bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell Culture Isolation of Piscine Nodavirus (Betanodavirus) in Fish-Rearing Seawater
Authors: Nishi Shinnosuke , Yamashita Hirofumi , Kawato Yasuhiko , Nakai Toshihiro 
Published: February 2016

ABSTRACT

Piscine nodavirus (betanodavirus) is the causative agent of viral nervous necrosis (VNN) in a variety of cultured fish species, particularly marine fish. In the present study, we developed a sensitive method for cell culture isolation of the virus from seawater and applied the method to a spontaneous fish-rearing environment. The virus in seawater was concentrated by an iron-based flocculation method and subjected to isolation with E-11 cells. A real-time reverse transcriptase PCR (RT-PCR) assay was used to quantify the virus in water. After spiking into seawater was performed, a betanodavirus strain (redspotted grouper nervous necrosis virus [RGNNV] genotype) was effectively recovered in the E-11 cells at a detection limit of approximately 10
5
copies (equivalent to 10
2
50% tissue culture infective doses [TCID
50
])/liter seawater. In an experimental infection of juvenile sevenband grouper (
Epinephelus septemfasciatus
) with the virus, the virus was isolated from the drainage of a fish-rearing tank when the virus level in water was at least approximately 10
5
copies/liter. The application of this method to sevenband grouper-rearing floating net pens, where VNN prevailed, resulted in the successful isolation of the virus from seawater. No differences were found in the partial sequences of the coat protein gene (
RNA2
) between the clinical virus isolates of dead fish and the cell-cultured virus isolates from seawater, and the viruses were identified as RGNNV. The infection experiment showed that the virus isolates from seawater were virulent to sevenband grouper. These results showed direct evidence of the horizontal transmission of betanodavirus via rearing water in marine aquaculture.
Dominant Tree Species and Soil Type Affect the Fungal Community Structure in a Boreal Peatland Forest
Authors: Sun Hui , Terhonen Eeva , Kovalchuk Andriy , Tuovila Hanna , Chen Hongxin , Oghenekaro Abbot O. , Heinonsalo Jussi , Kohler Annegret , Kasanen Risto , Vasander Harri , Asiegbu Fred O. 
Published: February 2016

ABSTRACT

Boreal peatlands play a crucial role in global carbon cycling, acting as an important carbon reservoir. However, little information is available on how peatland microbial communities are influenced by natural variability or human-induced disturbances. In this study, we have investigated the fungal diversity and community structure of both the organic soil layer and buried wood in boreal forest soils using high-throughput sequencing of the internal transcribed spacer (ITS) region. We have also compared the fungal communities during the primary colonization of wood with those of the surrounding soils. A permutational multivariate analysis of variance (PERMANOVA) confirmed that the community composition significantly differed between soil types (
P
< 0.001) and tree species (
P
< 0.001). The distance-based linear models analysis showed that environmental variables were significantly correlated with community structure (
P
< 0.04). The availability of soil nutrients (Ca [
P
= 0.002], Fe [
P
= 0.003], and P [
P
= 0.003]) within the site was an important factor in the fungal community composition. The species richness in wood was significantly lower than in the corresponding soil (
P
< 0.004). The results of the molecular identification were supplemented by fruiting body surveys. Seven of the genera of
Agaricomycotina
identified in our surveys were among the top 20 genera observed in pyrosequencing data. Our study is the first, to our knowledge, fungal high-throughput next-generation sequencing study performed on peatlands; it further provides a baseline for the investigation of the dynamics of the fungal community in the boreal peatlands.
Diversity, Productivity, and Stability of an Industrial Microbial Ecosystem
Authors: Beyter Doruk , Tang Pei-Zhong , Becker Scott , Hoang Tony , Bilgin Damla , Lim Yan Wei , Peterson Todd C. , Mayfield Stephen , Haerizadeh Farzad , Shurin Jonathan B. , Bafna Vineet , McBride Robert 
Published: February 2016

ABSTRACT
Managing ecosystems to maintain biodiversity may be one approach to ensuring their dynamic stability, productivity, and delivery of vital services. The applicability of this approach to industrial ecosystems that harness the metabolic activities of microbes has been proposed but has never been tested at relevant scales. We used a tag-sequencing approach with bacterial small subunit rRNA (16S) genes and eukaryotic internal transcribed spacer 2 (ITS2) to measuring the taxonomic composition and diversity of bacteria and eukaryotes in an open pond managed for bioenergy production by microalgae over a year. Periods of high eukaryotic diversity were associated with high and more-stable biomass productivity. In addition, bacterial diversity and eukaryotic diversity were inversely correlated over time, possibly due to their opposite responses to temperature. The results indicate that maintaining diverse communities may be essential to engineering stable and productive bioenergy ecosystems using microorganisms.
Lactococcus lactis LMG2081 Produces Two Bacteriocins, a Nonlantibiotic and a Novel Lantibiotic
Authors: Mirkovic Nemanja , Polovic Natalija , Vukotic Goran , Jovcic Branko , Miljkovic Marija , Radulovic Zorica , Diep Dzung B. , Kojic Milan 
Published: February 2016

ABSTRACT

Bacteriocin producers normally possess dedicated immunity systems to protect themselves from their own bacteriocins.
Lactococcus lactis
strains LMG2081 and BGBM50 are known as lactococcin G producers. However, BGBM50 was sensitive to LMG2081, which indicated that LMG2081 might produce additional bacteriocins that are not present in BGBM50. Therefore, whole-genome sequencing of the two strains was performed, and a lantibiotic operon (called
lctLMG
) was identified in LMG2081 but not in BGBM50. The
lctLMG
operon contains six open reading frames; the first three genes,
lmgA
,
lmgM
, and
lmgT
, are involved in the biosynthesis and export of bacteriocin, while the other three genes,
lmgF
,
lmgE
, and
lmgG
, are involved in lantibiotic immunity. Mutational analysis confirmed that the
lctLMG
operon is responsible for the additional antimicrobial activity. Specifically, site-directed mutation within this operon rendered LMG2081 inactive toward BGBM50. Subsequent purification and electrospray ionization–time of flight mass spectrometric analysis confirmed that the lantibiotic bacteriocin called lacticin LMG is exported as a 25-amino-acid peptide. Lacticin LMG is highly similar to the lacticin 481 group. It is interesting that a bacteriocin producer produces two different classes of bacteriocins, whose operons are located in the chromosome and a plasmid.
Electroacupuncture Improves Memory and Protects Neurons by Regulation of the Autophagy Pathway in a Rat Model of Alzheimer—s Disease
Authors: Guo Hai-dong , Zhu Jing , Tian Jin-xin , Shao Shui-jin , Xu Yan-wu , Mou Fang-fang , Han Xiao-jing , Yu Zhi-hua , Chen Jiu-lin , Zhang Da-yong , Zhang Li-sheng , Cui Guo-hong 
Published: February 2016

Background Acupuncture is a potential therapy for Alzheimer's disease (AD), but its clinical effects and underlying mechanisms are not fully understood. Emerging evidence suggests autophagy is involved in β-amyloid (Aβ) clearance. We hypothesised that electroacupuncture (EA) treatment of AD involves the autophagy pathway in rats. Methods We injected 2μl Aβ1–40 bilaterally into the hippocampi of 42 rats to establish AD. Rats remained untreated (AD group, n=14) or received 24 EA treatments at GV20+BL23 over 28 days from day 7 post-injection with/without co-treatment with 3-methyladenine (3-MA), an autophagy inhibitor (AD+EA+3-MA and AD+EA groups, respectively, n=14 each). Cognitive function was evaluated by Morris water maze (MWM) testing. Hippocampi were examined by transmission electron microscopy (TEM) and stained with haematoxylin and eosin/transferase dUTP nick end labelling (TUNEL) to assess neuronal morphology/apoptosis, respectively. Protein expression of Beclin-1, LC3 and Aβ1-40 was examined. Results In the MWM test, the AD+EA group showed an improvement in parameters consistent with improved learning/memory compared to untreated AD rats, and 3-MA attenuated these effects. EA mitigated cellular apoptosis resulting from Aβ infusion in the CA1 region and enhanced LC3II/LC3I ratios and Beclin-1 expression. Numerous autophagosome precursors and enlarged autophagosomes were observed by TEM in the hippocampi of EA-treated rats. Reduced Aβ levels, and co-localisation of Aβ and LC3II, were observed following EA treatment by immunofluorescence staining. EA+3-MA treated rats had much higher TUNEL-positive neurons, lower LC3II/LC3I ratios and Beclin-1 expression, and elevated Aβ levels compared with EA alone. Conclusions EA reduces neuronal apoptosis, enhances degradation of Aβ, and improves learning/memory in AD rats by upregulating the autophagy pathway.
Understanding quit decisions in primary care: a qualitative study of older GPs
Authors: Sansom Anna , Calitri Raff , Carter Mary , Campbell John 
Published: February 2016

ObjectiveTo investigate the reasons behind intentions to quit direct patient care among experienced general practitioners (GPs) aged 50–60 years.Design and settingQualitative study based on semistructured interviews with GPs in the South West region of England. Transcribed interviews were analysed thematically.Participants23 GPs aged 50–60 years: 3 who had retired from direct patient care before age 60, and 20 who intended to quit direct patient care within the next 5 years.ResultsThe analysis identified four key themes: early retirement is a viable option for many GPs; GPs have employment options other than undertaking direct patient care; GPs report feeling they are doing an (almost) undoable job; and GPs may have other aspirations that pull them away from practice. Findings from this study confirmed those from earlier research, with high workload, ageing and health, family and domestic life, and organisational change all influencing GPs’ decisions about when to retire/quit direct patient care. However, in addition, GPs expressed feelings of insecurity and uncertainty regarding the future of general practice, low morale, and issues regarding accountability (appraisal and revalidation) and governance. Suggestions about how to help retain GPs within the active clinical workforce were offered, covering individual, practice and organisational levels.ConclusionsThis research highlights aspects of the current professional climate for GPs that are having an impact on retirement decisions. Any future changes to policy or practice to help retain experienced GPs will benefit from this informed understanding of GPs’ views. Key factors to take into account include: making the GP workload more manageable; managing change sympathetically; paying attention to GPs’ own health; improving confidence in the future of general practice; and improving GP morale.
Reservoir characterization using electrofacies analysis in the sandstone reservoir of the Norne Field (offshore Norway)
Authors: Correia Gil G. , Schiozer Denis J. 
Published: February 2016

The Norne Field reservoir sandstone comprises Early–Middle Jurassic interbedded sandstones and shales to massive sandstones with some thin continuous cemented interlayers. A detailed characterization of the geological heterogeneities through electrofacies analysis, together with the simulation grid refinement, has been used to derive representative facies and petrophysical models (porosity, net-to-gross (NtG) and permeability).
An electrofacies database was created comprising six rock types, ranging from cemented carbonates through shales and into clean sandstones. In the absence of available cored sections, the electrofacies scheme was validated by the geological and petrophysical reports of 26 wells using gamma-ray, neutron and density logs. An artificial neural network algorithm enabled the probabilistic discrimination of the different types of electrofacies, with a sampling rate of 0.125 m. This high-resolution electrofacies database, together with a high-resolution geomodel grid, enabled us to map the fine-scale heterogeneities mainly materialized by decimetre shales and cemented layers that could represent stratigraphic barriers to vertical fluid displacement.
The high-resolution datasets created in this study will form the working basis on which to perform a probabilistic and multi-objective history matching guided by production and 4D seismic data, and assisted by geostatistical parameterization techniques.
IFNγ and CCL2 Cooperate to Redirect Tumor-Infiltrating Monocytes to Degrade Fibrosis and Enhance Chemotherapy Efficacy in Pancreatic Carcinoma
Authors: Long Kristen B. , Gladney Whitney L. , Tooker Graham M. , Graham Kathleen , Fraietta Joseph A. , Beatty Gregory L. 
Published: February 2016

Abstract
Dense fibrosis and a robust macrophage infiltrate are key therapeutic barriers in pancreatic ductal adenocarcinoma (PDAC). CD40 activation can circumvent these barriers by inducing macrophages, originating from peripheral blood monocytes, to deplete fibrosis. The precise mechanism and therapeutic implications of this antifibrotic activity, though, remain unclear. Here, we report that IFNγ and CCL2 released systemically in response to a CD40 agonist cooperate to redirect a subset of Ly6C+CCR2+ monocytes/macrophages to infiltrate tumors and deplete fibrosis. Whereas CCL2 is required for Ly6C+ monocyte/macrophage infiltration, IFNγ is necessary for tumor-infiltrating monocytes/macrophages to shift the profile of matrix metalloproteinases (MMP) in tumors, leading to MMP-dependent fibrosis degradation. In addition, MMP13-dependent loss of extracellular matrix components induced by a CD40 agonist increased PDAC sensitivity to chemotherapy. Our findings demonstrate that fibrosis in PDAC is a bidirectional process that can be rapidly altered by manipulating a subset of tumor-infiltrating monocytes, leading to enhanced chemotherapy efficacy.
Significance: We report that CD40 agonists improve chemotherapy efficacy in pancreatic carcinoma by redirecting tumor-infiltrating monocytes/macrophages to induce fibrosis degradation that is dependent on MMPs. These findings provide novel insight into the plasticity of monocytes/macrophages in cancer and their capacity to regulate fibrosis and modulate chemotherapy efficacy in pancreatic carcinoma. Cancer Discov; 6(4); 400–13. ©2016 AACR.
This article is highlighted in the In This Issue feature, p. 331
Inhibition of Soluble Tumor Necrosis Factor Prevents Chemically Induced Carcinogenesis in Mice
Authors: Sobo-Vujanovic Andrea , Vujanovic Lazar , DeLeo Albert B. , Concha-Benavente Fernando , Ferris Robert L. , Lin Yan , Vujanovic Nikola L. 
Published: February 2016

AbstractTNF is a potent promoter of carcinogenesis and potentially important target for cancer prevention. TNF is produced as functionally distinct transmembrane and soluble molecules (tmTNF and sTNF, respectively), but their individual roles in carcinogenesis are unexplored. We investigated the participation of tmTNF and sTNF in chemically induced carcinogenesis in mice. We found that injection of XPro1595, a dominant-negative TNF biologic (DN-TNF) and specific antagonist of sTNF, decreased tumor incidence and growth, and prolonged survival of 3-methylcholanthrene (MCA)–injected mice. Similar results were obtained following the exclusion of both TNF forms by either TNF-receptor 2–Fc fusion protein (TNFR2-Fc) treatment or TNF gene deletion. In addition, gene deletion of TNFR1, which is preferentially triggered by sTNF, was temporarily blocked, whereas gene deletion of TNFR2, which is preferentially triggered by tmTNF, enhanced MCA-induced carcinogenesis. Concomitantly with carcinogenesis induction, MCA increased circulating IL1α, accumulation of myeloid-derived suppressor cells (MDSC), STAT3 phosphorylation, and immunosuppression in the spleen. In sharp contrast, DN-TNF treatment dramatically decreased IL1α and increased the essential immunoregulatory cytokines IL1β, IL12p70, and IL17 in the peripheral blood of MCA-injected mice. In addition, MDSC accumulation, STAT3 phosphorylation, and immunosuppression in MCA-injected mice were prevented by DN-TNF treatment, TNFR2-Fc treatment, and/or gene deletion of TNF or TNFR1, but not deletion of TNFR2. These findings reveal that sTNF is both an essential promoter of carcinogenesis and a pivotal regulator of MDSCs, and indicate that sTNF could be a significant target for cancer prevention and therapy. Cancer Immunol Res; 4(5); 441–51. ©2016 AACR.
Systematic Characterization of Long Noncoding RNAs Reveals the Contrasting Coordination of
Cis
- and
Trans
-Molecular Regulation in Human Fetal and Adult Hearts
Authors: He Chunjiang , Hu Hanyang , Wilson Kitchener D. , Wu Haodi , Feng Jing , Xia Siyu , Churko Jared , Qu Kun , Chang Howard Y. , Wu Joseph C. 
Published: February 2016

Background—

The molecular regulation of heart development is regulated by
cis
- and
trans
-factors acting on the genome and epigenome. As a class of important regulatory RNAs, the role of long noncoding RNAs (lncRNAs) in human heart development is still poorly understood. Furthermore, factors that interact with lncRNAs in this process are not well characterized.

Methods and Results—
Using RNA sequencing, we systematically define the contrasting lncRNA expression patterns between fetal and adult hearts. We report that lncRNAs upregulated in adult versus fetal heart have different sequence features and distributions. For example, the adult heart expresses more sense lncRNAs compared with fetal heart. We also report the coexpression of lncRNAs and neighboring coding genes that have important functions in heart development. Importantly, the regulation of lncRNA expression during fetal to adult heart development seems to be due, in part, to the coordination of specific developmental epigenetic modifications, such as H3K4me1 and H3k4me3. The expression of promoter-associated lncRNAs in adult and fetal hearts also seems to be related to these epigenetic states. Finally, transcription factor–binding analysis suggests that lncRNAs are directly regulating cardiac gene expression during development.

Conclusions—
We provide a systematic analysis of lncRNA control of heart development that gives clues to the roles that specific lncRNAs play in fetal and adult hearts.
Sex Differences in Cardiovascular Disease Risk of Ghanaian‐ and Nigerian‐Born West African Immigrants in the United States: The Afro‐Cardiac Study
Authors: Commodore‐Mensah Yvonne , Hill Martha , Allen Jerilyn , Cooper Lisa A. , Blumenthal Roger , Agyemang Charles , Himmelfarb Cheryl Dennison 
Published: February 2016

Background

The number of African immigrants in the United States grew 40‐fold between 1960 and 2007, from 35 355 to 1.4 million, with a large majority from West Africa. This study sought to examine the prevalence of cardiovascular disease (
CVD
) risk factors and global
CVD
risk and to identify independent predictors of increased
CVD
risk among West African immigrants in the United States.

Methods and Results

This cross‐sectional study assessed West African (Ghanaian and Nigerian) immigrants aged 35–74 years in the Baltimore–Washington metropolitan area. The mean age of participants was 49.5±9.2 years, and 58% were female. The majority (95%) had ≥1 of the 6
CVD
risk factors. Smoking was least prevalent, and overweight or obesity was most prevalent, with 88% having a body mass index (in kg/m
2
) ≥25; 16% had a prior diagnosis of diabetes or had fasting blood glucose levels ≥126 mg/
dL
. In addition, 44% were physically inactive. Among women, employment and health insurance were associated with odds of 0.09 (95%
CI
0.033–0.29) and 0.25 (95%
CI
0.09–0.67), respectively, of having a Pooled Cohort Equations estimate ≥7.5% in the multivariable logistic regression analysis. Among men, higher social support was associated with 0.90 (95%
CI
0.83–0.98) lower odds of having ≥3
CVD
risk factors but not with having a Pooled Cohort Equations estimate ≥7.5%.

Conclusions

The prevalence of
CVD
risk factors among West African immigrants was particularly high. Being employed and having health insurance were associated with lower
CVD
risk in women, but only higher social support was associated with lower
CVD
risk in men.
Tetrahydrobiopterin Supplementation Improves Endothelial Function But Does Not Alter Aortic Stiffness in Patients With Rheumatoid Arthritis
Authors: Mäki‐Petäjä Kaisa M. , Day Lisa , Cheriyan Joseph , Hall Frances C. , Östör Andrew J. K. , Shenker Nicholas , Wilkinson Ian B. 
Published: February 2016

Background

Rheumatoid arthritis is a systemic inflammatory condition associated with increased cardiovascular risk that may be due to underlying endothelial dysfunction and subsequent aortic stiffening. We hypothesized that supplementation with tetrahydrobiopterin (
BH
4
) would recouple endothelial nitric oxide synthase and thus improve endothelial function and consequently reduce aortic stiffness.

Methods and Results

We conducted 2 randomized, double‐blinded, placebo‐controlled crossover studies examining 2 separate regimens: an acute regimen, with a single dose of
BH
4
400 mg versus placebo (n=18), and a short‐term regimen, composed of a 1‐week treatment with
BH
4
400 mg once daily versus placebo (n=15). Flow‐mediated dilatation and aortic pulse wave velocity were studied 4 times, before and after each treatment phase. Acute
BH
4
supplementation led to an improvement of flow‐mediated dilatation, whereas placebo had no effect (mean±
SD
of effect difference 2.56±4.79%;
P
=0.03). Similarly, 1‐week treatment with
BH
4
improved endothelial function, but there was no change with placebo (mean±
SD
of effect difference 3.50±5.05%;
P
=0.02). There was no change in aortic pulse wave velocity following acute or short‐term
BH
4
supplementation or placebo (mean±
SD
of effect difference: acute 0.09±0.67 m/s,
P
=0.6; short‐term 0.03±1.46 m/s,
P
=0.9).

Conclusion

Both acute and short‐term supplementation with oral
BH
4
improved endothelial function but not aortic stiffness. This result suggests that
BH
4
supplementation may be beneficial for patients with rheumatoid arthritis by improving endothelial dysfunction and potentially reducing risk of cardiovascular disease. There appears to be no causal relationship between endothelial function and aortic stiffness, suggesting that they occur in parallel, although they may share common risk factors such as inflammation.
Spatial and temporal distribution of bats (Chiroptera) in bright summer nights
Authors: Michaelsen Tore Christian 
Published: February 2016

Most bat species show plasticity in their choice of habitat and landscape. This study focuses on the distribution and activity of bats along the hillsides and onto the shores of a low salinity marine Norwegian fiord at 62°N. Ultrasound was recorded using D500 detectors in June and July at 42 different sites from the shoreline and up the hillsides to around 200 m. Detectors were placed in well-preserved woodlands. Only Pipistrellus sp., northern bats Eptesicus nilssonii and bats of the Myotis genus were common. There was a clear non-linear spatial distribution pattern along these slopes, with a pronounced increase in the number of recorded bats at short distances from the shore. On all six nights, the detector closest to the shore had the highest number of recorded bats. A pattern was also seen in bat distribution over time. Pipistrellus sp., northern bats and Myotis species all had a peak near the shore during the darkest part of the night, which is around 01.35 h in mid-summer at this latitude. At greater distances, Pipistrellus sp. and northern bats had a peak around 40 minutes to one hour before the darkest part of the night, respectively. Here, Myotis spp. peaked about an hour after 01.35.