bluuebunny/crossref_metadata_2025 huggingface dataset:
CD8+T Cell-Related Gene Biomarkers in Macular Edema of Diabetic Retinopathy
Authors: Huang Jing , Zhou Qiong
Published: July 2022

Background

CD8+T lymphocytes have a strong pro-inflammatory effect in all parts of the tissue, and some studies have demonstrated that its concentration in the vitreous increased significantly, suggesting that CD8+T cells play a pivotal role in the inflammatory response of diabetic retinopathy (DR). However, the infiltration of CD8+T cells in the DR retina, especially in diabetic macular edema (DME), and its related genes are still unclear.

Methods

Download the GSE16036 dataset from the Gene Expression Omnibus (GEO) database. The ImmuCellAI program was performed to evaluate the abundance of 24 immune cells including CD8+T cells. The CD8+T cell-related genes (DECD8+TRGs) between non-proliferative diabetic retinopathy (NPDR) and DME were detectedviadifference analysis and correlation analysis. Enrichment analysis and protein-protein interaction (PPI) network mapping were implemented to explore the potential function of DECD8+TRGs. Lasso regression, support vector machine recursive feature elimination (SVM-RFE), CytoHubba plug-in and MCODE plug-in in Cytoscape software, and Weighted Gene Co-Expression Network Analysis (WGCNA) were performed to comprehensively analyze and obtain Hub DECD8+TRGs. Hub DECD8+TRGs expression patterns were further validated in other two DR-related independent datasets. The CD8+TRG score was defined as the genetic characterization of Hub DECD8+TRGs using the GSVA sample scoring method, which can be administered to distinguish early and advanced diabetic nephropathy (DN) as well as normal and DN. Finally, the transcription level of DECD8+TRGs in DR model mouse were verified by quantitative real-time PCR (qPCR).

Results

A total of 371 DECD8+TRGs were identified, of which 294 genes were positively correlated and only 77 genes were negatively correlated. Eight genes (IKZF1, PTPRC, ITGB2, ITGAX, TLR7, LYN, CD74, SPI1) were recognized as Hub DECD8+TRGs. DR and DN, which have strong clinical correlation, have been proved to be associated with CD8+T cell-related hub genes by multiple independent data sets. Hub DECD8+TRGs can not only distinguish PDR from normal and DN from normal, but also play a role in the early and progressive stages of the two diseases (NPDR vs DME, Early DN vs Advanced DN). The qPCR transcription level and trend of Hub DECD8+TRGs in DR mouse model was basically the same as that in human transcriptome.

Conclusion

This study not only increases our understanding of the molecular mechanism of CD8+T cells in the progression of DME, but also expands people’s cognitive vision of the molecular mechanism of crosstalk of CD8+T cells in the eyes and kidneys of patients with diabetes.
A predictive scoring system for proximal junctional kyphosis after posterior internal fixation in elderly patients with chronic osteoporotic vertebral fracture: A single-center diagnostic study
Authors: Du Xing , Jiang Guanyin , Zhu Yong , Luo Wei , Ou Yunsheng
Published: July 2022

Objective

To establish a predictive scoring system for proximal junctional kyphosis (PJK) after posterior internal fixation in elderly patients with chronic osteoporotic vertebral fracture (COVF).

Materials and methods

The medical records of 88 patients who were diagnosed with COVF and underwent posterior internal fixation in our hospital from January 2013 to December 2017 were retrospectively analyzed. The included patients were divided into two groups according to whether they suffered PJK after surgery, namely, the PJK group (25 cases) and non-PJK group (63 cases). The following clinical characteristics were recorded and analyzed: age, gender, body mass index (BMI), bone mineral density (BMD), smoking history, fracture segment, proximal junction angle, sagittal vertebral axis, pelvic incidence (PI)–lumbar lordosis (LL), pelvic tilt (PT), sacral slope (SS), posterior ligamentous complex (PLC) injury, upper instrumented vertebra, lower instrumented vertebra, and the number of fixed segments. The prevalence of these clinical characteristics in the PJK group was evaluated, and the scoring system was established using logistic regression analysis. The performance of the scoring system was also prospectively validated.

Results

The predictive scoring system was established based on five clinical characteristics confirmed as significant predictors of PJK, namely, age > 70 years, BMI > 28 kg/m2, BMD < −3.5 SD, preoperative PI-LL > 20°, and PLC injury. PJK showed a significantly higher score than non-PJK (7.80 points vs. 2.83 points, t=9.556, P<0.001), and the optimal cutoff value for the scoring system was 5 points. The sensitivity and specificity of the scoring system for predicting postoperative PJK were 80.00% and 88.89%, respectively, in the derivation set and 75.00% and 80.00% in the validation set.

Conclusion

The predictive scoring system was confirmed with satisfactory sensitivity and specificity in predicting PJK after posterior internal fixation in elderly COVF patients. The risk of postoperative PJK in patients with a score of 6–11 is high, while the score of 0–5 is low.
Dual protective role of velutin against articular cartilage degeneration and subchondral bone loss via the p38 signaling pathway in murine osteoarthritis
Authors: Wang Kelei , Lu Xuanyuan , Li Xinyu , Zhang Yufeng , Xu Rongjian , Lou Yun , Wang Yanben , Zhang Tan , Qian Yu
Published: July 2022

Osteoarthritis (OA) is a common degenerative joint condition associated with inflammation and characterized by progressive degradation of the articular cartilage and subchondral bone loss in the early stages. Inflammation is closely associated with these two major pathophysiological changes in OA. Velutin, a flavonoid family member, reportedly exerts anti-inflammatory effects. However, the therapeutic effects of velutin in OA have not yet been characterized. In this study, we explore the effects of velutin in an OA mouse model. Histological staining and micro-CT revealed that velutin had a protective effect against cartilage degradation and subchondral bone loss in an OA mouse model generated by surgical destabilization of the medial meniscus (DMM). Additionally, velutin rescued IL-1β-induced inflammation in chondrocytes and inhibited RANKL-induced osteoclast formation and bone resorption in vitro. Mechanistically, the p38 signaling pathway was found to be implicated in the inhibitory effects of velutin. Our study reveals the dual protective effects of velutin against cartilage degradation and subchondral bone loss by inhibiting the p38 signaling pathway, thereby highlighting velutin as an alternative treatment for OA.
An online tool for predicting ovarian reserve based on AMH level and age: A retrospective cohort study
Authors: Han Yong , Xu Huiyu , Feng Guoshuang , Wang Haiyan , Alpadi Kannan , Chen Lixue , Zhang Mengqian , Li Rong
Published: July 2022

Purpose

To establish a more convenient ovarian reserve model with anti-Müllerian hormone (AMH) level and age (the AA model), with blood samples taken at any time in the menstrual cycle.

Methods

We have established this AA model for predicting ovarian reserve using the AMH level and age. The outcome variable was defined as poor ovarian response (POR) with <5 oocytes retrieved during assisted reproductive technology treatment cycles. Least Absolute Shrinkage and Selection Operator logistic regression with 5-fold cross validation methods was applied to construct the model, and that with the lowest scaled log-likelihood was selected as the final one.

Results

The areas under the receiver operating characteristic curve for the training, inner, and external validation sets were 0.862, 0.843, and 0.854 respectively. The main effects of AMH level and age contributing to the prediction of POR were 95.3% and 1.8%, respectively. The incidences of POR increased with its predicted probability in both the model building and in external validation datasets, indicating its stability. An online website-based tool for assessing the score of ovarian reserve (http://121.43.113.123:9999) has been developed.

Conclusions

Based on external validation data, the AA model performed well in predicting POR, and was more cost-effective and convenient than our previous published models.
Case Report: Insulinoma Co-Existing With Type 2 Diabetes – Advantages and Challenges of Treatment With Endoscopic Ultrasound-Guided Radiofrequency Ablation
Authors: Chang Johnny Yau-Cheung , Woo Chariene Shao-Lin , Lui David Tak-Wai , Fung Matrix Man-Him , Lee Alan Chun-Hong , Leung Eunice Ka-Hong , Woo Yu-Cho , Chow Wing-Sun , Lam Karen Siu-Ling , Tan Kathryn Choon-Beng , Lee Chi-Ho
Published: July 2022

The coexistence of insulinoma and type 2 diabetes is rare and the diagnostic process is often challenging. Continuous glucose monitoring system devices, which are more readily available nowadays, provide a useful tool for the diagnosis and evaluation of treatment response. Curative surgery is often the mainstay of treatment for insulinoma. Here, we report a Chinese patient with insulinoma diagnosed simultaneously with type 2 diabetes. His insulinoma was managed with endoscopic ultrasound guided-radiofrequency ablation (EUS-RFA) and the patient achieved complete resolution of hypoglycaemic episodes. The case illustrates that while EUS-RFA is an emerging non-invasive treatment modality for pancreatic lesions, limitations exist especially when histological confirmation is essential.
Fifth Generation Mobile Communication Technology Network Attack Defense Based on Software Defined network Technology in Power Internet of Things
Authors: Li Tong , Zhao Hai , Song Shouyou , Yang Chao , Du Chunlai , Liu Yang
Published: July 2022

The purpose is to guarantee the security of fifth generation mobile communication technology (5G) network in power Internet of Things environment and improve the ability of wireless network communication to resist attacks. First, in terms of attack prevention, the 5G network security structure is proposed to replace the plaintext information commonly used in the original system with Ciphertext based on software defined network (SDN), thereby alleviating the security risks of the data dimension. Second, concerning attack detection, the signal is identified by using the imperfections and differences of equipment manufacturing based on the above security structure, preventing the attacker from further harming the sensitive data leaked. Researchers found that the SDN-based 5G network attack prevention scheme avoids the centralized exposure of sensitive data, improves security, reduces computational overhead, and simplifies encryption logic. Without affecting the bandwidth, the existing 5G network system is greatly prevented from attacks. The detection mechanism is not limited by the low-dimensional feature space, and it demonstrates strong robustness and stability. It can effectively detect the attacks on 5G network system in power Internet of Things (IoT). This study provides an important reference for the protection of 5G communication network attacks under IoT.
Responses of Functional and Taxonomic Phytoplankton Diversity to Environmental Gradients in Subtropical and Tropical Reservoirs
Authors: Santos Juliana B. O. , Brasil Jandeson , Huszar Vera L. M.
Published: July 2022

Understanding the influence of environmental conditions on biodiversity is a major task in ecology. We investigated how phytoplankton taxonomic (TD) and functional (FD) diversities vary with environmental factors in eight subtropical and tropical reservoirs. We hypothesized that i) environmental variables affect phytoplankton TD and FD; ii) FD provides better relationships to environmental changes than TD, and; iii) indices based on biomass are better related to the environment than those based on identities. The relationships between phytoplankton diversities and environmental drivers were assessed through generalized linear models. Our hypotheses were partly confirmed. TD and FD were, in fact, dependent on the environment, with higher values occurring in warmer, clearer, and more enriched systems, under lower zooplankton grazing pressure; but FD based on identities was not predicted better from environmental conditions than TD based on identities. As expected, indices based on biomass are better related to the environment than their counterpart based on identities.
Ciliates in man-made mountain reservoirs
Authors: Sommer Fabian , Sonntag Bettina , Rastl Nikolai , Summerer Monika , Tartarotti Barbara
Published: July 2022

Climate warming has multiple effects on an environment. Especially the Alpine region is affected by changing conditions, which do not only have ecological but also economic impacts in respect to winter sports tourism. Due to higher environmental temperatures and less precipitation, artificial snow making is becoming increasingly important and consequently, mountain reservoirs for water storage are built. In these systems, planktonic communities are not only influenced by the naturally harsh environmental conditions of the alpine region, but also by severe changes in water level fluctuations due to water withdrawal and re-filling within short time periods. Information on planktonic communities and species traits in such man-made water bodies is nonexistent. Here, we focused on ciliates, a group of unicellular protists known to adapt and respond rapidly to changing environmental conditions. Simultaneously, we identified abiotic and other biotic factors that shaped these microbial communities. We investigated the species composition, abundance and species traits of ciliates in eleven mountain reservoirs in the Tyrolean Alps, Austria, and hypothesized that these communities differed significantly from natural ones. The mountain reservoirs were investigated twice during the ice-free season and water chemistry, chlorophyll a, bacteria, zooplankton, and ciliates were sampled. We detected 48 ciliate taxa in total, with an average of five taxa per mountain reservoir. A wide range of abundance (summer: 24 to >15,600 Ind L−1; autumn: 38 to ∼7,500 Ind L−1) and no clear pattern in the community composition was found, most likely due to water level fluctuations and the source of water used for filling the mountain reservoirs. The ciliate abundance was significantly affected by pH, nutrients, but also water transparency and potential predators (crustaceans). Planktonic ciliates dominated the mountain reservoirs and, surprisingly, mixotrophic species, typically found in natural (alpine) lakes, were only rarely observed. Our data suggest that in these fast-changing systems, local factors seem to be more important than regional ones.
Soil Organic Carbon Pool and the Production of Goji Berry (Lycium barbarum L.) as Affected by Different Fertilizer Combinations Under Drip Fertigation
Authors: Wang Fang , Li Wenhui , Lin Yanmin , Nan Xiongxiong , Yuan Jingjing
Published: July 2022

Goji berries (Lycium barbarum L.), widely planted in arid to semi-arid regions, are a functional resource characterized by a homology of medicine and food. Changing extensive water and fertilizer management practices to drip fertigation is one of the most cost-effective ways to achieve the sustainable development of the Goji berry industry. This study explores the effects of different fertilizer combinations on the soil organic carbon pool and L. barbarum yield under drip fertigation in Ningxia, northwestern China. A two-year field experiment (2017–2019) was conducted using different levels of drip nitrogen (40, 60, and 80 mg L−1) and phosphorus (10, 20, and 30 mg L−1) fertigation. Compared with traditional manual fertilization (control), soil organic carbon contents in the 0–20, 20–40, and 40–60 cm layers increased by 33.6–144.4, 39.6–136.8, and 14.0–73.6%, respectively, across all fertigation treatments. With increasing levels of fertigation, the easily oxidizable organic carbon content increased most prominently in the 0–20 cm soil layer and reached the highest value (538 mg kg−1) under treatment with 60 mg L−1 nitrogen plus 10 mg L−1 phosphorus. The microbial biomass carbon contents in the 20–60 cm soil layer was markedly higher under treatment with 60 mg L−1 nitrogen plus 30 mg L−1 phosphorus compared with other treatments. Fertigation increased the soil carbon pool management index and L. barbarum yield. The highest two-year average yield (13,890 kg ha−1) was obtained under treatment with 60 mg L−1 nitrogen plus 30 mg L−1 phosphorus. These findings suggest that drip fertigation with 60 mg L−1 nitrogen plus 30 mg L−1 phosphorus is the optimal practice for carbon sequestration and sustainable production of L. barbarum in arid regions.
A study on the impact of extreme weather on the poverty vulnerability of farming households—evidence from six counties in the hubei and yunnan provinces of china
Authors: Chen Zhi , Yan Han , Yang Chao
Published: July 2022

By using micro-farm household survey data from six counties in the Hubei and Yunnan provinces, warm days, heavy precipitation, and consecutive dry days were selected as extreme weather measures, and the RClimDex software was used to empirically examine the impacts of extreme weather on farm household poverty vulnerability by setting percentile thresholds to measure extreme weather indicators in each district and county in 2017. Based on the improved Department for International Development sustainable livelihoods analysis framework, the entropy value method was used to synthesize the variables in the farm household sustainable livelihood capacity to examine their mediating effects. The results were as follows: 1) Extreme weather significantly affected farm household poverty vulnerability. Warm days were significantly and negatively related to farmers’ poverty vulnerability, while total heavy precipitation and consecutive dry days were significantly and positively related to farmers’ poverty vulnerability. 2) The impacts of extreme weather on farmers with different vulnerability characteristics varied. 3) The sustainable livelihood capacity of farm households played a partially mediating role in the process of extreme weather indicators of persistent drought index affecting the poverty vulnerability of farm households. 4) As compared to rural households engaged in non-agricultural industries, agricultural production and operation-based farming households were more vulnerable to shocks from extreme weather. Accordingly, we recommended that to improve farmers’ climate resilience, differentiated policies should be adopted according to local conditions; climate-sensitive vulnerable groups should be identified; agricultural insurance coverage should be expanded; farmers should be guided into entrepreneurship; and equalization of public services should be equalized so as to avoid farmers becoming impoverished due to extreme weather.
The Progressive Correlation Between Carbon Emission, Economic Growth, Energy Use, and Oil Consumption by the Most Prominent Contributors to Travel and Tourism GDPs
Authors: Khan Aarif Mohammad , Basit Asma , Khan Uzma , Khan Muhammad Kamran
Published: July 2022

Travel and tourism have glimpsed a significant and promising implication for economic development. Despite the commendatory implication of tourism, it levies a stringent environmental cost such as environmental degeneration. Hence, this study will incorporate the 18 countries out of the top 20 travel and tourism contributors to economic growth to assess the progressive correlation between tourist arrival, economic growth, energy consumption, and oil consumption on carbon emission by applying panel ARDL spanning from 1995 to 2019. The outcome of the panel ARDL reveals that both periods have witnessed that the endogenous variables have a substantial and positive impact on environmental degradation except for tourism as it indicates −0.22 and −0.48% in the long and short run, having a rate of adjustment as −0.52 toward the equilibrium. The simultaneous quantile regression reveals that in the 50 and 75 percentiles, the effect of tourism has a negative impact, which contradicts the PMG findings. These determinations suggest that the policymakers look for more manageable and environmentally sound tourism and economic growth procedures to safeguard the sustainable environment in the studied countries.
High Confident Evaluation for Smart City Services
Authors: Sheng Hao , Zhang Yang , Wang Wei , Shan Zhiguang , Fang Yufei , Lyu Weifeng , Xiong Zhang
Published: July 2022

This study aims to analyze massive data in cities through data vitalization, and quantitatively evaluate smart city services, so as to promote the construction and development of smart cities. Due to the great difference between cities, a single evaluation method cannot accurately describe the development of a city. In this study, we classify cities by multiple labels according to various bases to give cities comprehensive description. Then, a Multi-level Service Evaluation System (MSES) is introduced. It considers individual weights to cities with different characteristics and evaluates the smart city services from different aspects. In addition to putting forward the iterative development of smart city services, a Maturity Model-based Service Evaluation (MMSE) framework is proposed based on the evaluation results of the MSES. It constructs a standardized and high confident evaluation framework to analyze the current state of cities and make feedback to the government policies. Finally, we take 10 cities in China to demonstrate the effectiveness of MMSE during the development of smart city services.
Sustainability Assessment of Marine Economy in China: Spatial Distributions of Marine Environmental Governance Entities in Shanghai
Authors: Yang Debin , Geng Hong , Fu Yan-Kai , Zhu Ting
Published: July 2022

The amount of investment in marine environmental governance (MEG) is growing fast in China, which brought the prosperity of environmental treatment entities (e.g., water treatment enterprises and port pollution control institutions). Based on spatial big data, this paper adopted kernel density method, standard deviational ellipse, and nearest neighbor index to explore the spatial distribution pattern of MEG entities in Shanghai from 2005 to 2021. Several conclusions emerged from this study: (1) From 2005 to 2021, the new MEG entities in Shanghai have increased by more than 10 times; (2) The analysis showed that the nearest neighbor index of Shanghai’s MEG entities was larger than 0.2, with Z values all being lower than −30, indicating that the spatial agglomeration characteristics in Shanghai was significant at an alpha level of 1%. (3) Chongming District, Pudong New District, Fengxian District, and Minhang District were the core agglomeration areas. (4) The standard deviational ellipse analysis suggested that the distribution of Shanghai MEG entities from 2005 to 2021 showed an obvious pattern of spreading from the center to both the north and south. This results in an industrial belt along the Huangpu River. This paper argues that the spatial distribution of MEG entities in Shanghai confirms the central place theory, which highlights the network characteristics that combine centrality with spreading to the surrounding areas.
Understanding conflict and co-existence among Spiti Bhot community and large carnivores in high Himalaya: The case of Himalayan wolves
Authors: Lyngdoh Salvador , Habib Bilal
Published: July 2022

The wolves in the Hindukush–Himalayan region belong to one of the most basal lineages ofCanis lupus, yet little is known about their ecology and behavior. In this study, we determine wolf movement and analyze diet patterns in contrast with studies from within its distribution range. We determine conflict perception and identify hotspots using ecological, social, and remotely sensed information. Wolf diet (n= 283 scats) constituted mostly of domestic prey (79%), while wild prey constituted 17.8% of the wolf diet. Interview-based questionnaire surveys revealed that 55% of the respondents claimed to have seen wolves. Over 98% of the respondents claimed wolves as a possible threat to various livestock in the study area. Marginal response curves through the MaxEnt model showed that wolf hotspots were positive in response to their density of location, landuse-landcover, village population, village density, and depredation. Comparisons between scat- and questionnaire-based depredation data showed that the perceived levels of depredation by wolves differed significantly from the actual proportion of livestock prey species consumed by wolves (χ2 = 99.64,p-value < 0.0001). Wolf conflict hotspots showed a very high conflict zone area of 36 km2, high conflict zone of 62 km2, medium conflict zone of 196 km2, and low conflict zone of 3,636 km2. Future conflict mitigation strategies may focus on such areas primarily to reduce livestock losses and enhance conservation outcomes. Negative perceptions toward wolves can be managed through a holistic conservation action plan in concert with the existing snow leopard conservation program alongside local traditions that do not hinder livelihood security.
Full-Length Spatial Transcriptomics Reveals the Unexplored Isoform Diversity of the Myocardium Post-MI
Authors: Boileau Etienne , Li Xue , Naarmann-de Vries Isabel S , Becker Christian , Casper Ramona , Altmüller Janine , Leuschner Florian , Dieterich Christoph
Published: July 2022

We introduce Single-cell Nanopore Spatial Transcriptomics (scNaST), a software suite to facilitate the analysis of spatial gene expression from second- and third-generation sequencing, allowing to generate a full-length near-single-cell transcriptional landscape of the tissue microenvironment. Taking advantage of the Visium Spatial platform, we adapted a strategy recently developed to assign barcodes to long-read single-cell sequencing data for spatial capture technology. Here, we demonstrate our workflow using four short axis sections of the mouse heart following myocardial infarction. We constructed a de novo transcriptome using long-read data, and successfully assigned 19,794 transcript isoforms in total, including clinically-relevant, but yet uncharacterized modes of transcription, such as intron retention or antisense overlapping transcription. We showed a higher transcriptome complexity in the healthy regions, and identified intron retention as a mode of transcription associated with the infarct area. Our data revealed a clear regional isoform switching among differentially used transcripts for genes involved in cardiac muscle contraction and tissue morphogenesis. Molecular signatures involved in cardiac remodeling integrated with morphological context may support the development of new therapeutics towards the treatment of heart failure and the reduction of cardiac complications.
Pan-cancer analysis of the FAM83 family and its association with prognosis and tumor microenvironment
Authors: Yuan Shangkun , Huang Zhisheng , Qian Xiaoying , Wang Yong , Fang Chen , Chen Renfang , Zhang Xinwei , Xiao Zhehao , Wang Qian , Yu Biao , Li Yong
Published: July 2022

Family with sequence similarity 83 (FAM83) is a newly identified family of oncogenes whose members play important roles in signaling and cancer progression. However, a thorough understanding of the FAM83 family in tumors is still lacking. Here, we performed a comprehensive analysis of the expression levels of the FAM83 family across cancers and patient prognoses using bioinformatics methods. We found that the expression levels of FAM83 family genes were upregulated in most tumors, and importantly, high expression levels of FAM83 family genes were related to poor prognosis in most tumors. In addition, we analyzed the relationship of FAM83 family genes with immune subtypes and the tumor microenvironment (TME). The results showed that FAM83 family genes were significantly associated with immune infiltrative subtypes and to varying degrees with the level of stromal cell infiltration and tumor stem cells. Finally, our study also showed the relationship between FAM83 family genes and drug sensitivity. Therefore, this pan-cancer analysis demonstrates the critical role of FAM83 family genes in tumor development and provides new clues for therapeutic strategies for cancer.
Profiling a Community-Specific Function Landscape for Bacterial Peptides Through Protein-Level Meta-Assembly and Machine Learning
Authors: Vajjala Mitra , Johnson Brady , Kasparek Lauren , Leuze Michael , Yao Qiuming
Published: July 2022

Small proteins, encoded by small open reading frames, are only beginning to emerge with the current advancement of omics technology and bioinformatics. There is increasing evidence that small proteins play roles in diverse critical biological functions, such as adjusting cellular metabolism, regulating other protein activities, controlling cell cycles, and affecting disease physiology. In prokaryotes such as bacteria, the small proteins are largely unexplored for their sequence space and functional groups. For most bacterial species from a natural community, the sample cannot be easily isolated or cultured, and the bacterial peptides must be better characterized in a metagenomic manner. The bacterial peptides identified from metagenomic samples can not only enrich the pool of small proteins but can also reveal the community-specific microbe ecology information from a small protein perspective. In this study, metaBP (Bacterial Peptides for metagenomic sample) has been developed as a comprehensive toolkit to explore the small protein universe from metagenomic samples. It takes raw sequencing reads as input, performs protein-level meta-assembly, and computes bacterial peptide homolog groups with sample-specific mutations. The metaBP also integrates general protein annotation tools as well as our small protein-specific machine learning module metaBP-ML to construct a full landscape for bacterial peptides. The metaBP-ML shows advantages for discovering functions of bacterial peptides in a microbial community and increases the yields of annotations by up to five folds. The metaBP toolkit demonstrates its novelty in adopting the protein-level assembly to discover small proteins, integrating protein-clustering tool in a new and flexible environment of RBiotools, and presenting the first-time small protein landscape by metaBP-ML. Taken together, metaBP (and metaBP-ML) can profile functional bacterial peptides from metagenomic samples with potential diverse mutations, in order to depict a unique landscape of small proteins from a microbial community.
CD8TCEI-EukPath: A Novel Predictor to Rapidly Identify CD8+ T-Cell Epitopes of Eukaryotic Pathogens Using a Hybrid Feature Selection Approach
Authors: Hu Rui-Si , Wu Jin , Zhang Lichao , Zhou Xun , Zhang Ying
Published: July 2022

Computational prediction to screen potential vaccine candidates has been proven to be a reliable way to provide guarantees for vaccine discovery in infectious diseases. As an important class of organisms causing infectious diseases, pathogenic eukaryotes (such as parasitic protozoans) have evolved the ability to colonize a wide range of hosts, including humans and animals; meanwhile, protective vaccines are urgently needed. Inspired by the immunological idea that pathogen-derived epitopes are able to mediate the CD8+ T-cell-related host adaptive immune response and with the available positive and negative CD8+ T-cell epitopes (TCEs), we proposed a novel predictor called CD8TCEI-EukPath to detect CD8+ TCEs of eukaryotic pathogens. Our method integrated multiple amino acid sequence-based hybrid features, employed a well-established feature selection technique, and eventually built an efficient machine learning classifier to differentiate CD8+ TCEs from non-CD8+ TCEs. Based on the feature selection results, 520 optimal hybrid features were used for modeling by utilizing the LightGBM algorithm. CD8TCEI-EukPath achieved impressive performance, with an accuracy of 79.255% in ten-fold cross-validation and an accuracy of 78.169% in the independent test. Collectively, CD8TCEI-EukPath will contribute to rapidly screening epitope-based vaccine candidates, particularly from large peptide-coding datasets. To conduct the prediction of CD8+ TCEs conveniently, an online web server is freely accessible (http://lab.malab.cn/∼hrs/CD8TCEI-EukPath/).
Affective Risk Associated With Menstrual Cycle Symptom Change
Authors: Kiesner Jeff , Eisenlohr-Moul Tory A. , Vidotto Giulio
Published: July 2022

In the present study we test whether cyclical changes in affective symptoms of the menstrual cycle are associated with higher mean levels of those same symptoms. Using prospective daily reports across two full menstrual cycles, from two samples of female University students (n = 213; n = 163), we applied both quartic polynomial regressions and cosine regressions to model cyclical change in symptoms, and to test for mean-level differences in symptoms across the resulting trajectory patterns. Counter to prior findings, but consistent with theoretical expectations, these results show that females who experience menstrual cycle-related changes in affect (whether a perimenstrual or mid-cycle increase) are at risk for higher average levels of affective symptoms. These results suggest that the mid-cycle group should be recognized as a target for future research that is associated with increased risk for chronic negative affective symptoms.
Chemokines in progression, chemoresistance, diagnosis, and prognosis of colorectal cancer
Authors: Zou Qian , Lei Xue , Xu Aijing , Li Ziqi , He Qinglian , Huang Xiujuan , Xu Guangxian , Tian Faqing , Ding Yuanlin , Zhu Wei
Published: July 2022

Plenty of factors affect the oncogenesis and progression of colorectal cancer in the tumor microenvironment, including various immune cells, stromal cells, cytokines, and other factors. Chemokine is a member of the cytokine superfamily. It is an indispensable component in the tumor microenvironment. Chemokines play an antitumor or pro-tumor role by recruitment or polarization of recruiting immune cells. Meanwhile, chemokines, as signal molecules, participate in the formation of a cross talk among signaling pathways and non-coding RNAs, which may be involved in promoting tumor progression. In addition, they also function in immune escape. Chemokines are related to drug resistance of tumor cells and may even provide reference for the diagnosis, therapy, and prognosis of patients with colorectal cancer.
Role of the mucin-like glycoprotein FCGBP in mucosal immunity and cancer
Authors: Liu Qiao , Niu Xia , Li Yang , Zhang Jia-rui , Zhu Shao-jun , Yang Qi-yuan , Zhang Wei , Gong Li
Published: July 2022

IgGFc-binding protein (FCGBP) is a mucin first detected in the intestinal epithelium. It plays an important role in innate mucosal epithelial defense, tumor metastasis, and tumor immunity. FCGBP forms disulfide-linked heterodimers with mucin-2 and members of the trefoil factor family. These formed complexes inhibit bacterial attachment to mucosal surfaces, affect the motility of pathogens, and support their clearance. Altered FCGBP expression levels may be important in the pathologic processes of Crohn’s disease and ulcerative colitis. FCGBP is also involved in regulating the infiltration of immune cells into tumor microenvironments. Thus, the molecule is a valuable marker of tumor prognosis. This review summarizes the functional relevance and role of FCGBP in immune responses and disease development, and highlights the potential role in diagnosis and predicting tumor prognosis.
The landscape of chimeric antigen receptor T cell therapy in breast cancer: Perspectives and outlook
Authors: Zhang Hao , Zhu Shuangli , Deng Wanjun , Li Rui , Zhou Haiting , Xiong Huihua
Published: July 2022

Chimeric antigen receptor-T (CAR-T) cell therapy is a revolutionary adoptive cell therapy, which could modify and redirect T cells to specific tumor cells. Since CAR-T cell therapy was first approved for B cell-derived malignancies in 2017, it has yielded unprecedented progress in hematological tumors and has dramatically reshaped the landscape of cancer therapy in recent years. Currently, cumulative evidence has demonstrated that CAR-T cell therapy could be a viable therapeutic strategy for solid cancers. However, owing to the immunosuppressive tumor microenvironment (TME) and heterogenous tumor antigens, the application of CAR-T cell therapy against solid cancers requires circumventing more challenging obstacles. Breast cancer is characterized by a high degree of invasiveness, malignancy, and poor prognosis. The review highlights the underlying targets of CAR-T cell therapy in breast cancer, summarizes the challenges associated with CAR-T cell therapy, and proposes the strategies to overcome these challenges, which provides a novel approach to breast cancer treatment.
Effectiveness and Waning of Protection With Different SARS-CoV-2 Primary and Booster Vaccines During the Delta Pandemic Wave in 2021 in Hungary (HUN-VE 3 Study)
Authors: Vokó Zoltán , Kiss Zoltán , Surján György , Surján Orsolya , Barcza Zsófia , Wittmann István , Molnár Gergő Attila , Nagy Dávid , Müller Veronika , Bogos Krisztina , Nagy Péter , Kenessey István , Wéber András , Polivka Lőrinc , Pálosi Mihály , Szlávik János , Rokszin György , Müller Cecília , Szekanecz Zoltán , Kásler Miklós
Published: July 2022

Background

In late 2021, the pandemic wave was dominated by the Delta SARS-CoV-2 variant in Hungary. Booster vaccines were offered for the vulnerable population starting from August 2021.

Methods

The nationwide HUN-VE 3 study examined the effectiveness and durability of primary immunization and single booster vaccinations in the prevention of SARS-CoV-2 infection, Covid-19 related hospitalization and mortality during the Delta wave, compared to an unvaccinated control population without prior SARS-CoV-2 infection.

Results

The study population included 8,087,988 individuals who were 18–100 years old at the beginning of the pandemic. During the Delta wave, after adjusting for age, sex, calendar day, and chronic diseases, vaccine effectiveness (VE) of primary vaccination against registered SARS-CoV-2 infection was between 11% to 77% and 18% to 79% 14–120 days after primary immunization in the 16–64 and 65–100 years age cohort respectively, while it decreased to close to zero in the younger age group and around 40% or somewhat less in the elderly after 6 months for almost all vaccine types. In the population aged 65–100 years, we found high, 88.1%–92.5% adjusted effectiveness against Covid-19 infection after the Pfizer-BioNTech, and 92.2%–95.6% after the Moderna booster dose, while Sinopharm and Janssen booster doses provided 26.5%–75.3% and 72.9%–100.0% adjusted VE, respectively. Adjusted VE against Covid-19 related hospitalization was high within 14–120 days for Pfizer-BioNTech: 76.6%, Moderna: 83.8%, Sputnik-V: 78.3%, AstraZeneca: 73.8%, while modest for Sinopharm: 45.7% and Janssen: 26.4%. The waning of protection against Covid-19 related hospitalization was modest and booster vaccination with mRNA vaccines or the Janssen vaccine increased adjusted VE up to almost 100%, while the Sinopharm booster dose proved to be less effective. VE against Covid-19 related death after primary immunization was high or moderate: for Pfizer-BioNTech: 81.5%, Moderna: 93.2%, Sputnik-V: 100.0%, AstraZeneca: 84.8%, Sinopharm: 58.6%, Janssen: 53.3%). VE against this outcome also showed a moderate decline over time, while booster vaccine types restored effectiveness up to almost 100%, except for the Sinopharm booster.

Conclusions

The HUN-VE 3 study demonstrated waning VE with all vaccine types for all examined outcomes during the Delta wave and confirmed the outstanding benefit of booster vaccination with the mRNA or Janssen vaccines, and this is the first study to provide clear and comparable effectiveness results for six different vaccine types after primary immunization against severe during the Delta pandemic wave.
Human Lung Fibroblasts Exhibit Induced Inflammation Memory via Increased IL6 Gene Expression and Release
Authors: Yap Jennifer Maries Go , Ueda Takashi , Kanemitsu Yoshihiro , Takeda Norihisa , Fukumitsu Kensuke , Fukuda Satoshi , Uemura Takehiro , Tajiri Tomoko , Ohkubo Hirotsugu , Maeno Ken , Ito Yutaka , Oguri Testsuya , Ugawa Shinya , Niimi Akio
Published: July 2022

Fibroblasts of different origins are known to possess stromal memory after inflammatory episodes. However, there are no studies exploring human lung fibroblast memory which may predict a subsequent inflammatory response in chronic respiratory diseases and COVID-19. MRC-5 and HF19 human lung fibroblast cell lines were treated using different primary and secondary stimulus combinations: TNFα–WD–TNFα, Poly (I:C)–WD–TNFα, TNFα–WD–Poly (I:C), or LPS–WD–TNFα with a 24-h rest period (withdrawal period; WD) between the two 24-h stimulations. TLR3 and NF-κB inhibitors were used to determine pathways involved. The effect of SARS-Cov-2 spike protein to inflammatory response of lung fibroblasts was also investigated. mRNA expressions of genes and IL6 release were measured using qRT-PCR and ELISA, respectively. Statistical significance was determined by using one- or two-way ANOVA, followed by Bonferroni’s post hoc analysis for comparison of multiple groups. Preexposure with Poly (I:C) significantly increased TNFα-induced IL6 gene expression and IL6 release in both cell lines, while it affected neither gene expressions of IL1B, IL2, IL8, and MMP8 nor fibrosis-related genes: ACTA2, COL1A1, POSTN, and TGFB1. Inhibition of TLR3 or NF-κB during primary stimulation significantly downregulated IL6 release. Simultaneous treatment of MRC-5 cells with SARS-CoV-2 spike protein further increased TNFα-induced IL6 release; however, preexposure to Poly (I:C) did not affect it. Human lung fibroblasts are capable of retaining inflammatory memory and showed an augmented response upon secondary exposure. These results may contribute to the possibility of training human lung fibroblasts to respond suitably on inflammatory episodes after viral infection.
Orange Chromide, Pseudetroplus maculatus (Bloch., 1795): A Potential Euryhaline Fish Model to Evaluate Climate Change Adaptations in Fishes
Authors: Padinhate Purayil Suresh Babu , Thomas Shilta M. , Anirudhan Anuraj , Sidhick Jeena Nikarthil , Kandiyil Asokan Pillaru , Ebeneezar Sanal , Ignatius Boby , Achamveetil Gopalakrishnan
Published: July 2022

Orange chromide, Pseudetroplus maculatus is a euryhaline species with both ornamental and food value. The species has several attributes similar to other fish model organisms such as smaller size, repeated breeding, ease of maintenance, and higher fecundity. A salinity tolerance study was performed in different salinities (0, 15, and 35 ppt) in triplicate introducing 10 fishes each (5.4 ± 0.08 g) in 12 plastic tanks of 60 L water-holding capacity. Fish were fed with commercial feed (1.2 mm and 40% protein) at 5% of body weight twice daily for 45 days. No significant variation (p< 0.05) in growth and survival was observed during the study indicating the wide salinity tolerance for the species. Experimental breeding of the species in freshwater and seawater (35 ppt) revealed the ability of the species to breed in varying salinities. Lenience in captive broodstock development, pair formation, and year-round natural breeding makes the seed production of the species easier. Characteristics such as multiple spawnings, a prolonged incubation period (48 to 72 hours) useful for elaborative embryonic studies, shorter larval development cycle (25 to 30 days), and better acceptance of live feed (Artemia nauplii and flakes) and commercial feed by the larvae make the species a potential euryhaline ornamental fish model to assess the physiological changes at different salinities. Minimal input requirements and lower capital and operational investments for the seed production of the species make it an ideal model organism for studying the impact of climatic and environmental changes on fish farming in different habitats.
Influence of Rising Water Temperature on the Temperate Seagrass Species Eelgrass (Zostera marina L.) in the Northeast USA
Authors: Plaisted Holly K. , Shields Erin C. , Novak Alyssa B. , Peck Christopher P. , Schenck Forest , Carr Jillian , Duffy Paul A. , Evans N. Tay , Fox Sophia E. , Heck Stephen M. , Hudson Robbie , Mattera Trevor , Moore Kenneth A. , Neikirk Betty , Parrish David B. , Peterson Bradley J. , Short Frederick T. , Tinoco Amanda I.
Published: July 2022

Sea surface temperature (SST) has increased worldwide since the beginning of the 20th century, a trend which is expected to continue. Changes in SST can have significant impacts on marine biota, including population-level shifts and alterations in community structure and diversity, and changes in the timing of ecosystem events. Seagrasses are a group of foundation species that grow in shallow coastal and estuarine systems, where they provide many ecosystem services. Eelgrass, Zostera marina L., is the dominant seagrass species in the Northeast United States of America (USA). Multiple factors have been cited for losses in this region, including light reduction, eutrophication, and physical disturbance. Warming has the potential to exacerbate seagrass loss. Here, we investigate regional changes in eelgrass presence and abundance in relation to local water temperature using monitoring data from eight sites in the Northeastern USA (New Hampshire to Maryland) where a consistent monitoring protocol, SeagrassNet, has been applied. We use a hurdle model consisting of a generalized additive mixed model (GAMM) with binomial and beta response distributions for modeling eelgrass presence and abundance, respectively, in relation to the local summer average water temperature. We show that summer water temperature one year prior to monitoring is a significant predictor of eelgrass presence, but not abundance, on a regional scale. Above average summer temperatures correspond to a decrease in probability of eelgrass presence (and increased probability of eelgrass absence) the following year. Cooler than average temperatures in the preceding year, down to approximately 0.5°C below the site average, are associated with the highest predicted probability of eelgrass presence. Our findings suggest vulnerability in eelgrass meadows of the Northeast USA and emphasize the value of unified approaches to seagrass monitoring, conservation and management at the seascape scale.
Insight Into the Relation Between Nutritional Benefits of Aquaculture Products and its Consumption Hazards: A Global Viewpoint
Authors: Arshad Naufal , Samat Narimah , Lee Lai Kuan
Published: July 2022

Aquaculture plays a huge role in supporting the needs and demands of fish and other aquatic organisms globally. Being a vital contributor in the fisheries sector, aquatic sources derived from the aquaculture industry are well-known for their high nutritive values that are compromised with high-quality protein, essential omega-3 fatty acids, vitamins, and minerals. Aquaculture has also widened fish availability to regions and countries with limited access to farmed species, leading to improved nutrition and food security. However, the presence of dangerous contaminants, notably heavy metals, endocrine disrupting compounds, polycyclic aromatic hydrocarbons, microplastics, as well as antimicrobial drug residues, has been detected in the aquaculture products. In conjunction, the risk–benefit assessment (RBA) approach has been proposed to be used as a meaningful tool for evaluating the health impacts of the consumption of aquatic sources on the targeted population. This narrative review outlines a compilation of aquaculture products as a nutritional source for human consumption. The aquaculture industry is well-appreciated, especially in low-income countries, for achieving sustainable food security. The organoleptics and preferences of aquaculture products as means of dietary variations were demonstrated. The damaging contaminants contained in the commercially available aquaculture products were quantitatively outlined. Furthermore, the adaptation of the risk–benefit approach underlying its potent impacts on public health concerns, with its current challenges and limitations, is elucidated.