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Potato is the third most important food crop in the world. Diverse pathogens threaten sustainable crop production but can be controlled, in many cases, through the deployment of disease resistance genes belonging to the family of nucleotide-binding, leucine-rich-repeat (NLR) genes.To identify functional NLRs in established varieties, we have successfully established SMRT-AgRenSeq in tetraploid potatoes and have further enhanced the methodology by including dRenSeq in an approach that we term SMRT-AgRenSeq-d. The inclusion of dRenSeq enables the filtering of candidates after the association analysis by establishing a presence/absence matrix across resistant and susceptible potatoes that is translated into an F1 score. Using a SMRT-RenSeq based sequence representation of the NLRome from the cultivar Innovator, SMRT-AgRenSeq-d analyses reliably identified the late blight resistance benchmark genesR1, R2-like, R3aandR3bin a panel of 117 varieties with variable phenotype penetrations. All benchmark genes were identified with an F1 score of 1 which indicates absolute linkage in the panel.When applied to the elusive nematode disease resistance geneGpa5that controls the Potato Cyst Nematode (PCN) speciesGlobodera pallida(pathotypes Pa2/3), SMRT-AgRenSeq-d identified nine strong candidates. These map to the previously established position on potato chromosome 5 and are potential homologs of the late blight resistance geneR1.Assuming that NLRs are involved in controlling many types of resistances, SMRT-AgRenSeq-d can readily be applied to diverse crops and pathogen systems. In potato, SMRT-AgRenSeq-d lends itself, for example, to further study the elusive PCN resistancesH1orH3for which phenotypic data exist.

This work was supported by the Rural & Environment Science & Analytical Services (RESAS) Division of the Scottish Government through project JHI-B1-1, the Biotechnology and Biological Sciences Research Council (BBSRC) through award BB/S015663/1 and the Royal Society through award NAF\R1\201061. MS and LHB were supported through the East of Scotland Bioscience Doctoral Training Partnership (EASTBIO DTP), funded by the BBSRC award BB/T00875X/1. YW was supported through the CSC scholarship program, China. Background : In the ten years since the initial publication of the RenSeq protocol, the method has proved to be a powerful tool for studying disease resistance in plants and providing target genes for breeding programmes. Since the initial publication of the methodology, it has continued to be developed as new technologies have become available and the increased availability of computing power has made new bioinformatic approaches possible. Most recently, this has included the development of a k-mer based association genetics approach, the use of PacBio HiFi data, and graphical genotyping with diagnostic RenSeq. However, there is not yet a unified workflow available and researchers must instead configure approaches from various sources themselves. This makes reproducibility and version control a challenge and limits the ability to perform these analyses to those with bioinformatics expertise. Results : Here we present HISS, consisting of three workflows which take a user from raw RenSeq reads to the identification of candidates for disease resistance genes. These workflows conduct the assembly of enriched HiFi reads from an accession with the resistance phenotype of interest. A panel of accessions both possessing and lacking the resistance are then used in an association genetics approach (AgRenSeq) to identify contigs positively associated with the resistance phenotype. Candidate genes are then identified on these contigs and assessed for their presence or absence in the panel with a graphical genotyping approach that uses dRenSeq. These workflows are implemented via Snakemake, a python-based workflow manager. Software dependencies are either shipped with the release or handled with conda. All code is freely available and is distributed under the GNU GPL-3.0 license. Conclusions : HISS provides a user-friendly, portable, and easily customised approach for identifying novel disease resistance genes in plants. It is easily installed with all dependencies handled internally or shipped with the release and represents a significant improvement in the ease of use of these bioinformatics analyses. Publisher PDF

Transcriptomics is being increasingly applied to generate new insight into the interactions between plants and their pathogens. For the wheat yellow (stripe) rust pathogen (Puccinia striiformis f. sp. tritici, Pst) RNA-based sequencing (RNA-Seq) has proved particularly valuable, overcoming the barriers associated with its obligate biotrophic nature. This includes the application of RNA-Seq approaches to study Pst and wheat gene expression dynamics over time and the Pst population composition through the use of a novel RNA-Seq based surveillance approach called “field pathogenomics”. As a dual RNA-Seq approach, the field pathogenomics technique also provides gene expression data from the host, giving new insight into host responses. However, this has created a wealth of data for interrogation. Results: Here, we used the field pathogenomics approach to generate 538 new RNA-Seq datasets from Pst-infected field wheat samples, doubling the amount of transcriptomics data available for this important pathosystem. We then analysed these datasets alongside 66 RNA-Seq datasets from four Pst infection time-courses and 420 Pst-infected plant field and laboratory samples that were publicly available. A database of gene expression values for Pst and wheat was generated for each of these 1024 RNA-Seq datasets and incorporated into the development of the rust expression browser (http://www.rust-expression.com). This enables for the first time simultaneous ‘point-and-click’ access to gene expression profiles for Pst and its wheat host and represents the largest database of processed RNA-Seq datasets available for any of the three Puccinia wheat rust pathogens. We also demonstrated the utility of the browser through investigation of expression of putative Pst virulence genes over time and examined the host plants response to Pst infection. Conclusions: The rust expression browser offers immense value to the wider community, facilitating data sharing and transparency and the underlying database can be continually expanded as more datasets become publicly available. EEA Bordenave Fil: Adams, Thomas M.. John Innes Centre. Norwich Research Park; Reino Unido Fil: Olsson, Tjelvar S.G. John Innes Centre. Norwich Research Park; Reino Unido Fil: Ramírez-González, Ricardo H. John Innes Centre. Norwich Research Park; Reino Unido Fil: Bryant, Ruth. RAGT Seeds Ltd.; Reino Unido Fil: Bryson, Rosie. BASF SE. Agricultural Centre; Alemania Fil: Campos, Pablo Eduardo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Bordenave; Argentina Fil: Fenwick, Paul. Limagrain UK Ltd.; Reino Unido Fil: Feuerhelm, David. Syngenta Seeds Ltd.; Reino Unido Fil: Hayes, Charlotte. Elsoms Wheat Ltd.; Reino Unido Fil: Henriksson, Tina. Lantmännen Lantbruk; Suecia Fil: Hubbard, Amelia. NIAB; Reino Unido Fil: Jevtić, Radivoje. Institute of Field and Vegetable Crops; Serbia Fil: Judge, Christopher. NIAB; Reino Unido Fil: Kerton, Matthew. DSV United Kingdom Ltd.; Reino Unido Fil: Lage, Jacob. KWS UK Limited; Reino Unido Fil: Lewis, Clare M. John Innes Centre. Norwich Research Park; Reino Unido Fil: Lilly, Christine. Frontier Agriculture; Reino Unido Fil: Meidan, Udi. Hazera Seeds Ltd.; Israel Fil: Novoselović, Dario. Agricultural Institute Osijek; Croacia Fil: Patrick, Colin. Masstock Arable (UK) Ltd.; Reino Unido Fil: Wanyera, Ruth. Kenya Agricultural and Livestock Research Organization; Kenia Fil: Saunders, Diane G.O. John Innes Centre. Norwich Research Park; Reino Unido

Puccinia striiformisf. sp.tritici(Pst) is the causative agent of wheat yellow rust disease, affecting wheat production worldwide. In order to effectively manage this disease, it is important to monitor the genotypes present through surveillance programs. Additionally, the use of public, open source tools such as the Nextstrain toolkit allow for rapid and efficient sharing of data from surveillance programmes. Here we present a Nextstrain instance forPst, which will be a valuable resource for understanding and tracking the distribution of specific genotypes of this important pathogen.

In this Perspective, the author presents his vision of scholarship as consisting of hierarchically nested levels of specialization, each level offering its own perspective and value. He argues that in an era of increasingly sophisticated analysis tools, modern scholarship tends to proceed largely unaware of the benefits of conducting research at the higher, more general levels of the hierarchy. Drawing upon his own research and that of others, he gives examples of the manner in which generalist scholarship may proceed, the type of unique insights it uncovers, and the wisdom afforded us via an awareness of where our scholarship resides within the hierarchy.

In 2003, Arkansas became the first state to require body mass index (BMI) testing in public schools to raise awareness of the growing obesity epidemic among children and adolescents. Limited information exists regarding the effectiveness of school-based BMI screening programs. The purpose of this study was to determine if BMI health report cards affected parents’ knowledge or actions regarding their child’s health and to determine the accuracy of parents’ perceptions of their child as underweight, normal weight, or overweight according to their child’s BMI. A questionnaire was developed with the help of physical educators, pediatricians, and exercise scientists to determine parents’ perceptions and behaviors regarding BMI report cards. The questionnaire was distributed to parents/guardians of children who sought medical care at two pediatrician’s offices in Arkansas. Based on responses to survey questions, parents are not making changes to their child’s diet and exercise habits if their child is classified as “at risk” or “overweight.” However, parents did report that BMI health report cards are influencing their knowledge about their child’s health. The majority of parents in the study (approximately 66%) did not accurately perceive their child’s BMI category.

BACKGROUND Obesity in children and adolescents has become one of the most critical public health problems in the United States. Schools may play an important role in raising awareness and possibly slowing the obesity epidemic. METHODS The purpose of this study was to gather information on parents' perception and use of body mass index (BMI) report cards provided by public schools through the administration of a questionnaire. The questionnaire was developed with the assistance of physical educators, pediatricians, and exercise scientists. The questionnaires were backpacked home with 1127 students in 6 Arkansas public schools. Parents completed and returned 404 questionnaires. RESULTS Findings indicate that parents are supportive of schools reporting BMI and providing information on healthier lifestyles. However, most parents reported not making any adjustment to their child's diet and physical activity habits based on the BMI reports. Approximately half of parents (55%) thought the BMI report accurately reflected their child's health status. Approximately half of the parents reported their child's BMI report led them to think about their family's health habits. CONCLUSIONS Although parents do support receiving BMI information from schools, many did not indicate using the data to initiate changes such as increased physical activity or healthy eating.

The republican model of social rights in France invokes the heritage of the Revolution. The meaning of this legacy is complex for several reasons. The articulation of rights during the Revolution took different forms in theory; practice fell short of aspirations. The political legacy of social rights drew strength from Enlightenment sources and from older antecedents such as the Erasmian humanism of Juan Luis Vives. Tracing the evolution of social rights in France since the Revolution, the historian encounters continuities both in the statement of principles and in the obstacles to their realization. At the same time, new players contend with challenges unforeseen by the leaders of the first French republic. Le modèle républicain de la protection sociale en France s'inscrit dans l'héritage de la Révolution. Or, il faut préciser d'abord que le moment de sa conception n'est pas établi et qu'une recherche de paternité nécessiterait une approche historique de longue durée. Le fons et origo du droit social remonte au siècle des Lumières et dans une tradition plus lointaine que l'on peut qualifier d'érasmienne. Quand on trace les réalisations du droit social depuis l'époque révolutionnaire, on retrouve les qualités et les défauts de son ascendance. D'autre part, il faut reconnaître les apports multiples et les trébuchements d'une société et d'un état qui ne se sont pas révélés révolutionnaires sans réserve. Les réticences et les démarches nouvelles de la politique sociale contemporaine font état d'un monde imprévisible aux militants de 1789, 1793 et 1795. Pourtant, l'appel des droits universels a maintenant un retentissement mondial.

NiTi shape memory alloy thin films from separate evaporation sources are produced. One micron films with a gradient of Ni–Ti ratios are fabricated at temperatures of 200 °C with a deposition rate of 8.3 A/s. A single e-beam evaporation system combined with a thermal evaporation source is used to create a co-evaporation process. The evaporation rate of the nickel in the evaporation source is allowed to develop a steady state, and then the e-beam evaporation of the titanium is controlled to maintain the correct rate and desired ratio. The resulting thin films that exhibit the two-way shape memory effect had approximately a 50% concentration of titanium as measured by energy dispersive spectroscopy (EDS).

An experimental investigation addressing the effect of the release of dissolved noncondensables on the heat transfer in a long, heated microchannel subject to subcooled liquid forced convection was conducted. The convection heat transfer coefficients near the exit of a copper microchannel with 0.76 mm inner diameter and 16 cm heated length, subject to forced-flow cooling by subcooled water, were measured. The range of experimental parameters were: wall heat flux=0.5–2.5 MW/m2; liquid velocity=2.07 to 8.53 m/s; channel exit pressure=5.9 bar. Experiments were performed with degassed water and water saturated with air. The convection heat transfer coefficients obtained with degassed water were systematically under predicted by the widely-used Dittus–Boelter correlation for turbulent pipe flow. The presence of dissolved air in water could increase the heat transfer coefficients by as much as 17%, despite the fact that the maximum increase in the coolant velocity due to the noncondensable gas release was only a few percent. The heat transfer enhancement increased with increasing the heat flux and decreasing the liquid velocity.

Turbulent, single-phase forced convection of water in circular microchannels with diameters of 0.76 and 1.09 mm has been investigated. The data show that the Nusselt numbers for the microchannels are higher than those predicted by traditional large channel correlations. Based on the data obtained in this investigation, along with earlier data for smaller diameter channels, a generalized correlation for the Nusselt number for turbulent, single-phase, forced convection in circular microchannels has been developed. The diameter, Reynolds number, and Prandtl number ranges are 0.102–1.09 mm, 2.6 × 103−2.3 × 104, and 1.53–6.43, respectively. With a confidence level of greater than 95%, differences between experimental and predicted Nusselt number values are less than ± 18.6%.

One of the most important resources available in the field of fluid mechanics, the Moody Chart gives Darcy friction factor as a function of Reynolds number and relative roughness. The experimentalists who generated the data correlated in the Moody Chart, however, roughened pipe surfaces by coating their internal surfaces with a monolayer of sand, the pipe wall roughness being defined as the average diameter of the sand grains. Thus, the sand-grain roughness values required for use with the Moody Chart are not derived from any direct measure of roughness using modern surface characterization equipment, such as an optical profilometer. Using direct measurements of surface roughness in fluid flow calculations may therefore result in significant error. In this paper we present a simple algorithm with which various measured surface roughness parameters can be converted to equivalent sand-grain roughness. For nearly every surface roughness value converted to equivalent sand-grain roughness using the algorithm, better agreement with fluid flow experiments is seen over using the raw roughness value.

Comeau, MJ, Lawson, PM, Graves, MM, Church, JB, and Adams II, TM. Visualization of the passive sink phenomenon in nonexercising muscle using 2 sampling sites: consequences for assessment and training. J Strength Cond Res 25(10): 2926–2930, 2011—Sampling sites for determining lactate concentration [La 2 ] have been debated for years. To date, none of the research that has been completed has taken into consideration the muscle group that is active during exercise, sample site, and the passivity of nonexercising muscle, collectively. The purpose of this study was to determine if this passive sink phenomenon could be visualized by using common sampling methods immediately after exercise and during the recovery period from 2 sample sites. Eleven male cyclists completed a subject-specific trial on a Velotron cycle ergometer. Plasma [La 2 ] was measured from the finger and toe immediately postexercise and every 5 minutes after, for 25 minutes after the cycling trial. All 3 analyses were significant (p , 0.05) with the sample site 3 sample time interaction, sample time main effect, and sample site main effect being reported, respectively: Wilks’ l = 0.079, F (5,6) = 13.932, p = 0.003, Wilks’ l = 0.012, F (5,6) = 94.804, p = 0.000, and Wilks’ l = 0.492, F (1,10) = 10.316, p = 0.009. Post hoc paired t-tests on computed mean differences between sample sites for each sample time revealed statistically significant differences (p , 0.05) between several time intervals. Further analysis also revealed significant differences (p , 0.05) in the sample site main effect at each collection time. Blood lactate samples need to be obtained from the limb containing the exercising muscle(s) to negate the passive sink effect that has been observed to occur in nonexercising muscles. This recommendation needs to be followed to better establish future training volumes and outcomes.

We have learned much about the substrate and ways of adding layers to it. We next turn our attention to creating and transferring patterns onto the substrate and/or these layers. In so doing we lay the foundation of creating actual structures with specific geometries. The primary tool used to accomplish this is photolithography, which is essentially an optical printing process.

A transducer is a device that converts power from one form to another for purposes of measurement or control. Historically, the word “transducer” referred only to devices that converted mechanical stimuli such as force or pressure into an electrical signal, usually voltage. Today the definition has been broadened to include all forms of input stimuli—mechanical, electrical, fluidic, or thermal—and output signals other than electrical.

We have explored the nature of the silicon substrate, seen how to tailor its composition by doping it, how to deposit thin film layers, and also how to create and transfer patterns using photolithography. We next turn our attention to using the substrate, thin film deposition, and pattern transfer processes to create the actual structures that make up a MEMS device. This shaping of materials into structural elements is commonly known as micromachining.

Utilization of MEMS devices that employ fluids offers many advantages over macroscale devices, including enhanced portability and performance, as well as allowing for increased integration and automation. The array of microscale devices that incorporate fluids is large, and includes inkjet printer heads, devices used for DNA amplification, a variety of sensors, and a number of emerging technologies such as the use of microneedles for drug delivery. The use of fluids at the microscale is also becoming increasingly important in thermal management, particularly through the use of microfluidic devices to cool electronic components. Power generation via microscale turbomachinery and even microrocket engines are currently under development as well. Figure 12.1 gives yet another application, the use of controlled fluid flow to grow crystals.

A model is a system for interpreting, explaining, describing, thinking about and designing…another system. The models we will use are mathematical, generally involving geometry, trigonometry, calculus, statistics, and sometimes numerical and computer methods. The systems we model are (big surprise) MEMS!

One of the most important techniques employed in microfabrication is the addition of a thin layer of material to an underlying layer. Added layers may form part of the MEMS structure, serve as a mask for etching, or serve as a sacrificial layer.

Due to the small scales encountered in MEMS and microfluidic devices, surface tension can play a significant role in the device physics. As such, many microscale devices have exploited surface tension forces to serve as passive valves and to move fluids. Surprisingly, few models for surface tension driven flow seem to have been developed. In this study a theoretical mathematical model for surface tension driven flow through a capillary of an arbitrary cross section is derived. The model is based on macroscopic mass and momentum balances, allowing for different physical insights to be drawn compared to approaches starting with the Navier-Stokes equations. Expressions for flow length and velocity are derived for both frictionless flow and for flow with wall friction. For frictionless flow the result of surface tension force is to increase the momentum of the fluid by constantly drawing mass into the capillary at a constant characteristic velocity. In the case of flow with wall friction, a characteristic time scale can be calculated. For times on the order of the characteristic time scale, the flow velocity exponentially decays from the characteristic velocity, whereas for larger times the velocity shows an inverse power law dependence. The model well predicts flow behaviour for previously published experiments in which the characteristic time is small. For systems in which the characteristic time is larger, the model may show improved performance over previous models.

(1993). The Effects of Conceptually Based Physical Education Programs on Attitudes and Exercise Habits of College Alumni after 2 to 11 Years of Follow-Up. Research Quarterly for Exercise and Sport: Vol. 64, No. 2, pp. 208-212.