bluuebunny/crossref_metadata_2025_split huggingface dataset:
Benjamin’s gravity current into an ambient fluid with an open surface
Authors: Ungarish Marius 
Published: July 2017

We present the solution of the idealized steady-state gravity current of height $h$ and density $\unicode[STIX]{x1D70C}_{1}$ that propagates into an ambient motionless fluid of height $H$ and density $\unicode[STIX]{x1D70C}_{2}$ with an upper surface open to the atmosphere (open channel) at high Reynolds number. The current propagates with speed $U$ and causes a depth decrease $\unicode[STIX]{x1D712}$ of the top surface. This is a significant extension of Benjamin’s (J. Fluid Mech., vol. 31, 1968, pp. 209–248) seminal solution for a fixed-top channel ($\unicode[STIX]{x1D712}=0$). In the present case, the determination of $\unicode[STIX]{x1D712}$ is part of the problem. The dimensionless parameters of the problem are $a=h/H$ and $r=\unicode[STIX]{x1D70C}_{2}/\unicode[STIX]{x1D70C}_{1}$. We show that a control-volume analysis determines $\tilde{\unicode[STIX]{x1D712}}=\unicode[STIX]{x1D712}/H$ and $\mathit{Fr}=U/(g^{\prime }h)^{1/2}$ as functions of $a$ and $r$, where $g^{\prime }=(r^{-1}-1)g$ is the reduced gravity. The system satisfies balance of volume and momentum (explicitly), and vorticity (implicitly). We develop two branches (models) of solution for the control-volume balances. The first assumes that the outflow velocity $u_{2}$ is $z$-independent, accompanied by a similarly homogeneous headloss; this model is exactly the counterpart of Benjamin’s solution ($z$ is the vertical coordinate). The second model assumes that $u_{2}$ increases from $0$ in a layer of finite thickness $\unicode[STIX]{x1D702}$ (say) above the $z=h$ interface, and the headloss occurs in this layer only (a vortex wake). The $\mathit{Fr},\tilde{\unicode[STIX]{x1D712}}$ results of these models are in excellent agreement, and this increases the confidence concerning the physical relevance of the analysis. (The solution is obtained numerically.) The predicted flows are in general dissipative, and thus physically energetically valid only for $a\leqslant a_{max}(r)\approx 0.5r$, where non-negative dissipation appears. In this range of validity, the open-surface $\mathit{Fr}(a,r)$ is smaller than Benjamin’s $\mathit{Fr}_{b}(a)$, but the reduction is not dramatic, typically a few per cent. The current with thickness $h=a_{max}H$ is energy conserving. For given $r$, the energy conserving $a_{max}(r)$ provides the maximum height depression $\tilde{\unicode[STIX]{x1D712}}_{max}(r)\approx 0.45r^{1/4}(1-r)$. The largest possible depression is $\tilde{\unicode[STIX]{x1D712}}_{max}\approx 0.25$ at $r\approx 0.20$, and this corresponds to the minimum of $\mathit{Fr}(a,r)/\mathit{Fr}_{b}(a)$ which is approximately 0.75. For $r<0.68$, the propagation is subcritical; for $r>0.68$, the subcritical flow condition reduces the applicability slightly to $a\leqslant a_{\mathit{crit}}\approx 0.345$. For a Boussinesq system with $r\approx 1$, we obtain $\tilde{\unicode[STIX]{x1D712}}\ll 1$, and the present $\mathit{Fr}$, dissipation and $a_{\mathit{crit}}$ results differ only slightly from Benjamin’s classical predictions, as expected.
Increased serum ferritin levels are independently associated with carotid atherosclerosis in women
Authors: Xu Haiyan , Song Yanqi , Xu Jing , Gu Yeqing , Zhang Qing , Liu Li , Meng Ge , Wu Hongmei , Xia Yang , Bao Xue , Shi Hongbin , Su Qian , Fang Liyun , Yu Fei , Yang Huijun , Sun Shaomei , Wang Xing , Zhou Ming , Jia Qiyu , Wang Guolin , Song Kun , Wu Yuntang , Sun Zhong , Niu Kaijun 
Published: July 2017

AbstractPrevious studies have supported the theory that there is a positive association between ferritin and carotid atherosclerosis in Western people. Diet plays an important role in determining serum ferritin concentration. Asian dietary patterns are different from Western dietary patterns, implying that there may be a difference in the association of ferritin with carotid atherosclerosis between Asian and Western people. However, few studies focus on the association between ferritin and carotid atherosclerosis among Asians. The aim of this study was to investigate how serum ferritin levels are associated with carotid atherosclerosis in an Asian adult population. A cross-sectional assessment was performed in 8302 adults in Tianjin, China. Carotid intima-media thickness (IMT) and plaques were assessed using ultrasonography, and serum ferritin was measured using the protein chip-chemiluminescence method. Multiple logistic regression analysis was used to examine the association between quartiles of serum ferritin concentration and carotid atherosclerosis. In the present study, the overall prevalence of IMT and carotid plaques in participants is 29·2 and 22·7 %, respectively. In women, after adjustments for potentially confounding factors, the OR of IMT and carotid plaques by increasing serum ferritin quartiles were 1·00, 1·39 (95 % CI 0·98–1·99), 1·39 (95 % CI 0·99–1·97), 1·81 (95 % CI 1·30–2·55) (Pfor trend<0·001) and 1·00, 1·24 (95 % CI 0·89–1·73), 1·18 (95 % CI 0·85–1·65), 1·59 (95 % CI 1·15–2·20) (Pfor trend<0·01), respectively. However, no association was found between serum ferritin and carotid atherosclerosis in men. The study demonstrated that increased serum ferritin levels are independently associated with IMT and carotid plaques in Asian women but not in Asian men.
Supplementation with Lactobacillus paracasei or Pediococcus pentosaceus does not prevent diarrhoea in neonatal pigs infected with Escherichia coli F18
Authors: Andersen Anders D. , Cilieborg Malene S. , Lauridsen Charlotte , Mørkbak Anne Louise , Sangild Per Torp 
Published: July 2017

AbstractInfectious diarrhoea is a worldwide problem in newborns. Optimal bacterial colonisation may enhance gut maturation and protect against pathogenic bacteria after birth. We hypothesised that lactic acid bacteria (LAB) administration prevents pathogen-induced diarrhoea in formula-fed newborns. Newborn caesarean-delivered, colostrum-deprived term piglets on parenteral nutrition for the first 15 h, were used as models for sensitive newborn infants. A commercially available probiotic strain, Lactobacillus paracasei F19 (LAP, 2·6×108 colony-forming units (CFU)/kg per d) and a novel LAB isolate, Pediococcus pentosaceus (PEP, 1·3×1010 CFU/kg per d), were administered for 5 d with or without inoculation of the porcine pathogen, Escherichia coli F18 (F18, 1010 CFU/d). This resulted in six treatment groups: Controls (n 9), LAP (n 10), PEP (n 10), F18 (n 10), F18–LAP (n 10) and F18–PEP (n 10). The pathogen challenge increased diarrhoea and density of F18 in the intestinal mucosa (P<0·05). LAB supplementation further increased the diarrhoea score, relative to F18 alone (P<0·01). Intestinal structure and permeability were similar among groups, whereas brush border enzymes were affected in variable intestinal regions with decreased activities in most cases after F18 and LAB inoculation. Bacterial density in colon mucosa increased after F18 inoculation (P<0·05) but was unaffected by LAB supplementation. In colon contents, acetic and butyric acids were increased by PEP (P<0·05). The LAB used in this study failed to reduce E. coli-induced diarrhoea in sensitive newborn pigs. In vulnerable newborns there may be a delicate balance among bacterial composition and load, diet and the host. Caution may be required when administering LAB to compromised newborns suffering from enteric infections.
Transferrin saturation concentrations associated with telomeric ageing: a population-based study
Authors: Shin Chol , Baik Inkyung 
Published: July 2017

AbstractThere are limited data on the association between Fe overload and leucocyte telomere length (LTL), known as a useful biomarker of the replicative ageing of cells. The aim of the study was to evaluate associations between Fe-status biomarkers and LTL. A cross-sectional study included 1174 men and women aged 50–79 years who provided blood samples for assays of Fe-status biomarkers including ferritin, transferrin saturation (TSAT), total Fe-binding capacity (TIBC) and relative LTL. They were free of hepatitis, potential infection or Fe deficiency. In multiple linear regression analysis adjusted for potential confounding variables, log-transformed LTL was positively associated with TIBC (adjusted coefficient estimate for its highest quartile: 0·17 (se 0·03), P<0·001) and inversely associated with TSAT (adjusted coefficient estimate for its third and fourth quartiles: −0·09 (se 0·03), P<0·01). These associations were consistent after additional adjustment for serum concentrations of high-sensitivity C-reactive protein, alanine transaminase and aspartate transaminase. In particular, participants with not only abnormally high concentrations (>45 %) but also with high-normal concentrations (35–45 %) of TSAT had shorter LTL compared with those with low-normal concentrations (<30 %) (P<0·05). We also observed that less-active or obese persons with high TSAT concentrations had shorter LTL than others. Our findings that cellular ageing is influenced not only by Fe overload but also by high-normal concentrations of TSAT support the hypothesis regarding the detrimental effects of labile Fe, which has a potent pro-oxidant activity in the body.
Erratum: Regulation of infection efficiency in a globally abundant marine Bacteriodetes virus
Authors: Howard-Varona Cristina , Roux Simon , Dore Hugo , Solonenko Natalie E , Holmfeldt Karin , Markillie Lye M , Orr Galya , Sullivan Matthew B 
Published: July 2017

Abstract
Correction to: The ISME Journal (2017) 11, 284–295; doi:10.1038/ismej.2016.81 In the title of the article, ‘Bacteriodetes’ is misspelled. The proper spelling is ‘Bacteroidetes’.
Silk micrococoons for protein stabilisation and molecular encapsulation
Authors: Shimanovich Ulyana , Ruggeri Francesco S. , De Genst Erwin , Adamcik Jozef , Barros Teresa P. , Porter David , Müller Thomas , Mezzenga Raffaele , Dobson Christopher M. , Vollrath Fritz , Holland Chris , Knowles Tuomas P. J. 
Published: July 2017

AbstractNaturally spun silks generate fibres with unique properties, including strength, elasticity and biocompatibility. Here we describe a microfluidics-based strategy to spin liquid native silk, obtained directly from the silk gland of Bombyx mori silkworms, into micron-scale capsules with controllable geometry and variable levels of intermolecular β-sheet content in their protein shells. We demonstrate that such micrococoons can store internally the otherwise highly unstable liquid native silk for several months and without apparent effect on its functionality. We further demonstrate that these native silk micrococoons enable the effective encapsulation, storage and release of other aggregation-prone proteins, such as functional antibodies. These results show that native silk micrococoons are capable of preserving the full activity of sensitive cargo proteins that can aggregate and lose function under conditions of bulk storage, and thus represent an attractive class of materials for the storage and release of active biomolecules.
Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells
Authors: Byrne Ashley , Beaudin Anna E. , Olsen Hugh E. , Jain Miten , Cole Charles , Palmer Theron , DuBois Rebecca M. , Forsberg E. Camilla , Akeson Mark , Vollmers Christopher 
Published: July 2017

AbstractUnderstanding gene regulation and function requires a genome-wide method capable of capturing both gene expression levels and isoform diversity at the single-cell level. Short-read RNAseq is limited in its ability to resolve complex isoforms because it fails to sequence full-length cDNA copies of RNA molecules. Here, we investigate whether RNAseq using the long-read single-molecule Oxford Nanopore MinION sequencer is able to identify and quantify complex isoforms without sacrificing accurate gene expression quantification. After benchmarking our approach, we analyse individual murine B1a cells using a custom multiplexing strategy. We identify thousands of unannotated transcription start and end sites, as well as hundreds of alternative splicing events in these B1a cells. We also identify hundreds of genes expressed across B1a cells that display multiple complex isoforms, including several B cell-specific surface receptors. Our results show that we can identify and quantify complex isoforms at the single cell level.
A shape-shifting redox foldase contributes to Proteus mirabilis copper resistance
Authors: Furlong Emily J. , Lo Alvin W. , Kurth Fabian , Premkumar Lakshmanane , Totsika Makrina , Achard Maud E. S. , Halili Maria A. , Heras Begoña , Whitten Andrew E. , Choudhury Hassanul G. , Schembri Mark A. , Martin Jennifer L. 
Published: July 2017

AbstractCopper resistance is a key virulence trait of the uropathogen Proteus mirabilis. Here we show that P. mirabilis ScsC (PmScsC) contributes to this defence mechanism by enabling swarming in the presence of copper. We also demonstrate that PmScsC is a thioredoxin-like disulfide isomerase but, unlike other characterized proteins in this family, it is trimeric. PmScsC trimerization and its active site cysteine are required for wild-type swarming activity in the presence of copper. Moreover, PmScsC exhibits unprecedented motion as a consequence of a shape-shifting motif linking the catalytic and trimerization domains. The linker accesses strand, loop and helical conformations enabling the sampling of an enormous folding landscape by the catalytic domains. Mutation of the shape-shifting motif abolishes disulfide isomerase activity, as does removal of the trimerization domain, showing that both features are essential to foldase function. More broadly, the shape-shifter peptide has the potential for ‘plug and play’ application in protein engineering.
Accumulating the hydride state in the catalytic cycle of [FeFe]-hydrogenases
Authors: Winkler Martin , Senger Moritz , Duan Jifu , Esselborn Julian , Wittkamp Florian , Hofmann Eckhard , Apfel Ulf-Peter , Stripp Sven Timo , Happe Thomas 
Published: July 2017

AbstractH2 turnover at the [FeFe]-hydrogenase cofactor (H-cluster) is assumed to follow a reversible heterolytic mechanism, first yielding a proton and a hydrido-species which again is double-oxidized to release another proton. Three of the four presumed catalytic intermediates (Hox, Hred/Hred and Hsred) were characterized, using various spectroscopic techniques. However, in catalytically active enzyme, the state containing the hydrido-species, which is eponymous for the proposed heterolytic mechanism, has yet only been speculated about. We use different strategies to trap and spectroscopically characterize this transient hydride state (Hhyd) for three wild-type [FeFe]-hydrogenases. Applying a novel set-up for real-time attenuated total-reflection Fourier-transform infrared spectroscopy, we monitor compositional changes in the state-specific infrared signatures of [FeFe]-hydrogenases, varying buffer pH and gas composition. We selectively enrich the equilibrium concentration of Hhyd, applying Le Chatelier’s principle by simultaneously increasing substrate and product concentrations (H2/H+). Site-directed manipulation, targeting either the proton-transfer pathway or the adt ligand, significantly enhances Hhyd accumulation independent of pH.
Validation of the XDP–MDSP rating scale for the evaluation of patients with X-linked dystonia-parkinsonism
Authors: Pasco Paul Matthew D. , Jamora Roland Dominic G. , Rosales Raymond L. , Diesta Cid Czarina E. , Ng Arlene R. , Teleg Rosalia A. , Go Criscely L. , Lee Lillian , Fernandez Hubert H. 
Published: July 2017

AbstractX-linked dystonia-parkinsonism(XDP) is a neurodegenerative disorder endemic to the Philippines. A rating scale was developed by the authors under the guidance of the Movement Disorder Society of the Philippines (MDSP) to assess XDP severity and progression, functional impact, and response to treatment in future clinical trials. Our main objective was to validate our new scale, the XDP–MDSP scale. The initial validation process included pragmatic testing to XDP patients followed by a modified Delphi procedure with an international advisory panel of dystonia, parkinsonism and scale development experts. Pearson correlation was used to assess construct validity of our new scale versus the assess construct validity of our new scale versus standard dystonia, parkinsonism, non-motor and functional scales; and also to assess divergent validity against behavioral and cognitive scales. The 37-item XDP–MDSP scale has five parts: I-dystonia, II-parkinsonism, III-non-motor features, IV-ADL, and V-global impression. After initial validation, the scale was administered to 204 XDP patients. Inter-domain correlation for the first four parts was acceptable. The correlation between these domains and the global rating was slightly lower. Correlations between Parts I, II, III, and IV versus standard dystonia, parkinsonism, non-motor and functional scales were acceptable with values ranging from 0.323 to 0.428. For divergent validity, a significant correlation was seen with behavioral scales. No significant correlation was noted with the cognitive scale. The proposed XDP–MDSP scale is internally valid but the global rating subscale may need to be modified or eliminated. While there is convergent validity, divergent validation was successful only on cognitive and not behavioral scales. The frequent co-occurrence of anxiety and depression, and its effect on the motor and functional state, may explain this finding.
Identification of the ESKAPE pathogens by mass spectrometric analysis of microbial membrane glycolipids
Authors: Leung Lisa M. , Fondrie William E. , Doi Yohei , Johnson J. Kristie , Strickland Dudley K. , Ernst Robert K. , Goodlett David R. 
Published: July 2017

AbstractRapid diagnostics that enable identification of infectious agents improve patient outcomes, antimicrobial stewardship, and length of hospital stay. Current methods for pathogen detection in the clinical laboratory include biological culture, nucleic acid amplification, ribosomal protein characterization, and genome sequencing. Pathogen identification from single colonies by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analysis of high abundance proteins is gaining popularity in clinical laboratories. Here, we present a novel and complementary approach that utilizes essential microbial glycolipids as chemical fingerprints for identification of individual bacterial species. Gram-positive and negative bacterial glycolipids were extracted using a single optimized protocol. Extracts of the clinically significant ESKAPE pathogens: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. were analyzed by MALDI-TOF-MS in negative ion mode to obtain glycolipid mass spectra. A library of glycolipid mass spectra from 50 microbial entries was developed that allowed bacterial speciation of the ESKAPE pathogens, as well as identification of pathogens directly from blood bottles without culture on solid medium and determination of antimicrobial peptide resistance. These results demonstrate that bacterial glycolipid mass spectra represent chemical barcodes that identify pathogens, potentially providing a useful alternative to existing diagnostics.
Transcriptomes and expression profiling of deep-sea corals from the Red Sea provide insight into the biology of azooxanthellate corals
Authors: Yum Lauren K. , Baumgarten Sebastian , Röthig Till , Roder Cornelia , Roik Anna , Michell Craig , Voolstra Christian R. 
Published: July 2017

AbstractDespite the importance of deep-sea corals, our current understanding of their ecology and evolution is limited due to difficulties in sampling and studying deep-sea environments. Moreover, a recent re-evaluation of habitat limitations has been suggested after characterization of deep-sea corals in the Red Sea, where they live at temperatures of above 20 °C at low oxygen concentrations. To gain further insight into the biology of deep-sea corals, we produced reference transcriptomes and studied gene expression of three deep-sea coral species from the Red Sea, i.e.Dendrophylliasp.,Eguchipsammia fistula, andRhizotrochus typus. Our analyses suggest that deep-sea coral employ mitochondrial hypometabolism and anaerobic glycolysis to manage low oxygen conditions present in the Red Sea. Notably, we found expression of genes related to surface cilia motion that presumably enhance small particle transport rates in the oligotrophic deep-sea environment. This is the first study to characterize transcriptomes andin situgene expression for deep-sea corals. Our work offers several mechanisms by which deep-sea corals might cope with the distinct environmental conditions present in the Red Sea As such, our data provide direction for future research and further insight to organismal response of deep-sea coral to environmental change and ocean warming.
Multiplication rate variation in the human malaria parasite Plasmodium falciparum
Authors: Murray Lee , Stewart Lindsay B. , Tarr Sarah J. , Ahouidi Ambroise D. , Diakite Mahamadou , Amambua-Ngwa Alfred , Conway David J. 
Published: July 2017

AbstractIt is important to understand intrinsic variation in asexual blood stage multiplication rates of the most virulent human malaria parasite, Plasmodium falciparum. Here, multiplication rates of long-term laboratory adapted parasite clones and new clinical isolates were measured, using a newly standardised assay of growth from low starting density in replicate parallel cultures with erythrocytes from multiple different donors, across multiple cycles. Multiplication rates of long-term established clones were between 7.6 and 10.5 fold per 48 hours, with clone Dd2 having a higher rate than others (clones 3D7, HB3 and D10). Parasite clone-specific growth was then analysed in co-culture assays with all possible heterologous pairwise combinations. This showed that co-culture of different parasites did not affect their replication rates, indicating that there were no suppressive interactions operating between parasites. Multiplication rates of eleven new clinical isolates were measured after a few weeks of culture, and showed a spectrum of replication rates between 2.3 and 6.0 fold per 48 hours, the entire range being lower than for the long-term laboratory adapted clones. Multiplication rate estimates remained stable over time for several isolates tested repeatedly up to three months after culture initiation, indicating considerable persistence of this important trait variation.
Analysis of somatic mutations across the kinome reveals loss-of-function mutations in multiple cancer types
Authors: Kumar Runjun D. , Bose Ron 
Published: July 2017

AbstractIn this study we use somatic cancer mutations to identify important functional residues within sets of related genes. We focus on protein kinases, a superfamily of phosphotransferases that share homologous sequences and structural motifs and have many connections to cancer. We develop several statistical tests for identifying Significantly Mutated Positions (SMPs), which are positions in an alignment with mutations that show signs of selection. We apply our methods to 21,917 mutations that map to the alignment of human kinases and identify 23 SMPs. SMPs occur throughout the alignment, with many in the important A-loop region, and others spread between the N and C lobes of the kinase domain. Since mutations are pooled across the superfamily, these positions may be important to many protein kinases. We select eleven mutations from these positions for functional validation. All eleven mutations cause a reduction or loss of function in the affected kinase. The tested mutations are from four genes, including two tumor suppressors (TGFBR1 and CHEK2) and two oncogenes (KDR and ERBB2). They also represent multiple cancer types, and include both recurrent and non-recurrent events. Many of these mutations warrant further investigation as potential cancer drivers.