bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimal planting density of Agave for maximising aboveground biomass: A systematic literature review
Authors: Crawford William , Tan Daniel K. Y. , Van Ogtrop Floris 
Published: December 2022

There are hundreds of species of Agaves found globally in natural and anthropogenic systems. Agaves are used to produce fibres, alcoholic beverages like tequila, and in biofuel production. The objectives of this study were to assess the research available into Agave planting density and to use PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) to suggest an optimum planting density for the highest dry aboveground productivity. Background research into Agave planting densities found little data on the effect of planting density on biomass production, with most studies focusing on other independent variables affecting productivity. There were 13 data points included in the analysis. The meta-analysis suggested that the optimal planting density of Agave is approximately 2,600 plants ha−1, which provides optimal dry aboveground biomass of 28.8 Mg ha−1 yr−1. These findings provide a framework for further experimentation in Australian conditions using a Nelder design density experiment to ground-truth the meta-analysis.
Performance evaluation and clinical validation of optimized nucleotide MALDI-TOF-MS for mycobacterial identification
Authors: Li Baiying , Zhu Chi , Sun Lifang , Dong Hang , Sun Yaping , Cao Shangzhi , Zhen Libo , Qi Qi , Zhang Quanquan , Mo Ting , Wang Huijie , Qiu Meihua , Song Chao , Cai Qingshan 
Published: December 2022

ObjectiveTo evaluate the performance and validate the diagnostic value of a nucleotide matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS) with the analysis process optimized in identification of mycobacterium species.MethodsThe optimized analysis process was used for mycobacterial identification in the nucleic MALDI-TOF-MS. 108 samples were used for assessing the performance of nucleic MALDI-TOF-MS, including 25 reference standards, 37 clinical isolates, 37 BALF, and 9 plasmids. The BALF of 38 patients suspected of pulmonary mycobacterial infection was collected for validation. Clinical etiological diagnosis was used as the gold standard to evaluate the diagnostic value of nucleotide MALDI-TOF-MS.ResultsThe sensitivity, specificity, and accuracy of the nucleotide MALDI-TOF-MS in mycobacterial identification were 96.91%, 100% and 97.22%, respectively, and the limit of detection for mycobacterium tuberculosis (MTB) was 50 bacteria/mL. Among 38 patients suspected of pulmonary mycobacterial infection, 33 were diagnosed with pulmonary tuberculosis infection, and 5 with non-mycobacterial infection. In clinical validation, the positive rates of MALDI-TOF-MS, Xpert MTB/RIF, culture and AFS in BALF of patients diagnosed with tuberculosis infection were 72.7%, 63.6%, 54.5% and 27.3%, respectively. The sensitivity/specificity of MALDI-TOF-MS, Xpert, culture and AFS in diagnosing MTB were 72.7%/100%, 63.6%/100%, 54.5%/100%, 27.3%/100%, with the areas under the curve of 0.864, 0.818, 0.773, and 0.636, respectively.ConclusionOptimized nucleotide MALDI-TOF-MS has satisfactory sensitivity, specificity and low LOD in the identification of mycobacteria, which may serve as a potential assay for mycobacterial identification.
Effect of alirocumab and evolocumab on all-cause mortality and major cardiovascular events: A meta-analysis focusing on the number needed to treat
Authors: Wang Hong-Fei , Mao Yu-Cheng , Xu Xin-Yi , Zhao Si-Yu , Han Dan-Dan , Ge Shi-Yao , Song Kai , Geng Chang , Tian Qing-Bao 
Published: December 2022

AimsThe efficacy of anti-proprotein convertase subtilisin/Kexin type 9 (PCSK9) monoclonal antibodies in patients with atherosclerotic cardiovascular disease (ASCVD) remains unclear. Therefore, this study aims to assess the effect of PCSK9 inhibitors (alirocumab and evolocumab) on ASCVD patients considering the number needed to treat (NNT).MethodsWe reviewed randomized controlled trials (RCTs) which compared the effects of alirocumab or evolocumab and placebo or standards of care. All articles were published in English up to May 2022. Using random effect models, we estimated risk ratios (RRs), NNT, and 95% confidence intervals (CI).ResultsWe incorporated 12 RCTs with 53 486 patients total, of which 27 674 received PCSK9 inhibitors and 25 812 received placebos. The mean follow-up duration was 1.56 years. The effect of PCSK9 inhibitors on major adverse cardiovascular events (MACE) was statistically significant, and the corresponding mean NNT was 36. Alirocumab reduced the risk of MACE, stroke, and coronary revascularization; the corresponding mean NNT were 37, 319, and 107, respectively. Evolocumab positively affected MACE, myocardial infarction, stroke, and coronary revascularization; the corresponding mean NNT were 32, 78, 267, and 65, respectively. The effects of alirocumab or evolocumab on all-cause mortality and cardiovascular mortality were not statistically significant.ConclusionThis study suggests that preventing one patient from MACE needed to treat 36 patients with ASCVD with PCSK9 inhibitors for 1.56 years. Both alirocumab and evolocumab reduced MACE, stroke, and coronary revascularization. Evolocumab had a positive effect on myocardial infarction, but no effects were noted for alirocumab. In addition, alirocumab may not be as effective as evolocumab. NNT visualizes the magnitude of efficacy to assist in clinical decisions.Systematic review registration[https://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=344908], identifier [CRD42022344908].
Psychological burden predicts new-onset diabetes in men: A longitudinal observational study in the Fukushima Health Management Survey after the Great East Japan earthquake
Authors: Hirai Hiroyuki , Nagao Masanori , Ohira Tetsuya , Maeda Masaharu , Okazaki Kanako , Nakano Hironori , Hayashi Fumikazu , Harigane Mayumi , Suzuki Yuriko , Takahashi Atsushi , Sakai Akira , Kazama Junichiro J. , Hosoya Mitsuaki , Yabe Hirooki , Yasumura Seiji , Ohto Hitoshi , Kamiya Kenji , Shimabukuro Michio 
Published: December 2022

BackgroundThe burden of psychological distress and post-traumatic stress disorder (PTSD) has been suggested as a factor in developing type 2 diabetes mellitus. However, longitudinal features in psychological distress- and PTSD-related new-onset diabetes mellitus have not been thoroughly evaluated.MethodsThe association between probable depression and probable PTSD and the risk of developing new-onset diabetes mellitus was evaluated in a 7-year prospective cohort of evacuees of the Great East Japan Earthquake in 2011. Probable depression was defined as a Kessler 6 scale (K6) ≥ 13 and probable PTSD as a PTSD Checklist—Stressor-Specific Version (PCL-S) ≥ 44.ResultsThe log-rank test for the Kaplan–Meier curve for new-onset diabetes mellitus was significant between K6 ≥ 13 vs. &lt; 13 and PCL-S ≥ 44 vs. &lt; 44 in men but not in women. In men, both K6 ≥ 13 and PCL-S ≥ 44 remained significant in the Cox proportional hazards model after multivariate adjustment for established risk factors and disaster-related factors, including evacuation, change in work situation, sleep dissatisfaction, and education.ConclusionThe post-disaster psychological burden of probable depression and probable PTSD was related to new-onset diabetes in men but not in women. In post-disaster circumstances, prevention strategies for new-onset diabetes might consider sex differences in terms of psychological burden.
A systematic review of lived experiences of people with polycystic ovary syndrome highlights the need for holistic care and co-creation of educational resources
Authors: Lau Gar Mun , Elghobashy Mirna , Thanki Mansi , Ibegbulam Shirley , Latthe Pallavi , Gillett Caroline D. T. , O’Reilly Michael W. , Arlt Wiebke , Lindenmeyer Antje , Kempegowda Punith ,   PCOS SEva Working Group
Published: December 2022

IntroductionPCOS-related literature is mostly dominated by the medical perspective. However, the condition’s lifelong, far reaching, and multifaceted impacts highlight the importance to gain the perspectives from those with PCOS. Therefore, we performed a systematic review to explore the current literatures and gaps around the experiences and perceptions of those living with PCOSMethodA comprehensive search of seven electronic databases was conducted between July and October 2021. A total 34 from 1615 screened articles were included in this systematic review and subsequently coded using NVivo 12 software. The quality of individual studies was assessed by adaptation to the Critical Appraisal Skills Program (CASP) quality assessment tool.ResultsFive domains were generated from the data: Signs/Symptoms, Diagnosis, Management, Perceptions, Resources and Improving Outcomes. Dissatisfaction surrounding the experience of diagnosis was common. Concerns surrounded perceived lack of knowledge from healthcare professionals and delays in diagnosis. Individual studies on adults and adolescents shared similar feelings. The consensus was found to be that current management was vague and generalised. Symptoms such as hirsutism, obesity, irregular menstruation challenge personal and societal expectations of femininity. Online PCOS resources are popular amongst those with PCOS but most of them lack evidence. A call for more culturally specific resources was found to be common ground amongst those with PCOS.ConclusionOverall dissatisfaction amongst adults and adolescents regarding their diagnostic journey of PCOS. Tailored and culturally specific PCOS advice and management is necessary and can be achieved through co-creation of resources between healthcare professionals and those with PCOS.Systematic review registrationhttps://www.crd.york.ac.uk/prospero/, identifier CRD42021272371.
Influential factors of urinary arsenic levels in the population residing close to one heavy-industrial area in Taiwan - A case study
Authors: Kaewlaoyoong Acharee , Huang Shih-Ting , Wang Shu-Li , Sun Chien-Wen , Chen Jia-Jen , Kuo Chao-Hung , Hung Chih-Hsing , Chen Szu-Chia , Liang Ching-Chao , Tsai Hsiao-Wen , Wu Chia-Fang , Lin Wen-Yi , Wu Ming-Tsang 
Published: December 2022

The public in southwestern Taiwan’s Kaohsiung City have expressed concern over risk of arsenic (As) to people living in six villages of that city nearby a coastal heavy-industrial area. To investigate, we first analyzed urinary total As (TAs) levels in 328 adult subjects from the Nutrition and Health Survey in Taiwan in 2005-2008 (NAHSIT 2005-8). We found the top three highest median urinary TAs levels in residents from the Penghu islands (150.90 µg/L, n = 21) and the upper northern region (78.04 µg/L, n = 56) and the southern region (75.21 µg/L, n = 33) of Taiwan. Then, urinary TAs levels in 1,801 and 1,695 voluntary adult residents of the above-mentioned six villages in 2016 and 2018 respectively were compared with those from the top three highest TAs levels of NAHSIT 2005-8. Median urinary As levels were 84.60 µg/L in 2016 and 73.40 µg/L in 2018, similar to those in the southern region of Taiwan, but far below those in the Penghu islands (p &lt; 0.05). Finally, in 2020, we interviewed 116 healthy adult residents from the same six villages and analyzed one-spot urine samples of total inorganic-related As (TiAs), a summation of As3+, As5+, monomethylarsonic acid, and dimethylarsinic acid. Subjects consuming seafood 2 days before urine sampling (n = 15) were significantly higher TiAs levels than those not (n = 101, p = 0.028). These findings suggest that seafood consumption is probably the main source of urinary TAs and TiAs in people residing close to that coastal heavy-industrial area.
Prognostic implications of necroptosis-related long noncoding RNA signatures in muscle-invasive bladder cancer
Authors: Jiang Kan , Wu Lingyun , Yin Xin , Tang Qiuying , Yin Jie , Zhou Ziyang , Yu Hao , Yan Senxiang 
Published: December 2022

Background: Bladder cancer (BLCA) is the sixth most common cancer in men, with an increasing incidence of morbidity and mortality. Necroptosis is a type of programmed cell death and plays a critical role in the biological processes of bladder cancer (BLCA). However, current studies focusing on long noncoding RNA (lncRNA) and necroptosis in cancer are limited, and there is no research about necroptosis-related lncRNAs (NRLs) in BLCA.Methods: We obtained the RNA-seq data and corresponding clinical information of BLCA from The Cancer Genome Atlas (TCGA) database. The seven determined prognostic NLRs were analyzed by several methods and verified by RT-qPCR. Then, a risk signature was established based on the aforementioned prognostic NLRs. To identify it, we evaluated its prognostic value by Kaplan–Meier (K-M) survival curve and receiver operating characteristics (ROC) curve analysis. Moreover, the relationships between risk signature and clinical features, functional enrichment, immune landscape, and drug resistance were explored as well.Results: We constructed a signature based on seven defined NLRs (HMGA2-AS1, LINC02489, ETV7-AS1, EMSLR, AC005954.1, STAG3L5P-PVRIG2P-PILRB, and LINC02178). Patients in the low-risk cohort had longer survival times than those in the high-risk cohort, and the area under the ROC curve (AUC) value of risk signature was higher than other clinical variables. Functional analyses, the infiltrating level of immune cells and functions, ESTIMATE score, and immune checkpoint analysis all indicated that the high-risk group was in a relatively immune-activated state. In terms of treatments, patients in the high-risk group were more sensitive to immunotherapy, especially anti-PD1/PD-L1 immunotherapy and conventional chemotherapy.Conclusion: The novel NLR signature acts as an invaluable tool for predicting prognosis, immune microenvironment, and drug resistance in muscle-invasive bladder cancer (MIBC) patients.
FCGR2C: An emerging immune gene for predicting sepsis outcome
Authors: Liu Si , Zhang Yao Lu , Zhang Lu Yao , Zhao Guang Ju , Lu Zhong Qiu 
Published: December 2022

BackgroundSepsis is a life-threatening disease associated with immunosuppression. Immunosuppression could ultimately increase sepsis mortality. This study aimed to identify the prognostic biomarkers related to immunity in sepsis.MethodsPublic datasets of sepsis downloaded from the Gene Expression Omnibus (GEO) database were divided into the discovery cohort and the first validation cohort. We used R software to screen differentially expressed genes (DEGs) and analyzed DEGs’ functional enrichment in the discovery dataset. Immune-related genes (IRGs) were filtered from the GeneCards website. A Lasso regression model was used to screen candidate prognostic genes from the intersection of DEGs and IRGs. Then, the candidate prognostic genes with significant differences were identified as prognostic genes in the first validation cohort. We further validated the expression of the prognostic genes in the second validation cohort of 81 septic patients recruited from our hospital. In addition, we used four immune infiltration methods (MCP-counter, ssGSEA, ImmuCellAI, and CIBERSORT) to analyze immune cell composition in sepsis. We also explored the correlation between the prognostic biomarker and immune cells.ResultsFirst, 140 genes were identified as prognostic-related immune genes from the intersection of DEGs and IRGs. We screened 18 candidate prognostic genes in the discovery cohort with the lasso regression model. Second, in the first validation cohort, we identified 4 genes (CFHR2, FCGR2C, GFI1, and TICAM1) as prognostic immune genes. Subsequently, we found that FCGR2C was the only gene differentially expressed between survivors and non-survivors in 81 septic patients. In the discovery and first validation cohorts, the AUC values of FCGR2C were 0.73 and 0.67, respectively. FCGR2C (AUC=0.84) had more value than SOFA (AUC=0.80) and APACHE II (AUC=0.69) in evaluating the prognosis of septic patients in our recruitment cohort. Moreover, FCGR2C may be closely related to many immune cells and functions, such as B cells, NK cells, neutrophils, cytolytic activity, and inflammatory promotion. Finally, enrichment analysis showed that FCGR2C was enriched in the phagosome signaling pathway.ConclusionFCGR2C could be an immune biomarker associated with prognosis, which may be a new direction of immunotherapy to reduce sepsis mortality.
Single-cell multiomics revealed the dynamics of antigen presentation, immune response and T cell activation in the COVID-19 positive and recovered individuals
Authors: Chattopadhyay Partha , Khare Kriti , Kumar Manish , Mishra Pallavi , Anand Alok , Maurya Ranjeet , Gupta Rohit , Sahni Shweta , Gupta Ayushi , Wadhwa Saruchi , Yadav Aanchal , Devi Priti , Tardalkar Kishore , Joshi Meghnad , Sethi Tavpritesh , Pandey Rajesh 
Published: December 2022

IntroductionDespite numerous efforts to describe COVID-19's immunological landscape, there is still a gap in our understanding of the virus's infections after-effects, especially in the recovered patients. This would be important to understand as we now have huge number of global populations infected by the SARS-CoV-2 as well as variables inclusive of VOCs, reinfections, and vaccination breakthroughs. Furthermore, single-cell transcriptome alone is often insufficient to understand the complex human host immune landscape underlying differential disease severity and clinical outcome.MethodsBy combining single-cell multi-omics (Whole Transcriptome Analysis plus Antibody-seq) and machine learning-based analysis, we aim to better understand the functional aspects of cellular and immunological heterogeneity in the COVID-19 positive, recovered and the healthy individuals.ResultsBased on single-cell transcriptome and surface marker study of 163,197 cells (124,726 cells after data QC) from the 33 individuals (healthy=4, COVID-19 positive=16, and COVID-19 recovered=13), we observed a reduced MHC Class-I-mediated antigen presentation and dysregulated MHC Class-II-mediated antigen presentation in the COVID-19 patients, with restoration of the process in the recovered individuals. B-cell maturation process was also impaired in the positive and the recovered individuals. Importantly, we discovered that a subset of the naive T-cells from the healthy individuals were absent from the recovered individuals, suggesting a post-infection inflammatory stage. Both COVID-19 positive patients and the recovered individuals exhibited a CD40-CD40LG-mediated inflammatory response in the monocytes and T-cell subsets. T-cells, NK-cells, and monocyte-mediated elevation of immunological, stress and antiviral responses were also seen in the COVID-19 positive and the recovered individuals, along with an abnormal T-cell activation, inflammatory response, and faster cellular transition of T cell subtypes in the COVID-19 patients. Importantly, above immune findings were used for a Bayesian network model, which significantly revealed FOS, CXCL8, IL1β, CST3, PSAP, CD45 and CD74 as COVID-19 severity predictors.DiscussionIn conclusion, COVID-19 recovered individuals exhibited a hyper-activated inflammatory response with the loss of B cell maturation, suggesting an impeded post-infection stage, necessitating further research to delineate the dynamic immune response associated with the COVID-19. To our knowledge this is first multi-omic study trying to understand the differential and dynamic immune response underlying the sample subtypes.
Predicting diagnostic gene expression profiles associated with immune infiltration in patients with lupus nephritis
Authors: Wang Lin , Yang Zhihua , Yu Hangxing , Lin Wei , Wu Ruoxi , Yang Hongtao , Yang Kang 
Published: December 2022

ObjectiveTo identify potential diagnostic markers of lupus nephritis (LN) based on bioinformatics and machine learning and to explore the significance of immune cell infiltration in this pathology.MethodsSeven LN gene expression datasets were downloaded from the GEO database, and the larger sample size was used as the training group to obtain differential genes (DEGs) between LN and healthy controls, and to perform gene function, disease ontology (DO), and gene set enrichment analyses (GSEA). Two machine learning algorithms, least absolute shrinkage and selection operator (LASSO) and support vector machine-recursive feature elimination (SVM-RFE), were applied to identify candidate biomarkers. The diagnostic value of LN diagnostic gene biomarkers was further evaluated in the area under the ROC curve observed in the validation dataset. CIBERSORT was used to analyze 22 immune cell fractions from LN patients and to analyze their correlation with diagnostic markers.ResultsThirty and twenty-one DEGs were screened in kidney tissue and peripheral blood, respectively. Both of which covered macrophages and interferons. The disease enrichment analysis of DEGs in kidney tissues showed that they were mainly involved in immune and renal diseases, and in peripheral blood it was mainly enriched in cardiovascular system, bone marrow, and oral cavity. The machine learning algorithm combined with external dataset validation revealed that C1QA(AUC = 0.741), C1QB(AUC = 0.758), MX1(AUC = 0.865), RORC(AUC = 0.911), CD177(AUC = 0.855), DEFA4(AUC= 0.843)and HERC5(AUC = 0.880) had high diagnostic value and could be used as diagnostic biomarkers of LN. Compared to controls, pathways such as cell adhesion molecule cam, and systemic lupus erythematosus were activated in kidney tissues; cell cycle, cytoplasmic DNA sensing pathways, NOD-like receptor signaling pathways, proteasome, and RIG-1-like receptors were activated in peripheral blood. Immune cell infiltration analysis showed that diagnostic markers in kidney tissue were associated with T cells CD8 and Dendritic cells resting, and in blood were associated with T cells CD4 memory resting, suggesting that CD4 T cells, CD8 T cells and dendritic cells are closely related to the development and progression of LN.ConclusionC1QA, C1QB, MX1, RORC, CD177, DEFA4 and HERC5 could be used as new candidate molecular markers for LN. It may provide new insights into the diagnosis and molecular treatment of LN in the future.
The spatial distribution of cystic echinococcosis in Italian ruminant farms from routine surveillance data
Authors: Entezami Mahbod , Nocerino Martina , Widdicombe Jo , Bosco Antonio , Cringoli Giuseppe , Casulli Adriano , Iacono Giovanni Lo , Rinaldi Laura , Prada Joaquin M. 
Published: December 2022

IntroductionCystic echinococcosis (CE) is a zoonotic parasite caused by the cestode Echinococcus granulosus sensu lato (s.l.) which predominantly affects livestock. The disease is endemic in central-southern and insular Italy, with CE particularly infecting sheep, goats, cattle, and water buffalo. The spatial distribution of CE in endemic regions is not widely understood, with surveillance efforts varying across the region.MethodsIn this study, we investigated the spatial distribution of CE in livestock using samples from farms across different livestock species using a Stochastic Partial Differential Equations (SPDE) model. Samples were collected during a survey conducted in the area of central-southern and insular Italy between the years 2019 – 2021.ResultsA total of 3141 animal samples (126 goats, 601 sheep and 2414 cattle and water buffalo) were inspected for Echinococcus s.l. cysts through routine surveillance in abattoirs by postmortem visual examination, palpation and incision of target organs. The geographic location of the farm of origin (a total of 2,878) for each sample was recorded. CE prevalence of 46.0% (1,323/2,878) was estimated at the farm level with 78.3% (462/590) of farms with sheep, 28.6% (36/126) of farms with goats, 36.5% (747/2,049) of farms with cattle, and 23.5% (102/434) of farms with water buffalo infected.DiscussionThe spatial model evaluated the probability of infection in farms across the sampled regions, with the distribution of CE showing high clustering of infected cattle farms in Sardinia and Sicily regions, and sheep farms in Salerno province (Campania region). The output of this study can be used to identify CE hot-spots and to improve surveillance and control programs in endemic areas of Italy.