Miracle-dz/UniFAR-FTUs huggingface dataset:
The use and reporting of airline passenger data for infectious disease modelling: a systematic review

Background A variety of airline passenger data sources are used for modelling the international spread of infectious diseases. Questions exist regarding the suitability and validity of these sources. Aim We conducted a systematic review to identify the sources of airline passenger data used for these purposes and to assess validation of the data and reproducibility of the methodology. Methods Articles matching our search criteria and describing a model of the international spread of human infectious disease, parameterised with airline passenger data, were identified. Information regarding type and source of airline passenger data used was collated and the studies’ reproducibility assessed. Results We identified 136 articles. The majority (n = 96) sourced data primarily used by the airline industry. Governmental data sources were used in 30 studies and data published by individual airports in four studies. Validation of passenger data was conducted in only seven studies. No study was found to be fully reproducible, although eight were partially reproducible. Limitations By limiting the articles to international spread, articles focussed on within-country transmission even if they used relevant data sources were excluded. Authors were not contacted to clarify their methods. Searches were limited to articles in PubMed, Web of Science and Scopus. Conclusion We recommend greater efforts to assess validity and biases of airline passenger data used for modelling studies, particularly when model outputs are to inform national and international public health policies. We also recommend improving reporting standards and more detailed studies on biases in commercial and open-access data to assess their reproducibility.
Loss and gain of sexual reproduction in the same stick insect

The outcome of competition between different reproductive strategies within a single species can be used to infer selective advantage of the winning strategy. Where multiple populations have independently lost or gained sexual reproduction it is possible to investigate whether the advantage is contingent on local conditions. In the New Zealand stick insect Clitarchus hookeri, three populations are distinguished by recent change in reproductive strategy and we determine their likely origins. One parthenogenetic population has established in the United Kingdom and we provide evidence that sexual reproduction has been lost in this population. We identify the sexual population from which the parthenogenetic population was derived, but show that the UK females have a post‐mating barrier to fertilisation. We also demonstrate that two sexual populations have recently arisen in New Zealand within the natural range of the mtDNA lineage that otherwise characterizes parthenogenesis in this species. We infer independent origins of males at these two locations using microsatellite genotypes. In one population, a mixture of local and nonlocal alleles suggested males were the result of invasion. Males in another population were most probably the result of loss of an X chromosome that produced a male phenotype in situ. Two successful switches in reproductive strategy suggest local competitive advantage for outcrossing over parthenogenetic reproduction. Clitarchus hookeri provides remarkable evidence of repeated and rapid changes in reproductive strategy, with competitive outcomes dependent on local conditions.
Antithrombin III Contributes to the Protective Effects of Fresh Frozen Plasma Following Hemorrhagic Shock by Preventing Syndecan-1 Shedding and Endothelial Barrier Disruption.

BACKGROUND Endothelial dysfunction during hemorrhagic shock (HS), is associated with loss of cell-associated syndecan-1 (Sdc1) and hyperpermeability. Fresh frozen plasma (FFP) preserves Sdc1 and reduces permeability following HS, although the key mediators remain unknown. Antithrombin III (ATIII) is a plasma protein with potent anti-inflammatory and endothelial protective activity. We hypothesized that the protective effects of FFP on endothelial Sdc1 and permeability are mediated, in part, through ATIII. METHODS ATIII and Sdc1 were measured in severely injured patients upon admission (N = 125) and hospital day 3 (N = 90) for correlation analysis. In vitro effects of ATIII on human lung microvascular endothelial cells (HLMVECs) were determined by pre-treating cells with vehicle, FFP, ATIII-deficient FFP, or purified ATIII followed by TNFα stimulation. Sdc1 expression was measured by immunostaining and permeability by electrical impedance. To determine the role of ATIII in vivo, male mice were subjected to a fixed pressure exsanguination model of HS, followed by resuscitation with FFP, ATIII-deficient FFP, or ATIII-deficient FFP with ATIII repletion. Lung Sdc1 expression was assessed by immunostaining. RESULTS Pearson correlation analysis showed a significant negative correlation between plasma levels of Sdc1 and ATIII (R = -0.62; p < 0.0001) in injured patients on hospital day 3. Also, in vitro, FFP and ATIII prevented TNFα-induced permeability (p < 0.05 vs TNFα) in HLMVECs. ATIII-deficient FFP had no effect; however, ATIII restoration reestablished its protective effects in a dose-dependent manner. Similarly, FFP and ATIII prevented TNFα-induced Sdc1 shedding in HLMVECs, however ATIII-deficient FFP did not. In mice, Sdc1 expression was increased following FFP resuscitation (1.7 ± 0.5, p < 0.01) vs. HS alone (1.0 ± 0.3), however, no improvement was seen following ATIII-deficient FFP treatment (1.3 ± 0.4, p = 0.3). ATIII restoration improved Sdc1 expression (1.5 ± 0.9, p < 0.05) similar to that of FFP resuscitation. CONCLUSIONS ATIII plays a role in FFP-mediated protection of endothelial Sdc1 expression and barrier function, making it a potential therapeutic target to mitigate HS-induced endothelial dysfunction. Further studies are needed to elucidate the mechanisms by which ATIII protects the endothelium.
The impact of glycated hemoglobin on risk of hypertension: a Mendelian randomization study using UK Biobank.

BACKGROUND Observational studies suggest higher glycated hemoglobin (HbA1c) associated with higher hypertension risk although these associations could be confounded. We examined the relation using a Mendelian randomization design in a large Biobank, the UK Biobank. METHODS We identified 38 single nucleotide polymorphisms (SNPs) strongly and independently related to HbA1c from a large genome wide association study (n = 123 665) and applied them to the UK Biobank (n = 376 644). We used inverse variance weighting (IVW) to assess the relation of HbA1c with risk of hypertension (defined using the American College of Cardiology/American Heart Association 2017 guidelines), and SBP and DBP. Sensitivity analyses included Mendelian randomization-Egger, weighted median, Mendelian randomization pleiotropy residual sum and outlier and exclusion of pleiotropic SNPs. RESULTS HbA1c was not clearly associated with hypertension risk using IVW (odds ratio 1.11, 95% confidence interval 0.76-1.62) in the main analysis. However, Mendelian randomization pleiotropy residual sum and outlier suggested potential horizontal pleiotropy. After excluding potentially invalid SNPs, HbA1c was associated with hypertension risk (IVW odds ratio 1.22 per %, 95% confidence interval 1.01-1.46), with consistent estimates from sensitivity analyses. HbA1c was positively associated with SBP in some, but not all analyses, albeit with directionally consistent estimates. The relation with DBP was unclear. CONCLUSION Our study suggests HbA1c may increase hypertension risk and could be one underlying mechanistic pathway between HbA1c and coronary artery disease risk.
Nutrient Patterns, Cognitive Function, and Decline in Older Persons: Results from the Three-City and NuAge Studies

Dietary patterns, or the combination of foods and beverages intake, have been associated with better cognitive function in older persons. To date, no study has investigated the link between a posteriori nutrient patterns based on food intake, and cognitive decline in longitudinal analyses. The aim of this study was to evaluate the relationship between nutrient patterns and cognitive function and decline in two longitudinal cohorts of older persons from France and Canada. The study sample was composed of participants from the Three-City study (3C, France) and the Quebec Longitudinal Study on Nutrition and Successful Aging (NuAge, Quebec, Canada). Both studies estimated nutritional intakes at baseline, and carried out repeated measures of global cognitive function for 1,388 and 1,439 individuals, respectively. Nutrient patterns were determined using principal component analysis methodology in the two samples, and their relation with cognitive function and decline was estimated using linear mixed models. In 3C, a healthy nutrient pattern, characterized by higher intakes of plant-based foods, was associated with a higher global cognitive function at baseline, as opposed to a Western nutrient pattern, which was associated with lower cognitive performance. In NuAge, we also found a healthy nutrient pattern and a Western pattern, although no association was observed with either of these patterns in the Canadian cohort. No association between any of the nutrient patterns and cognitive decline was observed in either cohort. There is a need for longitudinal cohorts focusing on nutrient patterns with substantial follow-up, in order to evaluate more accurately associations between nutrition and cognition in older persons.
Gastrointestinal involvement in systemic sclerosis: an update.

PURPOSE OF REVIEW This review provides important updates in systemic sclerosis (SSc)-related gastrointestinal disease, specifically focusing on the most recent literature. RECENT FINDINGS In the past year, several studies were published that present interesting insights into SSc and gastrointestinal disease. Studies focusing on newly identified risk factors, novel approaches to diagnosis and assessment of disease activity, survival and quality of life demonstrate progress in our understanding of this challenging area. Additional data on specific SSc gastrointestinal-related topics, such as the link between gastrointestinal and pulmonary disease, nutrition, and the microbiome, are also now available. SUMMARY SSc gastrointestinal disease is heterogeneous in its clinical presentation, which presents a challenge in diagnosis and management. In the past year, several studies have evaluated risk factors and clinical features associated with specific gastrointestinal complications in SSc. Objective gastrointestinal testing may help to identify specific SSc gastrointestinal subgroups and provide diagnostic accuracy to guide targeted therapies. Survival in very early SSc is affected by the severity of gastrointestinal involvement. Other important gastrointestinal subsets, including patients with esophageal disease and interstitial lung disease, should carefully be considered when developing a management plan for this patient population.
Melatonin inhibits the inflammation and apoptosis in rats with diabetic retinopathy via MAPK pathway.

The article "Melatonin inhibits the inflammation and apoptosis in rats with diabetic retinopathy via MAPK pathway, by Y. Ma, Q. Zhao, Y. Shao, M. -Z. Cao, M. Zhao, D. Wang, published in Eur Rev Med Pharmacol Sci 2019; 23 (3 Suppl): 1-8-DOI: 10.26355/eurrev_201908_18620-PMID: 31389568" has been withdrawn from the authors. The Publisher apologizes for any inconvenience this may cause. https://www.europeanreview. org/article/18620.
Specialization of small non-conjugative plasmids in Escherichia coli according to their family types

We undertook a comprehensive comparative analysis of a collection of 30 small (<25 kb) non-conjugative Escherichia coli plasmids previously classified by the gene sharing approach into 10 families, as well as plasmids found in the National Center for Biotechnology Information (NCBI) nucleotide database sharing similar genomic sequences. In total, 302 mobilizable (belonging to 2 MOBrep and 5 MOBRNA families) and 106 non-transferable/relaxase-negative (belonging to three ReLRNA families) plasmids were explored. The most striking feature was the specialization of the plasmid family types that was not related to their transmission mode and replication system. We observed a range of host strain specificity, from narrow E. coli host specificity to broad host range specificity, including a wide spectrum of Enterobacteriaceae . We found a wide variety of toxin/antitoxin systems and colicin operons in the plasmids, whose numbers and types varied according to the plasmid family type. The plasmids carried genes conferring resistance spanning almost all of the antibiotic classes, from those to which resistance developed early, such as sulphonamides, to those for which resistance has only developed recently, such as colistin. However, the prevalence of the resistance genes varied greatly according to the family type, ranging from 0 to 100 %. The evolutionary history of the plasmids based on the family type core genes showed variability within family nucleotide divergences in the range of E. coli chromosomal housekeeping genes, indicating long-term co-evolution between plasmids and host strains. In rare cases, a low evolutionary divergence suggested the massive spread of an epidemic plasmid. Overall, the importance of these small non-conjugative plasmids in bacterial adaptation varied greatly according to the type of family they belonged to, with each plasmid family having specific hosts and genetic traits.
A Narrative Role of Vitamin D and Its Receptor: With Current Evidence on the Gastric Tissues

Vitamin D is a major steroid hormone that is gaining attention as a therapeutic molecule. Due to the general awareness of its importance for the overall well-being, vitamin D deficiency (VDD) is now recognized as a major health issue. The main reason for VDD is minimal exposure to sunlight. The vitamin D receptor (VDR) is a member of the steroid hormone receptors that induces a cascade of cell signaling to maintain healthy Ca2+ levels that serve to regulate several biological functions. However, the roles of vitamin D and its metabolism in maintaining gastric homeostasis have not yet been completely elucidated. Currently, there is a need to increase the vitamin D status in individuals worldwide as it has been shown to improve musculoskeletal health and reduce the risk of chronic illnesses, including some cancers, autoimmune and infectious diseases, type 2 diabetes mellitus, neurocognitive disorders, and general mortality. The role of vitamin D in gastric homeostasis is crucial and unexplored. This review attempts to elucidate the central role of vitamin D in preserving and maintaining the overall health and homeostasis of the stomach tissue.
Visualization of sequential conversion of human intermediately reprogrammed stem cells into iPS cells

Analysis of gene expression in single cells is required to understand somatic cell reprogramming into human induced pluripotent stem cells (iPSCs). To facilitate this, we established intermediately reprogrammed stem cells (iRSCs), pre‐iPSC lines. The iRSC‐iPSC conversion system enables the reproducible monitoring of reprogramming events and the analysis of progressive gene expression profiles using single‐cell microarray analysis and genome editing. Here, single‐cell microarray analysis showed the stage‐specific sequential gene activation during the conversion of iRSCs into iPSCs, using OCT4, TDGF1 and E‐CADHERIN as marker genes. Out of 75 OCT4‐related genes, which were significantly up‐regulated after the activation of OCT4, and entry into the mesenchymal‐to‐epithelial transition (MET), LIN28 (LIN28A) and FOXO1 were selected for applying to gene expression visualization. Multicolored visualization was achieved by the genome editing of LIN28 or FOXO1 with mCherry into OCT4‐GFP iRSCs. Fluorescent analysis of gene activity in individual cells showed that OCT4 was dispensable for maintenance, but required for activation, of the LIN28 and FOXO1 expression in reprogramming.
Costs associated with follicular lymphoma among individuals diagnosed with non-Hodgkin lymphoma: a longitudinal analysis using SEER-Medicare data

Abstract There is limited information on the cost burden associated with follicular lymphoma (FL) and how it compares to other non-Hodgkin lymphoma (NHL) subtypes. We examined the direct medical costs associated with FL and estimated the incremental 3-year cost of FL compared to other NHL subtypes. Using the linked Surveillance, Epidemiology and End Results-Medicare dataset, we identified 16,691 NHL patients aged 66 years or older who were diagnosed with NHL between 2007 and 2013. The mean 3-year cost among the full NHL sample was $120,120 (standard error (SE) 839). The mean 3-year cost per patient was $114,443 (SE 1738) for FL and $121,402 (SE 950) for non-FL subtypes. The incremental 3-year cost of FL compared to non-FL was US$-5458 (95% confidence interval: US$-9325 to US$-1590). Longitudinally, FL was less costly than other NHL subtypes in the first year only, and became more expensive in the second and third years.
Laser ablation and topical drug delivery: a review of recent advances

ABSTRACT Introduction: The ablative laser can be used as an effective approach for enhancing drug permeation via the skin. The enhancement mechanisms of laser-assisted drug permeation are the direct ablation of the superficial skin, optical breakdown by a photomechanical wave, and a photothermal effect. Areas covered: This review describes the development of laser-assisted drug delivery in the recent 5 years. This review systematically introduces the concepts and enhancement mechanisms of the technique, highlighting the potential of the laser approach for increasing drug absorption via the skin. A recent advance of this approach is the use of fractional laser offering limited skin damage and short recovery time. Another sign of progress regarding laser-assisted drug delivery in the recent 5 years is the clinical trials for treating various dermatological disorders. Expert opinion: The potential use of the laser-assisted approach affords a novel treatment for topical drug application with significant efficacy. Although many clinical studies have been performed, further studies using a large group for patients are needed to confirm and clarify the findings in the in vitro or animal experiments. The laser-assisted delivery should be optimized to achieve skin targeting without the risk of diffusion into circulation.
Reply to Measuring Under‐ and Over‐Use of Medications

consistent with the results of a recent meta-analysis that showed that interventions designed to improve suboptimal prescribing/adherence reduced the risk of any ADR by 25%. Second, we would like to debate the notion implied by authors that our implicit instrument, the assessment of underutilization (AOU), “overestimates medication benefits and underestimate harms. ” Literature examples the authors used to support their argument were published after the dates of the data the AOU was applied in the two studies cited (ie, mid-1990s to early 2000s). Readers should also know that the AOU, which has demonstrated good interrater reliability and was used as a process outcome measure in several intervention trials, has been continuously updated since then to take into account multimorbidity and limited life expectancy (available on request). Moreover, the START criteria, also cited as being potentially problematic, were updated in 2015 (version 2) and have now been supplemented by the newer STOPPFrail criteria that also take into account limited life expectancy. Finally, we agree with the authors that it is important to stepwise address unnecessary/potentially inappropriate medications that take into account patients’ wishes and their current functional status and life expectancy prior to addressing medication nonadherence and/or underprescribing of necessary drugs so one can avoid further issues with “inappropriate polypharmacy” and related adverse health outcomes.
Mycobacterium tuberculosis requires glyoxylate shunt and reverse methylcitrate cycle for lactate and pyruvate metabolism

Bacterial nutrition is an essential aspect of host–pathogen interaction. For the intracellular pathogen Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis in humans, fatty acids derived from lipid droplets are considered the major carbon source. However, many other soluble nutrients are available inside host cells and may be used as alternative carbon sources. Lactate and pyruvate are abundant in human cells and fluids, particularly during inflammation. In this work, we study Mtb metabolism of lactate and pyruvate combining classic microbial physiology with a ‘multi‐omics’ approach consisting of transposon‐directed insertion site sequencing (TraDIS), RNA‐seq transcriptomics, proteomics and stable isotopic labelling coupled with mass spectrometry‐based metabolomics. We discovered that Mtb is well adapted to use both lactate and pyruvate and that their metabolism requires gluconeogenesis, valine metabolism, the Krebs cycle, the GABA shunt, the glyoxylate shunt and the methylcitrate cycle. The last two pathways are traditionally associated with fatty acid metabolism and, unexpectedly, we found that in Mtb the methylcitrate cycle operates in reverse, to allow optimal metabolism of lactate and pyruvate. Our findings reveal a novel function for the methylcitrate cycle as a direct route for the biosynthesis of propionyl‐CoA, the essential precursor for the biosynthesis of the odd‐chain fatty acids.
CORR Insights®: Does Knee Flexion Influence the Relationship between the Femoral Tunnel and the Lateral Anatomic Structures During ACL Reconstruction?

Only after decades of studies systematically unraveling the structure and function of the native ACL [5] did orthopaedic surgeons accept anatomic ACL reconstruction as a suitable surgical procedure. Independent drilling of the femoral tunnel,most commonly through an anteromedial portal, consistently positions the tunnel within the anatomic footprint, which better restores the knee kinematics compared to a non-anatomic graft placed through transtibial drilling [8, 9]. While exhaustive research efforts have been made to understand the effects of intercondylar tunnel position on knee kinematics and clinical outcomes following ACL reconstruction, far less is known about the effect of drilling techniques on the position of the lateral structures of the femur relative to the tunnel outlet. Through cadaveric dissection, Laprade and colleagues [10] described the relative positions and sizes of several posterolateral knee structures. More recent studies, utilizing both three-dimensional (3-D) models and cadaveric specimens, investigated tunnel outlet position relative to posterolateral knee structures when drilling was performed through an anteromedial portal [4, 12]. Using angles such as 90°, 110°, 130°, but never exceeding 135° of knee flexion, these studies found that drilling under high knee-flexion angles reduced the risk of violating lateral structures [4, 12]. In another cadaveric in vitro study, Basdekis and colleagues [2] recommended against maximal knee flexion when drilling due to high variability in the maximum flexion angle achieved across specimens, as well as higher tunnel acuity. In the current study, Chung and colleagues [3] retrospectively studied CT 3D reconstructed knee models of patients who underwent anatomic single-bundle ACL reconstruction with a transportal technique using quadruple hamstring autografts. Although the knees were maximally flexed at the time of femoral tunnel drilling, the knee flexion angle measured during surgery varied across three groups of patients: < 120°, 120° to 129°, and $ 130°. Chung and colleagues [3] found a safe window of 121° to 131° in which the risk of the tunnel outlet violating any posterolateral structure was minimized. These findings provide clinical evidence for the aforementioned cadaveric studies in which knee flexion angles # 90° or $ 130° were associated with increased risk of either violating lateral structures or variable tunnel positioning.