bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metal nanoparticle induced hormetic activation: a novel mechanism of homeopathic medicines
Authors: Chikramane Prashant S. , Suresh Akkihebbal K. , Kane Shantaram G. , Bellare Jayesh R. 
Published: July 2017

Background: High-potency homeopathic remedies, 30c and 200c have enormous dilution factors of 1060 and 10400 respectively. Therefore, the presence of physical entities in them is inconceivable. As a result, their efficacy is highly debated and often dismissed as a placebo. Despite several hypotheses postulated to explain the claimed homeopathic efficacy, none have satisfactorily answered the qualms of the sceptics. Against all beliefs and principles of conventional dilution, we have shown that nanoparticles (NPs) of the starting metals are unequivocally found in the 30c and 200c remedies at concentrations of a few pg/ml. In this paper, our aim was to answer the important question of whether such negligible metal concentrations elicit a biological response.Methods: Metal-based homeopathic medicines (30c and 200c) were analysed at doses between 0.003%v/v and 10%v/v in in-vitro HepG2 cell-line. Upon treatment, cell response was estimated by MTT assay, FACS and total intracellular protein. Experiments were performed to discern whether the hormesis was a cell-activation or a proliferation effect.Results: Remedies at doses containing a few femtograms/ml levels of the starting metals induced a proliferation-independent hormetic activation by increasing the intracellular protein synthesis. The metal concentrations (at fg/ml) were a billion-fold lower than the studies with synthetic NPs (at μg/ml). Further, we also highlight a few plausible mechanisms initiating a hormetic response at a billion-fold lower dose.Conclusions: Hormetic activation has been shown for the first time with standard homeopathic high-potency remedies. These findings should have a profound effect in understanding these extreme dilutions from a biological perspective.
L-arginine Attenuates Hypobaric Hypoxia-Induced Increase in Ornithine Decarboxylase 1
Authors: Yuhong Li , Zhengzhong Bai , Feng Tang , Quanyu Yang , Ge Ri-Li 
Published: July 2017

Background Chronic hypoxia-induced pulmonary hypertension and vascular remodeling have been shown to be associated with ornithine decarboxylase 1 (ODC1). However, few animal studies have investigated the role of ODC1 in acute hypoxia. Objectives We investigated ODC1 gene expression, morphologic and functional changes, and the effect of L-arginine as an attenuator in lung tissues of rats exposed to acute hypobaric hypoxia at a simulated altitude of 6000 m. Methods Sprague-Dawley rats exposed to simulated hypobaric hypoxia (6000 m) for 24, 48, or 72 hours were treated with L-arginine (L-arginine group, 20 mg/100 g intraperitoneal; n=15) or untreated (non–L-arginine group, n=15). Control rats (n=5) were maintained at 2260 m in a normal environment for the same amount of time but were treated without L-arginine. The mean pulmonary artery pressure was measured by PowerLab system. The morphologic and immunohistochemical changes in lung tissue were observed under a microscope. The mRNA and protein levels of ODC1 were measured by real-time polymerase chain reaction and Western-blot, respectively. Results Hypobaric hypoxia induced pulmonary interstitial hyperemia and capillary expansion in the lungs of rats exposed to acute hypoxia at 6000 m. The mean pulmonary artery pressure and the mRNA and protein levels of ODC1 were significantly increased, which could be attenuated by treatment with L-arginine. Conclusions L-arginine attenuates acute hypobaric hypoxia-induced increase in mean pulmonary artery pressure and ODC1 gene expression in lung tissues of rats. ODC1 gene contributes to the development of hypoxic pulmonary hypertension.
Flow control with rotating cylinders
Authors: Schulmeister James C. , Dahl J. M. , Weymouth G. D. , Triantafyllou M. S. 
Published: July 2017

We study the use of small counter-rotating cylinders to control the streaming flow past a larger main cylinder for drag reduction. In a water tunnel experiment at a Reynolds number of 47 000 with a three-dimensional and turbulent wake, particle image velocimetry (PIV) measurements show that rotating cylinders narrow the mean wake and shorten the recirculation length. The drag of the main cylinder was measured to reduce by up to 45 %. To examine the physical mechanism of the flow control in detail, a series of two-dimensional numerical simulations at a Reynolds number equal to 500 were conducted. These simulations investigated a range of control cylinder diameters in addition to rotation rates and gaps to the main cylinder. Effectively controlled simulated flows present a streamline that separates from the main cylinder, passes around the control cylinder, and reattaches to the main cylinder at a higher pressure. The computed pressure recovery from the separation to reattachment points collapses with respect to a new scaling, which indicates that the control mechanism is viscous.
Turbulent thermal convection over rough plates with varying roughness geometries
Authors: Xie Yi-Chao , Xia Ke-Qing 
Published: July 2017

We present a systematic investigation of the effects of roughness geometry on turbulent Rayleigh–Bénard convection (RBC) over rough plates with pyramid-shaped and periodically distributed roughness elements. Using a parameter $\unicode[STIX]{x1D706}$ defined as the height of a roughness element over its base width, the heat transport, the flow dynamics and the local temperatures are measured for the Rayleigh number range $7.50\times 10^{7}\leqslant Ra\leqslant 1.31\times 10^{11}$ and Prandtl numbers $Pr$ from 3.57 to 23.34 at four values of $\unicode[STIX]{x1D706}$ (0.5, 1.0, 1.9 and 4.0). It is found that the heat transport scaling, i.e. $Nu\sim Ra^{\unicode[STIX]{x1D6FC}}$ where $Nu$ is the Nusselt number, may be classified into three regimes in turbulent RBC over rough plates. In Regime I, the system is in a dynamically smooth state. The heat transport scaling is the same as that in a smooth cell. In Regimes II and III, the heat transport is enhanced. When $\unicode[STIX]{x1D706}$ is increased from 0.5 to 4.0, $\unicode[STIX]{x1D6FC}$ increases from 0.36 to 0.59 in Regime II and it increases from 0.30 to 0.50 in Regime III. The experiment thus clearly demonstrates that the heat transport scaling in turbulent RBC can be manipulated using $\unicode[STIX]{x1D706}$ in the heat transport enhanced regime. Previous studies suggest that the transition to heat transport enhanced regime, i.e. from Regime I to Regime II, occurs when the thermal boundary layer (BL) thickness becomes smaller than the roughness height. Direct measurements of the viscous BL in the present study suggest that the transition from Regime II to Regime III is likely a result of the viscous BL thickness becoming smaller than the roughness height. The scaling exponent of the Reynolds number $Re$ with respect to $Ra$ changes from 0.471 to 0.551 when $\unicode[STIX]{x1D706}$ is increased from 0.5 to 4.0, suggesting a change of the dynamics of the large-scale circulation. Interestingly, the transition from Regime II to Regime III in terms of the heat transport scaling is not reflected in the $Re$ scaling with $Ra$. It is also found that increasing $\unicode[STIX]{x1D706}$ increases the clustering of thermal plumes which effectively increases the plume lifetime. This leads to a great increase in the probability of observing large temperature fluctuations in the bulk flow, which corresponds to the formation of more coherent plumes or plume clusters that are ultimately responsible for the enhanced heat transport.
A one-dimensional model for tidal array design based on three-scale dynamics
Authors: Gupta Vikrant , Young Anna M. 
Published: July 2017

In order to make the extraction of tidal current energy economically viable, the power production per turbine must be optimised in each tidal array. Furthermore, the impact of power extraction on the marine flow environment must be understood. These two aims mean that designers must be able to model different configurations of a tidal array in order to create the most efficient, least invasive arrangement. In this paper, an analytical model is developed for array design in idealised rectangular tidal channels with idealised turbines. The model includes the effects of (i) local blockage, (ii) surface deformation and (iii) added drag due to the installation of the array. While these effects have been accounted for individually in past work, the model presented here is the first to include all three such that the interaction between different effects can be understood. Results are presented for optimal local blockage and turbine resistance as functions of inherent channel drag coefficient, channel length and Froude number at various global blockage values. It will be shown that it is necessary to model the effects of local blockage and added drag simultaneously in order to obtain the design parameters of a tidal array (global blockage, local blockage and turbine resistance), which will maximise the power extraction per turbine. Neglecting either effect will lead to an array design with lower power extraction than the optimum, the addition of unnecessary extra turbines and higher lost power from the array.
Loud ethics and quiet morality among Muslim healers in Eastern Africa
Authors: Parkin David 
Published: July 2017

AbstractThe professional ethics of biomedicine in Eastern Africa are usually sharply distinguished from the everyday moral concerns of patients, who may interpret healthcare treatment differently from their doctors. Biomedical doctors’ pronouncements adhere to the ethical demands of formal training, while ordinary people form their own moral ideas about biomedicine, with the two discourses meeting only during medical-moral crises. The voice of biomedicine, therefore, is metaphorically loud compared with that of everyday talk. This hegemonic duality of biomedicine is less evident in traditional Islamic healing, where patients sometimes negotiate the moral implications of sickness with their healers, and where Islamic medical ethics may be transmitted to younger apprentices interpersonally through life histories and narrative. The differences in volume between healers’ and patients’ moral voices are thus less pronounced, though not absent. Nevertheless, both are subject to the higher authority of Islam, whose holy texts and clerics are the final arbiters of the symptoms, cause and consequences of sickness. It is speculated that the emerging power, influence and stronger voice of radical Wahhabism could create a hegemonic medical ethical duality based more strictly than at present on religiously prescribed practice.
Adult attachment and paranoia: an experimental investigation
Authors: Hutton Jane , Ellett Lyn , Berry Katherine 
Published: July 2017

AbstractAttachment theory may develop understanding of the occurrence and maintenance of persecutory delusions. This study investigates the role of dispositional attachment and contextually primed secure base attachment representations in the occurrence of paranoid thinking. Sixty participants were randomly allocated to one of three conditions: a secure attachment priming condition, a positive affect condition, or a neutral control condition. Following priming, all participants were exposed to a paranoia induction. State paranoia was measured at baseline and following the paranoia induction. Dispositional insecure attachment was associated with both trait and state paranoid thinking. Contrary to predictions, the secure attachment prime did not appear to buffer paranoid thinking and had a negative impact for participants with high levels of attachment anxiety, highlighting the potentially aversive effects of exposure to secure attachment material in those with existing insecure attachment styles.
RETRACTED ARTICLE: Inhibition of microRNA-214 promotes epithelial–mesenchymal transition process and induces interstitial cystitis in postmenopausal women by upregulating Mfn2
Authors: Lv Jian-Wei , Wen Wei , Jiang Chen , Fu Qi-Bo , Gu Yin-Jun , Lv Ting-Ting , Li Zhen-Dong , Xue Wei 
Published: July 2017

AbstractOur study aims to investigate the roles that microRNA-214 (miR-214) plays in the epithelial mesenchymal transition (EMT) process and the development of interstitial cystitis (IC) in postmenopausal women by targeting Mitofusin 2 (Mfn2). IC bladder tissues and adjacent normal bladder tissues were collected from postmenopausal women. Immunohistochemistry (IHC) staining was conducted. The target relationship between miR-214 and Mfn2 was determined by a dual luciferase reporter gene assay. Adipose-derived mesenchymal stem cells (ADMSCs) were extracted from postmenopausal rats and assigned to the blank, mimics, miR-214 inhibitors, mimics negative control (NC), inhibitors NC, Mfn2 siRNA, miR-214 inhibitors and Mfn2 siRNA groups. Exosomes secreted by transfected ADMSCs were instilled into the bladders of postmenopausal rats. The expression of miR-214 and Mfn2 mRNA and EMT markers was assessed by qRT-PCR and western blotting. It was confirmed that Mfn2 was the target gene of miR-214 in IC. Compared with the normal bladder tissues, miR-214 decreased, but Mfn2 increased in IC bladder tissues. Compared with the blank group, the expression of miR-214 and the expression levels of N-cadherin, Fibronectin, Twist1, Snail and Vimentin mRNA and protein increased, whereas the expression levels of Mfn2, E-cadherin and ZO-1 mRNA and protein decreased in the miR-214 mimics and Mfn2 groups. The expression of MiR-214 and the expression levels of N-cadherin, Fibronectin, Twist1, Snail and Vimentin mRNA and protein decreased, whereas the expression levels of Mfn2, E-cadherin and ZO-1 mRNA and protein increased in the miR-214 inhibitors group. Our findings indicate that the inhibition of miR-214 promotes the EMT process and contributes to bladder wall fibrosis by up-regulating Mfn2, thus leading to the occurrence of IC in postmenopausal women.
Novel chaperonins are prevalent in the virioplankton and demonstrate links to viral biology and ecology
Authors: Marine Rachel L , Nasko Daniel J , Wray Jeffrey , Polson Shawn W , Wommack K Eric 
Published: July 2017

Abstract
Chaperonins are protein-folding machinery found in all cellular life. Chaperonin genes have been documented within a few viruses, yet, surprisingly, analysis of metagenome sequence data indicated that chaperonin-carrying viruses are common and geographically widespread in marine ecosystems. Also unexpected was the discovery of viral chaperonin sequences related to thermosome proteins of archaea, indicating the presence of virioplankton populations infecting marine archaeal hosts. Virioplankton large subunit chaperonin sequences (GroELs) were divergent from bacterial sequences, indicating that viruses have carried this gene over long evolutionary time. Analysis of viral metagenome contigs indicated that: the order of large and small subunit genes was linked to the phylogeny of GroEL; both lytic and temperate phages may carry group I chaperonin genes; and viruses carrying a GroEL gene likely have large double-stranded DNA (dsDNA) genomes (&gt;70 kb). Given these connections, it is likely that chaperonins are critical to the biology and ecology of virioplankton populations that carry these genes. Moreover, these discoveries raise the intriguing possibility that viral chaperonins may more broadly alter the structure and function of viral and cellular proteins in infected host cells.
Marine archaeal dynamics and interactions with the microbial community over 5 years from surface to seafloor
Authors: Parada Alma E , Fuhrman Jed A 
Published: July 2017

Abstract
Marine archaea are critical contributors to global carbon and nitrogen redox cycles, but their temporal variability and microbial associations across the water column are poorly known. We evaluated seasonal variability of free living (0.2–1 μm size fraction) Thaumarchaea Marine Group I (MGI) and Euryarchaea Marine Group II (MGII) communities and their associations with the microbial community from surface to seafloor (890 m) over 5 years by 16S rRNA V4-V5 gene sequencing. MGI and MGII communities demonstrated distinct compositions at different depths, and seasonality at all depths. Microbial association networks at 150 m, 500 m and 890 m, revealed diverse assemblages of MGI (presumed ammonia oxidizers) and Nitrospina taxa (presumed dominant nitrite oxidizers, completing the nitrification process), suggesting distinct MGI-Nitrospina OTUs are responsible for nitrification at different depths and seasons, and depth- related and seasonal variability in nitrification could be affected by alternating MGI-Nitrospina assemblages. MGII taxa also showed distinct correlations to possibly heterotrophic bacteria, most commonly to members of Marine Group A, Chloroflexi, Marine Group B, and SAR86. Thus, both MGI and MGII likely have dynamic associations with bacteria based on similarities in activity or other interactions that select for distinct microbial assemblages over time. The importance of MGII taxa as members of the heterotrophic community previously reported for photic zone appears to apply throughout the water column.
Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation
Authors: Svartström Olov , Alneberg Johannes , Terrapon Nicolas , Lombard Vincent , de Bruijn Ino , Malmsten Jonas , Dalin Ann-Marie , EL Muller Emilie , Shah Pranjul , Wilmes Paul , Henrissat Bernard , Aspeborg Henrik , Andersson Anders F 
Published: July 2017

Abstract
The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to 11 prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall composition of the metagenome, with dominance of the phyla Bacteroidetes and Firmicutes. Unlike in other ruminants, Spirochaetes constituted a significant proportion of the community and our analyses indicate that the corresponding strains are primarily pectin digesters. Pectin-degrading genes were also common in MAGs of Ruminococcus, Fibrobacteres and Bacteroidetes and were overall overrepresented in the moose microbiome compared with other ruminants. Phylogenomic analyses revealed several clades within the Bacteriodetes without previously characterized genomes. Several of these MAGs encoded a large numbers of dockerins, a module usually associated with cellulosomes. The Bacteroidetes dockerins were often linked to CAZymes and sometimes encoded inside polysaccharide utilization loci, which has never been reported before. The almost 100 CAZyme-annotated genomes reconstructed in this study provide an in-depth view of an efficient lignocellulose-degrading microbiome and prospects for developing enzyme technology for biorefineries.
Uncultivated microbes in need of their own taxonomy
Authors: Konstantinidis Konstantinos T , Rosselló-Móra Ramon , Amann Rudolf 
Published: July 2017

Abstract
The great majority of microbial species remains uncultured, severely limiting their taxonomic characterization and thus communication among scientists. Although Candidatus was devised as a provisional category to classify uncultured taxa, it has not been widely accepted owing to technical limitations and lack of priority of Candidatus names in the official nomenclature. High-throughput sequencing provides the potential for data-rich taxonomic descriptions of uncultivated microbes, comparable in quality to those of cultured organisms. In order to fully realize this potential, standards and guidelines on how to perform these descriptions are needed. Here we aimed to outline these standards and draw the roadmap for a new genome-based taxonomy that, at least initially, would be parallel but highly convergent to the one in existence for isolates. In particular, we recommend the use of DNA genome sequences, recovered by population binning or single-cell techniques, as the basis for (i) identification and phylogenetic placement, (ii) bioinformatics-based functional and thus phenotypic predictions, as well as (iii) type material. We also recommend the implementation of an independent nomenclatural system for uncultivated taxa, following the same nomenclature rules as those for cultured Bacteria and Archaea but with its own list of validly published names. If widely adopted, this system will not only facilitate a comprehensive characterization of the ‘uncultivated majority’, but also provide a unified catalogue of validly published names, thereby avoiding synonyms and confusion. We also suggest that a committee of experts, supported by an international microbiological society, should be formed to govern the new classification system.
A genomic perspective on stoichiometric regulation of soil carbon cycling
Authors: Hartman Wyatt H , Ye Rongzhong , Horwath William R , Tringe Susannah G 
Published: July 2017

Abstract
Similar to plant growth, soil carbon (C) cycling is constrained by the availability of nitrogen (N) and phosphorus (P). We hypothesized that stoichiometric control over soil microbial C cycling may be shaped by functional guilds with distinct nutrient substrate preferences. Across a series of rice fields spanning 5–25% soil C (N:P from 1:12 to 1:70), C turnover was best correlated with P availability and increased with experimental N addition only in lower C (mineral) soils with N:P⩽16. Microbial community membership also varied with soil stoichiometry but not with N addition. Shotgun metagenome data revealed changes in community functions with increasing C turnover, including a shift from aromatic C to carbohydrate utilization accompanied by lower N uptake and P scavenging. Similar patterns of C, N and P acquisition, along with higher ribosomal RNA operon copy numbers, distinguished that microbial taxa positively correlated with C turnover. Considering such tradeoffs in genomic resource allocation patterns among taxa strengthened correlations between microbial community composition and C cycling, suggesting simplified guilds amenable to ecosystem modeling. Our results suggest that patterns of soil C turnover may reflect community-dependent metabolic shifts driven by resource allocation strategies, analogous to growth rate–stoichiometry coupling in animal and plant communities.