bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phenotypic and Genotypic Description of Sedimenticola selenatireducens Strain CUZ, a Marine (Per)Chlorate-Respiring Gammaproteobacterium, and Its Close Relative the Chlorate-Respiring Sedimenticola Strain NSS
Authors: Carlström Charlotte I. , Loutey Dana E. , Wang Ouwei , Engelbrektson Anna , Clark Iain , Lucas Lauren N. , Somasekhar Pranav Y. , Coates John D. 
Published: February 2015

ABSTRACT

Two (per)chlorate-reducing bacteria, strains CUZ and NSS, were isolated from marine sediments in Berkeley and San Diego, CA, respectively. Strain CUZ respired both perchlorate and chlorate [collectively designated (per)chlorate], while strain NSS respired only chlorate. Phylogenetic analysis classified both strains as close relatives of the gammaproteobacterium
Sedimenticola selenatireducens
. Transmission electron microscopy (TEM) and scanning electron microscopy (SEM) preparations showed the presence of rod-shaped, motile cells containing one polar flagellum. Optimum growth for strain CUZ was observed at 25 to 30°C, pH 7, and 4% NaCl, while strain NSS grew optimally at 37 to 42°C, pH 7.5 to 8, and 1.5 to 2.5% NaCl. Both strains oxidized hydrogen, sulfide, various organic acids, and aromatics, such as benzoate and phenylacetate, as electron donors coupled to oxygen, nitrate, and (per)chlorate or chlorate as electron acceptors. The draft genome of strain CUZ carried the requisite (per)chlorate reduction island (PRI) for (per)chlorate respiration, while that of strain NSS carried the composite chlorate reduction transposon responsible for chlorate metabolism. The PRI of strain CUZ encoded a perchlorate reductase (Pcr), which reduced both perchlorate and chlorate, while the genome of strain NSS included a gene for a distinct chlorate reductase (Clr) that reduced only chlorate. When both (per)chlorate and nitrate were present, (per)chlorate was preferentially utilized if the inoculum was pregrown on (per)chlorate. Historically, (per)chlorate-reducing bacteria (PRB) and chlorate-reducing bacteria (CRB) have been isolated primarily from freshwater, mesophilic environments. This study describes the isolation and characterization of two highly related marine halophiles, one a PRB and the other a CRB, and thus broadens the known phylogenetic and physiological diversity of these unusual metabolisms.
Cyanobacterial Blue Color Formation during Lysis under Natural Conditions
Authors: Arii Suzue , Tsuji Kiyomi , Tomita Koji , Hasegawa Masateru , Bober Beata , Harada Ken-Ichi 
Published: February 2015

ABSTRACT

Cyanobacteria produce numerous volatile organic compounds (VOCs), such as β-cyclocitral, geosmin, and 2-methylisoborneol, which show lytic activity against cyanobacteria. Among these compounds, only β-cyclocitral causes a characteristic color change from green to blue (blue color formation) in the culture broth during the lysis process. In August 2008 and September 2010, the lysis of cyanobacteria involving blue color formation was observed at Lake Tsukui in northern Kanagawa Prefecture, Japan. We collected lake water containing the cyanobacteria and investigated the VOCs, such as β-cyclocitral, β-ionone, 1-propanol, 3-methyl-1-butanol, and 2-phenylethanol, as well as the number of cyanobacterial cells and their damage and pH changes. As a result, the following results were confirmed: the detection of several VOCs, including β-cyclocitral and its oxidation product, 2,2,6-trimethylcyclohexene-1-carboxylic acid; the identification of phycocyanin based on its visible spectrum; the lower pH (6.7 and 5.4) of the lysed samples; and characteristic morphological change in the damaged cyanobacterial cells. We also encountered the same phenomenon on 6 September 2013 in Lake Sagami in northern Kanagawa Prefecture and obtained almost the same results, such as blue color formation, decreasing pH, damaged cells, and detection of VOCs, including the oxidation products of β-cyclocitral. β-Cyclocitral derived from
Microcystis
has lytic activity against
Microcystis
itself but has stronger inhibitory activity against other cyanobacteria and algae, suggesting that the VOCs play an important role in the ecology of aquatic environments.
Evidence of the Internalization of Animal Caliciviruses via the Roots of Growing Strawberry Plants and Dissemination to the Fruit
Authors: DiCaprio Erin , Culbertson Doug , Li Jianrong 
Published: February 2015

ABSTRACT

Human norovirus (NoV) is the leading cause of foodborne disease in the United States, and epidemiological studies have shown that fresh produce is one of the major vehicles for the transmission of human NoV. However, the mechanisms of norovirus contamination and persistence in fresh produce are poorly understood. The objective of this study is to determine whether human NoV surrogates, murine norovirus (MNV-1) and Tulane virus (TV), can attach and become internalized and disseminated in strawberries grown in soil. The soil of growing strawberry plants was inoculated with MNV-1 and TV at a level of 10
8
PFU/plant. Leaves and berries were harvested over a 14-day period, and the viral titer was determined by plaque assay. Over the course of the study, 31.6% of the strawberries contained internalized MNV-1, with an average titer of 0.81 ± 0.33 log
10
PFU/g. In comparison, 37.5% of strawberries were positive for infectious TV, with an average titer of 1.83 ± 0.22 log
10
PFU/g. A higher percentage (78.7%) of strawberries were positive for TV RNA, with an average titer of 3.15 ± 0.51 log
10
RNA copies/g as determined by real-time reverse transcriptase quantitative PCR (RT-qPCR). In contrast, no or little virus internalization and dissemination were detected when TV was inoculated into bell peppers grown in soil. Collectively, these data demonstrate (i) virally contaminated soils can lead to the internalization of virus via plant roots and subsequent dissemination to the leaf and fruit portions of growing strawberry plants and (ii) the magnitude of internalization is dependent on the type of virus and plant.
Metatranscriptomic Evidence for Co-Occurring Top-Down and Bottom-Up Controls on Toxic Cyanobacterial Communities
Authors: Steffen Morgan M. , Belisle B. Shafer , Watson Sue B. , Boyer Gregory L. , Bourbonniere Richard A. , Wilhelm Steven W. 
Published: February 2015

ABSTRACT

Little is known about the molecular and physiological function of co-occurring microbes within freshwater cyanobacterial harmful algal blooms (cHABs). To address this, community metatranscriptomes collected from the western basin of Lake Erie during August 2012 were examined. Using sequence data, we tested the hypothesis that the activity of the microbial community members is independent of community structure. Predicted metabolic and physiological functional profiles from spatially distinct metatranscriptomes were determined to be ≥90% similar between sites. Targeted analysis of
Microcystis aeruginosa
, the historical causative agent of cyanobacterial harmful algal blooms over the past ∼20 years, as well as analysis of
Planktothrix agardhii
and
Anabaena cylindrica
, revealed ongoing transcription of genes involved in microcystin toxin synthesis as well as the acquisition of both nitrogen and phosphorus, nutrients often implicated as independent bottom-up drivers of eutrophication in aquatic systems. Transcription of genes involved in carbon dioxide (CO
2
) concentration and metabolism also provided support for the alternate hypothesis that high-pH conditions and dense algal biomass result in CO
2
-limiting conditions that further favor cyanobacterial dominance. Additionally, the presence of
Microcystis
-specific cyanophage sequences provided preliminary evidence of possible top-down virus-mediated control of cHAB populations. Overall, these data provide insight into the complex series of constraints associated with
Microcystis
blooms that dominate the western basin of Lake Erie during summer months, demonstrating that multiple environmental factors work to shape the microbial community.
Host Erythrocyte Environment Influences the Localization of Exported Protein 2, an Essential Component of the Plasmodium Translocon
Authors: Meibalan Elamaran , Comunale Mary Ann , Lopez Ana M. , Bergman Lawrence W. , Mehta Anand , Vaidya Akhil B. , Burns James M. 
Published: February 2015

ABSTRACT

Malaria parasites replicating inside red blood cells (RBCs) export a large subset of proteins into the erythrocyte cytoplasm to facilitate parasite growth and survival. PTEX, the parasite-encoded translocon, mediates protein transport across the parasitophorous vacuolar membrane (PVM) in
Plasmodium falciparum
-infected erythrocytes. Proteins exported into the erythrocyte cytoplasm have been localized to membranous structures, such as Maurer's clefts, small vesicles, and a tubovesicular network. Comparable studies of protein trafficking in
Plasmodium vivax
-infected reticulocytes are limited. With
Plasmodium yoelii
-infected reticulocytes, we identified exported protein 2 (Exp2) in a proteomic screen of proteins putatively transported across the PVM. Immunofluorescence studies showed that
P. yoelii
Exp2 (
Py
Exp2) was primarily localized to the PVM. Unexpectedly,
Py
Exp2 was also associated with distinct, membrane-bound vesicles in the reticulocyte cytoplasm. This is in contrast to
P. falciparum
in mature RBCs, where
P. falciparum
Exp2 (
Pf
Exp2) is exclusively localized to the PVM. Two
P. yoelii
-exported proteins, PY04481 (encoded by a
pyst-a
gene) and PY06203 (
Py
pAg-1), partially colocalized with these
Py
Exp2-positive vesicles. Further analysis revealed that with
P. yoelii
,
Plasmodium berghei
, and
P. falciparum
, cytoplasmic Exp2-positive vesicles were primarily observed in CD71
+
reticulocytes versus mature RBCs. In transgenic
P. yoelii
17X parasites, the association of hemagglutinin-tagged
Py
Exp2 with the PVM and cytoplasmic vesicles was retained, but the
pyexp2
gene was refractory to deletion. These data suggest that the localization of Exp2 in mouse and human RBCs can be influenced by the host cell environment. Exp2 may function at multiple points in the pathway by which parasites traffic proteins into and through the reticulocyte cytoplasm.
Pretreatment lymphocyte–monocyte ratio as a potential prognostic factor in a cohort of patients with upper tract urothelial carcinoma
Authors: Hutterer Georg C , Sobolev N , Ehrlich Georg C , Gutschi Thomas , Stojakovic Tatjana , Mannweiler Sebastian , Pummer Karl , Zigeuner Richard , Pichler Martin , Dalpiaz Orietta 
Published: February 2015

AimsTo investigate the potential prognostic impact of the lymphocyte–monocyte ratio (LMR) in a large European cohort of patients with localised upper urinary tract urothelial carcinoma (UTUC). The LMR as an indicator of systemic inflammatory response has been shown to represent a potential prognostic factor in various types of human cancers. Up to date, the prognostic significance of the LMR in UTUC has not been evaluated.MethodsClinico-pathological data from 182 non-metastatic patients with UTUC, operated between 1990 and 2012 at a single tertiary academic centre, were evaluated retrospectively. Pretreatment LMR was assessed 1 day before surgery. Patients were categorised using an LMR cut-off value of 2.0 according to a calculation by receiver-operating curve analysis. Patients’ overall survival (OS) was assessed using the Kaplan–Meier method. To evaluate the independent prognostic significance of the LMR, a multivariate proportional Cox regression model was applied for OS.ResultsIn multivariate analyses, age on the date of surgery (<65 vs ≥65 years, HR=2.10, 95% CI 1.22 to 3.64), pathological T-stage (pT1 vs pT2–4, HR=2.15, 95% CI 1.26 to 3.67), as well as the LMR (<2 vs ≥2, HR=0.56, 95% CI 0.35 to 0.92) were independent predictors of OS of patients with UTUC.ConclusionsIn the cohort studied, patients with an elevated (≥2) preoperative LMR had a subsequently longer OS after radical surgery for UTUC, compared with those with a low (<2) preoperative LMR. Thus, we believe this parameter might be considered an additional prognostic factor in UTUC in the future.
Underuse of an invasive strategy for patients with diabetes with acute coronary syndrome: a nationwide study
Authors: Gustafsson Ida , Hvelplund Anders , Hansen Kim Wadt , Galatius Søren , Madsen Mette , Jensen Jan Skov , Tilsted Hans-Henrik , Terkelsen Christian Juhl , Jensen Lisette Okkels , Jørgensen Erik , Madsen Jan Kyst , Abildstrøm Steen Zabell 
Published: February 2015

BackgroundGuidelines recommend an early invasive strategy for patients with diabetes with acute coronary syndromes (ACS). We investigated if patients with diabetes with ACS are offered coronary angiography (CAG) and revascularisation to the same extent as patients without diabetes.Methods and resultsThe study is a nationwide cohort study linking Danish national registries containing information on healthcare. The study population comprises all patients hospitalised with first-time ACS in Denmark during 2005–2007 (N=24 952). Diabetes was defined as claiming of a prescription for insulin and/or oral hypoglycaemic agents within 6 months prior to the ACS event. Diabetes was present in 2813 (11%) patients. Compared with patients without diabetes, patients with diabetes were older (mean 69 vs 67 years, p<0.0001), less often males (60% vs 64%, p=0.0001) and had more comorbidity. Fewer patients with diabetes underwent CAG: cumulative incidence 64% vs 74% for patients without diabetes, HR=0.72 (95% CI 0.69 to 0.76, p<0.0001); adjusted for age, sex, previous revascularisation and comorbidity HR=0.78 (95% CI 0.74 to 0.82, p<0.0001). More patients with diabetes had CAG showing two-vessel or three-vessel disease (53% vs 38%, p<0.0001). However, revascularisation after CAG revealing multivessel disease was less likely in patients with diabetes (multivariable adjusted HR=0.76, 95% CI 0.68 to 0.85, p<0.0001).ConclusionsIn this nationwide cohort of patients with incident ACS, patients with diabetes were found to be less aggressively managed by an invasive treatment strategy. The factors underlying the decision to defer an invasive strategy in patients with diabetes are unclear and merit further investigation.
Evaluation and management of hypersensitivity reactions to chemotherapy agents
Authors: Tham Elizabeth Huiwen , Cheng Yew Kuang , Tay Miah Hiang , Alcasabas Ana Patricia , Shek Lynette Pei-Chi 
Published: February 2015

ABSTRACT
Hypersensitivity reactions to chemotherapy drugs pose significant difficulties in management, especially when no suitable alternative is available or acceptable and delay in continuation of treatment may be life-threatening. Such reactions may be IgE- or non-IgE-mediated and have varied manifestations. Timely recognition and treatment of life-threatening hypersensitivity reactions are essential. Identification of patients at high risk of developing hypersensitivity reactions allows risk stratification to guide clinical decision-making. Skin testing for carboplatin hypersensitivity has good predictive value but is not yet established for oxaliplatin and taxane hypersensitivity. Rapid desensitisation may be considered if no suitable alternative drug is available. Available protocols have shown good safety and efficacy but must be performed in an appropriate setting with adequate monitoring. There are many avenues for research into the utility of skin testing for other chemotherapy agents as well as in vitro tests.
Stratigraphic relations of Santorini’s intracaldera fill and implications for the rate of post-caldera volcanism
Authors: Johnston E. N. , Sparks R. S. J. , Nomikou P. , Livanos I. , Carey S. , Phillips J. C. , Sigurdsson H. 
Published: February 2015

We propose a new volcanological interpretation of Santorini’s intracaldera fill deposits as revealed by seismic reflection profiles. This interpretation, along with supplementary gravity and geophysical studies, reveals three distinct volcaniclastic units (1–3). From top to bottom these units are attributed to (1) modern infilling sediment, (2) shallow marine phreatomagmatic volcanism associated with the relatively recent formation of the Kameni Islands, and (3) downfaulted ‘Minoan’ pyroclastic deposits, which formed during caldera collapse towards the end of the Bronze Age eruption. Estimates of the volumes of the seismic units and Kameni Islands yield a dense rock equivalent magma volume of 4.85 ± 0.7 km
3
. The average rate of volcanism over the past
c
. 3641 years is estimated at 1.3 ×10
−3
km
3
a
−1
, and is similar to the rate since the AD 1707 eruption of 1.2 ×10
−3
km
3
a
−1
based on historical lava volume estimates.
Sedimentology and magnetic susceptibility of recent sediments from New Caledonia
Authors: Jadot Hélène , Boulvain Frédéric 
Published: February 2015

Abstract
The interpretation of the primary origin of the minerals carrying the magnetic susceptibility (MS) signal from ancient rocks suffers notably from the scarcity of studies on Recent sediments. To bring new data, a study of tropical coastal sediments of New Caledonia was undertaken. This island is surrounded by a nearly uninterrupted reef barrier, isolating a wide lagoon from the open ocean. The erosion of extremely varied rocks (from mantle rocks to laterites) produces different types of detrital sediments, which are mixed with the indigenous precipitated carbonates. This generates different types of coastal sediments, detrital- or carbonate-dominated or mixed. More than 300 samples were analysed for grain size, nature of sediment, MS and geochemistry (major elements). The first results show that: (a) carbonate sands and carbonate silts are characterized by lower MS than detrital sediments; (b) the MS signal of mixed sediments is mostly influenced by the proportion of detrital sediments; (c) MS is directly correlated with Mn and Fe content; (d) beachrocks are characterized by lower MS than equivalent loose sediment; (e) the MS signal of carbonate sediments is locally positively correlated with granulometry; (f) there is no MS change between surface and 20 cm deep samples; and (g) when the subsurface sediment is reducing, the MS is higher than that from surface sediment.
Forcing factors of the magnetic susceptibility signal in lagoonal and subtidal depositional cycles from the Zachełmie section (Eifelian, Holy Cross Mountains, Poland)
Authors: Grabowski J. , Narkiewicz M. , De Vleeschouwer D. 
Published: February 2015

Abstract

Eifelian dolomites in the Zachełmie Quarry exhibit metre-scale depositional cyclicity, both in the lower, lagoonal part of the section and in the upper, shallow subtidal portion. Magnetic properties were studied in 30 samples (at
c.
1 m intervals), including magnetic susceptibility (MS) and anhysteretic and isothermal remanent magnetization. The rock magnetic parameters are compared with the results of thin-section study and elemental chemistry. The forcing factors driving the MS pattern are identified. The MS signal is mostly related to a finely dispersed hematite, controlled by terrigenous input. Magnetite plays a subordinate role and it is confined to less terrigenous horizons relatively enriched in uranium and phosphorus. Results of high-resolution (
c.
8 cm intervals) MS field measurements show a good correlation with depositional shallowing-upwards cycles, especially in the lagoonal part of the section, where variations of rock magnetic properties and geochemical (redox and productivity) indices are very small. High MS values occur in the bottom part of the cycles and they decrease upwards. Time-series analyses of the MS signal reveal the dominance of
c.
1.7 m cycles, grouped into
c.
10 m bundles. The former cycles probably reflect precession-driven changes in monsoonal intensity, whereas the latter may have been controlled by 100 kyr eccentricity.
Tectonic and magmatic segmentation of the Global Ocean Ridge System: a synthesis of observations
Authors: Carbotte Suzanne M. , Smith Deborah K. , Cannat Mathilde , Klein Emily M. 
Published: February 2015

Abstract
Mid-ocean ridges display tectonic segmentation defined by discontinuities of the axial zone, and geophysical and geochemical observations suggest segmentation of the underlying magmatic plumbing system. Here, observations of tectonic and magmatic segmentation at ridges spreading from fast to ultraslow rates are reviewed in light of influential concepts of ridge segmentation, including the notion of hierarchical segmentation, spreading cells and centralized v. multiple supply of mantle melts. The observations support the concept of quasi-regularly spaced principal magmatic segments, which are 30–50 km long on average at fast- to slow-spreading ridges and fed by melt accumulations in the shallow asthenosphere. Changes in ridge properties approaching or crossing transform faults are often comparable with those observed at smaller offsets, and even very small discontinuities can be major boundaries in ridge properties. Thus, hierarchical segmentation models that suggest large-scale transform fault-bounded segmentation arises from deeper level processes in the asthenosphere than the finer-scale segmentation are not generally supported. The boundaries between some but not all principal magmatic segments defined by ridge axis geophysical properties coincide with geochemical boundaries reflecting changes in source composition or melting processes. Where geochemical boundaries occur, they can coincide with discontinuities of a wide range of scales.
A method for characterizing basement rocks from borehole images
Authors: Murray Ann 
Published: February 2015

Abstract

Basement rocks tend to have negligible primary (rock matrix) porosity and, where present, almost all porosity is fracture-related. An insight into fracture type and distribution is therefore of importance when attempting to predict potential flow zones in hydrocarbon reservoirs. In the absence of core, borehole images provide a proven means of characterizing fractures within basement rocks. This paper will concentrate upon the classification and characterization of basement structural elements, including fractures, faults and breccias, versus lithological elements, such as foliations and intrusion boundaries from borehole images. In addition, suggestions of how to differentiate present-day
in-situ
stress indicators from natural fractures will be made as these features may provide important information regarding open fracture set orientations. Examples of microresistivity and acoustic borehole images acquired in fractured igneous basement rocks from oil wells in Yemen will be presented together with a suggested methodology for their interpretation. The discussion will be based on hydrocarbon reservoirs; however, the methodology outlined can potentially have wider applications in, for example, groundwater pollution prevention schemes or groundwater extraction, radioactive waste disposal, geothermal energy resources and deep-drilling research programmes.