Miracle-dz/UniFAR-FTUs huggingface dataset:
Percutaneous Coronary Intervention For Bifurcation Coronary Lesions.The 15th Consensus Document from the European Bifurcation Club.

The 15th European Bifurcation Club (EBC) meeting was held in Barcelona in October 2019 and it facilitated a renewed consensus on coronary bifurcation lesions (CBL) and unprotected left main (LM) percutaneous interventions. Bifurcation stenting techniques continue to be refined, developed and tested. It remains evident that provisional approach with optional side-branch treatment utilising T, T and small protrusion (TAP) or culotte continue to provide flexible options for the majority of CBL patients. Debate persists regarding the optimal treatment of side branches, including assessment of clinical significance and thresholds for bail-out treatment. In more complex CBL, especially when involving the LM, adoption of dedicated 2-stent techniques should be considered. Operators using such techniques have to be fully familiar with their procedural steps and should acknowledge associated limitations and challenges. When using 2-stent techniques, failure to perform a final kissing inflation is regarded as a technical failure, since it may jeopardize clinical outcome. The development of novel technical tools and drug regimens deserve attention. In particular, intra-coronary imaging, bifurcation simulation, drug-eluting balloon technology and tailored anti-platelet therapy are identified as promising tools to enhance clinical outcomes. In conclusion, the evolution of a broad spectrum of bifurcation PCI components have resulted from studies extending from bench testing to randomised controlled trials. However, further advances are still needed to achieve the ambitious goal of optimizing the clinical outcomes for every patient undergoing PCI on a CBL.
mMGE: a database for human metagenomic extrachromosomal mobile genetic elements

Abstract Extrachromosomal mobile genetic elements (eMGEs), including phages and plasmids, that can move across different microbes, play important roles in genome evolution and shaping the structure of microbial communities. However, we still know very little about eMGEs, especially their abundances, distributions and putative functions in microbiomes. Thus, a comprehensive description of eMGEs is of great utility. Here we present mMGE, a comprehensive catalog of 517 251 non-redundant eMGEs, including 92 492 plasmids and 424 759 phages, derived from diverse body sites of 66 425 human metagenomic samples. About half the eMGEs could be further grouped into 70 074 clusters using relaxed criteria (referred as to eMGE clusters below). We provide extensive annotations of the identified eMGEs including sequence characteristics, taxonomy affiliation, gene contents and their prokaryotic hosts. We also calculate the prevalence, both within and across samples for each eMGE and eMGE cluster, enabling users to see putative associations of eMGEs with human phenotypes or their distribution preferences. All eMGE records can be browsed or queried in multiple ways, such as eMGE clusters, metagenomic samples and associated hosts. The mMGE is equipped with a user-friendly interface and a BLAST server, facilitating easy access/queries to all its contents easily. mMGE is freely available for academic use at: https://mgedb.comp-sysbio.org.
Inhibition of ACSL4 attenuates ferroptotic damage after pulmonary ischemia‐reperfusion

Lung ischemia‐reperfusion (IR) injury is a common clinical pathology associated with high mortality. Ferroptosis, a novel mode of cell death elicited by iron‐dependent phospholipid peroxidation, has been implicated in ischemic events. Acyl‐CoA synthetase long‐chain family member 4 (ACSL4) is one of the main enzymes in pro‐ferroptotic lipid metabolism. In this study, the involvement of ferroptotic death in different durations of reperfusion was evaluated by assessing the iron content, malondialdehyde, and glutathione levels, ferroptosis‐related protein expression, and mitochondria morphology. The roles of ferroptosis‐specific inhibitor, liproxastin‐1 (Lip‐1), and ACSL4 modulation in a preventive regimen were assessed in vivo and in vitro. The hallmarks of pulmonary function, such as histological lung injury score, wet/dry ratio, and oxygenation index, were evaluated as well. Results showed that lung IR increased the tissue iron content and lipid peroxidation accumulation, along with key protein (GPX4 and ACSL4) expression alteration during reperfusion. Pretreatment with Lip‐1 inhibited ferroptosis and ameliorated lung IR‐induced injury in animal and cell models. In addition, administering ACSL4 inhibitor rosiglitazone before ischemia diminished the ferroptotic damage in IR‐injured lung tissue, consistent with the protective effect of ACSL4 knockdown on lung epithelial cells subjected to hypoxia/reoxygenation. Thus, this study delineated that IR‐induced ferroptotic cell death in lung tissue and ACSL4 were correlated with this process. Inhibition of ferroptosis and ACSL4 mitigated the ferroptotic damage in IR‐induced lung injury by reducing lipid peroxidation and increasing the glutathione and GPX4 levels.
Who Joins the Franchise, Affiliation Model of Hospital Networks? An Analysis of Hospital and Market Characteristics of Members

Joining nonownership based, organization-driven networks and alliances is a common strategy for hospitals to pursue yet little is known about what types of hospitals join these collaborations, due in part to challenges in identifying members. One novel network form that has recently emerged, and made identification feasible, is franchise-like “affiliation networks” in which affiliate hospitals pay an annual membership fee that allows access to the clinical expertise and resources of high-status, nationally ranked sponsor hospitals. Affiliation networks and their members publicize affiliation. Using 2006-2015 data on United States’ hospitals, we find hospitals with higher patient acuity, teaching hospitals, and hospitals located in areas of higher utilization intensity were more likely to join an affiliation network. Joining affiliation networks does not appear to be in response to highly competitive markets because hospitals in less competitive environments are more likely to join and hospitals with higher net incomes are more likely to join.
Physiological stabilization, community characterization, and nitrogen degradation dynamics in an anammox consortium from estuarine sediments

Anammox is a cost‐effective and sustainable process for nitrogen removal; however, the production of a physiologically stable inoculum is a critical point in the start‐up process. In this work, estuarine sediments were used as incubation seeds to obtain cultures with stable anammox activity. Assays were performed in batch cultures fed with stoichiometric amounts of ammonium and nitrite, analyzing physiological response variables and the microbial community. Estuarine sediments showed a stable anammox process after 90 days, consuming ammonium and nitrite simultaneously with concomitant generation of N2 and nitrate in stoichiometric amounts. In kinetic assays, substrates were fully consumed after 210 hr, exhibiting N2 and nitrate yields of 0.85 and 0.10, respectively. The microbial community analysis using PCR‐DGGE indicated the presence of uncultured anammox bacteria and members of the genus Candidatus Jettenia. The results evidenced the achievement of anammox cultures, although their start‐up and kinetic characteristics were less favorable than those recorded in man‐made systems.
Effects of salt concentration, pH, and their interaction on plant growth, nutrient uptake, and photochemistry of alfalfa (Medicago sativa) leaves

ABSTRACT In order to explore the main limiting factors affecting the growth and physiological function of alfalfa under salt and alkali stress, the effect of the salt and alkali stress on the growth and physiological function of alfalfa was studied. The results showed that effects of the excessive salt concentration (100 and 200 mM) on the growth and physiological characteristics were significantly greater than that of pH (7.0 and 9.0). Under 100 mM salt stress, there was no significant difference in the growth and photosynthetic function between pH 9.0 and pH 7.0. Under the 200 mM salt concentration the absorption of Na+ by alfalfa treated at the pH 9.0 did not increase significantly compared with absorption at the pH 7.0. However, the higher pH directly reduced the root activity, leaf’s water content, and N-P-K content also decreased significantly. The PSII and PSI activities decreased with increasing the salt concentration, especially the damage degree of PSI. Although the photoinhibition of PSII was not significant, PSII donor and electron transfer from the Q A to Q B of the PSII receptor sides was inhibited. In a word, alfalfa showed relatively strong salt tolerance capacity, at the 100 mM salt concentration, even when the pH reached 9.0. Thus, the effect on the growth and photosynthetic function was not significant. However, at 200 mM salt concentration, pH 9.0 treatment caused damage to root system and the photosynthetic function in leaves of alfalfa was seriously injured.
Priming for enhanced ARGONAUTE2 activation accompanies induced resistance to cucumber mosaic virus in Arabidopsis thaliana

Abstract Systemic acquired resistance (SAR) is a broad‐spectrum disease resistance response that can be induced upon infection from pathogens or by chemical treatment, such as with benzo‐(1,2,3)‐thiadiazole‐7‐carbothioic acid S‐methyl ester (BTH). SAR involves priming for more robust activation of defence genes upon pathogen attack. Whether priming for SAR would involve components of RNA silencing remained unknown. Here, we show that upon leaf infiltration of water, BTH‐primed Arabidopsis thaliana plants accumulate higher amounts of mRNA of ARGONAUTE (AGO)2 and AGO3, key components of RNA silencing. The enhanced AGO2 expression is associated with prior‐to‐activation trimethylation of lysine 4 in histone H3 and acetylation of histone H3 in the AGO2 promoter and with induced resistance to the yellow strain of cucumber mosaic virus (CMV[Y]). The results suggest that priming A. thaliana for enhanced defence involves modification of histones in the AGO2 promoter that condition AGO2 for enhanced activation, associated with resistance to CMV(Y). Consistently, the fold‐reduction in CMV(Y) coat protein accumulation by BTH pretreatment was lower in ago2 than in wild type, pointing to reduced capacity of ago2 to activate BTH‐induced CMV(Y) resistance. A role of AGO2 in pathogen‐induced SAR is suggested by the enhanced activation of AGO2 after infiltrating systemic leaves of plants expressing a localized hypersensitive response upon CMV(Y) infection. In addition, local inoculation of SAR‐inducing Pseudomonas syringae pv. maculicola causes systemic priming for enhanced AGO2 expression. Together our results indicate that defence priming targets the AGO2 component of RNA silencing whose enhanced expression is likely to contribute to SAR.
The involvement of p38 gamma MAPK in pathological cardiac hypertrophy

s British Society for Cardiovascular Research, Reading, 2014 A Loonat, F Hunt, S H Choi, E D Martin, N T Hertz, R Levin, K M Shokat, A L Burlingame, M S Marber and J E Clark. Elucidating the role of p38γ in pathological cardiac hypertrophy. Heart (2014) British Society for Cardiovascular Research, London, 2014 M Thomas, S Uddin, A Loonat, M Marber, J Clark. P38γ mitogen-activated protein kinase is a mediator of pathological cardiac hypertrophy. Heart (2014) The Biomedical Basis of Elite Performance, London, 2012 K. D. Tilgner, A. Loonat, M. Marber, J. E. Clark. Ablation of p38γ-MAPK reduces cardiac remodelling following pressure overload. Proc Physiol Soc (2012)
The Diabetes Location, Environmental Attributes, and Disparities Network: Protocol for Nested Case Control and Cohort Studies, Rationale, and Baseline Characteristics

Background Diabetes prevalence and incidence vary by neighborhood socioeconomic environment (NSEE) and geographic region in the United States. Identifying modifiable community factors driving type 2 diabetes disparities is essential to inform policy interventions that reduce the risk of type 2 diabetes. Objective This paper aims to describe the Diabetes Location, Environmental Attributes, and Disparities (LEAD) Network, a group funded by the Centers for Disease Control and Prevention to apply harmonized epidemiologic approaches across unique and geographically expansive data to identify community factors that contribute to type 2 diabetes risk. Methods The Diabetes LEAD Network is a collaboration of 3 study sites and a data coordinating center (Drexel University). The Geisinger and Johns Hopkins University study population includes 578,485 individuals receiving primary care at Geisinger, a health system serving a population representative of 37 counties in Pennsylvania. The New York University School of Medicine study population is a baseline cohort of 6,082,146 veterans who do not have diabetes and are receiving primary care through Veterans Affairs from every US county. The University of Alabama at Birmingham study population includes 11,199 participants who did not have diabetes at baseline from the Reasons for Geographic and Racial Differences in Stroke (REGARDS) study, a cohort study with oversampling of participants from the Stroke Belt region. Results The Network has established a shared set of aims: evaluate mediation of the association of the NSEE with type 2 diabetes onset, evaluate effect modification of the association of NSEE with type 2 diabetes onset, assess the differential item functioning of community measures by geographic region and community type, and evaluate the impact of the spatial scale used to measure community factors. The Network has developed standardized approaches for measurement. Conclusions The Network will provide insight into the community factors driving geographical disparities in type 2 diabetes risk and disseminate findings to stakeholders, providing guidance on policies to ameliorate geographic disparities in type 2 diabetes in the United States. International Registered Report Identifier (IRRID) DERR1-10.2196/21377
Prospective assessment of subclinical cardiovascular damage and associated factors in liver transplant recipients

Cardiovascular (CV) disease plays a major role after liver transplantation (LT). This prospective study assessed subclinical CV damage after LT by measuring pulse wave velocity (PWV), intima‐media thickness (IMT) and left‐ventricular mass index (LVMI) and characterized associated risk factors. We included 112 patients with a median of 1.8 years after LT (q1–q3 0.9–9.2). Fifty‐three percent (n = 59) of patients had ≥2 annual assessments (median follow‐up 1.6 years, q1–q3 1.1–2.0), with a total of 195 assessments. We found increased PWV (indicating arteriosclerosis) in 16% (n = 17), elevated IMT in 5% (n = 5; indicating atherosclerosis) and increased LVMI in 25% (n = 24; indicating left‐ventricular hypertrophy). A linear mixed model analysis using all 195 assessments revealed that higher age and systolic blood pressure (BP) were associated with higher PWV (β = 0.069, P < 0.001 and β = 0.022, P = 0.005) and higher IMT (β = 0.005, P < 0.001 and β = 0.001, P = 0.029), while higher body mass index was associated with higher IMT (β = 0.004, P = 0.023). Higher systolic BP (β = 0.200, P = 0.034), male sex (β = 8.847, P = 0.031) and lower glomerular filtration rate (β = −0.288, P < 0.001) were associated with higher LVMI. Our data highlight not only the rate of subclinical CV damage in LT patients, but also the impact of classical CV risk factors (such as BP and body mass index) which outweighed LT‐related factors. These modifiable risk factors are suitable targets for interventions to reduce CV morbidity in LT patients.
Restoration of the apoptosis pathways’ proteins levels after orchiectomy in testicular tumour patients

Seminal plasma proteins already demonstrated to reflect the testicular environment function and important regulatory mechanisms. However, it is crucial to understand which of these proteins participate in probable altered pathways in testicular germ cell tumours and after unilateral orchiectomy. In this study, we proposed to verify, by a multiplex approach, the levels of DNA damage and apoptosis pathways’ proteins, in seminal plasma of men before and after unilateral orchiectomy, and also in control men. Comparing pre‐ and post‐orchiectomy groups, just the apoptosis pathways’ proteins presented different levels, in which Bad was lower and Bcl2, Akt, caspase‐9, p53 and caspase‐8 were higher after orchiectomy. When comparing pre‐ and post‐orchiectomy groups with control, both presented lower levels of ChK1, Chk2, H2AX, p53 and p21, for DNA damage pathway. Regarding the apoptosis pathway, lower levels of JNK, Bcl2, Akt, caspase‐9, p53 and caspase‐8 and higher levels of Bad were observed before orchiectomy. The post‐orchiectomy group did not differ from controls, demonstrating a probable restoration on its proteins levels. We can conclude that testicular tumours can alter both of the assessed pathways, and its removal is associated with a probable restoration of the apoptosis pathway.
Network based conditional genome wide association analysis of human metabolomics

Background Genome-wide association studies (GWAS) have identified hundreds of loci influencing complex human traits, however, their biological mechanism of action remains mostly unknown. Recent accumulation of functional genomics (‘omics’) including metabolomics data opens up opportunities to provide a new insight into the functional role of specific changes in the genome. Functional genomic data are characterized by high dimensionality, presence of (strong) statistical dependencies between traits, and, potentially, complex genetic control. Therefore, analysis of such data asks for development of specific statistical genetic methods. Results We propose a network-based, conditional approach to evaluate the impact of genetic variants on omics phenotypes (conditional GWAS, cGWAS). For each trait of interest, based on biological network, we select a set of other traits to be used as covariates in GWAS. The network could be reconstructed either from biological pathway databases or directly from the data. We evaluated our approach using data from a population-based KORA study (n=1,784, 1.7 M SNPs) with measured metabolomics data (151 metabolites) and demonstrated that our approach allows for identification of up to five additional loci not detected by conventional GWAS. We show that this gain in power is achieved through increased precision of genetic effect estimates, and in presence of specific ‘contra-intuitive’ pleiotropic scenarios (when genetic and environmental sources of covariance are acting in opposite manner). We justify existence of such scenarios, and discuss possible applications of our method beyond metabolomics. Conclusions We demonstrate that in context of metabolomics network-based, conditional genome-wide association analysis is able to dramatically increase power of identification of loci with specific ‘contra-intuitive’ pleiotropic architecture. Our method has modest computational costs, can utilize summary level GWAS data, and is applicable to other omics data types. We anticipate that application of our method to new and existing data sets will facilitate progress in understanding genetic bases of control of molecular and complex phenotypes. Short abstract We propose a network-based, conditional approach for genome-wide analysis of multivariate omics phenotypes. Our methods can incorporate prior biological knowledge about biological pathways from external sources. We evaluated our approach using metabolomics data and demonstrated that our approach has bigger power and allows for identification of additional loci. We show that gain in power is achieved through increased precision of genetic effect estimates, and in presence of specific ‘contra-intuitive’ pleiotropic scenarios (when genetic and environmental sources of covariance are acting in opposite manner). We justify existence of such scenarios, and discuss possible applications of our method beyond metabolomics.
In silico Analysis to Identify Synteny in Bacterial Signatures of Iron Nanoparticles Synthesizing Bacteria Contributing to Big Data

Isolation of bacteria from new sources has been initiated and different types of bacteria have been reported from various types of metal mines, extreme environments, ocean beds, amorphous solids, effluents etc (Francois et al., 2012). Various bacterial species such as Actinobacter sp. , Escherichia coli, Klebsiella pneumonia, Lactobacillus spp. , Bacillus cereus, Corynebacterium sp. , and Pseudomonas sp. undergoes intracellular and extracellular mechanism to synthesize metallic nanoparticles (Mohanpuria et al., 2008; Tollamadugu et al., 2011). It is very interesting to add that various metal nanoparticles synthesizing bacteria has been added to list with respect to iron, gold, silver, copper, selenium, titanium etc (Li et al., 2011). Traditional method of classification was carried out according to similarities and differences in their phenotypic characteristics, International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 6 Number 9 (2017) pp. 356-367 Journal homepage: http://www.ijcmas. com
A CAUTIONARY NOTE ON THE USE OF MNA-DERIVED TRAPPABILITY METRICS IN WILDLIFE PROGRAMMES, AS EXEMPLIFIED BY THE CASE OF THE EUROPEAN BADGER (MELES MELES)

Minimum Number Alive (MNA) is a widely used index of abundance and trappability in mark-recapture programmes. MNA is a negatively-biased abundance index, and is sensitive to capture probability and the capture session number. This suggests that MNA-trappability will be positively-biased, and that the extent of the bias will vary with true trappability and trapping regime. Inappropriate use of the index may therefore lead to over-optimistic estimates of trappability. In this note, we highlight the dangers of using MNA-trappability for wildlife practitioners. Using closed-population stochastic simulation, we verify that MNA-trappability indeed provides over-optimistic estimates, especially when true trappability is <70% and the number of trapping occasions is small (<7). Using severely-biased trappability estimates could have serious consequences for wildlife conservation, management or vaccination studies. We specifically discuss the implications of this finding in relation to control programmes of the European badger Meles meles and recommend that future studies, where possible, use multiple metrics of trappability to assess the consistency of results across estimators.
Composition and properties of Apis mellifera honey: A review

Honey is a natural sweetener with a complex composition. Honey features vary depending on the botanical source and geographical origin, as well as climatic, processing and storage conditions. Honey is mainly composed of carbohydrates and water, parameters that influence its shelf life and some of its properties, including color, flavor, density, viscosity, hygroscopicity, and crystallization. Honey also contains small amounts of other components, such as nitrogen compounds, organic acids, minerals, vitamins, Maillard reaction products, volatile compounds, and several bioactive substances that affect sensory and physical characteristics, as well as biological potential. This review summarizes the literature about the composition and main properties of honey. It also describes the use of honey as a biomonitor for collecting information about the environment, identifying environmental contamination and assessing the level of soil, water, plant and air pollution.