Multi-contrast imaging and digital refocusing on a mobile microscope with a domed LED array

We demonstrate the design and application of an add-on device for improving the diagnostic and research capabilities of CellScope--a low-cost, smartphone-based point-of-care microscope. We replace the single LED illumination of the original CellScope with a programmable domed LED array. By leveraging recent advances in computational illumination, this new device enables simultaneous multi-contrast imaging with brightfield, darkfield, and phase imaging modes. Further, we scan through illumination angles to capture lightfield datasets, which can be used to recover 3D intensity and phase images without any hardware changes. This digital refocusing procedure can be used for either 3D imaging or software-only focus correction, reducing the need for precise mechanical focusing during field experiments. All acquisition and processing is performed on the mobile phone and controlled through a smartphone application, making the computational microscope compact and portable. Using multiple samples and different objective magnifications, we demonstrate that the performance of our device is comparable to that of a commercial microscope. This unique device platform extends the field imaging capabilities of CellScope, opening up new clinical and research possibilities

Metabolic effects of elevated temperature on organic acid degradation in ripening <em>Vitis vinifera</em> fruit

First published online: September 1, 2014Berries of the cultivated grapevine Vitis vinifera are notably responsive to temperature, which can influence fruit quality and hence the future compatibility of varieties with their current growing regions. Organic acids represent a key component of fruit organoleptic quality and their content is significantly influenced by temperature. The objectives of this study were to (i) manipulate thermal regimes to realistically capture warming-driven reduction of malate content in Shiraz berries, and (ii) investigate the mechanisms behind temperature-sensitive malate loss and the potential downstream effects on berry metabolism. In the field we compared untreated controls at ambient temperature with longer and milder warming (2-4 °C differential for three weeks; Experiment 1) or shorter and more severe warming (4-6 °C differential for 11 days; Experiment 2). We complemented field trials with control (25/15 °C) and elevated (35/20 °C) day/night temperature controlled-environment trials using potted vines (Experiment 3). Elevating maximum temperatures (4-10 °C above controls) during pre-véraison stages led to higher malate content, particularly with warmer nights. Heating at véraison and ripening stages reduced malate content, consistent with effects typically seen in warm vintages. However, when minimum temperatures were also raised by 4-6 °C, malate content was not reduced, suggesting that the regulation of malate metabolism differs during the day and night. Increased NAD-dependent malic enzyme activity and decreased phosphoenolpyruvate carboxylase and pyruvate kinase activities, as well as the accumulation of various amino acids and γ-aminobutyric acid, suggest enhanced anaplerotic capacity of the TCA cycle and a need for coping with decreased cytosolic pH in heated fruit.C. Sweetman, V. O. Sadras, R. D. Hancock, K. L. Soole and C. M. For

Jewish Identity and Religious Revival in Post-Soviet Cuba

No Abstrac

Explaining pre-emptive acclimation by linking information to plant phenotype

We review mechanisms for pre-emptive acclimation in plants and propose a conceptual model linking developmental and evolutionary ecology with the acquisition of information through sensing of cues and signals. The idea is that plants acquire much of the information in the environment not from individual cues and signals but instead from their joint multivariate properties such as correlations. If molecular signalling has evolved to extract such information, the joint multivariate properties of the environment must be encoded in the genome, epigenome, and phenome. We contend that multivariate complexity explains why extrapolating from experiments done in artificial contexts into natural or agricultural systems almost never works for characters under complex environmental regulation: biased relationships among the state variables in both time and space create a mismatch between the evolutionary history reflected in the genotype and the artificial growing conditions in which the phenotype is expressed. Our model can generate testable hypotheses bridging levels of organization. We describe the model and its theoretical bases, and discuss its implications. We illustrate the hypotheses that can be derived from the model in two cases of pre-emptive acclimation based on correlations in the environment: the shade avoidance response and acclimation to drought.Peer reviewe

Compared to conventional, ecological intensive management promotes beneficial proteolytic soil microbial communities for agro-ecosystem functioning under climate change-induced rain regimes

Projected climate change and rainfall variability will affect soil microbial communities, biogeochemical cycling and agriculture. Nitrogen (N) is the most limiting nutrient in agroecosystems and its cycling and availability is highly dependent on microbial driven processes. In agroecosystems, hydrolysis of organic nitrogen (N) is an important step in controlling soil N availability. We analyzed the effect of management (ecological intensive vs. conventional intensive) on N-cycling processes and involved microbial communities under climate change-induced rain regimes. Terrestrial model ecosystems originating from agroecosystems across Europe were subjected to four different rain regimes for 263 days. Using structural equation modelling we identified direct impacts of rain regimes on N-cycling processes, whereas N-related microbial communities were more resistant. In addition to rain regimes, management indirectly affected N-cycling processes via modifications of N-related microbial community composition. Ecological intensive management promoted a beneficial N-related microbial community composition involved in N-cycling processes under climate change-induced rain regimes. Exploratory analyses identified phosphorus-associated litter properties as possible drivers for the observed management effects on N-related microbial community composition. This work provides novel insights into mechanisms controlling agro-ecosystem functioning under climate change

Effects of the source:sink ratio on the phenotypic plasticity of stem water potential in olive (Olea europaea L.)

The aims of this work were to quantify (i) the effect of the source:sink ratio on stem water potential (SWP) and (ii) the phenotypic plasticity of SWP and its relationship to oil yield components in olive. Trees with a 3-fold variation in the source:sink ratio (crown volume/fruit number per tree) were monitored in 2007–2008 and 2008–2009 in a fully irrigated orchard in Mendoza, Argentina. The combination of rainfall, irrigation, and evaporative demand led to a steady SWP largely above –1.65 MPa in 2007–2008 and a marked seasonal decline from –1.13 MPa to –2.04 MPa in trees with a medium and low source:sink ratio in 2008–2009. Plasticity was quantified as the slope of the norm of reaction for each trait. Across seasons, trees with a high source:sink ratio had a higher SWP than their counterparts with a medium and low source:sink ratio. Plasticity of SWP was highest in olives with a low source:sink ratio (slope=1.28) and lowest for trees with a high source:sink ratio (slope=0.76). The average SWP for each source:sink ratio and season was unrelated to both the source:sink ratio and yield components. On the other hand, the plasticity of SWP was positively associated with fruit number and negatively associated with the source:sink ratio, fruit weight, and fruit oil weight. The plasticity of the SWP was unrelated to SWP per se. It is concluded that understanding the effect of the source:sink ratio on plant water relations would benefit from a dual perspective considering the trait per se and its plasticity. A dual approach would also allow for more robust plant-based indicators for irrigation.EEA JunínFil: Trentacoste, Eduardo Rafael. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Junín; ArgentinaFil: Sadras, Victor Oscar. South Australian Research & Development Institute; AustraliaFil: Puertas, Carlos Marcelo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Junín; Argentin

Future opportunities for crop physiology in fruit production

This paper outlines some of the challenges and opportunities for whole plant and crop physiologists to contribute to enhanced and more efficient fruit production in the coming years. The rapid advances in molecular biology provide both an opportunity (especially to improve understanding of physiological processes in crop production) and a challenge (to use this knowledge to advance production in real farm situations). Similar or even greater opportunities are being provided by other developing technologies, especially the rapidly increasing power and availability of powerful computing and communications technology and smartphones which provide real opportunities to contribute to improved crop and farm management. In addition the rapid development of novel 'remote' or 'proximal' sensing technologies, including the use of unmanned aerial vehicles and on-tractor sensors for crop monitoring and stress diagnosis also holds great promise. These and other advances are discussed in the context of their potential for improving both crop breeding and orchard management, drawing on examples from a wide range of crops. The potential of these scientific advances will be put in the context of other factors relating to the advance of horticultural knowledge including the availability of funding and the training of young scientists.</p

Secular identification : the case of BINA and its secular yeshiva

The clashing perspectives over Jewishness in Israel, on the one side an orthodox minority that is a major political player, on the other a secular majority that is politically fragmented, is a cause of constant tension in Israeli Jewish society. In Israel, Jewishness with its religious overtones overlaps with national sentiments. This overlap is one aspect of the Israeli secular story, orthodox monopoly over the state\u2019s Jewish character is another. The Jewish renewal movement in Israel looks to bridge, and reestablish a reciprocal relationship, between the national and religious aspects of Israeliness with Hebrew culture based on the Hebrew Bible as the common core. The movement calls upon secular Jewish individuals to challenge the Jewish orthodoxy monopoly in Israel. Furthermore, it calls for secular individuals to reclaim ownership and with it authority over Jewish culture, recreating Jewishness in their own secular image. What exactly is that secular image that is to mold Jewishness into a contemporary frame of reference, is in fact the subject of this dissertation. In this work, I carry out an analysis of group identification based on secular principles. I argue that group identification based in secularity facilitates inclusive environment; however, it does not guarantee inclusion. Looking at BINA and its secular yeshiva in the south of Tel-Aviv, I introduce ethnographic data showing how secular sensibilities challenge current understanding of group belonging and boundaries. The binary notion secular-religious forms the basis for understanding the secular by both layman and experts. In Israel\u2019s socio-political atmosphere orthodoxy has become equated with religiosity, leading many to believe that secularity and Jewishness are mutually exclusive. However this study shows that the ethnographic findings about BINA and its secular yeshiva prove otherwise. The coupling of the term secular and yeshiva is a socio-political claim against Jewish orthodox monopoly in Israel. BINA proudly claims its in-between status, representing both the secular and Jewishness, not as oppositions but simply as different cultural frameworks coming together to form BINA, and in turn these frameworks are being reimagined through BINA, embodying the processual nature of culture. Two themes guide my investigation of BINA: the ways the secular informs its operations as a Jewish educational institution, and the relationship between the collective and the individual in the secular institute. Concentrating on five secular modes of operation \u2013 literacy, multiplicity, contextual truth, activism and sovereignty, I show how Jewish inclusiveness is facilitated. I use two tracks to make my arguments regarding secular groupness: BINA\u2019s teachings and BINA\u2019s operations as an institution. Analyzing BINA\u2019s teaching I demonstrate how secular sensibilities are transmitted to students. Furthermore, I show how these secular sensibilities encourage a more inclusive perception of Jewish groupness. BINA\u2019s institutional dynamics offer a window on the way secular sensibilities guide the interplay between the individual and the collective.I argue for a new model for group identification that is more flexible and thus more inclusive. I introduce and explore the notion of inclusive groupness as a voluntary collective individualism, which achieves group cohesion through its very dynamism, flexibility and ability to foster change. The model of inclusive groupness is based on two principles: fidelity, and debate and negotiation.Thesis (Ph. D.)--Michigan State University. Anthropology, 2016Includes bibliographical references (pages 173-181

What is cost-efficient phenotyping? Optimizing costs for different scenarios

Progress in remote sensing and robotic technologies decreases the hardware costs of phenotyping. Here, we first review cost-effective imaging devices and environmental sensors, and present a trade-off between investment and manpower costs. We then discuss the structure of costs in various real-world scenarios. Hand-held low-cost sensors are suitable for quick and infrequent plant diagnostic measurements. In experiments for genetic or agronomic analyses, (i) major costs arise from plant handling and manpower; (ii) the total costs per plant/microplot are similar in robotized platform or field experiments with drones, hand-held or robotized ground vehicles; (iii) the cost of vehicles carrying sensors represents only 5–26% of the total costs. These conclusions depend on the context, in particular for labor cost, the quantitative demand of phenotyping and the number of days available for phenotypic measurements due to climatic constraints. Data analysis represents 10–20% of total cost if pipelines have already been developed. A trade-off exists between the initial high cost of pipeline development and labor cost of manual operations. Overall, depending on the context and objsectives, “cost-effective” phenotyping may involve either low investment (“affordable phenotyping”), or initial high investments in sensors, vehicles and pipelines that result in higher quality and lower operational costs

CRP 2020 Reviews: WHEAT

In 2020 the CGIAR CAS Secretariat is conducting independent reviews of the 12 CGIAR Research Programs (CRPs), including this one of WHEAT. The reviews will provide information on quality of science and effectiveness in each CRP. This review covers the Phase II years of 2017 through 2019, with a view to identifying lessons for future research modalities