bluuebunny/crossref_metadata_2025_split huggingface dataset:
Black-grass (Alopecurus myosuroides) in cereal multispectral detection by UAV
Authors: Cox Jonathan , Li Xiaodong , Fox Charles , Coutts Shaun 
Published: July 2023

AbstractSite-specific weed management (on the scale of a few meters or less) has the potential to greatly reduce pesticide use and its associated environmental and economic costs. A prerequisite for site-specific weed management is the availability of accurate maps of the weed population that can be generated quickly and cheaply. Improvements and cost reductions in unmanned aerial vehicles (UAVs) and camera technology mean these tools are now readily available for agricultural use. We used UAVs to collect aerial images captured in both RGB and multispectral formats of 12 cereal fields (wheat [Triticum aestivumL.] and barley [Hordeum vulgareL.]) across eastern England. These data were used to train machine learning models to generate prediction maps of locations of black-grass (Alopecurus myosuroidesHuds.), a prolific weed in UK cereal fields. We tested machine learning and data set resampling methods to obtain the most accurate system for predicting the presence and absence of weeds in new out-of-sample fields. The accuracy of the system in predicting the absence ofA. myosuroidesis 69% and its presence above 5 g in weight with 77% accuracy in new out-of-sample fields. This system generates prediction maps that can be used by either agricultural machinery or autonomous robotic platforms for precision weed management. Improvements to the accuracy can be made by increasing the number of fields and samples in the data set and the length of time over which data are collected to gather data across the entire growing season.
Pillars of Cloud‐Based Earth Observation Science Education
Authors: Crowley Morgan A. , Stuhlmacher Michelle , Trochim Erin D. , Van Den Hoek Jamon , Pasquarella Valerie J. , Szeto Sabrina H. , Howarth Jeffrey T. , Platt Rud , Roy Samapriya , Tellman Beth , Chakraborty T. C. , Ignatius Amber , Cherrington Emil , Markert Kel , Wu Qiusheng , Madhusudan M. D. , Mayer Timothy , Cardille Jeffrey A. , Erickson Tyler , Moore Rebecca , Clinton Nicholas E. , Saah David 
Published: July 2023

AbstractEarth observation (EO) is undergoing a paradigm shift with the development of cloud‐based analytical platforms supporting EO data collection and access, parallel processing, easier communication of results, and expanded accessibility. As the global community of users and the diversity of applications grow, there is a clear need for expanded educational capacity to leverage these developments and increase the impact of EO research and teaching. Drawing upon extensive conversations between educators, practitioners, and researchers, we propose three pillars that must be prioritized to prepare students, researchers, and professionals to take full advantage of the cloud‐based EO paradigm and guide future growth.
Impacts of air pollution and meteorological conditions on dry eye disease among residents in a northeastern Chinese metropolis: a six-year crossover study in a cold region
Authors: Lu Cheng-Wei , Fu Jing , Liu Xiu-Fen , Cui Zhi-Hua , Chen Wei-Wei , Guo Li , Li Xiao-Lan , Ren Yu , Shao Fei , Chen Li-Na , Hao Ji-Long 
Published: July 2023

AbstractThe purpose of this study is to explore the associations among dry eye disease (DED), air pollution, and meteorological conditions in the cold region of a northeastern Chinese metropolis (i.e., Changchun). Data on ambient air pollutants and meteorological parameters as well as diagnosed DED outpatients during 2015–2021 were collected. The associations between DED and environmental factors were analysed at multiple time scales using various statistical methods (i.e., correlation, regression and machine learning). Among the 10,809 DED patients (21,617 eyes) studied, 64.60% were female and 35.40% were male. A higher frequency of DED was observed in March and April, followed by January, August and October. Individual and multiple factor models showed the positive importance of particles with aerodynamic diameters <10 μm (PM10), carbon monoxide (CO), and ozone (O3) among normal air pollutants and air pressure (AP), air temperature (AT) and wind speed (WS) among normal meteorological parameters. Air pollutants (PM10, nitrogen dioxide: NO2) and meteorological parameters (AT, AP) have combined impacts on DED occurrence. For the first time, we further explored the associations of detailed components of atmospheric particles and DED, suggesting potential emission sources, including spring dust from bare soil and roads and precursor pollutants of summer O3 formation from vehicles and industry in Northeast China. Our results revealed the quantitative associations among air pollutants, meteorological conditions and DED outpatients in cold regions, highlighting the importance of coordinated policies in air pollution control and climate change mitigation.
Trans-ancestry meta-analysis of genome wide association studies of inhibitory control
Authors: Arnatkeviciute Aurina , Lemire Mathieu , Morrison Claire , Mooney Michael , Ryabinin Peter , Roslin Nicole M. , Nikolas Molly , Coxon James , Tiego Jeggan , Hawi Ziarih , Fornito Alex , Henrik Walter , Martinot Jean-Luc , Martinot Marie-Laure Paillère , Artiges Eric , Garavan Hugh , Nigg Joel , Friedman Naomi P. , Burton Christie , Schachar Russell , Crosbie Jennifer , Bellgrove Mark A. 
Published: July 2023

AbstractDeficits in effective executive function, including inhibitory control are associated with risk for a number of psychiatric disorders and significantly impact everyday functioning. These complex traits have been proposed to serve as endophenotypes, however, their genetic architecture is not yet well understood. To identify the common genetic variation associated with inhibitory control in the general population we performed the first trans-ancestry genome wide association study (GWAS) combining data across 8 sites and four ancestries (N = 14,877) using cognitive traits derived from the stop-signal task, namely – go reaction time (GoRT), go reaction time variability (GoRT SD) and stop signal reaction time (SSRT). Although we did not identify genome wide significant associations for any of the three traits, GoRT SD and SSRT demonstrated significant and similar SNP heritability of 8.2%, indicative of an influence of genetic factors. Power analyses demonstrated that the number of common causal variants contributing to the heritability of these phenotypes is relatively high and larger sample sizes are necessary to robustly identify associations. In Europeans, the polygenic risk for ADHD was significantly associated with GoRT SD and the polygenic risk for schizophrenia was associated with GoRT, while in East Asians polygenic risk for schizophrenia was associated with SSRT. These results support the potential of executive function measures as endophenotypes of neuropsychiatric disorders. Together these findings provide the first evidence indicating the influence of common genetic variation in the genetic architecture of inhibitory control quantified using objective behavioural traits derived from the stop-signal task.
The spatiotemporal dynamics of spatially variable genes in developing mouse brain revealed by a novel computational scheme
Authors: Hong Yingzhou , Song Kai , Zhang Zongbo , Deng Yuxia , Zhang Xue , Zhao Jinqian , Jiang Jun , Zhang Qing , Guo Chunming , Peng Cheng 
Published: July 2023

AbstractTo understand how brain regions form and work, it is important to explore the spatially variable genes (SVGs) enriched in specific brain regions during development. Spatial transcriptomics techniques provide opportunity to select SVGs in the high-throughput way. However, previous methods neglected the ranking order and combinatorial effect of SVGs, making them difficult to automatically select the high-priority SVGs from spatial transcriptomics data. Here, we proposed a novel computational pipeline, called SVGbit, to rank the individual and combinatorial SVGs for marker selection in various brain regions, which was tested in different kinds of public datasets for both human and mouse brains. We then generated the spatial transcriptomics and immunohistochemistry data from mouse brain at critical embryonic and neonatal stages. The results show that our ranking and clustering scheme captures the key SVGs which coincide with known anatomic regions in the developing mouse brain. More importantly, SVGbit can facilitate the identification of multiple gene combination sets in different brain regions. We identified three dynamical sub-regions which can be segregated by the staining of Sox2 and Calb2 in thalamus, and we also found that Nr4a2 expression gradually segregates the neocortex and hippocampus during the development. In summary, our work not only reveals the spatiotemporal dynamics of individual and combinatorial SVGs in developing mouse brain, but also provides a novel computational pipeline to facilitate the selection of marker genes from spatial transcriptomics data.
A BAHD-type acyltransferase concludes the biosynthetic pathway of non-bitter glycoalkaloids in ripe tomato fruit
Authors: Sonawane Prashant D. , Gharat Sachin A. , Jozwiak Adam , Barbole Ranjit , Heinicke Sarah , Almekias-Siegl Efrat , Meir Sagit , Rogachev Ilana , Connor Sarah E. O’ , Giri Ashok P. , Aharoni Asaph 
Published: July 2023

AbstractTomato is the highest value fruit and vegetable crop worldwide, yet produces α-tomatine, a renowned toxic and bitter-tasting anti-nutritional steroidal glycoalkaloid (SGA) involved in plant defense. A suite of modifications during tomato fruit maturation and ripening converts α-tomatine to the non-bitter and less toxic Esculeoside A. This important metabolic shift prevents bitterness and toxicity in ripe tomato fruit. While the enzymes catalyzing glycosylation and hydroxylation reactions in the Esculeoside A pathway have been resolved, the proposed acetylating step remains, to date, elusive. Here, we discovered that GAME36 (GLYCOALKALOID METABOLISM36), a BAHD-type acyltransferase catalyzes SGA-acetylation in cultivated and wild tomatoes. This finding completes the elucidation of the core Esculeoside A biosynthetic pathway in ripe tomato, allowing reconstitution of Esculeoside A production in heterologous microbial and plant hosts. The involvement of GAME36 in bitter SGA detoxification pathway points to a key role in the evolution of sweet-tasting tomato as well as in the domestication and breeding of modern cultivated tomato fruit.
Locomotion modulates olfactory learning through proprioception in C. elegans
Authors: Zhan Xu , Chen Chao , Niu Longgang , Du Xinran , Lei Ying , Dan Rui , Wang Zhao-Wen , Liu Ping 
Published: July 2023

AbstractLocomotor activities can enhance learning, but the underlying circuit and synaptic mechanisms are largely unknown. Here we show that locomotion facilitates aversive olfactory learning in C. elegans by activating mechanoreceptors in motor neurons, and transmitting the proprioceptive information thus generated to locomotion interneurons through antidromic-rectifying gap junctions. The proprioceptive information serves to regulate experience-dependent activities and functional coupling of interneurons that process olfactory sensory information to produce the learning behavior. Genetic destruction of either the mechanoreceptors in motor neurons, the rectifying gap junctions between the motor neurons and locomotion interneurons, or specific inhibitory synapses among the interneurons impairs the aversive olfactory learning. We have thus uncovered an unexpected role of proprioception in a specific learning behavior as well as the circuit, synaptic, and gene bases for this function.
Neuroprotective role for RORA in Parkinson’s disease revealed by analysis of post-mortem brain and a dopaminergic cell line
Authors: Al-Zaid Felwah S. , Hurley Michael J. , Dexter David T. , Gillies Glenda E. 
Published: July 2023

AbstractParkinson’s disease (PD) is almost twice as prevalent in men, which has largely been attributed to neuroprotective effect of oestradiol in women. RORA (retinoic acid receptor-related orphan receptor alpha) regulates the transcription of central aromatase, the enzyme responsible for local oestradiol synthesis, simultaneously, RORA expression is regulated by sex hormones. Moreover, RORA protects neurones against oxidative stress, a key mechanism contributing to the loss of dopaminergic neurones in PD. Therefore, we hypothesized that there would be sex differences in RORA expression in the substantia nigra pars compacta (SNpc), which could contribute to sex differences observed in PD prevalence and pathogenesis. In a case control study, qPCR and western blot analyses were used to quantify gene and protein expression in the SNpc of post-mortem brains (n = 14 late-stage PD and 11 age and sex matched controls). The neuroprotective properties of a RORA agonist were then investigated directly using a cell culture toxin-based model of PD coupled with measures of viability, mitochondrial function and apoptosis. RORA was expressed at significantly higher levels in the SNpc from control females’ brains compared to males. In PD, we found a significant increase in SNpc RORA expression in male PD compared to female PD. Treatment with a RORA agonist showed a significant neuroprotection in our cell culture model of PD and revealed significant effects on intracellular factors involved in neuronal survival and demise. This study is the first to demonstrate a sex specific pattern of RORA protein and gene expression in the SNpc of controls post-mortem human brains, and to show that this is differentially altered in male and female PD subjects, thus supporting a role for RORA in sex-specific aspects of PD. Furthermore, our in vitro PD model indicates mechanisms whereby a RORA agonist exerts its neuroprotective effect, thereby highlighting the translational potential for RORA ligands in PD.
Exact electronic states with shallow quantum circuits from global optimisation
Authors: Burton Hugh G. A. , Marti-Dafcik Daniel , Tew David P. , Wales David J. 
Published: July 2023

AbstractQuantum computers promise to revolutionise molecular electronic simulations by overcoming the exponential memory scaling. While electronic wave functions can be represented using a product of fermionic unitary operators, the best ansatz for strongly correlated electronic systems is far from clear. In this contribution, we construct universal wave functions from gate-efficient, spin symmetry-preserving fermionic operators by introducing an algorithm that globally optimises the wave function in the discrete ansatz design and continuous parameter spaces. Our approach maximises the accuracy that can be obtained with near-term quantum circuits and provides a practical route for designing ansätze in the future. Numerical simulations for strongly correlated molecules, including water and molecular nitrogen, and the condensed-matter Hubbard model, demonstrate the improved accuracy of gate-efficient quantum circuits for simulating strongly correlated chemistry.
Influence of inter-stimulus interval on 40-Hz auditory steady-state response in patients with schizophrenia
Authors: Choi Kang-Min , Im Chang-Hwan , Yang Chaeyeon , Lee Hyun Seo , Kim Sungkean , Lee Seung-Hwan 
Published: July 2023

AbstractDecreased 40-Hz auditory steady-state response (ASSR) is believed to reflect abnormal gamma oscillation in patients with schizophrenia (SZ). However, previous studies have reported conflicting results due to variations in inter-stimulus interval (ISI) used. In this study, we aimed to investigate the influence of varying ISI on the 40-Hz ASSR, particularly for patients with SZ and healthy controls (HCs). Twenty-four SZ patients (aged 40.8 ± 13.9 years, male: n = 11) and 21 HCs (aged 33.3 ± 11.3 years, male: n = 8) were recruited. For every participant, 40-Hz ASSRs were acquired for three different stimulus types: 500, 2000, and 3500 ms of ISIs. Two conventional ASSR measures (total power and inter-trial coherence, ITC) were calculated. Several additional ASSR measures were also analyzed: (i) ISI-dependent power; (ii) power onset slope; (iii) power centroid latency; (iv) ISI-dependent ITC; (v) ITC onset slope (500, 2000, 3500 ms); (vi) ITC centroid latency (500, 2000, 3500 ms). As ISI increased, total power and ITC increased in patients with SZ but decreased in HCs. In addition, patients with SZ showed higher ISI-dependent ITC, which was positively correlated with the psychotic symptom severity. The abnormal ITC onset slope and centroid latency for the ISI-500 ms condition were associated with cognitive speed decline in patients with SZ. Our study confirmed that the 40-Hz ASSR could be severely influenced by ISI. Furthermore, our results showed that the additional ASSR measures (ISI-dependent ITC, ITC onset slope, ITC centroid latency) could represent psychotic symptom severity or impairment in cognitive function in patients with SZ.
Exposure of iPSC-derived human microglia to brain substrates enables the generation and manipulation of diverse transcriptional states in vitro
Authors: Dolan Michael-John , Therrien Martine , Jereb Saša , Kamath Tushar , Gazestani Vahid , Atkeson Trevor , Marsh Samuel E. , Goeva Aleksandrina , Lojek Neal M. , Murphy Sarah , White Cassandra M. , Joung Julia , Liu Bingxu , Limone Francesco , Eggan Kevin , Hacohen Nir , Bernstein Bradley E. , Glass Christopher K. , Leinonen Ville , Blurton-Jones Mathew , Zhang Feng , Epstein Charles B. , Macosko Evan Z. , Stevens Beth 
Published: July 2023

AbstractMicroglia, the macrophages of the brain parenchyma, are key players in neurodegenerative diseases such as Alzheimer’s disease. These cells adopt distinct transcriptional subtypes known as states. Understanding state function, especially in human microglia, has been elusive owing to a lack of tools to model and manipulate these cells. Here, we developed a platform for modeling human microglia transcriptional states in vitro. We found that exposure of human stem-cell-differentiated microglia to synaptosomes, myelin debris, apoptotic neurons or synthetic amyloid-beta fibrils generated transcriptional diversity that mapped to gene signatures identified in human brain microglia, including disease-associated microglia, a state enriched in neurodegenerative diseases. Using a new lentiviral approach, we demonstrated that the transcription factor MITF drives a disease-associated transcriptional signature and a highly phagocytic state. Together, these tools enable the manipulation and functional interrogation of human microglial states in both homeostatic and disease-relevant contexts.
Genome-wide identification of accessible chromatin regions by ATAC-seq upon induction of the transcription factor bZIP11 in Arabidopsis
Authors: Hellens Alicia M. , Humphreys Jazmine L. , Fichtner Franziska , Tanurdžić Miloš , Beveridge Christine A. , Barbier François F. 
Published: July 2023

AbstractBasic leucine zipper 11 (bZIP11) is a transcription factor that is activated under low energy conditions in plants and plays a crucial role in enabling plants to adapt to starvation situations. Although previous results indicate that bZIP11 regulates chromatin accessibility based on evidence obtained from single genomic loci, to what extent this transcription factor regulates the chromatin landscape at the whole genome level remains unknown. Here we addressed this by performing an ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) on Arabidopsis thaliana (Arabidopsis) leaf protoplasts to obtain a profile of chromatin patterning in response upon bZIP11 induction. We identified, on average, 10,000 differentially accessible regions upon bZIP11 induction, corresponding to over 8,420 different genes out of the 25,000 genes present in the Arabidopsis genome. Our study provides a resource for understanding how bZIP11 regulates the genome at the chromatin level and provides an example of the impact of a single transcription factor on a whole plant genome.
A multi-predator trophic database for the California Current Large Marine Ecosystem
Authors: Bizzarro Joseph J. , Dewitt Lynn , Wells Brian K. , Curtis K. Alexandra , Santora Jarrod A. , Field John C. 
Published: July 2023

AbstractThe California Current Trophic Database (CCTD) was developed at NOAA Southwest Fisheries Science Center in collaboration with numerous diet data contributors. We compiled the CCTD from twenty-four data sets, representing both systematic collections and directed trophic studies. Diet composition data, including stomach and scat samples, were obtained from 105,694 individual predators among 143 taxa collected throughout the California Current Large Marine Ecosystem (CCLME) from 1967–2019. Predator taxa consist of squids (n = 5), elasmobranchs (n = 13), bony fishes (n = 118), and marine mammals (n = 7). Extensive time series are available for some predators (e.g., California Sea Lion, Pacific Hake, Chinook Salmon). The CCTD represents the largest compilation of raw trophic data within the CCLME, allowing for more refined analyses and modeling studies within this region. Our intention is to further augment and periodically update the dataset as additional historical or contemporary data become available to increase its utility and impact.
A paired dataset of T1- and T2-weighted MRI at 3 Tesla and 7 Tesla
Authors: Chen Xiaoyang , Qu Liangqiong , Xie Yifang , Ahmad Sahar , Yap Pew-Thian 
Published: July 2023

AbstractBrain magnetic resonance imaging (MRI) provides detailed soft tissue contrasts that are critical for disease diagnosis and neuroscience research. Higher MRI resolution typically comes at the cost of signal-to-noise ratio (SNR) and tissue contrast, particularly for more common 3 Tesla (3T) MRI scanners. At ultra-high magnetic field strength, 7 Tesla (7T) MRI allows for higher resolution with greater tissue contrast and SNR. However, the prohibitively high costs of 7T MRI scanners deter their widespread adoption in clinical and research centers. To obtain higher-quality images without 7T MRI scanners, algorithms that can synthesize 7T MR images from 3T MR images are under active development. Here, we make available a dataset of paired T1-weighted and T2-weighted MR images at 3T and 7T of 10 healthy subjects to facilitate the development and evaluation of 3T-to-7T MR image synthesis models. The quality of the dataset is assessed using image quality metrics implemented in MRIQC.
Towards automated long-term acoustic monitoring of endangered river dolphins: a case study in the Brazilian Amazon floodplains
Authors: Erbs Florence , Gaona Marina , van der Schaar Mike , Zaugg Serge , Ramalho Emiliano , Houser Dorian , André Michel 
Published: July 2023

AbstractUsing passive acoustic monitoring (PAM) and convolutional neural networks (CNN), we monitored the movements of the two endangered Amazon River dolphin species, the boto (Inia geoffrensis) and the tucuxi (Sotalia fluviatilis) from main rivers to floodplain habitats (várzea) in the Mamirauá Reserve (Amazonas, Brazil). We detected dolphin presence in four main areas based on the classification of their echolocation clicks. Using the same method, we automatically detected boat passages to estimate a possible interaction between boat and dolphin presence. Performance of the CNN classifier was high with an average precision of 0.95 and 0.92 for echolocation clicks and boats, respectively. Peaks of acoustic activity were detected synchronously at the river entrance and channel, corresponding to dolphins seasonally entering the várzea. Additionally, the river dolphins were regularly detected inside the flooded forest, suggesting a wide dispersion of their populations inside this large area, traditionally understudied and particularly important for boto females and calves. Boats overlapped with dolphin presence 9% of the time. PAM and recent advances in classification methods bring a new insight of the river dolphins’ use of várzea habitats, which will contribute to conservation strategies of these species.