bluuebunny/crossref_metadata_2025 huggingface dataset:
Increased levels of endogenous retroviruses trigger fibroinflammation and play a role in kidney disease development
Authors: Dhillon Poonam , Mulholland Kelly Ann , Hu Hailong , Park Jihwan , Sheng Xin , Abedini Amin , Liu Hongbo , Vassalotti Allison , Wu Junnan , Susztak Katalin
Published: February 2023

Inflammation is a common feature of all forms of chronic kidney disease; however, the underlying mechanism remains poorly understood. Evolutionarily inherited endogenous retroviruses (ERVs) have the potential to trigger an immune reaction. Comprehensive RNA-sequencing of control and diseased kidneys from human and mouse disease models indicated higher expression of transposable elements (TEs) and ERVs in diseased kidneys. Loss of cytosine methylation causing epigenetic derepression likely contributes to an increase in ERV levels. Genetic deletion/pharmacological inhibition of DNA methyltransferase 1 (DNMT1) induces ERV expression. In cultured kidney tubule cells, ERVs elicit the activation of cytosolic nucleotide sensors such as RIG-I, MDA5, and STING. ERVs expressions in kidney tubules trigger RIG-I/STING, and cytokine expression, and correlate with the presence of immune cells. Genetic deletion of RIG-I or STING or treatment with reverse transcriptase inhibitor ameliorates kidney fibroinflammation. Our data indicate an important role of epigenetic derepression-induced ERV activation triggering renal fibroinflammation.
Quantifying PON1 on HDL with nanoparticle-gated electrokinetic membrane sensor for accurate cardiovascular risk assessment
Authors: Kumar Sonu , Maniya Nalin , Wang Ceming , Senapati Satyajyoti , Chang Hsueh-Chia
Published: February 2023

Cardiovascular disease-related deaths (one-third of global deaths) can be reduced with a simple screening test for better biomarkers than the current lipid and lipoprotein profiles. We propose using a highly atheroprotective subset of HDL with colocalized PON1 (PON1-HDL) for superior cardiovascular risk assessment. However, direct quantification of HDL proteomic subclasses are complicated by the peroxides/antioxidants associated with HDL interfering with redox reactions in enzymatic calorimetric and electrochemical immunoassays. Hence, we developed an enzyme-free Nanoparticle-Gated Electrokinetic Membrane Sensor (NGEMS) platform for quantification of PON1-HDL in plasma within 60 min, with a sub-picomolar limit of detection, 3–4 log dynamic range and without needing sample pretreatment or individual-sample calibration. Using NGEMS, we report our study on human plasma PON1-HDL as a cardiovascular risk marker with AUC~0.99 significantly outperforming others (AUC~0.6–0.8), including cholesterol/triglycerides tests. Validation for a larger cohort can establish PON1-HDL as a biomarker that can potentially reshape cardiovascular landscape.
Sample multiplexing-based targeted pathway proteomics with real-time analytics reveals the impact of genetic variation on protein expression
Authors: Yu Qing , Liu Xinyue , Keller Mark P. , Navarrete-Perea Jose , Zhang Tian , Fu Sipei , Vaites Laura P. , Shuken Steven R. , Schmid Ernst , Keele Gregory R. , Li Jiaming , Huttlin Edward L. , Rashan Edrees H. , Simcox Judith , Churchill Gary A. , Schweppe Devin K. , Attie Alan D. , Paulo Joao A. , Gygi Steven P.
Published: February 2023

Targeted proteomics enables hypothesis-driven research by measuring the cellular expression of protein cohorts related by function, disease, or class after perturbation. Here, we present a pathway-centric approach and an assay builder resource for targeting entire pathways of up to 200 proteins selected from >10,000 expressed proteins to directly measure their abundances, exploiting sample multiplexing to increase throughput by 16-fold. The strategy, termed GoDig, requires only a single-shot LC-MS analysis, ~1 µg combined peptide material, a list of up to 200 proteins, and real-time analytics to trigger simultaneous quantification of up to 16 samples for hundreds of analytes. We apply GoDig to quantify the impact of genetic variation on protein expression in mice fed a high-fat diet. We create several GoDig assays to quantify the expression of multiple protein families (kinases, lipid metabolism- and lipid droplet-associated proteins) across 480 fully-genotyped Diversity Outbred mice, revealing protein quantitative trait loci and establishing potential linkages between specific proteins and lipid homeostasis.
Genetic and pharmacologic inhibition of ALDH1A3 as a treatment of β-cell failure
Authors: Son Jinsook , Du Wen , Esposito Mark , Shariati Kaavian , Ding Hongxu , Kang Yibin , Accili Domenico
Published: February 2023

Type 2 diabetes (T2D) is associated with β-cell dedifferentiation. Aldehyde dehydrogenase 1 isoform A3 (ALHD1A3) is a marker of β-cell dedifferentiation and correlates with T2D progression. However, it is unknown whether ALDH1A3 activity contributes to β-cell failure, and whether the decrease of ALDH1A3-positive β-cells (A+) following pair-feeding of diabetic animals is due to β-cell restoration. To tackle these questions, we (i) investigated the fate of A+ cells during pair-feeding by lineage-tracing, (ii) somatically ablated ALDH1A3 in diabetic β-cells, and (iii) used a novel selective ALDH1A3 inhibitor to treat diabetes. Lineage tracing and functional characterization show that A+ cells can be reconverted to functional, mature β-cells. Genetic or pharmacological inhibition of ALDH1A3 in diabetic mice lowers glycemia and increases insulin secretion. Characterization of β-cells following ALDH1A3 inhibition shows reactivation of differentiation as well as regeneration pathways. We conclude that ALDH1A3 inhibition offers a therapeutic strategy against β-cell dysfunction in diabetes.
Achiral organoiodine-functionalized helical polyisocyanides for multiple asymmetric dearomative oxidations
Authors: Wu Zong-Quan , Song Xue , Li Yan-Xiang , Zhou Li , Zhu Yuan-Yuan , Chen Zheng , Liu Na
Published: February 2023

Immobilizing organocatalyst onto helical polymers not only facilitates the catalyst recycling from homogeneous reactions, but also boosts enantioselectivity. In this work, achiral organoiodine-functionalized single left- and right-handed helical polyisocyanides were prepared from the same monomers, which catalyzed three asymmetric oxidations gave the desired products in high yields and excellent enantioselectivity. The enantiomeric excess of the target products was up to 95%. Remarkably, the enantioselectivity can be switched by reversing the helicity of the polymer backbone. The polymer catalysts can be facilely recovered and recycled in different asymmetric oxidations with maintained excellent activity and enantioselectivity.
3-Mercaptopyruvate sulfur transferase is a protein persulfidase
Authors: Pedre Brandán , Talwar Deepti , Barayeu Uladzimir , Schilling Danny , Luzarowski Marcin , Sokolowski Mikolaj , Glatt Sebastian , Dick Tobias P.
Published: February 2023

Protein S-persulfidation (P-SSH) is recognized as a common posttranslational modification. It occurs under basal conditions and is often observed to be elevated under stress conditions. However, the mechanism(s) by which proteins are persulfidated inside cells have remained unclear. Here we report that 3-mercaptopyruvate sulfur transferase (MPST) engages in direct protein-to-protein transpersulfidation reactions beyond its previously known protein substrates thioredoxin and MOCS3/Uba4, associated with H2S generation and transfer RNA thiolation, respectively. We observe that depletion of MPST in human cells lowers overall intracellular protein persulfidation levels and identify a subset of proteins whose persulfidation depends on MPST. The predicted involvement of these proteins in the adaptation to stress responses supports the notion that MPST-dependent protein persulfidation promotes cytoprotective functions. The observation of MPST-independent protein persulfidation suggests that other protein persulfidases remain to be identified.
Trajetorias: a dataset of environmental, epidemiological, and economic indicators for the Brazilian Amazon
Authors: Rorato Ana C. , Dal’Asta Ana Paula , Lana Raquel Martins , dos Santos Ricardo B. N. , Escada Maria Isabel S. , Vogt Camila M. , Neves Tatiana Campos , Barbosa Milton , Andreazzi Cecilia S. , dos Reis Izabel C. , Fernandes Danilo A. , da Silva-Nunes Mônica , de Souza Anielli R. , Monteiro Antonio M. V. , Codeço Claudia T.
Published: February 2023

The Trajetorias dataset is a harmonized set of environmental, epidemiological, and poverty indicators for all municipalities of the Brazilian Legal Amazon (BLA). This dataset is the result of a scientific synthesis research initiative conducted by scientists from several natural and social sciences fields, consolidating multidisciplinary indicators into a coherent dataset for integrated and interdisciplinary studies of the Brazilian Amazon. The dataset allows the investigation of the association between the Amazonian agrarian systems and their impacts on environmental and epidemiological changes, furthermore enhancing the possibilities for understanding, in a more integrated and consistent way, the scenarios that affect the Amazonian biome and its inhabitants.
Short-term sedimentation dynamics in mesotidal marshes
Authors: Carrasco A. Rita , Kombiadou Katerina , Matias Ana
Published: February 2023

One of the key questions about wetlands resilience to sea-level rise is whether sediment supply will be enough to keep them coping with growing inundation levels. To address this question, researchers have put a lot of effort into field data collection and ecogeomorphic modelling, in an attempt to identify the tipping points of marsh survival. This study uses fieldwork data to characterize the sediment fluxes between the tidal flats and salt marshes, in the Ria Formosa lagoon (Portugal). Sediment fluxes were measured from the tidal channel towards the mid-upper marsh, during neap and spring tide conditions. The flow magnitude was measured, and induced transport was determined based on shear velocities. Deposition rates, instantaneous suspended sediment and near-bed velocities were linked through theoretical formulas and used to characterize time-averaged conditions for sediment delivery and deposition to the site. The results showed that suspended sediment concentrations and sediment deposition varied across the transect with no specific relation to elevation. Maximum water depths were recorded in the vegetated tidal flat, and the maximum currents were flood dominated, in the order of 0.20 m/s, in the low marsh due to flow-plant interactions and an increase of turbulence. Deposition rates ranged between 20 to 45 g/m2/hr, after a complete tidal cycle, and were higher in the mid-upper marsh. Hydroperiod was not the main contributor to sediment deposition in the study area. Sediment transport was tidally driven, strongly two-dimension during the cycle, and highly influenced by the vegetation. Measurements of marsh sediment flux obtained in our work are diverse from the ones found in the literature and evidence the importance of considering spatio-temporal variability of vegetated platforms in assessing overall marsh bed level changes.
Sustainable synthesis of graphene sand composite from waste cooking oil for dye removal
Authors: Abdullah Sani Nor Syazwani , Ang Wei Lun , Mohammad Abdul Wahab , Nouri Alireza , Mahmoudi Ebrahim
Published: February 2023

Waste cooking oil (WCO) appears to be a potential carbonaceous source for synthesizing graphene sand composite (GSC) adsorbent in removing pollutants. This study presents a green synthesis method of GSC using WCO as a sustainable carbon source for the synthesis of GSC through the thermal graphitization method. Characterization analysis conducted on GSCWCOverified the successful coating of WCO onto the sand surface and conversion to graphene, which possessed distinct functional groups and features of graphene materials. GSCWCOadsorbent effectiveness in removing Congo Red dye through batch adsorption was studied under the influence of different initial concentrations (20 to 100 mg/L), and the optimum pH (pH 2 to 10), contact time (5 to 240 min), and temperature (25 to 45 °C) were investigated. The GSCWCOshowed removal rates of 91.5% achieved at an initial dye concentration of 20 mg L−1, 1.0 g of adsorbent dosage, a temperature of 25 °C, and 150 min of contact time. The GSCWCOexhibited a maximum capacity of 5.52 mg g−1, was well-fitted to the Freundlich isotherm model with an R2value of 0.989 and had an adsorption mechanism that followed the pseudo-second-order kinetic model. Negative values of enthalpy (ΔH) and Gibbs free energy (ΔG) revealed that CR adsorption onto GSCWCOwas a spontaneous and exothermic process. The presence of functional groups on the surface of GSCWCOwith such interactions (π–π attractive forces, hydrophobic forces, and hydrogen bonding) was responsible for the anionic dye removal. Regeneration of GSCWCOadsorbent declined after four cycles, possibly due to the chemisorption of dyes with GSC that resulted in inefficient adsorption. Being a waste-to-wealth product, GSCWCOpossessed great potential to be used for water treatment and simultaneously benefited the environment through the effort to reduce the excessive discharge of WCO.
Degradation of 1-alkyl-3-methylimidazolium tetrafluoroborate in an ultrasonic zero-valent zinc and activated carbon micro-electrolysis system
Authors: Lyu Ping , Guo Wan , Qi Hang , Yuan Xiang , Ma Jinqi , Xu Xingmin , Zhou Haimei
Published: February 2023

Increased attention has been given to the removal of ionic liquids (ILs) from natural water environments. In this work, 5 kinds of 1-alkyl-3-methylimidazoliumtetrafluoroborate ([Cnmim][BF4] (n = 2, 4, 6, 8, 10)) ILs were degraded in an ultrasonic zero-valent zinc (ZVZ) and activated carbon (AC) micro-electrolysis system. Optimization of degradation conditions and the degradation levels were studied by high performance liquid chromatography, the surface morphology of the ZVZ and AC changed before and after the reaction were observed by scanning electron microscope. The degradation intermediates were detected by gas chromatography- mass spectrometry and ion chromatography, and inferred the degradation pathway. The degradation effect of [C4mim][BF4] was best with ultrasonic assistance, pH 3 and an AC/ZVZ ratio of 1:1. The degradation of [Cnmim][BF4] in aqueous solution exceeded 91.7% in 120 min, and the mineralization level exceeded 88.9%. The surface of smooth and dense ZVZ particles became loose flocculent and the porous surface of AC became larger and rougher after reaction. The degradation pathway suggested that the imidazolium ring was sulfurized or oxidized, and then the ring was opened to form N-alkyl formamide and N-methyl formamide. ZVZ/AC micro-electrolysis combined with ultrasonic irradiation is an effective method to remove ILs, which provides new insight into IL degradation.
Contrasting patterns of population structure of Bulwer’s petrel (Bulweria bulwerii) between oceans revealed by statistical phylogeography
Authors: Silva Mónica C. , Catry Paulo , Bried Joël , Kawakami Kazuto , Flint Elizabeth , Granadeiro José P.
Published: February 2023

The patterns of population divergence of mid-latitude marine birds are impacted by only a few biogeographic barriers to dispersal and the effect of intrinsic factors, such as fidelity to natal colonies or wintering grounds, may become more conspicuous. Here we describe, for the first time, the phylogeographic patterns and historical demography of Bulwer’s petrel Bulweria bulwerii and provide new insights regarding the drivers of species diversification in the marine environment. We sampled Bulwer’s petrels from the main breeding colonies and used a statistical phylogeography approach based on surveying nuclear and mitochondrial loci (~ 9100 bp) to study its mechanisms of global diversification. We uncovered three highly differentiated groups including the Western Pacific, the Central Pacific and the Atlantic. The older divergence occurred within the Pacific Ocean, ca. 850,000 ya, and since then the W Pacific group has been evolving in isolation. Conversely, divergence between the Central Pacific and Atlantic populations occurred within the last 200,000 years. While the Isthmus of Panama is important in restricting gene flow between oceans in Bulwer’s petrels, the deepest phylogeographic break is within the Pacific Ocean, where oceanographic barriers are key in driving and maintaining the remarkable structure found in this highly mobile seabird. This is in contrast with the Atlantic, where no structure was detected. Further data will provide insights regarding the extent of lineage divergence of Bulwer’s petrels in the Western Pacific.
Heterogeneity of interaction strengths and its consequences on ecological systems
Authors: Jackson Zachary , Xue BingKan
Published: February 2023

Ecosystems are formed by networks of species and their interactions. Traditional models of such interactions assume a constant interaction strength between a given pair of species. However, there is often significant trait variation among individual organisms even within the same species, causing heterogeneity in their interaction strengths with other species. The consequences of such heterogeneous interactions for the ecosystem have not been studied systematically. As a theoretical exploration, we analyze a simple ecosystem with trophic interactions between two predators and a shared prey, which would exhibit competitive exclusion in models with homogeneous interactions. We consider several scenarios where individuals of the prey species differentiate into subpopulations with different interaction strengths. We show that in all these cases, whether the heterogeneity is inherent, reversible, or adaptive, the ecosystem can stabilize at a new equilibrium where all three species coexist. Moreover, the prey population that has heterogeneous interactions with its predators reaches a higher density than it would without heterogeneity, and can even reach a higher density in the presence of two predators than with just one. Our results suggest that heterogeneity may be a naturally selected feature of ecological interactions that have important consequences for the stability and diversity of ecosystems.
Designing plant–transparent agrivoltaics
Authors: Stallknecht Eric J. , Herrera Christopher K. , Yang Chenchen , King Isaac , Sharkey Thomas D. , Lunt Richard R. , Runkle Erik S.
Published: February 2023

Covering greenhouses and agricultural fields with photovoltaics has the potential to create multipurpose agricultural systems that generate revenue through conventional crop production as well as sustainable electrical energy. In this work, we evaluate the effects of wavelength-selective cutoffs of visible and near-infrared (biologically active) radiation using transparent photovoltaic (TPV) absorbers on the growth of three diverse, representative, and economically important crops: petunia, basil, and tomato. Despite the differences in TPV harvester absorption spectra, photon transmission of photosynthetically active radiation (PAR; 400–700 nm) is the most dominant predictor of crop yield and quality. This indicates that different wavebands of blue, red, and green are essentially equally important to these plants. When the average photosynthetic daily light integral is > 12 mol m–2 d–1, basil and petunia yield and quality is acceptable for commercial production. However, even modest decreases in TPV transmission of PAR reduces tomato growth and fruit yield. These results identify crop-specific design requirements that exist for TPV harvester transmission and the necessity to maximize transmission of PAR to create the most broadly applicable TPV greenhouse harvesters for diverse crops and geographic locations. We determine that the deployment of 10% power conversion efficiency (PCE) plant-optimized TPVs over approximately 10% of total agricultural and pasture land in the U.S. would generate 7 TW, nearly double the entire energy demand of the U.S.
Reynolds nano fluid model for Casson fluid flow conveying exponential nanoparticles through a slandering sheet
Authors: Nadeem Sohail , Ishtiaq Bushra , Ben Hamida Mohamed Bechir , Almutairi Shahah , Ghazwani Hassan Ali , Eldin Sayed M. , Al-Shafay A. S.
Published: February 2023

Nanofluids with their augmented thermal characteristics exhibit numerous implementations in engineering and industrial fields such as heat exchangers, microelectronics, chiller, pharmaceutical procedures, etc. Due to such properties of nanofluids, a mathematical model of non-Newtonian Casson nanofluid is analyzed in this current study to explore the steady flow mechanism with the contribution of water-based Aluminum oxide nanoparticles. A stretchable surface incorporating variable thickness is considered to be the source of the concerning fluid flow in two-dimension. An exponential viscosity of the nanofluid is proposed to observe the fluid flow phenomenon. Different models of viscosity including Brinkman and Einstein are also incorporated in the flow analysis and compared with the present exponential model. The physical flow problem is organized in the boundary layer equations which are further tackled by the execution of the relevant similarity transformations and appear in the form of ordinary nonlinear differential equations. The different three models of nanofluid viscosity exhibit strong graphical and tabulated relations with each other relative to the various aspects of the flow problem. In all concerned models of the viscosity, the deteriorating nature of the velocity field corresponding to the Casson fluid and surface thickness parameters is observed.
Multimodal single-cell analyses of peripheral blood mononuclear cells of COVID-19 patients in Japan
Authors: Kashima Yukie , Mizutani Taketoshi , Nakayama-Hosoya Kaori , Moriyama Saya , Matsumura Takayuki , Yoshimura Yoshihiro , Sasaki Hiroaki , Horiuchi Hiroshi , Miyata Nobuyuki , Miyazaki Kazuhito , Tachikawa Natsuo , Takahashi Yoshimasa , Suzuki Tadaki , Sugano Sumio , Matano Tetsuro , Kawana-Tachikawa Ai , Suzuki Yutaka
Published: February 2023

SARS-CoV-2 continues to spread worldwide. Patients with COVID-19 show distinct clinical symptoms. Although many studies have reported various causes for the diversity of symptoms, the underlying mechanisms are not fully understood. Peripheral blood mononuclear cells from COVID-19 patients were collected longitudinally, and single-cell transcriptome and T cell receptor repertoire analysis was performed. Comparison of molecular features and patients’ clinical information revealed that the proportions of cells present, and gene expression profiles differed significantly between mild and severe cases; although even among severe cases, substantial differences were observed among the patients. In one severely-infected elderly patient, an effective antibody response seemed to have failed, which may have caused prolonged viral clearance. Naïve T cell depletion, low T cell receptor repertoire diversity, and aberrant hyperactivation of most immune cell subsets were observed during the acute phase in this patient. Through this study, we provided a better understanding of the diversity of immune landscapes and responses. The information obtained from this study can help medical professionals develop personalized optimal clinical treatment strategies for COVID-19.
A mechanistic understanding of the effects of polyethylene terephthalate nanoplastics in the zebrafish (Danio rerio) embryo
Authors: Bashirova Narmin , Poppitz David , Klüver Nils , Scholz Stefan , Matysik Jörg , Alia A.
Published: February 2023

Plastic pollution, especially by nanoplastics (NPs), has become an emerging topic due to the widespread existence and accumulation in the environment. The research on bioaccumulation and toxicity mechanism of NPs from polyethylene terephthalate (PET), which is widely used for packaging material, have been poorly investigated. Herein, we report the first use of high-resolution magic-angle spinning (HRMAS) NMR based metabolomics in combination with toxicity assay and behavioural end points to get systems-level understanding of toxicity mechanism of PET NPs in intact zebrafish embryos. PET NPs exhibited significant alterations on hatching and survival rate. Accumulation of PET NPs in larvae were observed in liver, intestine, and kidney, which coincide with localization of reactive oxygen species in these areas. HRMAS NMR data reveal that PET NPs cause: (1) significant alteration of metabolites related to targeting of the liver and pathways associated with detoxification and oxidative stress; (2) impairment of mitochondrial membrane integrity as reflected by elevated levels of polar head groups of phospholipids; (3) cellular bioenergetics as evidenced by changes in numerous metabolites associated with interrelated pathways of energy metabolism. Taken together, this work provides for the first time a comprehensive system level understanding of toxicity mechanism of PET NPs exposure in intact larvae.
Characterisation of a cyclic peptide that binds to the RAS binding domain of phosphoinositide 3-kinase p110α
Authors: Ismail Mohamed , Martin Stephen R. , George Roger , Houghton Francesca , Kelly Geoff , Chaleil Raphaël A. G. , Anastasiou Panayiotis , Wang Xinyue , O’Reilly Nicola , Federico Stefania , Joshi Dhira , Nagaraj Hemavathi , Cooley Rachel , Hui Ning Sze , Molina-Arcas Miriam , Hancock David C. , Tavassoli Ali , Downward Julian
Published: February 2023

P110α is a member of the phosphoinositide 3-kinase (PI3K) enzyme family that functions downstream of RAS. RAS proteins contribute to the activation of p110α by interacting directly with its RAS binding domain (RBD), resulting in the promotion of many cellular functions such as cell growth, proliferation and survival. Previous work from our lab has highlighted the importance of the p110α/RAS interaction in tumour initiation and growth. Here we report the discovery and characterisation of a cyclic peptide inhibitor (cyclo-CRVLIR) that interacts with the p110α-RBD and blocks its interaction with KRAS. cyclo-CRVLIR was discovered by screening a “split-intein cyclisation of peptides and proteins” (SICLOPPS) cyclic peptide library. The primary cyclic peptide hit from the screen initially showed a weak affinity for the p110α-RBD (Kd about 360 µM). However, two rounds of amino acid substitution led to cyclo-CRVLIR, with an improved affinity for p110α-RBD in the low µM (Kd 3 µM). We show that cyclo-CRVLIR binds selectively to the p110α-RBD but not to KRAS or the structurally-related RAF-RBD. Further, using biophysical, biochemical and cellular assays, we show that cyclo-CRVLIR effectively blocks the p110α/KRAS interaction in a dose dependent manner and reduces phospho-AKT levels in several oncogenic KRAS cell lines.
Design, development and application of a compact robotic transplanter with automatic seedling picking mechanism for plug-type seedlings
Authors: Khadatkar Abhijit , Pandirwar A. P. , Paradkar V.
Published: February 2023

Automation of agricultural operation such as seedling transplanting is needed to ensure efficient as well as timely operation. Robotics is the area that needs to be focused for the future of automatic seedling transplanter. This paper presents the design, development as well as working of the robotic transplanter (RT) for plug seedlings. The developed RT consists of three systems: (1) robot initiation; (2) seedling picking mechanism (SPM); and (3) vehicle movement system (VMS). The SPM consists of a main frame, manipulator, end-effector and control unit. Whereas, the VMS is having photoelectric sensor, robot controller and DC motor. The stepper motors were mounted on the main frame for movement in XY direction. The manipulator was on the crossbar that used to move the end-effector in Z-axis. The pick-up mechanism consists of an end-effector having jaw-type gripper controlled by servo motor. The control unit consists of microchip 16F877 and the system is controlled with computer programming. The gripper moves to each seedling in the pro-tray, grasp and pick-up the seedling, moves to the delivery point and then release the seedling. The manipulator was tested and analyzed for pickup and releasing of 96 seedlings with soil base from pro-tray. The initial experimental result showed that the seedling success rate, leakage rate and successful transplanting of 30 days old chilli seedling was 95.1%, 7.6% and 90.3%, respectively. Robotic technology seems to be expensive but the scope lies in the non-availability or high cost of manual labour and to ensure timeliness of repetitive field operations.
Extra-viral DNA in adeno-associated viral vector preparations induces TLR9-dependent innate immune responses in human plasmacytoid dendritic cells
Authors: Bucher Kirsten , Rodríguez-Bocanegra Eduardo , Wissinger Bernd , Strasser Torsten , Clark Simon J. , Birkenfeld Andreas L. , Siegel-Axel Dorothea , Fischer M. Dominik
Published: February 2023

Adeno-associated viral (AAV) vector suspensions produced in either human derived HEK cells or in Spodoptera frugiperda (Sf9) insect cells differ in terms of residual host cell components as well as species-specific post-translational modifications displayed on the AAV capsid proteins. Here we analysed the impact of these differences on the immunogenic properties of the vector. We stimulated human plasmacytoid dendritic cells with various lots of HEK cell-produced and Sf9 cell-produced AAV-CMV-eGFP vectors derived from different manufacturers. We found that AAV8-CMV-eGFP as well as AAV2-CMV-eGFP vectors induced lot-specific but not production platform-specific or manufacturer-specific inflammatory cytokine responses. These could be reduced or abolished by blocking toll-like receptor 9 signalling or by enzymatically reducing DNA in the vector lots using DNase. Successful HEK cell transduction by DNase-treated AAV lots and DNA analyses demonstrated that DNase did not affect the integrity of the vector but degraded extra-viral DNA. We conclude that both HEK- and Sf9-cell derived AAV preparations can contain immunogenic extra-viral DNA components which can trigger lot-specific inflammatory immune responses. This suggests that improved strategies to remove extra-viral DNA impurities may be instrumental in reducing the immunogenic properties of AAV vector preparations.
The ferroptosis signature predicts the prognosis and immune microenvironment of nasopharyngeal carcinoma
Authors: Zhou Ji , Guo Tianyao , Zhou Lin , Bao Meihua , Wang Lin , Zhou Wenhu , Tan Shan , Li Guangyi , He Binsheng , Guo Zhen
Published: February 2023

Nasopharyngeal carcinoma (NPC) is a cancer with a high metastatic rate and poor prognosis. Growing studies suggest that ferroptosis take part in the development of tumours. At the same time, the connection between ferroptosis-related genes (FRGs) and the prognosis of NPC remains unclear. In this study, we explored the dysregulated FRGs between normal control and tumour samples of NPC. Firstly, 14 of 36 differentially expressed FRGs were identified in NPC tissues compared to normal tissues, among which ABCC1, GLS2, CS and HMGCR were associated with poor prognosis for patients. The four ferroptosis genes were used for consensus cluster analysis and two risk-related FRGs (ABCC1 and GLS2) were used in a risk model. The ROC curve revealed the good predictive performance of this risk signature. Multivariate analysis revealed that risk score and intratumoral TILs were independent risk factors linked to prognosis. Additionally, our results suggested that the risk signature was attached to the immune microenvironment. Moreover, the NPC patients with high risk were sensitive to chemotherapeutic drugs including axitinib, docetaxel, embelin, epothilone.B, parthenolide, thapsigargin, tipifarnib, vinorelbine. Finally, the expression of ABCC1 and GLS2 was validated in NPC tissues using immunohistochemistry. Together, these results revealed ferroptosis may be a potential biomarker in NPC and representing a promising future direction in prognosis and therapeutic strategy for the treatment of NPC.
Risk of dementia and mild cognitive impairment in older adults with a criminal background: a population-based register study in Sweden
Authors: Solares Carmen , Garcia-Argibay Miguel , Chang Zheng , Dobrosavljevic Maja , Larsson Henrik , Andershed Henrik
Published: February 2023

Criminal behaviour has previously been associated with an increased risk for several mental health problems, but little is known about the association between criminal behaviour and dementia. We aimed to examine how the criminal background (type of crime, number of convictions, length of the sentence) is associated with dementia and mild cognitive impairment (MCI), and how mental and physical health disorders and educational attainment influenced these associations. A nationwide cohort of 3,617,028 individuals born between 1932 and 1962 were linked with criminal and medical records using Swedish national registers. We used Cox regression models to examine the associations. Increased risks for dementia (Hazard ratios (HRs) 1.54, 95% confidence interval (CI) 1.50–1.57) and MCI (1.55, 1.50–1.61) were found in individuals with criminal background, particularly among those who committed violent or several crimes, or with long sentences. After full adjustment of covariates, the associations attenuated but remained statistically significant for dementia (1.25, 1.22–1.28) and MCI (1.27, 1.22–1.32). The attenuation was mostly explained by mental health problems -depression, anxiety, schizophrenia spectrum disorders, substance use disorder (SUD), and bipolar disorder- (dementia: 1.34, 1.31–1.37; MCI: 1.35, 1.30–1.40). SUD contributed the most to attenuate the associations. Our results may provide important insights to health and penal systems by showing the importance of considering the severity of the criminal background and life-course mental health when assessing the risk of neurodegenerative disorders.
Distributed compact plasma reactor decontamination for planetary protection in space missions
Authors: Choudhury Bhaswati , Revazishvili Tamara , Lozada Maria , Roy Sarthak , Mastro Emma Noelle , Portugal Sherlie , Roy Subrata
Published: February 2023

This paper presents a proof-of-concept study establishing effectiveness of the Active Plasma Sterilizer (APS) for decontamination in planetary protection. The APS uses Compact Portable Plasma Reactors (CPPRs) to produce surface dielectric barrier discharge, a type of cold plasma, using ambient air to generate and distribute reactive species like ozone used for decontamination. Decontamination tests were performed with pathogenic bacteria (Escherichia coli and Bacillus subtilis) on materials (Aluminum, Polycarbonate, Kevlar and Orthofabric) relevant to space missions. Results show that the APS can achieve 4 to 5 log reductions of pathogenic bacteria on four selected materials, simultaneously at 11 points within 30 min, using power of 13.2 ± 2.22 W. Spatial decontamination data shows the APS can uniformly sterilize several areas of a contaminated surface within 30 min. Ozone penetration through Kevlar and Orthofabric layers was achieved using the CPPR with no external agent assisting penetration. Preliminary material compatibility tests with SEM analysis of the APS exposed materials showed no significant material damage. Thus, this study shows the potential of the APS as a light-weight sustainable decontamination technology for planetary protection with advantages of uniform spatial decontamination, low processing temperatures, low exposure times, material compatibility and the ability to disinfect porous surfaces.
Fetal bovine serum, an important factor affecting the reproducibility of cell experiments
Authors: Liu Shuai , Yang Wei , Li Yunlei , Sun Changqing
Published: February 2023

Fetal bovine serum (FBS) is a natural medium used in cell cultures containing the large amount of nutrients necessary for cell growth and is often used for in vitro cultures of animal cells. Although FBS plays a vital role in cell cultures, there are small molecules contained within FBS that remain unidentified, and their effects on cultured cells is poorly understood. Here, we report that different brands of FBS have varying influences on the background expression of IL-8, not TNFα and IL1β in epithelial cells. The endogenous small molecules in FBS and ERK pathways may contribute to these effects. In addition, FBS form the IL-8 stimulation and IL-8 non-responsive groups have different metabolome profiles. Overall, our study suggests that metabolites in FBS should be included in the quantitative considerations when conducting cell experiments, especially immune-related experiments, to improve the repeatability of experimental results in scientific papers; IL-8 could thus be an important factor in selecting FBS.
CT-based data generation for foreign object detection on a single X-ray projection
Authors: Andriiashen Vladyslav , van Liere Robert , van Leeuwen Tristan , Batenburg K. Joost
Published: February 2023

Although X-ray imaging is used routinely in industry for high-throughput product quality control, its capability to detect internal defects has strong limitations. The main challenge stems from the superposition of multiple object features within a single X-ray view. Deep Convolutional neural networks can be trained by annotated datasets of X-ray images to detect foreign objects in real-time. However, this approach depends heavily on the availability of a large amount of data, strongly hampering the viability of industrial use with high variability between batches of products. We present a computationally efficient, CT-based approach for creating artificial single-view X-ray data based on just a few physically CT-scanned objects. By algorithmically modifying the CT-volume, a large variety of training examples is obtained. Our results show that applying the generative model to a single CT-scanned object results in image analysis accuracy that would otherwise be achieved with scans of tens of real-world samples. Our methodology leads to a strong reduction in training data needed, improved coverage of the combinations of base and foreign objects, and extensive generalizability to additional features. Once trained on just a single CT-scanned object, the resulting deep neural network can detect foreign objects in real-time with high accuracy.
Severe SARS-Cov2 pneumonia in vaccinated patients: a multicenter cohort study
Authors: Mirouse Adrien , Friol Alice , Moreau Anne-Sophie , Jung Boris , Jullien Edouard , Bureau Côme , Djibré Michel , de Prost Nicolas , Zafrani Lara , Argaud Laurent , Reuter Danielle , Calvet Laure , de Montmollin Etienne , Benghanem Sarah , Pichereau Claire , Pham Tai , Cacoub Patrice , Biard Lucie , Saadoun David
Published: February 2023

Vaccination reduces risk of infection, hospitalization, and death due to SARS-Cov2. Vaccinated patients may however experience severe SARS-Cov2 disease. The objective was to describe clinical features of vaccinated patients requiring intensive care unit (ICU) admission due to SARS-Cov2 infection and compare them to a published cohort of unvaccinated patients. We performed a multicenter cohort study of patients with severe SARS-Cov2 disease admitted to 15 ICUs in France between January and September 2021. 100 consecutive vaccinated patients (68 (68%) men, median age 64 [57–71]) were included. Immunosuppression was reported in 38 (38%) patients. Among available serologies at ICU admission, 64% exhibited an optimal antibody level. Median SOFA score at ICU admission was 4 [4–6.3] and median PaO2/FiO2 ratio was 84 [69–128] mmHg. A total of 79 (79%) and 18 (18%) patients received high flow nasal oxygen and non-invasive mechanical ventilation, respectively. Invasive mechanical ventilation (IMV) was initiated in 48 (48%) with a median duration of 11 [5–19] days. During a median ICU length-of-stay of 8 [4–20] days, 31 (31%) patients died. Age (OR per 5-years increment 1.38 CI95% [1.02–1.85], p = 0.035), and SOFA at ICU admission (OR 1.40 CI95% [1.14–1.72] per point, p = 0.002) were independently associated with mortality. When compared to a cohort of 1316 unvaccinated patients (72% men, median age 63 [53–71]), vaccinated patients exhibited less frequently diabetes (16 [16%] vs. 351 [27%], p = 0.029) but were more frequently immunosuppressed (38 [38%] vs. 109 (8.3%), p < 0.0001), had more frequently chronic kidney disease (24 [24%] vs. 89 (6.8%), p < 0.0001), chronic heart failure (16 [16%] vs. 58 [4.4%], p < 0.0001), and chronic liver disease (3 [3%] vs. 8 [0.6%], p = 0.037) compared to unvaccinated patients. Despite similar severity, vaccinated patients required less frequently IMV at ICU day 1 and during ICU stay (23 [23%] vs. 785 [59.7%], p < 0.0001, and 48 [48%] vs. 930 [70.7%], p < 0.0001, respectively). There was no difference concerning ICU mortality (31 [31%] vs. 379 [28.8%], p = 0.64). Severe SARS-Cov2 infection after vaccination occurs mainly in patients with immunosuppression, chronic kidney, heart or liver failure. Age and disease severity are independently associated with mortality.
Different functional networks underlying human walking with pulling force fields acting in forward or backward directions
Authors: Ogawa Tetsuya , Obata Hiroki , Yokoyama Hikaru , Kawashima Noritaka , Nakazawa Kimitaka
Published: February 2023

Walking with pulling force fields acting at the body center of mass (in the forward or backward directions) is compatible with inclined walking and is used in clinical practice for gait training. From the perspective of known differences in the motor strategies that underlie walking with the respective force fields, the present study elucidated whether the adaptation acquired by walking on a split-belt treadmill with either one of the force fields affects subsequent walking in a force field in the opposite directions. Walking with the force field induced an adaptive and de-adaptive behavior of the subjects, with the aspect evident in the braking and propulsive impulses of the ground reaction force (difference in the peak value between the left and right sides for each stride cycle) as parameters. In the parameters, the adaptation acquired during walking with a force field acting in one direction was transferred to that in the opposite direction only partially. Furthermore, the adaptation that occurred while walking in a force field in one direction was rarely washed out by subsequent walking in a force field in the opposite direction and thus was maintained independently of the other. These results demonstrated possible independence in the neural functional networks capable of controlling walking in each movement task with an opposing force field.
Relationship between brain metastasis and thyroid transcription factor 1
Authors: Kut Engin , Menekşe Serkan
Published: February 2023

Brain metastases (BMs) are common in lung adenocarcinomas (ACs). Thyroid transcription factor 1 (TTF-1) is important in the diagnosis of AC. This study aimed to examine the relationship between TTF-1 and BM for the first time in literature. The data of 137 patients with AC that developed BM between 2009 and 2020 were retrospectively analyzed. A total of 137 patients, 120 (87.6%) male, and 17 (12.4%) female were examined. Their mean age was 59.78 ± 0.82 years. The Eastern Cooperative Oncology Group (ECOG) performance score was 0–1 (< 2) for 39 (28.5%) patients and 2–4 (≤ 2) for 98 (71.5%). TTF-1 was positive in 100 (73%) patients and negative in 37 (27%). More than five BMs were present in 102 (74.4%) patients and less than five in 35 (25.6%). All the patients received whole-brain radiotherapy. None of the patients was suitable for surgery or radiosurgery. The median survival time was 6.4 [95% confidence interval (CI), 5.67–7.1] months. The survival time was 7 (95% CI, 5.91–8.09) months for the TTF-1 (+) patients and 5.8 (95% CI, 4.1–7.5) months for the TTF-1 (−) patients. In the univariate analysis, there was a significant relationship between survival time and age (p = 0.047), TTF-1 (p = 0.024), and ECOG performance score (p = 0.002). The multivariance analysis revealed a significant relationship between survival and TTF-1 (p = 0.034) and ECOG score (p = 0.007). We found a correlation between survival time and ECOG performance score and TTF-1. TTF-1 can be used as a biomarker to monitor prognosis in the follow-up and treatment of patients with AC that develop BM.
High frequency beam oscillation keyhole dynamics in laser melting revealed by in-situ x-ray imaging
Authors: Wu Ziheng , Tang Guannan , Clark Samuel J. , Meshkov Andrey , Roychowdhury Subhrajit , Gould Benjamin , Ostroverkhov Victor , Adcock Thomas , Duclos Steven J. , Fezzaa Kamel , Immer Christopher , Rollett Anthony D.
Published: February 2023

The metal additive manufacturing industry is actively developing instruments and strategies to enable higher productivity, optimal build quality, and controllable as-built microstructure. A beam controlling technique, laser oscillation has shown potential in all these aspects in laser welding; however, few attempts have been made to understand the underlying physics of the oscillating keyholes/melt pools which are the prerequisites for these strategies to become a useful tool for laser-based additive manufacturing processes. Here, to address this gap, we utilized a synchrotron-based X-ray operando technique to image the dynamic keyhole oscillation in Ti-6Al-4V using a miniature powder bed fusion setup. We found good agreement between the experimental observations and simulations performed with a validated Lattice Boltzmann multiphysics model. The study revealed the continuous and periodic fluctuations in the characteristic keyhole parameters that are unique to the oscillating laser beam processing and responsible for the chevron pattern formation at solidification. In particular, despite the intrinsic longer-range fluctuation, the oscillating technique displayed potential for reducing keyhole instability, mitigating porosity formation, and altering surface topology. These insights on the oscillating keyhole dynamics can be useful for the future development and application of this technique.
The projected future degradation in air quality is caused by more abundant natural aerosols in a warmer world
Authors: Gomez James , Allen Robert J. , Turnock Steven T. , Horowitz Larry W. , Tsigaridis Kostas , Bauer Susanne E. , Olivié Dirk , Thomson Erik S. , Ginoux Paul
Published: February 2023

Previous studies suggest that greenhouse gas-induced warming can lead to increased fine particulate matter concentrations and degraded air quality. However, significant uncertainties remain regarding the sign and magnitude of the response to warming and the underlying mechanisms. Here, we show that thirteen models from the Coupled Model Intercomparison Project Phase 6 all project an increase in global average concentrations of fine particulate matter in response to rising carbon dioxide concentrations, but the range of increase across models is wide. The two main contributors to this increase are increased abundance of dust and secondary organic aerosols via intensified West African monsoon and enhanced emissions of biogenic volatile organic compounds, respectively. Much of the inter-model spread is related to different treatment of biogenic volatile organic compounds. Our results highlight the importance of natural aerosols in degrading air quality under current warming, while also emphasizing that improved understanding of biogenic volatile organic compounds emissions due to climate change is essential for numerically assessing future air quality.