bluuebunny/crossref_metadata_2025_split huggingface dataset:
The low diverse gastric microbiome of the jellyfish Cotylorhiza tuberculata is dominated by four novel taxa
Authors: Viver Tomeu , Orellana Luis H. , Hatt Janet K. , Urdiain Mercedes , Díaz Sara , Richter Michael , Antón Josefa , Avian Massimo , Amann Rudolf , Konstantinidis Konstantinos T. , Rosselló‐Móra Ramon 
Published: April 2017

SummaryCotylorhiza tuberculata is an important scyphozoan jellyfish producing population blooms in the Mediterranean probably due to pelagic ecosystem's decay. Its gastric cavity can serve as a simple model of microbial–animal digestive associations, yet poorly characterized. Using state‐of‐the‐art metagenomic population binning and catalyzed reporter deposition fluorescence in situ hybridization (CARD‐FISH), we show that only four novel clonal phylotypes were consistently associated with multiple jellyfish adults. Two affiliated close to Spiroplasma and Mycoplasma genera, one to chlamydial ‘Candidatus Syngnamydia’, and one to bacteroidetal Tenacibaculum, and were at least one order of magnitude more abundant than any other bacteria detected. Metabolic modelling predicted an aerobic heterotrophic lifestyle for the chlamydia, which were found intracellularly in Onychodromopsis‐like ciliates. The Spiroplasma‐like organism was predicted to be an anaerobic fermenter associated to some jellyfish cells, whereas the Tenacibaculum‐like as free‐living aerobic heterotroph, densely colonizing the mesogleal axis inside the gastric filaments. The association between the jellyfish and its reduced microbiome was close and temporally stable, and possibly related to food digestion and protection from pathogens. Based on the genomic and microscopic data, we propose three candidate taxa: ‘Candidatus Syngnamydia medusae’, ‘Candidatus Medusoplasma mediterranei’ and ‘Candidatus Tenacibaculum medusae’.
The life sulfuric: microbial ecology of sulfur cycling in marine sediments
Authors: Wasmund Kenneth , Mußmann Marc , Loy Alexander 
Published: April 2017

SummaryAlmost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular‐ and ecosystem‐level processes. Sulfur‐transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate‐rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep‐subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle.
Precision medicine and pharmacogenetics: what does oncology have that addiction medicine does not?
Authors: Kranzler Henry R. , Smith Rachel V. , Schnoll Robert , Moustafa Afaf , Greenstreet‐Akman Emma 
Published: April 2017

AbstractBackground and aimsPrecision, personalized or stratified medicine, which promises to deliver the right treatment to the right patient, is a topic of international interest in both the lay press and the scientific literature. A key aspect of precision medicine is the identification of biomarkers that predict the response to medications (i.e. pharmacogenetics). We examined why, despite the great strides that have been made in biomarker identification in many areas of medicine, only in oncology has there been substantial progress in their clinical implementation. We also considered why progress in this effort has lagged in addiction medicine.MethodsWe compared the development of pharmacogenetic biomarkers in oncology, cardiovascular medicine (where developments are also promising) and addictive disorders.ResultsThe first major reason for the success of oncologic pharmacogenetics is ready access to tumor tissue, which allows in‐vitro testing and insights into cancer biology. The second major reason is funding, with cancer research receiving, by far, the largest allocation by the National Institutes of Health (NIH) during the past two decades. The second largest allocation of research funding has gone to cardiovascular disease research. Addictions research received a much smaller NIH funding allocation, despite the major impact that tobacco use, alcohol consumption and illicit drug use have on the public health and healthcare costs.ConclusionsGreater support for research on the personalized treatment of addictive disorders can be expected to yield disproportionately large benefits to the public health and substantial reductions in healthcare costs.
Association of external cephalic version before term with late preterm birth
Authors: Poole Kristie L. , McDonald Sarah D. , Griffith Lauren E. , Hutton Eileen K. ,   the Early ECV Pilot and ECV2 Trial Collaborative Group
Published: April 2017

AbstractIntroductionWhile evidence suggests that beginning an external cephalic version (ECV) before term (340/7 to 366/7 weeks) compared with after term may be associated with an increase in late preterm birth (340/7 to 366/7 weeks), it remains unknown what might account for this risk. The objective of the present study is to further investigate the association between ECV before term and late preterm birth.Material and methodsSecondary analysis of data collected from the international, multicenter Early ECV trials. We evaluated the relation between ECV exposure and late preterm birth (340/7 to 366/7 weeks), as well as whether additional risk factors for preterm birth (such as maternal age, height, body mass index, parity, placental location, and perinatal mortality rate) moderated this relation. Generalized linear mixed methods were used to account for center effect and adjust for covariates.ResultAmong 1765 women with breech pregnancies and without a prior preterm birth, 749 (42.4%) received at least one ECV before term. Exposure to an ECV before term was not associated significantly independently with odds of preterm birth. However, placenta location moderated the association between early ECV exposure and late preterm birth. The odds of preterm birth in women who were exposed to an ECV before term and who also had an anterior placenta were doubled (OR 2.05; 95% CI 1.12–3.71; p = 0.02).ConclusionIn a large cohort of women without known risks for preterm birth, those with an anterior placenta who undergo an ECV before term constitute a subgroup at particular risk for late preterm birth.
Impact of adverse drug events and treatment satisfaction on patient adherence with antihypertensive medication – a study in ambulatory patients
Authors: Berhe Derbew Fikadu , Taxis Katja , Haaijer‐Ruskamp Flora M. , Mulugeta Afework , Mengistu Yewondwossen Tadesse , Burgerhof Johannes G. M. , Mol Peter G. M. 
Published: April 2017

AimsThe aim of the present study was to evaluate the impact of adverse drug events (ADEs) and treatment satisfaction on antihypertensive medication adherence.MethodsA cross‐sectional study was conducted in six public hospitals in Ethiopia. We included adult ambulatory patients on antihypertensive medication. Adherence was measured using the eight‐point Morisky Medication Adherence Scale, which categorizes as low (0–5), medium (6–7) and high (8) adherence. Treatment satisfaction was measured using the Treatment Satisfaction Questionnaire for Medication (TSQM) version 1.4, which included questions about ADEs. Data were analysed using generalized ordered logistic regression with 95% confidence intervals (CIs).ResultsWe included 925 out of 968 patients. Overall, 42% of patients scored low, 37% medium and 21% high adherence. Satisfaction with treatment was low, with a mean (standard deviation) TSQM score for global satisfaction of 51 (14). A total of 193 (21%) patients experienced 421 ADEs – mainly dyspeptic symptoms (12%), headache (11%) and cough (11). Experiencing more ADEs reduced the odds of being adherent [low vs. medium/high: odds ratio (OR) OR1 0.77 (95% CI 0.67, 0.89), and low/medium vs. high: OR2 0.55 (05% CI 0.41, 0.73)]. Being more satisfied increased the odds of being adherent [low vs. medium/high: OR1 1.02 (95% CI 1.01, 1.03)]. Taking medication >1 year [OR1 = 2, 0.60 (95% CI 0.43, 0.83)] and taking calcium channel blockers [OR1 = 2 0.71 (95% CI 0.54, 0.92)] decreased the odds for both low vs. medium/high and low/medium vs. high adherence.ConclusionsOnly one in five patients reported perfect (high) adherence to their antihypertensive treatment regimen. Experiencing ADEs and being dissatisfied with treatment were associated with lower adherence. In addition to addressing treatment satisfaction and drug safety in first‐world countries, these should also be addressed in resource‐poor settings, within patient consultations, to enhance adherence.
Iron‐chelating therapy with deferasirox in transfusion‐dependent, higher risk myelodysplastic syndromes: a retrospective, multicentre study
Authors: Musto Pellegrino , Maurillo Luca , Simeon Vittorio , Poloni Antonella , Finelli Carlo , Balleari Enrico , Ricco Alessandra , Rivellini Flavia , Cortelezzi Agostino , Tarantini Giuseppe , Villani Oreste , Mansueto Giovanna , Milella Maria R. , Scapicchio Daniele , Marziano Gioacchino , Breccia Massimo , Niscola Pasquale , Sanna Alessandro , Clissa Cristina , Voso Maria T. , Fenu Susanna , Venditti Adriano , Santini Valeria , Angelucci Emanuele , Levis Alessandro 
Published: April 2017

SummaryIron chelation is controversial in higher risk myelodysplastic syndromes (HR‐MDS), outside the allogeneic transplant setting. We conducted a retrospective, multicentre study in 51 patients with transfusion‐dependent, intermediate‐to‐very high risk MDS, according to the revised international prognostic scoring system, treated with the oral iron chelating agent deferasirox (DFX). Thirty‐six patients (71%) received azacitidine concomitantly. DFX was given at a median dose of 1000 mg/day (range 375–2500 mg) for a median of 11 months (range 0·4–75). Eight patients (16%) showed grade 2–3 toxicities (renal or gastrointestinal), 4 of whom (8%) required drug interruption. Median ferritin levels decreased from 1709 μg/l at baseline to 1100 μg/l after 12 months of treatment (P = 0·02). Seventeen patients showed abnormal transaminase levels at baseline, which improved or normalized under DFX treatment in eight cases. One patient showed a remarkable haematological improvement. At a median follow up of 35·3 months, median overall survival was 37·5 months. The results of this first survey of DFX in HR‐MDS are comparable, in terms of safety and efficacy, with those observed in lower‐risk MDS. Though larger, prospective studies are required to demonstrate real clinical benefits, our data suggest that DFX is feasible and might be considered in a selected cohort of HR‐MDS patients.
The 2016 revised World Health Organization definition of ‘myelodysplastic syndrome with isolated del(5q)’; prognostic implications of single versus double cytogenetic abnormalities
Authors: Gurney Mark , Patnaik Mrinal M. , Hanson Curtis A. , Litzow Mark R. , Al‐Kali Aref , Ketterling Rhett P. , Tefferi Ayalew , Gangat Naseema 
Published: April 2017

SummaryThe definition of the myelodysplastic syndrome (MDS) subtype ‘MDS with isolated del(5q)’ was expanded to include cases with one additional non‐chromosome 7 based cytogenetic abnormality in the 2016 revised World Health Organization classification. This study applied the revised definition to a large primary MDS cohort, and evaluated the prognostic impact of the additional cytogenetic abnormality. Seventy‐two of 1067 patients (7%) met the ‘MDS with isolated del(5q)’ criteria, 11 (1%) of whom had an additional cytogenetic abnormality. There was no survival difference between patients in whom del(5q) occurred alone, compared to those with one additional cytogenetic abnormality (P = 0·52).
Skeletal muscle analyses: agreement between non‐contrast and contrast CT scan measurements of skeletal muscle area and mean muscle attenuation
Authors: van der Werf Anne , Dekker Ingeborg M. , Meijerink Martijn R. , Wierdsma Nicolette J. , de van der Schueren Marian A. E. , Langius Jacqueline A. E. 
Published: April 2017

SummaryLow skeletal muscle area (SMA) and muscle radiation attenuation (MRA) have been associated with poor prognosis in various patient populations. Both non‐contrast and contrast CT scans are used to determine SMA and MRA. The effect of the use of a contrast agent on SMA and MRA is unknown. Therefore, we investigated agreement between these two scan options. SMA and MRA of 41 healthy individuals were analysed on a paired non‐contrast and contrast single CT scan, and agreement between paired scan results was assessed with use of Bland–Altman plots, intraclass correlation coefficients (ICCs), standard error of measurements (SEM) and smallest detectable differences at a 95% confidence level (SDD95). Analyses were stratified by tube voltage. Difference in SMA between non‐contrast and contrast scans made with a different tube voltage was 7·0 ± 7·5 cm2; for scans made with the same tube voltage this was 2·3 ± 1·7 cm2. Agreement was excellent for both methods: ICC: 0·952, SEM: 7·2 cm2, SDD95: 19·9 cm2 and ICC: 0·997, SEM: 2·0 cm2, SDD95: 5·6 cm2, respectively. MRA of scans made with a different tube voltage differed 1·3 ± 11·3 HU, and agreement was poor (ICC: 0·207, SEM: 7·9 HU, SDD95: 21·8 HU). For scans made with the same tube voltage the difference was 6·7 ± 3·2 HU, and agreement was good (ICC: 0·682, SEM: 5·3 HU, SDD95: 14·6 HU). In conclusion, SMA and MRA can be slightly influenced by the use of contrast agent. To minimise measurement error, image acquisition parameters of the scans should be similar.
Aspects of carotid structure and function in health and different stages of chronic kidney disease
Authors: Asp Anna M. , Wallquist Carin , Rickenlund Anette , Hylander Britta , Jacobson Stefan H. , Caidahl Kenneth , Eriksson Maria J. 
Published: April 2017

SummaryIntroductionArterial remodelling and stiffening have been demonstrated in end‐stage renal disease (ESRD). The presence of vascular alterations in earlier‐stage chronic kidney disease (CKD) is less studied. We evaluated vascular structure and function in mild‐to‐moderate CKD (stages 2–3) compared with healthy subjects and advanced CKD (stages 4–5).MethodsCarotid ultrasound was performed in 103 non‐dialysis CKD patients and 54 healthy controls. Carotid intima‐media thickness (CIMT) and common carotid artery (CCA) diameter were measured. Strain, stiffness and the pressure‐strain elastic modulus (Ep) of the right CCA were calculated.ResultsThere was no significant difference in CCA diameter between CKD 2–3 and controls. The CCA diameter was larger in CKD 4–5 compared with CKD 2–3 and controls (CKD 4–5, 6·50 ± 0·79 mm versus CKD 2–3, 6·08 ± 0·56 mm, P = 0·003; and versus controls 5·97 ± 0·53 mm, P<0·001). However, after adjustments, the difference in CCA diameter was valid only for older ages and also dependent on systolic blood pressure (SBP). There were no significant differences in CIMT, strain or stiffness between the groups, but Ep was higher in CKD 4–5 compared with controls (P = 0·006).ConclusionIn mild‐to‐moderate CKD, there were no significant differences in carotid artery structure or function compared with healthy subjects. Only patients with advanced CKD and older ages showed signs of arterial remodelling. Our study indicates that vascular alterations occur in advanced CKD, with SBP and age as important contributing factors.
Attenuation and modification of the ballast water microbial community during voyages into the Canadian Arctic
Authors: Johansson Mattias L. , Chaganti Subba Rao , Simard Nathalie , Howland Kimberly , Winkler Gesche , Rochon André , Laget Frederic , Tremblay Pascal , Heath Daniel D. , MacIsaac Hugh J. 
Published: April 2017

AbstractAimBallast water is a major vector of non‐indigenous species introductions world‐wide. Our understanding of population dynamics of organisms entrained in ballast is largely limited to studies of zooplankton and phytoplankton. Bacteria are more numerous and diverse than zooplankton or phytoplankton, yet remain comparatively understudied. We apply a metagenomics approach to characterize changes in the microbial ballast water community over the course of three voyages on one ship, and assess the effects of ballast water exchange (BWE), spring/summer sampling month and time since voyage start.LocationQuebec City and Deception Bay, Quebec, and the coastal marine region offshore of eastern Canada.MethodsWe used universal primers to Ion Torrent sequence a fragment of the bacterial 16S ribosomal DNA for samples collected over three voyages of one ship between Quebec City and Deception Bay in June, July and August 2015. We compared richness (total number of species in the community) and diversity (accounts for both species abundance and evenness) using linear mixed‐effects analysis and compared community composition using non‐metric multidimensional scaling and permutational multivariate analysis of variance. Initial comparisons were between months. Subsequent analyses focused on each month separately.ResultsIon Torrent sequencing returned c. 2.9 million reads and revealed monthly differences in diversity and richness, and in community structure in ballast water. June had higher richness and diversity than either July or August, and showed most clearly the effect of BWE on the microbial community.Main conclusionsOur results suggest that environmental conditions associated with different spring/summer sampling months drive differences in microbial diversity in ballast water. This study showed that BWE removes some components of the freshwater starting microbial community and replaces them with other taxa. BWE also changed proportional representation of some microbes without removing them completely. It appears that some taxa are resident in ballast tanks and are not removed by BWE.
Effect of alpha‐lipoic acid on endometrial implants in an experimental rat model
Authors: Pınar Neslihan , Soylu Karapınar Oya , Özcan Oğuzhan , Özgür Tümay , Bayraktar Suphi 
Published: April 2017

AbstractTo investigate the antioxidant and anti‐inflammatory effects of alpha‐lipoic acid (ALA) in the treatment of endometriosis in an experimental rat model by evaluating biochemical and histopathologic parameters. Experimental endometriosis was induced by the peritoneal implantation of autologous endometrial tissue. The rats were randomly divided into two groups with eight rats each. Group I was intraperitoneally administered ALA 100 mg/kg/day for 14 days. Group II was intraperitoneally administered saline solution at the same dosage and over the same period. Endometrial implant volume was measured in both groups both pre‐ and post‐treatment. Tumor necrosis factor alpha (TNF‐α) was measured in peritoneal fluid. Total antioxidant status (TAS), total oxidant status (TOS), and oxidative stress index (OSI) were assessed in serum. The implants were histopathologically evaluated. In the ALA group, the serum TOS and OSI levels, the endometrial implant volumes, the TNF‐α levels in serum and peritoneal fluid, and the histopathologic scores were significantly lower compared to the control group (P < 0.05). Alpha‐lipoic acid may have a therapeutic potential in the treatment of endometriosis due to its antioxidant and anti‐inflammatory effects.
A Global Synthesis of Managing Groundwater Dependent Ecosystems Under Sustainable Groundwater Policy
Authors: Rohde Melissa M. , Froend Ray , Howard Jeanette 
Published: April 2017

AbstractGroundwater is a vital water supply worldwide for people and nature. However, species and ecosystems that depend on groundwater for some or all of their water needs, known as groundwater dependent ecosystems (GDEs), are increasingly becoming threatened worldwide due to growing human water demands. Over the past two decades, the protection and management of GDEs have been incorporated into several water management policy initiatives worldwide including jurisdictions within Australia, the European Union, South Africa, and the United States. Among these, Australia has implemented the most comprehensive framework to manage and protect GDEs through its water policy initiatives. Using a science‐based approach, Australia has made good progress at reducing uncertainty when selecting management thresholds for GDEs in their water management plans. This has been achieved by incorporating appropriate metrics for GDEs into water monitoring programs so that information gathered over time can inform management decisions. This adaptive management approach is also accompanied by the application of the “Precautionary Principle” in cases where insufficient information on GDEs exist. Additionally, the integration of risk assessment into Australia's approach has enabled water managers to prioritize the most valuable and vulnerable ecologic assets necessary to manage GDEs under Australia's national sustainable water management legislation. The purpose of this paper is to: (1) compare existing global policy initiatives for the protection and management of GDEs; (2) synthesize Australia's adaptive management approach of GDEs in their state water plans; and (3) highlight opportunities and challenges of applying Australia's approach for managing GDEs under other water management policies worldwide.
PD‐L1 expression in extrahepatic cholangiocarcinoma
Authors: Walter Dirk , Herrmann Eva , Schnitzbauer Andreas A , Zeuzem Stefan , Hansmann Martin Leo , Peveling‐Oberhag Jan , Hartmann Sylvia 
Published: April 2017

AimsTo investigate the expression of the programmed cell death 1 (PD‐1) receptor–programmed cell death ligand 1 (PD‐L1) pathway and the clinicopathological characteristics in extrahepatic cholangiocarcinoma (eCCA).Methods and resultsTissue samples from patients with eCCA [n = 69; perihilar cholangiocarcinoma (CCA), 40; and distal CCA, 29] who underwent surgical resection in the period from 2007 to 2015 were evaluated for PD‐1, PD‐L1, CD3 and CD163 expression, and correlations with clinicopathological characteristics, including survival data, were determined. PD‐L1 was found on both tumour cells of eCCA (8/69, 11.6%) and tumour‐associated macrophages (21/69, 30.4%). Significant correlations of PD‐L1 expression on cancer cells with venous invasion (P = 0.031) and poor differentiation of the tumour (P = 0.048) were observed. In 19 of 69 (27.5%) samples, tumour‐infiltrating lymphocytes (TILs) expressed PD‐1, whereas infiltration with CD3‐positive and CD163‐positive cells was found in 63 of 69 (91.3%) and 68 of 69 (98.6%) cases, respectively. The presence of fewer than five CD3‐positive cells per high‐power field was significantly correlated with poorer differentiation (P = 0.015) and venous invasion (P < 0.001) of CCA. PD‐L1 expression was not correlated with patient survival, but PD‐L1 expression on tumour cells combined with low infiltration of CD3‐positive TILs was associated with an unfavourable outcome (P = 0.027).ConclusionOnly a small number of eCCA patients are PD‐L1‐positive, which might be important for future application of PD‐1/PD‐L1‐targeted immune‐modulating therapy in these patients. A small subgroup of eCCAs with PD‐L1 expression and low lymphocytic infiltration showed more invasive growth and worse overall survival.