bluuebunny/crossref_metadata_2025_split huggingface dataset:
Yellowstone Lake: high‐energy geochemistry and rich bacterial diversity
Authors: Clingenpeel Scott , Macur Richard E. , Kan Jinjun , Inskeep William P. , Lovalvo Dave , Varley John , Mathur Eric , Nealson Kenneth , Gorby Yuri , Jiang Hongchen , LaFracois Toben , McDermott Timothy R. 
Published: March 2011

SummaryYellowstone Lake is central to the balanced functioning of the Yellowstone ecosystem, yet little is known about the microbial component of its food chain. A remotely operated vehicle provided video documentation (http://www.tbi.montana.edu/media/videos/) and allowed sampling of dilute surface zone waters and enriched lake floor hydrothermal vent fluids. Vent emissions contained substantial H2S, CH4, CO2 and H2, although CH4 and H2 levels were also significant throughout the lake. Pyrosequencing and near full‐length sequencing of Bacteria 16S rRNA gene diversity associated with two vents and two surface water environments demonstrated that this lake contains significant bacterial diversity. Biomass was size‐fractionated by sequentially filtering through 20‐µm‐, 3.0‐µm‐, 0.8‐µm‐ and 0.1‐µm‐pore‐size filters, with the > 0.1 to < 0.8 µm size class being the focus of this study. Major phyla included Acidobacteria, Actinobacteria, Bacteroidetes, α‐ and β‐Proteobacteria and Cyanobacteria, with 21 other phyla represented at varying levels. Surface waters were dominated by two phylotypes: the Actinobacteria freshwater acI group and an α‐Proteobacteria clade tightly linked with freshwater SAR11‐like organisms. We also obtained evidence of novel thermophiles and recovered Prochlorococcus phylotypes (97–100% identity) in one near surface photic zone region of the lake. The combined geochemical and microbial analyses suggest that the foundation of this lake's food chain is not simple. Phototrophy presumably is an important driver of primary productivity in photic zone waters; however, chemosynthetic hydrogenotrophy and methanotrophy are likely important components of the lake's food chain.
The Pseudomonas aeruginosa opportunistic pathogen and human infections
Authors: de Bentzmann Sophie , Plésiat Patrick 
Published: March 2011

SummaryPseudomonas aeruginosa, a Gram‐negative environmental species and an opportunistic microorganism, establishes itself in vulnerable patients, such as those with cystic fibrosis or hospitalized in intensive care units. It has become a major cause of nosocomial infections worldwide (about 10% of all such infections in most European Union hospitals) and a serious threat to Public Health. The overuse and misuse of antibiotics have also led to the selection of resistant strains against which very few therapeutic options exist. How an environmental species can cause human infections remains a key question that still needs elucidation despite the incredibly high progress that has been made in the P. aeruginosa biology over the past decades. The workshop belonging to Current trends in Biomedicine series, which was held under the sponsorship of the Universidad International de Andalucia between the 8th and the 10th November 2010 brought in the most recent advances in the environmental life of P. aeruginosa, the human P. aeruginosa infections, the new animal models to study Pseudomonas infections, the new genetic aspects including metabolomics, genomics and bioinformatics and the community lifestyle named biofilm that accounts for P. aeruginosa persistence in humans. This workshop organized by Soeren Molin (Danemark), Juan‐Luis Ramos (Spain) and Sophie de Bentzmann (France) gathered 46 researchers coming from 11 European and American countries in a small format and was hosted in the ‘Sede Antonio Machado’ in Baeza. It was organized in seven sessions covering animal models for P. aeruginosa pathogenesis, resistance to drugs, regulatory potency including small RNA, two component systems, extracytoplasmic function sigma factors and trancriptional regulators, new therapies emerging from dissection of molecular mechanisms, and evolutionary mechanisms of P. aeruginosa strains in patients.
Strict and direct transcriptional repression of the pobA gene by benzoate avoids 4‐hydroxybenzoate degradation in the pollutant degrader bacterium Cupriavidus necator JMP134
Authors: Donoso Raúl A. , Pérez‐Pantoja Danilo , González Bernardo 
Published: March 2011

SummaryAs other environmental bacteria, Cupriavidus necator JMP134 uses benzoate as preferred substrate in mixtures with 4‐hydroxybenzoate, strongly inhibiting its degradation. The mechanism underlying this hierarchical use was studied. A C. necator benA mutant, defective in the first step of benzoate degradation, is unable to metabolize 4‐hydroxybenzoate when benzoate is also included in the medium, indicating that this substrate and not one of its catabolic intermediates is directly triggering repression. Reverse transcription polymerase chain reaction analysis revealed that 4‐hydroxybenzoate 3‐hydroxylase‐encoding pobA transcripts are nearly absent in presence of benzoate and a fusion of pobA promoter to lacZ reporter confirmed that benzoate drastically decreases the transcription of this gene. Expression of pobA driven by a heterologous promoter in C. necator benA mutant, allows growth on 4‐hydroxybenzoate in presence of benzoate, overcoming its repressive effect. In contrast with other bacteria, regulators of benzoate catabolism do not participate in repression of 4‐hydroxybenzoate degradation. Moreover, the effect of benzoate on pobA promoter can be observed in heterologous strains with the sole presence of PobR, the transcriptional activator of pobA gene, indicating that PobR is enough to fully reproduce the phenomenon. This novel mechanism for benzoate repression is probably mediated by direct action of benzoate over PobR.
Energy metabolism and multiple respiratory pathways revealed by genome sequencing of Desulfurispirillum indicum strain S5
Authors: Rauschenbach Ines , Yee Nathan , Häggblom Max M. , Bini Elisabetta 
Published: March 2011

SummaryDesulfurispirillum indicum strain S5, a novel obligate anaerobe belonging to the phylum Chrysiogenetes, is a dissimilatory selenate‐, selenite‐, arsenate‐, nitrate‐ and nitrite‐reducing bacterium. The circular genome of this metabolically versatile bacterium is 2.9 Mbp, with a G+C content of 56.1% and 2619 predicted protein‐coding genes. Genome analysis uncovered the components of the electron transport chain, providing important insights into the ability of D. indicum to adapt to different conditions, by coupling the oxidation of various electron donors to the reduction of a wide range of electron acceptors. Sequences encoding the subunits of dehydrogenases and enzymes with roles in the oxidation of several electron donors, including acetate, pyruvate and lactate were identified. Furthermore, five terminal oxidoreductase complexes were encoded in the D. indicum genome. Phylogenetic analyses of their catalytic subunits, operon structure and co‐transcription of subunit‐coding genes indicate a likely role of three of them as respiratory arsenate reductase (Arr), periplasmic nitrate reductase (Nap) and the membrane‐bound nitrate reductase (Nar). This study is the first description and annotation of the genome of a dissimilatory selenate‐ and arsenate‐respiring organism, and D. indicum represents the first sequenced member of its phylum. Our analysis demonstrates the complexity of the microorganism's respiratory system, provides the basis for the functional analysis of metalloid oxyanions respiration and expands our knowledge of the deep branching phylum of Chrysiogenetes.
Biological nitrogen fixation in acidic high‐temperature geothermal springs in Yellowstone National Park, Wyoming
Authors: Hamilton Trinity L. , Lange Rachel K. , Boyd Eric S. , Peters John W. 
Published: March 2011

SummaryThe near ubiquitous distribution of nifH genes in sediments sampled from 14 high‐temperature (48.0–89.0°C) and acidic (pH 1.90–5.02) geothermal springs in Yellowstone National Park suggested a role for the biological reduction of dinitrogen (N2) to ammonia (NH3) (e.g. nitrogen fixation or diazotrophy) in these environments. nifH genes from these environments formed three unique phylotypes that were distantly related to acidiphilic, mesophilic diazotrophs. Acetylene reduction assays and 15N2 tracer studies in microcosms containing sediments sampled from acidic and high‐temperature environments where nifH genes were detected confirmed the potential for biological N2 reduction in these environments. Rates of acetylene reduction by sediment‐associated populations were positively correlated with the concentration of NH4+, suggesting a potential relationship between NH4+ consumption and N2 fixation activity. Amendment of microcosms with NH4+ resulted in increased lag times in acetylene reduction assays. Manipulation of incubation temperature and pH in acetylene reduction assays indicated that diazotrophic populations are specifically adapted to local conditions. Incubation of sediments in the presence of a N2 headspace yielded a highly enriched culture containing a single nifH phylotype. This phylotype was detected in all 14 geothermal spring sediments examined and its abundance ranged from ∼780 to ∼6800 copies (g dry weight sediment)−1, suggesting that this organism may contribute N to the ecosystems. Collectively, these results for the first time demonstrate thermoacidiphilic N2 fixation in the natural environment and extend the upper temperature for biological N2 fixation in terrestrial systems.
Androgen deprivation therapy in prostate cancer: are rising concerns leading to falling use?
Authors: Krahn Murray , Bremner Karen E. , Tomlinson George , Luo Jin , Ritvo Paul , Naglie Gary , Alibhai Shabbir M.H. 
Published: March 2011

Study Type – Therapy (cohort)Level of Evidence 2bWhat’s known on the subject? and What does the study add?Androgen deprivation therapy was originally used for metastatic prostate cancer but is now used to treat all stages of the disease. Once considered to be relatively harmless, androgen deprivation therapy was associated with impaired cognitive function, anemia, loss of muscle strength, osteoporotic fractures, diabetes, and cardiovascular disease by the year 2000.In a large, population‐based sample of prostate cancer patients, the numbers initiating androgen deprivation therapy increased from 1995 to 2001 and then sharply declined to 2005, but the rate of initiation among eligible prevalent cases steadily decreased over that period. Monotherapy with luteinizing hormone‐releasing hormone agonists became the dominant type of androgen deprivation therapy. Changes may be related to fewer cases of late stage disease, potential adverse effects, and new evidence for selected indications and regimens.OBJECTIVE• To describe patterns of initiation of androgen deprivation therapy (ADT) in a population‐based cohort of patients with prostate cancer.PATIENTS AND METHODS• All patients with prostate cancer in Ontario, Canada, who started ≥90 days of ADT at age ≥66 years in 1995–2005 were classified by ADT regimen: medical castration [oestrogen and/or luteinizing hormone‐releasing hormone (LHRH) agonist); orchidectomy; antiandrogen monotherapy; combined androgen blockade (CAB) medical (medical castration plus antiandrogen); CAB surgical (orchidectomy plus antiandrogen).• Indications for ADT were as follows: neoadjuvant (short‐term before prostatectomy or radiation therapy); adjuvant (long‐term with prostatectomy or radiation therapy); metastatic disease; biochemical recurrence; primary (localized disease); other.• We examined trends in ADT regimen and indication over time.RESULTS• The number of patients initiating ADT increased from 1995 to 2001 (2106–2916 per year) and declined thereafter to 2200–2300 annually (total n= 26 809).• However, prostate cancer prevalence doubled over these years, and the rate of ADT initiation decreased from 16 to 7 per 100 person‐years.• Patterns varied by regimen and indication. Medical castration increased from 12% of all ADT in 1995 to 47% in 2005; orchidectomy decreased from 17 to 4%. Use for metastatic disease remained stable, but adjuvant therapy increased from <3% of all ADT in 1995 to 13% in 2005. Primary therapy was the most common indication, but decreased over time.CONCLUSIONS• ADT initiation has fallen and marked changes occurred in treatment patterns for prostate cancer.• Changes might be driven by increasing awareness of potential harms and costs, and by new evidence supporting ADT for specific indications.
Meta‐analysis showing the beneficial effect of α‐blockers on ureteric stent discomfort
Authors: Lamb Alastair D. , Vowler Sarah L. , Johnston Richard , Dunn Nick , Wiseman Oliver J. 
Published: March 2011

Study Type – Therapy (systematic review)Level of Evidence 1aWhat’s known on the subject? and What does the study add?Ureteric stents cause significant discomfort and this is probably related to ureteric smooth muscle spasm and trigonal irritation. Alpha‐adrenoceptor antagonists reduce smooth muscle activity and are already widely used in medical expulsive therapy to aid passage of ureteric calculi.This meta‐analysis incorporating five randomized controlled trials provides evidence that alpha‐adrenoceptor antagonists reduce stent‐related pain and storage symptoms as assessed by the Ureteric Stent Symptoms Questionnaire (USSQ).OBJECTIVES
To evaluate the efficacy of α‐blockers with respect to improving stent‐related symptoms.
Ureteric stents remain a source of marked discomfort and their placement is often required after certain ureteroscopic procedures or in the acute setting. This analysis identifies and reviews the several studies that have investigated the role of α‐blockers after stent placement.
MATERIALS AND METHODS
Pubmed/Medline, EMBASE, CINAHL and Cochrane Library databases were scrutinized using standard MeSH headings.
Randomized or controlled trials comparing α‐blockers with control or standard therapy were included.
In all studies, patients completed the Ureteral Stent Symptom Questionnaire (USSQ).
The study data were independently reviewed by two assessors.
RESULTS
In total, five studies of varying quality were identified, including 461 patients receiving either tamsulosin or alfuzosin, or control.
On meta‐analysis, all five studies showed a reduction in USSQ urinary symptom score and body pain scores. There was mean reduction of 8.4 (95% CI, 5.6–11.1) in the urinary symptom score and 7.2 (95% CI, 2.5–11.8) in the body pain score.
In three studies, the numbers of patients experiencing stent related pain were stated: 45% (51/114) of patients receiving an α‐blocker experienced painful episodes within the follow‐up period defined for that study compared to 76% (88/116) in the control groups, which is equivalent to a relative risk of pain of 0.59 (95% confidence interval, 0.47–0.71).
There were also reductions in other aspects of the USSQ, such as the general health score and sexual matters score, although these were not statistically significant or uniformly reported.
CONCLUSION
There is evidence that α‐blockers provide an improvement in discomfort after placement of a ureteric stent.
R11, a novel cell‐permeable peptide, as an intravesical delivery vehicle
Authors: Hsieh Jer‐Tsong , Zhou Jian , Gore Crystal , Zimmern Philippe 
Published: March 2011

What’s known on the subject? and What does the study add?Efficient transfer of macromolecules such as proteins or nucleic acids or small molecules with charged or hydrophilic properties across cellular membranes is one of the major problems in cell biology and drug delivery. A cell‐permeable peptide, a short peptide with 9–12 amino acids, appears to be a potential carrier for delivering macro‐ or small molecules. Our study unveils a unique cell permeable peptide for developing intravesical therapy of new agent.OBJECTIVE• To test the uptake efficiency of R11, a cell‐permeable peptide (CPP), administered intravesically for effective drug delivery.METHODS• We used an approved in vivo model (an athymic nude mouse model) to test synthetic R11 conjugated with fluorescein isothiocyanate (FITC) at concentrations of 1 nM and 5 nM. Controls received FITC without CPP conjugation.• The mice were instilled with R11 for 30 min and killed 3 or 24 h later to harvest bladders for the measurement of CPP uptake and tissue localization using frozen sections.• Bladder uptake specificity was determined using the mean values of relative FITC intensity with each tissue weight.RESULTS• Although the uptake of R11 varied among the mice, a 2‐ to 6‐fold higher amount of R11 was detected in the bladder at 3 and 24 h after intravesical instillation at 1‐nM or 5‐nM concentrations than was detected in the bladders of each mouse control group or in other organs.• Examination of tissue sections further confirmed the localization of R11 in the lamina propria of the bladder wall.CONCLUSION• Because of its high affinity for the bladder, both systemically as reported in previous studies and after intravesical instillation as reported in the present study, R11 should be further tested in animal models as a delivery vector for agents used in treating bladder diseases.
The importance of alcoholic beverage type for suicide in Japan: A time‐series analysis, 1963–2007
Authors: NORSTRÖM THOR , STICKLEY ANDREW , SHIBUYA KENJI 
Published: March 2011

AbstractBackground.Japan has one of the highest suicide rates in the world. Cohort analysis has suggested that alcohol consumption is a risk factor for suicide in Japan. However, this relationship has not been observed at the population level when a measure of per capita total alcohol consumption has been analysed. The present study employed a time‐series analysis to examine whether these contradictory findings may be due to the existence of beverage‐specific effects on suicide.Methods.An autoregressive integrated moving average model was used to assess the relationship between the consumption of different types of alcohol and suicide rates from 1963 to 2007. The data comprised age‐adjusted suicide rates for the ages 15–69, and information on beverage‐specific alcohol consumption per capita (15+). The unemployment rate was included as a control variable.Results.During 1963–2007, male suicide rates increased substantially whereas female rates decreased slightly. Consumption of distilled spirits was significantly related to male suicide rates (but not in women) with a 1 L increase in consumption associated with a 21.4% (95% confidence interval: 3.2–42.9) increase in male suicide rates. There was no statistically significant relationship between suicide and any other form of alcohol consumption (beer, wine, other alcohol).Conclusion.This is the first study that has shown an association between spirits consumption and male suicide in Japan. Potentially beneficial policy changes include increasing spirits prices through taxation, reducing the physical availability of alcohol and discouraging the practice of heavy drinking.[Norström T, Stickley A, Shibuya K. The importance of alcoholic beverage type for suicide in Japan: A time‐series analysis, 1963–2007.Drug Alcohol Rev2012;31:251–256]
Characteristics of the actions by which 5‐HT affects electrical and mechanical activities in rabbit jugular vein
Authors: Itoh Takeo , Kajikuri Junko 
Published: March 2011

BACKGROUND AND PURPOSE 5‐HT is known to be a potent vasospasmogenic agonist in various arteries. However, in veins the vasomodulating actions of 5‐HT, and the underlying mechanisms, remain to be fully clarified. Here, we characterized the actions by which 5‐HT affects electrical and mechanical activities in the rabbit jugular vein.EXPERIMENTAL APPROACH Membrane potential and isometric tension were measured in endothelium‐intact and ‐denuded preparations. Localization of 5‐HT receptor subtypes was examined immunohistochemically.KEY RESULTS 5‐HT induced a transient then a small, sustained smooth muscle cell hyperpolarization in endothelium‐intact strips. In endothelium‐denuded strips, 5‐HT induced only a sustained hyperpolarization, and this was changed to a depolarization by the selective 5‐HT7 receptor inhibitor SB269970. This depolarization was inhibited by the 5‐HT2A receptor blocker sarpogrelate. 5‐HT induced a relaxation of PGF2α‐induced contracted strips that was similar in endothelium‐intact and ‐denuded preparations. The latter relaxation was changed to contraction by SB269970 and this contraction was inhibited by sarpogrelate. Immunoreactive responses against endothelial and smooth muscle 5‐HT2A receptors and smooth muscle 5‐HT7 receptors were identified in the vein. The 5‐HT‐induced relaxation of the PGF2α contraction was inhibited by the cAMP‐dependent protein kinase inhibitor Rp‐cAMPS and by the AC inhibitor SQ22536.CONCLUSIONS AND IMPLICATIONS These results indicate that 5‐HT activates both smooth muscle 5‐HT7 receptors (to produce relaxation) and smooth muscle 5‐HT2A receptors (to produce contraction) in rabbit jugular vein. We suggest that in this particular vein, the 5‐HT2A receptor‐induced depolarization and contraction are masked by the 5‐HT7 receptor‐induced responses, possibly via actions mediated by cAMP.
The thienotriazolodiazepine Ro 11‐1464 increases plasma apoA‐I and promotes reverse cholesterol transport in human apoA‐I transgenic mice
Authors: Zanotti I , Maugeais C , Pedrelli M , Gomaraschi M , Salgam P , Calabresi L , Bernini F , Kempen H 
Published: March 2011

BACKGROUND AND PURPOSE Ro 11‐1464 is a thienotriazolodiazepine previously described to selectively stimulate apolipoprotein A‐I (apoA‐I) production and mRNA level in human liver cells. Here, we studied its effects upon oral administration to human apoA‐I transgenic (hapoA‐I) mice.EXPERIMENTAL APPROACH HapoA‐I mice were treated for 5 days with increasing doses of Ro 11‐1464. Macrophage reverse cholesterol transport (mph‐RCT) was assessed by following [3H]‐cholesterol mobilization from pre‐labelled i.p. injected J774 macrophages to plasma, liver and faeces. Effects on plasma lipids, apoproteins, lecithin‐cholesterol : acyltransferase (LCAT) and liver enzymes, as well as on faecal excretion of cholesterol and bile salts, and on liver lipids and mRNA contents were determined.KEY RESULTS Treatment with Ro 11‐1464 300 mg·kg−1·day−1 resulted in a nearly 2‐fold increase in plasma apoA‐I, a 2‐ to 3‐fold increase in the level of large sized‐pre‐β high‐density lipoprotein and a 3‐fold selective up‐regulation of hepatic apoA‐I mRNA, but a marked decrease in all plasma lipids and LCAT activity. Mpm‐RCT was decreased in blood but markedly increased in faecal sterols (4‐fold) and bile acids (1.7‐fold). However, liver weight and liver enzymes in plasma were also increased, in parallel with an increase in liver cholesterol ester content (all these effect being significant).CONCLUSION AND IMPLICATIONS In this model Ro 11‐1464 causes increased hepatic expression and plasma levels of apoA‐I and a suppression of LCAT, and a marked enhancement of reverse cholesterol transport, but also some symptoms of liver toxicity. The compound may therefore be a prototype for a next generation of anti‐atherosclerotic medicines.