bluuebunny/crossref_metadata_2025 huggingface dataset:
Red cell distribution width (RDW) is correlated to time of oxygen desaturation < 90% and length of sleep apneas in patients with sleep disorder breathing (SDB) and acute heart failure with preserved ejection fraction (HFpEF)
Authors: Stamerra Cosimo A. , D'Elia Emilia , Gori Mauro , Roncali Federica , Cereda Alberto , Gavazzi Antonello , Ferri Claudio , Senni Michele
Published: February 2023

Background

Heart failure with preserved ejection fraction (HFpEF) is very frequently associated to sleep breathing disorders (SDB). Red blood cell distribution width (RDW) has been shown to be a potential inflammatory index linked to the degree of hypoxia and oxidative stress.

Aim

To identify the existence of a possible relationship between sleep apnea, oxygen saturation (SaO2) and RDW in a population of subjects affected by acute HFpEF (AHFpEF).

Methods

AHFpEF patients with known history of SDB were enrolled and performed blood chemistry, echocardiography, and 24-h polysomnography (PSG).

Results

A total of 34 acute HFpEF patients (mean age 72.8 +/−8.63) were enrolled in the study. A control group of 24 non-HF patients were considered. Compared to controls, HFpEF patients showed a higher mean apnea hypopnea index (AHI), with prevalence of central apneas. A moderate to severe desaturation pattern was observed in AHFpEF vs. controls. RDW was significantly higher in AHFpEF patients vs. controls (mean value 14.7 +/−2.6 % vs. 9.1 +/−2.2, p < 0.05). In AHFpEF, RDW showed a positive correlation with time of SaO2 < 90% (r = 0.35, p = 0.04), and with mean length of apneic events (60 +/−28 s, r = 0.29, p = 0.03).

Conclusion

In patients with AHFpEF and SDB, a dependence relationship between RDW and duration of oxygen desaturation was observed, as if oxidative stress and inflammation related to RDW increase could also be linked to severity of sleep disorders in this population.
Drought- and heatwave-associated compound extremes: A review of hotspots, variables, parameters, drivers, impacts, and analysis frameworks
Authors: Afroz Mahnaz , Chen Gang , Anandhi Aavudai
Published: February 2023

Droughts and heatwaves are rising concerns with regard to the frequent formation of the compound or concurrent extremes (CEs), which can cause greater havoc than an individual event of a higher magnitude. Recently, they have been frequently detected to form CEs together or with other events (e.g., floods, aridity, and humidity events) concurrently or with spatiotemporal lags. Therefore, this systematic review assesses these CEs by reviewing the following aspects: CE hotspots, events, and variable combinations that form CEs; frequently analyzed CE parameters (e.g., frequency and severity); large-scale modes of climate variability (CV) as drivers alongside the approaches to relate them to CEs; and CE impacts (e.g., yield loss and fire risk) alongside the impact integration approaches from 166 screened publications. Additionally, three varied analysis frameworks of CEs are summarized to highlight the different analysis components of drought- and heatwave-associated CEs, which is the novelty of this study. The analysis frameworks vary with regard to the three major assessment objectives: only CE parameters (event–event), driver association (event–driver), and impacts (event–impact). According to this review, the most frequently reported hotspots of these CEs in global studies are southern Africa, Australia, South America, and Southeast Asia. In regional studies, several vital hotspots (e.g., Iberian Peninsula, Balkans, and Mediterranean Basin) have been reported, some of which have not been mentioned in global studies because they usually report hotspots as broader regions. In addition, different event combinations (e.g., drought and heatwave; and heatwave and stagnation) are analyzed by varying the combination of variables, namely, temperature, precipitation, and their derived indices. Thus, this study presents three major analysis frameworks and components of drought- and heatwave-associated CE analysis for prospective researchers.
Response of summer maize growth to drought-flood abrupt alternation
Authors: Bi Wuxia , Weng Baisha , Yan Denghua , Zhang Dawei , Liu Cuishan , Shi Xiaoliang , Jing Lanshu , Yan Siying , Wang Hao
Published: February 2023

Extreme events normally have negative effects on crop growth. Many studies have reported findings on drought and flood events, while only sparse studies have focused on new types of extreme events, such as drought-flood abrupt alternation (DFAA). We attempted to gain an insight on the effects of DFAA over two-year field experiment on biomass, grain yield and quality, then simulated the yield loss to DFAA in history and future in summer maize planting area in the Northern Anhui Plain. Results show that DFAA significantly reduced root biomass and shoot biomass by 77.1% and 60.1% compared with that in the control systems. The negative effect lasted until mature stage. The grain yield loss was 14.1%–38.4% in different DFAA treatments. The numerical simulation reveals that the average annual yield loss due to DFAA has been increasing in the Northern Anhui Plain, with 21.19%–30.98% during 1964–2017, 14.10%–33.40% during 2020–2050. The spatial distribution of yield loss changed as well. This study increases our knowledge of the effects of DFAA on crop production and highlights the need to consider the targeted countermeasures.
Reconstruction of proto-type basin and tectono-paleogeography of Tarim block in early Paleozoic
Authors: Zhong Ziqi , Xia Jinkai , Huang Shaoying , Luo Caiming , Chang Haining , Li Xiang , Wei Lunyan , Zhang Hao
Published: February 2023

Tarim Basin is a large, superimposed basin rich in petroleum resources, which has experienced many stages of complex tectonic-sedimentary evolution. As the basic geological study of the Tarim Basin, the proto-type basin and tectono-paleogeographic evolution are of great significance for understanding the distribution of petroleum reservoirs in the superimposed basin and provide tectonic background and theoretical guidance for petroleum exploration. According to the residual thickness map, as well as other lithofacies and seismic data, the scopes of the proto-type basin are determined by the marginal facies method and the thickness trend method, and the shortening amounts are calculated by the balanced cross-section method. Based on these data and previous works, four proto-type basin maps of Tarim Basin in present-day geographic coordinates and four tectono-paleogeographic maps of Tarim Basin in paleogeographic coordinates during the early Paleozoic are reconstructed, which directly show the changes of sedimentary and uplift-depression pattern caused by the transformation of the tectonic environment from extension to compression. In the Cambrian, the Tarim Basin was controlled by the extensional tectonic environment, with the sedimentary framework of “carbonate platform in the west, deep-water basin in the east”. At the end of the Ordovician, the Kudi Ocean and the North Altyn Ocean were closed, and the Central and South Kunlun terrane and the Altyn-Qilian terrane were collaged with the Tarim block, which directly led to the transformation of the uplift-depression pattern in the Tarim Basin from east-west differentiation to north-south differentiation, thus changing the sedimentary environment of the Tarim Basin in the late Ordovician to Silurian.
Seasonal constraints on the burial of organic carbon in the eutrophic Lake Taihu
Authors: Xu Yanhong , He Yuxin , Pang Jiali , Sun Yongge
Published: February 2023

Eutrophication alters the function of lake ecosystems through phytoplankton blooms and is a major contributor to organic carbon (OC) burial in lakes worldwide. Although Lake Taihu is notable for its severe eutrophication yet low OC burial, why cyanobacteria-derived OC is ineffectively buried in the lake is unknown. Because seasonal hydrological and ecological dynamics in eutrophic lacustrine ecosystems would significantly modify the preservation and degradation behaviors of OC, seasonal variations in paired particulate samples from both the water column and surface sediment are critical in evaluating cyanobacteria-derived OC burial. In this study, we present the steroid results of water and sediments collected from Meiliang Bay in Lake Taihu across cyanobacteria-bloom and decay seasons (from May 2018 to June 2019) to investigate constraints on the seasonal burial of autochthonous and allochthonous OC. The results indicate that cyanobacteria contribute a considerable amount of OC to the water body in the cyanobacterial bloom season, while terrestrial OC becomes the main contributor during the cyanobacterial decay season. Although OC degradation occurs throughout the water column, substantially more OC degradation was observed at the water-sediment interface. The extensive degradation of OC in the bloom season eventually reverses the seasonal distribution characteristics of particulate OC in the water column, leading to less accumulation of OC under the background of higher cyanobacteria-derived OC input. The combined effect of OC bioavailability, temperature, oxygen exposure, and more importantly microorganism activities, accounts for much higher OC degradation rates in the bloom season. Similar phenomena were observed in subtropical shallow lakes with high primary productivity, suggesting that eutrophication might have a limited influence on OC burial when compared to other factors related to OC degradation.
Evolution characteristics of impact weather system and SST signals during years of anomalous Meiyu onset over the Yangtze-Huaihe River Basin
Authors: Jin Xiaoxia , Ma Yutong , Liu Mei , Zhong Shanshan
Published: February 2023

This article investigates the climatic characteristics of Meiyu over the Yangtze-Huaihe River Basin and the primary impact system based on Meiyu onset data from 1954 to 2020, precipitation during the Meiyu Period, NCEP/NCAR reanalysis data, sea surface temperature (SST) data of NOAA, and western Pacific subtropical high (sub-high) data provided by the National Climate Center. The main analytical method used is synthetic analysis. The results indicate that the Meiyu onset date has enormous interannual variation. The date of the earliest Meiyu emergence is 27 days prior to the latest. There is a strong relationship between the duration of Meiyu and rainfall. The start of Meiyu correlates with the northward motion of the South Asia High, the northward jump of the westerly jet, the northward jump of the subtropical high, and the northward motion of the low-level jet. In the early Meiyu years featured in this study, the northward jump of the aforementioned systems occurred earlier and the position of the westerly jet shifted from 34–35°N to 38–40°N, which is much further north than its position under typical climatic circumstances. From late May to early June, the subtropical high was extraordinarily powerful, the ridgeline reached 20°N, and its position was further to the north. In years with a late Meiyu onset, the position of the westerly jet and the ridgeline were further south than the climatological average from early to late June; the jump to the north was not evident until late June. In addition, SST anomalies of the Indian Ocean and Pacific Ocean are significant external forcing variables that influence the Meiyu start date. The high SST of the equatorial Indian Ocean and the equatorial tropical eastern Pacific in the autumn of the preceding year and the high SST of the equatorial Indian Ocean in the spring of that year are prophase indicators of an early Meiyu start in the Yangtze-Huaihe River Basin.
“They just wanted to move on”: A qualitative study on the experiences of Black students in classroom discussions on race
Authors: Stewart Ashley Marie
Published: February 2023

The current study used qualitative methods to explore what classroom conversations around race and social justice look like for Black high school students and the role of technology in these conversations at a time when most students were engaged in hybrid or distance learning. Through semi-structured interviews, 16 students recounted their experiences discussing contemporary racial justice issues in school. Participants recalled experiences throughout their schooling in traditional classrooms and more recent incidents in the context of distance learning. Findings revealed that Black students take on much of the labor of educating their classmates and teachers about racial justice issues in class. They also highlighted the importance of safety when having these conversations. Concerning those discussions occurring in virtual settings, students described how technology promoted an environment in which Black students felt safer having these dialogues. Findings from this study emphasize the complex roles that Black students play in cultivating learning environments that raise the critical racial consciousness of everyone in the classroom, including teachers. Digital classrooms and spaces can also potentially serve as an environment in which Black students feel safe to explore and express their perspectives fully. These findings also further highlight the need to build the capacity of educators to facilitate conversations and hold space for all students to make sense of and cope when issues of racial injustice are at play and affecting students’ lives and mental health.
Identification of thyroid hormone response genes in the remodeling of dorsal muscle during Microhyla fissipes metamorphosis
Authors: Liu Lusha , Liu Qi , Zou Xue , Chen Qiheng , Wang Xungang , Gao Zexia , Jiang Jianping
Published: February 2023

Introduction

Extensive morphological, biochemical, and cellular changes occur during anuran metamorphosis, which is triggered by a single hormone, thyroid hormone (TH). The function of TH is mainly mediated through thyroid receptor (TR) by binding to the specific thyroid response elements (TREs) of direct response genes, in turn regulating the downstream genes in the cascade. The remodeling of dorsal skeletal muscle during anuran metamorphosis provides the perfect model to identify the immediate early and direct response genes that are important during apoptosis, proliferation, and differentiation of the muscle.

Methods

In our current study, we performed Illumina sequencing combined with single-molecule real-time (SMRT) sequencing in the dorsal muscle of Microhyla fissipes after TH, cycloheximide (CHX), and TH_CHX treatment.

Results and Discussion

We first identified 1,245 differentially expressed transcripts (DETs) after TH exposure, many of which were involved in DNA replication, protein processing in the endoplasmic reticulum, cell cycle, apoptosis, p53 signaling pathway, and protein digestion and absorption. In the comparison of the TH group vs. control group and TH_CHX group vs. CHX group overlapping gene, 39 upregulated and 6 downregulated genes were identified as the TH directly induced genes. Further analysis indicated that AGGTCAnnTnAGGTCA is the optimal target sequence of target genes for TR/RXR heterodimers in M. fissipes. Future investigations on the function and regulation of these genes and pathways should help to reveal the mechanisms governing amphibian dorsal muscle remodeling. These full-length and high-quality transcriptomes in this study also provide an important foundation for future studies in M. fissipes metamorphosis.
Network pharmacology and experimental validation to explore the potential mechanism of Sanjie Zhentong Capsule in endometriosis treatment
Authors: Guo Ruoyi , Yi Zhihui , Wang Yun , Wang Li
Published: February 2023

Purpose

Sanjie Zhentong Capsule (SZC) is gradually becoming widely used in the treatment of endometriosis (EMs) and has demonstrated an excellent curative effect in the clinic. However, the active components and mechanisms of Sanjie Zhentong Capsule (SZC) in the treatment of endometriosis (EMs) remain unclear, and further research is needed to explore the effects of Sanjie Zhentong Capsule (SZC).

Materials and methods

First, a drug target database of Sanjie Zhentong capsule (SZC) was established by consulting the TCMSP database and related literature. An endometriosis (EMs) disease target database was then established by consulting the GeneCards, OMIM and Drug Bank databases. The overlapping genes of SZC and EMs were determined, and protein-protein interactions (PPIs), gene ontology (GO) and Kyoto Gene and Genome Encyclopedia (KEGG) analyses were performed to predict the potential therapeutic mechanisms. Molecular docking was used to observe whether the key active ingredients and targets predicted by network pharmacology had good binding energy. Finally, in vitro experiments such as CCK-8, flow cytometry and RT-PCR assays were carried out to preliminarily verify the potential mechanisms.

Results

Through the construction of a pharmacological network, we identified a total of 28 active components in SZC and 52 potential therapeutic targets. According to GO and KEGG enrichment analyses, the effects of SZC treatment may be related to oxidative stress, steroid metabolism, apoptosis and proliferation. We also experimentally confirmed that SZC can regulate the expression of steroid hormone biosynthesis-related genes, inhibit ectopic endometrial stromal cell (EESC) proliferation and oxidative stress, and promote apoptosis.

Conclusion

This study explored the potential mechanism of SZC in the treatment of EMs through network pharmacology and experiments, providing a basis for further future research on SZC in the treatment of EMs.
Circulating biomarkers during progression to type 1 diabetes: A systematic review
Authors: Brenu Ekua W. , Harris Mark , Hamilton-Williams Emma E.
Published: February 2023

Aim

Progression to type 1 diabetes (T1D) is defined in stages and clinical disease is preceded by a period of silent autoimmunity. Improved prediction of the risk and rate of progression to T1D is needed to reduce the prevalence of diabetic ketoacidosis at presentation as well as for staging participants for clinical trials. This systematic review evaluates novel circulating biomarkers associated with future progression to T1D.

Methods

PubMed, Ovid, and EBSCO databases were used to identify a comprehensive list of articles. The eligibility criteria included observational studies that evaluated the usefulness of circulating markers in predicting T1D progression in at-risk subjects <20 years old.

Results

Twenty-six studies were identified, seventeen were cohort studies and ten were case control studies. From the 26 studies, 5 found evidence for protein and lipid dysregulation, 11 identified molecular markers while 12 reported on changes in immune parameters during progression to T1D. An increased risk of T1D progression was associated with the presence of altered gene expression, immune markers including regulatory T cell dysfunction and higher short-lived effector CD8+ T cells in progressors.

Discussion

Several circulating biomarkers are dysregulated before T1D diagnosis and may be useful in predicting either the risk or rate of progression to T1D. Further studies are required to validate these biomarkers and assess their predictive accuracy before translation into broader use.

Systematic review registration

https://www.crd.york.ac.uk/prospero, identifier (CRD42020166830).
A low-carbon-oriented multi-time-scale dispatching strategy of multi-energy heterogeneous loads in clean heating scenarios of green residences
Authors: Li Zekun , Sun Yi , Li Jiajun , Xiong Kui , Liang Siyuan , Shen Yaqi
Published: February 2023

Clean energy utilization is important for the improvement of energy structure. At present, photothermal and electrothermal conversion technologies are becoming increasingly applied in many homes, which can thus be regarded as green residences. To meet the heating demand of green residences, solar hot water systems and electricity-to-heat (E2H) conversion devices, such as ground source heat pumps electric heating stoves and electric water heaters are widely installed to provide a clean form of heat. Besides, common loads, such as lighting, washing, and electric vehicles are daily loads in green residences. The above electric and thermal loads are regarded as multi-energy heterogeneous loads MEHLs can be used to decarbonize green residences by optimizing energy dispatch through flexible control. In this study, a novel energy structure of green residences was extended through the combination of SHWs, E2H, GSHPs, and EVs, as well as rooftop photovoltaic systems. Then, to minimize carbon emissions, a residential energy dispatching model was designed from day-ahead and real-time scales and a low-carbon-oriented multi-energy heterogeneous loads coordinated control strategy was proposed. Finally, to mitigate the residents’ loss of comfort caused by MEHL control, the indoor environment and water tank temperatures and the state of charge of EVs were regarded as special constraints. The simulation revealed that the proposed strategy can reduce carbon emissions by 33.07% and meet the basic demand for residential heat and electricity. Additionally, the strategy has good applicability for decarbonizing green residences.
Research on carbon flow traceability system for distribution network based on blockchain and power flow calculation
Authors: Sun Heyang , Li Tong , Yang Chao , Zhang Yingli , Song Jinliang , Lei Zhenjiang , Gong Gangjun , Liu Yang
Published: February 2023

With the proposal of the two-carbon goal, energy conservation and emission reduction will become the focus of China’s energy system in the future for a long time to come. The establishment of a complete and efficient carbon traceability system will play an important role in promoting carbon emission reduction in the power system. Based on blockchain, this paper uses the consensus mechanism, time stamp, decentralization features, smart contract and other functions of blockchain, combined with the power flow calculation and the characteristics related to carbon emission and active power of the generator set, to obtain the corresponding carbon emission intensity of the generator set and carbon flow rate. It realizes the calculation and tracing of carbon emission flow in power distribution network and ensures the reliability of carbon traceability results, high efficiency of information transmission and transparency of traceability process. Firstly, based on the characteristics of the master-slave multi-chain structure in the consortium chain, In this paper, high-voltage substation nodes are the main chain nodes, and carbon flow tracing and calculation are carried out for the associated low-voltage substations, and the information of high-voltage or low-voltage substation nodes is guaranteed to be tamper-free through the hash anchoring method. The master-slave multi-chain model adopted in this paper is that the main chain adopts EA-DPoS (Evaluation and Agent-DPoS) algorithm, the slave chain adopts improved PBFT algorithm, and the comprehensive evaluation and reward and punishment mechanism are introduced to complete the consensus. Secondly, considering the security requirements of the power system data and the fact that some nodes of the distribution network do not have powerful computing resources comparable to those of the power grid company or major nodes, this paper encrypts and decrypts relevant data in the main chain node by combining the smart contract of blockchain. Meanwhile, cloud service providers with computing resources are responsible for generator power distribution combined with power flow calculation and carbon emission intensity calculation of the generator set. The power grid company adopts the cloud computing framework based on the double check mechanism to calculate the carbon flow rate while verifying the correct calculation results of the cloud service provider, and finally realizes the safe and accurate tracing of the carbon flow of the distribution network.
Microplastics in a pelagic squid (Dosidicus gigas) from the Eastern tropical Pacific Ocean: Characteristics, spatial variation, and preliminary risk assessment
Authors: Wang Yaxin , Chen Xinjun
Published: February 2023

Despite concerns about the environmental impact of microplastics (MPs), knowledge of MP contamination levels in pelagic squid is lacking. This study investigated the stomach of an ecologically and commercially important but poorly known squid species, the jumbo squid Dosidicus gigas, found in the tropical and Southern temperate Pacific. We examined the characteristics and spatial distribution of MPs in fifty D. gigas (16.0–37.8 cm mantle length) and assessed potential MP pollution risks. MPs were detected in 50.0% of specimens and had an average abundance of 0.88 ± 1.12 items/individual and 0.24 ± 0.36 items/g stomach weight, and were sized 58.42–2,944.85 μm. The MPs were dominated by polyethylene terephthalate (31.82%) in polymer type, fragments (54.55%) and fibers (43.18%) in shape, and blue (59.59%) in color. All specimens could be evaluated as low risk. No statistically significant correlations were found between the MP abundances and D. gigas stomach weight, stomach fullness index, distance from the coast, and mantle length. While regression analyses showed that fuller stomachs contained larger MPs. Spatial variations in shape and polymer composition suggest that low-density fibrous MPs could be easily transported offshore by upwelling and/or ocean currents. These results indicate intraspecific variation in D. gigas MP contaminants and underscore the need to assess the potential site-specific ecotoxicological consequences of increased plastic pollution to pelagic squid.
Simulations reveal climate and legacy effects underlying regional beta diversity in alpine vegetation
Authors: Malanson George P. , Pansing Elizabeth R. , Testolin Riccardo , Jiménez-Alfaro Borja
Published: February 2023

Introduction

Whether the distribution and assembly of plant species are adapted to current climates or legacy effects poses a problem for their conservation during ongoing climate change. The alpine regions of southern and central Europe are compared to those of the western United States and Canada because they differ in their geographies and histories.

Methods

Individual-based simulation experiments disentangled the role of geography in species adaptations and legacy effects in four combinations: approximations of observed alpine geographies vs. regular lattices with the same number of regions (realistic and null representations), and virtual species with responses to either climatic or simple spatial gradients (adaptations or legacy effects). Additionally, dispersal distances were varied using five Gaussian kernels. Because the similarity of pairs of regional species pools indicated the processes of assembly at extensive spatiotemporal scales and is a measure of beta diversity, this output of the simulations was correlated to observed similarity for Europe and North America.

Results

In North America, correlations were highest for simulations with approximated geography and location-adapted species; those in Europe had their highest correlation with the lattice pattern and climate-adapted species. Only SACEU correlations were sensitive to dispersal limitation.

Discussion

The southern and central European alpine areas are more isolated and with more distinct climates to which species are adapted. In the western United States and Canada, less isolation and more mixing of species from refugia has caused location to mask climate adaptation. Among continents, the balance of explanatory factors for the assembly of regional species pools will vary with their unique historical biogeographies, with isolation lessening disequilibria.
Decomposition rate as an emergent property of optimal microbial foraging
Authors: Manzoni Stefano , Chakrawal Arjun , Ledder Glenn
Published: February 2023

Decomposition kinetics are fundamental for quantifying carbon and nutrient cycling in terrestrial and aquatic ecosystems. Several theories have been proposed to construct process-based kinetics laws, but most of these theories do not consider that microbial decomposers can adapt to environmental conditions, thereby modulating decomposition. Starting from the assumption that a homogeneous microbial community maximizes its growth rate over the period of decomposition, we formalize decomposition as an optimal control problem where the decomposition rate is a control variable. When maintenance respiration is negligible, we find that the optimal decomposition kinetics scale as the square root of the substrate concentration, resulting in growth kinetics following a Hill function with exponent 1/2 (rather than the Monod growth function). When maintenance respiration is important, optimal decomposition is a more complex function of substrate concentration, which does not decrease to zero as the substrate is depleted. With this optimality-based formulation, a trade-off emerges between microbial carbon-use efficiency (ratio of growth rate over substrate uptake rate) and decomposition rate at the beginning of decomposition. In environments where carbon substrates are easily lost due to abiotic or biotic factors, microbes with higher uptake capacity and lower efficiency are selected, compared to environments where substrates remain available. The proposed optimization framework provides an alternative to purely empirical or process-based formulations for decomposition, allowing exploration of the effects of microbial adaptation on element cycling.
Identification of a basement membrane-based risk scoring system for prognosis prediction and individualized therapy in clear cell renal cell carcinoma
Authors: Tang Yanlin , Ye Chujin , Zeng Jiayi , Zhu Ping , Cheng Shouyu , Zeng Weinan , Yang Bowen , Liu Yanjun , Yu Yuming
Published: February 2023

Clear cell renal cell carcinoma (ccRCC) belongs to one of the 10 most frequently diagnosed cancers worldwide and has a poor prognosis at the advanced stage. Although multiple therapeutic agents have been proven to be curative in ccRCC, their clinical application was limited due to the lack of reliable biomarkers. Considering the important role of basement membrane (BM) in tumor metastasis and TME regulation, we investigated the expression of BM-related genes in ccRCC and identified prognostic BM genes through differentially expression analysis and univariate cox regression analysis. Then, BM-related ccRCC subtypes were recognized through consensus non-negative matrix factorization based on the prognostic BM genes and evaluated with regard to clinical and TME features. Next, utilizing the differentially expressed genes between the BM-related subtypes, a risk scoring system BMRS was established after serial analysis of univariate cox regression analysis, lasso regression analysis, and multivariate cox regression analysis. Time-dependent ROC curve revealed the satisfactory prognosis predictive capacity of BMRS with internal, and external validation. Multivariate analysis proved the independent predictive ability of BMRS and a BMRS-based nomogram was constructed for clinical application. Some featured mutants were discovered through genomic analysis of the BMRS risk groups. Meanwhile, the BMRS groups were found to have distinct immune scores, immune cell infiltration levels, and immune-related functions. Moreover, with the help of data from The Cancer Immunome Atlas (TCIA) and Genomics of Drug Sensitivity in Cancer (GDSC), the potential of BMRS in predicting therapeutic response was evaluated and some possible therapeutic compounds were proposed through ConnectivityMap (CMap). For the practicability of BMRS, we validated the expression of BMRS-related genes in clinical samples. After all, we identified BM-related ccRCC subtypes with distinct clinical and TME features and constructed a risk scoring system for the prediction of prognosis, therapeutic responses, and potential therapeutic agents of ccRCC. As ccRCC systemic therapy continues to evolve, the risk scoring system BMRS we reported may assist in individualized medication administration.
Rare copy number variation analysis identifies disease-related variants in atrioventricular septal defect patients
Authors: Hu Huan , Geng Zilong , Zhang Shasha , Xu Yuejuan , Wang Qingjie , Chen Sun , Zhang Bing , Sun Kun , Lu Yanan
Published: February 2023

Atrioventricular septal defect (AVSD) is a deleterious subtype of congenital heart diseases (CHD) characterized by atrioventricular canal defect. The pathogenic genetic changes of AVSD remain elusive, particularly for copy number variation (CNV), a large segment variation of the genome, which is one of the major forms of genetic variants resulting in congenital heart diseases. In the present study, we recruited 150 AVSD cases and 100 healthy subjects as controls for whole exome sequencing (WES). We identified total 4255 rare CNVs using exon Hidden Markov model (XHMM) and screened rare CNVs by eliminating common CNVs based on controls and Database of Genomic Variants (DGV). Each patient contained at least 9 CNVs, and the CNV burden was prominently presented in chromosomes 19,22,21&16. Small CNVs (<500 kb) were frequently observed. By leveraging gene-based burden test, we further identified 20 candidate AVSD-risk genes. Among them, DYRK1A, OBSCN and TTN were presented in the core disease network of CHD and highly and dynamically expressed in the heart during the development, which indicated they possessed the high potency to be AVSD-susceptible genes. These findings not only provided a roadmap for finally unveiling the genetic cause of AVSD, but also provided more resources and proofs for clinical genetics.
Geographic distribution, clinical epidemiology and genetic diversity of the human oncogenic retrovirus HTLV-1 in Africa, the world’s largest endemic area
Authors: Gessain Antoine , Ramassamy Jill-Léa , Afonso Philippe V. , Cassar Olivier
Published: February 2023

The African continent is considered the largest high endemic area for the oncogenic retrovirus HTLV-1 with an estimated two to five million infected individuals. However, data on epidemiological aspects, in particular prevalence, risk factors and geographical distribution, are still very limited for many regions: on the one hand, few large-scale and representative studies have been performed and, on the other hand, many studies do not include confirmatory tests, resulting in indeterminate serological results, and a likely overestimation of HTLV-1 seroprevalence. For this review, we included the most robust studies published since 1984 on the prevalence of HTLV-1 and the two major diseases associated with this infection in people living in Africa and the Indian Ocean islands: adult T-cell leukemia (ATL) and tropical spastic paraparesis or HTLV-1-associated myelopathy (HAM/TSP). We also considered most of the book chapters and abstracts published at the 20 international conferences on HTLV and related viruses held since 1985, as well as the results of recent meta-analyses regarding the status of HTLV-1 in West and sub-Saharan Africa. Based on this bibliography, it appears that HTLV-1 distribution is very heterogeneous in Africa: The highest prevalences of HTLV-1 are reported in western, central and southern Africa, while eastern and northern Africa show lower prevalences. In highly endemic areas, the HTLV-1 prevalence in the adult population ranges from 0.3 to 3%, increases with age, and is highest among women. In rural areas of Gabon and the Democratic Republic of the Congo (DRC), HTLV-1 prevalence can reach up to 10-25% in elder women. HTLV-1-associated diseases in African patients have rarely been reported in situ on hospital wards, by local physicians. With the exception of the Republic of South Africa, DRC and Senegal, most reports on ATL and HAM/TSP in African patients have been published by European and American clinicians and involve immigrants or medical returnees to Europe (France and the UK) and the United States. There is clearly a huge underreporting of these diseases on the African continent. The genetic diversity of HTLV-1 is greatest in Africa, where six distinct genotypes (a, b, d, e, f, g) have been identified. The most frequent genotype in central Africa is genotype b. The other genotypes found in central Africa (d, e, f and g) are very rare. The vast majority of HTLV-1 strains from West and North Africa belong to genotype a, the so-called ‘Cosmopolitan’ genotype. These strains form five clades roughly reflecting the geographic origin of the infected individuals. We have recently shown that some of these clades are the result of recombination between a-WA and a-NA strains. Almost all sequences from southern Africa belong to Transcontinental a-genotype subgroup.
RASGRP2 is a potential immune-related biomarker and regulates mitochondrial-dependent apoptosis in lung adenocarcinoma
Authors: Liu Yongting , Ouyang Yanhong , Feng Ziyang , Jiang Zhaohui , Ma Jiayao , Zhou Xin , Cai Changjing , Han Ying , Zeng Shan , Liu Shanshan , Shen Hong
Published: February 2023

Background

Ras guanine nucleotide-releasing protein 2 (RASGRP2), one of the guanine nucleotide exchange factors (GEFs), has attracted much attention in recent years. However, the correlation between RASGRP2 and immune infiltration and malignant features in lung adenocarcinoma (LUAD) has rarely been mentioned.

Methods

The Limma package and the LASSO regression model were performed to screen for differentially expressed genes. Data from the TCGA and 5 GEO databases were used to explore the expression level of RASGRP2 in LUAD patients. A weighted co-expression network and LinkFinder module were established to find the related genes of RASGRP2. The ESTIMATE algorithm was used to analyze the correlation between RASGRP2 and immune infiltration in LUAD. Tumor-infiltrating immune cells were sorted and sequenced at the single-cell level to analyze differences in RASGRP2. Real-time PCR and immunohistochemistry were performed in the real-world cohort to verify the expression of RASGRP2 and its correlation with immune-related genes. Clone formation and EdU assays were used to verify the proliferation ability. The proportion of apoptotic cells was analyzed by flow cytometry. Observation of mitochondrial membrane potential (MMP) changes by fluorescence microscopy.

Results

Our results suggested that decreased RASGRP2 was associated with worse clinical parameters and prognosis in LUAD patients. And we constructed a FLI1-HSA-miR-1976-RASGRP2 transcriptional network to support the role of RASGRP2. Enrichment analysis revealed that RASGRP2 was involved in lymphocyte activation and leukocyte adhesion. RASGRP2 was found to be positively correlated with the infiltration of most immune cells, immunoregulators, and chemokines in a subsequent study. Meanwhile, the real-world cohort confirmed that the expression levels of PDCD1, CTLA4, CD40LG, CCL14, CXCR5, and CCR7 were higher in the high-RASGRP2 expression group. Cytological experiments proved that RASGRP2 inhibited cell proliferation in LUAD by regulating mitochondrial-dependent apoptosis.

Conclusion

RASGRP2 was a potential immune-related biomarker of LUAD. In addition, RASGRP2 was involved in the malignant progression of LUAD through the regulation of mitochondrial-dependent apoptosis.
Precision-engineering of subunit vaccine particles for prevention of infectious diseases
Authors: Chen Shuxiong , Pounraj Saranya , Sivakumaran Nivethika , Kakkanat Anjali , Sam Gayathri , Kabir Md. Tanvir , Rehm Bernd H. A.
Published: February 2023

Vaccines remain the best approach for the prevention of infectious diseases. Protein subunit vaccines are safe compared to live-attenuated whole cell vaccines but often show reduced immunogenicity. Subunit vaccines in particulate format show improved vaccine efficacy by inducing strong immune responses leading to protective immunity against the respective pathogens. Antigens with proper conformation and function are often required to induce functional immune responses. Production of such antigens requiring post-translational modifications and/or composed of multiple complex domains in bacterial hosts remains challenging. Here, we discuss strategies to overcome these limitations toward the development of particulate vaccines eliciting desired humoral and cellular immune responses. We also describe innovative concepts of assembling particulate vaccine candidates with complex antigens bearing multiple post-translational modifications. The approaches include non-covalent attachments (e.g. biotin-avidin affinity) and covalent attachments (e.g. SpyCatcher-SpyTag) to attach post-translationally modified antigens to particles.
Chlorophyll and POC in polar regions derived from spaceborne lidar
Authors: Zhang Zhenhua , Chen Peng , Zhong Chunyi , Xie Congshuang , Sun Miao , Zhang Siqi , Chen Su , Wu Danchen
Published: February 2023

Polar regions have the most productive ecosystems in the global ocean but are vulnerable to global climate changes. Traditionally, the long-term changes occurred in an ecosystem are studied by using satellite-derived estimates of passive ocean color remote sensing measurements. However, this technology is severely limited by the inability to observe high-latitude ocean areas during lengthy polar nights. The spaceborne lidar can address the limitations and provide a decade of uninterrupted polar observations. This paper presents an innovative feed-forward neural network (FFNN) model for the inversion of subsurface particulate backscatter coefficients (bbp), chlorophyll concentration (Chl), and total particulate organic carbon (POC) from the spaceborne lidar. Non-linear relationship between lidar signal and bio-optical parameters was estimated through FFNN. The inversion results are in good agreement with biogeochemical Argo data, indicating the accuracy of the method. The annual cycles of Chl and POC were then analyzed based on the inversion results. We find that Chl, bbp, and POC have similar interannual variability but there are some subtle differences between them. Light limitation appears to be a dominant factor controlling phytoplankton growth in polar regions according to the results. Overall, the combined analysis of bbp, Chl, and POC contributes to a comprehensive understanding of interannual variability in the ecosystem in polar regions.
Exploring reconfiguration of trends in CPUE to model sustainable TAC options for the pivotal YSLME anchovy fishery
Authors: Han Qingpeng , Shan Xiujuan , Jin Xianshi , Gorfine Harry
Published: February 2023

Sustainable utilization of exploited fish stocks generally relies on characterizing key aspects of their population dynamics using mathematical models to evaluate their stock status. In this study, the Anchovy population (Engraulis japonicus) in the Yellow Sea large marine ecosystem (YSLME) was evaluated by using the ‘Just Another Bayesian Biomass Assessment’ (JABBA) model. Catch and the anchovy scientific survey biomass index data from 1989 to 2021 in its nominal or raw form, plus three adjusted CPUE trends using data acquired from the China Fishery Statistical Yearbook were each used to fit JABBA to explore the performance of reconfigured CPUE for setting a total allowable catch (TAC) quota to sustain the YSLME commercial anchovy fishery. Results showed contrasting trends in estimated biomass from the fishery independent surveys, and nominal and reconfigured commercial fishery CPUE, with the latter producing the most plausible results. The JABBA output based on the scientific survey biomass index indicated a 56.7% probability that the anchovy stock is currently healthy with 1.04B2021/BMSYand 0.51F2021/FMSYratios, whereas JABBA estimates based on the nominal commercial CPUE-based were overly optimistic (100% probability stock was healthy). JABBA outputs based on the first two reconfigured CPUEs (FacpueyandFECcpuey) countered this overoptimism, with the survey biomass index-based assessment results lying between the extremes. This improvement in the modelled assessment was achieved because the reconfigured CPUE time series accommodated technological progress in fishing vessels and gear performance. Therefore, in instances where survey biomass index data are unavailable, we recommend using the two improved fishery CPUEs and combining the results of the two assessments to guide fishery management. Management reference points, however, should preferably be based on the more conservative of the two reconfigured CPUEs as a precautionary approach for setting a total allowable catch (TAC) whilst concomitantly considering the role of anchovy as prey for other economically important fish in the system.We encourage researchers to extensively review and improve the quality and availability of fisheries statistical data worldwide in the shared endeavour towards obtaining more realistic stock assessments.
Comprehensive evaluation of growth characteristics, nitrogen removal capacity, and nutritional properties of three diet microalgae
Authors: Zhang Lin , Han Jichang , Ma Shuonan , Zhang Yuanbo , Wang Yumeng , Xu Jilin
Published: February 2023

Nitrogen is one of the main pollution sources in aquaculture system. Microalgae are considered as one of the ideal bio-absorbents used in wastewater purification, due to their nitrogen removal capacity and more importantly nutritional value. Nannochloropsis oceanica, Cyclotella atomus, and Conticribra weissflogii are famous as diet microalgae. However, estimation of nitrogen removal capability and concomitant nutritional properties of the three species have been rarely reported, which was performed in this study. N. oceanica, C. atomus, and C. weissflogii were cultivated with two initial nitrate-N concentration, noted as NC (13.85 mg·L–1) and NW (5 mg·L–1) groups, respectively. All the three microalgal strains in NC group showed higher maximum cell density, specific growth rate, and biomass concentration, maximal quantum yield of PSII (Fv/Fm), total Chlorophyll and carotenoids contents than that in NW group. These results confirmed the importance of nitrogen for microalgal biomass generation and photosynthetic performance. From Fv/Fm, N. oceanica has better adaptability towards nitrogen depletion compared to other two selected strains. The three microalgae exhibited significantly stronger nitrate-N absorption efficiencies in NC group at the same timepoint, compared to NW. Analyzing the average amount of nitrate-N absorbed by each cell daily, C. weissflogii gained the largest value, followed successively by C. atomus and N. oceanica, likely due to species specificity. Moreover, three strains removed 90% of nitrate-N within five days and 99% of that within seven days, showing splendid nitrogen removal potentials. These results confirmed the feasibility of removing nitrogen from wastewater with the selected three microalgae. Nutritional properties of microalgal biomass were also investigated. For the three species, lower nitrate-N was beneficial for the production of soluble sugar, total lipid, and saturated fatty acid, while higher nitrate-N led to more soluble protein and polyunsaturated fatty acid. In summary, N. oceanica, C. atomus, and C. weissflogii all showed strong nitrogen removal capacity, whose growth characteristics and nutritional properties varied with nitrogen concentration. In practical application for assimilating nitrogen, these findings could provide some references for the selection of suitable microalgae species in order to satisfy different nutritional requirements of various aquatic animals.