Descriptive oceanography during the Frontal Air‐Sea Interaction Experiment: Medium‐ to large‐scale variability

Medium‐ and large‐scale oceanographic variability in the Sargasso Sea is examined during the Frontal Air‐Sea Interaction Experiment (FASINEX), focusing primarily on processes that influence the formation of subtropical fronts. From Fall to Spring the mean meridional gradient of meridional Ekman transport in the Subtropical Convergence Zone (STCZ) enhances the meridional sea surface temperature (Ts) gradients between 26° and 32°N. In the presence of this enhanced mean gradient, baroclinic eddies with zonal wavelengths of ≈800 km and periods of ≈200 days exert the dominant influence on the formation of subtropical fronts at medium and large scales. These eddies generate westward propagating Ts anomaly features with the same dominant wavelengths and periods. They are confined between 26° and 32°N and have amplitudes that occasionally exceed ±1°C. Ts fronts tend to be found within bands ≈200 km wide that roughly follow the periphery of these anomaly features. Deformation in the horizontal eddy current field is primarily responsible for the existence of these frontal bands. The migration of the strong front originally bracketed by the FASINEX moored array was related to the westward propagation of the larger‐scale eddy/anomaly/frontal‐band pattern. The moored array was located within a warm‐anomaly feature during most of the experiment, which produced exceptionally warm conditions in the upper ocean. These anomalies are confined between 26° and 32°N, not only because the relatively large seasonal mean Tsy there allows horizontal eddy currents to force strong anomalies, but also because the baroclinic eddies with wavelengths of ≈800 km and periods of ≈200 days are confined to the STCZ. Large meridional variability exists in many properties of the eddy field, much of which can be traced to the influence of the Sargasso Sea mean current field on eddy variability

Effect of Homocysteine-Lowering Nutrients on Blood Lipids: Results from Four Randomised, Placebo-Controlled Studies in Healthy Humans

BACKGROUND: Betaine (trimethylglycine) lowers plasma homocysteine, a possible risk factor for cardiovascular disease. However, studies in renal patients and in obese individuals who are on a weight-loss diet suggest that betaine supplementation raises blood cholesterol; data in healthy individuals are lacking. Such an effect on cholesterol would counteract any favourable effect on homocysteine. We therefore investigated the effect of betaine, of its precursor choline in the form of phosphatidylcholine, and of the classical homocysteine-lowering vitamin folic acid on blood lipid concentrations in healthy humans. METHODS AND FINDINGS: We measured blood lipids in four placebo-controlled, randomised intervention studies that examined the effect of betaine (three studies, n = 151), folic acid (two studies, n = 75), and phosphatidylcholine (one study, n = 26) on plasma homocysteine concentrations. We combined blood lipid data from the individual studies and calculated a weighted mean change in blood lipid concentrations relative to placebo. Betaine supplementation (6 g/d) for 6 wk increased blood LDL cholesterol concentrations by 0.36 mmol/l (95% confidence interval: 0.25–0.46), and triacylglycerol concentrations by 0.14 mmol/l (0.04–0.23) relative to placebo. The ratio of total to HDL cholesterol increased by 0.23 (0.14–0.32). Concentrations of HDL cholesterol were not affected. Doses of betaine lower than 6 g/d also raised LDL cholesterol, but these changes were not statistically significant. Further, the effect of betaine on LDL cholesterol was already evident after 2 wk of intervention. Phosphatidylcholine supplementation (providing approximately 2.6 g/d of choline) for 2 wk increased triacylglycerol concentrations by 0.14 mmol/l (0.06–0.21), but did not affect cholesterol concentrations. Folic acid supplementation (0.8 mg/d) had no effect on lipid concentrations. CONCLUSIONS: Betaine supplementation increased blood LDL cholesterol and triacylglycerol concentrations in healthy humans, which agrees with the limited previous data. The adverse effects on blood lipids may undo the potential benefits for cardiovascular health of betaine supplementation through homocysteine lowering. In our study phosphatidylcholine supplementation slightly increased triacylglycerol concentrations in healthy humans. Previous studies of phosphatidylcholine and blood lipids showed no clear effect. Thus the effect of phosphatidylcholine supplementation on blood lipids remains inconclusive, but is probably not large. Folic acid supplementation does not seem to affect blood lipids and therefore remains the preferred treatment for lowering of blood homocysteine concentrations

Performance of the CMS Cathode Strip Chambers with Cosmic Rays

The Cathode Strip Chambers (CSCs) constitute the primary muon tracking device in the CMS endcaps. Their performance has been evaluated using data taken during a cosmic ray run in fall 2008. Measured noise levels are low, with the number of noisy channels well below 1%. Coordinate resolution was measured for all types of chambers, and fall in the range 47 microns to 243 microns. The efficiencies for local charged track triggers, for hit and for segments reconstruction were measured, and are above 99%. The timing resolution per layer is approximately 5 ns

I don't think general practice should be the front line: Experiences of general practitioners working with refugees in South Australia

Introduction Many refugees arrive in Australia with complex health needs. In South Australia (SA), providing initial health care to refugees is the responsibility of General Practitioners (GPs) in private practice. Their capacity to perform this work effectively for current newly arrived refugees is uncertain. The aim of this study was to document the challenges faced by GPs in private practice in SA when providing initial care to refugees and to discuss the implications of this for policy relating to optimising health care services for refugees. Methods Semi-structured interviews with twelve GPs in private practice and three Medical Directors of Divisions of General Practice. Using a template analysis approach the interviews were coded and analysed thematically. Results Multiple challenges providing care to refugees were found including those related to: (1) refugee health issues; (2) the GP-refugee interaction; and (3) the structure of general practice. The Divisions also reported challenges assisting GPs to provide effective care related to a lack of funding and awareness of which GPs required support. Although respondents suggested a number of ways that GPs could be assisted to provide better initial care to refugees, strong support was voiced for the initial care of refugees to be provided via a specialist refugee health service. Conclusion GPs in this study were under-resourced, at both an individual GP level as well as a structural level, to provide effective initial care for refugees. In SA, there are likely to be a number of challenges attempting to increase the capacity of GPs in private practice to provide initial care. An alternative model is for refugees with multiple and complex health care needs as well as those with significant resettlement challenges to receive initial health care via the existing specialist refugee health service in Adelaide.David R Johnson, Anna M Ziersch, Teresa Burges

Performance and Operation of the CMS Electromagnetic Calorimeter

The operation and general performance of the CMS electromagnetic calorimeter using cosmic-ray muons are described. These muons were recorded after the closure of the CMS detector in late 2008. The calorimeter is made of lead tungstate crystals and the overall status of the 75848 channels corresponding to the barrel and endcap detectors is reported. The stability of crucial operational parameters, such as high voltage, temperature and electronic noise, is summarised and the performance of the light monitoring system is presented

Dynamics of Socioeconomic Risk Factors for Neglected Tropical Diseases and Malaria in an Armed Conflict

Armed conflict and war and infectious diseases are globally among the leading causes of human suffering and premature death. Moreover, they are closely interlinked, as an adverse public health situation may spur violent conflict, and violent conflict may favor the spread of infectious diseases. The consequences of this vicious cycle are increasingly borne by civilians, often as a hidden and hence neglected burden. We analyzed household data that were collected before and after an armed conflict in a rural part of western Côte d'Ivoire, and investigated the dynamics of socioeconomic risk factors for neglected tropical diseases (NTDs) and malaria. We identified a worsening of the sanitation infrastructure, decreasing use of protective measures against mosquito bites, and increasing difficulties to reach public health care infrastructure. In contrast, household crowding, the availability of soap, and the accessibility of comparatively simple means of health care provision (e.g., traditional healers and community health workers) seemed to be more stable. Knowledge about such dynamics may help to increase crisis-proofness of critical infrastructure and public health systems, and hence mitigate human suffering due to armed conflict and war

SILEX: a fast and inexpensive high-quality DNA extraction method suitable for multiple sequencing platforms and recalcitrant plant species

[EN] Background The use of sequencing and genotyping platforms has undergone dramatic improvements, enabling the generation of a wealth of genomic information. Despite this progress, the availability of high-quality genomic DNA (gDNA) in sufficient concentrations is often a main limitation, especially for third-generation sequencing platforms. A variety of DNA extraction methods and commercial kits are available. However, many of these are costly and frequently give either low yield or low-quality DNA, inappropriate for next generation sequencing (NGS) platforms. Here, we describe a fast and inexpensive DNA extraction method (SILEX) applicable to a wide range of plant species and tissues. Results SILEX is a high-throughput DNA extraction protocol, based on the standard CTAB method with a DNA silica matrix recovery, which allows obtaining NGS-quality high molecular weight genomic plant DNA free of inhibitory compounds. SILEX was compared with a standard CTAB extraction protocol and a common commercial extraction kit in a variety of species, including recalcitrant ones, from different families. In comparison with the other methods, SILEX yielded DNA in higher concentrations and of higher quality. Manual extraction of 48 samples can be done in 96 min by one person at a cost of 0.12 euro/sample of reagents and consumables. Hundreds of tomato gDNA samples obtained with either SILEX or the commercial kit were successfully genotyped with Single Primer Enrichment Technology (SPET) with the Illumina HiSeq 2500 platform. Furthermore, DNA extracted fromSolanum elaeagnifoliumusing this protocol was assessed by Pulsed-field gel electrophoresis (PFGE), obtaining a suitable size ranges for most sequencing platforms that required high-molecular-weight DNA such as Nanopore or PacBio. Conclusions A high-throughput, fast and inexpensive DNA extraction protocol was developed and validated for a wide variety of plants and tissues. SILEX offers an easy, scalable, efficient and inexpensive way to extract DNA for various next-generation sequencing applications including SPET and Nanopore among others.This research has been funded by the European Union's Horizon 2020 research and innovation programme under grant agreement No 677379 (Linking genetic resources, genomes and phenotypes of Solanaceous crops; G2P-SOL). David Alonso is grateful to Universitat Politecnica de Valencia for a predoctoral (PAID-01-16) contract under the Programa de Ayudas de Investigacion y Desarrollo initiative. Mariola Plazas is grateful to Generalitat Valenciana and Fondo Social Europeo for a postdoctoral grant (APOSTD/2018/014). Pietro Gramazio is grateful to Japan Society for the Promotion of Science for a Postdoctoral Grant (P19105, FY2019 JSPS Postdoctoral Fellowship for Research in Japan (Standard)). The Spanish Ministerio de Educacion, Cultura y Deporte funded a predoctoral fellowship granted to Edgar Garcia-Fortea (FPU17/02389).Vilanova Navarro, S.; Alonso-Martín, D.; Gramazio, P.; Plazas Ávila, MDLO.; García-Fortea, E.; Ferrante, P.; Schmidt, M.... (2020). SILEX: a fast and inexpensive high-quality DNA extraction method suitable for multiple sequencing platforms and recalcitrant plant species. Plant Methods. 16(1):1-11. https://doi.org/10.1186/s13007-020-00652-yS111161Scheben A, Batley J, Edwards D. Genotyping-by-sequencing approaches to characterize crop genomes: choosing the right tool for the right application. Plant Biotechnol J. 2017;15:149–61.Jung H, Winefield C, Bombarely A, Prentis P, Waterhouse P. Tools and strategies for long-read sequencing and de novo assembly of plant genomes. Trends Plant Sci. 2019;24:700–24.Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE. 2011;6:e19379.Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE. 2008;3:e3376.Scaglione D, Pinosio S, Marroni F, Centa E, Fornasiero A, Magris G, Scalabrin S, Cattonaro F, Taylor G, Morgante M. Single primer enrichment technology as a tool for massive genotyping: a benchmark on black poplar and maize. Ann Bot. 2019;124:543–51.Barchi L, Acquadro A, Alonso D, Aprea G, Bassolino L, Demurtas O, Ferrante P, Gramazio P, Mini P, Portis E, Scaglione D, Toppino L, Vilanova S, Díez MJ, Rotino G, Lanteri S, Prohens J, Giuliano G. Single primer enrichment technology (SPET) for high-throughput genotyping in tomato and eggplant germplasm. Front Plant Sci. 2019;10:1005.Vaillancourt B, Buell CR. High molecular weight DNA isolation method from diverse plant species for use with Oxford Nanopore sequencing. bioRxiv. 2019;1:783159.Anderson CB, Franzmayr BK, Hong SW, Larking AC, van Stijn TC, Tan R, Moraga R, Faville M, Griffiths A. Protocol: a versatile, inexpensive, high-throughput plant genomic DNA extraction method suitable for genotyping-by-sequencing. Plant Methods. 2018;14:75.Rana MM, Aycan M, Takamatsu T, Kaneko K, Mitsui T, Itoh K. Optimized nuclear pellet method for extracting next-generation sequencing quality genomic DNA from fresh leaf tissue. Methods Protoc. 2019;2:54.Doyle JJ, Doyle JL. Isolation of plant DNA from fresh tissue. Focus. 1990;12:13–5.Healey A, Furtado A, Cooper T, Henry RJ. Protocol: a simple method for extracting next-generation sequencing quality genomic DNA from recalcitrant plant species. Plant Methods. 2014;10:21.Martínez-González CR, Ramírez-Mendoza R, Jiménez-Ramírez J, Gallegos-Vázquez C, Luna-Vega I. Improved method for genomic DNA extraction for Opuntia Mill. (Cactaceae). Plant Methods. 2017;13:82.Barbier FF, Chabikwa TG, Ahsan MU, Cook SE, Powell R, Tanurdzic M, Beveridge C. A phenol/chloroform-free method to extract nucleic acids from recalcitrant, woody tropical species for gene expression and sequencing. Plant Methods. 2019;15:62.Souza DC, Teixeira TA. A simple and effective method to obtain high DNA quality and quantity from Cerrado plant species. Mol Biol Rep. 2019;46:4611–5.Kovačević N. Magnetic beads based nucleic acid purification for molecular biology applications. Sample preparation techniques for soil, plant, and animal samples. In: Micic M, editor. Springer Protoc Handb. 2016;53–67.Martin SL, Parent JS, Laforest M, Page E, Kreiner JM, James T. Population genomic approaches for weed science. Plants. 2019;8:354.Zhou Y, Zhang Y, He W, Wang J, Peng F, Huang L, Zhao S, Deng W. Rapid regeneration and reuse of silica columns from PCR purification and gel extraction kits. Sci Rep. 2018;8:12870.Park HJ, Cho H, Jung HS, Cho BH, Lee MY. Development of a DNA isolation device using poly(3,4-dihydroxy-l-phenylalanine)-coated swab for on-site molecular diagnostics. Sci Rep. 2019;9:8144.Boom R, Sol CJ, Salimans MM, Jansen CL, Wertheim-van Dillen PM, van der Noordaa J. Rapid and simple method for purification of nucleic acids. J Clin Microbiol. 1990;28:495–503.Carter MJ, Milton ID. An inexpensive and simple method for DNA purifications on silica particles. Nucleic Acids Res. 1993;21:1044.Carvalho J, Puertas G, Gaspar J, Azinheiro S, Diéguez L, Garrido-Maestu A, Vázquez M, Barros-Velázquez J, Cardoso S, Padro M. Highly efficient DNA extraction and purification from olive oil on a washable and reusable miniaturized device. Anal Chim Acta. 2018;1020:30–40.Branton D, Deamer D, Quick J, Loman NJ. DNA extraction strategies for nanopore sequencing. Nanopore Seq. World Sci. 2019;1:91–105.Cheng H, Zhang K, Libera J, De La Cruz M, Bedzyk M. Polynucleotide adsorption to negatively charged surfaces in divalent salt solutions. Biophys J. 2016;90:1164–74.Shi B, Shin Y, Hassanali A, Singer S. DNA Binding to the Silica Surface. J Phys Chem B. 2015;119:11030–40.Katevatis C, Fan A, Klapperich CM. Low concentration DNA extraction and recovery using a silica solid phase. PLoS ONE. 2017;12:e0176848.Green MR, Sambrook J. Isolation and quantification of DNA. Cold Spring Harb Protoc. 2018;2018:403–14.Toole K, Roffey P, Young E, Cho K, Shaw T, Smith M, Blagojevic N. Evaluation of commercial forensic DNA extraction kits for decontamination and extraction of DNA from biological samples contaminated with radionuclides. Forensic Sci Int. 2019;302:109867.Piskata Z, Servusova E, Babak V, Nesvadbova M, Borilova G. The quality of DNA isolated from processed food and feed via different extraction procedures. Molecules. 2019;24:1188.Xia Y, Chen F, Du Y, Liu C, Bu G, Xin Y, Boye L. A modified SDS-based DNA extraction method from raw soybean. Biosci Rep. 2019;39:2.Akkurt M. Comparison between modified DNA extraction protocols and commercial isolation kits in grapevine (Vitis vinifera L.). Genet Mol Res. 2012;11:2343–51.Marsal G, Baiges I, Canals JM, Zamora F, Fort F. A Fast, efficient method for extracting DNA from leaves, stems, and seeds of Vitis vinifera L. Am J Enol Vitic. 2011;62:376–81.Abdel-Latif A, Osman G. Comparison of three genomic DNA extraction methods to obtain high DNA quality from maize. Plant Methods. 2017;13:1.Huang J, Ge X, Sun M. Modified CTAB protocol using a silica matrix for isolation of plant genomic DNA. Biotechniques. 2000;28:432–4.Rogstad SH. Plant DNA extraction using silica. Plant Mol Biol Report. 2012;21:463.Li J-F, Li L, Sheen J. Protocol: a rapid and economical procedure for purification of plasmid or plant DNA with diverse applications in plant biology. Plant Methods. 2010;6:1.Li J-F, Sheen J. DNA purification from multiple sources in plant research with homemade silica resins. Humana Press. 2012;862:53–9.Vandeventer PE, Lin JS, Zwang TJ, Nadim A, Johal MS, Niemz A. Multiphasic DNA adsorption to silica surfaces under varying buffer, pH, and ionic strength conditions. J Phys Chem B. 2012;116:5661–70.Boesenberg-Smith KA, Pessarakli MM, Wolk DM. Assessment of DNA yield and purity: an overlooked detail of PCR troubleshooting. Clin Microbiol Newsl. 2012;34:1–6.Emaus MN, Clark KD, Hinners P, Anderson JL. Preconcentration of DNA using magnetic ionic liquids that are compatible with real-time PCR for rapid nucleic acid quantification. Anal Bioanal Chem. 2018;410:4135–44.Dumschott K, Schmidt MHW, Chawla HS, Snowdon R, Usadel B. Oxford Nanopore sequencing: new opportunities for plant genomics? J Exp Bot. 2020;eraa263Knapp S, Sagona E, Carbonell AKZ, Chiarini F. A revision of the Solanum elaeagnifolium clade (Elaeagnifolium clade; subgenus Leptostemonum, Solanaceae). PhytoKeys. 2017;84:1–104.García-Fortea E, Gramazio P, Vilanova S, Fita A, Mangino G, Villanueva G, Arrones A, Knapp S, Prohens J, Plazas M. First successful backcrossing towards eggplant (Solanum melongena) of a New World species, the silverleaf nightshade (S. elaeagnifolium), and characterization of interspecific hybrids and backcrosses. Sci Hort. 2019;246:563–73.Ihaka R, Gentleman R. R: a language for data analysis and graphics. J Comput Graph Stat. 1996;5:3299–314.Wickham H. ggplot2: Elegant graphics for data analysis. New York: Springer-Verlag; 2016.Ponti G, Maccaferri M, Manfredini M, Kaleci S, Mandrioli M, Pellacani G, Ozben T, Depenni R, Bianchi G, Pirola G, Tomasi A. The value of fluorimetry (Qubit) and spectrophotometry (NanoDrop) in the quantification of cell-free DNA (cfDNA) in malignant melanoma and prostate cancer patients. Clin Chim Acta. 2018;479:14–9.Lakshmi R, Baskar V, Ranga U. Extraction of superior-quality plasmid DNA by a combination of modified alkaline lysis and silica matrix. Anal Biochem. 1999;272:109–12.Taylor JI, Hurst CD, Davies MJ, Sachsinger N, Bruce IJ. Application of magnetite and silica–magnetite composites to the isolation of genomic DNA. J Chromatogr A. 2000;890:159–66.Prodělalová J, Rittich B, Španová A, Petrová K, Beneš MJ. Isolation of genomic DNA using magnetic cobalt ferrite and silica particles. J Chromatogr A. 2004;1056:43–8.Shan Z, Jiang Y, Guo M, Bennett JC, Li X, Tian H, Oakes K, Zhang, Zhou Y, Huang Q, Chen H. Promoting DNA loading on magnetic nanoparticles using a DNA condensation strategy. Colloids Surfaces B Biointerfaces. 2015;125:247–54.Greco M, Sáez C, Brown M, Bitonti M. A simple and effective method for high quality co-extraction of genomic DNA and total RNA from low biomass Ectocarpus siliculosus, the model brown alga. PLoS ONE. 2014;9:e96470.Schrader C, Schielke A, Ellerbroek L, Johne R. PCR inhibitor – occurrence, properties and removal. J Appl Microbiol. 2012;113:1014–26.Demeke T, Adams RP. The effects of plant polysaccharides and buffer additives on PCR. Biotechniques. 1992;12:332–4.Asami DK, Hong YJ, Barrett DM, Mitchell AE. Comparison of the total phenolic and ascorbic acid content of freeze-dried and air-dried marionberry, strawberry, and corn grown using conventional, organic, and sustainable agricultural practices. J Agric Food Chem. 2003;51:1237–41.Schmidt M, Vogel A, Denton A, Istace B, Wormit A, van de Geest H, Bolger M, Alseekh S, Maß J, Pfaff C, Schurr U, Chetelat R, Maumus F, Aury J, Koren S, Fernie A, Zamir D, Bolger A, Usadel B. De novo assembly of a new Solanum pennellii accession using nanopore sequencing. Plant cell. 2017;29:2336–48

The Prevalence of Sexually Transmitted Infections in Papua New Guinea: A Systematic Review and Meta-Analysis

Patellofemoral osteoarthritis (PF OA) is more prevalent than previously thought and contributes to patient's suffering from knee OA. Synthesis of prevalence data can provide estimates of the burden of PF OA

Matrix Metalloproteinases in Cytotoxic Lymphocytes Impact on Tumour Infiltration and Immunomodulation

To efficiently combat solid tumours, endogenously or adoptively transferred cytotoxic T cells and natural killer (NK) cells, need to leave the vasculature, traverse the interstitium and ultimately infiltrate the tumour mass. During this locomotion and migration in the three dimensional environment many obstacles need to be overcome, one of which is the possible impediment of the extracellular matrix. The first and obvious one is the sub-endothelial basement membrane but the infiltrating cells will also meet other, both loose and tight, matrix structures that need to be overridden. Matrix metalloproteinases (MMPs) are believed to be one of the most important endoprotease families, with more than 25 members, which together have function on all known matrix components. This review summarizes what is known on synthesis, expression patterns and regulation of MMPs in cytotoxic lymphocytes and their possible role in the process of tumour infiltration. We also discuss different functions of MMPs as well as the possible use of other lymphocyte proteases for matrix degradation