bluuebunny/crossref_metadata_2025 huggingface dataset:
Universal quantum obfuscation for quantum non-linear functions
Authors: Pan Chuyue , Shang Tao , Zhang Yuanjing
Published: January 2023

Research on quantum cryptography has burgeoned in the recent decades and combined quantum mechanics and cryptography theory. Among the existing quantum cryptographic primitives, quantum obfuscation is an emergent force to be reckoned with. Quantum obfuscation means obfuscating a circuit by quantum mechanics to improve security. It is used to hide functionality and prevent the reverse engineering of quantum circuits. However, research studies on the construction of quantum obfuscation are relatively immature due to its difficulty in implementation and application. Also, the obfuscation for quantum non-linear functions has not been suggested yet, although quantum non-linear functions cover a wide range of quantum functions that can be obfuscated. In this paper, we initiate a universal definition of quantum obfuscation which utilizes quantum teleportation to construct an obfuscator and interpreter for quantum non-linear functions. Furthermore, we demonstrate the validity of applying the obfuscation to the quantum asymmetric encryption scheme and rigorously prove that the encryption realized by quantum obfuscation satisfies IND (indistinguishability)-security. This work provides a positive possibility of quantum obfuscation for quantum non-linear functions and will complement the theory of both quantum obfuscation and quantum asymmetric encryption.
A robust self-referenced 2D nyquist ghost correction for different MRI-biomarker measurements based on multi-band interleaved EPI
Authors: Liu Xiaoxi , Chen Shihui , Cui Di , Hui Edward S. , Chan Queenie , Chen Nan-Kuei , Chang Hing-Chiu
Published: January 2023

Purpose: To enable 2D Nyquist ghost correction for multi-band interleaved echo-planar imaging (EPI) without reference scan.

Methods: 2D phase errors between positive and negative echo were directly measured from the multi-band interleaved EPI data acquired with alternating readout polarity, and then corrected by using multiplexed sensitivity encoding (MUSE) framework. The proposed method was tested on brain data acquired with and without multi-band imaging under different multi-shot factors (4, 8, and 16). In addition, the 2D phase corrections for the interleaved EPI data acquired with 2D zoomed-FOV, 2D reduced-FOV, or 3D multi-band imaging were also performed with the proposed method. The performance of our proposed method was assessed with single-to-noise ratio (SNR) and ghost-to-signal ratio (GSR), and then compared with an iterative 2D phase correction method. The g-factor penalty of the proposed 2D Nyquist ghost correction method associated with 2D phase error was also evaluated. The feasibility of the proposed method was evaluated in diffusion MRI and multi-echo fMRI where quantitative biomarkers with high quality are desired.

Results: The proposed method successfully suppressed the ghost artifacts for the multi-shot interleaved EPI data acquired with different multi-shot factors, 2D and 3D multi-band acquisitions, zoomed-FOV, or reduced-FOV. Compared with the iterative method, our proposed method showed lower GSR and comparable SNR performance. Through g-factor penalty simulation, the proposed method showed less than 9% of overall SNR loss associated with a maximum y-linear phase error of π. The residual aliasing artifact was effectively eliminated in the quantitative biomarkers (ADC, FA and dynamic T2*) when applying the proposed method in diffusion imaging and multi-echo fMRI.

Conclusion: The proposed method can perform robust 2D Nyquist ghost correction for multi-band multi-shot interleaved EPI without reference scan, and thus can be a generalized 2D ghost correction method for multi-shot interleaved EPI based acquisitions and applications.
RETRACTED: Mixed convective heat transfer in a power-law fluid in a square enclosure: Higher order finite element solutions
Authors: Bilal S. , Khan Noor Zeb , Fatima Iqra , Riaz Arshad , Ansari Ghulam Jillani , Alhazmi Sharifah E. , El-Din ElSayed M. Tag
Published: January 2023

Incorporation of momentum gradients produced due to inertial motion of the lid along with the presence of temperature differences in the configuration make the physical problem more significant. The joint variation of momentum and thermal diffusion in diversified natural liquids is recognized as mixed convection. Valuable attention has been received by such a phenomenon in different areas of science and technology such as in wind current–based solar receivers, electronic instruments, control of emergency shutdown in reactors, thermal exchangers, oceanic currents, control of atmospheric pollution, and so on. So, the main focus is to contemplate hydrothermal characteristics of a power-law fluid contained in a square cavity with the movement of the upper lid and being thermally adiabatic. The other extremities are considered to be at rest, and the base wall is prescribed with uniform/non-uniform temperature distributions. The governing formulation of the problem is handled by executing a finite element approach. Hybrid meshing is performed for domain discretization, and weak variational formulation is utilized for formulation discretization. Second-degree polynomials are employed as the interpolation function, providing information about velocity and temperature distributions at boundary and intermediate nodes. The system of finalized non-linear equations is resolved by using the Paradiso software. The results for velocity and temperature distributions are attained comparatively for uniformly and non-uniformly heated profiles. The kinetic energy and average Nusselt number are also computed against flow concerning variables. From the attained graphical and tabular data, it is deduced that by increasing the Reynolds number, inertial forces dominate over buoyancy forces and the effect of lid movement is prominent on flow characteristics. It is also inferred that for the shear thickening case and for all values of the Reynolds number, the average Nusselt number shows a constant behavior.
Full characterization of spontaneous parametric down conversion in non-ideal quarter-wavelength semiconductor Bragg reflection waveguide
Authors: Niu Bin , Qian Cheng , Jing Xu , Wan Chenquan , Kong Yuechan , Chen Tangsheng , Liu Yichen , Lu Liangliang
Published: January 2023

Entangled photons are important for testing foundations of quantum physics and are at the heart of quantum technology. Integrated photonics has overwhelming dominance in terms of density and performance, making it a promise route for scalable quantum information processing. AlGaAs-based materials having large second-order non-linearities, direct bandgap and strong electro-optical effect can offer distinct advantages in quantum light source. Here we report a non-ideal quarter-wavelength Bragg reflection waveguide for generating three types of spontaneous parametric down-conversion processes. A general solution to the dispersion equation is derived and employed for designing high efficiency devices by taking into account the influence of core layer aluminium concentration. We further design and fabricate a Bragg reflection waveguide sample based on the analysis, and experimentally characterize its phase matching types and spectral brightness. Our work paves the path for the development of portable quantum light sources.
Agent-based models in cellular systems
Authors: Pleyer Jonas , Fleck Christian
Published: January 2023

This mini-review discusses agent-based models as modeling techniques for studying pattern formation of multi-cellular systems in biology. We introduce and compare different agent-based model frameworks with respect to spatial representation, microenvironment, intracellular and extracellular reactions, cellular properties, implementation, and practical use. The guiding criteria for the considered selection of agent-based model frameworks are that they are actively maintained, well documented, and provide a model development workflow.
Characterization of sclerostin’s response within white adipose tissue to an obesogenic diet at rest and in response to acute exercise in male mice
Authors: Kurgan Nigel , Baranowski Bradley , Stoikos Joshua , MacNeil Adam J. , Fajardo Val A. , MacPherson Rebecca E. K. , Klentrou Panagiota
Published: January 2023

Introduction: It is well established that sclerostin antagonizes the anabolic Wnt signalling pathway in bone, however, its physiological role in other tissues remains less clear. This study examined the effect of a high-fat diet (HFD) on sclerostin content and downstream markers of the Wnt signaling pathway (GSK3β and β-catenin) within subcutaneous inguinal white adipose tissue (iWAT), and visceral epididymal WAT (eWAT) depots at rest and in response to acute aerobic exercise.

Methods: Male C57BL/6 mice (n = 40, 18 weeks of age) underwent 10 weeks of either a low-fat diet (LFD) or HFD. Within each diet group, mice were assigned to either remain sedentary (SED) or perform 2 h of endurance treadmill exercise at 15 m min−1 with 5° incline (EX), creating four groups: LFD + SED (N = 10), LFD + EX (N = 10), HFD + SED (N = 10), and HFD + EX (N = 10). Serum and WAT depots were collected 2 h post-exercise.

Results: Serum sclerostin showed a diet-by-exercise interaction, reflecting HFD + EX mice having higher concentration than HFD + SED (+31%, p = 0.03), and LFD mice being unresponsive to exercise. iWAT sclerostin content decreased post-exercise in both 28 kDa (−31%, p = 0.04) and 30 kDa bands (−36%, main effect for exercise, p = 0.02). iWAT β-catenin (+44%, p = 0.03) and GSK3β content were higher in HFD mice compared to LFD (+128%, main effect for diet, p = 0.005). Monomeric sclerostin content was abolished in eWAT of HFD mice (−96%, main effect for diet, p < 0.0001), was only detectable as a 30 kDa band in LFD mice and was unresponsive to exercise. β-catenin and GSK3β were both unresponsive to diet and exercise within eWAT.

Conclusion: These results characterized sclerostin’s content to WAT depots in response to acute exercise, which appears to be specific to a reduction in iWAT and identified a differential regulation of sclerostin’s form/post-translational modifications depending on diet and WAT depot.
Symbiont coordinates stem cell proliferation, apoptosis, and morphogenesis of gut symbiotic organ in the stinkbug-Caballeronia symbiosis
Authors: Jang Seonghan , Matsuura Yu , Ishigami Kota , Mergaert Peter , Kikuchi Yoshitomo
Published: January 2023

The bean bug Riptortus pedestris obtains a specific bacterial symbiont, Caballeronia insecticola (Burkholderia insecticola), from the environmental soil and harbors it in the posterior midgut region that is composed of hundreds of crypts. While newly hatched aposymbiotic insects possess primordial midgut crypts with little or no lumen, colonization of C. insecticola triggers swift development of the symbiotic organ, forming enlarged and opened crypts, and the symbiont subsequently fills the luminal cavities of those mature crypts. The cellular processes of crypt development triggered by C. insecticola colonization are poorly understood. Here we identified a fundamental mechanism of the symbiont-mediated midgut development by investigating cell cycles of intestinal epithelial cells. Intestinal stem cells of the bean bug are located and proliferate at the crypt base. Differentiated enterocytes migrate upward along the epithelial cell layer of the crypt as the midgut develops, induction of apoptosis in enterocytes primarily occurred on the tip side of the crypts, and apoptotic cells then eventually were shed from the crypts into the hemolymph. The proliferation rate of the stem cells at the base of the crypts was low while a high apoptotic rate was observed at the crypt tip in aposymbiotic insects, resulting in undeveloped short crypts. On the contrary, the gut-colonizing C. insecticola promoted the proliferation of the stem cells at the base of crypts and simultaneously inhibited apoptosis at the tip of crypts, resulting in a net growth of the crypts and the generation of a crypt lumen that becomes colonized by the bacterial symbiont. These results demonstrated that the Caballeronia symbiont colonization induces the development of the midgut crypts via finely regulating the enterocyte cell cycles, enabling it to stably and abundantly colonize the generated spacious crypts of the bean bug host.
Peak appearance time in pulse waveforms of intracranial pressure and cerebral blood flow velocity
Authors: Ziółkowski Arkadiusz , Pudełko Agata , Kazimierska Agnieszka , Uryga Agnieszka , Czosnyka Zofia , Kasprowicz Magdalena , Czosnyka Marek
Published: January 2023

The shape of the pulse waveforms of intracranial pressure (ICP) and cerebral blood flow velocity (CBFV) typically contains three characteristic peaks. It was reported that alterations in cerebral hemodynamics may influence the shape of the pulse waveforms by changing peaks’ configuration. However, the changes in peak appearance time (PAT) in ICP and CBFV pulses are only described superficially. We analyzed retrospectively ICP and CBFV signals recorded in traumatic brain injury patients during decrease in ICP induced by hypocapnia (n = 11) and rise in ICP during episodes of ICP plateau waves (n = 8). All three peaks were manually annotated in over 48 thousand individual pulses. The changes in PAT were compared between periods of vasoconstriction (expected during hypocapnia) and vasodilation (expected during ICP plateau waves) and their corresponding baselines. Correlation coefficient (rS) analysis between mean ICP and mean PATs was performed in each individual recording. Vasodilation prolonged PAT of the first peaks of ICP and CBFV pulses and the third peak of CBFV pulse. It also accelerated PAT of the third peak of ICP pulse. In contrast, vasoconstriction shortened appearance time of the first peaks of ICP and CBFV pulses and the second peak of ICP pulses. Analysis of individual recordings demonstrated positive association between changes in PAT of all three peaks in the CBFV pulse and mean ICP (rS range: 0.32–0.79 for significant correlations). Further study is needed to test whether PAT of the CBFV pulse may serve as an indicator of changes in ICP–this may open a perspective for non-invasive monitoring of alterations in mean ICP.
The effects of 4-Phenylbutyric acid on ER stress during mouse tooth development
Authors: Lee Eui-Seon , Aryal Yam Prasad , Kim Tae-Young , Pokharel Elina , Kim Ji-Youn , Yamamoto Hitoshi , An Chang-Hyeon , An Seo-Young , Jung Jae-Kwang , Lee Youngkyun , Ha Jung-Hong , Sohn Wern-Joo , Kim Jae-Young
Published: January 2023

Introduction: During tooth development, proper protein folding and trafficking are significant processes as newly synthesized proteins proceed to form designated tissues. Endoplasmic reticulum (ER) stress occurs inevitably in tooth development as unfolded and misfolded proteins accumulate in ER. 4-Phenylbutyric acid (4PBA) is a FDA approved drug and known as a chemical chaperone which alleviates the ER stress. Recently, several studies showed that 4PBA performs therapeutic effects in some genetic diseases due to misfolding of proteins, metabolic related-diseases and apoptosis due to ER stress. However, the roles of 4PBA during odontogenesis are not elucidated. This study revealed the effects of 4PBA during molar development in mice.

Methods: We employed in vitro organ cultivation and renal transplantation methods which would mimic the permanent tooth development in an infant period of human. The in vitro cultivated tooth germs and renal calcified teeth were examined by histology and immunohistochemical analysis.

Results and Discussion: Our results revealed that treatment of 4PBA altered expression patterns of enamel knot related signaling molecules, and consequently affected cellular secretion and patterned formation of dental hard tissues including dentin and enamel during tooth morphogenesis. The alteration of ER stress by 4PBA treatment during organogenesis would suggest that proper ER stress is important for pattern formation during tooth development and morphogenesis, and 4PBA as a chemical chaperone would be one of the candidate molecules for dental and hard tissue regeneration.
Vascular smooth muscle cells in intimal hyperplasia, an update
Authors: Déglise Sébastien , Bechelli Clémence , Allagnat Florent
Published: January 2023

Arterial occlusive disease is the leading cause of death in Western countries. Core contemporary therapies for this disease include angioplasties, stents, endarterectomies and bypass surgery. However, these treatments suffer from high failure rates due to re-occlusive vascular wall adaptations and restenosis. Restenosis following vascular surgery is largely due to intimal hyperplasia. Intimal hyperplasia develops in response to vessel injury, leading to inflammation, vascular smooth muscle cells dedifferentiation, migration, proliferation and secretion of extra-cellular matrix into the vessel’s innermost layer or intima. In this review, we describe the current state of knowledge on the origin and mechanisms underlying the dysregulated proliferation of vascular smooth muscle cells in intimal hyperplasia, and we present the new avenues of research targeting VSMC phenotype and proliferation.
Postnatal Osterix but not DMP1 lineage cells significantly contribute to intramembranous ossification in three preclinical models of bone injury
Authors: Buettmann Evan G. , Yoneda Susumu , Hu Pei , McKenzie Jennifer A. , Silva Matthew J.
Published: January 2023

Murine models of long-bone fracture, stress fracture, and cortical defect are used to discern the cellular and molecular mediators of intramembranous and endochondral bone healing. Previous work has shown that Osterix (Osx+) and Dentin Matrix Protein-1 (DMP1+) lineage cells and their progeny contribute to injury-induced woven bone formation during femoral fracture, ulnar stress fracture, and tibial cortical defect repair. However, the contribution of pre-existing versus newly-derived Osx+ and DMP1+ lineage cells in these murine models of bone injury is unclear. We addressed this knowledge gap by using male and female 12-week-old, tamoxifen-inducible Osx Cre_ERT2 and DMP1 Cre_ERT2 mice harboring the Ai9 TdTomato reporter allele. To trace pre-existing Osx+ and DMP1+ lineage cells, tamoxifen (TMX: 100 mg/kg gavage) was given in a pulse manner (three doses, 4 weeks before injury), while to label pre-existing and newly-derived lineage Osx+ and DMP1+ cells, TMX was first given 2 weeks before injury and continuously (twice weekly) throughout healing. TdTomato positive (TdT+) cell area and cell fraction were quantified from frozen histological sections of injured and uninjured contralateral samples at times corresponding with active woven bone formation in each model. We found that in uninjured cortical bone tissue, Osx Cre_ERT2 was more efficient than DMP1 Cre_ERT2 at labeling the periosteal and endosteal surfaces, as well as intracortical osteocytes. Pulse-labeling revealed that pre-existing Osx+ lineage and their progeny, but not pre-existing DMP1+ lineage cells and their progeny, significantly contributed to woven bone formation in all three injury models. In particular, these pre-existing Osx+ lineage cells mainly lined new woven bone surfaces and became embedded as osteocytes. In contrast, with continuous dosing, both Osx+ and DMP1+ lineage cells and their progeny contributed to intramembranous woven bone formation, with higher TdT+ tissue area and cell fraction in Osx+ lineage versus DMP1+ lineage calluses (femoral fracture and ulnar stress fracture). Similarly, Osx+ and DMP1+ lineage cells and their progeny significantly contributed to endochondral callus regions with continuous dosing only, with higher TdT+ chondrocyte fraction in Osx+versus DMP1+ cell lineages. In summary, pre-existing Osx+ but not DMP1+ lineage cells and their progeny make up a significant amount of woven bone cells (particularly osteocytes) across three preclinical models of bone injury. Therefore, Osx+ cell lineage modulation may prove to be an effective therapy to enhance bone regeneration.
Increased sizes and improved qualities of tibia bones by myostatin mutation in Japanese quail
Authors: Lee Joonbum , Tompkins Yuguo , Kim Dong-Hwan , Kim Woo Kyun , Lee Kichoon
Published: January 2023

Production of large amounts of meat within a short growth period from modern broilers provides a huge economic benefit to the poultry industry. However, poor bone qualities of broilers caused by rapid growth are considered as one of the problems in the modern broilers industry. After discovery and investigation of myostatin (MSTN) as an anti-myogenic factor to increase muscle mass by targeted knockout in various animal models, additional positive effects of MSTN mutation on bone qualities have been reported in MSTN knockout mice. Although the same beneficial effects on muscle gain by MSTN mutation have been confirmed in MSTN mutant quail and chickens, bone qualities of the MSTN mutant birds have not been investigated, yet. In this study, tibia bones were collected from MSTN mutant and wild-type (WT) quail at 4 months of age and analyzed by Micro-Computed Tomography scanning to compare size and strength of tibia bone and quality parameters in diaphysis and metaphysis regions. Length, width, cortical thickness, and bone breaking strength of tibia bones in the MSTN mutant group were significantly increased compared to those of the WT group, indicating positive effects of MSTN mutation on tibia bone sizes and strength. Furthermore, bone mineral contents and bone volume of whole diaphysis, diaphyseal cortical bone, whole metaphysis, and metaphyseal trabecular and cortical bones were significantly increased in the MSTN mutant group compared to the WT group, indicating increased mineralization in the overall tibia bone by MSTN mutation. Especially, higher bone mineral density (BMD) of whole diaphysis, higher total surface of whole metaphysis, and higher BMD, trabecular thickness, and total volume of metaphyseal trabecular bones in the MSTN mutant group compared to the WT group suggested improvements in bone qualities and structural soundness of both diaphysis and metaphysis regions with significant changes in trabecular bones by MSTN mutation. Taken together, MSTN can be considered as a potential target to not only increase meat yield, but also to improve bone qualities that can reduce the incidence of leg bone problems for the broiler industry.
Acute resistance exercise training does not augment mitochondrial remodelling in master athletes or untrained older adults
Authors: Marshall Ryan Neil , McKendry James , Smeuninx Benoit , Seabright Alex Peter , Morgan Paul T. , Greig Carolyn , Breen Leigh
Published: January 2023

Background: Ageing is associated with alterations to skeletal muscle oxidative metabolism that may be influenced by physical activity status, although the mechanisms underlying these changes have not been unraveled. Similarly, the effect of resistance exercise training (RET) on skeletal muscle mitochondrial regulation is unclear.

Methods: Seven endurance-trained masters athletes ([MA], 74 ± 3 years) and seven untrained older adults ([OC]. 69 ± 6 years) completed a single session of knee extension RET (6 x 12 repetitions, 75% 1-RM, 120-s intra-set recovery). Vastus lateralis muscle biopsies were collected pre-RET, 1 h post-RET, and 48h post-RET. Skeletal muscle biopsies were analyzed for citrate synthase (CS) enzyme activity, mitochondrial content, and markers of mitochondrial quality control via immunoblotting.

Results: Pre-RET CS activity and protein content were ∼45% (p < .001) and ∼74% greater in MA compared with OC (p = .006). There was a significant reduction (∼18%) in CS activity 48 h post-RET (p < .05) in OC, but not MA. Pre-RET abundance of individual and combined mitochondrial electron transport chain (ETC) complexes I-V were significantly greater in MA compared with OC, as were markers of mitochondrial fission and fusion dynamics (p-DRP-1Ser616, p-MFFSer146, OPA-1 & FIS-1, p < .05 for all). Moreover, MA displayed greater expression of p-AMPKThr172, PGC1α, TFAM, and SIRT-3 (p < .05 for all). Notably, RET did not alter the expression of any marker of mitochondrial content, biogenesis, or quality control in both OC and MA.

Conclusion: The present data suggest that long-term aerobic exercise training supports superior skeletal muscle mitochondrial density and protein content into later life, which may be regulated by greater mitochondrial quality control mechanisms and supported via superior fission-fusion dynamics. However, a single session of RET is unable to induce mitochondrial remodelling in the acute (1h post-RET) and delayed (48 h post-RET) recovery period in OC and MA.
Apelin-17 to diagnose idiopathic pulmonary arterial hypertension: A biomarker study
Authors: Foris Vasile , Kovacs Gabor , Avian Alexander , Bálint Zoltán , Douschan Philipp , Ghanim Bahil , Klepetko Walter , Olschewski Andrea , Olschewski Horst
Published: January 2023

Background: NT-proBNP and GDF-15 are established blood-derived biomarkers for risk assessment in pulmonary hypertension (PH), despite limited sensitivity and specificity. Apelin has a crucial function in endothelial homeostasis, thus it might represent a new biomarker for PH. However, there are numerous circulating apelin isoforms, and their potential role in this setting is unknown. This study evaluated different apelin isoforms in PH patients and prospectively evaluated the role of apelin-17 in comparison with NT-proBNP and GDF-15 as diagnostic marker in idiopathic pulmonary arterial hypertension (IPAH).

Methods: Based on our pilot study, we performed a power calculation for apelin-13, apelin-17, apelin-36, as predictor of IPAH vs healthy controls. Apelin-17 provided the best discriminatory power, and accordingly, we enrolled n = 31 patients with IPAH and n = 31 matched healthy controls in a prospective study. NT-proBNP and GDF-15 was determined in all patients. ROC curve analysis was performed to assess the diagnostic value of the markers and their combinations.

Results: Apelin-17, NT-proBNP, and GDF-15 were significantly elevated in IPAH patients as compared to controls (p < .001). Apelin-17 detected IPAH with a sensitivity of 68% and a specificity of 93% at a cut-off value of >1,480 pg/ml (AUC 0.86, 95%CI:0.76–0.95) as compared to GDF-15 (sensitivity 86%; specificity 72%, AUC 0.81 (95%CI:0.7–0.92)) and NT-proBNP (sensitivity 86%; specificity 72% (AUC 0.85, 95%CI:0.75–0.95)). Combinations of these markers could be used to increase either specificity or sensitivity.

Conclusion: Apelin-17 appears to be suitable blood derived diagnostic marker for idiopathic pulmonary arterial hypertension.
Towards making the fields talks: A real-time cloud enabled IoT crop management platform for smart agriculture
Authors: Thilakarathne Navod Neranjan , Bakar Muhammad Saifullah Abu , Abas Pg Emerolylariffion , Yassin Hayati
Published: January 2023

Agriculture is the primary and oldest industry in the world and has been transformed over the centuries from the prehistoric era to the technology-driven 21st century, where people are always solving complex problems with the aid of technology. With the power of Information and Communication Technologies (ICTs), the world has become a global village, where every digital object that prevails in the world is connected to each other with the Internet of Things (IoT). The fast proliferation of IoT-based technology has revolutionized practically every sector, including agriculture, shifting the industry from statistical to quantitative techniques. Such profound transformations are reshaping traditional agricultural practices and generating new possibilities in the face of various challenges. With the opportunities created, farmers are now able to monitor the condition of crops in real time. With the automated IoT solutions, farmers can automate tasks in the farmland, as these solutions are capable of making precise decisions based on underlying challenges and executing actions to overcome such difficulties, alerting farmers in real-time, eventually leading to increased productivity and higher harvest. In this context, we present a cloud-enabled low-cost sensorized IoT platform for real-time monitoring and automating tasks dealing with a tomato plantation in an indoor environment, highlighting the necessity of smart agriculture. We anticipate that the findings of this study will serve as vital guides in developing and promoting smart agriculture solutions aimed at improving productivity and quality while also enabling the transition to a sustainable environment.
An integrated genomic and biochemical approach to investigate the potentiality of heirloom tomatoes: Breeding resources for food quality and sustainable agriculture
Authors: Tripodi Pasquale , D’Alessandro Antonietta , Francese Gianluca
Published: January 2023

A revival of interest in traditional varieties reflects the change in consumer preferences and the greater awareness of the quality of locally grown products. As ancient cultivars, heirlooms have been selected for decades in specific habitats and represent nowadays potential germplasm sources to consider for breeding high-quality products and cultivation in sustainable agriculture. In this study, 60 heirloom tomato (Solanum lycopersicum L.) accessions, including diverse varietal types (beefsteak, globe, oxheart, plum, and cherry), were profiled over two seasons for the main chemical and biochemical fruit traits. A medium–high level of heritability was found for all traits ranging from 0.52 for soluble solids to 0.99 for fruit weight. The average content of ascorbic acid was ~31 mg 100 g−1 of fw in both seasons, while the greatest variability was found for carotenoids with peaks of 245.65 μg g−1 of fw for total lycopene and 32.29 μg g−1 of fw for β-carotene. Dissection of genotypic (G) and seasonal (Y) factors highlighted genotype as the main source of variation for all traits. No significant effect of Y and G × Y was found for ascorbic acid and fruit weight, respectively, whereas a high influence of Y was found on the variation of lycopene. Molecular fingerprinting was performed using the 10K SolCAP array, yielding a total of 7,591 SNPs. Population structure, phylogenetic relationships, and principal components analysis highlighted a differentiation of plum and cherry genotypes with respect to the beefsteak and globe types. These results were confirmed by multivariate analysis of phenotypic traits, shedding light on how breeding and selection focused on fruit characteristics have influenced the genetic and phenotypic makeup of heirlooms. Marker–trait association showed 11 significantly associated loci for β-carotene and fruit weight. For β-carotene, a single variant on chromosome 8 was found at 12 kb to CCD8, a cleavage dioxygenase playing a key role in the biosynthesis of apocarotenoids. For fruit weight, a single association was located at less than 3 Mbp from SLSUN31 and fw11.3, two candidates involved in the increasing of fruit mass. These results highlight the potentiality of heirlooms for genetic improvement and candidate gene identification.
Na+/K+-ATPase regulates the K+/Na+ homeostasis in the intertidal macroalgae, Neoporphyra haitanensis, in response to salt stress
Authors: Chen Qi , Xu Kai , Xu Yan , Ji Dehua , Chen Changsheng , Xie Chaotian , Wang Wenlei
Published: January 2023

In plants under hypersaline stress, the main transporter that extrudes sodium ions (Na+) is the Na+/H+ antiporter SOS1. Different from land plants, the intertidal macroalgae, Neopyropia/Neoporphyra contains an animal-type Na+/K+-ATPase as well as the SOS1 system. However, the contribution of Na+/K+-ATPase to the K+/Na+ homeostasis of intertidal macroalgae remains unclear. In this study, we analyzed the function of Na+/K+-ATPase in the response of Neoporphyra haitanensis to salt stress from the perspective of ion transport dynamics. Both the transcript level of NhNKA2 and enzyme activity of Na+/K+-ATPase increased in the early response of N. haitanensis thalli to hypersaline stress. Addition of ouabain, an inhibitor of Na+/K+-ATPase, resulted in Na+ accumulation in the cells, severe K+ leakage from the thalli, and then remarkably disturbed the K+/Na+ homeostasis in N. haitanensis thalli. This disruption might induce a significant decrease in photosynthesis and a severe oxidative damage in thalli. Accordingly, these results suggested that the important role of Na+/K+-ATPase in the resistance of intertidal macroalgae to hypersaline stress, and shed light on the diversity of K+/Na+ homeostasis maintenance mechanisms in plants.
Ten new high-quality genome assemblies for diverse bioenergy sorghum genotypes
Authors: Voelker William G. , Krishnan Krittika , Chougule Kapeel , Alexander Louie C. , Lu Zhenyuan , Olson Andrew , Ware Doreen , Songsomboon Kittikun , Ponce Cristian , Brenton Zachary W. , Boatwright J. Lucas , Cooper Elizabeth A.
Published: January 2023

Introduction

Sorghum (Sorghum bicolor (L.) Moench) is an agriculturally and economically important staple crop that has immense potential as a bioenergy feedstock due to its relatively high productivity on marginal lands. To capitalize on and further improve sorghum as a potential source of sustainable biofuel, it is essential to understand the genomic mechanisms underlying complex traits related to yield, composition, and environmental adaptations.

Methods

Expanding on a recently developed mapping population, we generated de novo genome assemblies for 10 parental genotypes from this population and identified a comprehensive set of over 24 thousand large structural variants (SVs) and over 10.5 million single nucleotide polymorphisms (SNPs).

Results

We show that SVs and nonsynonymous SNPs are enriched in different gene categories, emphasizing the need for long read sequencing in crop species to identify novel variation. Furthermore, we highlight SVs and SNPs occurring in genes and pathways with known associations to critical bioenergy-related phenotypes and characterize the landscape of genetic differences between sweet and cellulosic genotypes.

Discussion

These resources can be integrated into both ongoing and future mapping and trait discovery for sorghum and its myriad uses including food, feed, bioenergy, and increasingly as a carbon dioxide removal mechanism.
Convergent evolution of the annual life history syndrome from perennial ancestors
Authors: Hjertaas Ane C. , Preston Jill C. , Kainulainen Kent , Humphreys Aelys M. , Fjellheim Siri
Published: January 2023

Despite most angiosperms being perennial, once-flowering annuals have evolved multiple times independently, making life history traits among the most labile trait syndromes in flowering plants. Much research has focused on discerning the adaptive forces driving the evolution of annual species, and in pinpointing traits that distinguish them from perennials. By contrast, little is known about how ‘annual traits’ evolve, and whether the same traits and genes have evolved in parallel to affect independent origins of the annual syndrome. Here, we review what is known about the distribution of annuals in both phylogenetic and environmental space and assess the evidence for parallel evolution of annuality through similar physiological, developmental, and/or genetic mechanisms. We then use temperate grasses as a case study for modeling the evolution of annuality and suggest future directions for understanding annual-perennial transitions in other groups of plants. Understanding how convergent life history traits evolve can help predict species responses to climate change and allows transfer of knowledge between model and agriculturally important species.
Current trends and insights on EMS mutagenesis application to studies on plant abiotic stress tolerance and development
Authors: Chen Liuzhu , Duan Liu , Sun Minghui , Yang Zhuo , Li Hongyu , Hu Keming , Yang Hong , Liu Li
Published: January 2023

Ethyl methanesulfonate (EMS)-induced mutagenesis is a powerful tool to generate genetic resource for identifying untapped genes and characterizing the function of genes to understand the molecular basis of important agronomic traits. This review focuses on application of contemporary EMS mutagenesis in the field of plant development and abiotic stress tolerance research, with particular focuses on reviewing the mutation types, mutagenesis site, mutagen concentration, mutagenesis duration, the identification and characterization of mutations responsible for altered stress tolerance responses. The application of EMS mutation breeding combined with genetic engineering in the future plant breeding and fundamental research was also discussed. The collective information in this review will provide good insight on how EMS mutagenesis is efficiently applied to improve abiotic stress tolerance of crops with the utilization of Next-generation sequencing (NGS) for mutation identification.
Phenotypic variation of a new synthetic allotetraploid Arabidopsis kamchatica enhanced in natural environment
Authors: Shimizu-Inatsugi Rie , Morishima Aki , Mourato Beatriz , Shimizu Kentaro K. , Sato Yasuhiro
Published: January 2023

The phenotypic variation of vegetative organs and reproductive organs of newly synthesized and natural Arabidopsis kamchatica genotypes was investigated in both a controlled environment and a natural environment in an experimental garden. When we compared the variation of their leaf shape as a vegetative organ, the synthetic A. kamchatica individuals grown in the garden showed larger variation compared with the individuals incubated in a growth chamber, suggesting enhanced phenotypic variation in a natural fluctuating environment. In contrast, the natural A. kamchatica genotypes did not show significant change in variation by growth condition. The phenotypic variation of floral organs by growth condition was much smaller in both synthetic and natural A. kamchatica genotypes, and the difference in variation width between the growth chamber and the garden was not significant in each genotype as well as among genotypes. The higher phenotypic variation in synthetic leaf may imply flexible transcriptomic regulation of a newly synthesized polyploid compared with a natural polyploid.
Maize-soybean intercropping at optimal N fertilization increases the N uptake, N yield and N use efficiency of maize crop by regulating the N assimilatory enzymes
Authors: Nasar Jamal , Zhao Chang Jiang , Khan Rayyan , Gul Hina , Gitari Harun , Shao Zeqiang , Abbas Ghulam , Haider Imran , Iqbal Zafar , Ahmed Waqas , Rehman Raheela , Liang Qing Ping , Zhou Xun Bo , Yang Juan
Published: January 2023

Introduction

Surplus use of chemical nitrogen (N) fertilizers to increase agricultural Q9 production causes severe problems to the agricultural ecosystem and environment. This is contrary to N use efficiency and sustainable agricultural production.

Methods

Hence, this study was designed to investigate the effect of maizesoybean intercropping on N uptake, N yield, N utilization use efficiency, and the associated nitrogen assimilatory enzymes of maize crops under different N fertilization for two consecutive years 2021-2022.

Results

The findings of the study showed that intercropping at the optimal N rate (N1) (250 kg N ha-1) increased significantly maize grain yield by 30 and 34%, residue yield by 30 and 37%, and 100-grain weight by 33 and 39% in the year 2021 and 2022, respectively. As compared with mono-cropping, at this optimal N rate, the respective increase (of maize’s crop N yield indices) for 2021 and 2022 were 53 and 64% for grain N yield, and 53 and 68% for residue N yield. Moreover, intercropping at N1 resulted in higher grain N content by 28 and 31%, residue N content by 18 and 22%, and total N uptake by 65 and 75% in 2021 and 2022, respectively. The values for the land equivalent ratio for nitrogen yield (LERN) were greater than 1 in intercropping, indicating better utilization of N under the intercropping over mono-cropping. Similarly, intercropping increased the N assimilatory enzymes of maize crops such as nitrate reductase (NR) activity by 19 and 25%, nitrite reductase (NiR) activity by 20 and 23%, and glutamate synthase activity (GOGAT) by 23 and 27% in 2021 and 2022, respectively. Consequently, such increases resulted in improved nitrogen use efficiency indices such as N use efficiency (NUE), partial factor nitrogen use efficiency (PFNUE), nitrogen uptake efficiency (NUpE), and nitrogen agronomic efficiency (NAE) under intercropping than mono-cropping.

Conclusion

Thus, this suggests that maize-soybean intercropping under optimal N fertilization can improve the nitrogen status and nitrogen use efficiency of maize crops by regulating the nitrogen assimilatory enzymes, thereby enhancing its growth and yield. Therefore, prioritizing intercropping over an intensive mono-cropping system could be a better option for sustainable agricultural production.
Genome-wide characterization of the SHORT INTER-NODES/STYLISH and Shi-Related Sequence family in Gossypium hirsutum and functional identification of GhSRS21 under salt stress
Authors: Sun Chendong , Yu Li , Zhang Shuojun , Gu Qijuan , Wang Mei
Published: January 2023

Saline stress is a significant factor that caused crop growth inhibition and yield decline. SHORT INTERNODES/STYLISH (SHI/STY) and SHI-RELATED SEQUENCE (SRS) transcription factors are specific to plants and share a conserved RING-like zinc-finger domain (CX2CX7CX4CX2C2X6C). However, the functions of SHI/STY and SRS genes in cotton responses to salt stress remain unclear. In this study, 26 GhSRSs were identified in Gossypium hirsutum, which further divided into three subgroups. Phylogenetic analysis of 88 SRSs from8 plant species revealed independent evolutionary pattern in some of SRSs derived from monocots. Conserved domain and subcellular location predication of GhSRSs suggested all of them only contained the conserved RING-like zinc-finger domain (DUF702) domain and belonged to nucleus-localized transcription factors except for the GhSRS22. Furthermore, synteny analysis showed structural variation on chromosomes during the process of cotton polyploidization. Subsequently, expression patterns of GhSRS family members in response to salt and drought stress were analyzed in G. hirsutum and identified a salt stress-inducible gene GhSRS21. The GhSRS21 was proved to localize in the nuclear and silencing it in G. hirsutum increased the cotton resistance to salt using the virus-induced gene silencing (VIGS) system. Finally, our transcriptomic data revealed that GhSRS21 negatively controlled cotton salt tolerance by regulating the balance between ROS production and scavenging. These results will increase our understanding of the SRS gene family in cotton and provide the candidate resistant gene for cotton breeding.
Utilization of functional agro-waste residues for oyster mushroom production: Nutritions and active ingredients in healthcare
Authors: Zeng Xu , Li Jiaxue , Lyu Xinkai , Chen Tongyao , Chen Juan , Chen Xiaomei , Guo Shunxing
Published: January 2023

A large amount of agro-industrial residues are produced from the planting, production and processing of traditional Chinese herbs. As a tonic, edible, and economical herb, Codonopsis pilosula root has been extensively developed into medicine and functional food. However, thousands of tons of aerial parts (stems, leaves, flowers and fruits) have been directly discarded after harvest each year. To utilise agro-wastes, Pleurotus ostreatus was cultivated on a basal substrate supplemented with C. pilosula stems and leaves (CSL). Physicochemical analyses revealed that the basal substrate mixed with CSL was more abundant in cellulose, hemicellulose, and most of micronutrients such as K, Ca, Mg, S, Fe, Zn and Mo. After the first flush, the fruit bodies in CSL group exhibited a higher fresh weight, a wider average pileus diameter and a lower moisture level. Nutrition analyses presented a higher protein content and a lower fat content in mushrooms from CSL group compared with control group. Interestingly, 14 amino acids (glutamine, arginine, valine, leucine, and etc.) and 3 micronutrients (Se, Fe and Zn) were increased after CSL addition to the substrate. Based on untargeted metabolomics, a total of 710 metabolites were annotated. Compared with control group, there were 142 and 117 metabolites significantly increased and decreased in the CSL group. Most of them were grouped into classes of amino acids and peptids, fatty acids, carbohydrates, terpenoids, and etc. Moreover, an abundance of phytometabolites from Codonopsis were detected in P. ostreatus from CSL group, including polyacetylenes or polyenes, flavonoids, alkaloids, terpenoids, organic acids, and etc. UPLC-MS/MS results demonstrated that lobetyolin content in the CSL group samples was 0.0058%. In summary, the aerial parts of C. pilosula processed for use in the production of edible mushroom is an emerging strategy to converting agricultural waste into functional foods.
YOLO-P: An efficient method for pear fast detection in complex orchard picking environment
Authors: Sun Han , Wang Bingqing , Xue Jinlin
Published: January 2023

Introduction

Fruit detection is one of the key functions of an automatic picking robot, but fruit detection accuracy is seriously decreased when fruits are against a disordered background and in the shade of other objects, as is commmon in a complex orchard environment.

Methods

Here, an effective mode based on YOLOv5, namely YOLO-P, was proposed to detect pears quickly and accurately. Shuffle block was used to replace the Conv, Batch Norm, SiLU (CBS) structure of the second and third stages in the YOLOv5 backbone, while the inverted shuffle block was designed to replace the fourth stage’s CBS structure. The new backbone could extract features of pears from a long distance more efficiently. A convolutional block attention module (CBAM) was inserted into the reconstructed backbone to improve the robot’s ability to capture pears’ key features. Hard-Swish was used to replace the activation functions in other CBS structures in the whole YOLOv5 network. A weighted confidence loss function was designed to enhance the detection effect of small targets.

Result

At last, model comparison experiments, ablation experiments, and daytime and nighttime pear detection experiments were carried out. In the model comparison experiments, the detection effect of YOLO-P was better than other lightweight networks. The results showed that the module’s average precision (AP) was 97.6%, which was 1.8% higher than the precision of the original YOLOv5s. The model volume had been compressed by 39.4%, from 13.7MB to only 8.3MB. Ablation experiments verified the effectiveness of the proposed method. In the daytime and nighttime pear detection experiments, an embedded industrial computer was used to test the performance of YOLO-P against backgrounds of different complexities and when fruits are in different degrees of shade.

Discussion

The results showed that YOLO-P achieved the highest F1 score (96.1%) and frames per second (FPS) (32 FPS). It was sufficient for the picking robot to quickly and accurately detect pears in orchards. The proposed method can quickly and accurately detect pears in unstructured environments. YOLO-P provides support for automated pear picking and can be a reference for other types of fruit detection in similar environments.