bluuebunny/crossref_metadata_2025 huggingface dataset:
Nanocellulose coated paper diagnostic to measure glucose concentration in human blood
Authors: Hossain Laila , De Francesco Marisa , Tedja Patricia , Tanner Joanne , Garnier Gil
Published: November 2022

A new generation of rapid, easy to use and robust colorimetric point of care (POC) nanocellulose coated-paper sensors to measure glucose concentration in blood is presented in this study. The cellulose gel containing the enzyme with co-additive is coated and dried onto a paper substrate. Nanocellulose gel is used to store, immobilize and stabilize enzymes within its structure to prolong enzyme function and enhance its availability. Here, we immobilize glucose oxidase within the gel structure to produce a simple colorimetric blood glucose sensor. Increase in blood glucose concentration increases the concentration of reaction product which decreases the system pH detected by the pH indicative dye entrapped in the nanocellulose gel. The sensor produces a color change from red to orange as pH decreases due to the enzymatic reaction of glucose into gluconic acid and hydrogen peroxide. This sensor can measure glucose concentrations of 7–13 mM (medical range for diabetes control) at temperatures of 4°C–40°C. Stability tests confirm that no denaturation of enzyme occurs by measuring enzyme activity after 4 weeks. A prototype device is designed to instantly measure the glucose concentration from blood in a two steps process: 1) red blood cell separation and 2) quantification of glucose by color change. This study demonstrates nanocellulose sensor as an economical, robust, and sensitive diagnostic technology platform for a broad spectrum of diseases.
Comparative glycoproteomics study on the surface of SKOV3 versus IOSE80 cell lines
Authors: Zhou Ying , Cai Xiaoyu , Wu Linwen , Lin Nengming
Published: November 2022

Objective:Site-and structure-specific quantitative N-glycoproteomics study of differential cell-surface N-glycosylation of ovarian cancer SKOV3 cells with the non-cancerous ovarian epithelial IOSE80 cells as the control.

Methods:C18-RPLC-MS/MS (HCD with stepped normalized collision energies) was used to analyze the 1: 1 mixture of labeled intact N-glycopeptides from SKOV3 and IOSE80 cells, and the site- and structure-specific intact N-glycopeptide search engine GPSeeker was used to conduct qualitative and quantitative search on the obtained raw datasets.

Results:With the control of the spectrum-level false discovery rate ≤1%, 13,822 glycopeptide spectral matches coming from 2,918 N-glycoproteins with comprehensive N-glycosite and N-glycan structure information were identified; 3,733 N-glycosites and 3,754 N-glycan sequence structures were confirmed by site-determining and structure-diagnostic fragment ions, respectively. With the control of no less than two observations among the three technical replicates, fold change ≥1.5, andp-value ≤ 0.05, 746 DEPGs in SKOV3 cells relative to IOSE80 cells were quantified, where 421 were upregulated and 325 downregulated.

Conclusion:Differential cell-surface N-glycosylation of ovarian cancer SKOV3 cells were quantitatively analyzed by isotopic labeling and site- and structure-specific N-glycoproteomics. This discovery study provides putative N-glycoprotein biomarker candidates for future validation study using multiple reaction monitoring and biochemical methods.
Recent advances in the synthesis of TS-1 zeolite
Authors: Luan Huimin , Xu Cheng , Wu Qinming , Xiao Feng-Shou
Published: November 2022

Heteroatomic zeolites as an important class of zeolites, have been widely applied in industrially catalytic processes due to their unique properties. As one of the most representative heteroatomic zeolites, titanosilicate zeolites have been extensively used in the selective oxidations of organic substrates with H2O2 such as cyclohexanone ammoximation, epoxidation of alkenes, and phenol hydroxylation. In this review, recent advances in the synthesis of TS-1 zeolite are briefly summarized, including use of low-cost raw materials (organic templates, silicon, and titanium sources), development of new synthesis routes (post-treatment synthesis, dry-gel conversion synthesis, solvent-free synthesis, and microwave-assisted synthesis), and new strategy for enhanced mass transfer in TS-1 crystals (synthesis of hierarchical and nanosized TS-1 zeolite). This review might help researchers to have a deep understanding on the synthesis of TS-1 zeolite and provide a new opportunity for the design and preparation of highly efficient TS-1 catalysts in the future.
Respiratory immune status and microbiome in recovered COVID-19 patients revealed by metatranscriptomic analyses
Authors: Meng Huan , Wang Shuang , Tang Xiaomeng , Guo Jingjing , Xu Xinming , Wang Dagang , Jin Fangfang , Zheng Mei , Yin Shangqi , He Chaonan , Han Ying , Chen Jin , Han Jinyu , Ren Chaobo , Gao Yantao , Liu Huifang , Wang Yajie , Jin Ronghua
Published: November 2022

Coronavirus disease 2019 (COVID-19) is currently a severe threat to global public health, and the immune response to COVID-19 infection has been widely investigated. However, the immune status and microecological changes in the respiratory systems of patients with COVID-19 after recovery have rarely been considered. We selected 72 patients with severe COVID-19 infection, 57 recovered from COVID-19 infection, and 65 with non-COVID-19 pneumonia, for metatranscriptomic sequencing and bioinformatics analysis. Accordingly, the differentially expressed genes between the infected and other groups were enriched in the chemokine signaling pathway, NOD-like receptor signaling pathway, phagosome, TNF signaling pathway, NF-kappa B signaling pathway, Toll-like receptor signaling pathway, and C-type lectin receptor signaling pathway. We speculate that IL17RD, CD74, and TNFSF15 may serve as disease biomarkers in COVID-19. Additionally, principal coordinate analysis revealed significant differences between groups. In particular, frequent co-infections with the genera Streptococcus, Veillonella, Gemella, and Neisseria, among others, were found in COVID-19 patients. Moreover, the random forest prediction model with differential genes showed a mean area under the curve (AUC) of 0.77, and KCNK12, IL17RD, LOC100507412, PTPRT, MYO15A, MPDZ, FLRT2, SPEG, SERPINB3, and KNDC1 were identified as the most important genes distinguishing the infected group from the recovered group. Agrobacterium tumefaciens, Klebsiella michiganensis, Acinetobacter pittii, Bacillus sp. FJAT.14266, Brevundimonas naejangsanensis, Pseudopropionibacterium propionicum, Priestia megaterium, Dialister pneumosintes, Veillonella rodentium, and Pseudomonas protegens were selected as candidate microbial markers for monitoring the recovery of COVID patients. These results will facilitate the diagnosis, treatment, and prognosis of COVID patients recovering from severe illness.
Vaginal Lactobacillus iners abundance is associated with outcome in antibiotic treatment of bacterial vaginosis and capable of inhibiting Gardnerella
Authors: Zhou Rui , Lu Jingjing , Wang Jun , Xiao Bingbing
Published: November 2022

Bacterial vaginosis is characterized as a polymicrobial dysbiosis with the loss of Lactobacillus spp. and growth of multiple anerobic bacteria, including Gardnerella, Prevotella and Atopobium ranked as the top three most abundant. A total of nine Gardnerella genomospecies have been identified, yet the association between their distribution or any exact Lactobacillus species with BV occurrence or prognosis remains controversial. A total of 308 patients and 62 healthy women who sought annual examinations were recruited, with 130 BV patients and 41 healthy women who met our inclusion criteria finally included. Vaginal samples were used for microscopic examination, 16S rRNA sequencing, bacterial culture and isolation. Isolates of Gardnerella vaginalis, Fannyhessae vaginae (used to be called Atopobium vaginae) and Lactobacillus iners were used for competition tests. We found that the relative abundances of Gardnerella, Prevotella and Atopobium were elevated in BV patients compared to healthy people (p<0.0001), yet no significant differences were found among patients with different clinical outcomes (p>0.05). Seven out of nine Gardnerella genomospecies were present in both BV patients and healthy women, and the relative abundances of all detected genomospecies were higher in BV patients (p<0.05). Cured patients possessed higher GS03 than intermediate and failed patients (p=0.005, 0.0337). L. iners was significantly higher in cured patients than in the other two groups (p=0.0021, p<0.0001), and its ability to inhibit the growth of G. vaginalis and F. vaginae was validated. In summary, seven Gardnerella genomospecies were detected in Chinese BV patients, but no association of its distribution and BV occurrence or prognosis was found. The relative abundance of L. iners was higher in cured patients, and its antimicrobial activity against G. vaginalis and F. vaginae was validated through in vitro inhibition experiment. L. iners could become a predictive indicator of clinical outcomes of BV patients, and its antimicrobial function might be beneficial to BV patients.
Differential affinity chromatography reveals a link between Porphyromonas gingivalis–induced changes in vascular smooth muscle cell differentiation and the type 9 secretion system
Authors: Phillips Priscilla L. , Wu Xiao-jun , Reyes Leticia
Published: November 2022

Porphyromonas gingivalis is implicated in adverse pregnancy outcome. We previously demonstrated that intrauterine infection with various strains of P. gingivalis impairs the physiologic remodeling of the uterine spiral arteries (IRSA) during pregnancy, which underlies the major obstetrical syndromes. Women diagnosed with IRSA also have a greater risk for premature cardiovascular disease in later life. The dysregulated plasticity of vascular smooth muscle cells (VSMCs) is present in both IRSA and premature cardiovascular events. We hypothesized that VSMCs could serve as a bait to identify P. gingivalis proteins associated with dysregulated VSMC plasticity as seen in IRSA. We first confirmed that dams with P. gingivalis A7UF-induced IRSA also show perturbed aortic smooth muscle cell (AoSMC) plasticity along with the P. gingivalis colonization of the tissue. The in vitro infection of AoSMCs with IRSA-inducing strain A7UF also perturbed AoSMC plasticity that did not occur with infection by non-IRSA-inducing strain W83. Far-Western blotting with strain W83 and strain A7UF showed a differential binding pattern to the rat aorta and primary rat AoSMCs. The affinity chromatography/pull-down assay combined with mass spectrometry was used to identify P. gingivalis/AoSMC protein interactions specific to IRSA. Membrane proteins with a high binding affinity to AoSMCs were identified in the A7UF pull-down but not in the W83 pull-down, most of which were the outer membrane components of the Type 9 secretion system (T9SS) and T9SS cargo proteins. Additional T9SS cargo proteins were detected in greater abundance in the A7UF pull-down eluate compared to W83. None of the proteins enriched in the W83 eluate were T9SS components nor T9SS cargo proteins despite their presence in the prey preparations used in the pull-down assay. In summary, differential affinity chromatography established that the components of IRSA-inducing P. gingivalis T9SS as well as its cargo directly interact with AoSMCs, which may play a role in the infection-induced dysregulation of VSMC plasticity. The possibility that the T9SS is involved in the microbial manipulation of host cell events important for cell differentiation and tissue remodeling would constitute a new virulence function for this system.
Real-time multiple target segmentation with multimodal few-shot learning
Authors: Khoshboresh-Masouleh Mehdi , Shah-Hosseini Reza
Published: November 2022

Deep learning-based target segmentation requires a big training dataset to achieve good results. In this regard, few-shot learning a model that quickly adapts to new targets with a few labeled support samples is proposed to tackle this issue. In this study, we introduce a new multimodal few-shot learning [e.g., red-green-blue (RGB), thermal, and depth] for real-time multiple target segmentation in a real-world application with a few examples based on a new squeeze-and-attentions mechanism for multiscale and multiple target segmentation. Compared to the state-of-the-art methods (HSNet, CANet, and PFENet), the proposed method demonstrates significantly better performance on the PST900 dataset with 32 time-series sets in both Hand-Drill, and Survivor classes.
The chronic coronary syndrome—Heart failure roundabout: A multimodality imaging workflow approach
Authors: Lala Radu I. , Mercea Simona , Jipa Radu A. , Puschita Maria , Pop-Moldovan Adina
Published: November 2022

Heart failure (HF) is a complex syndrome of considerable burden with high mortality and hospitalization rates. Approximately two-thirds of patients with HF have ischemic etiology, which makes crucial the identification of relevant coronary artery disease (CAD). Moreover, patients with chronic coronary syndrome (CCS) can first show signs of dyspnea and left ventricular (LV) dysfunction. If establishing a diagnosis of HF and consequent management is clear enough, it will not be the same when it comes to recommendations for etiology assessment. Ischemic heart disease is the most studied disease by cardiac multimodality imaging with excellent diagnostic performance. Based on this aspect, the high prevalence of CAD, the worst outcome—HF patients should undergo a diagnostic work-up using these multimodality imaging techniques. The aim of this mini-review is to provide insights on multimodality imaging for diagnosing CCS in patients with new onset of HF and propose a diagnostic work-up based on current international studies and guidelines.
Machine learning opportunities to conduct high-fidelity earthquake simulations in multi-scale heterogeneous geology
Authors: Lehmann Fanny , Gatti Filippo , Bertin Michaël , Clouteau Didier
Published: November 2022

The 2019 Le Teil earthquake is an illustrative example of a moderate (MW4.9) yet damaging event, occurring at shallow depth (≈1 km) in a region with little to no geophysical data available. Therefore, using a high-fidelity wave propagation code, we performed numerical simulations of the Le Teil earthquake in a highly uncertain framework, investigating several seismic sources and geological set-ups. With respect to the former aspect, a point-source model and an extended kinematic fault model were compared. The latter aspect was investigated by comparing a 1D-layered to a 3D geological model. Those models were enhanced with random fluctuations, in order to obtain three alternative non-stationary random geological fields. The synthetic waveforms obtained from regional geophysical models were globally coherent with the recorded ones. The extended fault source model seemed more realistic than the point-source model. In addition, some geological random fields improved the synthetics’ agreement with the recordings. However, the three random field samplings led to a high variability in induced ground motion responses. Given the computational burden of high-fidelity simulations, we used two dimensionality reduction methods, namely the Principal Component Analysis (PCA) and a deep neural network (3D UNet), to investigate this variability. The methods were applied to a database of 40,000 3D geological random fields. Both the PCA and the 3D UNet condensed the variability of the 3D geological fields into a few components. These were sufficient to reconstruct the original fields with great accuracy. More importantly, the seismic response arising from the propagation throughout the reconstructed fields was in excellent agreement with the response of the original geological fields in more than 75% of the dataset. By building a structured ensemble of complex geological fields from their reduced representation, it may become possible to find a relationship between the reduced representation and the generated ground motion. Thus, our study proves the interest of dimensionality reduction to perform uncertainty analyses in complex geological media.
Building archean cratonic roots
Authors: Jain Charitra , Rozel Antoine B. , van Hunen Jeroen , Chin Emily J. , Manjón-Cabeza Córdoba Antonio
Published: November 2022

Geophysical, geochemical, and geological investigations have attributed the stable behaviour of Earth’s continents to the presence of their Archean cratonic roots. These roots are likely composed of melt-depleted, low density residual peridotite with high magnesium number (Mg#), while devolatilisation from the upper mantle during magmatic events might have made these roots more viscous and intrinsically stronger than the convecting mantle. Several conceptual dynamic and petrological models of craton formation have been proposed. Dynamic models invoke far-field shortening or mantle melting events, e.g., by mantle plumes, to create melt-depleted and thick cratons. Compositional buoyancy and rheological modifications have also been invoked to create long-lived stable cratonic lithosphere. However, these conceptual models have not been tested in a dynamically self-consistent model. In this study, we present global thermochemical models of craton formation with coupled core-mantle-crust evolution driven entirely by gravitational forces. Our results with melting and crustal production (both oceanic and continental) show that formation of cratonic roots can occur through naturally occurring lateral compression and thickening of the lithosphere in a self-consistent manner, without the need to invoke far-field tectonic forces. Plume impingements, and gravitational sliding creates thrusting of lithosphere to form thick, stable, and strong lithosphere that has a strong resemblance to the Archean cratons that we can still observe today at the Earth’s surface. These models also suggest the recycling of denser eclogitic crust by delamination and dripping processes. Within our computed parameter space, a variety of tectonic regimes are observed which also transition with time. Based on these results, we propose that a ridge-only regime or a sluggish-lid regime might have been active on Earth during the Archean Eon as they offer favourable dynamics and conditions for craton formation.
A FFAR1 full agonist restores islet function in models of impaired glucose-stimulated insulin secretion and diabetic non-human primates
Authors: Rady Brian , Liu Jianying , Huang Hui , Bakaj Ivona , Qi Jenson , Lee S. P. , Martin Tonya , Norquay Lisa , Player Mark , Pocai Alessandro
Published: November 2022

The free fatty acid receptor 1 (FFAR1/GPR40) mediates fatty acid-induced insulin secretion from pancreatic β-cells. At least 3 distinct binding sites exist on the FFAR1 receptor and numerous synthetic ligands have been investigated for their anti-diabetic actions. Fasiglifam, binds to site-1 and stimulates intra-cellular calcium release and improves glycemic control in diabetic patients. Recently, small molecule FFAR1 agonists were discovered which bind to site-3, stimulating both intra-cellular calcium and cAMP, resulting in insulin and glucagon-like peptide-1 (GLP-1) secretion. The ability of our site-3 FFAR1 agonist (compound A) to control blood glucose was evaluated in spontaneously diabetic cynomolgus monkeys during an oral glucose tolerance test. In type-2 diabetic (T2D) animals, significant reductions in blood glucose and insulin were noted. To better understand the mechanism of these in vivo findings, we evaluated the effect of compound A in islets under several conditions of dysfunction. First, healthy human and non-human primate islets were treated with compound A and showed potentiation of insulin and glucagon secretion from both species. Next, we determined glucose-responsive insulin secretion under gluco-lipotoxic conditions and from islets isolated from type-2 diabetic humans. Despite a dysfunctional phenotype that failed to secrete insulin in response to glucose, site-3 FFAR1 agonism not only enhanced insulin secretion, but restored glucose responsiveness across a range of glucose concentrations. Lastly, we treated ex vivo human islets chronically with a sulfonylurea to induce secondary beta-cell failure. Again, this model showed reduced glucose-responsive insulin secretion that was restored and potentiated by site-3 FFAR1 agonism. Together these data suggest a mechanism for FFAR1 where agonists have direct effects on islet hormone secretion that can overcome a dysfunctional T2D phenotype. These unique characteristics of FFAR1 site-3 agonists make them an appealing potential therapy to treat type-2 diabetes.
The promising role of risk scoring system for Cushing syndrome: Time to reconsider current screening recommendations
Authors: Lam-Chung CE. , Cuevas-Ramos D.
Published: November 2022

Despite the current screening approach for Cushing syndrome (CS), delayed diagnosis is common due to broad spectrum of presentation, poor discriminant symptoms featured in diabetes and obesity, and low clinical index of suspicion. Even if initial tests are recommended to screen CS, divergent results are not infrequent. As global prevalence of type 2 diabetes and obesity increases, CS may not be frequent enough to back routine screening to avoid false-positive results. This represents a greater challenge in countries with limited health resources. The development of indexes incorporates clinical features and biochemical data that are largely used to provide a tool to predict the presence of disease. In clinical endocrinology, indexes have been used in Graves’ ophthalmology, hirsutism, and hypothyroidism. The use of clinical risk scoring system may assist clinicians in discriminating CS in the context of at-risk populations and, thus, may provide a potential intervention to decrease time to diagnosis. Development and validation of clinical model to estimate pre-test probability of CS in different geographic source population may help to establish regional prediction model for CS. Here, we review on the latest progress in clinical risk scoring system for CS and attempt to raise awareness for the use, validation, and/or development of clinical risk scores in CS.
How big data drives green economic development: Evidence from China
Authors: Wang Li , Wu Yuhan , Huang Zeyu , Wang Yanan
Published: November 2022

Big data can improve production efficiency and optimize resource allocation, which is conductive to achieve sustainable development. This paper explores the impact of big data on green economic development. The global MINDW-MML model is used to measure green economic development and text analysis method is used to quantify the development of big data. An empirical study is conducted based on the panel data from 30 provinces in China from 2011 to 2018. Results show that, big data promotes the development of green economy and plays a greater role in facilitating technological progress than improving efficiency. As for sub-indicators of big data, cloud computing, Internet of things, artificial intelligence, and Hadoop positively affect technological progress, while blockchain can improve efficiency. In addition, the positive role of big data in promoting green technological progress and green efficiency will vary according to geographical location, the intensity of environmental governance and the development of digital financial inclusion. As moving into the good phase of the economy, big data is more inclined to enhance green technological progress, while in a sluggish phase, it improves green efficiency more. These findings point the way forward for sustainable development. The Chinese government can actively build information infrastructure and improve the technical level and application capacity of big data.
Progress and prospect of ecological risks of land use change
Authors: Cao Congjie , Song Wei
Published: November 2022

Ecological risks reflect the extent to which ecosystems are threatened by human activities and environmental changes. Changes in land use/land cover can have profound impacts on the regional ecological environment, such as land desertification, soil erosion, a sharp reduction in forest resources, and biodiversity loss. To objectively reveal the current research status, we conducted an econometric analysis of relevant research papers from 1991 to 2021, published in Web of Science. The results are as follows: 1) In the past 30 years, the number of publications in the field of ecological risks of land use change increased, and the period from 1991 to 2021 can be divided into three stages: the budding period from 1991 to 2008, the rising period from 2009 to 2015, and the high-yield period from 2016 to 2021. 2) Research in this field covered 104 countries or regions, mainly in Asia, the Americas, and Europe. The top three cited countries were the US, China, and the UK. 3) The high-frequency keywords of land use change in the field of ecological risks mainly included “land use”, “management”, “climate change”, and “risk and ecology”. Keywords frequently appeared in Tree Map, such as “dynamics”, “framework”, and “model”, indicating the main research methods in this field. Based on the results, we suggest that for the future development of this research field, the evaluation method system should be improved and multidisciplinary research should be strengthened, ultimately exploring new ways to solve the current ecological problems.
Study on the effect of industrial structure transformation on regional ecological efficiency in ecological economic zone under carbon peaking and carbon neutrality strategy
Authors: Wang Yan , Wang Ladi
Published: November 2022

As the main strategy for the coordinated development of China’s ecological economy in the future, the carbon peaking and carbon neutrality strategy is an important response strategy to solve the two major problems of China’s urbanization process: the industrial structure is biased toward tradition and the economic development is biased toward high carbon. Under this development prospect, how to coordinate ecological development and economic development through the transformation of the industrial structure and form a unified development situation is an important issue for the development of the ecological economy. To solve this problem, the research starts with the theory of industrial structure change and ecological efficiency, puts forward two kinds of ecological efficiency assumptions, and establishes a mathematical model based on the C-D production function and cost function for the impact of industrial structure change on ecological efficiency. On this basis, a spatial model is formed, and empirical analysis is carried out for the important domestic ecological economic zone - the Yangtze River Economic Belt. The research results show that the industrial structure of the eco-economic zone will have a significant positive impact on ecological efficiency. At the same time, under the effect of inter-city cooperation, ecological efficiency has a significant spatial spillover effect. At the same time, the spatial lag factor and spatial error factor of urban agglomeration in the Yangtze River Delta are significant at the 10% and 5% levels, and the spatial lag factor and spatial error factor of urban agglomeration in the middle and long reaches are significant at the 5% level. It can be seen that the spatial dependence and linkage of ecological effects are strong, and there is a relatively significant interaction.
Activation of pheromone-sensitive olfactory neurons by plant volatiles in the moth Agrotis ipsilon does not occur at the level of the pheromone receptor protein
Authors: Vandroux Paul , Li Zibo , Capoduro Rémi , François Marie-Christine , Renou Michel , Montagné Nicolas , Jacquin-Joly Emmanuelle
Published: November 2022

In moths, mate finding relies on female-emitted sex pheromones that the males have to decipher within a complex environmental odorant background. Previous studies have shown that interactions of both sex pheromones and plant volatiles can occur in the peripheral olfactory system, and that some plant volatiles can activate the pheromone-specific detection pathway. In the noctuid moth Agrotis ipsilon, plant volatiles such as heptanal activate the receptor neurons tuned to the pheromone component (Z)7-12:OAc. However, the underlying mechanisms remain totally unknown. Following the general rule that states that one olfactory receptor neuron usually expresses only one type of receptor protein, a logic explanation would be that the receptor protein expressed in (Z)7-12:OAc-sensitive neurons recognizes both pheromone and plant volatiles. To test this hypothesis, we first annotated odorant receptor genes in the genome of A. ipsilon and we identified a candidate receptor putatively tuned to (Z)7-12:OAc, named AipsOR3. Then, we expressed it in Drosophila olfactory neurons and determined its response spectrum to a large panel of pheromone compounds and plant volatiles. Unexpectedly, the receptor protein AipsOR3 appeared to be very specific to (Z)7-12:OAc and was not activated by any of the plant volatiles tested, including heptanal. We also found that (Z)7-12:OAc responses of Drosophila neurons expressing AipsOR3 were not affected by a background of heptanal. As the Drosophila olfactory sensilla that house neurons in which AipsOR3 was expressed contain other olfactory proteins – such as odorant-binding proteins – that may influence its selectivity, we also expressed AipsOR3 in Xenopus oocytes and confirmed its specificity and the lack of activation by plant volatiles. Altogether, our results suggest that a still unknown second odorant receptor protein tuned to heptanal and other plant volatiles is expressed in the (Z)7-12:OAc-sensitive neurons of A. ipsilon.
Two lines of defense in the pupas of ichneumonid wasp parasitoids associated with spider hosts
Authors: Korenko Stanislav , Sýkora Jakub , Kostro-Ambroziak Agata , Pekár Stano
Published: November 2022

Insects in the pupal stage are vulnerable to various predators because the pupa is immobile. The pupas of parasitoid ichneumonid wasps (Ichneumonidae) associated with spider hosts have evolved two lines of defense against predators, namely a cocoon spun by the parasitoid larva and a web provided by the spider host. The web is derived from a normal or modified spider web built by the spider under manipulation by the penultimate instar of the parasitoid wasp. In laboratory experiments, we tested the efficacy of these two defensive lines using six potential predators with two different types of mouthparts coming from three foraging guilds. The presence of the cocoon significantly reduced predation. Scavengers with chewing mouthparts, e.g., cockroaches and crickets, attacked and consumed pupas within both sparse and strong cocoon walls. Scavengers with piercing mouthparts were able to attack pupas in cocoons with a sparse wall, but not with a strong wall. Collectors and true predators showed no interest in cocoons. The presence of a web increased pupa protection by up to 80% when the web was on the ground and by up to 95% when the web was in the air. Only scavengers with chewing mouthparts were able to reach and consume pupas sheltered by the web. We provide the first evidence of how the two lines of defense contribute to parasitoid defense during the pupal stage.
Scrutinizing the paleoecological record of the Maya forest
Authors: Ford Anabel
Published: November 2022

Human expansion into and occupation of the New World coincided with the great transition from the Pleistocene to the Holocene epoch, yet questions remain about how we detect human presence in the paleoecological record. In the Maya area of southern Mesoamerica, archeological evidence of the human imprint is largely invisible until ∼4,000 years ago. How do environmental changes after that time correspond and relate to human impacts? Are the archeological signatures of initial settlements in the Early Preclassic detected? Later, by ∼2,000 years ago when the Maya had fully settled the landscape, how does the evidence of forest compositional changes relate to human intervention? This paper evaluates published paleoecological data in light of the rise of the Maya civilization and reflects on interpretations of how swidden agriculture and the milpa cycle impacted the environment. Evaluating the contrast between the long archeological sequence of successful Maya development and paleoecological interpretations of destructive human-induced environmental impacts requires a concordance among pollen data, archeological evidence, ethnohistoric observations, ethnological studies of traditional Maya land use, and the historical ecology of the Maya forest today.
Causal effects of homocysteine levels on the components of sarcopenia: A two-sample mendelian randomization study
Authors: Yu Hongwei , Luo Gan , Sun Tianwei , Tang Qiong
Published: November 2022

Background: Currently, it is unclear whether there is a causal association between genetically predicted plasma homocysteine (Hcy) levels and the risk of sarcopenia. We performed a Mendelian randomization (MR) study to assess the association between circulating Hcy levels and the components [grip strength, walking pace, and appendicular lean mass (ALM)] of sarcopenia.

Methods: Independent single nucleotide polymorphisms (SNPs) significantly associated with plasma Hcy levels served as instrumental variables. Summary-level data regarding the components of sarcopenia. Were obtained from the UK Biobank. Inverse variance weighted (IVW) as the primary method was used for Mendelian randomization (MR) analysis. We also use four models, weighted median, MR-Egger regression, Maximum likelihood, and Penalised weighted median, as supplementary methods to IVW. The MR-Egger intercept test, Cochran’s Q test, and “leave-one-out” sensitivity analysis were performed to evaluate the horizontal pleiotropy, heterogeneities, and stability of the causal association between Hcy levels and the components of sarcopenia.

Results: The IVW-MR analysis suggested significant negative associations of increased plasma Hcy levels with grip strength (right: effect = −0.036, SE = 0.032, p = 5.53E-4; left: effect = −0.045, SE = 0.010, p = 1.45E-5), walking pace (effect = −0.038, SE = 0.011, p = 3.18E-4), and ALM (effect = −0.058, 0.013, p = 1.03E-5). However, there were no significant associations of decreased plasma Hcy levels with grip strength (right: effect = 0.005, SE = 0.021, p = 0.82; left: effect = −0.006, SE = 0.014, p = 0.64), walking pace (effect = 0.01, 0.020, p = 0.61), or ALM (effect = -0.034, SE = 0.018, p = 0.06).The accuracy and robustness of these findings were confirmed by sensitivity tests.

Conclusion: Increased circulating Hcy levels were associated with lower grip strength, slower walking pace, and decreased ALM.
Coexpression network analysis of human candida infection reveals key modules and hub genes responsible for host-pathogen interactions
Authors: Naik Surabhi , Mohammed Akram
Published: November 2022

Invasive fungal infections are a significant reason for morbidity and mortality among organ transplant recipients. Therefore, it is critical to investigate the host and candida niches to understand the epidemiology of fungal infections in transplantation. Candida albicans is an opportunistic fungal pathogen that causes fatal invasive mucosal infections, particularly in solid organ transplant patients. Therefore, identifying and characterizing these genes would play a vital role in understanding the complex regulation of host-pathogen interactions. Using 32 RNA-sequencing samples of human cells infected with C. albicans, we developed WGCNA coexpression networks and performed DESeq2 differential gene expression analysis to identify the genes that positively correlate with human candida infection. Using hierarchical clustering, we identified 5 distinct modules. We studied the inter- and intramodular gene network properties in the context of sample status traits and identified the highly enriched genes in the correlated modules. We identified 52 genes that were common in the most significant WGCNA turquoise module and differentially expressed genes in human endothelial cells (HUVEC) infection vs. control samples. As a validation step, we identified the differentially expressed genes from the independent Candida-infected human oral keratinocytes (OKF6) samples and validated 30 of the 52 common genes. We then performed the functional enrichment analysis using KEGG and GO. Finally, we performed protein-protein interaction (PPI) analysis using STRING and CytoHubba from 30 validated genes. We identified 8 hub genes (JUN, ATF3, VEGFA, SLC2A1, HK2, PTGS2, PFKFB3, and KLF6) that were enriched in response to hypoxia, angiogenesis, vasculogenesis, hypoxia-induced signaling, cancer, diabetes, and transplant-related disease pathways. The discovery of genes and functional pathways related to the immune system and gene coexpression and differential gene expression analyses may serve as novel diagnostic markers and potential therapeutic targets.
TLsub: A transfer learning based enhancement to accurately detect mutations with wide-spectrum sub-clonal proportion
Authors: Zheng Tian
Published: November 2022

Mutation detecting is a routine work for sequencing data analysis and the trading of existing tools often involves the combinations of signals on a set of overlapped sequencing reads. However, the subclonal mutations, which are reported to contribute to tumor recurrence and metastasis, are sometimes eliminated by existing signals. When the clonal proportion decreases, signals often present ambiguous, while complicated interactions among signals break the IID assumption for most of the machine learning models. Although the mutation callers could lower the thresholds, false positives are significantly introduced. The main aim here was to detect the subclonal mutations with high specificity from the scenario of ambiguous sample purities or clonal proportions. We proposed a novel machine learning approach for filtering false positive calls to accurately detect mutations with wide spectrum subclonal proportion. We have carried out a series of experiments on both simulated and real datasets, and compared to several state-of-art approaches, including freebayes, MuTect2, Sentieon and SiNVICT. The results demonstrated that the proposed method adapts well to different diluted sequencing signals and can significantly reduce the false positive when detecting subclonal mutations. The codes have been uploaded at https://github.com/TrinaZ/TL-fpFilter for academic usage only.
Comparison of detection methods and genome quality when quantifying nuclear mitochondrial insertions in vertebrate genomes
Authors: Triant Deborah A. , Pearson William R.
Published: November 2022

The integration of mitochondrial genome fragments into the nuclear genome is well documented, and the transfer of these mitochondrial nuclear pseudogenes (numts) is thought to be an ongoing evolutionary process. With the increasing number of eukaryotic genomes available, genome-wide distributions of numts are often surveyed. However, inconsistencies in genome quality can reduce the accuracy of numt estimates, and methods used for identification can be complicated by the diverse sizes and ages of numts. Numts have been previously characterized in rodent genomes and it was postulated that they might be more prevalent in a group of voles with rapidly evolving karyotypes. Here, we examine 37 rodent genomes, and an additional 26 vertebrate genomes, while also considering numt detection methods. We identify numts using DNA:DNA and protein:translated-DNA similarity searches and compare numt distributions among rodent and vertebrate taxa to assess whether some groups are more susceptible to transfer. A combination of protein sequence comparisons (protein:translated-DNA) and BLASTN genomic DNA searches detect 50% more numts than genomic DNA:DNA searches alone. In addition, higher-quality RefSeq genomes produce lower estimates of numts than GenBank genomes, suggesting that lower quality genome assemblies can overestimate numts abundance. Phylogenetic analysis shows that mitochondrial transfers are not associated with karyotypic diversity among rodents. Surprisingly, we did not find a strong correlation between numt counts and genome size. Estimates using DNA: DNA analyses can underestimate the amount of mitochondrial DNA that is transferred to the nucleus.
Identification of immune-related features involved in Duchenne muscular dystrophy: A bidirectional transcriptome and proteome-driven analysis
Authors: Wu Xuan , Dong Nan , Yu Liqiang , Liu Meirong , Jiang Jianhua , Tang Tieyu , Zhao Hongru , Fang Qi
Published: November 2022

Background

We aimed to investigate the biological mechanism and feature genes of Duchenne muscular dystrophy (DMD) by multi-omics and experimental verification strategy.

Methods

We integrated the transcriptomic and proteomic methods to find the differentially expressed mRNAs (DEMs) and proteins (DEPs) between DMD and Control groups. Weighted gene co-expression network analysis (WGCNA) was then used to identify modules of highly correlated genes and hub genes. In the following steps, the immune and stromal cells infiltrations were accomplished by xCELL algorithm. Furthermore, TF and miRNA prediction were performed with Networkanalyst. ELISA, western blot and external datasets were performed to verify the key proteins/mRNAs in DMD patient and mouse. Finally, a nomogram model was established based on the potential biomarkers.

Results

4515 DEMs and 56 DEPs were obtained from the transcriptomic and proteomic study respectively. 14 common genes were identified, which is enriched in muscle contraction and inflammation-related pathways. Meanwhile, we observed 33 significant differences in the infiltration of cells in DMD. Afterwards, a total of 22 miRNAs and 23 TF genes interacted with the common genes, including TFAP2C, MAX, MYC, NFKB1, RELA, hsa-miR-1255a, hsa-miR-130a, hsa-miR-130b, hsa-miR-152, and hsa-miR-17. In addition, three genes (ATP6AP2, CTSS, and VIM) showed excellent diagnostic performance on discriminating DMD in GSE1004, GSE3307, GSE6011 and GSE38417 datasets (all AUC > 0.8), which is validated in patients (10 DMD vs. 10 controls), DMD with exon 55 mutations, mdx mouse, and nomogram model.

Conclusion

Taken together, ATP6AP2, CTSS, and VIM play important roles in the inflammatory response in DMD, which may serve as diagnostic biomarkers and therapeutic targets.
Crosstalk between cytotoxic CD8+ T cells and stressed cardiomyocytes triggers development of interstitial cardiac fibrosis in hypertensive mouse hearts
Authors: Brassington Kurt , Kanellakis Peter , Cao Anh , Toh Ban-Hock , Peter Karlheinz , Bobik Alex , Kyaw Tin
Published: November 2022

Aims

Cardiac fibrosis is central to heart failure (HF), especially HF with preserved ejection fraction (HFpEF), often caused by hypertension. Despite fibrosis causing diastolic dysfunction and impaired electrical conduction, responsible for arrhythmia-induced sudden cardiac death, the mechanisms are poorly defined and effective therapies are lacking. Here we show that crosstalk between cardiac cytotoxic memory CD8+ T cells and overly stressed cardiomyocytes is essential for development of non-ischemic hypertensive cardiac fibrosis.

Methods and results

CD8 T cell depletion in hypertensive mice, strongly attenuated CF, reduced cardiac apoptosis and improved ventricular relaxation. Interaction between cytotoxic memory CD8+ T cells and overly stressed cardiomyocytes is highly dependent on the CD8+ T cells expressing the innate stress-sensing receptor NKG2D and stressed cardiomyocytes expressing the NKG2D activating ligand RAE-1. The interaction between NKG2D and RAE-1 results in CD8+ T cell activation, release of perforin, cardiomyocyte apoptosis, increased numbers of TGF-β1 expressing macrophages and fibrosis. Deleting NKG2D or perforin from CD8+ T cells greatly attenuates these effects. Activation of the cytoplasmic DNA-STING-TBK1-IRF3 signaling pathway in overly stressed cardiomyocytes is responsible for elevating RAE-1 and MCP-1, a macrophage attracting chemokine. Inhibiting STING activation greatly attenuates cardiomyocyte RAE-1 expression, the cardiomyocyte apoptosis, TGF-β1 and fibrosis.

Conclusion

Our data highlight a novel pathway by which CD8 T cells contribute to an early triggering mechanism in CF development; preventing CD8+ T cell activation by inhibiting the cardiomyocyte RAE-1-CD8+ T cell-NKG2D axis holds promise for novel therapeutic strategies to limit hypertensive cardiac fibrosis.
Are homeostatic mechanisms aiding the reconstitution of the T-cell pool during lymphopenia in humans?
Authors: Baliu-Piqué Mariona , Tesselaar Kiki , Borghans José A. M.
Published: November 2022

A timely recovery of T-cell numbers following haematopoietic stem-cell transplantation (HSCT) is essential for preventing complications, such as increased risk of infection and disease relapse. In analogy to the occurrence of lymphopenia-induced proliferation in mice, T-cell dynamics in humans are thought to be homeostatically regulated in a cell density-dependent manner. The idea is that T cells divide faster and/or live longer when T-cell numbers are low, thereby helping the reconstitution of the T-cell pool. T-cell reconstitution after HSCT is, however, known to occur notoriously slowly. In fact, the evidence for the existence of homeostatic mechanisms in humans is quite ambiguous, since lymphopenia is often associated with infectious complications and immune activation, which confound the study of homeostatic regulation. This calls into question whether homeostatic mechanisms aid the reconstitution of the T-cell pool during lymphopenia in humans. Here we review the changes in T-cell dynamics in different situations of T-cell deficiency in humans, including the early development of the immune system after birth, healthy ageing, HIV infection, thymectomy and hematopoietic stem cell transplantation (HSCT). We discuss to what extent these changes in T-cell dynamics are a side-effect of increased immune activation during lymphopenia, and to what extent they truly reflect homeostatic mechanisms.
Seed bank dynamics and quality in the seagrass Halophila ovalis along estuarine salinity gradients—a case in the Swan-Canning Estuary
Authors: Gu Ruiting , Statton John , Rahmawati Susi , Hovey Renae , Zhou Yi , Tang Jianwu , Yu Shuo , Kendrick Gary A.
Published: November 2022

The seed bank of Halophila ovalis is crucial for resilience to disturbance through re-establishment. Understanding seasonal changes in abundance and quality of seeds in natural seed banks is critical for seed-based restoration. We selected an estuary in southwestern Australia and investigated the seasonal changes of seed distribution and viability in H. ovalis seed banks. We also adapted an X-ray viability test used for terrestrial seeds to test the viability of H. ovalis seeds. We then simulated the effect of low salinity on seed viability through a short-term indoor experiment. Seed density was significantly different between sites and seasons (0 to 43590 seeds·m-2), and the highest seed density in the seed banks was found after the reproductive season (May). The proportion of viable seeds in the seed bank was less than 22%, and was not subjected to substantial seasonal variability. The density of seeds in the seed bank decreased in spring, which indicated winter conditions were not prompt seed loss. We also predicted that extreme rainfall events and the resulting extremely low salinity would significantly reduce seed viability, and could decrease in seed germination; limit population recruitment. As it rapidly colonizes marine sediments from seeds, H. ovalis was considered an ideal seagrass for restoration purposes. Our results provide physiological information for H. ovalis seed banks to support seed-based restoration plans. Such understanding would enable accurate predictions about seagrass population resilience to extreme climate events in estuaries, where variable and extremely low salinity may limit seagrass population recovery from seeds through decreasing their viability.