bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spectral discrimination of crops and weeds using deep learning assisted by wavelet transform and statistical preprocessing
Authors: Mohammadi Vahid , Minaei Saeid , Gouton Pierre , Mahdavian Ali Reza , Khoshtaghaza Mohammad Hadi 
Published: November 2024

AbstractAutomatic detection and removal of weeds is a challenging task that requires precise sensors. While crops and weeds possess similar features in terms of appearance, they can be discriminated based on spectral information. This can be done because any object has its own specific spectral signature based on its physical structure and chemical contents. This study examined the use of wavelet transform and deep learning for discrimination of weeds from crops. A total of 626 spectral reflectances in the range of 380 to 1,000 nm were obtained for three crops (cucumber [Cucumis sativus L.], tomato [Solanum lycopersicum L.], and bell pepper [Capsicum annuum L.]) and five different weeds (bindweed [Convolvulus spp.], purple nutsedge [Cyperus rotundus L.], narrowleaf plantain [Plantago lanceolata L.], common cinquefoil [Potentilla simplex Michx.], and garden sorrel [Rumex acetosa L.]). Morse wavelet was employed to decompose the spectra and extract the scalograms, which are the RGB representations of the spectral data. Two deep convolutional neural networks (i.e., GoogLeNet and SqueezNet) were employed for the recognition of crops and weeds. In addition, six common classifiers, including linear discriminant analysis, quadratic discriminant analysis, linear support vector machine, quadratic support vector machine, artificial neural networks, and k-nearest neighbors classifier (KNN), were used for the task of crop/weed discrimination to build the comparison with the proposed method. The error of prediction gradually decreased, and a 100% correct classification was achieved after 258 iterations. Analysis showed that SqueezNet provided classification of 100% accuracy, while GoogLeNet’s accuracy was 97.8% for the test set. Among the common classifiers, KNN provided the highest accuracy (i.e., 100%). This study showed that the proposed method can be successfully utilized for classification of crops and weeds.
Emergence of multiple resistance to EPSPS and ALS herbicides in smooth pigweed (Amaranthus hybridus): a growing concern in Brazil
Authors: de Oliveira Claudia , M. Mathioni Sandra , Witter Ana Paula Werkhausen , Nalin Daniel , N. Lemes Lúcio , G. Ozorio Eduardo , Storniolo Adegas Fernando , Silvério de Oliveira Rubem 
Published: November 2024

AbstractRecently, farmers in Brazil have observed a decline in efficacy of glyphosate, chlorimuron, and imazethapyr control of smooth pigweed (Amaranthus hybridus L.). The objectives of this study were to quantify the resistance of Amaranthus in Brazil to glyphosate and acetolactate synthase (ALS)-inhibiting herbicides, elucidate the mechanism of resistance, and assess the frequency of shifts in sensitivity to glyphosate and chlorimuron in Brazil. Dose–response assays were conducted in a greenhouse with glyphosate, chlorimuron, and imazethapyr. This was followed by sequencing of the EPSPS and ALS genes. Additionally, 740 Amaranthus populations across several Brazilian states were monitored over 4 yr, subjected to a single discriminatory dose of glyphosate and chlorimuron. The populations BR18Asp051 and BR21Asp205 were resistant to glyphosate, chlorimuron, and imazethapyr. The elevated resistance level to glyphosate in these populations is attributed to multiple amino acid substitutions (TAP-IVS) in the EPSPS gene; and cross-resistance to sulfonylureas and imidazolinones is conferred by the Trp-574-Leu substitution in the ALS gene in both populations. Overall, resistance distribution indicated that 88% of the sampled populations were considered sensitive to glyphosate, while 66% were sensitive to chlorimuron. Furthermore, 10% of the samples demonstrated multiple resistance to both active ingredients. A shift in glyphosate sensitivity was observed in four states in Brazil; however, sensitivity shifts to chlorimuron were more widely dispersed in Brazilian agricultural regions.
Effects of goosegrass (Eleusine indica) competition on strawberry growth and yield
Authors: Buzanini Ana C. , Boyd Nathan S. 
Published: November 2024

AbstractGoosegrass [Eleusine indica (L.) Gaertn.] is one of the most problematic weeds in plasticulture strawberry [Fragaria × ananassa (Weston) Duchesne ex Rozier (pro sp.) [chiloenis × virginiana]] production systems in Florida. A 2-yr trial was implemented to evaluate the effects of different E. indica densities on strawberry growth and yield. Eleusine indica densities evaluated were 0, 0.4, 0.8, 1.9, 2.7, and 3.8 plants m−2 equally distributed on the plastic-mulched bed top within the strawberry transplant holes. Eleusine indica density did not affect E. indica height or biomass. However, E. indica seed production was positively correlated with E. indica density in Season 1 and negatively correlated with E. indica density in Season 2. A negative linear regression was observed between E. indica density and strawberry yield in both seasons. For each increase in E. indica plants per square meter, strawberry yield was reduced by 316 and 2,356 kg ha−1 for Seasons 1 and 2, respectively. Our results highlight the importance of achieving adequate E. indica management to minimize yield losses.
Efficient Model Calibration Using Submodels
Authors: Vermeulen P. T. M. , Janssen G. M. C. M. , Kroon T. 
Published: November 2024

AbstractGroundwater models tend to become increasingly detailed to accommodate increasing data availability and higher accuracy demands from stakeholders. As runtimes increase almost quadratically with the number of model cells, this makes the models ever more computationally demanding. This high computational demand introduces challenges for the history‐matching (calibration) process as this is an algorithmic process that needs hundreds or thousands of model‐runs to obtain the model sensitivities needed to estimate parameters. Model runs may take hours or days to complete which in fact, is often a reason to discard the history‐matching all together. As a solution, we present a practical approach to use sub‐modeling in combination with parallelization for automatic history‐matching. Therefore a large model is subdivided into smaller models to carry out the sensitivity simulations. With a realistic case the method is elaborated, after which the method is demonstrated in the history‐matching of the transient Dutch National Groundwater Flow model. In this manner the model, which consisted of over 12 million model cells, could be optimized using 416 sub‐models and altogether 2,188 parameters in 1 week. This would take years to complete in a conventional way.
Toward a Universal Model of Hyporheic Exchange and Nutrient Cycling in Streams
Authors: Monofy Ahmed , Grant Stanley B. , Boano Fulvio , Rippy Megan A. , Gomez‐Velez Jesus D. , Kaushal Sujay S. , Hotchkiss Erin R. , Shelton Sydney 
Published: November 2024

AbstractIn this paper we demonstrate that several ubiquitous hyporheic exchange mechanisms can be represented simply as a one‐dimensional diffusion process, where the diffusivity decays exponentially with depth into the streambed. Based on a meta‐analysis of 106 previously published laboratory measurements of hyporheic exchange (capturing a range of bed morphologies, hydraulic conditions, streambed properties, and experimental approaches) we find that the reference diffusivity and mixing length‐scale are functions of the permeability Reynolds Number and Schmidt Number. These dimensionless numbers, in turn, can be estimated for a particular stream from the median grain size of the streambed and the stream's depth, slope, and temperature. Application of these results to a seminal study of nitrate removal in 72 headwater streams across the United States, reveals: (a) streams draining urban and agricultural landscapes have a diminished capacity for in‐stream and in‐bed mixing along with smaller subsurface storage zones compared to streams draining reference landscapes; (b) under steady‐state conditions nitrate uptake in the streambed is primarily biologically controlled; and (c) median reaction timescales for nitrate removal in the hyporheic zone are 0.5 and 20 hr for uptake by assimilation and denitrification, respectively. While further research is needed, the simplicity and extensibility of the framework described here should facilitate cross‐disciplinary discussions and inform reach‐scale studies of pollutant fate and transport and their scale‐up to watersheds and beyond.
Measurements of F1‐ Region Ionosphere State Variables at Arecibo Through Quasi Height‐Independent Exhaustive Fittings of the Incoherent Scatter Ion‐Line Spectra
Authors: Li Yanlin , Zhou Qihou 
Published: November 2024

AbstractWe discuss an exhaustive search approach to fit the incoherent scatter spectrum (ISS) in the F1‐region for molecular ion fraction (fm), ion temperature (Ti), and electron temperature (Te). The commonly used “full profile” approach for F1‐region measurements parameterizes the molecular ion fraction as a function of altitude and fits all the related heights for the state variables. In our approach, we fit the ISS at each height for fm, Ti, Te, and ion velocity (Vi) independently. Our exhaustive search method finds all the major local minima at each altitude. Although a parameterized function is used to guide the algorithm in finding the best solution, the fitting parameters retain their local characteristics. Despite that fitting fm, Ti, and Te without constraints requires Doppler shift to be accurately determined and the ISS signal‐to‐noise ratio higher than the full‐profile method, simulations show that Ti, Te, and fm can be recovered within a few percent accuracy with a moderate signal‐to‐noise ratio. We apply the exhaustive search approach to the Arecibo high‐resolution incoherent scatter radar data taken on 13 September 2014. The derived ion and electron temperatures are sensitive enough to reveal thermosphere gravity waves commonly seen in the electron density previously. Our method is more robust than previous height‐independent fitting methods. Comparison with another Arecibo program indicates our results are likely more accurate. Simultaneous high‐resolution measurements of Ti, Te, fm, Vi, and electron concentration (Ne) in our approach open new opportunities for synergistic studies of the F1‐region dynamics and chemistry.
Significant Midlatitude Plasma Density Peaks and Dual‐Hemisphere SED During the 10–11 May 2024 Super Geomagnetic Storm
Authors: Aa Ercha , Zhang Shun‐Rong , Lei Jiuhou , Huang Fuqing , Erickson Philip J. , Coster Anthea J. , Luo Bingxian , Kerr Robert B. 
Published: November 2024

AbstractThis study investigates midlatitude ionospheric variations during the super geomagnetic storm on 10–11 May 2024, utilizing multi‐instrument data from ground‐based sources (Global Navigation Satellite Systems receivers and a Fabry–Perot Interferometer) and space‐based measurements (Swarm and DMSP). We observed several distinct density gradient structures in the midlatitude ionosphere, with the main findings summarized as follows: (a) Significant zonal plasma density enhancements developed continuously in local dusk across the American‐Pacific‐Asian longitude sectors around geomagnetic latitude. These midlatitude peaks exhibited a wide longitudinal extension exceeding 150 and a prolonged duration of 12–15 hr during the late main phase and early recovery phase of the storm. (b) Strong storm‐enhanced density (SED) was observed in both hemispheres yet with different longitudinal and universal time preferences. In the Northern Hemisphere, significant SED occurred over the American longitude sector during 20:30–22:30 UT on May 10. In the Southern Hemisphere, pronounced SED was observed not only in the American longitudes during 20:30–22:30 UT on May 10 but also in the Australian longitude sector during 02:00–04:00 UT on May 11.
The Neoproterozoic Mozambique Belt in the Gol Mountains (N Tanzania): Structural Analysis of Amphibolite and Granulite‐Facies Nappe Tectonites From a Crustal Orogenic Channel
Authors: Eguíluz L. , Puelles P. , Tarriño A. , Ábalos B. 
Published: November 2024

AbstractA structural analysis of the Gol Mountains of North Tanzania is presented in which we identify and characterize a sheet‐like deformation‐localization zone of regional scale. Syn‐metamorphic rock‐deformation within the localization zone gave rise to widespread tectonite development under high‐T in lower‐mid crustal realms. Regional foliations and mineral/stretching lineations, and associated non‐coaxial mineral petrofabrics can be correlated with ductile flow shear planes. At the macro‐scale these structures are genetically connected with tangential movement zones involving large a‐type and sheath folds, thrusts and ductile shear zones, and hydrothermal quartz megaveins plastically deformed. The dimension of the area affected by this structural style is c. 30 km across the Mozambique Belt and >50 km parallel to it. The associated tectonic displacements likely attained several tens of km in the context of an overall W‐directed tectonic vergence transversal to the Mozambique Belt orogenic trend. It is interpreted as a segment of a mid‐lower crustal orogenic channel active during late Ediacaran amalgamation of the Congo‐Tanzania Archean Craton (and its discontinuous fringe of Paleoproterozoic and Mesoproterozoic orogens) with the amalgamated arcs and terranes of the Arabian‐Nubian Shield.
Physiological and pathological roles of the transcriptional kinases CDK12 and CDK13 in the central nervous system
Authors: Pitolli Consuelo , Marini Alberto , Sette Claudio , Pagliarini Vittoria 
Published: November 2024

AbstractThe cyclin-dependent kinases 12 (CDK12) and 13 (CDK13) govern several steps of gene expression, including transcription, RNA processing and translation. The main target of CDK12/13 is the serine 2 residue of the carboxy-terminal domain of RNA polymerase II (RNAPII), thus influencing the directionality, elongation rate and processivity of the enzyme. The CDK12/13-dependent regulation of RNAPII activity influences the expression of selected target genes with important functional roles in the proliferation and viability of all eukaryotic cells. Neuronal cells are particularly affected by the loss of CDK12/13, as result of the high dependency of neuronal genes on RNAPII processivity for their expression. Deregulation of CDK12/13 activity strongly affects brain physiology by influencing the stemness potential and differentiation properties of neuronal precursor cells. Moreover, mounting evidence also suggest the involvement of CDK12/13 in brain tumours. Herein, we discuss the functional role(s) of CDK12 and CDK13 in gene expression regulation and highlight similarities and differences between these highly homologous kinases, with particular attention to their impact on brain physiology and pathology. Lastly, we provide an overview of CDK12/13 inhibitors and of their efficacy in brain tumours and other neoplastic diseases.
Structural basis of MICAL autoinhibition
Authors: Horvath Matej , Schrofel Adam , Kowalska Karolina , Sabo Jan , Vlasak Jonas , Nourisanami Farahdokht , Sobol Margarita , Pinkas Daniel , Knapp Krystof , Koupilova Nicola , Novacek Jiri , Veverka Vaclav , Lansky Zdenek , Rozbesky Daniel 
Published: November 2024

AbstractMICAL proteins play a crucial role in cellular dynamics by binding and disassembling actin filaments, impacting processes like axon guidance, cytokinesis, and cell morphology. Their cellular activity is tightly controlled, as dysregulation can lead to detrimental effects on cellular morphology. Although previous studies have suggested that MICALs are autoinhibited, and require Rab proteins to become active, the detailed molecular mechanisms remained unclear. Here, we report the cryo-EM structure of human MICAL1 at a nominal resolution of 3.1 Å. Structural analyses, alongside biochemical and functional studies, show that MICAL1 autoinhibition is mediated by an intramolecular interaction between its N-terminal catalytic and C-terminal coiled-coil domains, blocking F-actin interaction. Moreover, we demonstrate that allosteric changes in the coiled-coil domain and the binding of the tripartite assembly of CH-L2α1-LIM domains to the coiled-coil domain are crucial for MICAL activation and autoinhibition. These mechanisms appear to be evolutionarily conserved, suggesting a potential universality across the MICAL family.
Multimodal scanning of genetic variants with base and prime editing
Authors: Belli Olivier , Karava Kyriaki , Farouni Rick , Platt Randall J. 
Published: November 2024

AbstractMutational scanning connects genetic variants to phenotype, enabling the interrogation of protein functions, interactions and variant pathogenicity. However, current methodologies cannot efficiently engineer customizable sets of diverse genetic variants in endogenous loci across cellular contexts in high throughput. Here, we combine cytosine and adenine base editors and a prime editor to assess the pathogenicity of a broad spectrum of variants in the epithelial growth factor receptor gene (EGFR). Using pooled base editing and prime editing guide RNA libraries, we install tens of thousands of variants spanning the full coding sequence of EGFR in multiple cell lines and assess the role of these variants in tumorigenesis and resistance to tyrosine kinase inhibitors. Our EGFR variant scan identifies important hits, supporting the robustness of the approach and revealing underappreciated routes to EGFR activation and drug response. We anticipate that multimodal precision mutational scanning can be applied broadly to characterize genetic variation in any genetic element of interest at high and single-nucleotide resolution.
Computational investigation of the effect of BODIPY labelling on peptide-membrane interaction
Authors: de Jong-Hoogland Dominique , Ulmschneider Jacob , Ulmschneider Martin 
Published: November 2024

AbstractOptical monitoring of peptide binding to live cells is hampered by the abundance of naturally occurring fluorophores such as tryptophan. Unnatural amino acids incorporating synthetic fluorophores such as BODIPY overcome these optical limitations. A drawback to using fluorophores in lipid binding peptide design is their propensity to override other interactions, potentially causing the peptides to lose their binding selectivity. Here, the binding strength of a selection of peptides incorporating a variety of BODIPY derivatized amino acids has been studied via molecular dynamics simulations to quantify the impact of BODIPY incorporation on peptide-membrane binding behaviour.
Energy saving analysis for pump-motor set in water purification plant using variable speed drive
Authors: Salama Mohamed Adel Esmaeel , El-Naggar Nada Mohamed , Abu-Zaid Salama 
Published: November 2024

AbstractThe induction motor is known to be the most reliable motor in the industry and is also the most energy-consuming load worldwide. It is noticeable in some production areas that the use of a high-capacity induction motor is not required at some operating times, and therefore it is important to control the speed of the induction motor to suit the operating requirements and obtain highly efficient performance. This paper presents a case study of a drinking water purification plant that uses a variable speed drive (VSD) as a speed controller for one of its induction motors to drive the pump. The VSD is connected to the motor in question to regulate its speed and maintain the external pressure of the station at an appropriate value that ensures water delivery to all branches of the network. 24-hour power consumption measurements of the respective engine with and without the use of a VSD are studied and analyzed to determine the potential for energy savings. Finally, a case study simulation is presented to compare the simulation results with the actual results.
Genetic remodeling of soil diazotrophs enables partial replacement of synthetic nitrogen fertilizer with biological nitrogen fixation in maize
Authors: Martinez-Feria Rafael , Simmonds Maegen B. , Ozaydin Bilge , Lewis Stacey , Schwartz Allison , Pluchino Alex , McKellar Megan , Gottlieb Shayin S. , Kayatsky Tasha , Vital Richelle , Mehlman Sharon E. , Caron Zoe , Colaianni Nicholas R. , Ané Jean-Michel , Maeda Junko , Infante Valentina , Karlsson Bjorn H. , McLimans Caitlin , Vyn Tony , Hanson Brendan , Verhagen Garrett , Nevins Clayton , Reese Lori , Otyama Paul , Robinson Alice , Learmonth Timothy , Miller Christine M. F. , Havens Keira , Tamsir Alvin , Temme Karsten 
Published: November 2024

AbstractIncreasing biological nitrogen (N) fixation (BNF) in maize production could reduce the environmental impacts of N fertilizer use, but reactive N in the rhizosphere of maize limits the BNF process. Using non-transgenic methods, we developed gene-edited strains of Klebsiella variicola (Kv137-2253) and Kosakonia sacchari (Ks6-5687) bacteria optimized for root-associated BNF and ammonium excretion in N-rich conditions. The aim of this research was to elucidate the mechanism of action of these strains. We present evidence from in vitro, in planta and field experiments that confirms that our genetic remodeling strategy derepresses BNF activity in N-rich systems and increases ammonium excretion by orders of magnitude above the respective wildtype strains. BNF is demonstrated in controlled environments by the transfer of labeled 15N2 gas from the rhizosphere to the chlorophyll of inoculated maize plants. This was corroborated in several 15N isotope tracer field experiments where inoculation with the formulated, commercial-grade product derived from the gene-edited strains (PIVOT BIO PROVEN® 40) provided on average 21 kg N ha-1 to the plant by the VT-R1 growth stages. Data from small-plot and on-farm trials suggest that this technology can improve crop N status pre-flowering and has potential to mitigate the risk of yield loss associated with a reduction in synthetic N fertilizer inputs.