Miracle-dz/UniFAR-FTUs huggingface dataset:
Sex difference in incidence of gastric cancer: an international comparative study based on the Global Burden of Disease Study 2017

Objectives To investigate sex difference in global gastric cancer incidence by year, age and socioeconomical status. Design An international comparative study. Setting We obtained the global and national sex-specific incidence of gastric caner by year and age from the Global Burden of Disease Study 2017. The human development index (HDI) in 2017 as an indicator of national socioeconomical status was extracted from the Human Development Report. Main outcome measures Sex-specific incidence of gastric cancer was compared by year and age at the global level. Linear regression analyses were performed to explore socioeconomic-associated sex difference in gastric cancer incidence. Results Despite declining incidence of global gastric cancer in both sexes between 1990 and 2017, relative sex difference showed an increasing trend, with male to female ratios of age-standardised incidence rates (ASRs) rising from 1.86 to 2.20. Sex difference was almost negligible under 45 years of age and relative difference maximised in the age range of 65–69 years with male to female ratios of ASRs being 2.74. Both absolute sex difference (standardised β=0.256, p<0.001) and relative difference (standardised β=0.387, p<0.001) in ASRs were positively associated with HDI. Conclusions This study revealed that decreasing incidence of global gastric cancer was accompanied by widening sex difference in the past few decades. Men always had higher incidence than women. Greater sex difference was found in older age and in more developed countries. These findings highlight the importance of making sex-sensitive health policy to cope with the global gastric cancer burden.
Selection constraints determine preference for A/U-ending codons in Taxus contorta.

Unequal utilization of synonymous codons is a well-known phenomenon among living organisms. This phenomenon plays a major role in the enhancement of the accuracy and efficiency of translation. Gymnosperms are rarely paid attention in this aspect. Understanding the degree of and determining the forces influencing the codon usage bias (CUB) in Taxus contorta, an endangered Himalayan gymnosperm, will prove useful in interpreting the evolutionary characteristics of this species. Using RNAseq data, 93,790 assembled transcripts were clustered into 32,701 unigenes. Around 13,061 full-length sequences were utilized for the analysis of CUB. Compositional properties showed that GC-content ranged from 28.76% to 65.22%, with an average value of 44.28%, suggesting an AT-rich genome. The mean ENC (effective number of codons) value revealed that CUB is not strong in T. contorta. The preferred codons tended to be A/U ending, whereas the avoided codons tended to be G/C ending. A P2 index of 0.54 and a Mutation Responsive Index (MRI) value of -0.02 in addition to the results revealed by the neutrality, ENC, and parity plots showed that natural selection is a predominating factor governing CUB. Mutational pressure, gene length, hydropathiciy, aromaticity, and nucleotide composition influence CUB weakly.
Transposon Mutagenesis Screen of Klebsiella pneumoniae Identifies Multiple Genes Important for Resisting Antimicrobial Activities of Neutrophils in Mice

Klebsiella pneumoniae is a Gram-negative bacterial pathogen that causes a range of infections, including pneumonias, urinary tract infections, and septicemia, in otherwise healthy and immunocompromised patients. K. pneumoniae has become an increasing concern due to the rise and spread of antibiotic-resistant and hypervirulent strains. However, its virulence determinants remain understudied. To identify novel K. pneumoniae virulence factors needed to cause pneumonia, a high-throughput screen was performed with an arrayed library of over 13,000 K. pneumoniae transposon insertion mutants in the lungs of wild-type (WT) and neutropenic mice using transposon sequencing (Tn-seq). ABSTRACT Klebsiella pneumoniae is a Gram-negative bacterial pathogen that causes a range of infections, including pneumonias, urinary tract infections, and septicemia, in otherwise healthy and immunocompromised patients. K. pneumoniae has become an increasing concern due to the rise and spread of antibiotic-resistant and hypervirulent strains. However, its virulence determinants remain understudied. To identify novel K. pneumoniae virulence factors needed to cause pneumonia, a high-throughput screen was performed with an arrayed library of over 13,000 K. pneumoniae transposon insertion mutants in the lungs of wild-type (WT) and neutropenic mice using transposon sequencing (Tn-seq). Insertions in 166 genes resulted in K. pneumoniae mutants that were significantly less fit in the lungs of WT mice than in those of neutropenic mice. Of these, mutants with insertions in 51 genes still had significant defects in neutropenic mice, while mutants with insertions in 52 genes recovered significantly. In vitro screens using a minilibrary of K. pneumoniae transposon mutants identified putative functions for a subset of these genes, including in capsule content and resistance to reactive oxygen and nitrogen species. Lung infections in mice confirmed roles in K. pneumoniae virulence for the ΔdedA, ΔdsbC, ΔgntR, Δwzm-wzt, ΔyaaA, and ΔycgE mutants, all of which were defective in either capsule content or growth in reactive oxygen or nitrogen species. The fitness of the ΔdedA, ΔdsbC, ΔgntR, ΔyaaA, and ΔycgE mutants was higher in neutropenic mouse lungs, indicating that these genes encode proteins that protect K. pneumoniae against neutrophil-related effector functions.
Music Lessons: Exploring the Role and Meaning of Music for Older Adults with Dementia

ABSTRACT An aging population and increasing rates of dementia point to the need for alternative strategies that allow individuals to age in place. This multiple case study explored, from an insider’s perspective, the role and meaning of music for individuals with dementia who are aging in place. Methods were semi-structured interviews, observations, and videos. The study’s central theme is connection, with three types of “connectors” – self, partner, and music – as subthemes. Connection to self involves present moment awareness, accessing memories, and self-expression. Connection to partner builds on self-connection and spending time together with music. Lastly, the connection to music builds on the previous two subthemes as well as the desire to keep things “normal”. This study provides insight into the growing body of interdisciplinary literature dedicated to dementia, music, aging in place, and contemplative practices, as well as implications for aging and caring for someone with dementia.
Fire synchronizes flowering and boosts reproduction in a widespread but declining prairie species

Significance We address a critical conservation concern: the loss of native plant species in fire-dependent ecosystems. Reduced fire frequency in ecosystems such as the North American prairie contributes to local extinctions. The leading hypothesis is that woody and large herbaceous species outcompete other species in the absence of fire. However, alternative mechanisms have not been investigated. In our 21-y study of a model prairie plant, Echinacea angustifolia, we demonstrate that fires synchronize reproduction, leading to increased mating opportunities and improved reproduction. Fire synchronizes flowering both among and within years, nearly doubling seed production. These findings demonstrate a potentially widespread mechanism by which fire can enhance plant reproduction, promote population growth, and maintain plant diversity in fire-dependent ecosystems worldwide. Fire is an important determinant of habitat structure and biodiversity across ecosystems worldwide. In fire-dependent communities, similar to the North American prairie, fire suppression contributes to local plant extinctions. Yet the demographic mechanisms responsible for species loss have not been directly investigated. We conducted a 21-y longitudinal study of 778 individual plants of Echinacea angustifolia, a widespread perennial species with chronically limited mating opportunities, to explore how fire affects reproduction. In a large preserve, with management units on different burn schedules, we investigated Echinacea mating scenes, which quantify isolation from potential mates and overlap in the timing of flowering, to determine the extent to which fire influences the potential for sexual reproduction. We demonstrate that fire consistently increased mating opportunities by synchronizing reproductive effort. Each fire occurred during fall or spring and stimulated flowering in the subsequent summer, thus synchronizing reproduction among years and increasing the proximity of potential mates after a fire. Greater within-season flowering synchrony in postfire mating scenes further increased mating potential. The improved postfire mating scene enhanced reproduction by increasing pollination efficiency. Seed set in scenes postfire exceeded other scenes by 55%, and annual fecundity nearly doubled (88% increase). We predict the reproductive benefits of synchronized flowering after fire can alleviate mate-finding Allee effects, promote population growth, and forestall local extirpation in small populations of Echinacea and many other prairie species. Furthermore, the synchronization of flowering by burning may improve mating opportunities, reproduction, and the likelihood of persistence for many other plant species in fire-dependent habitats.
Unlocking the potential for digital mental health technologies in the UK: a Delphi exercise

Background Digitally enabled services can contribute to the support, treatment and prevention of mental health difficulties; however, questions remain regarding how we can most usefully harness such technology in primary and secondary mental healthcare settings. Aims To identify barriers and facilitators to enable the potential of digital mental health in England, Scotland, Wales and Northern Ireland. Method A three-round Delphi exercise was carried out online with 16 participants from across the four nations of the UK representing the following stakeholder groups: service providers, health professionals, policymakers, lived experience, small and medium enterprises and academics. Qualitative data were collected in the first round (80 fragments) that were then coded to produce a 26-item round-two questionnaire for participant rating. Participants were given the opportunity to reconsider their scores in light of the group responses in round three. Results Eight statements under the following five themes reached consensus with median scores between 8 and 10 (i.e. important/very important): co-production; the human element; data security; funding; and regulation. Conclusions The Delphi process allowed consensus to be achieved regarding the factors that experts consider important for harnessing technology in primary and secondary mental healthcare. Knowledge of these factors can help users and providers of mental health services negotiate how best to move forward with digitally enabled systems of care.
Landscape context affects the sustainability of organic farming systems

Significance Organic agriculture promotes environmental and socioeconomic sustainability to a greater degree than conventional agriculture. However, it is unknown whether effects of organic agriculture on sustainability metrics such as biodiversity, crop yields, and profitability vary across the diverse landscapes where organic farming is practiced. We addressed this using a global meta-analysis spanning 60 crops. Organic sites had greater biodiversity than conventional ones, with the largest benefits in landscapes with large field sizes. In contrast, while organic sites also had greater profits, the largest benefits occurred in landscapes with small fields. The ecological sustainability benefits of organic agriculture are most pronounced in landscapes typified by more intensive agriculture, while economic benefits are likely influenced by socioeconomic factors and yields. Organic agriculture promotes sustainability compared to conventional agriculture. However, the multifunctional sustainability benefits of organic farms might be mediated by landscape context. Assessing how landscape context affects sustainability may aid in targeting organic production to landscapes that promote high biodiversity, crop yields, and profitability. We addressed this using a meta-analysis spanning 60 crop types on six continents that assessed whether landscape context affected biodiversity, yield, and profitability of organic vs. conventional agroecosystems. We considered landscape metrics reflecting landscape composition (percent cropland), compositional heterogeneity (number and diversity of cover types), and configurational heterogeneity (spatial arrangement of cover types) across our study systems. Organic sites had greater biodiversity (34%) and profits (50%) than conventional sites, despite lower yields (18%). Biodiversity gains increased as average crop field size in the landscape increased, suggesting organic farms provide a “refuge” in intensive landscapes. In contrast, as crop field size increased, yield gaps between organic and conventional farms increased and profitability benefits of organic farming decreased. Profitability of organic systems, which we were only able to measure for studies conducted in the United States, varied across landscapes in conjunction with production costs and price premiums, suggesting socioeconomic factors mediated profitability. Our results show biodiversity benefits of organic farming respond differently to landscape context compared to yield and profitability benefits, suggesting these sustainability metrics are decoupled. More broadly, our results show that the ecological, but not the economic, sustainability benefits of organic agriculture are most pronounced in more intensive agricultural landscapes.
Identification of key biomarkers and immune infiltration in the synovial tissue of osteoarthritis by bioinformatics analysis

Background Osteoarthritis (OA) is the most common chronic degenerative joint disease and is mainly characterized by cartilage degeneration, subcartilage bone hyperplasia, osteophyte formation and joint space stenosis. Recent studies showed that synovitis might also be an important pathological change of OA. However, the molecular mechanisms of synovitis in OA are still not well understood. Objective This study was designed to identify key biomarkers and immune infiltration in the synovial tissue of osteoarthritis by bioinformatics analysis. Materials and Methods The gene expression profiles of GSE12021, GSE55235 and GSE55457 were downloaded from the GEO database. The differentially expressed genes (DEGs) were identified by the LIMMA package in Bioconductor, and functional enrichment analyses were performed. A protein-protein interaction network (PPI) was constructed, and module analysis was performed using STRING and Cytoscape. The CIBERSORT algorithm was used to analyze the immune infiltration of synovial tissue between OA and normal controls. Results A total of 106 differentially expressed genes, including 68 downregulated genes and 38 upregulated genes, were detected. The PPI network was assessed, and the most significant module containing 14 hub genes was identified. Gene Ontology analysis revealed that the hub genes were significantly enriched in immune cell chemotaxis and cytokine activity. KEGG pathway analysis showed that the hub genes were significantly enriched in the rheumatoid arthritis signaling pathway, IL-17 signaling pathway and cytokine-cytokine receptor interaction signaling pathway. The immune infiltration profiles varied significantly between osteoarthritis and normal controls. Compared with normal tissue, OA synovial tissue contained a higher proportion of memory B cells, naive CD4+ T cells, regulatory T cells, resting dendritic cells and resting mast cells, while naive CD4+ T cells, activated NK cells, activated mast cells and eosinophils contributed to a relatively lower portion (P > 0.05). Finally, the expression levels of 11 hub genes were confirmed by RT-PCR. Conclusion The hub genes and the difference in immune infiltration in synovial tissue between osteoarthritis and normal controls might provide new insight for understanding OA development.
Physical Exercise Combined With CPAP in Subjects Who Underwent Surgical Myocardial Revascularization: A Randomized Clinical Trial

BACKGROUND: Aerobic exercise and CPAP benefit patients in the postoperative period of cardiac surgery. To our knowledge, the association of aerobic exercise on an exercise bicycle with CPAP has not yet been demonstrated. Therefore, we aimed to evaluate the effectiveness of physical exercise on a cycle ergometer combined with CPAP in the postoperative period after coronary artery bypass graft surgery. METHODS: This was a randomized clinical trial, with recruitment from May 2017 to December 2017 (registered in the Brazilian Clinical Trials Registry: RBR-69CDYF). The step group (n = 16 subjects) started rehabilitation in the immediate postoperative period with breathing exercises and passive mobilization in the sitting position, progressing to active exercises, ambulation, and stair training. For the intervention group (n = 15 subjects), dynamic exercises on a cycle ergometer combined with CPAP were added to the step program from the second to the fourth postoperative day in a single daily session. RESULTS: Functional capacity decreased in both groups, but this reduction was not significant in the intervention group (P = .11). The length of stay in ICU was lower in the intervention group (P = .050). In both groups there was a decrease in maximum inspiratory and expiratory pressure, as well as in the 1-min sit-to-stand test on the fourth postoperative day compared to the preoperative period. CONCLUSIONS: Physical exercise combined with CPAP promoted the maintenance of functional capacity and reduced the length of stay in the ICU.
Plasma exchange in patients with acute and acute-on-chronic liver failure: A systematic review

BACKGROUND Acute liver failure (ALF) and acute-on-chronic liver (ACLF) carry high short-term mortality rate, and may result from a wide variety of causes. Plasma exchange has been shown in a randomized control trial to improve survival in ALF especially in patients who did not receive a liver transplant. Other cohort studies demonstrated potential improvement in survival in patients with ACLF. AIM To assess utility of plasma exchange in liver failure and its effect on mortality in patients who do not undergo liver transplantation. METHODS Databases MEDLINE via PubMed, and EMBASE were searched and relevant publications up to 30 March, 2019 were assessed. Studies were included if they involved human participants diagnosed with liver failure who underwent plasma exchange, with or without another alternative non-bioartificial liver assist device. RESULTS Three hundred twenty four records were reviewed, of which 62 studies were found to be duplicates. Of the 262 records screened, 211 studies were excluded. Fifty-one articles were assessed for eligibility, for which 7 were excluded. Twenty-nine studies were included for ALF only, and 9 studies for ACLF only. Six studies included both ALF and ACLF patients. A total of 44 publications were included. Of the included publications, 2 were randomized controlled trials, 14 cohort studies, 12 case series, 16 case reports. All of three ALF studies which looked at survival rate or survival days reported improvement in outcome with plasma exchange. In two out of four studies where plasma exchange-based liver support systems were compared to standard medical treatment (SMT) for ACLF, a biochemical improvement was seen. Survival in the non-transplanted patients was improved in all four studies in patients with ACLF comparing plasma exchange vs SMT. Using the aforementioned studies, plasma exchange based therapy in ACLF compared to SMT improved survival in non-transplanted patients at 30 and 90-d with a pooled OR of 0.60 (95%CI 0.46-0.77, P < 0.01). CONCLUSION The level of evidence for use of high volume plasma exchange in selected ALF cases is high. Plasma exchange in ACLF improves survival at 30-and 90-d in non-transplanted patients. Further well-designed randomized control trials will need to be carried out to ascertain the optimal duration and amount of plasma exchange required and assess if the use of high volume plasma exchange can be extrapolated to patients with ACLF.
Pre‐treatment systemic immune‐inflammation index is a useful prognostic indicator in patients with breast cancer undergoing neoadjuvant chemotherapy

The systemic immune‐inflammation index (SII = N × P/L) based on neutrophil (N), platelet (P) and lymphocyte (L) counts is used to predict the survival of patients with malignant tumours and can fully reflect the balance between host inflammatory and immune status. This study is conducted to explore the potential prognostic significance of SII in patients with breast cancer undergoing neoadjuvant chemotherapy (NACT). A total of 262 patients with breast cancer received NACT were enrolled in this study. According to the receiver operating characteristic curve, the optimal cut‐off value of SII was divided into two groups: low SII group (<602 × 109/L) and high SII group (≥602 × 109/L). The associations between breast cancer and clinicopathological variables by SII were determined by chi‐squared test or Fisher's exact test. The Kaplan‐Meier plots and log‐rank test were used to determine clinical outcomes of disease‐free survival (DFS) and overall survival (OS). The prognostic value of SII was analysed by univariate and multivariate Cox proportional hazards regression models. The toxicity of NACT was accessed by National Cancer Institute Common Toxicity Criteria (NCICTC). According to univariate and multivariate Cox regression survival analyses, the results showed that the value of SII had prognostic significance for DFS and OS. The patients with low SII value had longer DFS and OS than those with high SII value (31.11 vs 40.76 months, HR: 1.075, 95% CI: 0.718‐1.610, P = .006; 44.47 vs 53.68 months, HR: 1.051, 95% CI: 0.707‐1.564, P = .005, respectively). The incidence of DFS and OS in breast cancer patients with low SII value was higher than that in those patients with high SII value in 3‐, 5‐ and 10‐year rates. The common toxicities after NACT were haematological and gastrointestinal reaction, and there were no differences by SII for the assessment of side effects of neoadjuvant chemotherapy. Meanwhile, the results also proved that breast cancer patients with low SII value and high Miller and Payne grade (MPG) survived longer than those breast cancer with high SII value and low MPG grade. In patients without lymph vessel invasion, these breast cancer patients with low SII value had better prognosis and lower recurrence rates than those with high SII value. Pre‐treatment SII with the advantage of reproducible, convenient and non‐invasive was a useful prognostic indicator for breast cancer patients undergoing neoadjuvant chemotherapy and is a promising biomarker for breast cancer on treatment strategy decisions.