bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sediment toxicity and contaminants in the Kattegat and Skagerrak
Authors: Dave Göran , Nilsson Eva 
Published: November 2008

Abstract
Sediment bioassays have usually been applied to sediments from sites close to known sources of pollution such as harbours or major industrial sites. In this study sediment bioassays were conducted on samples from 120 sites in the Kattegat and Skagerrak (North Sea) at water depths ranging from 4 to 682 m. Sediment toxicity to Daphnia magna, expressed as immobility after 48 h exposure to 16% sediment (wet weight) ranged from 0 to 95%. Sediment toxicty to Nitocra spinipes, expressed as the 96 h LC50 for sediment in water, ranged from 0.61 to 88% dry weight. The responses obtained in duplicate bioassay test vessels showed good correlation (r = 0.7–0.8), but toxicity to Daphnia was not correlated with toxicity to Nitocra. High sediment toxicity was not restricted to areas close to industrial sites and harbours, but was found also in open sea areas. Analysed sediment concentrations of contaminants (heavy metals, organochlorines and polyaromatic hydrocarbons) at 25 of these 120 sites were tested for correlation with sediment toxicity, but no correlations, or rather weak ones, were found. Further, the concentrations of single contaminants were usually below those, which are considered harmful to aquatic organisms (tentative sediment quality criteria). Therefore, none of the single analysed contaminants seems to cause the observed sediment toxicity. No improvement in correlation was achieved when using an additive model of joint toxicity between different groups of contaminants and the combined toxicity to Daphnia and Nitocra. Therefore, the cause of the sediment toxicity is so far unknown, and no hazard assessment based on the analysed contaminants was warranted. The average immobility of Daphnia after exposure to 16% sediment (wet weight) for 48 h was 29%, and the average 96 h LC50 for Nitocra exposed to various concentrations of sediment was 11.4% (dry weight) of sediment in dilution water. A tentative hazard assessment based on these average results from both bioassays suggested that sediment toxicity in the Kattegat and Skagerrak must be reduced by on average four times to approach a Predicted Effect Level (PEL) allowing 50% survival.
Summer Peaks in the Incidences of Gram-Negative Bacterial Infection Among Hospitalized Patients
Authors: Perencevich Eli N. , McGregor Jessina C. , Shardell Michelle , Furuno Jon P. , Harris Anthony D. , Morris J. Glenn , Fisman David N. , Johnson Judith A. 
Published: November 2008

Objective.Recognition of seasonal trends in hospital infections may improve diagnosis, use of empirical therapy, and infection prevention interventions. There are very few data available regarding the seasonal variability of these infections. We quantified the seasonal variation in the incidences of hospital infection caused by common bacterial pathogens and estimated the association between temperature changes and infection rates.Methods.A cohort of all adult patients admitted to the University of Maryland Medical Center during the period from 1998 through 2005 was analyzed. Time-series analyses were used to estimate the association of the number of infections per month caused by Pseudomonas aeruginosa, Acinetobacter baumannii, Enterobacter cloacae, Escherichia coli, Staphylococcus aureus, and enterococci with season and temperature, while controlling for long-term trends.Results.There were 218,594 admissions to the index hospital, and analysis of 26,624 unique clinical cultures that grew the organisms of interest identified increases in the mean monthly rates of infection caused by P. aeruginosa (28% of isolates recovered; P < .01), E. cloacae (46%; P < .01), E. coli (12%; P < .01), and A. baumannii (21%; P = .06). For each 10°F increase, we observed a 17% increase in the monthly rates of infection caused by P. aeruginosa (P = .01) and A. baumanii (P = .05).Conclusion.Significantly higher rates of gram-negative infection were observed during the summer months, compared with other seasons. For some pathogens, higher temperatures were associated with higher infection rates, independent of seasonality. These findings have important implications for infection prevention, such as enhanced surveillance during the warmer months, and for choice of empirical antimicrobial therapy among hospitalized adults. Future, quasi-experimental investigations of gram-negative infection prevention initiatives should control for seasonal variation.
Otolith shape analysis: its application for discriminating between stocks of Irish Sea and Celtic Sea herring (Clupea harengus) in the Irish Sea
Authors: Burke Nóirín , Brophy Deirdre , King Pauline A. 
Published: November 2008

Abstract
Burke, N., Brophy, D., and King, P. A. 2008. Otolith shape analysis: its application for discriminating between stocks of Irish Sea and Celtic Sea herring (Clupea harengus) in the Irish Sea. – ICES Journal of Marine Science, 65: 1670–1675. The extensive movement of Celtic Sea juvenile Atlantic herring (Clupea harengus) during the first year of life into the Irish Sea results in two stocks of herring living together on Irish Sea nursery grounds: the resident autumn-spawned juveniles that originate in the Irish Sea, and the winter-spawned juveniles that hatch in the Celtic Sea and drift into the Irish Sea as larvae. Measurements of otolith increment width can be used to distinguish between the fast-growing winter-spawned and the slow-growing autumn-spawned stocks, but this method can be time-consuming. Otolith shape analysis is investigated as an alternative method for discriminating between seasonal spawning stocks. Juvenile herring collected from nursery grounds in the Irish Sea in 2006 were classified as autumn- or winter-spawned using increment width measurements. Otolith shape was defined using shape indices and Fourier descriptors. Juveniles were classified successfully to hatch type with a high degree of accuracy (86–87%) using shape variables. The potential use of otolith shape analysis for identifying Celtic Sea juvenile herring in the Irish Sea and its possible use for other mixed-herring stock assessments are discussed.
Regulatory T cells fail to suppress CD4+ T‐bet+ T cells in relapsing multiple sclerosis patients
Authors: Frisullo Giovanni , Nociti Viviana , Iorio Raffaele , Patanella Agata K. , Caggiula Marcella , Marti Alessandro , Sancricca Cristina , Angelucci Francesco , Mirabella Massimiliano , Tonali Pietro A. , Batocchi Anna P. 
Published: November 2008

SummaryMultiple sclerosis (MS) is a chronic inflammatory demyelinating disease of the central nervous system and a defect in the regulatory T‐cell subset seems to be involved in the pathogenesis of the disease. Foxp3 is a transcription factor that is selectively expressed in CD4+ CD25+ regulatory T cells and is required for their development and function. T‐bet is a key transcription factor for the development of T helper 1 (Th1) cells. We found that both the percentage of circulating CD4+ CD25+ Foxp3+ cells and Foxp3 expression were lower in relapsing‐remitting (RR) MS patients during relapses than during remission. Otherwise, the percentage of CD4+ T‐bet+ T cells and T‐bet expression in CD4+ T cells were higher in relapsing than in remitting RRMS patients. CD4+ CD25+ T cells both from relapsing and from remitting RRMS patients showed significantly less capacity than corresponding cells from healthy subjects to suppress autologous CD4+ CD25− T‐cell proliferation, despite a similar Foxp3 expression level. CD4+ CD25+ T cells from healthy subjects and patients in remission clearly reduced T‐bet mean fluorescence intensity (MFI) in CD4+ CD25− T cells up to a ratio of 1:10, whereas CD4+ CD25+ T cells from patients in relapse were able to reduce T‐bet expression only at a high ratio. Our data indicate that the increased number of regulatory T (T‐reg) cells and the increased Foxp3 expression in circulating CD4+ CD25+ T cells may contribute to the maintenance of tolerance in the remission phase of MS. Moreover, the inhibitory capacity of CD4+ CD25+ T cells seems to be impaired in relapsing patients under inflammatory conditions, as shown by the high levels of T‐bet expression in CD4+ T cells.
Induction of copper/zinc‐superoxide dismutase by CCL5/CCR5 activation causes tumour necrosis factor‐α and reactive oxygen species production in macrophages
Authors: Qiu Lei , Ding Li , Huang Jin , Wang Dong , Zhang Junping , Guo Baoyu 
Published: November 2008

SummaryUsing two‐dimensional sodium dodecyl sulphate–polyacrylamide gel electrophoresis, we found that copper/zinc superoxide dismutase (Cu/Zn‐SOD, SOD‐1) was induced in constructed CCR5 stably transfected HEK 293 cells, but not in mock cells, treated with CCL5. CCL5‐induced SOD‐1 expression was also confirmed in HEK 293‐CCR5 cells and CCR5‐positive granulocyte–macrophage colony‐stimulating factor‐induced human macrophages and murine macrophage RAW264.7 cells. CCL5 and CCR5 interaction induced SOD‐1 expression mainly via MEK–ERK activation. In addition, we provided evidence that upregulation of SOD‐1 by CCL5/CCR5 activation occurred in parallel with the increased release of tumour necrosis factor‐α and nitric oxide and production of intracellular reactive oxygen species as well as enhanced nuclear factor‐κB transcriptional activity in CCR5‐positive RAW264.7 cells. Conversely, the MEK1/2 inhibitor PD98059 significantly inhibited SOD‐1 expression with the decrease of these biological responses. More importantly, inhibition of SOD‐1 activity by disulfiram also strongly inhibited the CCL5‐induced biological effects. These data suggest that SOD‐1 mediates CCR5 activation by CCL5 and that pharmacological modulation of SOD‐1 may be beneficial to CCR5‐associated diseases.
Acetylcholinesterase genes in the basal Hexapod Orchesella villosa
Authors: Nardi F. , Barazzuoli B. , Ciolfi S. , Carapelli A. , Dallai R. , Frati F. 
Published: November 2008

AbstractAcetylcholinesterase (AChE) is a key enzyme of the cholinergic nerve system. Of the two forms found in insects, the predominant one is active in the synapses and is the target of organophosphate and carbamate insecticides, while the role of the second is currently unknown. Two acetylcholinesterase cDNAs from the basal hexapod Orchesella villosa have been characterized and compared with others reported form insects. One form conforms well to the typical structure, while the other is characterized by an unusual 3′ region. No amino acid mutation could be directly associated with known resistance mutations in other insect species or to a clear signal of selection in the distribution of alleles, although the action of some population process is suggested.
Estimation of infectious dose and viral shedding rates for infectious pancreatic necrosis virus in Atlantic salmon, Salmo salar L., post‐smolts
Authors: Urquhart K , Murray A G , Gregory A , O’Dea M , Munro L A , Smail D A , Shanks A M , Raynard R S 
Published: November 2008

AbstractInfectious dose and shedding rates are important parameters to estimate in order to understand the transmission of infectious pancreatic necrosis virus (IPNV). Bath challenge of Atlantic salmon post‐smolts was selected as the route of experimental infection as this mimics a major natural route of exposure to IPNV infection. Doses ranging from 102 to 10−4 50% end‐point tissue culture infectious dose (TCID50) mL−1 sea water were used to estimate the minimum infectious dose for a Scottish isolate of IPNV. The minimum dose required to induce infection in Atlantic salmon post‐smolts was <10−1 TCID50 mL−1 by bath immersion (4 h at 10 °C). The peak shedding rate for IPNV following intraperitoneal challenge using post‐smolts was estimated to be 6.8 × 103 TCID50 h−1 kg−1 and occurred 11 days post‐challenge. This information may be incorporated into mathematical models to increase the understanding of the dispersal of IPNV from marine salmon sites.
Deicing salt scaling resistance of concrete incorporating supplementary cementing materials: laboratory and field test data
Authors: Bouzoubaâ N. , Bilodeau A. , Fournier B. , Hooton R. D. , Gagné R. , Jolin M. 
Published: November 2008

In this study, sidewalk sections were made in the field using seven concrete mixtures, applying a finishing and curing practice that is commonly used in Montréal, Canada. For each of the sidewalk sections, large slabs (1.2 m × 1.2 m) were cast from which specimens were cored and tested in the laboratory for determining their basic mechanical properties and deicing salt scaling resistance following ASTM C672 test procedures. Also, during the casting of the sidewalk, companion specimens were cast on site, using concrete from the same batch, and were subjected to the same tests as the “cored” specimens. The resistance to deicing salt scaling of these “laboratory specimens” was evaluated according to ASTM C672 and to BNQ NQ 2621–900 (2002 standard of the province of Quebec, Canada) test procedures. The results were compared with the performance of the sidewalk sections after four winters of outdoor exposure. The visual evaluation of the sidewalks after four winters has confirmed the severity of the ASTM C672 procedure and the adequateness of the BNQ procedure to better evaluate the deicing salt scaling resistance of concrete made with supplementary cementing materials (SCMs). The field evaluation should, however, continue for a longer period of time to increase the confidence in the BNQ test or to allow for changes as needed.
Incidence of nontuberculous mycobacteria in four hot water systems using various types of disinfection
Authors: Sebakova Helena , Kozisek Frantisek , Mudra Radim , Kaustova Jarmila , Fiedorova Marie , Hanslikova Danuse , Nachtmannova Hana , Kubina Jaroslav , Vraspir Pavel , Sasek Jaroslav 
Published: November 2008

The objective of this study was to determine the incidence of nontuberculous mycobacteria (NTM) in hot water systems of 4 selected hospital settings. The hospitals provided the following types of disinfection for their hot water systems: hydrogen peroxide and silver, thermal disinfection, chlorine dioxide, and no treatment (control). In each building, 6 samples were collected from 5 sites during a 3 month period. NTM were detected in 56 (46.7%) of 120 samples; the CFU counts ranged from 10 to 1625 CFU/L. The detected NTM species were the pathogens Mycobacterium kansasii , Mycobacterium xenopi , and Mycobacterium fortuitum and the saprophyte Mycobacterium gordonae. The most common to be isolated was M. xenopi, which was present in 51 samples. The hot water systems differed significantly in the incidence of NTM. NTM were not detected in the system treated by thermal disinfection, and a relatively low incidence (20% positive samples) was found in the system disinfected with chlorine dioxide. However, a high incidence was found in the control system with no additional disinfection (70% positives) and in the system using hydrogen peroxide and silver (97% positives). Water temperatures above 50 °C significantly limited the occurrence of NTM.
In vitro activity of essential oils extracted from plants used as spices against fluconazole-resistant and fluconazole-susceptible Candida spp.
Authors: Pozzatti Patrícia , Scheid Liliane Alves , Spader Tatiana Borba , Atayde Margareth Linde , Santurio Janio Morais , Alves Sydney Hartz 
Published: November 2008

In the present study, the antifungal activity of selected essential oils obtained from plants used as spices was evaluated against both fluconazole-resistant and fluconazole-susceptible Candida spp. The Candida species studied were Candida albicans , Candida dubliniensis , Candida tropicalis , Candida glabrata , and Candida krusei. For comparison purposes, they were arranged in groups as C. albicans, C. dubliniensis, and Candida non-albicans. The essential oils were obtained from Cinnamomum zeylanicum Breyn, Lippia graveolens HBK, Ocimum basilicum L., Origanum vulgare L., Rosmarinus officinalis L., Salvia officinalis L., Thymus vulgaris L., and Zingiber officinale . The susceptibility tests were based on the M27-A2 methodology. The chemical composition of the essential oils was obtained by gas chromatography – mass spectroscopy and by retention indices. The results showed that cinnamon, Mexican oregano, oregano, thyme, and ginger essential oils have different levels of antifungal activity. Oregano and ginger essential oils were found to be the most and the least efficient, respectively. The main finding was that the susceptibilities of fluconazole-resistant C. albicans, C. dubliniensis, and Candida non-albicans to Mexican oregano, oregano, thyme, and ginger essential oils were higher than those of the fluconazole-susceptible yeasts (P < 0.05). In contrast, fluconazole-resistant C. albicans and Candida non-albicans were less susceptible to cinnamon essential oil than their fluconazole-susceptible counterparts (P < 0.05). A relationship between the yeasts’ susceptibilities and the chemical composition of the essential oils studied was apparent when these 2 parameters were compared. Finally, basil, rosemary, and sage essential oils did not show antifungal activity against Candida isolates at the tested concentrations.
Pacific lamprey climbing behavior
Authors: Reinhardt U. G. , Eidietis L. , Friedl S. E. , Moser M. L. 
Published: November 2008

New lamprey-friendly fishways feature inclined ramps that facilitate passage of Pacific lampreys ( Lampetra tridentata (Richardson, 1836)) over Bonneville Dam on the Columbia River, USA. We observed the lampreys moving against water at two flow volumes and on two ramps of 45° and 18° angles relative to horizontal. We documented climbing movements using high-speed video (125 frames/s). Lampreys advanced on the ramps by repeated cycles of attaching to the ramps by their sucker mouths (resting phase), bending their bodies into a W shape (stage II), and then, rapidly straightening the body to propel themselves up the ramp, with simultaneous brief (20–140 ms) release of suction (stage III). We inferred that lampreys were using burst swimming to propel themselves up the ramp, because we observed inflection points in the body curvature traveling toward the posterior of the body and the center of mass moving up, during stage III. This climbing behavior is not described for any other fish species. Vertical motion, relative to the ground, during each cycle of movement was greatest in the 45° ramp – low water flow volume treatment (mean of 0.07 L/cycle), but the movement upstream along the ramp plane was greatest on the 18° ramp, regardless of flow volume. These findings can be used to develop ramp designs that maximize lamprey climbing performance.
Whale Music: Anatomy of an Interspecies Duet
Authors: Rothenberg David 
Published: November 2008

ABSTRACT
The author played clarinet in accompaniment with a singing male humpback whale off the coast of Maui. A sound spectrogram suggests that the whale may have altered his song in response to the clarinet. This observation is consistent with the fact that humpback whales rapidly change their song during breeding season from week to week. A male humpback whale may be able to quickly match new pitched, musical sounds it has never heard before—a result different from those of most humpback whale playback experiments. This experiment suggests that interspecies music-making might be a valuable tool in helping understand the complex communication strategies of humpback whales, as well as in extending our own music making beyond the human realm.
Exploring valid reference genes for gene expression studies in Brachypodium distachyonby real-time PCR
Authors: Hong Shin-Young , Seo Pil Joon , Yang Moon-Sik , Xiang Fengning , Park Chung-Mo 
Published: November 2008

Abstract

Background
The wild grass species Brachypodium distachyon (Brachypodium hereafter) is emerging as a new model system for grass crop genomics research and biofuel grass biology. A draft nuclear genome sequence is expected to be publicly available in the near future; an explosion of gene expression studies will undoubtedly follow. Therefore, stable reference genes are necessary to normalize the gene expression data.

Results
A systematic exploration of suitable reference genes in Brachypodium is presented here. Nine reference gene candidates were chosen, and their gene sequences were obtained from the Brachypodium expressed sequence tag (EST) databases. Their expression levels were examined by quantitative real-time PCR (qRT-PCR) using 21 different Brachypodium plant samples, including those from different plant tissues and grown under various growth conditions. Effects of plant growth hormones were also visualized in the assays. The expression stability of the candidate genes was evaluated using two analysis software packages, geNorm and NormFinder. In conclusion, the ubiquitin-conjugating enzyme 18 gene (UBC18) was validated as a suitable reference gene across all the plant samples examined. While the expression of the polyubiquitin genes (Ubi4 and Ubi10) was most stable in different plant tissues and growth hormone-treated plant samples, the expression of the S-adenosylmethionine decarboxylase gene (SamDC) ranked was most stable in plants grown under various environmental stresses.

Conclusion
This study identified the reference genes that are most suitable for normalizing the gene expression data in Brachypodium. These reference genes will be particularly useful when stress-responsive genes are analyzed in order to produce transgenic plants that exhibit enhanced stress resistance.
Myonecrosis secondary to Clostridium Septicumin a patient with Occult Colon Malignancy: a case report
Authors: Gibson Michael A , Avgerinos Dimitrios V , Llaguna Omar H , Sheth Nitin D 
Published: November 2008

Abstract

Background
Gas gangrene is a relatively rare event that is typically associated with history of trauma. A non-traumatic history of gas gangrene has been associated with Clostridium septicum and cecal malignancy.

Case presentation
We present a case of a 54-year-old male patient who presented with myonecrosis secondary to Clostridium septicum septicemia and an occult cecal carcinoma.

Conclusion

C. septicum and its association with malignancy should be considered in any patient suffering from myonecrosis without a history of trauma.
Perceived risk of medicine side effects in users of a patient information website: A study of the use of verbal descriptors, percentages and natural frequencies
Authors: Knapp P. , Gardner P. H. , Carrigan N. , Raynor D. K. , Woolf E. 
Published: November 2008

Objectives. Research into the provision of patient information has demonstrated that, under certain conditions, patients overestimate the risks of medicine side effects. Gigerenzer and Edwards (2004) argue that ‘natural frequencies’ are a less confusing way of expressing risk information. Two experiments with users of an existing high profile patient information website, investigate the effectiveness of presenting medicine side‐effect risk information in different forms.Design. In both experiments participants were randomly allocated to one of the three conditions for representing risk information (a form of ‘natural frequency’, percentages and verbal descriptors).Method. Participants were recruited from users of the Cancer Research UK patient information website (Cancer Help UK). In Experiment 1, participants (N = 148) were asked to imagine that they had to take a chemotherapy drug (Taxol®) and were asked to estimate the risks of two side‐effects occurring. In Experiment 2 participants (N = 137) estimated the risk for three different side‐effects occurring with the painkiller ibuprofen.Results. In both experiments, verbal descriptions led to significantly higher estimations of risk compared to the other two formats. There was some evidence that people given information as frequencies were more accurate in their estimates than those given percentage information.Conclusions. These findings provide partial support for the advantages of a form of ‘natural frequencies’ when presenting side‐effects to patients. They also add weight to the growing body of research highlighting the deficiencies in using verbal descriptions of side‐effect risk alone.