bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reducing the short-term mortality of juvenile school prawns (Metapenaeus macleayi) discarded during trawling
Authors: Macbeth William G. , Broadhurst Matt K. , Paterson Brian D. , Wooden Michael E.L. 
Published: May 2006

Abstract
A field experiment was carried out in southeastern Australia to assess the short-term mortality and stress incurred by juvenile school prawns (Metapenaeus macleayi) discarded from an estuarine trawler. Some 35% of the prawns died up to 72 h after being caught in a trawl, exposed to air during sorting and separation from the retained catch (as per normal commercial procedures), then discarded into replicate cages. Total mortality was partitioned into that caused by trawling (about 16% of mortalities), and by subsequent sorting and grading (about 19%). Assuming that the majority of the non-penaeid bycatch is excluded from trawls (by the use of bycatch reduction devices), the latter mortalities could be almost eliminated by sorting and separating unwanted school prawns in water-filled compartments. Emersion stress was measured as concentrations of l-lactate in the haemolymph, which were elevated for at least 40 min following capture, but similar among all trawled treatments. l-lactate levels decreased within the first 24 h post-capture, then remained constant over at least the next 48 h, and were greater than baseline levels. The potential benefits associated with subtle changes to handling practices onboard estuarine trawlers are discussed.
Creation of trivalent transgenic watermelon resistant to virus infection
Authors: Sheng-Niao Niu , Xue-Sen Huang , Sek-Man Wong , Jia-Lin Yu , Fu-Xing Zhao , Da-Wei Li , Sheng-You Wang , Guang-Ming Zhai , Fan-Sheng Shi 
Published: May 2006

AbstractA trivalent vector containing genes of Watermelon mosaic virus (WMV) coat protein (CP), and replicase genes of Zucchini yellow mosaic virus (ZYMV) and Cucumber mosaic virus (CMV), was constructed for transformation of watermelon (Citrullus lanatus) plants, mediated by Agrobacterium tumefaciens. The integrated foreign genes were identified in the regenerated progenies by polymerase chain reaction (PCR) and Southern blots. The transformation efficiency was about 1.7‰. Resistance to virus infection was determined by mechanical inoculation in the greenhouse and by field trials. The transgenic watermelon lines showed different phenotypes of susceptible, resistant, immune or recovery from virus infections in the late growth stage. A relatively high level of resistance was shown by T3 plants of the line BH1-7. This result indicates the possibility of creating, by transgenic protocols, new varieties of watermelon resistant to viral infection.
Cloning of the obese gene (ob) of adipose tissue, and differences in ob gene expression with age of piglets
Authors: Yi-Zhen Wang , Xiao-Na Chu , Hai-Qing Huang , Fei-Fei Han , Jian-Xin Liu 
Published: May 2006

AbstractGenomic RNA was extracted from the subcutaneous adipose tissue of piglets (Duroc×Landrace×Tai-hu) at 1, 14, 28, 42 and 56 days of age, and obese gene (ob) mRNA was amplified using reverse transcriptase-polymerase chain reaction (RT-PCR). A DNA fragment of about 504 bp was obtained and the PCR product was cloned into a pGEM-T vector. The ob gene was isolated and sequenced from the positive clones screened. Sequence analysis suggested that this fragment was a partial sequence of ob cDNA, coding 167 amino acid residues, which constituted the major part of leptin mature protein. The gene homology of the fragment obtained in this study compared to the reported ob cDNA sequence in adipocytes of pig was 99.405%, and amino acid homology was 98.94%. Based on the ob gene clone, we successfully constructed an optimal semi-quantitative RT-PCR method. Using β-actin as the internal control, we investigated the difference of ob gene expression at different ages of piglets. Results showed that ob mRNA levels increased steadily at postnatal days 1–28 (preweaning), peaked at postnatal day 28, when piglets were weaned, and decreased from day 28 to 56.
Prelude&Fugue, predicting local protein structure, early folding regions and structural weaknesses
Authors: Kwasigroch Jean Marc , Rooman Marianne 
Published: May 2006

Abstract
Summary: Prelude&Fugue are bioinformatics tools aiming at predicting the local 3D structure of a protein from its amino acid sequence in terms of seven backbone torsion angle domains, using database-derived potentials. Prelude&Fugue computes all lowest free energy conformations of a protein or protein region, ranked by increasing energy, and possibly satisfying some interresidue distance constraints specified by the user. Prelude&Fugue detects sequence regions whose predicted structure is significantly preferred relative to other conformations in the absence of tertiary interactions. These programs can be used for predicting secondary structure, tertiary structure of short peptides, flickering early folding sequences and peptides that adopt a preferred conformation in solution. They can also be used for detecting structural weaknesses, i.e. sequence regions that are not optimal with respect to the tertiary fold.
Availability:
Contact: Jean.Marc.Kwasigroch@ulb.ac.be
HoSeqI: automated homologous sequence identification in gene family databases
Authors: Arigon Anne-Muriel , Perrière Guy , Gouy Manolo 
Published: May 2006

Abstract
Summary: We present a web service allowing to automatically assign sequences to homologous gene families from a set of databases. After identification of the most similar gene family to the query sequence, this sequence is added to the whole alignment and the phylogenetic tree of the family is rebuilt. Thus, the phylogenetic position of the query sequence in its gene family can be easily identified.
Availability:
Contact: arigon@biomserv.univ-lyon1.fr
Supplementary Information: Supplementary Data are available at Bioinformatics online.
Leishmania histone H1 overexpression delays parasite cell‐cycle progression, parasite differentiation and reduces Leishmania infectivity in vivo
Authors: Smirlis Despina , Bisti Sylvia N. , Xingi Evangelia , Konidou Georgia , Thiakaki Maria , Soteriadou Ketty P. 
Published: May 2006

SummaryEpisomal expression of Leishmania histone H1 sense mRNAs in Leishmania major promasigotes was found previously to result in overexpression of this molecule and to reduce parasite infectivity in vitro. Herein, we evaluated the in vivo infectivity of these transfectants, in BALB/c mice, and showed that it is dramatically reduced. No lesions were observed in this group of mice and this was associated with an extremely low number of parasites both in the footpad and in the draining lymph nodes. Interestingly, the transfectants‐reduced infectivity was associated with a delay in their cell‐cycle progression and differentiation to axenic amastigotes, assessed in vitro. Therefore, the dramatic reduction in their infectivity may be attributed to the above‐mentioned phenotypic modifications. As the metazoan linker histone H10 homologue is known to delay cell‐cycle progression in mammalian cells we investigated whether its Leishmania counterpart, which possesses homology to its C‐terminal region, when expressed in mammalian cells may also affect their cell‐cycle progression. It was thus shown that Leishmania histone H1 expressed in COS7 and NIH 3T3 cells, delays cell‐cycle progression in these cells too. The latter strengthens the phenotype observed in Leishmania and provides evidence that critical functions of histone H1 molecules are conserved throughout evolution.
Modelling spatial and environmental effects at the edge of the distribution: the red‐backed shrikeLanius collurioin Northern Portugal
Authors: Reino Luís , Beja Pedro , Heitor António C. 
Published: May 2006

ABSTRACTThis study examined the interplay of spatial and environmental effects shaping the range margin of the red‐backed shrike (Lanius collurio) in northern Portugal. The occurrence of shrikes in 10 × 10 km UTM squares was related to three sets of explanatory variables, reflecting environmental effects (climate and habitat), large‐scale spatial trends, and neighbourhood influences (considering an autologistic term); spatial variables were used as surrogates for historical and demographic factors. Multiple logistic regression models were built for each set, and then variation partitioning based on partial regressions isolated the unique and shared components of explained variation. The environmental model revealed a dominant influence of climate effects, with the occurrence of shrikes increasing with frost and thermal amplitude, declining with insolation, and responding unimodally to rainfall. There was a weaker influence of habitat conditions, though shrikes were more likely with increasing cover by annual crops and pastures, and decreasing forest cover. Only a relatively small proportion of explained variation was due to a ‘pure’ environmental component (10.4%), as most variation explained by environmental factors appeared spatially structured (51.9%). The unique contributions of spatial variables to the overall model were also small, though the neighbourhood effects appeared relatively stronger than large‐scale trends. Taken together, results suggested that the south‐western range margin of the red‐backed shrike was largely determined by spatially structured environmental factors. Nevertheless, there were also ‘pure’ environmental factors determining some isolate occurrences irrespective of any spatial structure, and ‘pure’ spatial factors that appeared to favour the occupation of squares surrounding the core distribution areas irrespective of environmental conditions. These results add to the growing evidence that both environmental and spatial factors need to be considered in predictive modelling of species range margins.
Incidence of positive pelvic lymph nodes in patients with prostate cancer, a prostate‐specific antigen (PSA) level of ≤10 ng/mL and biopsy Gleason score of ≤6, and their influence on PSA progression‐free survival after radical prostatectomy
Authors: WECKERMANN DOROTHEA , GOPPELT MARCUS , DORN ROBERT , WAWROSCHEK FRIEDHELM , HARZMANN ROLF 
Published: May 2006

OBJECTIVETo investigate how many men with low‐risk prostate cancer had positive lymph nodes detected by radio‐guided surgery and whether they had a higher biochemical relapse rate after radical prostatectomy, because in such patients most urologists dispense with operative lymph node staging, as nomograms indicate only a low percentage of lymph node metastases.PATIENTS AND METHODSThe study included 474 men with a prostate‐specific antigen (PSA) level of ≤ 10 ng/mL, biopsy Gleason score of ≤ 6 and positive biopsies in one (group 1, 315 men) or both lobes (group 2, 159 men); follow‐up data were available in 357 men. Men with adjuvant radiation or hormone therapy before the occurrence of biochemical relapse were excluded.RESULTSPositive lymph nodes were detected in 17 men in group 1, and in 18 in group 2. In more than half of the patients (19/35) these nodes were found outside the region of standard lymphadenectomy. Men with node‐positive disease had a higher biochemical relapse rate (P < 0.001). When the tumour was organ‐confined and well differentiated in node‐positive disease (Gleason score ≤ 6) the biochemical relapse rate was lower than in men with higher tumour stage and grade.CONCLUSIONSWhen dissecting pelvic lymph nodes, extended or sentinel lymphadenectomy should be preferred. Removing the diseased nodes could improve the PSA progression‐free survival, especially in well differentiated organ‐confined disease.
Restrictions on Provider Access in Health Plans and Socioeconomic Status
Authors: Deb Partha , Trivedi Pravin K. 
Published: May 2006

Objective. To model the socioeconomic determinants of restrictions on provider access and choices in health plans.Data Sources. Data from the 1996–97 Community Tracking Study are used. Publicly available enrollee data including enrollee reports of health care plan characteristics are linked with restricted use data with insurer reports of health plan characteristics.Study Design. This is an observational study. A mixed multinomial logit model is used to model the enrollees' choice between health plans, each plan being treated as a bundle of attributes formed from restrictions on provider access.Principal Findings. There are important differences between the enrollee responses and the insurer reports, which may be due to poor information dissemination on the part of health plans and/or lack of attention on the part of enrollees. There is no evidence of selection into plans with restrictive attributes on the basis of observed health status but there is evidence of selection on the basis of race, ethnicity, gender and other socioeconomic characteristics. Determinants of plan supply, i.e., employment characteristics, are the most important determinants of plan attribute choices.Conclusion. The finding suggests that plan designs optimized using “objective” knowledge and with the best intentions may not receive favorable reviews from enrollees because enrollees have different perceptions of these plans.
Reviews: Diagnosis and Management of Sleep Apnea Syndrome and Restless Legs Syndrome in Dialysis Patients
Authors: Novak Marta , Mendelssohn David , Shapiro Colin M. , Mucsi Istvan 
Published: May 2006

ABSTRACTSleep complaints are very common in patients with end‐stage renal disease (ESRD) and contribute to their impaired quality of life. Both obstructive and central sleep apnea syndromes are reported more often in patients on dialysis than in the general population. Impaired daytime functioning, sleepiness, and fatigue, as well as cognitive problems, are well known in patients with sleep apnea. Increasing evidence supports the pathophysiological role of sleep apnea in cardiovascular disorders, which are the leading cause of death in ESRD patients. Uremic factors may be involved in the pathogenesis of sleep apnea in this patient population and optimal dialysis may reduce disease severity. Furthermore, treatment with continuous positive airway pressure may improve quality of life and may help to manage hypertension in these patients. Secondary restless legs syndrome is highly prevalent in patients on maintenance dialysis. The pathophysiology of the disorder may also involve uremia‐related factors, iron deficiency, and anemia, but genetic and lifestyle factors might also play a role. The treatment of restless legs syndrome involves various pharmacologic approaches and might be challenging in severe cases. In this article we review the diagnosis and treatment of sleep apnea and restless legs syndrome, with a focus on dialysis patients. We also briefly review current data regarding sleep problems after transplantation, since these studies may indirectly shed light on the possible pathophysiological role of uremia or dialysis in the etiology of sleep disorders. Considering the importance of sleep disorders, more awareness among professionals involved in the care of patients on dialysis is necessary. Appropriate management of sleep disorders could improve the quality of life and possibly even impact upon survival of renal patients.
Burden of Clostridium Difficile‐Associated Diarrhea in a Long‐Term Care Facility
Authors: Laffan Alison M. , Bellantoni Michelle F. , Greenough William B. , Zenilman Jonathan M. 
Published: May 2006

OBJECTIVES: To describe the incidence and prevalence of Clostridium difficile–associated diarrhea (CDAD) in a long‐term care facility (LTCF).DESIGN: Retrospective review of CDAD cases between July 2001 and December 2003.SETTING: Two hundred two–bed LTCF affiliated with an academic medical center in Baltimore, Maryland.PARTICIPANTS: All residents of the facility during July 2001 to December 2003.MEASUREMENTS: Clinical and laboratory‐confirmed cases of CDAD.RESULTS: Incidence of CDAD ranged from 0 to 2.62 cases per 1,000 resident days. The highest rates were observed in residents of subacute units, whereas incidence was much lower on traditional nursing home units. Prevalence of CDAD at admission was greater on units (subacute and rehabilitative) where the majority of patients were admitted from hospital settings than on those where the majority of patients were admitted from the community (nursing home units). Recurrent disease occurred in 21.7% of patients with CDAD.CONCLUSION: CDAD remains a problem in the long‐term care setting, and importation from the acute care setting accounts for a large proportion of the C. difficile seen LTCFs. As the population continues to age, issues of disease and infection in long‐term care are expected to increase. New prevention and control strategies are needed to control the spread of CDAD in LTCFs.
The effect of β‐aminobutyric acid on the growth of herbivorous insects feeding on Brassicaceae
Authors: Hodge S. , Pope T.W. , Holaschke M. , Powell G. 
Published: May 2006

Abstract dl‐β‐Aminobutyric acid (BABA) is a nonprotein amino acid that can enhance defences in a variety of plants against a wide range of pathogens. BABA can also reduce infestation by phytopathogenic nematodes and has recently been shown to suppress the growth of aphids feeding on legumes. This investigation examined the effect of applying BABA as a root drench to a range of Brassicaceae, including Arabidopsis thaliana, on the performance of two species of aphid (Myzus persicae and Brevicoryne brassicae) and the larvae of two species of Lepidoptera (Trichoplusia ni and Plutella xylostella). Application of BABA reduced the performance of all four insect species, and inhibition of insects occurred on all the plants tested. The results illustrate that BABA‐induced resistance (BABA‐IR) can affect generalist and specialist insect herbivores and inhibit insects feeding with mandibulate as well as sap‐feeding mouthparts. The BABA‐induced suppression of B. brassicae and P. xylostella feeding on A. thaliana provides a means to further examine the mechanisms of BABA‐IR to insects using this model plant.
Radical Evil in the Lockean State: The Neglect of the Political Emotions
Authors: Nussbaum Martha 
Published: May 2006

AbstractAll modern liberal democracies have strong reasons to support an idea of toleration, understood as involving respect, not only grudging acceptance, and to extend it to all religious and secular doctrines, limiting only conduct that violates the rights of other citizens. There is no modern democracy, however, in which toleration of this sort is a stable achievement. Why is toleration, attractive in principle, so difficult to achieve? The normative case for toleration was well articulated by John Locke in his influential A Letter Concerning Toleration , although his attractive proposal thus rests on a fragile foundation. Kant did much more, combining a Lockean account of the state with a profound diagnosis of ‘radical evil’, the tendencies in all human beings to militate against stable toleration and respect. But Kant proposed no mechanism through which the state might mitigate the harmful influence of ‘radical evil’, thus rendering toleration stable. One solution to this problem was proposed by Rousseau, but it has deep problems. How, then, can a respectful pluralistic society shore up the fragile human basis of toleration, especially in a world in which we need to cultivate toleration not only within each state, but also among peoples and states, in this interlocking world?
Virtue Epistemology and Moral Luck
Authors: Silcox Mark 
Published: May 2006

AbstractThomas Nagel has proposed that the existence of moral luck mandates a general attitude of skepticism in ethics. One popular way of arguing against Nagel’s claim is to insist that the phenomenon of moral luck itself is an illusion , in the sense that situations in which it seems to occur may be plausibly re-described so as to show that agents need not be held responsible for the unlucky outcomes of their actions. Here I argue that this strategy for explaining away moral luck fails because it does not take account of the fact that agents in morally unlucky circumstances are uniformly subject to a very specific type of epistemic obligation. I then proceed to sketch out an alternative strategy for blocking the inference to skepticism, one that makes use of the distinctive explanatory resources provided by epistemic virtue theory.
Measuring nasal bacterial load and its association with otitis media
Authors: Smith-Vaughan Heidi , Byun Roy , Nadkarni Mangala , Jacques Nicholas A , Hunter Neil , Halpin Stephen , Morris Peter S , Leach Amanda J 
Published: May 2006

Abstract

Background
Nasal colonisation with otitis media (OM) pathogens, particularly Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis, is a precursor to the onset of OM. Many children experience asymptomatic nasal carriage of these pathogens whereas others will progress to otitis media with effusion (OME) or suppurative OM. We observed a disparity in the prevalence of suppurative OM between Aboriginal children living in remote communities and non-Aboriginal children attending child-care centres; up to 60% and <1%, respectively. This could not be explained by the less dramatic difference in rates of carriage of respiratory bacterial pathogens (80% vs 50%, respectively). In this study, we measured nasal bacterial load to help explain the different propensity for suppurative OM in these two populations.

Methods
Quantitative measures (colony counts and real-time quantitative PCR) of the respiratory pathogens S. pneumoniae, H. influenzae and M. catarrhalis, and total bacterial load were analysed in nasal swabs from Aboriginal children from remote communities, and non-Aboriginal children attending urban child-care centres.

Results
In both populations nearly all swabs were positive for at least one of these respiratory pathogens. Using either quantification method, positive correlations between bacterial load and ear state (no OM, OME, or suppurative OM) were observed. This relationship held for single and combined bacterial respiratory pathogens, total bacterial load, and the proportion of respiratory pathogens to total bacterial load. Comparison of Aboriginal and non-Aboriginal children, all with a diagnosis of OME, demonstrated significantly higher loads of S. pneumoniae and M. catarrhalis in the Aboriginal group. The increased bacterial load despite similar clinical condition may predict persistence of middle ear effusions and progression to suppurative OM in the Aboriginal population. Our data also demonstrated the presence of PCR-detectable non-cultivable respiratory pathogens in 36% of nasal swabs. This may have implications for the pathogenesis of OM including persistence of infection despite aggressive therapies.

Conclusion
Nasal bacterial load was significantly higher among Aboriginal children and may explain their increased risk of suppurative OM. It was also positively correlated with ear state. We believe that a reduction in bacterial load in high-risk populations may be required before dramatic reductions in OM can be achieved.