New phenotyping approach analyzes crop traits at the 3D level

Researchers devise a novel method for the accurate quantification of crop traits using multi-source data and time-series images

Peer-Reviewed Publication

NANJING AGRICULTURAL UNIVERSITY THE ACADEMY OF SCIENCE

 

IMAGE: (A) IMAGE PROCESSING PROCESS (ORTHORECTIFIED IMAGES OF MAIZE POPULATIONS IN THE FIELD AFTER PROCESSING WITH OPENDRONEMAP SOFTWARE, BINARIZED IMAGES, AND PLANT PROFILE EXTRACTION RESULTS). (B) POINT CLOUD OBTAINED FROM VELODYNE (TOP HALF) AND AN EXAMPLE OF THE IMAGE-ALIGNED POINT CLOUD (BOTTOM HALF). (EXAMPLES OF SEEDLING IMAGES AND TIME-SERIES POINT CLOUD ARE ALIGNED ACCORDING TO THE PROCESS.) (C) OVERVIEW OF TIME-SERIES DATA ALIGNMENT USING TIME-SERIES IMAGE ALIGNMENT AND DATA FUSION. view more 

CREDIT: PLANT PHENOMICS

The steady decline in cultivable land owing to the rapidly increasing global population has necessitated the use of efficient plant breeding methods that could be used to improve agricultural yields. However, in addition to genetic methods, we need approaches to control and improve complex crop traits. To this end, plant scientists make use of various cutting-edge imaging techniques that quantify crop traits (height, leaf shape, leaf color, etc.). Traditional imaging methods, however, are tedious, destructive, and non-sustainable. Moreover, since plants exist in a three-dimensional (3D) space, making accurate estimation is difficult using two-dimensional (2D) images.

The high throughput phenotyping (HTP) platform enables field data collection on a regular basis. It captures images using RGB (red, green, and blue) cameras and Light Detection and Ranging (LiDAR). The RGB camera produces high-resolution images from which traits such as canopy structure and the number and appearance of specific plant organs can be extracted. While RGB cameras are affected by light, LiDAR is not. As a result, LiDAR is widely used in self-driven vehicles for mapping and navigation. So, can LiDAR provide detailed descriptions of crop features as well?

To answer this question, scientists from China have now developed a rail-based field phenotyping technique that uses LiDAR for quantifying plant traits. The study led by Professor Xinyu Guo from National Engineering Research Center for Information Technology in Agriculture, China, was recently published in Plant Phenomics on 28 March 2023. Prof. Guo explains, “It is difficult to align the point cloud data and extract accurate phenotypic traits of plant populations. In this study, high-throughput, time-series raw data of field maize populations were collected using a field rail-based phenotyping platform with LiDAR and an RGB camera.”

The research team incorporated LiDAR into the design of the rail-based field phenotyping platform.  To achieve this, the research team used orthorectification, a process that converts raw field images into usable forms by removing sensor, motion, and terrain-related distortions. The rectified images were then used to accurately quantify various crop traits after subjecting them to algorithmic processing.

Next, the team used time-series-based high-throughput plant phenotyping to determine plant height in a maize field. This method entails studying field images captured at regular time intervals to perform non-destructive analysis of the desired plant traits (in this case, plant height).

“Alignment errors in time-series point cloud data were minimized by coupling field orthorectified images and point clouds. The proposed method integrates point cloud data acquisition, alignment, filtering, and segmentation algorithms,” adds Prof. Guo.

The results were impressive and reassuring: The plant heights of 13 maize cultivars obtained using the aforementioned technique strongly correlated with the manual measurements. In other words, plant height determined using the rail-based field phenotyping platform was in agreement with the height measured using established manual techniques. The research team also noted that the measurement accuracy increased when data acquired from multiple sources replaced single-source data.

Although effective, the technique has a few drawbacks. For example, during image acquisition, leaf crossing, shading, and overlapping result in partial data loss. The team is working to resolve these issues.

“The method can also be used to compare growth rates between cultivars or estimate botanical traits, which are features of interest to crop modelers and breeders. Therefore, this research can provide data supporting modern breeding,” concludes Prof. Guo. 

Kudos to the research team for their phenomenal innovations!      

###

Reference

Authors

Yinglun Li,1,2 Weiliang Wen,1,2 Jiangchuan Fan,1,2 Wenbo Gou,1,2 Shenghao Gu,1,2 Xianju Lu,1,2 Zetao Yu,2 Xiaodong Wang,2 and Xinyu Guo1,2

Affiliations

1Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.

2Beijing Key Lab of Digital Plant, National Engineering Research Center for Information Technology in Agriculture, Beijing 100097, China.

---

JOURNAL

Plant Phenomics

DOI

10.34133/plantphenomics.0043 

METHOD OF RESEARCH

Computational simulation/modeling

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Multi-Source Data Fusion Improves Time-Series Phenotype Accuracy in Maize under a Field High-Throughput Phenotyping Platform

ARTICLE PUBLICATION DATE

20-Apr-2023

Enhanced performance of oxygen vacancies on CO2 adsorption and activation over different phases of ZrO2

Peer-Reviewed Publication

HIGHER EDUCATION PRESS

 

IMAGE: ACTIVATION PROCESS OF CO2 ON C-ZRO2, T-ZRO2, M-ZRO2 SURFACES WITH THE PRESENCE OF OXYGEN VACANCIES view more 

CREDIT: HIGHER EDUCATION PRESS LIMITED COMPANY

Excessive use of fossil energy causes global warming and other environmental problems. To reduce the greenhouse effect, two major greenhouse gases-CO2 and CH4 as the feedback are used to produce syngas (CO and H2) by CO2-CH4 reforming technique (DRM). The key to DRM is the choice of catalyst. The catalyst for DRM reaction mainly consists of two parts: the active metal and the support, in which a suitable support plays an important role in promoting the reaction activity and stability. Currently, ZrO2 is considered as a promising catalyst support due to the presence of oxygen vacancies. However, studies on the effect of oxygen vacancies on the ZrO2 surface for CO2 adsorption and activation processes are still lacking.

A research group of Juntian Niu from Taiyuan University of Technology investigated the effect of oxygen vacancies for the adsorption and activation of CO2 on the surface ZrO2 by density functional theory (DFT) calculations. They found that the oxygen vacancies contribute greatly to both the adsorption and activation of CO2, and the essence lies in oxygen vacancies greatly facilitate the charge transfer from the ZrO2 surface to the CO2 molecule. Additionally, it was found that t-ZrO2 with the presence of oxygen vacancies is most favorable to the adsorption and activation of CO2 by the comparison of different ZrO2 crystalline phases.

The new findings elucidated the role of oxygen vacancies in CO2 adsorption and activation for the preparation of high-performance DRM reaction catalysts using ZrO2. Meanwhile, it provided guidance for the design of CO2 high-efficient catalysts at an atomic level.

These findings were published in Frontiers in Energy on February 28.

###

About Higher Education Press

Founded in May 1954, Higher Education Press Limited Company (HEP), affiliated with the Ministry of Education, is one of the earliest institutions committed to educational publishing after the establishment of P. R. China in 1949. After striving for six decades, HEP has developed into a major comprehensive publisher, with products in various forms and at different levels. Both for import and export, HEP has been striving to fill in the gap of domestic and foreign markets and meet the demand of global customers by collaborating with more than 200 partners throughout the world and selling products and services in 32 languages globally. Now, HEP ranks among China's top publishers in terms of copyright export volume and the world's top 50 largest publishing enterprises in terms of comprehensive strength.

The Frontiers Journals series published by HEP includes 28 English academic journals, covering the largest academic fields in China at present. Among the series, 12 have been indexed by SCI, 6 by EI, 2 by MEDLINE, 1 by A&HCI. HEP's academic monographs have won about 300 different kinds of publishing funds and awards both at home and abroad.

 

About Frontiers in Energy

Frontiers in Energy, a peer-reviewed international journal launched in January 2007, presents a unique platform for reporting the most advanced research and strategic thinking on energy technology. The Journal publishes review and mini-review articles, original research articles, perspective, news & highlights, viewpoints, comments, etc. by individual researchers and research groups. The journal is strictly peer-reviewed and accepts only original submissions in English. The scope of the Journal covers (but not limited to): energy conversion and utilization; renewable energy; energy storage; hydrogen and fuel cells; carbon capture, utilization and storage; advanced nuclear technology; smart grids and microgrids; power and energy systems; power cells and electric vehicles; building energy conservation, energy and environment; energy economy and policy, etc. Interdisciplinary papers are encouraged.

 

---

JOURNAL

Frontiers in Energy

DOI

10.1007/s11708-023-0867-7 

METHOD OF RESEARCH

Experimental study

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Enhanced performance of oxygen vacancies on CO2 adsorption and activation over different phases of ZrO2

UGA researchers use AI to discover new planet outside solar system

The exoplanet was detected using machine learning, a branch of artificial intelligence

Peer-Reviewed Publication

UNIVERSITY OF GEORGIA

A University of Georgia research team has confirmed evidence of a previously unknown planet outside of our solar system, and they used machine learning tools to detect it.

A recent study by the team showed that machine learning can correctly determine if an exoplanet is present by looking in protoplanetary disks, the gas around newly formed stars.

The newly published findings represent a first step toward using machine learning to identify previously overlooked exoplanets.

“We confirmed the planet using traditional techniques, but our models directed us to run those simulations and showed us exactly where the planet might be,” said Jason Terry, doctoral student in the UGA Franklin College of Arts and Sciences department of physics and astronomy and lead author on the study.

“When we applied our models to a set of older observations, they identified a disk that wasn't known to have a planet despite having already been analyzed. Like previous discoveries, we ran simulations of the disk and found that a planet could re-create the observation.”

According to Terry, the models suggested a planet’s presence, indicated by several images that strongly highlighted a particular region of the disk that turned out to have the characteristic sign of a planet — an unusual deviation in the velocity of the gas near the planet. 

“This is an incredibly exciting proof of concept. We knew from our previous work that we could use machine learning to find known forming exoplanets,” said Cassandra Hall, assistant professor of computational astrophysics and principal investigator of the Exoplanet and Planet Formation Research Group at UGA. “Now, we know for sure that we can use it to make brand new discoveries.”

The discovery highlights how machine learning has the power to enhance scientists’ work, utilizing artificial intelligence as an added tool to expand researchers’ accuracy and more efficiently economize their time when engaged in such a vast endeavor as investigating deep, outer space.

The models were able to detect a signal in data that people had already analyzed; they found something that previously had gone undetected.

“This demonstrates that our models — and machine learning in general — have the ability to quickly and accurately identify important information that people can miss. This has the potential to dramatically speed up analysis and subsequent theoretical insights,” Terry said. “It only took about an hour to analyze that entire catalog and find strong evidence for a new planet in a specific spot, so we think there will be an important place for these types of techniques as our datasets get even larger.” 

---

JOURNAL

The Astrophysical Journal

DOI

10.3847/1538-4357/acc737 

ARTICLE TITLE

Kinematic Evidence of an Embedded Protoplanet in HD 142666 Identified by Machine Learning

ARTICLE PUBLICATION DATE

21-Apr-2023

Is sex in space being taken seriously by the emerging space tourism sector?

Sex in space is a real possibility with the expected growth in space tourism over the next decade, says Cranfield University-led paper

Reports and Proceedings

CRANFIELD UNIVERSITY

• Sex in space is a real possibility with the expected growth in space tourism over the next decade, says Cranfield University-led paper
• Researchers say the expected motivations and behaviours of space tourists will differ from that of professional astronauts
• Green paper published today highlights the biological and commercial risk of human conception in space and urges open discussion of this among the space tourism sector and wider communities

It could be a crucial question posed by the expected growth in space tourism over the next decade – namely what would a human conception in space mean for the sector?

That’s the situation posed by an international group of scientists, clinicians and other interested parties, who have authored a consultative green paper led by David Cullen, Professor of Astrobiology & Space Biotechnology at Cranfield University.

It highlights that the emerging space tourism sector has not openly considered or discussed the risks of sex in space or prepared suitable mitigation approaches. It argues it is unrealistic to assume all future space tourists will abstain from sexual activities – opening the possibility of human conception and the early stages of human reproduction occurring in space.

This appears to pose several risks, those of a biological nature such as embryo developmental risks and those of a commercial nature such as liability, litigation, and reputational damage. The authors recommend that an open discussion is now needed within the space tourism industry to consider the risks.

Open discussion on human conception in space tourism is lacking

Professor Cullen from Cranfield University led the work. He said: “Our starting point was a throwaway comment about sex in space, but when we checked, we were surprised the sector has not openly considered the risks and this led to the study.”

The green paper strongly recommends that all the relevant parties involved in the space tourism sector enter into open discussions concerning the risks and mitigations, and develop and disseminate best practice approaches within the sector.

The findings of the study have been published today (24 April) as a green paper for community consultation.

Human reproduction outside of Earth should be taken seriously

Egbert Edelbroek, the head of SpaceBorn United, a Netherlands-based organisation researching human reproduction in space, helped to coordinate the study. He said: “Given the long-term importance of human reproduction beyond Earth, as humanity is trying to become a multi-planetary species, we need to take seriously the possible first step, whether this is planned, or especially if unplanned.”

Alex Layendecker, director of the Astrosexological Research Institute and a co-author of the green paper, said: “The sociological and cultural aspects are fascinating to consider, given the approaching shift from well-trained professional and private astronauts to true ‘space tourists’. That shift will encapsulate changes in motivations, social interactions, and behavioural norms, the impacts of which we need to take seriously.”

The paper will be debated in a parallel session alongside the upcoming Space Tourism Conference 2023 on 28 April in Los Angeles, USA.

 

Vaccine printer could help vaccines reach more people

The printer generates vaccine-filled microneedle patches that can be stored long-term at room temperature and applied to the skin

Peer-Reviewed Publication

MASSACHUSETTS INSTITUTE OF TECHNOLOGY

PrintEmail App

 

IMAGE: INSIDE THE PRINTER, A ROBOTIC ARM INJECTS INK INTO MICRONEEDLE MOLDS, AND A VACUUM CHAMBER BELOW THE MOLD SUCKS THE INK DOWN TO THE BOTTOM. PICTURED IS AN EXAMPLE OF THE MOLD. view more 

CREDIT: MIT

CAMBRIDGE, MA -- Getting vaccines to people who need them isn’t always easy. Many vaccines require cold storage, making it difficult to ship them to remote areas that don’t have the necessary infrastructure.

MIT researchers have come up with a possible solution to this problem: a mobile vaccine printer that could be scaled up to produce hundreds of vaccine doses in a day. This kind of printer, which can fit on a tabletop, could be deployed anywhere vaccines are needed, the researchers say.

“We could someday have on-demand vaccine production,” says Ana Jaklenec, a research scientist at MIT’s Koch Institute for Integrative Cancer Research. “If, for example, there was an Ebola outbreak in a particular region, one could ship a few of these printers there and vaccinate the people in that location.”

The printer produces patches with hundreds of microneedles containing vaccine. The patch can be attached to the skin, allowing the vaccine to dissolve without the need for a traditional injection. Once printed, the vaccine patches can be stored for months at room temperature.

In a study appearing today in Nature Biotechnology, the researchers showed they could use the printer to produce thermostable Covid-19 RNA vaccines that could induce a comparable immune response to that generated by injected RNA vaccines, in mice.

Jaklenec and Robert Langer, the David H. Koch Institute Professor at MIT and a member of the Koch Institute, are the senior authors of the study. The paper’s lead authors are former MIT postdoc Aurelien vander Straeten, former MIT graduate student Morteza Sarmadi ’21, and postdoc John Daristotle.

Printing vaccines

Most vaccines, including mRNA vaccines, have to be refrigerated while stored, making it difficult to stockpile them or send them to locations where those temperatures can’t be maintained. Furthermore, they require syringes, needles, and trained health care professionals to administer them.

To get around this obstacle, the MIT team set out to find a way to produce vaccines on demand. Their original motivation, before Covid-19 arrived, was to build a device that could quickly produce and deploy vaccines during outbreaks of diseases such as Ebola. Such a device could be shipped to a remote village, a refugee camp, or military base to enable rapid vaccination of large numbers of people.

Instead of producing traditional injectable vaccines, the researchers decided to work with a novel type of vaccine delivery based on patches about the size of a thumbnail, which contain hundreds of microneedles. Such vaccines are now in development for many diseases, including polio, measles, and rubella. When the patch is applied to the skin, the tips of the needles dissolve under the skin, releasing the vaccine.

“When Covid-19 started, concerns about vaccine stability and vaccine access motivated us to try to incorporate RNA vaccines into microneedle patches,” Daristotle says.

The “ink” that the researchers use to print the vaccine-containing microneedles includes RNA vaccine molecules that are encapsulated in lipid nanoparticles, which help them to remain stable for long periods of time.

The ink also contains polymers that can be easily molded into the right shape and then remain stable for weeks or months, even when stored at room temperature or higher. The researchers found that a 50/50 combination of polyvinylpyrrolidone and polyvinyl alcohol, both of which are commonly used to form microneedles, had the best combination of stiffness and stability.

Inside the printer, a robotic arm injects ink into microneedle molds, and a vacuum chamber below the mold sucks the ink down to the bottom, making sure that ink reaches all the way to the tips of the needles. Once the molds are filled, they take a day or two to dry. The current prototype can produce 100 patches in 48 hours, but the researchers anticipate that future versions could be designed to have higher capacity.

Antibody response

To test the long-term stability of the vaccines, the researchers first created an ink containing RNA that encodes luciferase, a fluorescent protein. They applied the resulting microneedle patches to mice after being stored at either 4 degrees Celsius or 25 degrees Celsius (room temperature) for up to six months. They also stored one batch of the particles at 37 degrees Celsius for one month.

Under all of these storage conditions, the patches induced a strong fluorescent response when applied to mice. In contrast, the fluorescent response produced by a traditional intramuscular injection of the fluorescent-protein-encoding RNA declined with longer storage times at room temperature.

Then, the researchers tested their Covid-19 microneedle vaccine. They vaccinated mice with two doses of the vaccine, four weeks apart, then measured their antibody response to the virus. Mice vaccinated with the microneedle patch had a similar response to mice vaccinated with a traditional, injected RNA vaccine.

The researchers also saw the same strong antibody response when they vaccinated mice with microneedle patches that had been stored at room temperature for up to three months.

“This work is particularly exciting as it realizes the ability to produce vaccines on demand,” says Joseph DeSimone, a professor of translational medicine and chemical engineering at Stanford University, who was not involved in the research. “With the possibility of scaling up vaccine manufacturing and improved stability at higher temperatures, mobile vaccine printers can facilitate widespread access to RNA vaccines.”

While this study focused on Covid-19 RNA vaccines, the researchers plan to adapt the process to produce other types of vaccines, including vaccines made from proteins or inactivated viruses.

“The ink composition was key in stabilizing mRNA vaccines, but the ink can contain various types of vaccines or even drugs, allowing for flexibility and modularity in what can be delivered using this microneedle platform,” Jaklenec says.

Other authors of the paper are Maria Kanelli, Lisa Tostanoski, Joe Collins, Apurva Pardeshi, Jooli Han, Dhruv Varshney, Behnaz Eshaghi, Johnny Garcia, Timothy Forster, Gary Li, Nandita Menon, Sydney Pyon, Linzixuan Zhang, Catherine Jacob-Dolan, Olivia Powers, Kevin Hall, Shahad Alsaiari, Morris Wolf, Mark Tibbitt, Robert Farra, and Dan Barouch.

###

The research was funded by the Biomedical Advanced Research and Development Authority (BARDA), the Belgian American Educational Foundation, Wallonia-Brussels International, the Bodossaki Foundation, the Onassis Foundation, the National Institutes of Health, and the Koch Institute Support (core) Grant from the National Cancer Institute.

  

The printer produces patches with hundreds of microneedles containing vaccine. The patch can be attached to the skin, allowing the vaccine to dissolve without the need for a traditional injection.

CREDIT

MIT

JOURNAL

Nature Biotechnology

DOI

10.1038/s41587-023-01774-z 

SUBJECT OF RESEARCH

Animals

ARTICLE TITLE

A microneedle vaccine printer for thermostable COVID-19 mRNA vaccines

ARTICLE PUBLICATION DATE

24-Apr-2023

Scientists have full state of a quantum liquid down cold

New research, using ultracold atoms, reveals particular properties of quantum systems

Peer-Reviewed Publication

NEW YORK UNIVERSITY

 

IMAGE: IN THE HEART OF THE EXPERIMENTAL SETUP SITS THE ATOMCHIP IN A VACUUM CHAMBER IN SCHMIEDMAYER LAB AT THE ATOMINSTITUT OF TU WIEN IN VIENNA. view more 

CREDIT: THOMAS SCHWEIGLER

A team of physicists has illuminated certain properties of quantum systems by observing how their fluctuations spread over time. The research offers an intricate understanding of a complex phenomenon that is foundational to quantum computing—a method that can perform certain calculations significantly more efficiently than conventional computing. 

“In an era of quantum computing it’s vital to generate a precise characterization of the systems we are building,” explains Dries Sels, an assistant professor in New York University’s Department of Physics and an author of the paper, which appears in the journal Nature Physics. “This work reconstructs the full state of a quantum liquid, consistent with the predictions of a quantum field theory—similar to those that describe the fundamental particles in our universe.”

Sels adds that the breakthrough offers promise for technological advancement.

“Quantum computing relies on the ability to generate entanglement between different subsystems, and that’s exactly what we can probe with our method,” he notes. “The ability to do such precise characterization could also lead to better quantum sensors—another application area of quantum technologies.”

The research team, which included scientists from Vienna University of Technology, ETH Zurich, Free University of Berlin, and the Max-Planck Institute of Quantum Optics, performed a tomography of a quantum system—the reconstruction of a specific quantum state with the aim of seeking experimental evidence of a theory.

The studied quantum system consisted of ultracold atoms—slow-moving atoms that make the movement easier to analyze because of their near-zero temperature—trapped on an atom chip. 

In their work, the scientists created two “copies” of this quantum system—cigar-shaped clouds of atoms that evolve over time without influencing each other. At different stages of this process, the team performed a series of experiments that revealed the two copies’ correlations.

“By constructing an entire history of these correlations, we can infer what is the initial quantum state of the system and extract its properties,” explains Sels. “Initially, we have a very strongly coupled quantum liquid, which we split into two so that it evolves as two independent liquids, and then we recombine it to reveal the ripples that are in the liquid.

“It’s like watching the ripples in a pond after throwing a rock in it and inferring the properties of the rock, such as its size, shape, and weight.”

An image and a video, along with captions and credits, depicting this process may be accessed from Google Drive. 

This research was supported by grants from the Air Force Office of Scientific Research (FA9550-21-1-0236) and the U.S. Army Research Office (W911NF-20-1-0163) as well as the Austrian Science Fund (FWF) and the German Research Research Foundation (DRG).

The interference between a pair of ultra-cold atomic clouds after free fall.

CREDIT

Bernhard Rauer

JOURNAL

Nature Physics

DOI

10.1038/s41567-023-02027-1 

METHOD OF RESEARCH

Experimental study

ARTICLE TITLE

Verification of the area law of mutual information in a quantum field simulator

ARTICLE PUBLICATION DATE

24-Apr-2023