bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-Wide Effects on Gene Expression Between Parental and Filial Generations of Trisomy 11 and 12 of Rice
Authors: Sun Shang , Liu Kai , Xue Chao , Hu Yingying , Yu Hengxiu , Qi Guoxiao , Chen Jijin , Li Xiya , Zhao Xinru , Gong Zhiyun 
Published: March 2023

AbstractAneuploid refers to the gene dosage imbalance due to copy number alterations. Aneuploidy is generally harmful to the growth, development and reproduction of organisms according to the numerous research. However, it has rarely been reported on whether aneuploid have a relevant pattern of genome expression between the parental and its offspring generations. In this study, mRNA sequencing analysis was performed on rice (Oryza sativa L.) primary trisomes 11 and 12, same primary trisomes and normal individuals in their filial generation. We systematically summarized the changes in gene expression patterns that occur on cis genes and on trans genes between parental and filial generations. In T11 and T12, the ratio of cis-gene expression showed intermediate type in parents and dosage compensation in filial generations, which maybe due to more genes being downregulated. The trans genes were also affected by aneuploidy and manifested as cis-related. The strains with normal chromosomes in filial generations, there are still aneuploid-sensitive genes differentially expressed in their genomes, indicating that the effect of aneuploidy is far-reaching and could not be easily eliminated. Meanwhile, among these differentially expressed genes, genes with low-expression level were more likely to be upregulated, while genes with medium- and high-expression level were easy to be downregulated. For the different types of rice aneuploid, upregulated genes were mainly associated with genomic imbalance while downregulated genes were mainly influenced by the specific added chromosome. In conclusion, our results provide new insights into the genetic characterization and evolution of biological aneuploidy genomes.
Exploration of lung mycobiome in the patients with non-small-cell lung cancer
Authors: Zhao Yiming , Yi Junqi , Xiang Juanjuan , Jia Wei , Chen Anqi , Chen Liyu , Zheng Leliang , Zhou Wen , Wu Minghua , Yu Zheng , Tang Jingqun 
Published: March 2023

AbstractAs the Human Microbiome Project (HMP) progresses, the relationship between microbes and human health has been receiving increasing attention. A growing number of reports support the correlation between cancer and microbes. However, most studies have focused on bacteria, rather than fungal communities. In this study, we studied the alteration in lung mycobiome in patients with non-small-cell lung cancer (NSCLC) using metagenomic sequencing and qPCR. The higher fungal diversity and more complex network were observed in the patients with NSCLC. In addition, Alternaria arborescens was found as the most relevant fungus to NSCLC, and the enrichment of it in cancerous tissue was also detected. This study proposes that the changes in fungal communities may be closely related to lung cancer, and provides insights into further exploration the relationship between lung cancer and fungi.
Morphological and physiological adaptation characteristics of lithophytic bryophytes to karst high calcium environment
Authors: Meng Wenping , Ran Jingcheng , Dai Quanhou , Tu Na , Leng Tingjiao , Ren Qingqing 
Published: March 2023

Abstract
Background
Lithophytic bryophytes grow on the rock surface, change the habitat on the rock surface through biological karstification, and provide a material basis for the growth of other plants. However, the surface calcium content of bare rock is high. The lithophytic bryophytes may have a special mechanism to adapt to the karst high calcium environment. The present study aimed to explore the physiological regulation process of karst lithophytic bryophytes under high calcium environment, and to provide scientific basis for revealing the maintenance mechanism of karst biodiversity.

Results
With the increase of Ca2+ concentration, the contents of Pro, SP and MDA of lithophytic bryophytes showed a downward—upward—downward trend. However, when Ca2+ ≥ 400 mmol/L, the contents of Pro and SP changed significantly at 1d, 2d, 3d, 5d and 7d with the extension of culture time, and lithophytic bryophytes died after 2 months of culture. Under different Ca2+ concentrations, the maximum SOD activity of lithophytic bryophytes is 1758.00 (U/g FW), the minimum is 92.60 (U/g FW), the maximum POD activity is 120.88 (U/g FW), and the minimum is 4.80 (U/g FW). The antioxidative activity of of Hyophila involuta are higher than that of Didymodon constrictus and Eurohypnum leptothallum, and its enzyme activity changed significantly with the increase of calcium concentration and time.At the same time, the contents of TChl, Chla, and Chlb in lithophytic bryophytes decreased with the increase of Ca2+ concentration. When Ca2+ = 400 mmol/L, the contents of TChl and Chla were the lowest, but when Ca2+ > 400 mmol/L, they began to increase. In addition, ABA is negatively correlated with TChl and Chla, and positively correlated with ROS. It shows that ABA has a certain role in regulating the adaptation of lithophytic bryophytes to high calcium environment.

Conclusions
Lithophytic bryophytes have strong calcium tolerance, and their physiological response to high calcium stress is different from vascular bundle plants. The general stress principle is not applicable to lithophytic bryophytes. The response of lithophytic bryophytes to the change of Ca2+concentration is slow, showing passive response or inert response.
A successful defence strategy in grapevine cultivar ‘Tocai friulano’ provides compartmentation of grapevine Flavescence dorée phytoplasma
Authors: Casarin Sofia , Vincenzi Simone , Esposito Antonella , Filippin Luisa , Forte Vally , Angelini Elisa , Bertazzon Nadia 
Published: March 2023

Abstract
Background
Flavescence dorée (FD) is a grapevine disease caused by phytoplasma and it is one of the most destructive pathologies in Europe. Nowadays, the only strategies used to control the epidemics are insecticides against vector, but more sustainable techniques are required. Completely resistant Vitis vinifera varieties have not been uncovered yet, but differences in susceptibility among cultivars and spontaneous recovery from FD symptoms have been observed. The grapevine cultivar ‘Tocai friulano’ shows very low susceptibility to FD but its defence strategy to counteract the phytoplasma spread has not been deciphered yet. In this work, the mechanisms occurring within ‘Tocai friulano’ FD-infected plants were examined in depth to identify the phytoplasma distribution and the defence pathways involved.

Results
In ‘Tocai friulano’ symptoms of FD-infection remained confined near the area where they appeared during all the vegetative season. Analyses of secondary phloem showed a total absence of FD phytoplasma (FDp) in the trunk and its disappearance in 2-year-old arms from July to November, which was different from ‘Pinot gris’, a highly susceptible variety.
Diverse modulations of defence genes and accumulation of metabolites were revealed in 1-year-old canes of ‘Tocai friulano’ FD-infected plants, depending on the sanitary status. Symptomatic portions showed high activation of both jasmonate- and salicylate-mediated responses, together with a great accumulation of resveratrol. Whereas activation of jasmonate-mediated response and high content of ε-viniferin were identified in asymptomatic 1-year-old cane portions close to the symptomatic ones.

Conclusion
Successful defence mechanisms activated near the symptomatic areas allowed the compartmentation of FD symptoms and phytoplasmas within the infected ‘Tocai friulano’ plants. These results could suggest specific agronomical practices to be adopted during FD management of this variety, and drive research of resistance genes against FD.
Season, storage and extraction method impact on the phytochemical profile of Terminalia ivorensis
Authors: Moomin Aliu , Russell Wendy R. , Knott Rachel M. , Scobbie Lorraine , Mensah Kwesi Boadu , Adu-Gyamfi Paa Kofi Tawiah , Duthie Susan J. 
Published: March 2023

Abstract
Background
Terminalia ivorensis (TI) is used in West African ethnomedicine for the treatment of conditions including ulcers, malaria and wounds. Despite its widespread use, the phytochemical profile of TI remains largely undetermined. This research investigated the effects of extraction method, season, and storage conditions on the phytochemical composition of TI to contribute towards understanding the potential benefits.

Methods
TI bark was collected in September 2014, September 2018 and February 2018 during the rainy or dry seasons in Eastern Region, Ghana. Samples were extracted sequentially with organic solvents (petroleum ether, chloroform, ethyl acetate and ethanol) or using water (traditional). Metabolites were identified by liquid chromatography–mass spectrometry/mass spectrometry and compared statistically by ANOVA.

Results
A total of 82 different phytochemicals were identified across all samples. A greater yield of the major phytochemicals (44%, p < 0.05) was obtained by water as compared with organic extraction. There was also a higher concentration of metabolites present in cold (63%, p < 0.05) compared with hot water extraction. A significantly (p < 0.05) higher number of phytochemicals were identified from TI collected in the dry (85%) compared to the rainy season (69%). TI bark stored for four years retained 84% of the major phytochemicals.

Conclusion
This work provides important information on composition and how this is modified by growing conditions, storage and method of extraction informing progress on the development of TI as a prophylactic formulation or medicine.
Study on the effectiveness and safety of ciprofol in anesthesia in gynecological day surgery: a randomized double-blind controlled study
Authors: Man Yan , Xiao Hongyi , Zhu Teng , Ji Fanceng 
Published: March 2023

Abstract
Backgroud
ciprofol is a new type of intravenous anesthetic, which is a tautomer of propofol, with the characteristics of less injection pain, less respiratory depression and higher potency, but little clinical experience. The aim of this study was to observe the efficacy and safety of the application of ciprofol in ambulatory surgery anesthesia in gynecology.

Methods
128 patients were selected to undergo gynecological day surgery under general anesthesia, and the patients were randomly divided into the ciprofol group and the propofol group, with 64 cases in each group. During anesthesia induction, the ciprofol group was infused at a time limit of 0.5 mg/kg for one minute, and the propofol group was infused at a time limit of 2 mg/kg for 1 min. The overall incidence of adverse events was the primary outcome for this study, while secondary outcomes included the success rate of anesthesia induction, the time of loss of consciousness, the time of awakening,top-up dose and frequency of use of rescue drugs.

Results
The overall incidence of adverse events was significantly lower in the ciprofol group compared with the propofol group (56.2% vs. 92.2%,P < 0.05). The success rate of anesthesia induction of ciprofol and propofol group was 100.0%. The time of loss of consciousness of the ciprofol group was longer than that of the propofol group (1.6 ± 0.4 min vs. 1.4 ± 0.2 min, P < 0.05). The time of awakening was not statistically significant (5.4 ± 2.8 min vs. 4.6 ± 1.6 min, P > 0.05). The number of drug additions and resuscitation drugs used were not statistically significant.

Conclusions
Compared with propofol, ciprofol had a similar anesthetic effect in gynecological ambulatory surgery, and the incidence of adverse events in the ciprofol group was lower.
Sub-clinical rheumatic heart disease (RHD) detected by hand-held echocardiogram in children participating in a school-based RHD prevention program in Tanzania
Authors: Chillo Pilly , Mutagaywa Reuben , Nkya Deogratias , Njelekela Marina , Kwesigabo Gideon , Kahabuka Febronia , Kerry Vanessa , Kamuhabwa Appolinary 
Published: March 2023

Abstract
Background
Rheumatic Heart Disease (RHD) continues to cause suffering and premature deaths in many sub-Saharan Africa (SSA) countries, where the disease is still endemic. RHD is largely preventable and determining its community burden is an important critical step in any RHD prevention program.

Methods
We conducted a cross-sectional study of 5–16 years old pupils from 11 primary schools participating in an RHD prevention program in 4 districts in Tanzania, between 2018 and 2019. At the school, all children were invited to participate after receiving consent from their parents/guardians. Participating children filled a questionnaire and were auscultated for cardiac murmurs. Echocardiographic screening was done by two experienced cardiologists, using a hand-held machine (V-Scan, GE®). All positive screening tests were stored for further examination by the same two cardiologists to reach to a consensus of definite, borderline or no RHD, using a modified World Heart Federation (WHF) criterion.

Results
Of the 6895 children invited, 4738 (68.7%) were screened and 4436 (64.3%) had complete data. The mean (SD) age was 10.04 (2.43) years, and 2422 (54.6%) were girls. Fifty three (1.2%) children were found to have a murmur. The proportion of children with trace or mild valvular regurgitation, sub-valvular/chordal thickening and valvular thickening/deformity were 8.3%, 1.3%, and 1.0%, respectively. Sub-clinical RHD was found in 95 children (59 definite and 36 borderline), giving a prevalence of 2.1%, [95% CI 1.7% – 2.6%]. Sub-clinical RHD was independently associated with female sex (aOR 1.83, 95% CI 1.18–2.85, p = 0.007), older age groups (aOR 1.73, 95% CI 1.10–2.72, p = 0.018 for age group 11–14 years; and aOR 3.02 95% CI 1.01–9.05, p = 0.048 for age group 15–16 years), as well as presence of a cardiac murmur, aOR 5.63 95% CI 2.31–13.69, p < 0.0001. None of the studied socio- or economic factors was associated with the presence of sub-clinical RHD in this study.

Conclusion
The prevalence of sub-clinical RHD among primary school children in Tanzania is 2.1%, similar to previous reports in SSA. Efforts to prevent and control RHD in our communities are highly warranted.
A new cure model that corrects for increased risk of non-cancer death: analysis of reliability and robustness, and application to real-life data
Authors: Botta Laura , Goungounga Juste , Capocaccia Riccardo , Romain Gaelle , Colonna Marc , Gatta Gemma , Boussari Olayidé , Jooste Valérie 
Published: March 2023

AbstractBackgroundNon-cancer mortality in cancer patients may be higher than overall mortality in the general population due to a combination of factors, such as long-term adverse effects of treatments, and genetic, environmental or lifestyle-related factors. If so, conventional indicators may underestimate net survival and cure fraction. Our aim was to propose and evaluate a mixture cure survival model that takes into account the increased risk of non-cancer death for cancer patients.MethodsWe assessed the performance of a corrected mixture cure survival model derived from a conventional mixture cure model to estimate the cure fraction, the survival of uncured patients, and the increased risk of non-cancer death in two settings of net survival estimation, grouped life-table data and individual patients’ data. We measured the model’s performance in terms of bias, standard deviation of the estimates and coverage rate, using an extensive simulation study. This study included reliability assessments through violation of some of the model’s assumptions. We also applied the models to colon cancer data from the FRANCIM network.ResultsWhen the assumptions were satisfied, the corrected cure model provided unbiased estimates of parameters expressing the increased risk of non-cancer death, the cure fraction, and net survival in uncured patients. No major difference was found when the model was applied to individual or grouped data. The absolute bias was < 1% for all parameters, while coverage ranged from 89 to 97%. When some of the assumptions were violated, parameter estimates appeared more robust when obtained from grouped than from individual data. As expected, the uncorrected cure model performed poorly and underestimated net survival and cure fractions in the simulation study. When applied to colon cancer real-life data, cure fractions estimated using the proposed model were higher than those in the conventional model, e.g. 5% higher in males at age 60 (57% vs. 52%).ConclusionsThe present analysis supports the use of the corrected mixture cure model, with the inclusion of increased risk of non-cancer death for cancer patients to provide better estimates of indicators based on cancer survival. These are important to public health decision-making; they improve patients’ awareness and facilitate their return to normal life.
Strong recommendations from low certainty evidence: a cross-sectional analysis of a suite of national guidelines
Authors: Chong Ming Chuen , Sharp Melissa K. , Smith Susan M. , O’Neill Michelle , Ryan Máirín , Lynch Rosarie , Mahtani Kamal R. , Clyne Barbara 
Published: March 2023

Abstract
Background
Clinical guidelines should be based on a thorough evaluation of the evidence and generally include a rating of the quality of evidence and assign a strength to recommendations. Grading of Recommendations Assessment, Development and Evaluation (GRADE) guidance warns against making strong recommendations when the certainty of the evidence is low or very low, but has identified five paradigmatic situations (e.g. life-threatening situations) where this may be justified.

Aims and objectives
We aimed to characterize the strength of recommendations and certainty of the evidence in Irish National Clinical Guidelines using the GRADE approach.

Methods
All National Clinical Guidelines from the National Clinical Effectiveness Committee (NCEC) website using the GRADE approach (fully or partially) were included. All recommendations and their corresponding certainty of the evidence, strength of recommendations and justifications were extracted. Authors classified instances of strong recommendations with low certainty evidence (referred to as discordant recommendations) into one of the five paradigmatic situations. Descriptive statistics were calculated.

Results
From the 29 NCEC Clinical Guidelines available at the time of analysis, we identified 8 guidelines using GRADE with a total of 240 recommendations; 38 recommendations did not use the GRADE approach and were excluded. Half of the included guidelines focused on emergency situations. In the final dataset of 202 recommendations, 151 (74.7%) were classified as strong and 51 (25.3%) as conditional. Of the 151 strong recommendations, 55 (36.4%) were supported by high or moderate certainty evidence and 96 (63.6%) by low or very low certainty evidence and were considered discordant. Of these 96 discordant recommendations, 55 (73.7%) were consistent with one of the five paradigmatic situations. However, none were specifically described as such within the guidelines.

Conclusions
The proportion of discordant recommendations identified in this analysis was higher than some previous international studies (range of all strong recommendations being discordant 30–50%), but similar to other guidelines focused on emergency situations. The majority of discordant recommendations could be mapped to one of the five situations, but no National Clinical Guideline explicitly referenced this. Guideline developers require further guidance to enable greater transparency in the reporting of the reasons for discordant recommendations.
Prognostic significance of the Naples prognostic score in colorectal cancer patients undergoing curative resection: a propensity score matching analysis
Authors: Sugimoto Atsushi , Fukuoka Tatsunari , Shibutani Masatsune , Kasashima Hiroaki , Kitayama Kishu , Ohira Masaichi , Maeda Kiyoshi 
Published: March 2023

Abstract
Background
Systemic inflammation is recognized as a hallmark of cancer that contributes to tumor development and progression in various malignancies. The Naples prognostic score (NPS) was established as a prognostic indicator for colorectal cancer (CRC). This study aims to examine the predictive value of the NPS for survival in CRC patients undergoing curative resection by a propensity score matching (PSM) analysis.

Methods
A total of 533 CRC patients were enrolled in this study. Overall survival (OS) and disease-free survival (DFS) were compared between high-NPS and low-NPS groups. A time-dependent receiver operator characteristic (ROC) curve analysis was conducted to calculate the area under curve (AUC) of the NPS for OS. A multivariable Cox-proportional hazards regression analysis and PSM analysis were used to identify independent prognostic factors for OS and DFS. We compared the predictive value of the NPS to that of the neutrophil-to-lymphocyte ratio (NLR), lymphocyte-to-monocyte ratio (LMR), platelet-to-lymphocyte ratio (PLR), Onodera prognostic nutritional index (PNI), and controlling nutritional status score (CONUT) for OS.

Results
High-NPS was significantly associated with worse OS and DFS. After PSM, 123 patients were included in each group. A multivariate analysis revealed that Age ≥ 68, ASA-PS ≥ 3, high NPS and undifferentiated tumor type were independently associated with OS, while high NPS, advanced T and N stage were independently associated with DFS after PSM. The NPS had the greatest AUC for OS in comparison to the NLR, LMR, PNI and CONUT.

Conclusions
We successfully validated the prognostic utility of the NPS for CRC patients after curative resection.