bluuebunny/crossref_metadata_2025_split huggingface dataset:
Data driven analysis of atmospheric methane concentrations as function of geographic, land cover type and season
Authors: Karoff Christoffer , Vara-Vela Angel Liduvino 
Published: March 2023

Over the last decade we have witnessed a rapid, so far unexplained, increase in the emission of methane to the atmosphere and this increase could lead to an acceleration of the ongoing climate changes. The increase is likely to originate from agriculture, but oil and gas production as well as wetlands are also under suspicion. The best way to quantify the emission of methane and other greenhouse gasses to our atmosphere is by using space based remote sensing. Here, we analyse 3 years of measurements of the column-averaged dry-air mole fraction of methane from the Tropospheric Monitoring Instrument on Sentinel-5P obtained with two different retrieval methods in order to evaluate the dependency on geographic, land cover type and season. The land cover types were obtained from the Moderate Resolution Imaging Spectroradiometer aboard the Terra and Aqua satellites and from the World Cover data product using observations from the Copernicus Sentinel-1 and Sentinel-2 missions. The analysis reveals that while the highest methane concentrations are generally found over croplands, the lowest are generally found over shrublands, which is in agreement with expectations. It is more surprising that the analysis also reveals lower than average methane concentrations over wetlands as wetlands are generally thought to be a major source of methane emission. Until this discrepancy is resolved the methane concentration over wetlands from the Tropospheric Monitoring Instrument on Sentinel-5P should be handled with caution. It is also found that the annual methane cycle, as seen in the measured methane concentrations, for croplands, shrublands and savannas is delayed in Africa compared to Asia.
High-fat diet causes undesirable bone regeneration by altering the bone marrow environment in rats
Authors: Cai Feiyu , Yusufu Aihemaitijiang , Liu Kai , Chen Wenjiao , Zhao Ruomei , Liu Yanshi , Liu Yi 
Published: March 2023

ObjectiveDiet structure has changed greatly over the last few decades, and high-calorie diets have become an integral part of people’s daily diet, as well as the important cause of obesity in society. Several organ systems, including the skeletal system, are seriously affected by high-fat-diets (HFD) in the world. There is, however, still a lack of knowledge about the effects of HFD on bone regeneration and the possible mechanisms involved. In this study, the difference in bone regeneration between rats under HFD and low-fat-diets (LFD) was evaluated by monitoring the process of bone regeneration in distraction osteogenesis (DO) model animals, as well as the possible mechanisms.MethodsA total of 40 Sprague Dawley (SD) rats (5 weeks old) were randomly divided into HFD group (n=20) and LFD group (n=20). Except for feeding methods, there were no differences between the two groups in terms of treatment conditions. All animals received the DO surgery eight weeks after starting to feed. After a delay of 5 days (latency phase), the active lengthening phase was performed for 10 days (0.25 mm/12 h), and the consolidation phase followed for 42 days. An observational study of bone included radioscopy (once a week), micro-computed tomography (CT), general morphology, biomechanics, histomorphometry, and immunohistochemistry.ResultThe results showed that HFD group had a higher body weight than LFD group after 8, 14, and 16 weeks of feeding. Furthermore, at the final observation, there were statistically significant differences between LFD group and HFD group in terms of total cholesterol (TC), triglycerides (TG), low-density lipoprotein (LDL), and high-density lipoprotein (HDL) levels. Additionally, observations on bone regeneration showed a slower regeneration and a lower biomechanical strength in HFD group than LFD group, based on radiography, micro-CT, general morphology, biomechanics, histomorphometry, and immunohistochemistry.ConclusionIn this study, HFD resulted in elevated blood lipids, increased adipose differentiation at the bone marrow level, and delayed bone regeneration. The pieces of evidence are beneficial to better understand the association between diet and bone regeneration and to adjust the diet optimally for fracture patients.
Post-fire recovery of soil organic carbon, soil total nitrogen, soil nutrients, and soil erodibility in rotational shifting cultivation in Northern Thailand
Authors: Arunrat Noppol , Sereenonchai Sukanya , Kongsurakan Praeploy , Iwai Chuleemas Boonthai , Yuttitham Monthira , Hatano Ryusuke 
Published: March 2023

The hill tribes in Thailand traditionally depend on rotational shifting cultivation (RSC). However, insufficient understanding remains on post-fire soil properties and soil erodibility (k-values) with fallow years. To address this gap, the levels of soil organic carbon (SOC), soil total nitrogen (STN), soil nutrients, and soil erodibility after fire in RSC were investigated. Topsoil (0–10 cm) samples from sites with 4 (RSC-4Y), 5 (RSC-5Y), and 7 (RSC-7Y) fallow years in Chiang Mai Province, northern Thailand, were taken at four time points: before burning, 5 min after burning, 9 months after burning, and 2 years after burning. Soil pH, electrical conductivity, and soil nutrient (available P, K, and Ca) levels were increased after burning and remained higher than the pre-burning levels for at least 2 years. The SOC stock decreased after burning in all fallow fields. At 2 years after burning, the SOC stock in RSC-4Y was higher than before burning, whereas in RSC-5Y and RSC-7Y, the levels had not reached the pre-fire levels. The STN stocks of all studied fields significantly decreased after burning and had not reached the pre-burning levels after 2 years. After burning, the topsoil of RSC-4Y was most susceptible to erosion. However, only in RSC-4Y, the k-value was unchanged at 2 years after burning. Three different approaches are recommended for post-fire land management: 1) farmers should not cut and remove the weeds and grasses at the soil surface, 2) burning should be performed around late winter or early summer (November–February) to inhibit complete combustion, and 3) contour-felled log erosion barriers should be made by using the trunks remaining after the fire to trap the sediment and slow down surface runoff.
Fine root biomass and morphology in a temperate forest are influenced more by canopy water addition than by canopy nitrogen addition
Authors: Li Wen , Wang Chuang , Liu Haowei , Wang Wenqian , Sun Ruomin , Li Mengke , Shi Yifei , Zhu Dandan , Du Wenzhi , Ma Lei , Fu Shenglei 
Published: March 2023

IntroductionIncreasing atmospheric N deposition and changes in precipitation patterns could profoundly impact forest community structure and ecosystem functions. However, most N and water (W) addition experiments have focused on direct N application to leaf litter or soil, neglecting canopy processes such as leaf evaporation and absorption.MethodsIn this study, we aimed to assess the effects of atmospheric N deposition and increased precipitation on the fine root biomass and morphology of plants in a temperate deciduous forest. To achieve this, we applied N and W above the forest canopy and quantified the seasonal dynamics (January, July, and October) of fine root biomass and morphology.ResultsOur results revealed that only canopy W addition significantly increased the biomass of fine roots in January compared to that in other seasons (p &lt; 0.05). We observed no significant interaction effect of N and W on fine root biomass. However, we found that the different growth seasons had a significant impact on the fine root biomass (p &lt; 0.001). The combined application of N and W significantly affected the root tip density (p = 0.002). Although canopy N addition was significantly positively correlated with available soil N (p &lt; 0.05), we detected no significant association with fine root biomass or morphology.DiscussionThe findings of this study indicated that fine root biomass and morphology, are affected to a greater extent by the provision of W than by N application. These findings provide a new perspective and a more precise understanding of the effects of the actual N deposition and precipitation on the dynamics of plant fine roots in forest ecosystems.
Case Report: Identification of a rare nonsense mutation in the POC1A gene by NGS in a diabetes mellitus patient
Authors: Li Dongfeng , Li Shihui , Zhou Jingjing , Zheng Lili , Liu Gui , Ding Chengzhang , Yuan Xingyun 
Published: March 2023

Objective: This study aimed to investigate the clinical and molecular biology of a patient with a type of diabetes mellitus caused by a mutation in the POC1A (OMIM number: 614783) gene and explore its pathogenesis and related characteristics.Methods: The patient was interviewed about his medical history and subjected to relevant examinations. Blood DNA samples were collected from the patient and his family members (parents) for trio whole-exome sequencing. Whole-exome sequencing was performed using the IDT xGen Exome Research Panel v1.0 whole-exome capture chip and sequenced using an Illumina NovaSeq 6,000 series sequencer (PE150); the sequencing coverage of the target sequence was not less than 99%. After systematic analysis and screening of the cloud platform for accurate diagnosis of genetic diseases, which integrated molecular biology annotation, biology, genetics, and clinical feature analysis, combined with a pathogenic mutation database, normal human genome database, and clinical feature database of 4,000 known genetic diseases, hundreds of thousands of gene variants were graded using the gene data analysis algorithm, a three-element grading system, and the American Society of Medical Genetics gene variant grading system. After polymerase chain reaction testing, the target sequence was verified by Sanger sequencing using an ABI3730 sequencer, and the verification result was obtained using sequence analysis software.Results: The patient had a peculiar face, a thin body, and a body mass index of 16.0 kg/m2. His fasting connecting peptide was 10.2 ug/L, his fasting insulin was 44 mIU/L, his fasting blood glucose was 10.5 mmol/L, and his glycosylated haemoglobin was 12.5%. After hospitalisation, the patient was given 0.75 g/d metformin tablets and 15 mg/d pioglitazone dispersible tablets, and his fasting blood glucose reduced to 9.2 mmol/L. After 48 U/L insulin treatment, the patient’s fasting blood glucose was reduced to 8.5 mmol/L. Genetic screening revealed that there was a pathogenic variant at the POC1A gene locus and a cytosine-to-thymine mutation at the G81 locus, turning the Arg to a termination codon and shortening the POC1A protein from 359 amino acids (aa) to 80 aa. No mutation was detected in the patient’s parents’ POC1A gene loci.Conclusion: The patient’s diabetes was caused by a POC1A gene mutation at the G81 locus, which is rarely reported in the clinic. The specific manifestations of this mutation need to be further investigated.
Discovering genetic linkage between periodontitis and type 1 diabetes: A bioinformatics study
Authors: Liu Junqi , Zhang Bo , Zhu Guanyin , Liu Chenlu , Wang Shuangcheng , Zhao Zhihe 
Published: March 2023

Background: Relationship between periodontitis (PD) and type 1 diabetes (T1D) has been reported, but the detailed pathogenesis requires further elucidation. This study aimed to reveal the genetic linkage between PD and T1D through bioinformatics analysis, thereby providing novel insights into scientific research and clinical treatment of the two diseases.Methods: PD-related datasets (GSE10334, GSE16134, GSE23586) and T1D-related datasets(GSE162689)were downloaded from NCBI Gene Expression Omnibus (GEO). Following batch correction and merging of PD-related datasets as one cohort, differential expression analysis was performed (adjusted p-value &lt;0.05 and ∣log2  fold change| &gt; 0.5), and common differentially expressed genes (DEGs) between PD and T1D were extracted. Functional enrichment analysis was conducted via Metascape website. The protein-protein interaction (PPI) network of common DEGs was generated in The Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database. Hub genes were selected by Cytoscape software and validated by receiver operating characteristic (ROC) curve analysis.Results: 59 common DEGs of PD and T1D were identified. Among these DEGs, 23 genes were commonly upregulated, and 36 genes were commonly downregulated in both PD- and T1D-related cohorts. Functional enrichment analysis indicated that common DEGs were mainly enriched in tube morphogenesis, supramolecular fiber organization, 9 + 0 non-motile cilium, plasma membrane bounded cell projection assembly, glomerulus development, enzyme-linked receptor protein signaling pathway, endochondral bone morphogenesis, positive regulation of kinase activity, cell projection membrane and regulation of lipid metabolic process. After PPI construction and modules selection, 6 hub genes (CD34, EGR1, BBS7, FMOD, IGF2, TXN) were screened out and expected to be critical in linking PD and T1D. ROC analysis showed that the AUC values of hub genes were all greater than 70% in PD-related cohort and greater than 60% in T1D-related datasets.Conclusion: Shared molecular mechanisms between PD and T1D were revealed in this study, and 6 hub genes were identified as potential targets in treating PD and T1D.
Clinical implications of gut microbiota and cytokine responses in coronavirus disease prognosis
Authors: Seong Hye , Kim Jun Hyoung , Han Young-Hee , Seo Ho Seong , Hyun Hak Jun , Yoon Jin Gu , Nham Eliel , Noh Ji Yun , Cheong Hee Jin , Kim Woo Joo , Lim Sooyeon , Song Joon Young 
Published: March 2023

ObjectivesSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects gut luminal cells through the angiotensin-converting enzyme-2 receptor and disrupts the gut microbiome. We investigated whether the gut microbiome in the early stage of SARS-CoV-2 infection was associated with the prognosis of coronavirus disease (COVID-19).MethodsThirty COVID-19 patients and 16 healthy controls were prospectively enrolled. Blood and stool samples and clinical details were collected on days 0 (enrollment), 7, 14, and 28. Participants were categorized into four groups by their clinical course.ResultsGut microbiota composition varied during the clinical course of COVID-19 and was closely associated with cytokine levels (p=0.003). A high abundance of the genus Dialister (linear discriminant analysis [LDA] effect size: 3.97856, p=0.004), species Peptoniphilus lacrimalis (LDA effect size: 4.00551, p=0.020), and Anaerococcus prevotii (LDA effect size: 4.00885, p=0.007) was associated with a good prognosis. Starch, sucrose, and galactose metabolism was highly activated in the gut microbiota of the poor prognosis group. Glucose-lowering diets, including whole grains, were positively correlated with a good prognosis.ConclusionGut microbiota may mediate the prognosis of COVID-19 by regulating cytokine responses and controlling glucose metabolism, which is implicated in the host immune response to SARS-CoV-2.
Chromosome 11q13 amplification correlates with poor response and prognosis to PD-1 blockade in unresectable hepatocellular carcinoma
Authors: Yan Kai , Zhang Ding , Chen Yanan , Lu Wenfeng , Huang Mengli , Cai Jinping , Chen Shiqing , Bei Ting , Bai Yuezong , Lv Jian , Fu Yong , Zhang Haibin 
Published: March 2023

Background &amp; aimsLittle is known about molecular biomarkers that predict the response and prognosis in unresectable hepatocellular carcinoma (HCC) treated with programmed death (PD)-1 inhibitors.MethodsA total of 62 HCC patients who underwent next-generation sequencing were retrospectively included in our department for this study. Patients with unresectable disease were subjected to systemic therapy. PD-1 inhibitors intervention (PD-1Ab) group and nonPD-1Ab group included 20 and 13 patients, respectively. Primary resistance was defined as initial on-treatment progression or progression with an initial stable disease of less than 6 months.ResultsChromosome 11q13 amplification (Amp11q13) was the most common copy number variation in our cohort. Fifteen (24.2%) patients harbored Amp11q13 in our dataset. Patients with Amp11q13 showed higher level of Des-γ-carboxy-prothrombin (DCP), tumor number and were more prone to be combined with portal vein tumor thrombosis (PVTT). In the PD-1Ab group, the proportion of progressive disease (PD) in patients with Amp11q13 was significantly higher than that in patients with nonAmp11q13 (100% vs 33.3%, P=0.03). In the nonPD-1Ab group, the proportion of PD in patients with Amp11q13 and nonAmp11q13 had no significant difference (0% vs 11.1%, P&gt;0.99). In the PD-1Ab group, the median progression-free survival (PFS) was 1.5 months in Amp11q13 patients vs 16.2 months in non-Amp11q13 patients (HR, 0.05; 95% CI 0.01-0.45; P = 0.0003). No significant difference was observed in the nonPD-1Ab group. Notably, we found that hyperprogressive disease (HPD) might be associated with Amp11q13. The increased density of Foxp3+ Treg cells in HCC patients with Amp11q13 might be one of potential mechanisms.ConclusionHCC patients with Amp11q13 are less likely to benefit from PD-1 blockade therapies. These findings may help guide the use of immunotherapy for HCC in routine clinical practice.
Soluble immune checkpoints as correlates for HIV persistence and T cell function in people with HIV on antiretroviral therapy
Authors: Chiu Chris Y. , Schou Maya D. , McMahon James H. , Deeks Steven G. , Fromentin Rémi , Chomont Nicolas , Wykes Michelle N. , Rasmussen Thomas A. , Lewin Sharon R. 
Published: March 2023

IntroductionIn people with HIV (PWH) both off and on antiretroviral therapy (ART), the expression of immune checkpoint (IC) proteins is elevated on the surface of total and HIV-specific T-cells, indicating T-cell exhaustion. Soluble IC proteins and their ligands can also be detected in plasma, but have not been systematically examined in PWH. Since T-cell exhaustion is associated with HIV persistence on ART, we aimed to determine if soluble IC proteins and their ligands also correlated with the size of the HIV reservoir and HIV-specific T-cell function.MethodsWe used multiplex bead-based immunoassay to quantify soluble programmed cell death protein 1 (PD-1), cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), lymphocyte activation gene-3 (LAG-3), T cell immunoglobulin domain and mucin domain 3 (TIM-3), PD-1 Ligand 1 (PD-L1) and PD-1 Ligand 2 (PD-L2) in plasma from PWH off ART (n=20), on suppressive ART (n=75) and uninfected controls (n=20). We also quantified expression of membrane-bound IC and frequencies of functional T-cells to Gag and Nef peptide stimulation on CD4+ and CD8+ T-cells using flow cytometry. The HIV reservoir was quantified in circulating CD4+ T-cells using qPCR for total and integrated HIV DNA, cell-associated unspliced HIV RNA and 2LTR circles.ResultsSoluble (s) PD-L2 level was higher in PWH off and on ART compared to uninfected controls. Higher levels of sPD-L2 correlated with lower levels of HIV total DNA and higher frequencies of gag-specific CD8+ T-cells expressing CD107a, IFNγ or TNFα. In contrast, the concentration of sLAG-3 was similar in uninfected individuals and PWH on ART, but was significantly elevated in PWH off ART. Higher levels of sLAG-3 correlated with higher levels of HIV total and integrated DNA, and lower frequency of gag-specific CD4+ T cells expressing CD107a. Similar to sLAG-3, levels of sPD-1 were elevated in PWH off ART and normalized in PWH on ART. sPD-1 was positively correlated with the frequency of gag-specific CD4+ T cells expressing TNF-a and the expression of membrane-bound PD-1 on total CD8+ T-cells in PWH on ART.DiscussionPlasma soluble IC proteins and their ligands correlate with markers of the HIV reservoir and HIV-specific T-cell function and should be investigated further in in large population-based studies of the HIV reservoir or cure interventions in PWH on ART.
Multicenter, single-arm, phase II study (CAP) of radiotherapy plus liposomal irinotecan followed by camrelizumab and anti-angiogenic treatment in advanced solid tumors
Authors: Shen Jie , Yan Jing , Du Juan , Li Xiaoqin , Wei Jia , Liu Qin , Yong Hongmei , Wang Xiaolu , Chang Xiaofeng , Ding Zhou , Sun Wu , Liu Chenxi , Zhu Sihui , Guo Jingyi , Li Huajun , Liu Ying , Zhang Wulou , Liu Zonghang , Li Rutian , Liu Baorui 
Published: March 2023

IntroductionCombination therapeutic mode is likely to be the key to enhance the efficacy of immunotherapy in a wider range of cancer patients. Herein, we conducted an open-label, single-arm, multicenter, phase II clinical trial that enrolled patients with advanced solid tumors who had progressed after standard treatments.MethodsRadiotherapy of 24 Gy/3 fractions/3-10 days was given to the targeted lesions. Liposomal irinotecan (80mg/m2, dose could be adjusted to 60 mg/m2 for intolerable cases) was intravenously (IV) administered once within 48 hours after radiotherapy. Then, camrelizumab (200mg IV, q3w) and anti-angiogenic drugs were given regularly until disease progression. The primary endpoint was objective response rate (ORR) in the target lesions evaluated by investigators per RECIST 1.1. The secondary endpoints were disease control rate (DCR) and treatment-related adverse events (TRAEs).ResultsBetween November 2020 and June 2022, 60 patients were enrolled. The median follow-up was 9.0 months (95% confidence interval (CI) 5.5-12.5). Of 52 evaluable patients, the overall ORR and DCR were 34.6% and 82.7%, respectively. Fifty patients with target lesions were evaluable, the ORR and DCR of the target lesions were 35.3% and 82.4%, respectively. The median progression-free survival was 5.3 months (95% CI 3.6, 6.2), and the median overall survival was not reached. TRAEs (all grades) occurred in 55 (91.7%) patients. The most common grade 3-4 TRAEs were lymphopenia (31.7%), anemia (10.0%), and leukopenia (10.0%).ConclusionThe combination of radiotherapy, liposomal irinotecan, camrelizumab, and anti-angiogenesis therapy demonstrated promising anti-tumor activity and well tolerance in various advanced solid tumors.Clinical trial registrationhttps://clinicaltrials.gov/ct2/home, identifier NCT04569916.