Close-range hyperspectral imaging of whole plants for digital phenotyping : Recent applications and illumination correction approaches
Mishra, Puneet ; Lohumi, Santosh ; Ahmad Khan, Haris ; Nordon, Alison - \ 2020
Computers and Electronics in Agriculture 178 (2020). - ISSN 0168-1699
Digital - High throughput - Non-destructive - Phenotyping - Spectroscopy
Digital plant phenotyping is emerging as a key research domain at the interface of information technology and plant science. Digital phenotyping aims to deploy high-end non-destructive sensing techniques and information technology infrastructures to automate the extraction of both structural and physiological traits from plants under phenotyping experiments. One of the promising sensor technologies for plant phenotyping is hyperspectral imaging (HSI). The main benefit of utilising HSI compared to other imaging techniques is the possibility to extract simultaneously structural and physiological information on plants. The use of HSI for analysis of parts of plants, e.g. plucked leaves, has already been demonstrated. However, there are several significant challenges associated with the use of HSI for extraction of information from a whole plant, and hence this is an active area of research. These challenges are related to data processing after image acquisition. The hyperspectral data acquired of a plant suffers from variations in illumination owing to light scattering, shadowing of plant parts, multiple scattering and a complex combination of scattering and shadowing. The extent of these effects depends on the type of plants and their complex geometry. A range of approaches has been introduced to deal with these effects, however, no concrete approach is yet ready. In this article, we provide a comprehensive review of recent studies of close-range HSI of whole plants. Several studies have used HSI for plant analysis but were limited to imaging of leaves, which is considerably more straightforward than imaging of the whole plant, and thus do not relate to digital phenotyping. In this article, we discuss and compare the approaches used to deal with the effects of variation in illumination, which are an issue for imaging of whole plants. Furthermore, future possibilities to deal with these effects are also highlighted.
Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls
Bodkhe, Rahul ; Shetty, Sudarshan A. ; Dhotre, Dhiraj P. ; Verma, Anil K. ; Bhatia, Khushbo ; Mishra, Asha ; Kaur, Gurvinder ; Pande, Pranav ; Bangarusamy, Dhinoth K. ; Santosh, Beena P. ; Perumal, Rajadurai C. ; Ahuja, Vineet ; Shouche, Yogesh S. ; Makharia, Govind K. - \ 2019
Frontiers in Microbiology 10 (2019). - ISSN 1664-302X
Recent studies on celiac disease (CeD) have reported alterations in the gut microbiome. Whether this alteration in the microbial community is the cause or effect of the disease is not well understood, especially in adult onset of disease. The first-degree relatives (FDRs) of CeD patients may provide an opportunity to study gut microbiome in pre-disease state as FDRs are genetically susceptible to CeD. By using 16S rRNA gene sequencing, we observed that ecosystem level diversity measures were not significantly different between the disease condition (CeD), pre-disease (FDR) and control subjects. However, differences were observed at the level of amplicon sequence variant (ASV), suggesting alterations in specific ASVs between pre-disease and diseased condition. Duodenal biopsies showed higher differences in ASVs compared to fecal samples indicating larger disruption of the microbiota at the disease site. The duodenal microbiota of FDR was characterized by significant abundance of ASVs belonging to Parvimonas, Granulicatella, Gemella, Bifidobacterium, Anaerostipes, and Actinomyces genera. The duodenal microbiota of CeD was characterized by higher abundance of ASVs from genera Megasphaera and Helicobacter compared to the FDR microbiota. The CeD and FDR fecal microbiota had reduced abundance of ASVs classified as Akkermansia and Dorea when compared to control group microbiota. In addition, predicted functional metagenome showed reduced ability of gluten degradation by CeD fecal microbiota in comparison to FDRs and controls. The findings of the present study demonstrate differences in ASVs and predicts reduced ability of CeD fecal microbiota to degrade gluten compared to the FDR fecal microbiota. Further research is required to investigate the strain level and active functional profiles of FDR and CeD microbiota to better understand the role of gut microbiome in pathophysiology of CeD.
Calcium Carbonate Packed Electrochemical Precipitation Column: New Concept of Phosphate Removal and Recovery
Lei, Yang ; Narsing, Santosh ; Saakes, Michel ; Weijden, Renata D. Van Der; Buisman, Cees J.N. - \ 2019
Environmental Science and Technology 53 (2019)18. - ISSN 0013-936X
Phosphorus (P) is a vital micronutrient element for all life forms. Typically, P can be extracted from phosphate rock. Unfortunately, the phosphate rock is a nonrenewable resource with a limited reserve on the earth. High levels of P discharged to water bodies lead to eutrophication. Therefore, P needs to be removed and is preferably recovered as an additional P source. A possible way to achieve this goal is by electrochemically induced phosphate precipitation with coexisting calcium ions. Here, we report a new concept of phosphate removal and recovery, namely a CaCO3 packed electrochemical precipitation column, which achieved improved removal efficiency, shortened hydraulic retention time, and substantially enhanced stability, compared with our previous electrochemical system. The concept is based on the introduction of CaCO3 particles, which facilitates calcium phosphate precipitation by buffering the formed H+ at the anode, releases Ca2+, acts as seeds, and establishes a high pH environment in the bulk solution in addition to that in the vicinity of the cathode. It was found that the applied current, the CaCO3 particle size, and the feed rate affect the removal of phosphate. Under optimized conditions (particle size, <0.5 mm; feed rate, 0.4 L/d; current, 5 mA), in a continuous flow system, the CaCO3 packed electrochemical precipitation column achieved 90 ± 5% removal of phosphate in 40 days and >50% removal over 125 days with little maintenance. The specific energy consumptions of this system lie between 29 and 61 kWh/kg P. The experimental results demonstrate the promising potential of the CaCO3 packed electrochemical precipitation column for P removal and recovery from P-containing streams.
Twenty-three unsolved problems in hydrology (UPH)–a community perspective
Blöschl, Günter ; Bierkens, Marc F.P. ; Chambel, Antonio ; Cudennec, Christophe ; Destouni, Georgia ; Fiori, Aldo ; Kirchner, James W. ; McDonnell, Jeffrey J. ; Savenije, Hubert H.G. ; Sivapalan, Murugesu ; Stumpp, Christine ; Toth, Elena ; Volpi, Elena ; Carr, Gemma ; Lupton, Claire ; Salinas, Josè ; Széles, Borbála ; Viglione, Alberto ; Aksoy, Hafzullah ; Allen, Scott T. ; Amin, Anam ; Andréassian, Vazken ; Arheimer, Berit ; Aryal, Santosh K. ; Baker, Victor ; Bardsley, Earl ; Barendrecht, Marlies H. ; Bartosova, Alena ; Batelaan, Okke ; Berghuijs, Wouter R. ; Beven, Keith ; Blume, Theresa ; Bogaard, Thom ; Borges de Amorim, Pablo ; Böttcher, Michael E. ; Boulet, Gilles ; Breinl, Korbinian ; Brilly, Mitja ; Brocca, Luca ; Buytaert, Wouter ; Castellarin, Attilio ; Castelletti, Andrea ; Chen, Xiaohong ; Chen, Yangbo ; Chen, Yuanfang ; Chifflard, Peter ; Claps, Pierluigi ; Clark, Martyn P. ; Collins, Adrian L. ; Croke, Barry ; Dathe, Annette ; David, Paula C. ; Barros, Felipe P.J. de; Rooij, Gerrit de; Baldassarre, Giuliano Di; Driscoll, Jessica M. ; Duethmann, Doris ; Dwivedi, Ravindra ; Eris, Ebru ; Farmer, William H. ; Feiccabrino, James ; Ferguson, Grant ; Ferrari, Ennio ; Ferraris, Stefano ; Fersch, Benjamin ; Finger, David ; Foglia, Laura ; Fowler, Keirnan ; Gartsman, Boris ; Gascoin, Simon ; Gaume, Eric ; Gelfan, Alexander ; Geris, Josie ; Gharari, Shervan ; Gleeson, Tom ; Glendell, Miriam ; Gonzalez Bevacqua, Alena ; González-Dugo, María P. ; Grimaldi, Salvatore ; Gupta, A.B. ; Guse, Björn ; Han, Dawei ; Hannah, David ; Harpold, Adrian ; Haun, Stefan ; Heal, Kate ; Helfricht, Kay ; Herrnegger, Mathew ; Hipsey, Matthew ; Hlaváčiková, Hana ; Hohmann, Clara ; Holko, Ladislav ; Hopkinson, Christopher ; Hrachowitz, Markus ; Illangasekare, Tissa H. ; Inam, Azhar ; Innocente, Camyla ; Istanbulluoglu, Erkan ; Jarihani, Ben ; Kalantari, Zahra ; Kalvans, Andis ; Khanal, Sonu ; Khatami, Sina ; Kiesel, Jens ; Kirkby, Mike ; Knoben, Wouter ; Kochanek, Krzysztof ; Kohnová, Silvia ; Kolechkina, Alla ; Krause, Stefan ; Kreamer, David ; Kreibich, Heidi ; Kunstmann, Harald ; Lange, Holger ; Liberato, Margarida L.R. ; Lindquist, Eric ; Link, Timothy ; Liu, Junguo ; Loucks, Daniel Peter ; Luce, Charles ; Mahé, Gil ; Makarieva, Olga ; Malard, Julien ; Mashtayeva, Shamshagul ; Maskey, Shreedhar ; Mas-Pla, Josep ; Mavrova-Guirguinova, Maria ; Mazzoleni, Maurizio ; Mernild, Sebastian ; Misstear, Bruce Dudley ; Montanari, Alberto ; Müller-Thomy, Hannes ; Nabizadeh, Alireza ; Nardi, Fernando ; Neale, Christopher ; Nesterova, Nataliia ; Nurtaev, Bakhram ; Odongo, Vincent O. ; Panda, Subhabrata ; Pande, Saket ; Pang, Zhonghe ; Papacharalampous, Georgia ; Perrin, Charles ; Pfister, Laurent ; Pimentel, Rafael ; Polo, María J. ; Post, David ; Prieto Sierra, Cristina ; Ramos, Maria Helena ; Renner, Maik ; Reynolds, José Eduardo ; Ridolfi, Elena ; Rigon, Riccardo ; Riva, Monica ; Robertson, David E. ; Rosso, Renzo ; Roy, Tirthankar ; Sá, João H.M. ; Salvadori, Gianfausto ; Sandells, Mel ; Schaefli, Bettina ; Schumann, Andreas ; Scolobig, Anna ; Seibert, Jan ; Servat, Eric ; Shafiei, Mojtaba ; Sharma, Ashish ; Sidibe, Moussa ; Sidle, Roy C. ; Skaugen, Thomas ; Smith, Hugh ; Spiessl, Sabine M. ; Stein, Lina ; Steinsland, Ingelin ; Strasser, Ulrich ; Su, Bob ; Szolgay, Jan ; Tarboton, David ; Tauro, Flavia ; Thirel, Guillaume ; Tian, Fuqiang ; Tong, Rui ; Tussupova, Kamshat ; Tyralis, Hristos ; Uijlenhoet, Remko ; Beek, Rens van; Ent, Ruud J. van der; Ploeg, Martine van der; Loon, Anne F. Van; Meerveld, Ilja van; Nooijen, Ronald van; Oel, Pieter R. van; Vidal, Jean Philippe ; Freyberg, Jana von; Vorogushyn, Sergiy ; Wachniew, Przemyslaw ; Wade, Andrew J. ; Ward, Philip ; Westerberg, Ida K. ; White, Christopher ; Wood, Eric F. ; Woods, Ross ; Xu, Zongxue ; Yilmaz, Koray K. ; Zhang, Yongqiang - \ 2019
Hydrological Sciences Journal 64 (2019)10. - ISSN 0262-6667 - p. 1141 - 1158.
hydrology - interdisciplinary - knowledge gaps - research agenda - science questions
This paper is the outcome of a community initiative to identify major unsolved scientific problems in hydrology motivated by a need for stronger harmonisation of research efforts. The procedure involved a public consultation through online media, followed by two workshops through which a large number of potential science questions were collated, prioritised, and synthesised. In spite of the diversity of the participants (230 scientists in total), the process revealed much about community priorities and the state of our science: a preference for continuity in research questions rather than radical departures or redirections from past and current work. Questions remain focused on the process-based understanding of hydrological variability and causality at all space and time scales. Increased attention to environmental change drives a new emphasis on understanding how change propagates across interfaces within the hydrological system and across disciplinary boundaries. In particular, the expansion of the human footprint raises a new set of questions related to human interactions with nature and water cycle feedbacks in the context of complex water management problems. We hope that this reflection and synthesis of the 23 unsolved problems in hydrology will help guide research efforts for some years to come.
Learning to cope with water variability through participatory monitoring: the case study of the Mountainous region, Nepal
Regmi, Santosh ; Bhusal, Jagat K. ; Gurung, Praju ; Zulkafli, Zed ; Karpouzoglou, T.D. ; Ochoa-Tocachi, Boris F. ; Buytaert, Wouter ; Mao, Feng - \ 2019
Meteorology Hydrology and Water Management 7 (2019)2. - ISSN 2299-3835 - 13 p.
Participatory monitoring allows communities to understand the use and management of local water resources and at the same time develop a sense of ownership of environmental information. The data generated through
participatory monitoring of stream flow and rainfall generate evidences to corroborate local people’s experiences with changing water resources patterns. In this study we evaluate the potential of participatory monitoring of hydrological
variables to improve scarce water supply utilization in agriculture. The case study site is the Mustang district in Nepal, which is located in the Upper Kaligandaki River Basin in the Himalayas with unique and complex geographical
and climatic features. This region is characterized by a semi-arid climate with total annual precipitation of less than 300 mm. Water supply, agricultural land, and livestock grazing are the key ecosystem services that underpin livelihood
security of the local population, particularly socio-economically vulnerable groups. An analysis of the measured stream flow data indicate that annual flow of water in the stream can meet the current crop irrigation water needs for
the agricultural land of the research site. The data provide local farmers a new way of understanding local water needs. Participatory monitoring would contribute to an optimization of the use of ecosystem services to support economic
development and livelihood improvement.
Water as “Time-Substance” : The Hydrosocialities of Climate Change in Nepal
Clark, Julian ; Gurung, Praju ; Chapagain, Prem Sagar ; Regmi, Santosh ; Bhusal, Jagat K. ; Karpouzoglou, Timothy ; Mao, Feng ; Dewulf, Art - \ 2017
Annals of the American Association of Geographers 107 (2017)6. - ISSN 2469-4452 - p. 1351 - 1369.
This article develops a novel theoretical framework to explain how water's situatedness relates to its political agency. Recent posthuman scholarship emphasizes these qualities but, surprisingly, no sustained analysis has been undertaken of this interrelation. Here we do so by theorizing water as a “time-substance” to reposition human hydrological struggles (including those exacerbated by climate change) around the topologies and temporalities rather than the spatialities of water. This innovative approach opens up new areas of geographical enquiry based on hydrosocial forms, hydrosocial transformations, and hydrosocial information (collectively referred to here as hydrosocialities). We contend that hydrosocialities enable the tracing of human–water relations that transcend times and scales and the matricial categories of subject and object to overcome the situated–agential binary of water. Drawing on two years of fieldwork in Mustang, Nepal, this conceptual framework is deployed to examine hydrosocialities in two remote mountain communities. We show hydrosocialities that comprise diverse water knowledge practices constituted from multiple points of proximity between the social and the hydrological in space and time. In turn, this conceptual framework underscores the importance of boundary objects in mediating water's situated–agential qualities. The article concludes that consequently boundary objects can play a crucial role in producing new practical hydrosocial politics of climate change mitigation and adaptation.
Soil protistology rebooted: 30 fundamental questions to start with
Geisen, Stefan ; Mitchell, Edward A.D. ; Wilkinson, David M. ; Adl, Sina ; Bonkowski, Michael ; Brown, Matthew W. ; Fiore-Donno, Anna Maria ; Heger, Thierry J. ; Jassey, Vincent E.J. ; Krashevska, Valentyna ; Lahr, Daniel J.G. ; Marcisz, Katarzyna ; Mulot, Matthieu ; Payne, Richard ; Singer, David ; Anderson, O.R. ; Charman, Dan J. ; Ekelund, Flemming ; Griffiths, Bryan S. ; Rønn, Regin ; Smirnov, Alexey ; Bass, David ; Belbahri, Lassaâd ; Berney, Cédric ; Blandenier, Quentin ; Chatzinotas, Antonis ; Clarholm, Marianne ; Dunthorn, Micah ; Feest, Alan ; Fernández, Leonardo D. ; Foissner, Wilhelm ; Fournier, Bertrand ; Gentekaki, Eleni ; Hájek, Michal ; Helder, Hans ; Jousset, Alexandre ; Koller, Robert ; Kumar, Santosh ; Terza, Antonietta La; Lamentowicz, Mariusz ; Mazei, Yuri ; Santos, Susana S. ; Seppey, Christophe V.W. ; Spiegel, Frederick W. ; Walochnik, Julia ; Winding, Anne ; Lara, Enrique - \ 2017
Soil Biology and Biochemistry 111 (2017). - ISSN 0038-0717 - p. 94 - 103.
Protists are the most diverse eukaryotes. These microbes are keystone organisms of soil ecosystems and
regulate essential processes of soil fertility such as nutrient cycling and plant growth. Despite this,
protists have received little scientific attention, especially compared to bacteria, fungi and nematodes in
soil studies. Recent methodological advances, particularly in molecular biology techniques, have made
the study of soil protists more accessible, and have created a resurgence of interest in soil protistology.
This ongoing revolution now enables comprehensive investigations of the structure and functioning of
soil protist communities, paving the way to a new era in soil biology. Instead of providing an exhaustive
review, we provide a synthesis of research gaps that should be prioritized in future studies of soil
protistology to guide this rapidly developing research area. Based on a synthesis of expert opinion we
propose 30 key questions covering a broad range of topics including evolution, phylogenetics, functional
ecology, macroecology, paleoecology, and methodologies. These questions highlight a diversity of topics
that will establish soil protistology as a hub discipline connecting different fundamental and applied
fields such as ecology, biogeography, evolution, plant-microbe interactions, agronomy, and conservation
biology. We are convinced that soil protistology has the potential to be one of the most exciting frontiers
Mountains Under Pressure: Evaluating Ecosystem Services and Livelihoods in the Upper Himalayan Region of Nepal
Bhusal, Jagat K. ; Chapagain, Prem Sagar ; Regmi, Santosh ; Gurung, Praju ; Zulkafli, Zed ; Karpouzoglou, T.D. ; Pandeya, Bhopal ; Buytaert, Wouter ; Clark, Julian - \ 2016
International Journal of Ecology and Environmental Sciences 42 (2016)3. - ISSN 0377-015X - p. 217 - 226.
water scarcity - poverty - adaptations - Trans-Himalaya - Upper Mustang
Natural resource-based livelihoods in mountainous regions are subject to new types of development as well as climate related pressures and vulnerabilities. On one hand, the integrity of the mountainous landscape is under pressure from the melting of glaciers, changes in water availability, rainfall patterns, and soil degradation. On the other hand, as mountainous environments become increasingly more important in national growth strategies and development priorities, new avenues for livelihoods and vulnerabilities become more pronounced. Climate change effects are expected to be disproportionately higher in mountainous regions. There is therefore a critical urgency to better comprehend these changes shaping mountainous environments and to better
assess future direct and indirect impacts on ecosystem services and livelihoods.
This article presents the results of an analysis of ecosystem services and livelihoods in the Upper Mustang region of Nepal. The region was selected for its particular trans-Himalayan location, development diversity, and climatic changes that have placed increasing pressure on local ecosystem services. We examine the central role of ecosystem services for remote mountain regions, particularly for the poor, the existing pressures on the key ecosystem services and local ways of adapting to climate-induced effect to ecosystem services and, cogeneration of the knowledge gaps and co-production of knowledge with communities to support local adaptation strategies. We adopted a combination of qualitative and quantitative analytical approaches. We found significant implications for local livelihoods and adaptation strategies with reference to water for farming, pasture productivity and livestock rearing, as well as tourism development. Additionally, we highlight knowledge gaps in assessing ecosystem services and opportunities for local monitoring that may close in on the gaps with an end goal of overcoming poverty.
Seepage analysis underneath the headwork of Chanda Mohana Irrigation Scheme, Sunsari, Nepal
Kaini, Santosh ; Hayde, L.G. ; Schultz, B. ; Marence, M. - \ 2011
In: Proceedings National Irrigation Seminar, Department of Irrigation/Nepal, International Network for Participatory Irrigation Management (INPIM)/Nepal and IWMI/Nepal. - - p. 21 - 21.
|Texture segmentation of broad-leaved dock (Rumex obtusifolius)
Atni Hiremath, Santosh - \ 2010
|Image texture analyses
Atni Hiremath, Santosh - \ 2010