007

Objective:  There are a number of unresolved issues in endometrial cytology. They include the significance of nuclear atypia for the diagnosis of grade1 adenocarcinoma (G1AC) and atypical endometrial hyperplasia (AEH), cytological criteria of endometrial hyperplasia without atypia, and recognition of stromal cell cluster (SC) and its distinction from epithelial cell cluster (EC).Methods:  We examined nuclear atypia, SC and EC in typical cases of five categories: normal endometrium (NEM), simple endometrial hyperplasia without atypia (SEH), complex endometrial hyperplasia without atypia (CEH), G1AC and grade2 adenocarcinoma (G2AC). We classified EC into four types: simple EC (SPEC), large regular EC (LREC), large irregular EC (LIEC) and small irregular EC (SIEC). Based on the results, we developed criteria of endometrial cytology and have evaluated 13 639 cases over 8 years.Results:  Nuclear atypia was significantly more frequent in G2AC than in any of the other four categories (P < 0.001). SC was significantly more frequent in NEM and SEH than in the other three categories (P < 0.001). G1AC and G2AC showed significantly higher frequency of LIEC than the other three categories (P < 0.001). CEH exhibited significantly higher frequency of LREC than the four categories (P < 0.001). The sensitivity and the specificity was 88.8% and 99.0% respectively.Conclusions:  We could diagnose G1AC, G2AC and CEH with high accuracy using the established criteria mainly based on SC and EC. We think that the criteria may facilitate an effective screening and an objective interpretation of endometrial samples.
Biological invasion alters regional nitrogen‐oxide emissions from tropical rainforests
Authors: HALL SHARON J. , ASNER GREGORY P. 
Published: October 2007

AbstractWe explored whether the invasion of an exotic, nitrogen (N) fixing tree into native Hawaiian tropical forests has altered regional emissions of nitrous oxide (N2O) and nitric oxide (NO), two atmospherically important trace gases produced by microorganisms in soils. Ecosystem processes, including nitrification and N‐oxide emissions, were not affected by Morella faya (formerly Myrica faya) invasion until it dominated the community with few native species in the overstory or understory. Remote‐sensing estimates of upper‐canopy leaf N concentration were strongly correlated to N‐oxide emissions in ecosystems at the mesic‐wet end of a precipitation gradient, where temperatures are warm, relatively constant, and N limits biological processes. In contrast, remotely sensed and field‐based canopy chemistry was not related to N‐oxide emissions in dry forest ecosystems where the seasonality of temperature and moisture exerted stronger control over soil gas fluxes. Thus, remote sensing of canopy N was useful for estimating the impact of M. faya on regional N‐oxide emissions only in regions receiving >1800 mm rainfall annually. Our estimates of N‐oxide emissions from M. faya are half as large and 35 times more precise than those made using traditional, plot‐level methods of extrapolation. Over the 40 years since its first occurrence in wet forests of Hawai'i Volcanoes National Park, M. faya has increased N‐oxide emissions 16‐fold, with its effects most pronounced in summer and at the N‐rich centers of dense, monospecific stands.
Water savings in mature deciduous forest trees under elevated CO2
Authors: LEUZINGER SEBASTIAN , KÖRNER CHRISTIAN 
Published: October 2007

AbstractStomatal conductance of plants exposed to elevated CO2 is often reduced. Whether this leads to water savings in tall forest‐trees under future CO2 concentrations is largely unknown but could have significant implications for climate and hydrology. We used three different sets of measurements (sap flow, soil moisture and canopy temperature) to quantify potential water savings under elevated CO2 in a ca. 35 m tall, ca. 100 years old mixed deciduous forest. Part of the forest canopy was exposed to 540 ppm CO2 during daylight hours using free air CO2 enrichment (FACE) and the Swiss Canopy Crane (SCC). Across species and a wide range of weather conditions, sap flow was reduced by 14% in trees subjected to elevated CO2, yielding ca. 10% reduction in evapotranspiration. This signal is likely to diminish as atmospheric feedback through reduced moistening of the air comes into play at landscape scale. Vapour pressure deficit (VPD)‐sap flow response curves show that the CO2 effect is greatest at low VPD, and that sap flow saturation tends to occur at lower VPD in CO2‐treated trees. Matching stomatal response data, the CO2 effect was largely produced by Carpinus and Fagus, with Quercus contributing little. In line with these findings, soil moisture at 10 cm depth decreased at a slower rate under high‐CO2 trees than under control trees during rainless periods, with a reversal of this trend during prolonged drought when CO2‐treated trees take advantage from initial water savings. High‐resolution thermal images taken at different heights above the forest canopy did detect reduced water loss through altered energy balance only at <5 m distance (0.44 K leaf warming of CO2‐treated Fagus trees). Short discontinuations of CO2 supply during morning hours had no measurable canopy temperature effects, most likely because the stomatal effects were small compared with the aerodynamic constraints in these dense, broad‐leaved canopies. Hence, on a seasonal basis, these data suggest a <10% reduction in water consumption in this type of forest when the atmosphere reaches 540% ppm CO2.
Climate change effects on organic matter decomposition rates in ecosystems from the Maritime Antarctic and Falkland Islands
Authors: BOKHORST S. , HUISKES A. , CONVEY P. , AERTS R. 
Published: October 2007

AbstractAntarctic terrestrial ecosystems have poorly developed soils and currently experience one of the greatest rates of climate warming on the globe. We investigated the responsiveness of organic matter decomposition in Maritime Antarctic terrestrial ecosystems to climate change, using two study sites in the Antarctic Peninsula region (Anchorage Island, 67°S; Signy Island, 61°S), and contrasted the responses found with those at the cool temperate Falkland Islands (52°S). Our approach consisted of two complementary methods: (1) Laboratory measurements of decomposition at different temperatures (2, 6 and 10 °C) of plant material and soil organic matter from all three locations. (2) Field measurements at all three locations on the decomposition of soil organic matter, plant material and cellulose, both under natural conditions and under experimental warming (about 0.8 °C) achieved using open top chambers. Higher temperatures led to higher organic matter breakdown in the laboratory studies, indicating that decomposition in Maritime Antarctic terrestrial ecosystems is likely to increase with increasing soil temperatures. However, both laboratory and field studies showed that decomposition was more strongly influenced by local substratum characteristics (especially soil N availability) and plant functional type composition than by large‐scale temperature differences. The very small responsiveness of organic matter decomposition in the field (experimental temperature increase < 1 °C) compared with the laboratory (experimental increases of 4 or 8 °C) shows that substantial warming is required before significant effects can be detected.
Identification of an anti‐idiotypic antibody that defines a B‐cell subset(s) producing xenoantibodies in primates
Authors: Fischer‐Lougheed Jacqueline , Gregory Clare , White Zena , Shulkin Irina , Gunthart Mirja , Kearns‐Jonker Mary 
Published: October 2007

SummarySynthetic anti‐idiotypic antibodies represent a potentially valuable tool for the isolation and characterization of B cells that produce xenoantibodies. An anti‐idiotypic antibody that binds to a subset of B cells producing antibodies encoded by the variable‐region heavy chain 3 (VH3) germline genes DP35 [immunoglobulin variable‐region heavy chain 3‐11 (IGHV3‐11)], DP‐53 and DP‐54 plus a small number of VH4 gene‐encoded antibodies in humans has recently been identified. These germline progenitors also encode xenoantibodies in humans. We tested whether the small, clearly defined group of B cells identified with this anti‐idiotypic antibody produce xenoantibodies in non‐human primates mounting active immune responses to porcine xenografts. Peripheral blood B cells were sorted by flow cytometry on the basis of phenotype, and cDNA libraries were prepared from each of these sorted groups of cells. Immunoglobulin VH gene libraries were prepared from the sorted cells, and the VH genes expressed in each of the sorted groups were identified by nucleic acid sequencing. Our results indicate that xenoantibody‐producing peripheral blood B cells, defined on the basis of binding to fluorescein isothiocyanate (FITC)‐conjugated galactose α(1,3) galactose–bovine serum albumin (Gal‐BSA) and the anti‐idiotypic antibody 2G10, used the IGHV3‐11 germline gene to encode xenoantibodies and were phenotypically CD11b+ (Mac‐1+) and CD5–. This novel reagent may be used in numerous applications including definition of xenoantibody‐producing B‐cell subsets in humans and non‐human primates and immunosuppression by depletion of B cells producing anti‐Gal xenoantibodies.
A bio‐molecular film ex‐vivo model to evaluate the influence of canal dimensions and irrigation variables on the efficacy of irrigation
Authors: Huang T.‐Y. , Gulabivala K. , Ng Y.‐L. 
Published: October 2007

AbstractAims  To devise an ex vivo model to test the efficacy of irrigation (static/dynamic) in removing a bio‐molecular film from root canal walls.Methodology  Forty human teeth with single straight canals were randomly allocated to two groups for static (n = 20) or dynamic (n = 20) irrigation. The root canals were prepared to different apical sizes (20, 40) and tapers (0.04, 0.08). The teeth were split longitudinally into two, stained collagen was applied to the canal surfaces and the tooth reassembled in a silicone matrix for dynamic or static irrigation. Digital images of the canal surface were taken before and after irrigation with 9, 18, 27 and 36 mL solution. The percentage of canal surface covered with stained collagen was quantified (ipWin4®). The data were analysed using paired t‐tests and linear regression models.Results  All the five explanatory variables: ‘volume of irrigant used’, ‘mode of irrigation’, ‘orientation of open port of needle’, ‘corono‐apical level of canal’ and ‘root canal dimension’ had a significant (P < 0.001) influence on outcome of irrigation. The corono‐apical level of canal was the most dominating factor. After irrigation, the apical third had 19.9% and 33.8% less area covered with the bio‐molecular film than the middle and coronal thirds respectively.Conclusions  The stained collagen bio‐molecular film could not be removed completely by either static or dynamic irrigation. Factors influencing removal, in rank order of decreasing priority, were: corono‐apical level, apical size and taper of canal preparation, and dynamic/static irrigation.