bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dissolution migration of gas, a mechanism to enrich ethane near the BSR and increase upwardly C1/C2 ratios in the hydrate-occurring zones: Insight from pore-scale experimental observation
Authors: Li Hui , Lu Xuekang , Wang Lin , Wang Wenjing , Li Tianhua , Lu Wanjun , Chen Yong 
Published: February 2023

Most experiments show that gas hydrates are often enriched in C2+ gases relative to the feeding gas source because of fractionation during hydrate crystallization directly from free gases and dissolved gases. However, sediments below and near the base of the gas hydrate stability zone (BGHSZ) in many ocean drilling program (ODP)/International Ocean Discovery Program (IODP) sites are relatively enriched in C2+ hydrocarbon gases, compared with the hydrate-occurring zone above. It is still unclear what kind of process causes the abrupt decreases in C1/C2+ ratios with the depth in headspace gas in sediments around seismic bottom-simulating reflector (BSR) and increasing upward C1/C2 ratios in the hydrate-occurring zone. To test the “dissolution/migration mechanism” and its links to the enrichment of ethane near the BSR and increasing upward C1/C2 ratios in the hydrate-occurring zone, we performed a series of pore-scale experimental observations, simulating the gas dissolution–migration–hydration processes, and investigated the effects of the composition of feeding gases and temperatures on the composition of the hydrate grown under the dissolution–migration mechanism. Hydrates are grown from aqueous fluids supplied by the migration of gases dissolved from the capillary-trapped free gas in a capillary high-pressure optical cell, with different supplying gases (90 mol% CH4 + 10 mol% C2H6, 80 mol% CH4 + 20 mol% C2H6) and a geothermal gradient (temperature from 278.15 to 293.15 K). The gas hydrate structure and composition were determined by quantitative Raman spectroscopy. Our study indicated that (1) under the dissolution–migration–hydration processes, the mole fraction of C2H6 in hydrates is depleted compared with gas sources, which confirms that the dissolution–migration of gases is a mechanism to enrich ethane near the BSR; (2) the proportion of C2H6 in structure I (sI) or structure II (sII) hydrates decreases with decreasing temperature, and decreasing temperature enlarges the difference of diffusion coefficient between methane and ethane and enhances the gas fractionation during migration, which could cause the increase upwardly C1/C2 ratios in the hydrate-occurring zone. A simplified geological model was proposed to explain the variability of hydrate composition with depth in the hydrate-occurring zone and the fractionation of gases near the BSR.
Characterization of the microbiota dynamics associated with Moniliophthora roreri, causal agent of cocoa frosty pod rot disease, reveals new viral species
Authors: Reyes Brayan Maudiel Diaz , Fonseca Paula Luize Camargos , Heming Neander Marcel , Conceição Lucas Barbosa de Amorim , Nascimento Katiucia Ticila de Souza , Gramacho Karina Peres , Arevalo-Gardini Enrique , Pirovani Carlos Priminho , Aguiar Eric Roberto Guimarães Rocha 
Published: February 2023

IntroductionTheobroma cacao, the cocoa tree, is a target for pathogens, such as fungi from the genera Phytophthora, Moniliophthora, Colletotrichum, Ceratocystis, among others. Some cacao pathogens are restricted to specific regions of the world, such as the Cacao swollen shoot virus (CSSV) in West African countries, while others are expanding geographically, such as Moniliophthora roreri in the Americas. M. roreri is one of the most threatening cacao pathogens since it directly attacks the cacao pods driving a significant reduction in production, and therefore economic losses. Despite its importance, the knowledge about the microenvironment of this pathogen and the cocoa pods is still poorly characterized.MethodsHerein we performed RNA sequencing of spores in differential stages of culture in a medium supplemented with cacao pod extract and mycelium collected of the susceptible variety ICT 7121 naturally infected by the pathogen to evaluate the diversity and transcriptional activity of microorganisms associated with the in vitro sporulation of M. roreri.ResultsOur data revealed a great variety of fungi and bacteria associated with M. roreri, with an exceptional diversity of individuals from the genus Trichoderma sp. Interestingly, the dynamics of microorganisms from different kingdoms varied proportionally, suggesting they are somehow affected by M. roreri culture time. We also identified three sequences similar to viral genomes from the Narnaviridae family, posteriorly confirmed by phylogenetic analysis as members of the genus Narnavirus. Screening of M. roreri public datasets indicated the virus sequences circulating in samples from Ecuador, suggesting a wide spread of these elements. Of note, we did not identify traces of the viral sequences in the M. roreri genome or DNA sequencing, restricting the possibility of these sequences representing endogenized elements.DiscussionTo the best of our knowledge, this is the first report of viruses infecting the fungus of the genus Moniliophthora and only the third description of viruses that are able to parasite elements from the Marasmiaceae family.
Identification of natural compounds as SARS-CoV-2 inhibitors via molecular docking and molecular dynamic simulation
Authors: Han Tiantian , Luo Ziqing , Ji Lichun , Wu Peng , Li Geng , Liu Xiaohong , Lai Yanni 
Published: February 2023

BackgroundBase mutations increase the contagiousness and transmissibility of the Delta and Lambda strains and lead to the severity of the COVID-19 pandemic. Molecular docking and molecular dynamics (MD) simulations are frequently used for drug discovery and relocation. Small molecular compounds from Chinese herbs have an inhibitory effect on the virus. Therefore, this study used computational simulations to investigate the effects of small molecular compounds on the spike (S) protein and the binding between them and angiotensin-converting enzyme 2 (ACE2) receptors.MethodsIn this study, molecular docking, MD simulation, and protein–protein analysis were used to explore the medicinal target inhibition of Chinese herbal medicinal plant chemicals on SARS-CoV-2. 12,978 phytochemicals were screened against S proteins of SARS-CoV-2 Lambda and Delta mutants.ResultsMolecular docking showed that 65.61% and 65.28% of the compounds had the relatively stable binding ability to the S protein of Lambda and Delta mutants (docking score ≤ −6). The top five compounds with binding energy with Lambda and Delta mutants were clematichinenoside AR2 (−9.7), atratoglaucoside,b (−9.5), physalin b (−9.5), atratoglaucoside, a (−9.4), Ochnaflavone (−9.3) and neo-przewaquinone a (−10), Wikstrosin (−9.7), xilingsaponin A (−9.6), ardisianoside G (−9.6), and 23-epi-26-deoxyactein (−9.6), respectively. Four compounds (Casuarictin, Heterophylliin D, Protohypericin, and Glansrin B) could interact with S protein mutation sites of Lambda and Delta mutants, respectively, and MD simulation results showed that four plant chemicals and spike protein have good energy stable complex formation ability. In addition, protein–protein docking was carried out to evaluate the changes in ACE2 binding ability caused by the formation of four plant chemicals and S protein complexes. The analysis showed that the binding of four plant chemicals to the S protein could reduce the stability of the binding to ACE2, thereby reducing the replication ability of the virus.ConclusionTo sum up, the study concluded that four phytochemicals (Casuarictin, Heterophylliin D, Protohypericin, and Glansrin B) had significant effects on the binding sites of the SARS-CoV-2 S protein. This study needs further in vitro and in vivo experimental validation of these major phytochemicals to assess their potential anti-SARS-CoV-2.Graphical abstract
Pseudorabies virus exploits N6-methyladenosine modification to promote viral replication
Authors: Yu Pei-Lun , Wu Rui , Cao San-Jie , Wen Yi-Ping , Huang Xiao-Bo , Zhao Shan , Lang Yi-Fei , Zhao Qin , Lin Ju-Chun , Du Sen-Yan , Yu Shu-Min , Yan Qi-Gui 
Published: February 2023

IntroductionPseudorabies virus (PRV) is the pathogenic virus of porcine pseudorabies (PR), belonging to the Herpesviridae family. PRV has a wide range of hosts and in recent years has also been reported to infect humans. N6-methyladenosine (m6A) modification is the major pathway of RNA post-transcriptional modification. Whether m6A modification participates in the regulation of PRV replication is unknown.MethodsHere, we investigated that the m6A modification was abundant in the PRV transcripts and PRV infection affected the epitranscriptome of host cells. Knockdown of cellular m6A methyltransferases METTL3 and METTL14 and the specific binding proteins YTHDF2 and YTHDF3 inhibited PRV replication, while silencing of demethylase ALKBH5 promoted PRV output. The overexpression of METTL14 induced more efficient virus proliferation in PRV-infected PK15 cells. Inhibition of m6A modification by 3-deazaadenosine (3-DAA), a m6A modification inhibitor, could significantly reduce viral replication.Results and DiscussionTaken together, m6A modification played a positive role in the regulation of PRV replication and gene expression. Our research revealed m6A modification sites in PRV transcripts and determined that m6A modification dynamically mediated the interaction between PRV and host.
Definition of a microbial signature as a predictor of endoscopic post-surgical recurrence in patients with Crohn’s disease
Authors: Oliver Lia , Camps Blau , Julià-Bergkvist David , Amoedo Joan , Ramió-Pujol Sara , Malagón Marta , Bahí Anna , Torres Paola , Domènech Eugeni , Guardiola Jordi , Serra-Pagès Mariona , Garcia-Gil Jesus , Aldeguer Xavier 
Published: February 2023

Background and aims: Although there are several effective drugs for the treatment of Crohn’s disease (CD), almost 70% of patients will require surgical resection during their lifetime. This procedure is not always curative, as endoscopic recurrence occurs in 65%–90% of patients in the first year after surgery. The aetiology of the recurrence is unknown; however, several studies have shown how the resident microbiota is modified after surgery. The aim of this study was to evaluate samples from patients with Crohn’s disease before and after an intestinal resection to determine whether there were differences in the abundance of different microbial markers, which may predict endoscopic recurrence at baseline.Methods: In this observational study, a stool sample was obtained from 25 patients with Crohn’s disease before undergoing surgery, recruited at three Catalan hospitals. From each sample, DNA was purified and the relative abundance of nine microbial markers was quantified using qPCR.Results: An algorithm composed of four microbial markers (E. coli, F. prausnitzii phylogroup I, Bacteroidetes, and Eubacteria) showed a sensitivity and specificity of 90.91% and 85.71%, respectively, and a positive and negative predictive value of 83.33% and 92.31%, respectively.Conclusion: A microbial signature to determine patients who will have post-surgical recurrence was identified. This tool might be very useful in daily clinical practice, allowing the scheduling of personalized therapy and enabling preventive treatment only in patients who really require it.
Asthma's effect on brain connectivity and cognitive decline
Authors: Wang Tao , Huang Xin , Wang Jun 
Published: February 2023

ObjectiveTo investigate the changes in dynamic voxel mirror homotopy connection (dVMHC) between cerebral hemispheres in patients with asthma.MethodsOur study was designed using a case-control method. A total of 31 subjects with BA and 31 healthy subjects with matching basic information were examined using rsfMRI. We also calculated and obtained the dVMHC value between the cerebral cortexes.ResultsCompared with the normal control group, the dVMHC of the lingual gyrus (Ling) and the calcarine sulcus (CAL), which represented the visual network (VN), increased significantly in the asthma group, while the dVMHC of the medial superior frontal gyrus (MSFG), the anterior/middle/posterior cingulate gyrus (A/M/PCG), and the supplementary motor area (SMA) of the sensorimotor network decreased significantly in the asthma group.ConclusionThis study showed that the ability of emotion regulation and the efficiency of visual and cognitive information processing in patients with BA was lower than in those in the HC group. The dVMHC analysis can be used to sensitively evaluate oxygen saturation, visual function changes, and attention bias caused by emotional disorders in patients with asthma, as well as to predict airway hyperresponsiveness, inflammatory progression, and dyspnea.
Opioid-induced short-term consciousness improvement in patients with disorders of consciousness
Authors: Ge Qianqian , Wang Yanjun , Zhuang Yutong , Li Qinghua , Han Ruquan , Guo Wenzhi , He Jianghong 
Published: February 2023

IntroductionEffective treatment to facilitate recovery from prolonged disorders of consciousness is a complex topic for the medical community. In clinical practice, we have found that a subset of patients has a short-term improvement of consciousness after general anesthesia.MethodsTo determine the clinical factors responsible for the consciousness improvement, we enrolled 50 patients with disorders of consciousness who underwent surgery from October 2021 to June 2022. Their states of consciousness were evaluated before surgery, within 48 h after surgery, and 3 months after surgery. Clinical-related factors and intraoperative anesthetic drug doses were collected and compared between patients with and without consciousness improvement. Independent associations between selected factors and postoperative improvement were assessed using multivariate logistical regression analyses.ResultsPostoperative short-term consciousness improvement was found in 44% (22/50) of patients, with significantly increased scores of auditory and visual subscales. Patients with traumatic etiology, a preoperative diagnosis of minimally conscious state, and higher scores in the auditory, visual, and motor subscales were more likely to have postoperative improvement. This short-term increase in consciousness after surgery correlated with patients’ abilities to communicate in the long term. Furthermore, the amount of opioid analgesic used was significantly different between the improved and non-improved groups. Finally, analgesic dose, etiology, and preoperative diagnosis were independently associated with postoperative consciousness improvement.DiscussionIn conclusion, postoperative consciousness improvement is related to the residual consciousness of the patient and can be used to evaluate prognosis. Administration of opioids may be responsible for this short-term improvement in consciousness, providing a potential therapeutic approach for disorders of consciousness.
Hepatoid adenocarcinoma of the stomach: CT findings
Authors: Yang Qian , Liu Yulin , Zhang Shuixia 
Published: February 2023

ObjectiveTo analyze the CT findings of hepatoid adenocarcinoma of the stomach (HAS) and improve the diagnosis accuracy of this condition.MethodsThe CT images of 22 pathologically confirmed HAS patients were analyzed retrospectively. We investigated the location of lesions, morphology, enhancement features, area of invasion into surrounding organs, lymph node metastasis, and venous tumor thrombus.ResultsAmong the 22 patients (17 men and 5 women, the mean age was 61.41 ± 9.83 years ranging from 36 to 80 years) with HAS; the morphology of tumors included mass (n = 5), focal ulcer (n = 7), and infiltrating ulcer (n = 10). Extraserous fat was invaded in 12 cases. Enhancement scans showed continuous enhancement in all cases. The CT values of unenhanced scan, the arterial phase, and the portal venous phase are 30.36 ± 6.46, 60.91 ± 17.80, and 75.64 ± 22.09 (Hounsfield Unit, HU), respectively. In six cases, the tumor infiltrated the surrounding organs: liver (n = 1), pancreas (n = 2), and both liver and pancreas (n = 3). In 16 out of 22 patients (72.3%), suspicious lymph node metastasis at CT imaging has then been confirmed by pathological specimens. Intrahepatic metastasis was found in 14 cases. Seven patients had venous tumor thrombus: three patients developed tumor thrombus in the main trunk and intrahepatic branches of the portal vein and two patients in the portal vein, splenic vein, and superior mesenteric vein simultaneously.ConclusionThe CT scans of HAS often show a thickened gastric wall and infiltrating ulceration. Infiltration into extraserosal fat is often seen. Enhancement scans show a continuous and progressive enhancement of lesions. Lymph node metastasis, intrahepatic metastasis, and portal vein tumor thrombus are common in HAS patients.
Preliminary study on CT contrast-enhanced radiomics for predicting central cervical lymph node status in patients with thyroid nodules
Authors: Kong Dan , Shan Wenli , Zhu Yan , Xu Qingqing , Duan Shaofeng , Guo Lili 
Published: February 2023

ObjectiveTo explore the feasibility of using a contrast-enhanced CT image-based radiomics model to predict central cervical lymph node status in patients with thyroid nodules.MethodsPretreatment clinical and CT imaging data from 271 patients with surgically diagnosed and treated thyroid nodules were retrospectively analyzed. According to the pathological features of the thyroid nodules and central lymph nodes, the patients were divided into three groups: group 1: papillary thyroid carcinoma (PTC) metastatic lymph node group; group 2: PTC nonmetastatic lymph node group; and group 3: benign thyroid nodule reactive lymph node group. Radiomics models were constructed to compare the three groups by pairwise classification (model 1: group 1 vs group 3; model 2: group 1 vs group 2; model 3: group 2 vs group 3; and model 4: group 1 vs groups (2 + 3)). The feature parameters with good generalizability and clinical risk factors were screened. A nomogram was constructed by combining the radiomics features and clinical risk factors. Receiver operating characteristic (ROC) curve, calibration curve and decision curve analysis (DCA) were performed to assess the diagnostic and clinical value of the nomogram.ResultsFor radiomics models 1, 2, and 3, the areas under the curve (AUCs) in the training group were 0.97, 0.96, and 0.93, respectively. The following independent clinical risk factors were identified: model 1, arterial phase CT values; model 2, sex and arterial phase CT values; model 3: none. The AUCs for the nomograms of models 1 and 2 in the training group were 0.98 and 0.97, respectively, and those in the test group were 0.95 and 0.87, respectively. The AUCs of the model 4 nomogram in the training and test groups were 0.96 and 0.94, respectively. Calibration curve analysis and DCA revealed the high clinical value of the nomograms of models 1, 2 and 4.ConclusionThe nomograms based on contrast-enhanced CT images had good predictive efficacy in classifying benign and malignant central cervical lymph nodes of thyroid nodule patients.
Minimal adverse outcomes of postnatal cytomegalovirus infection in term or moderate and late preterm infants
Authors: Chen Jie , Zhou Yineng , Tang Jie , Xu Chenyu , Chen Liping , Xu Biyun , Dai Yimin , Hu Yali , Zhou Yi-Hua 
Published: February 2023

ObjectiveThe aim of study was to investigate at what extent breastfeeding and vaginal delivery can increase mother-to-child transmission of cytomegalovirus (CMV) and to observe the clinical outcomes of postnatal infection in term or moderate and late preterm infants.MethodsIn this retrospective study of prospectively collected clinical data and serum samples, during 2012–2015, 380 women with CMV IgG positive/IgM negative and their 384 infants (4 twin pairs) with gestational age ≥32 weeks were included. CMV IgG and IgM were measured with enzyme-linked immunosorbent assay.ResultsOf 384 infants followed up at 10.2 ± 2.3 months age, 177 (46.1%) were defined with CMV infection based on the presence of higher CMV IgG levels than in their mothers. The infection rate in 190 breastfed infants was higher than in 194 formula-fed infants (62.6% vs. 29.9%, P &lt; 0.001). Vaginally delivered infants (172) had higher CMV infection rate than 212 infants delivered by caesarean section (55.2% vs. 38.7%, P = 0.001). Compared with formula feeding and caesarean section, breastfeeding and vaginal delivery increased postnatal CMV infection respectively (OR = 3.801, 95% CI 2.474–5.840, P &lt; 0.001; OR = 1.818, 95% CI 1.182–2.796, P = 0.007). Nevertheless, compared to uninfected infants, CMV-infected infants had comparable height and body weight and showed no adverse effect on the liver enzymes.ConclusionBreastfeeding and vaginal delivery can increase postnatal CMV infection; however, the infection does not influence the growth of the term infants or preterm infants with gestational age ≥32 weeks. Thus, breastfeeding should be encouraged in these infants regardless of maternal CMV IgG status.
Neonatal sclerosing cholangitis with novel mutations in DCDC2 (doublecortin domain-containing protein 2) in Chinese children
Authors: Wei Xia , Fang Yuan , Wang Jian-She , Wang Yi-Zhen , Zhang Yuan , Abuduxikuer Kuerbanjiang , Chen Lian 
Published: February 2023

BackgroundNeonatal sclerosing cholangitis (NSC) is a rare and severe autosomal recessive inherited liver disease with mutations in DCDC2, commonly requiring liver transplantation (LT) for decompensated biliary cirrhosis in childhood.MethodsThe information of four Chinese patients with NSC caused by mutations in DCDC2 from Children's Hospital of Fudan University were gathered. The four patients' clinicopathological and molecular features were summarized by clinical data, liver biopsy, immunohistochemical, and molecular genetic analysis.ResultsAll patients presented with jaundice, hepatosplenomegaly, hyperbilirubinemia and bile embolism, and high serum γ-glutamyl transferase activity (GGT). Liver biopsies revealed varying degrees of bile duct hyperplasia, portal-tract inflammation, and/or fibrosis. Whole-exome sequencing (WES) found novel heterozygous variants of c.1024-1G &gt; T /p.? and c.544G &gt; A /p. Gly182Arg in the DCDC2.ConclusionThis study expands the genetic spectrum of DCDC2 in NSC.