bluuebunny/crossref_metadata_2025 huggingface dataset:
Stage‐Slope‐Discharge Relationships Upstream of River Confluences Revealed by Satellite Altimetry
Authors: Liu Jun , Bauer‐Gottwein Peter , Frias Monica Coppo , Musaeus Aske Folkmann , Christoffersen Linda , Jiang Liguang
Published: November 2023

With increasing coverage, density, and accuracy of the global inland water altimetry record, remote sensing observations of water surface elevation (WSE) and water surface slope (WSS) are becoming available for the world's rivers. In steady, uniform flows, WSS is invariable, while there is a unique one‐to‐one relationship between WSE and discharge, the rating curve. While the assumptions of steady uniform flow are appropriate for many rivers, they are violated upstream of river confluences. We present a simple analytical hydraulic model of river confluences using the theory of steady, gradually varied flow. We apply the model to four river confluences in the Mississippi‐Missouri river system. We determine the spatial extent of the backwater‐affected zones and map WSE‐discharge and WSS‐discharge relationships. We show that coincident measurements of WSE and WSS from new satellite altimetry missions effectively constrain discharge estimates from space in the backwater‐affected zones upstream of river confluences.
Influence of endodontic motors on the behaviour of root canal shaping instruments: an in vitro comparative study
Authors: Reynette Clémentine , Giess Renaud , Davril Jeanne , Martrette Jean-Marc , Mortier Éric , Balthazard Rémy , Vincent Marin
Published: November 2023

Aims

The endodontic literature reports a lot of comparative study on endodontic instruments, concerning as well their geometry, instrumental dynamics, material, mechanical behavior or heat treatment. However, to our knowledge, no study has focused on the influence of endodontic motors on the shaping abilities of endodontic instruments. Thus, the aim of this study was to analyze the influence of the endodontic motors on root canal shaping instruments.

Method

Dual Move (MICRO-MEGA, Besançon, France), Canal Pro CL2i (COLTENE, Alstätten, Suisse), Canal Pro Jeni Motor (COLTENE, Alstätten, Suisse), Ai Motor (WOODPECKER, Guilin, China), Wave One motor (VDW, Postfach, Munich) and Smart A (WOODPECKER, Guilin, China) were pre-clinically compared in continuous rotation and reciprocating motion on a traction/compression bench using resin blocks. Canal shaping in continuous rotation and reciprocating motion were performed with One Curve and One RECI instruments (MICRO-MEGA, Besançon, France), respectively. The penetration/removal forces, making it possible to objectify the cutting effect and screwing effect of the instruments during root canal shaping, were analyzed.

Results

The results showed (i) that endodontic motors influence the mechanical behavior of endodontic instruments, (ii) that the influence of the motors is essentially felt during reciprocating motion and (iii) that the reciprocating angles influence the mechanical behavior of endodontic instruments.

Conclusion

Only endodontic instruments are widely studied in literature while endodontic motors have a direct influence on root canal treatment. This study analyzes the influence of the endodontic motors on root canal shaping instruments. This study tends to demonstrate that Jeni Motor could optimize the mechanical behavior of endodontic instruments.
Nuclear receptor corepressor 1 deficiency exacerbates asthma by modulating macrophage polarization
Authors: Hou Chenchen , Yan Lifeng , Sun Ke , Zhou Tianyu , Zou Yuxin , Xiong Weining , Duan Sheng-Zhong
Published: November 2023

Macrophage polarization plays an important role in asthma. Nuclear receptor corepressor 1 (NCOR1) plays an important role in metabolic and cardiovascular diseases by regulating the function of macrophages. The aim of this research was to examine the role and mechanism of macrophage NCOR1 in the development of asthma. We used ovalbumin (OVA) to induce macrophage NCOR1-deficient mice for asthma formation. Our results revealed that macrophage NCOR1 deficiency markedly enhanced allergic airway inflammation. In addition, NCOR1 deficiency in macrophages was found to enhance M2 polarization. Mechanistic studies suggested that NCOR1 promoted macrophage polarization by interacting with PPARγ, contributing to the pathogenesis of asthma. In conclusion, macrophage NCOR1 deficiency promoted the regulation of M2 programming by enhancing PPARγ expression to exacerbate asthma. Macrophage NCOR1 might be a potential target for the treatment of asthma.
Endosomal Arl4A attenuates EGFR degradation by binding to the ESCRT-II component VPS36
Authors: Lin Shin-Jin , Lin Ming-Chieh , Liu Tsai-Jung , Tsai Yueh-Tso , Tsai Ming-Ting , Lee Fang-Jen S.
Published: November 2023

Ligand-induced epidermal growth factor receptor (EGFR) endocytosis followed by endosomal EGFR signaling and lysosomal degradation plays important roles in controlling multiple biological processes. ADP-ribosylation factor (Arf)-like protein 4 A (Arl4A) functions at the plasma membrane to mediate cytoskeletal remodeling and cell migration, whereas its localization at endosomal compartments remains functionally unknown. Here, we report that Arl4A attenuates EGFR degradation by binding to the endosomal sorting complex required for transport (ESCRT)-II component VPS36. Arl4A plays a role in prolonging the duration of EGFR ubiquitinylation and deterring endocytosed EGFR transport from endosomes to lysosomes under EGF stimulation. Mechanistically, the Arl4A-VPS36 direct interaction stabilizes VPS36 and ESCRT-III association, affecting subsequent recruitment of deubiquitinating-enzyme USP8 by CHMP2A. Impaired Arl4A-VPS36 interaction enhances EGFR degradation and clearance of EGFR ubiquitinylation. Together, we discover that Arl4A negatively regulates EGFR degradation by binding to VPS36 and attenuating ESCRT-mediated late endosomal EGFR sorting.
Increased photosynthesis during spring drought in energy-limited ecosystems
Authors: Miller David L. , Wolf Sebastian , Fisher Joshua B. , Zaitchik Benjamin F. , Xiao Jingfeng , Keenan Trevor F.
Published: November 2023

Drought is often thought to reduce ecosystem photosynthesis. However, theory suggests there is potential for increased photosynthesis during meteorological drought, especially in energy-limited ecosystems. Here, we examine the response of photosynthesis (gross primary productivity, GPP) to meteorological drought across the water-energy limitation spectrum. We find a consistent increase in eddy covariance GPP during spring drought in energy-limited ecosystems (83% of the energy-limited sites). Half of spring GPP sensitivity to precipitation was predicted solely from the wetness index (R2 = 0.47, p < 0.001), with weaker relationships in summer and fall. Our results suggest GPP increases during spring drought for 55% of vegetated Northern Hemisphere lands ( >30° N). We then compare these results to terrestrial biosphere model outputs and remote sensing products. In contrast to trends detected in eddy covariance data, model mean GPP always declined under spring precipitation deficits after controlling for air temperature and light availability. While remote sensing products captured the observed negative spring GPP sensitivity in energy-limited ecosystems, terrestrial biosphere models proved insufficiently sensitive to spring precipitation deficits.
Preferential ice growth on grooved surface for crisscross-aligned graphene aerogel with large negative Poisson’s ratio
Authors: Li Meng , Zhao Nifang , Mao Anran , Wang Mengning , Shao Ziyu , Gao Weiwei , Bai Hao
Published: November 2023

Ice formation on solid surfaces is a ubiquitous process in our daily life, and ice orientation plays a critical role in anti-icing/deicing, organ cryo-preservation, and material fabrication. Although previous studies have shown that surface grooves can regulate the orientation of ice crystals, whether the parallel or perpendicular alignment to the grooves is still under debate. Here, we systematically investigate ice formation and its oriented growth on grooved surfaces through both in situ observation and theoretical simulation, and discover a remarkable size effect of the grooves. With the designability of surface groove patterns, the preferential growth of ice crystals is programmed for the fabrication of a crisscross-aligned graphene aerogel with large negative Poisson’s ratio. In addition, the size effect provides guidance for the design and fabrication of solid surfaces where the effective control of ice orientation is highly desired, such as efficient deicing, long time organ cryo-preservation, and ice-templated materials.
SPINK1-induced tumor plasticity provides a therapeutic window for chemotherapy in hepatocellular carcinoma
Authors: Man Ki-Fong , Zhou Lei , Yu Huajian , Lam Ka-Hei , Cheng Wei , Yu Jun , Lee Terence K. , Yun Jing-Ping , Guan Xin-Yuan , Liu Ming , Ma Stephanie
Published: November 2023

Tumor lineage plasticity, considered a hallmark of cancer, denotes the phenomenon in which tumor cells co-opt developmental pathways to attain cellular plasticity, enabling them to evade targeted therapeutic interventions. However, the underlying molecular events remain largely elusive. Our recent study identified CD133/Prom1 in hepatocellular carcinoma (HCC) tumors to mark proliferative tumor-propagating cells with cancer stem cell-like properties, that follow a dedifferentiation trajectory towards a more embryonic state. Here we show SPINK1 to strongly associate with CD133 + HCC, and tumor dedifferentiation. Enhanced transcriptional activity of SPINK1 is mediated by promoter binding of ELF3, which like CD133, is found to increase following 5-FU and cisplatin treatment; while targeted depletion of CD133 will reduce both ELF3 and SPINK1. Functionally, SPINK1 overexpression promotes tumor initiation, self-renewal, and chemoresistance by driving a deregulated EGFR-ERK-CDK4/6-E2F2 signaling axis to induce dedifferentiation of HCC cells into their ancestral lineages. Depleting SPINK1 function by neutralizing antibody treatment or in vivo lentivirus-mediated Spink1 knockdown dampens HCC cancer growth and their ability to resist chemotherapy. Targeting oncofetal SPINK1 may represent a promising therapeutic option for HCC treatment.
Distinct activation mechanisms of β-arrestin-1 revealed by 19F NMR spectroscopy
Authors: Zhai Ruibo , Wang Zhuoqi , Chai Zhaofei , Niu Xiaogang , Li Conggang , Jin Changwen , Hu Yunfei
Published: November 2023

β-Arrestins (βarrs) are functionally versatile proteins that play critical roles in the G-protein-coupled receptor (GPCR) signaling pathways. While it is well established that the phosphorylated receptor tail plays a central role in βarr activation, emerging evidence highlights the contribution from membrane lipids. However, detailed molecular mechanisms of βarr activation by different binding partners remain elusive. In this work, we present a comprehensive study of the structural changes in critical regions of βarr1 during activation using 19F NMR spectroscopy. We show that phosphopeptides derived from different classes of GPCRs display different βarr1 activation abilities, whereas binding of the membrane phosphoinositide PIP2 stabilizes a distinct partially activated conformational state. Our results further unveil a sparsely-populated activation intermediate as well as complex cross-talks between different binding partners, implying a highly multifaceted conformational energy landscape of βarr1 that can be intricately modulated during signaling.
TransformEHR: transformer-based encoder-decoder generative model to enhance prediction of disease outcomes using electronic health records
Authors: Yang Zhichao , Mitra Avijit , Liu Weisong , Berlowitz Dan , Yu Hong
Published: November 2023

Deep learning transformer-based models using longitudinal electronic health records (EHRs) have shown a great success in prediction of clinical diseases or outcomes. Pretraining on a large dataset can help such models map the input space better and boost their performance on relevant tasks through finetuning with limited data. In this study, we present TransformEHR, a generative encoder-decoder model with transformer that is pretrained using a new pretraining objective—predicting all diseases and outcomes of a patient at a future visit from previous visits. TransformEHR’s encoder-decoder framework, paired with the novel pretraining objective, helps it achieve the new state-of-the-art performance on multiple clinical prediction tasks. Comparing with the previous model, TransformEHR improves area under the precision–recall curve by 2% (p < 0.001) for pancreatic cancer onset and by 24% (p = 0.007) for intentional self-harm in patients with post-traumatic stress disorder. The high performance in predicting intentional self-harm shows the potential of TransformEHR in building effective clinical intervention systems. TransformEHR is also generalizable and can be easily finetuned for clinical prediction tasks with limited data.
Beet red food colourant can be produced more sustainably with engineered Yarrowia lipolytica
Authors: Thomsen Philip Tinggaard , Meramo Samir , Ninivaggi Lorenzo , Pasutto Eleonora , Babaei Mahsa , Avila-Neto Paulo Marcelo , Pastor Marc Cernuda , Sabri Peyman , Rago Daniela , Parekh Tanmay Utsav , Hunding Sara , Christiansen Laura Emilie Jul , Sukumara Sumesh , Borodina Irina
Published: November 2023

Synthetic food colourants are widely used in the food industry, but consumer concerns about safety and sustainability are driving a need for natural food-colour alternatives. Betanin, which is extracted from red beetroots, is a commonly used natural red food colour. However, the betanin content of beetroot is very low (~0.2% wet weight), which means that the extraction of betanin is incredibly wasteful in terms of land use, processing costs and vegetable waste. Here we developed a sustainability-driven biotechnological process for producing red beet betalains, namely, betanin and its isomer isobetanin, by engineering the oleaginous yeast Yarrowia lipolytica. Metabolic engineering and fermentation optimization enabled production of 1,271 ± 141 mg l−1 betanin and 55 ± 7 mg l−1 isobetanin in 51 h using glucose as carbon source in controlled fed-batch fermentations. According to a life cycle assessment, at industrial scale (550 t yr−1), our fermentation process would require significantly less land, energy and resources compared with the traditional extraction of betanin from beetroot crops. Finally, we apply techno-economic assessment to show that betanin production by fermentation could be economically feasible in the existing market conditions.
Estimation of gestating sows’ welfare status based on machine learning methods and behavioral data
Authors: Durand Maëva , Largouët Christine , de Beaufort Louis Bonneau , Dourmad Jean-Yves , Gaillard Charlotte
Published: November 2023

Estimating the welfare status at an individual level on the farm is a current issue to improve livestock animal monitoring. New technologies showed opportunities to analyze livestock behavior with machine learning and sensors. The aim of the study was to estimate some components of the welfare status of gestating sows based on machine learning methods and behavioral data. The dataset used was a combination of individual and group measures of behavior (activity, social and feeding behaviors). A clustering method was used to estimate the welfare status of 69 sows (housed in four groups) during different periods (sum of 2 days per week) of gestation (between 6 and 10 periods, depending on the group). Three clusters were identified and labelled (scapegoat, gentle and aggressive). Environmental conditions and the sows’ health influenced the proportion of sows in each cluster, contrary to the characteristics of the sow (age, body weight or body condition). The results also confirmed the importance of group behavior on the welfare of each individual. A decision tree was learned and used to classify the sows into the three categories of welfare issued from the clustering step. This classification relied on data obtained from an automatic feeder and automated video analysis, achieving an accuracy rate exceeding 72%. This study showed the potential of an automatic decision support system to categorize welfare based on the behavior of each gestating sow and the group of sows.
Olive stone as an eco-friendly bio-adsorbent for elimination of methylene blue dye from industrial wastewater
Authors: Alardhi Saja M. , Salih Hussein G. , Ali Nisreen S. , Khalbas Ali H. , Salih Issam K. , Saady Noori M. Cata , Zendehboudi Sohrab , Albayati Talib M. , Harharah Hamed N.
Published: November 2023

Adsorbents synthesized by activation and nanoparticle surface modifications are expensive and might pose health and ecological risks. Therefore, the interest in raw waste biomass materials as adsorbents is growing. In batch studies, an inexpensive and effective adsorbent is developed from raw olive stone (OS) to remove methylene blue (MB) from an aqueous solution. The OS adsorbent is characterized using scanning electron microscopy (SEM), Fourier Transform Infra-Red (FTIR), and Brunauer–Emmett–Teller (BET) surface area. Four isotherms are used to fit equilibrium adsorption data, and four kinetic models are used to simulate kinetic adsorption behavior. The obtained BET surface area is 0.9 m2 g−1, and the SEM analysis reveals significant pores in the OS sample that might facilitate the uptake of heavy compounds. The Langmuir and Temkin isotherm models best represent the adsorbtion of MB on the OS, with a maximum monolayer adsorption capacity of 44.5 mg g−1. The best dye color removal efficiency by the OS is 93.65% from an aqueous solution of 20 ppm at the OS doses of 0.2 g for 90 min contact time. The OS adsorbent serves in five successive adsorption cycles after a simple filtration-washing-drying process, maintaining MB removal efficiency of 91, 85, 80, and 78% in cycles 2, 3, 4, and 5, respectively. The pseudo second-order model is the best model to represent the adsorption process dynamics. Indeed, the pseudo second-order and the Elovich models are the most appropriate kinetic models, according to the correlation coefficient (R2) values (1.0 and 0.935, respectively) derived from the four kinetic models. The parameters of the surface adsorption are also predicted based on the mass transfer models of intra-particle diffusion and Bangham and Burt. According to the thermodynamic analysis, dye adsorption by the OS is endothermic and spontaneous. As a result, the OS material offers an efficient adsorbent for MB removal from wastewater that is less expensive, more ecologically friendly, and economically viable.
Characterization of cannabinoid plasma concentration, maternal health, and cytokine levels in a rat model of prenatal Cannabis smoke exposure
Authors: Black Tallan , Baccetto Sarah L. , Barnard Ilne L. , Finch Emma , McElroy Dan L. , Austin-Scott Faith V. L. , Greba Quentin , Michel Deborah , Zagzoog Ayat , Howland John G. , Laprairie Robert B.
Published: November 2023

Cannabis sativa has gained popularity as a “natural substance”, leading many to falsely assume that it is not harmful. This assumption has been documented amongst pregnant mothers, many of whom consider Cannabis use during pregnancy as benign. The purpose of this study was to validate a Cannabis smoke exposure model in pregnant rats by determining the plasma levels of cannabinoids and associated metabolites in the dams after exposure to either Cannabis smoke or injected cannabinoids. Maternal and fetal cytokine and chemokine profiles were also assessed after exposure. Pregnant Sprague–Dawley rats were treated daily from gestational day 6–20 with either room air, i.p. vehicle, inhaled high-Δ9-tetrahydrocannabinol (THC) (18% THC, 0.1% cannabidiol [CBD]) smoke, inhaled high-CBD (﻿0.7% THC, 13% CBD) smoke, 3 mg/kg i.p. THC, or 10 mg/kg i.p. CBD. Our data reveal that THC and CBD, but not their metabolites, accumulate in maternal plasma after repeated exposures. Injection of THC or CBD was associated with fewer offspring and increased uterine reabsorption events. For cytokines and chemokines, injection of THC or CBD up-regulated several pro-inflammatory cytokines compared to control or high-THC smoke or high-CBD smoke in placental and fetal brain tissue, whereas smoke exposure was generally associated with reduced cytokine and chemokine concentrations in placental and fetal brain tissue compared to controls. These results support existing, but limited, knowledge on how different routes of administration contribute to inconsistent manifestations of cannabinoid-mediated effects on pregnancy. Smoked Cannabis is still the most common means of human consumption, and more preclinical investigation is needed to determine the effects of smoke inhalation on developmental and behavioural trajectories.
On the reduction of mixed Gaussian and impulsive noise in heavily corrupted color images
Authors: Smolka Bogdan , Kusnik Damian , Radlak Krystian
Published: November 2023

In this paper, a novel approach to the mixed Gaussian and impulsive noise reduction in color images is proposed. The described denoising framework is based on the Non-Local Means (NLM) technique, which proved to efficiently suppress only the Gaussian noise. To circumvent the incapacity of the NLM filter to cope with impulsive distortions, a robust similarity measure between image patches, which is insensitive to the impact of impulsive corruption, was elaborated. To increase the effectiveness of the proposed approach, the blockwise NLM implementation was applied. However, instead of generating a stack of output images that are finally averaged, an aggregation strategy combining all weights assigned to pixels from the processing block was developed and proved to be more efficient. Based on the results of comparisons with the existing denoising schemes, it can be concluded that the novel filter yields satisfactory results when suppressing high-intensity mixed noise in color images. Using the proposed filter the image edges are well preserved and the details are retained, while impulsive noise is efficiently removed. Additionally, the computational burden is not significantly increased, compared with the classic NLM, which makes the proposed modification applicative for practical image denoising tasks.
Evaluating the stability of host-reference gene expression and simultaneously quantifying parasite burden and host immune responses in murine malaria
Authors: Browne Daniel J. , Kelly Ashton M. , Brady Jamie , Proietti Carla , Sarathkumara Yomani D. , Pattinson David J. , Doolan Denise L.
Published: November 2023

The efficacy of pre-erythrocytic stage malaria antigens or vaccine platforms is routinely assessed in murine models challenged with Plasmodium sporozoites. Relative liver-stage parasite burden is quantified using reverse transcription quantitative PCR (RTqPCR), which relies on constitutively expressed endogenous control reference genes. However, the stability of host-reference gene expression for RTqPCR analysis following Plasmodium challenge and immunization has not been systematically evaluated. Herein, we evaluated the stability of expression of twelve common RTqPCR reference genes in a murine model of Plasmodium yoelii sporozoite challenge and DNA-adenovirus IV 'Prime-Target' immunization. Significant changes in expression for six of twelve reference genes were shown by one-way ANOVA, when comparing gene expression levels among challenge, immunized, and naïve mice groups. These changes were attributed to parasite challenge or immunization when comparing group means using post-hoc Bonferroni corrected multiple comparison testing. Succinate dehydrogenase (SDHA) and TATA-binding protein (TBP) were identified as stable host-reference genes suitable for relative RTqPCR data normalisation, using the RefFinder package. We defined a robust threshold of 'partial-protection’ with these genes and developed a strategy to simultaneously quantify matched host parasite burden and cytokine responses following immunisation or challenge. This is the first report systematically identifying reliable host reference genes for RTqPCR analysis following Plasmodium sporozoite challenge. A robust RTqPCR protocol incorporating reliable reference genes which enables simultaneous analysis of host whole-liver cytokine responses and parasite burden will significantly standardise and enhance results between international malaria vaccine efficacy studies.
Redox-based ion-gating reservoir consisting of (104) oriented LiCoO2 film, assisted by physical masking
Authors: Shibata Kaoru , Nishioka Daiki , Namiki Wataru , Tsuchiya Takashi , Higuchi Tohru , Terabe Kazuya
Published: November 2023

Reservoir computing (RC) is a machine learning framework suitable for processing time series data, and is a computationally inexpensive and fast learning model. A physical reservoir is a hardware implementation of RC using a physical system, which is expected to become the social infrastructure of a data society that needs to process vast amounts of information. Ion-gating reservoirs (IGR) are compact and suitable for integration with various physical reservoirs, but the prediction accuracy and operating speed of redox-IGRs using WO3 as the channel are not sufficient due to irreversible Li+ trapping in the WO3 matrix during operation. Here, in order to enhance the computation performance of redox-IGRs, we developed a redox-based IGR using a (104) oriented LiCoO2 thin film with high electronic and ionic conductivity as a trap-free channel material. The subject IGR utilizes resistance change that is due to a redox reaction (LiCoO2 ⟺ Li1−xCoO2 + xLi+ + xe−) with the insertion and desertion of Li+. The prediction error in the subject IGR was reduced by 72% and the operation speed was increased by 4 times compared to the previously reported WO3, which changes are due to the nonlinear and reversible electrical response of LiCoO2 and the high dimensionality enhanced by a newly developed physical masking technique. This study has demonstrated the possibility of developing high-performance IGRs by utilizing materials with stronger nonlinearity and by increasing output dimensionality.
Distance and destination of retail meat alter multidrug resistant contamination in the United States food system
Authors: Innes Gabriel K. , Patton Andrew N. , Nachman Keeve E. , Casey Joan A. , Stapleton G. Sean , Abraham Alison G. , Price Lance B. , Tartof Sara Y. , Davis Meghan F.
Published: November 2023

Antibiotic-resistant infections are a global concern, especially those caused by multidrug-resistant (MDR) bacteria, defined as those resistant to more than three drug classes. The animal agriculture industry contributes to the antimicrobial resistant foodborne illness burden via contaminated retail meat. In the United States, retail meat is shipped across the country. Therefore, understanding geospatial factors that influence MDR bacterial contamination is vital to protect consumers and inform interventions. Using data available from the United States Food and Drug Administration’s National Antimicrobial Resistance Monitoring System (NARMS), we describe retail meat shipping distances using processor and retailer locations and investigated this distance as a risk factor for MDR bacteria meat contamination using log-binomial regression. Meat samples collected during 2012–2014 totaled 11,243, of which 4791 (42.61%) were contaminated with bacteria and 835 (17.43%) of those bacteria were MDR. All examined geospatial factors were associated with MDR bacteria meat contamination. After adjustment for year and meat type, we found higher prevalence of MDR contamination among meat processed in the south (relative adjusted prevalence ratio [aPR] 1.35; 95% CI 1.06–1.73 when compared to the next-highest region), sold in Maryland (aPR 1.12; 95% CI 0.95–1.32 when compared to the next-highest state), and shipped from 194 to 469 miles (aPR 1.59; 95% CI 1.31–1.94 when compared to meats that traveled < 194 miles). However, sensitivity analyses revealed that New York sold the meat with the highest prevalence of MDR Salmonella contamination (4.84%). In this secondary analysis of NARMS data, both geographic location where products were sold and the shipping distance were associated with microbial contamination on retail meat.
Metabolomics of early blight (Alternaria solani) susceptible tomato (Solanum lycopersicum) unfolds key biomarker metabolites and involved metabolic pathways
Authors: Singh Dhananjaya Pratap , Maurya Sudarshan , Yerasu Suresh Reddy , Bisen Mansi Singh , Farag Mohamed A. , Prabha Ratna , Shukla Renu , Chaturvedi Krishna Kumar , Farooqi Md. Samir , Srivastava Sudhir , Rai Anil , Sarma Birinchi Kumar , Rai Nagendra , Behera Tusar Kanti
Published: November 2023

Tomato (Solanum lycopersicum) is among the most important commercial horticultural crops worldwide. The crop quality and production is largely hampered due to the fungal pathogen Alternaria solani causing necrotrophic foliage early blight disease. Crop plants usually respond to the biotic challenges with altered metabolic composition and physiological perturbations. We have deciphered altered metabolite composition, modulated metabolic pathways and identified metabolite biomarkers in A. solani-challenged susceptible tomato variety Kashi Aman using Liquid Chromatography-Mass Spectrometry (LC–MS) based metabolomics. Alteration in the metabolite feature composition of pathogen-challenged (m/z 9405) and non-challenged (m/z 9667) plant leaves including 8487 infection-exclusive and 8742 non-infection exclusive features was observed. Functional annotation revealed putatively annotated metabolites and pathway mapping indicated their enrichment in metabolic pathways, biosynthesis of secondary metabolites, ubiquinone and terpenoid-quinones, brassinosteroids, steroids, terpenoids, phenylpropanoids, carotenoids, oxy/sphingolipids and metabolism of biotin and porphyrin. PCA, multivariate PLS-DA and OPLS-DA analysis showed sample discrimination. Significantly up regulated 481 and down regulated 548 metabolite features were identified based on the fold change (threshold ≥ 2.0). OPLS-DA model based on variable importance in projection (VIP scores) and FC threshold (> 2.0) revealed 41 up regulated discriminant metabolite features annotated as sphingosine, fecosterol, melatonin, serotonin, glucose 6-phosphate, zeatin, dihydrozeatin and zeatin-β-d-glucoside. Similarly, 23 down regulated discriminant metabolites included histidinol, 4-aminobutyraldehyde, propanoate, tyramine and linalool. Melatonin and serotonin in the leaves were the two indoleamines being reported for the first time in tomato in response to the early blight pathogen. Receiver operating characteristic (ROC)-based biomarker analysis identified apigenin-7-glucoside, uridine, adenosyl-homocysteine, cGMP, tyrosine, pantothenic acid, riboflavin (as up regulated) and adenosine, homocyctine and azmaline (as down regulated) biomarkers. These results could aid in the development of metabolite-quantitative trait loci (mQTL). Furthermore, stress-induced biosynthetic pathways may be the potential targets for modifications through breeding programs or genetic engineering for improving crop performance in the fields.
Species-specific gill’s microbiome of eight crab species with different breathing adaptations
Authors: Bacci Giovanni , Meriggi Niccolò , Cheng Christine L. Y. , Ng Ka Hei , Iannucci Alessio , Mengoni Alessio , Cavalieri Duccio , Cannicci Stefano , Fratini Sara
Published: November 2023

Transitions to physically different environments, such as the water-to-land transition, proved to be the main drivers of relevant evolutionary events. Brachyuran crabs evolved remarkable morphological, behavioral, and physiological adaptations to terrestrial life. Terrestrial species evolved new respiratory structures devoted to replace or support the gills, a multifunctional organ devoted to gas exchanges, ion-regulation and nitrogen excretion. It was hypothesized that microorganisms associated with respiratory apparatus could have facilitated the processes of osmoregulation, respiration, and elimination of metabolites along this evolutionary transition. To test if crab species with different breathing adaptations may host similar microbial communities on their gills, we performed a comparative targeted-metagenomic analysis, selecting two marine and six terrestrial crabs belonging to different families and characterised by different breathing adaptations. We analysed anterior and posterior gills separately according to their different and specific roles. Regardless of their terrestrial or marine adaptations, microbial assemblages were strongly species-specific indicating a non-random association between the host and its microbiome. Significant differences were found in only two terrestrial species when considering posterior vs. anterior gills, without any association with species-specific respiratory adaptations. Our results suggest that all the selected species are strongly adapted to the ecological niche and specific micro-habitat they colonise.
Comparative evaluation of 3D-printed and conventional implants in vivo: a quantitative microcomputed tomographic and histomorphometric analysis
Authors: Suh Hyemee , Lee Dongseob , Lee Jungwon , Seol Yang-Jo , Lee Yong-Moo , Koo Ki-Tae
Published: November 2023

In recent years, 3D-printing technology to fabricate dental implants has garnered widespread attention due to its patient-specific customizability and cost-effectiveness. This preclinical animal study analyzed the radiographic and histomorphometric outcomes of 3D-printed implants (3DIs) placed immediately after extraction and compared them to conventional implants (CIs). 3DIs and CIs of the same dimensions placed immediately were analyzed at 2, 6, and 12 weeks. The micro-computed tomography (micro-CT) analysis revealed statistically significant differences at 2 weeks in favor of 3DIs over the CIs in terms of bone volume/tissue volume (BV/TV), bone surface/bone volume (BS/BV), trabecular bone pattern factor (Tb.Pf), and structure model index (SMI). At 2 weeks, the mean bone-to-implant contact (BIC) of the 3DIs was greater than that of the CIs; the mean bone area fraction occupancy (BAFO) and the number of Haversian canals of the 3DIs showed no statistically significant differences compared to CIs at 2 weeks. At 6 and 12 weeks, there were no statistically significant differences between the 3DIs and CIs in any parameters. Within limitations, in the early stage of extraction socket healing, the 3DIs demonstrated a higher BIC than the CIs, presenting that 3DIs may be a potential option for immediate placement to enhance osseointegration.
C1QA and COMP: plasma-based biomarkers for early diagnosis of pancreatic neuroendocrine tumors
Authors: Gorai Priya Kumari , Bharti Prahalad Singh , Kumar Shashi , Rajacharya Girish H. , Bandyopadhyay Sabyasachi , Pal Sujoy , Dhingra Renu , Kumar Rakesh , Nikolajeff Fredrik , Kumar Saroj , Rani Neerja
Published: November 2023

Pancreatic Neuroendocrine tumors (PanNET) are challenging to diagnose and often detected at advanced stages due to a lack of specific and sensitive biomarkers. This study utilized proteomics as a valuable approach for cancer biomarker discovery; therefore, mass spectrometry-based proteomic profiling was conducted on plasma samples from 12 subjects (3 controls; 5 Grade I, 4 Grade II PanNET patients) to identify potential proteins capable of effectively distinguishing PanNET from healthy controls. Data are available via ProteomeXchange with the identifier PXD045045. 13.2% of proteins were uniquely identified in PanNET, while 60% were commonly expressed in PanNET and controls. 17 proteins exhibiting significant differential expression between PanNET and controls were identified with downstream analysis. Further, 5 proteins (C1QA, COMP, HSP90B1, ITGA2B, and FN1) were selected by pathway analysis and were validated using Western blot analysis. Significant downregulation of C1QA (p = 0.001: within groups, 0.03: control vs. grade I, 0.0013: grade I vs. grade II) and COMP (p = 0.011: within groups, 0.019: control vs grade I) were observed in PanNET Grade I & II than in controls. Subsequently, ELISA on 38 samples revealed significant downregulation of C1QA and COMP with increasing disease severity. This study shows the potential of C1QA and COMP in the early detection of PanNET, highlighting their role in the search for early-stage (Grade-I and Grade-II) diagnostic markers and therapeutic targets for PanNET.
An arrayed CRISPR knockout screen identifies genetic regulators of GLUT1 expression
Authors: Shi Yajuan , Katdare Ketaki A. , Kim Hyosung , Rosch Jonah C. , Neal Emma H. , Vafaie-Partin Sidney , Bauer Joshua A. , Lippmann Ethan S.
Published: November 2023

Glucose, a primary fuel source under homeostatic conditions, is transported into cells by membrane transporters such as glucose transporter 1 (GLUT1). Due to its essential role in maintaining energy homeostasis, dysregulation of GLUT1 expression and function can adversely affect many physiological processes in the body. This has implications in a wide range of disorders such as Alzheimer’s disease (AD) and several types of cancers. However, the regulatory pathways that govern GLUT1 expression, which may be altered in these diseases, are poorly characterized. To gain insight into GLUT1 regulation, we performed an arrayed CRISPR knockout screen using Caco-2 cells as a model cell line. Using an automated high content immunostaining approach to quantify GLUT1 expression, we identified more than 300 genes whose removal led to GLUT1 downregulation. Many of these genes were enriched along signaling pathways associated with G-protein coupled receptors, particularly the rhodopsin-like family. Secondary hit validation confirmed that removal of select genes, or modulation of the activity of a corresponding protein, yielded changes in GLUT1 expression. Overall, this work provides a resource and framework for understanding GLUT1 regulation in health and disease.
Enhanced thermoelectric properties of self-assembling ZnO nanowire networks encapsulated in nonconductive polymers
Authors: Volkova Margarita , Sondors Raitis , Bugovecka Lasma , Kons Artis , Avotina Liga , Andzane Jana
Published: November 2023

The near-room temperature thermoelectric properties of self-assembling ZnO nanowire networks before and after encapsulation in nonconductive polymers are studied. ZnO nanowire networks were synthesized via a two-step fabrication technique involving the deposition of metallic Zn networks by thermal evaporation, followed by thermal oxidation. Synthesized ZnO nanowire networks were encapsulated in polyvinyl alcohol (PVA) or commercially available epoxy adhesive. Comparison of electrical resistance and Seebeck coefficient of the ZnO nanowire networks before and after encapsulation showed a significant increase in the network's electrical conductivity accompanied by the increase of its Seebeck coefficient after the encapsulation. The thermoelectric power factor (PF) of the encapsulated ZnO nanowire networks exceeded the PF of bare ZnO networks by ~ 5 and ~ 185 times for PVA- and epoxy-encapsulated samples, respectively, reaching 0.85 μW m−1 K−2 and ZT ~ 3·10–6 at room temperature, which significantly exceeded the PF and ZT values for state-of-the-art non-conductive polymers based thermoelectric flexible films. Mechanisms underlying the improvement of the thermoelectrical properties of ZnO nanowire networks due to their encapsulation are discussed. In addition, encapsulated ZnO nanowire networks showed excellent stability during 100 repetitive bending cycles down to a 5 mm radius, which makes them perspective for the application in flexible thermoelectrics.
Insights into the recognition mechanism in the UBR box of UBR4 for its specific substrates
Authors: Jeong Da Eun , Lee Hye Seon , Ku Bonsu , Kim Cheol-Hee , Kim Seung Jun , Shin Ho-Chul
Published: November 2023

The N-end rule pathway is a proteolytic system involving the destabilization of N-terminal amino acids, known as N-degrons, which are recognized by N-recognins. Dysregulation of the N-end rule pathway results in the accumulation of undesired proteins, causing various diseases. The E3 ligases of the UBR subfamily recognize and degrade N-degrons through the ubiquitin-proteasome system. Herein, we investigated UBR4, which has a distinct mechanism for recognizing type-2 N-degrons. Structural analysis revealed that the UBR box of UBR4 differs from other UBR boxes in the N-degron binding sites. It recognizes type-2 N-terminal amino acids containing an aromatic ring and type-1 N-terminal arginine through two phenylalanines on its hydrophobic surface. We also characterized the binding mechanism for the second ligand residue. This is the report on the structural basis underlying the recognition of type-2 N-degrons by the UBR box with implications for understanding the N-end rule pathway.
Soy Protein Flavours
Authors: Li Jian , Li Xuejie , Di Taiju , Pang Xueli
Published: November 2023

Soybeans are one of the most widely grown crops in the world and provides the largest source of plant protein in the human diet due to its superior nutritional, economical, and functional base. They contain abundant plant-derived proteins, isoflavones, and other high-nutritional value ingredients, such as saponin and phytic acid. Soy protein isolates (SPI) have been widely used as functional ingredients in foods such as meats, sausages, breads, and beverages. Despite its high functionality, the typical grassy and beany off-flavours in SPI remain a major hurdle in expanding the use of SPI in mainstream food applications. The off-flavours associated with SPI have been recognized as beany, bitter, chalky, cardboard, astringent, toasted, nutty, and cereal-like. The volatile off-flavours are related to the oxidation of polyunsaturated fatty acids and several phytochemicals, such as isoflavones, saponins, phenolic acids, etc., and impart bitter and astringent tastes to SPI. Removing the off-flavours and improving the sensory quality of soybean products is a major technical challenge during the processing of soybean foods. For improving product quality, several treatments have been used for the removal or elimination of off-flavours, including physical methods, chemical methods, biological methods, and genetic engineering.
Pulse Protein Flavour
Authors: Xu Minwei , Chen Bingcan
Published: November 2023

Pulses (Fabaceae) have received great attention following the rising interest in plant-based foods. Although pulses have a high protein content, the off-flavours described as grassy, beany, and earthy have impeded the popularization of pulse proteins. This chapter reviews the volatile profiles of pulse proteins, including the molecules, sources, and interactions of pulse proteins and volatiles. In addition, it highlights the pulse protein profile, which could be related to pulse protein flavours. Moreover, recent research about the protein extraction process, including dry and wet processes and pulse processing technologies, is discussed. The research highlighted throughout this chapter is crucial for developing and popularizing pulse proteins as novel plant-based protein ingredients.
NMR of proteins and nucleic acids
Authors: Atkinson R. Andrew
Published: November 2023

A review of key publications from 2022, describing methodological developments and research applications of NMR of proteins and nucleic acids. Particularly novel approaches and reports of exceptional interest are highlighted.
Promoting nonsymmetric C–C coupling to valuable oxygenates without metal catalysts in alkali aqueous medium
Authors: Zhu Peidong , Wang Chunling , Zhong Heng , Yang Yang , Jin Fangming
Published: November 2023

Adjustable multi-carbon alkanoic acids/alcohols from formate without metal catalysts have been achieved via HCO* and HCOO− nonsymmetric C–C coupling in an alkali aqueous reaction.
Efficient post-synthesis incorporation and conjugation of reactive ketones in RNA via 2′-acylation
Authors: Shioi Ryuta , Xiao Lu , Fang Linglan , Kool Eric T.
Published: November 2023

Despite the broad utility of ketones in bioconjugation, few methods exist to introduce them into RNA.
First-principles studies on the electronic and photocatalytic water splitting properties of surface functionalized Y2C-based MXenes
Authors: Zhang Sheng-Yi , Shi Ni-Ping , Wang Chuan-Kui , Zhang Guang-Ping
Published: November 2023

A strategy is proposed that if one symmetric MXene is suitable for water reduction while another is suitable for water oxidation, then the corresponding Janus MXene may be promising for water splitting.
Effect of cyano-addition on the photoacidity switch in 5-cyano-8-amino-2-naphthol
Authors: Xie Jialin , Nealon Rachel E. , Egan Zelia T. , Takematsu Kana
Published: November 2023

Effect of cyano-addition on the photoacidity switch in 5-cyano-8-amino-2-naphthol: CN enhances but cannot override the NH2 off-switch for OH photoacidity in the substituted naphthol.
Stabilizing Pd–cerium oxide–aluminum oxide catalysts for methane oxidation by reduction pretreatments
Authors: Banerjee Anil C. , Proaño Laura , Alvarez Alexis , Rogers Imani , Park Jihyeon , Montgomery Maddison , Billor Mehmet Z. , Weckhuysen Bert M. , Monai Matteo
Published: November 2023

Pd–CeO2 based catalysts are state-of-the-art for methane oxidation, but deactivate due to Pd nanoparticle growth at high temperature.
Persulfate enhanced ciprofloxacin removal from water by laser-induced graphene-based electroconductive ultrafiltration membrane
Authors: Barbhuiya Najmul Haque , Misra Utkarsh , Kanwar Bhavana , Singh Swatantra P.
Published: November 2023

The ineffective removal of emerging pollutants by conventional treatment plants has necessitated the use of advanced treatment techniques such as electroconductive membranes.
Green synthesis of sulfur-containing polymers by carbon disulfide-based spontaneous multicomponent polymerization
Authors: Chen Xu , Qin Anjun , Tang Ben Zhong
Published: November 2023

A spontaneous multi-component polymerization of activated internal alkynes, amines, and CS2 was established. Similar to the ancient “tenon and mortise” structure, CS2 acts as a “wedge” to link the other two monomers to form sulfur-containing polymers.
The role of ceria/precious metal interfaces in catalysis
Authors: Melchionna Michele , Fornasiero Paolo
Published: November 2023

The popularity of ceria (CeO2) supports has been increasing over the last three decades on account of the rich redox chemistry of such an oxide.
A poly(2-ethylaniline) blend membrane for vanadium redox flow batteries
Authors: Bavdane Priyanka P. , Sreenath Sooraj , Nikumbe Devendra Y. , Bhatt Bhavana , Pawar Chetan M. , Dave Vidhiben , Nagarale Rajaram K.
Published: November 2023

Processable E-PANI polymer blend SPES membrane for enhancement of vanadium redox flow battery performance.
Intrafibrillar mineralization of type I collagen with calcium carbonate and strontium carbonate induced by polyelectrolyte–cation complexes
Authors: Zhang Yizhou , Wang Yiru , Zhang Zhengyi , Wang Zhe , Shao Changyu , Hannig Matthias , Zhou Zihuai , Fu Baiping
Published: November 2023

This article provides a feasible strategy for rapid intrafibrillar mineralization of collagen with CaCO3 and SrCO3. The CaCO3-mineralized collagen gels exhibited better biocompatibility and cell proliferation ability than SrCO3.
Tumor microenvironment-responsive degradable silica nanoparticles: design principles and precision theranostic applications
Authors: Zhang Junjie , Tang Kaiyuan , Liu Zilu , Zhang Zhijing , Duan Shufan , Wang Hui , Yang Hui , Yang Dongliang , Fan Wenpei
Published: November 2023

In this review, we categorize degradable silica nanoparticles into inorganic and organic types based on their framework components, highlight recent TME-responsive advancements, and discuss challenges in future research and clinical application.
Reactivity of azido terpyridine Pd(ii) and Pt(ii) complexes towards 4,4,4-trifluoro-2-butynoic acid: structural insight into the triazolato coordination mode
Authors: Mansour Ahmed M. , Radacki Krzysztof , Mostafa Gamal A. E. , Ali Essam A. , Shehab Ola R.
Published: November 2023

The binuclear azido terpyridine Pd(ii) complex underwent the catalyst-free cycloaddition coupling with alkyne affording triazolate analogues. The coordination mode of the triazolate ring was assigned with the aid of quantum chemical calculations.