bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid detection, classification and accurate alignment of up to a million or more related protein sequences
Authors: Neuwald Andrew F. 
Published: June 2009

AbstractMotivation: The patterns of sequence similarity and divergence present within functionally diverse, evolutionarily related proteins contain implicit information about corresponding biochemical similarities and differences. A first step toward accessing such information is to statistically analyze these patterns, which, in turn, requires that one first identify and accurately align a very large set of protein sequences. Ideally, the set should include many distantly related, functionally divergent subgroups. Because it is extremely difficult, if not impossible for fully automated methods to align such sequences correctly, researchers often resort to manual curation based on detailed structural and biochemical information. However, multiply-aligning vast numbers of sequences in this way is clearly impractical.Results: This problem is addressed using Multiply-Aligned Profiles for Global Alignment of Protein Sequences (MAPGAPS). The MAPGAPS program uses a set of multiply-aligned profiles both as a query to detect and classify related sequences and as a template to multiply-align the sequences. It relies on Karlin–Altschul statistics for sensitivity and on PSI-BLAST (and other) heuristics for speed. Using as input a carefully curated multiple-profile alignment for P-loop GTPases, MAPGAPS correctly aligned weakly conserved sequence motifs within 33 distantly related GTPases of known structure. By comparison, the sequence- and structurally based alignment methods hmmalign and PROMALS3D misaligned at least 11 and 23 of these regions, respectively. When applied to a dataset of 65 million protein sequences, MAPGAPS identified, classified and aligned (with comparable accuracy) nearly half a million putative P-loop GTPase sequences.Availability: A C++ implementation of MAPGAPS is available at http://mapgaps.igs.umaryland.edu.Contact: aneuwald@som.umaryland.eduSupplementary information: Supplementary data are available at Bioinformatics online.
ChromA: signal-based retention time alignment for chromatography–mass spectrometry data
Authors: Hoffmann Nils , Stoye Jens 
Published: June 2009

Abstract
Summary: We describe ChromA, a web-based alignment tool for chromatography–mass spectrometry data from the metabolomics and proteomics domains. Users can supply their data in open and standardized file formats for retention time alignment using dynamic time warping with different configurable local distance and similarity functions. Additionally, user-defined anchors can be used to constrain and speedup the alignment. A neighborhood around each anchor can be added to increase the flexibility of the constrained alignment. ChromA offers different visualizations of the alignment for easier qualitative interpretation and comparison of the data. For the multiple alignment of more than two data files, the center-star approximation is applied to select a reference among input files to align to.
Availability: ChromA is available at http://bibiserv.techfak.uni-bielefeld.de/chroma. Executables and source code under the L-GPL v3 license are provided for download at the same location.
Contact: stoye@techfak.uni-bielefeld.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Prevalence and seasonality of Hematodinium (Alveolata: Syndinea) in a Scottish crustacean community
Authors: Hamilton K. M. , Shaw P. W. , Morritt D. 
Published: June 2009

Abstract
Hamilton, K. M., Shaw, P. W., and Morritt, D. 2009. Prevalence and seasonality of Hematodinium (Alveolata: Syndinea) in a Scottish crustacean community. – ICES Journal of Marine Science, 66: 1837–1845. Protist parasites of the genus Hematodinium were detected in seven crustacean species (Cancer pagurus, Carcinus maenas, Liocarcinus depurator, Munida rugosa, Necora puber, Pagurus bernhardus, and Pagurus prideaux) from the Clyde Sea in Scotland. Seasonal screening of different tissues with sensitive molecular probes showed average infection of 3–23%, with prevalence reaching almost 60% in hermit crabs (P. bernhardus) and brachyuran hosts in spring and >30% in C. pagurus and N. puber in autumn. During summer, Hematodinium infections were rare. Hematodinium seemed to be present in all host sizes sampled. The infection was equally distributed between males and females in most host species, except C. maenas, where males seemed to be more susceptible to infection. PCR amplification of the Hematodinium ribosomal RNA gene in crustacean tissue detected the parasite most frequently in muscle, gills, and heart throughout the 2-year sampling period.
Relationship between body composition and bone mineral density (BMD) in perimenopausal Korean women
Authors: Kim C. J. , Oh K. W. , Rhee E. J. , Kim K. H. , Jo S. K. , Jung C. H. , Won J. C. , Park C. Y. , Lee W. Y. , Park S. W. , Kim S. W. 
Published: June 2009

SummaryObjectives  Osteoporosis is a disease that increases the fracture rates and it is the major cause of increased mortality and morbidity in the elderly people. To determine which component of body composition is most important to bone health, we analysed the relationship between elements of the body composition and bone mineral density (BMD) in Korean women.Design  Cross‐sectional clinical study.Patients  Totally 1694 women (mean age 51 years) were selected from subjects who participated in a medical check‐up program.Measurements  Body composition analysis was performed by segmental bioelectric impedance method and lean mass, fat mass and per cent body fat measured. Waist : hip ratio (WHR) was assessed as a marker for visceral fat. Lumbar spine (l‐spine) BMD was measured by dual X‐ray absorptiometry (DEXA). As menopausal status could not be confirmed in all subjects, we divided the subjects into two groups according to the age > 50 years and < 50 years.Results  Among the entire population, 599 subjects (35·4%) were osteopaenic and 229 subjects (13·5%) were osteoporotic. The bivariate correlation among the variables showed that weight had the highest correlation with fat mass. Mean lean mass was decreased and the WHR increased as the subjects progressed from normal to osteoporotic status; fat mass was the highest among the osteopaenic subjects. l‐spine BMD showed a positive correlation with lean mass, and a negative correlation with WHR by bivariate correlation analysis. However, fat mass had a negative correlation with l‐spine BMD only after adjustment for age and weight. Multiple regression analysis with l‐spine BMD as the dependent variable showed that age, height, fasting insulin, lean mass and WHR were significant determinants of the l‐spine BMD (R2 = 0·170, P < 0·05).Conclusion  In this Korean female population, l‐spine BMD showed a consistently positive correlation with lean mass and a negative correlation with WHR. Fat mass failed to show any consistent correlation with l‐spine BMD in this study population.
Disease activity in systemic lupus erythematosus is associated with an altered expression of low‐affinity Fcγ receptors and costimulatory molecules on dendritic cells
Authors: Carreño Leandro J. , Pacheco Rodrigo , Gutierrez Miguel A. , Jacobelli Sergio , Kalergis Alexis M. 
Published: June 2009

SummaryDendritic cells (DCs) play a pivotal role in the interface between immunity and maintenance of peripheral tolerance. The capture of immunoglobulin G (IgG)‐containing immune complexes (ICs) by low‐affinity Fcγ receptors (FcγRs) expressed on DCs may influence the immunogenicity/tolerogenicity of these cells, depending on the activating/inhibitory potential of FcγRs. Because of the key role that low‐affinity FcγRs play in determining the magnitude of the response in IC‐driven inflammation, these receptors are likely to play a role in autoimmune diseases, such as systemic lupus erythematosus (SLE). To evaluate if an altered expression of costimulatory molecules and/or FcγRs could account for disease severity, we evaluated the expression of these molecules on immature and mature DCs derived from peripheral blood monocytes of SLE patients and healthy donors. Our results show an increased expression of the costimulatory molecules CD40 and CD86. Furthermore, the ratio of CD86/CD80 is higher in SLE patients compared with healthy donors. Conversely, while the expression of activating FcγRs was higher on DCs from SLE patients, expression of inhibitory FcγRs was lower, compared with DCs obtained from healthy donors. As a result, the activating to inhibitory FcγR ratio was significantly higher in DCs from SLE patients. The altered ratio of activating/inhibitory FcγRs on mature DCs showed a significant correlation with the activity of SLE, as determined by the SLE Disease Activity Index (SLEDAI) score. We postulate that the increased ratio of activating/inhibitory FcγRs expressed on DCs from SLE patients can contribute to the failure of peripheral tolerance in the IC‐mediated phase of autoimmune pathogenesis.
Quantification and examination of depression‐related mental health literacy
Authors: Dunn Kirsten I. , Goldney Robert D. , Grande Eleonora Dal , Taylor Anne 
Published: June 2009

AbstractObjective  The aim of the study was to create an algorithm to measure depression‐related mental health literacy.Method  Participants were those recruited for the 1998 and 2004 South Australian Health Omnibus Surveys. Two unprompted questions were selected from a mental health literacy questionnaire and responses were quantified through allocation of scores agreed by a focus group of mental health professionals.Results  An application of the algorithm resulted in findings consistent with those of other research, providing face validity for the method developed. The application allowed for examination of overall levels of depression‐related mental health literacy, with improvement found between 1998 and 2004. Similarly, differences in overall literacy according to demographics were also uncovered.Conclusions  Tracking mental health literacy within populations is important as it has been shown to be related to individual help‐seeking as well as provision of support for those with a mental disorder. The method devised in this study allows for comparisons of literacy levels to be made across populations and time. It also offers increased capacity for statistical application.
Diurnal and seasonal variation in the carbon isotope composition of leaf dark‐respired CO2 in velvet mesquite (Prosopis velutina)
Authors: SUN WEI , RESCO VÍCTOR , WILLIAMS DAVID G. 
Published: June 2009

ABSTRACTWe evaluated diurnal and seasonal patterns of carbon isotope composition of leaf dark‐respired CO2 (δ13Cl) in the C3 perennial shrub velvet mesquite (Prosopis velutina) across flood plain and upland savanna ecosystems in the south‐western USA. δ13Cl of darkened leaves increased to maximum values late during daytime periods and declined gradually over night‐time periods to minimum values at pre‐dawn. The magnitude of the diurnal shift in δ13Cl was strongly influenced by seasonal and habitat‐related differences in soil water availability and leaf surface vapour pressure deficit. δ13Cl and the cumulative flux‐weighted δ13C value of photosynthates were positively correlated, suggesting that progressive 13C enrichment of the CO2 evolved by darkened leaves during the daytime mainly resulted from short‐term changes in photosynthetic 13C discrimination and associated shifts in the δ13C signature of primary respiratory substrates. The 13C enrichment of dark‐respired CO2 relative to photosynthates across habitats and seasons was 4 to 6‰ at the end of the daytime period (1800 h), but progressively declined to 0‰ by pre‐dawn (0300 h). The origin of night‐time and daytime variations in δ13Cl is discussed in terms of the carbon source(s) feeding respiration and the drought‐induced changes in carbon metabolism.
Sex‐related adaptive responses of Populus cathayana to photoperiod transitions
Authors: ZHAO HONGXIA , LI YAN , DUAN BAOLI , KORPELAINEN HELENA , LI CHUNYANG 
Published: June 2009

ABSTRACT Populus cathayana Rehd., a dioecious tree species, occupies a wide range of habitats in southwest China. Both males and females were grown under two regimes of photoperiod, from mid‐length to short‐day photoperiod (SD shift), or to long‐day photoperiod (LD shift). SD shift triggered leaf senescence in both males and females by decreasing net photosynthesis rate (A), transpiration (E), and chlorophyll pigment (Chl), non‐structural carbohydrate (NSC) and indoleacetic acid (IAA) contents, while increasing abscisic acid (ABA), malonaldehyde (MDA) and free proline (Pro) contents. The antioxidant enzyme (e.g. POD, CAT and SOD) activities and capability to maintain ultrastructural integrity also decreased under SD shift. Males exhibited faster leaf senescence than did females, as shown by greater decreases in A, E, Chl and IAA. However, males maintained a less senescent stage than did females, as indicated by higher values of A, Chl, NSC, IAA and antioxidant enzyme activities. Conversely, A, E, NSC and IAA contents and antioxidant enzyme activities were enhanced by lower O2•− in females, whereas reduced by higher O2•− in males under LD shift. Such sex‐dependent responses of P. cathayana to photoperiod transitions showed that males and females possess different adaptabilities, which may relate to sex‐specific leaf senescence speed under changing environments.
Frontiers in Clinical Immunology 2008
Authors: Deniz G. , Oral H. B. , Zouali M. 
Published: June 2009

AbstractIn recent years, investigations in immunology have led to progress in clinical medicine, including understanding transplant rejection, autoimmune diseases, immune deficiencies, inflammation, transplantation, cancer and the development of new vaccines. At a meeting recently held on the Mediterranean shore, advances in several facets of clinical immunology were the focus of discussion. Here, we highlight some of the debates that reflected advances in a variety of human immune disorders.
HUMAN STUDY: FOSB proteins in the orbitofrontal and dorsolateral prefrontal cortices of human alcoholics
Authors: Watanabe Hiroyuki , Henriksson Richard , Ohnishi Yoshinori N. , Ohnishi Yoko H. , Harper Clive , Sheedy Donna , Garrick Therese , Nyberg Fred , Nestler Eric J. , Bakalkin Georgy , Yakovleva Tatjana 
Published: June 2009

ABSTRACTThe transcription factor ΔFosB is accumulated in the addiction circuitry, including the orbitofrontal and medial prefrontal cortices of rodents chronically exposed to ethanol or other drugs of abuse, and has been suggested to play a direct role in addiction maintenance. To address this hypothesis in the context of substance dependence in humans, we compared the immunoreactivities of FOSB proteins in the orbitofrontal and dorsolateral prefrontal cortices (OFC and DLPFC respectively) between controls and alcoholics using semiquantitative immunoblotting. In both structures, we detected three forms of FOSB, one of which was ΔFOSB, but in neither case did their immunoreactivities differ between the groups. Our results indicate that the ΔFOSB immunoreactivity in the human brain is very low, and that it is not accumulated in the OFC and DLPFC of human alcoholics, suggesting that it may not be directly involved in addiction maintenance, at least not in ethanol dependence.
CLINICAL STUDY: Effect of saquinavir/ritonavir (1000/100 mg bid) on the pharmacokinetics of methadone in opiate‐dependent HIV‐negative patients on stable methadone maintenance therapy
Authors: Jamois Candice , Smith Patrick , Morrison Royce , Riek Myriam , Patel Arpna , Schmitt Christophe , Morcos Peter N. , Zhang Xiaoping 
Published: June 2009

ABSTRACTThis study was performed to determine the effect of two protease inhibitors, saquinavir (SQV, oral 1000 mg bid) boosted by ritonavir (RTV, oral 100 mg bid), on pharmacokinetics (PK) of methadone in opiate‐dependent HIV‐negative patients on stable methadone maintenance therapy. This was a two‐center, open‐label, one‐sequence cross‐over, multiple‐dose study in 13 HIV‐negative patients who were on stable methadone therapy (oral, 60–120 mg qd). All patients continued methadone treatment on days 2–15. All patients received SQV/RTV in combination with methadone from days 2–15. PK of methadone was assessed on day 1 (alone) and on day 15 when methadone treatment was combined with SQV/RTV at steady state. Twelve patients completed the study. Median age, body weight and height were 50 years (range: 24–54 years), 80 kg (range: 57–97 kg) and 174 cm (range: 163–189 cm), respectively. All patients were Caucasian, and 11 were smokers. Median methadone dose was 85 mg qd. Geometric mean area under curve of the plasma concentration‐time curve over 24 hour dosing interval (AUC0–24 hour) ratio of methadone with and without SQV/RTV was 0.81% (90% confidence interval: 71–91%). There was no significant plasma protein‐binding displacement of methadone by SQV/RTV. The combination of SQV/RTV and methadone was well tolerated. There were no clinically significant adverse events or significant changes in laboratory parameters, electrocardiograms or vital signs. The 19% decrease in R‐methadone AUC0–24 hour in the presence of SQV/RTV was not clinically relevant. There appears to be no need for methadone dose adjustment when methadone (60–120 mg qd) and SQV/RTV (1000/100 mg bid) are coadministered.
Donor profiles: demographic factors and their influence on the donor career
Authors: Veldhuizen I. J. T. , Doggen C. J. M. , Atsma F. , De Kort W. L. A. M. 
Published: June 2009

Background and objectives  Studying the contribution of demographic factors to the donor career provides important knowledge to be used for donor management. The aim of this study is to gain insight into donor characteristics, more specifically into the demographic profile of active vs. resigned donors, and multi‐gallon vs. occasional donors.Materials and methods  The study population consisted of all registered Dutch whole‐blood donors between 1 January 2004 and 1 January 2005 (N = 370 470). The effect of several blood donor characteristics and demographic variables on (i) resigning donating and (ii) being a multi‐gallon donor were assessed. Blood donor characteristics were extracted from the blood bank information system and included age, sex, blood group, number of donations and invitations. Demographic characteristics were constituted by population data on urbanization level, socio‐economic status (income, housing value), and ethnicity.Results  Men clearly resigned less often than women (odds ratio (OR) 0·73, 95% confidence interval (CI) 0·72–0·75). Being older than 24 years, having a high income, a high‐priced house, living in less urbanized areas or areas with relatively few ethnically diverse people also reduced the stopping risk. With respect to multi‐gallon donorship, men were five times more often multi‐gallon donor than women (OR 5·27, 95% CI 5·15–5·39) irrespective of the number of donation invitations. Furthermore, multi‐gallon donors appeared to live in urbanized areas and have a higher income than occasional donors.Conclusion  Our results show that different donor profiles can be distinguished. Differences between active and resigned donors include age, the number of donations, sex, socio‐economic‐status, ethnicity, and urbanization level. The factors highly associated with being a multi‐gallon donor are sex, age, socio‐economic status, and to a lesser extent urbanization level. Donor profiles do provide the blood bank with knowledge on their donor population, which may be used as valuable information for donor recruitment and retention policies.
Vaginal Ring and Round Ligament of the Uterus in the Female Cat
Authors: Watson A. 
Published: June 2009

SummaryThe peritoneum was examined for the existence of a vaginal ring and the round ligament of the uterus was dissected through the inguinal region in eleven embalmed adult female cats. In all cats, there was no evidence of a peritoneal evagination into the inguinal canal. There was no vaginal ring and no vaginal process. The round ligament of the uterus passed through the inguinal canal and disintegrated in the fascia a short distance beyond the superficial inguinal ring.
Physiological Responses and Dry Matter Partitioning of Summer Mungbean (Vigna radiata L.) Genotypes Subjected to Drought Conditions
Authors: Kumar A. , Sharma K. D. 
Published: June 2009

AbstractDrought is the most important limitation to summer mungbean production in the tropics and subtropics dependent on usually insufficient summer rainfall. As increased irrigation is not a viable answer to the problem, an economically and environmentally desirable solution is new varieties with drought tolerance. However, there is little genotypic information on drought tolerance in summer mungbean. The objectives of this study were to assess the genotypic differences in physiological traits and dry matter partitioning in mungbean and to measure the association of these traits with crop performance under drought conditions. Six mungbean genotypes were tested in drought micro plots at CCS Haryana Agricultural University, Hisar, India. A split plot design was used; two irrigation treatments (watered and droughted) in the main plots and six mungbean genotypes in the subplots with three replicate micro plots. Drought decreased leaf water status, rates of photosynthesis (Pn) and altered dry matter partitioning in different plant parts. Our results showed that Pn did not limit yield, but it was partitioning of dry matter governed by leaf water content (RWC) which influenced the final yield. RWC was positively correlated to the number of pods per plant and seed yield, genotypes maintaining high RWC produced higher seed yield. Therefore, the drought tolerance of summer mungbean was related to the maintenance of high RWC, which can be used as a physiological marker to identify and develop superior genotypes suited to drought‐prone environments.
Production and characterization of an amphidiploid line between Brassica rapa and a wild relative Diplotaxis tenuifolia
Authors: Jeong B. H. , Saga T. , Okayasu K. , Hattori G. , Kaneko Y. , Bang S. W. 
Published: June 2009

AbstractIntergeneric hybridization was performed between Brassica rapa and Diplotaxis tenuifolia following embryo rescue. Twenty‐three F1 hybrid plants were developed from the cross B. rapa × D. tenuifolia and confirmed to be amphihaploids with 21 chromosomes in mitosis. Chromosome doubling of F1 hybrids by colchicine treatment resulted into five amphidiploid plants which exhibited (20–21)II + (0–2)I at metaphase I (MI) of pollen mother cells. Sib‐crossing and/or open‐pollination among amphidiploid plants for more than four generations resulted in the development of an ADt‐06 line with reproductive systems capable of maintaining an amphidiploid line. The ADt‐06 line was intermediate in some morphological traits between two parental species, and was characterized by a slightly pungent taste as a physiological trait. Analyses for genomic DNA confirmed that this line was a hybrid between two species. This new amphidiploid ADt‐06 line could be a useful genetic resource for the breeding of new leafy salad vegetables.