bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction and Validation of a novel signature for Immune response prediction in clear cell Renal Cell Carcinoma
Authors: Wu Nan , Gui Ziwei , Du Juan , Shen Ningning , Yang Zhiqing , Yang Huijun , Zeng Zixin , Lu Wei , Leng Zijia , Wei Rong , Ma Wenxia , Wang Chen 
Published: November 2022

Abstract
Background
clear cell renal cell carcinoma (ccRCC) is the most common renal malignancy, although newly developing targeted therapy and immunotherapy have been showing promising effects in clinical treatment, the effective biomarkers for immune response prediction are still lacking. The study is to construct a gene signature according to ccRCC immune cells infiltration landscape, thus aiding clinical prediction of patients response to immunotherapy.
Methods
Firstly, ccRCC transcriptome expression profiles from Gene Expression Omnibus (GEO) database as well as immune related genes information from IMMPORT database were combine applied to identify the differently expressed meanwhile immune related candidate genes in ccRCC comparing to normal control samples. Then, based on protein-protein interaction network (PPI) and following module analysis of the candidate genes, a hub gene cluster was further identified for survival analysis. Further, LASSO analysis was applied to construct a signature which was in succession assessed with Kaplan-Meier survival, Cox regression and ROC curve analysis. Moreover, ccRCC patients were divided as high and low-risk groups based on the gene signature followed by the difference estimation of immune treatment response and exploration of related immune cells infiltration by TIDE and Cibersort analysis respectively among the two groups of patients.
Results
Based on GEO and IMMPORT databases, a total of 269 differently expressed meanwhile immune related genes in ccRCC were identified, further PPI network and module analysis of the 269 genes highlighted a 46 genes cluster. Next step, Kaplan-Meier and Cox regression analysis of the 46 genes identified 4 genes that were supported to be independent prognosis indicators, and a gene signature was constructed based on the 4 genes. Furthermore, after assessing its prognosis indicating ability by both Kaplan-Meier and Cox regression analysis, immune relation of the signature was evaluated including its association with environment immune score, Immune checkpoint inhibitors expression as well as immune cells infiltration. Together, immune predicting ability of the signature was preliminary explored.
Conclusions
Based on ccRCC genes expression profiles and multiple bioinformatic analysis, a 4 genes containing signature was constructed and the immune regulation of the signature was preliminary explored. Although more detailed experiments and clinical trials are needed before potential clinical use of the signature, the results shall provide meaningful insight into further ccRCC immune researches.
Relationships between fatigue differential experience and anxiety, depression, and serum hormones among Chinese cancer survivors: a cross-sectional study
Authors: Gu Shanshan , Xu Yun , Zhu Xiaoshu , Lam Anderson , Gong Lutian , Wang Jinghui , Guo Xinyu , Fu Li , Shi Jiyan , Liu Ketan 
Published: November 2022

Abstract
Purpose: Previous research has demonstrated that different cancer survivors with the same disease history or treatment may have different experiences of fatigue. This study aims to explore how demographic, oncological, sociological, psychological, and serum hormone levels interact to influence the distinct experiences of fatigue (CRF occurrence and fatigue degree).
Methods: A cross-sectional study carried out at the oncology outpatient and ward department of Xiyuan Hospital of China Academy of Chinese Medical Sciences recruited 306 cancer patients between January 2021 to December 2021. Differences between groups were examined using chi-square and nonparametric testing, and binary and ordered logistic regression were used to explore the factors related with the prevalence of CRF and the aggravation of fatigue, respectively.
Results: Among the 306 patients, 229 (74.8%) were diagnosed with CRF, including 94 (41.0%) with mild fatigue, 121 (52.8%) with moderate fatigue, and 14 (6.1%) with severe fatigue. Multivariate regression analysis showed that higher depression scores, aldosterone levels may increase the risk of CRF. Patients who are obese (BMI ≥ 28 kg/m2) may help to reduce the risk of CRF. Other contributing factors for increased levels of fatigue (p < 0.05) include being female, having anxiety, depression and high aldosterone levels.
Conclusion: CRF was a common symptom in cancer survivors. Gender, BMI, emotional state, aldosterone levels may be influential factors in the differential experience of fatigue.
Implications for Cancer Survivors: Pay attention to these influencing factors may help to better identify patients susceptible to fatigue and provide long-term, targeted interventions.
Target tumor therapy in human gastric cancer cell through the combination of docetaxel-loaded cationic lipid microbubbles and ultrasound-triggered microbubble destruction
Authors: Lai Bin , Ouyang Xi , Mao Shengxun , Cao Jiaqin , Li Honglang , Li Song , Wang Jiwei 
Published: November 2022

Abstract
It is well accepted that ultrasound-induced microbubble (USMB) cavitation is a promising method for drug delivery. Ultrasound-targeted destruction of cytotoxic drug-loaded lipid microbubbles (LMs) is used to promote the treatment of cancer. This study aimed to investigate the antitumor effects from combination of docetaxel-loaded cationic lipid microbubbles (DLLM+) and ultrasound (US)-triggered microbubble destruction (UTMD) on gastric cancer (GC). Here, the functional dose of DOC was identified as 1×10− 9 mol/L. We found that DLLM combined with UTMD group showed greater growth inhibition of the cultured human gastric cancer cells (HGCCs) when compared with other five groups by arresting the G2 / M phase in cell cycle. However, DLLM+ combined with UTMD showed a higher inhibition rate of tumor growth than DLLM combined with UTMD and that of the RC / CMV-p16 combined with UTMD in vitro and in vivo experiments. DLLM+ combined with UTMD significantly suppressed proliferation and promoted the apoptosis of HGCCs with more cells arrested in the G2 / M phase. In addition, DLLM+ combined with UTMD suppressed the proliferation and induced the apoptosis by arresting cells in the G2 / M phase, which leading to a great inhibition of GC progression. Thus, our results indicated that the combination of DLLM+ and UTMD might represent a novel and promising approach to chemotherapy for GC.
Simulation of suitable growth areas for the endangered species of Ephedra sinica in China
Authors: Liu Minxia , Li Le , Wang Siyuan , Xiao Shirui , Mi Jiale 
Published: November 2022

AbstractEphedra sinicais a rare and endangered species in China, and the survival environment ofEphedra sinicawas seriously threatening. Predicting the suitable growth areas and constructing ecological corridors forEphedra sinicain China will help to protect it scientifically. Based on 306 valid distribution records and 13 selected environmental factors, the maximum entropy (MaxEnt) model was used to simulate the current Habitat zones and potential future (2050 and 2070) Habitat zones ofEphedra sinicaunder four change scenarios. The minimum cumulative resistance (MCR) model was applied to extract important ecological corridors ofEphedra sinica. The results indicate that: (1) Under the current environment, the total area of the suitable habitat forEphedra sinicain China is 42.24×105km2, mainly distributed in Northwest China and North China. (2) Future expansion of the suitable area as the RCP (representative concentration pathway) rises. The center of mass of the Habitat zone moved northward from Shaanxi Province to Ordos City in Inner Mongolia Autonomous Region. (3) Of the 13 environmental factors selected, the primary factor was elevation (20.8%), followed by wettest month precipitation (18.2%) and temperature seasonality (15.2%). (4) Nineteen ecological corridors have been constructed, with a total corridor length of 430.2km, including seven long-distance passages and 12 short-distance corridors. All galleries are far from the artificial surface, mostly near high-altitude areas. In addition, the minimum cost distance has a good continuity within Ulanqab City, which can realize the connection between the Huitengxile grassland in the northwest of Ulanqab City and the Sumu Mountain Forest Park area in the southwest.
Estrogen regulates duodenal glucose absorption through the effect of estrogen receptor-α on glucose transporters
Authors: Shan Weixi , Ding Jianhong , Xie Rui , Du Qian , Chen Changmei , Liao Qiushi , Yang Xiaoxu , Lou Jun , Jin Zhe , Chen Mingkai , Xu Jingyu 
Published: November 2022

Abstract
Estrogen deficiency is an important reason for the obesity of menopause, but the specific mechanism is unclear. Here, we investigated the effect of estrogen on glucose absorption. The experiments were performed in human, mice and SCBN cells. We first observed the correlation between estrogen and blood glucose in women, which found that blood glucose was significantly higher in the premenstrual phase than in the preovulatory phase of young women. Similarly, with serum estradiol level decreased in ovariectomized (OVX) mice, ER-α and ER-β in the duodenum reduced, the weight, abdominal fat and blood glucose increased significantly. However, interestingly, the expression of SGLT1 and GLUT2 and the glucose absorption in duodenal decreased significantly. It was further confirmed that estrogen could significantly up-regulate the expression of SGLT1 and GLUT2 in SCBN cells, and this trend can be reversed after silencing ER-α, but it doesn’t work after silencing ER-β, suggesting ER-α may be the key receptor of estrogen regulating glucose transporter. Mechanism study found that estrogen downstream can activate PKC pathway. Overall, our findings indicate that estrogen promotes glucose absorption, estrogen and its receptor (ER-α) deficiency can inhibit the expression of SGLT1 and GLUT2 through PKC signaling pathway, thereby reducing the glucose absorption.
Wintering molecular changes in the brain of Calidris pusilla at lower latitude
Authors: Pereira Patrick Douglas Corrêa , Henrique Ediely Pereira , Costa Emanuel Ramos da , Silva Anderson de Jesus Falcão da , de Melo Mauro Andre Damasceno , Schneider Maria Paula Cruz , Burbano Rommel Mario Rodriguez , Diniz Daniel Guerreiro , Magalhães Nara Gyzely de Morais , Sherry David Francis , Diniz Cristovam Wanderley Picanço , Guerreiro-Diniz Cristovam 
Published: November 2022

Abstract
Background:
Migrant birds prepare differently to fly north for breeding in spring and for the flight to lower latitudes during autumn avoiding the cold and food shortages of the north hemisphere's harsh winter. The molecular events associated with these fundamental stages in the life history of migrants include the differential gene expression in different tissues. Semipalmated sandpipers (Calidris pusilla) are Artic breeding shorebirds that migrate to the coast of South America during non-breeding season. Thus, the adaptive molecular changes in the brain of these birds at lower latitudes have not yet been investigated in detail.
Results:
Here, we searched for differential gene expression in the brain of semipalmated sandpiper, of recent arrived birds (RA) from autumnal migration and that of individuals in the premigratory period (PM) in the spring. All individuals were collected in the tropical coastal of northern Brazil. We generated a De novo neurotranscriptome for C. pusilla individuals and compared gene expression across libraries for neurotranscriptome. To that end we mapped RNA-seq reads to the C. pusilla neurotranscriptome in a total of 4 brain samples each group. A total of 266,414 transcripts were reconstructed that yielded 615 differentially expressed genes in the brain of both groups.
Conclusions:
The present report revealed a remarkable differential gene expression in the brain of recently arrived and premigratory individuals. It also revealed molecular brain changes associated with the recovering of the 4 to 5 days long-distance uninterrupted flight across Atlantic Ocean and preparation for the long-distance multiple stopover spring migration.
Contemporary Management of Unexpected Arterial Thrombosis and Acute Limb Ischemia in a Young Male Patient with COVID-19: A Case Report and Literature Review
Authors: Aljabri Badr , Aldossary Mohammed 
Published: November 2022

Abstract
Background
The spread of severe acute respiratory syndrome coronavirus 2 has resulted in coronavirus disease 2019 (COVID-19) pandemic, raising significant concerns. COVID-19 can lead to thrombotic complications such as acute limb ischemia (ALI). In patients with COVID-19, thrombotic complications may increase the risk of morbidity and mortality. The frequency of ALI has reduced worldwide, and the hypercoagulable condition remains an infrequent cause of limb ischemia. Patients with COVID-19 have a 35–45% thromboembolic complication rate. In many studies, the virus launches a second attack between 7 and 14 days after symptom onset, possibly causing hypercoagulability. If conservative treatment fails, various surgical methods, including thromboembolectomy, thrombolysis, and thrombosuction, can be performed to treat ALI.
Case Presentation:
We report the case of a 37-year-old man who presented with a 2 weeks history of right foot pain, toes blackish discoloration, and numbness. He tested positive for COVID-19 10 days prior to his presentation. Computed tomography angiography (CTA) of the lower limbs revealed near-complete occlusion of the right popliteal artery with single-vessel posterior tibial artery runoff. The patient was brought to a hybrid operating room, and diagnostic angiography confirmed the diagnosis. He underwent popliteal artery thromboembolectomy and intraoperative thrombolysis through a posterior approach. A completion angiography demonstrated a patent popliteal artery with a 2-vessels patency to the foot. His postoperative recovery was uneventful. After surgery, the popliteal, anterior tibial, and posterior tibial arteries were all palpable. The patient was discharged home on antiplatelet therapy with frequent postoperative follow-ups during the last 1 year in our outpatient clinic.
Conclusions
In mild ALI symptoms, unfractionated heparin can be used with vigilant follow-up. Open and endovascular procedures are currently used to treat patients with acute limb ischemia, and technological advancements continue to make interventions easier and safer.
The utility of SUV max as an adaptation criterion for limited resection in stage IA non-small cell lung cancer
Authors: Motono Nozomu , Mizoguchi Takaki , Ishikawa Masahito , Iwai Shun , Iijima Yoshihito , Uramoto Hidetaka 
Published: November 2022

Abstract
Background
Although the consolidation diameter of a tumor on computed tomography (CT) is an adaptation criterion for limited resection in early-stage non-small cell lung cancer (NSCLC), whether the maximum standardized uptake value (SUVmax) is also an adaptation criterion for limited resection has not been evaluated.
Methods
In total, 478 NSCLC patients with clinical stage IA disease were analyzed, among whom 383 were used to perform a sub-analysis.
Results
Multivariate analysis showed that consolidation diameter (odds ratio [OR]: 3.05, p = 0.01), SUVmax (OR: 10.74, p = 0.02), and lymphatic invasion (OR: 10.34, p < 0.01) were risk factors for lymph node metastasis in clinical stage IA NSCLC patients. Furthermore, age (OR: 2.98, p = 0.03), SUVmax (OR: 13.07, p = 0.02), and lymphatic invasion (OR: 5.88, p = 0.02) were risk factors for lymph node metastasis in clinical stage IA lung adenocarcinoma patients according to multivariate analysis.
Conclusions
Consolidation diameter of a tumor on CT, SUVmax, and lymphatic invasion are risk factors for lymph node metastasis. These results suggest that for early-stage lung adenocarcinoma patients, SUVmax is more important for deciding the indication of limited resection.
Agroforestry species composition and growth of Black Cardamom in different habitats along altitudinal gradient, Bhutan
Authors: Koirala Bhakti Sharma , Suberi Bhagat , Sherub Karma , Chhetri Rekha , Gyeltshen Thubten 
Published: November 2022

Abstract
The composition and arrangement of agroforestry species at different altitudes play a vital environmental role in the growth of Black Cardamom crop. The present study assesses agroforestry tree species composition and the relationship between the growth of Black Cardamom and associated tree species. For this, the altitudes were sorted into three altitudinal ranges; low (850-1150 m), mid (1250-1550 m), and high (1650-1950 m) and in each altitudinal range three different habitats were assessed (Timber Tree (TT), Fodder tree (FT) and Mix tree (MT) habitats). In each altitudinal band, 16 plots were made for each habitat (TT, MT, FT) with a total of 144 plots sampled systematically with 20×20 m plot size within the selected altitudinal range (850 to 1950 m). The result of the study found 56 ecologically important agroforestry tree species under 32 families that are used as shade trees for Black Cardamom. The tree species preference of Black Cardamom changes based on the basal area of trees, altitudes, and habitat types (F(2, 33)=45.672, P=.000). The overall growth (R2=.95) was better in timber tree habitat at mid altitudes, where Alnus nepalensis was the dominating species having 41.40% canopy cover with low pest and disease-infested Black Cardamom stems, making it a suitable habitat for growth. The lower altitudinal band and all the mixed tree habitats were found to be unsuitable for Black Cardamom growth (p<0.05). Thus, while cultivating Black Cardamom it is important to select appropriate tree species, canopy cover, altitude, and habitat for optimum growth.
A coding variant in SULT1A2 gene: association with obesity and dyslipidemia in southern Chinese adults
Authors: Lv Hai-Yan , Shi Guifeng , Li Cai , Ye Ya-Fei , Chen Ya-Hong , Chen Li-Hua , Tung Tao-Hsin , Zhang Meixian 
Published: November 2022

Abstract
Background: A coding variant rs1059491 in the SULT1A2gene has been reported to be associated with childhood obesity. This study aimed to investigate the association of rs1059491 with risk of obesity and cardiometabolic abnormalities in adults.
Methods: This case-control study included 226 normal weight, 168 overweight and 72 obese adults who underwent a health examination in Taizhou, China. Genotyping of SULT1A2rs1059491 was performed by Sanger sequencing.
Results: The minor allele frequency of rs1059491 in the overweight combined obesity and control group was 0.0292 and 0.0686, respectively. No differences in weight and body mass index were detected between TT genotype and GT+GG genotype under the dominant model, but levels of serum triglyceride was significantly lower in G-allele carriers than non-G-allele carriers (1.02 (0.74–1.32) vs. 1.35 (0.83–2.13) mmol/L, P = 0.011). The GT+GG genotype of rs1059491 versus TT genotype reduced the risk of overweight and obesity by 54% (OR: 0.46, 95%CI: 0.22–0.96, P = 0.037) after adjusted for sex and age. Similar results were observed for hypertriglyceridemia (OR: 0.25, 95%CI: 0.08–0.74, P = 0.013) and dyslipidemia (OR: 0.37, 95%CI: 0.17–0.83, P = 0.015).
Conclusion: This study revealed that the coding variant rs1059491 is associated with decreased risk of obesity and dyslipidemia in southern Chinese adults. More studies are needed to validate the association in other populations and its underlying mechanisms.
Effect of agricultural management approaches on soil microbial diversity and crop production: A meta-analysis
Authors: Huang Jingyi , Zou Junliang , Xing Lei , Liu Yongjun , Liu Tianbo , Yin Huaqun , Liu Xueduan , Meng Delong 
Published: November 2022

Abstract
Background and Aims Microbial diversity is a critical topic that concerns sustainable agriculture and crop production. Anthropogenic activities have a nonnegligible influence on both soil microbial diversity and crop production. Little research has been conducted to quantify the beneficial relationships between microbial diversity and soil productivity.
Methods A meta-analysis based on 80 published papers was carried out to clarify the effects of anthropogenic activities including chemical fertilization (CF), organic fertilization (OF), intercropping or rotation (IC) and microbial treatment (MF), on soil microbial diversity and crop yield, and the relationship in between and summarized.
Results The results showed that CF had the greatest potential for improving crop yield, whereas it may cause reductions in soil microbial diversity. OF is a sustainable development strategy, which increases both soil microbial diversity and crop yield. Under IC treatment, soil bacterial community diversity was significantly positively correlated with crop productivity, and the average effects of the four management approaches on soil microbial diversity and crop productivity were significantly different under different conditions.
Conclusion Overall, our results have great guiding significance for ecological environment protection and crop economic benefits.
Comparative chloroplast genomes of Annonaceae species: Enlargement of plastomes in size, IR region, and gene content
Authors: Gan Yangying , Liu Xiaojing , Ping Jingyao , Peng Caixia 
Published: November 2022

AbstractIn recent years, the evolution and phylogeny of plastid genomes have attracted much attention from scholars all over the world. Annonaceae is the largest family in Magnoliales with the greatest diversity among and within genera. Thus comparative analyses of its plastomes will be informative. In this study, the complete chloroplast genome ofMiliusa glochidioideswas sequenced by next-generation sequencing technology. Using two Magnoliaceae species as out-group, a comparative analysis of the existing 13 Annonaceae plastomes was conducted, and a phylogenetic relationship was constructed based on four methods. Our results show that the Annonaceae plastomes have great variation in the evolution process. The genome size is between 159kb and 202kb while the gene content ranges from 127 to 165. The number of genes in the IR region is between 5 and 39. Plastomes underwent significant structural rearrangements, including one inversion and multiple large-scale expansion (6-20kb) in the lR region, and shrinkage and inversions in the SSC region. Compared with Magnoliaceae, two fragments (pafII-atpEand 5'-rps12-psbJ) were inversed in Annonaceae. The phylogenetic relationship based on 78 common protein genes showed thatCananga odoratawas located at the base of Annonaceae. Annonoideae was a monophyletic group, andChieniodendron hainanensewas located inside the Malmeoideae. A total of 737 simple sequence repeats (SSRs) were detected in the study, and the distribution of SSRs varied from species. It is mainly dominated by A/T bases (mononucleotide) and is located in the intergenic region. In conclusion, the plastomes of Annonaceae have undergone great variation during evolution, especially the large-scale expansion of the IR region. Our study provides more information for studying the plastome evolution of Annonaceae.