Miracle-dz/UniFAR-FTUs huggingface dataset:
LncRNA FAS-AS1 inhibits the progression of non-small cell lung cancer through regulating miR-19a-5p.

OBJECTIVE Non-small cell lung cancer (NSCLC) is one of the most common and deadly tumors in the world. LncRNA FAS-AS1 was abnormally expressed in various cancers, such as non-small cell lung cancer. However, the underlying mechanism of FAS-AS1 in NSCLC remains to be elucidated. MATERIALS AND METHODS The levels of FAS-AS1 and miR-19a-5p were measured using qRT-PCR in NSCLC cells. MTT and cell colony formation assays were performed to detect cell proliferative capacity. Transwell assay was carried out to measure cell migration and invasion. The relationship between FAS-AS1 and miR-19a-5p was confirmed using Luciferase reporter assay. Xenograft tumor experiment was conducted to detect the tumor growth in vivo. RESULTS FAS-AS1 was remarkably down-regulated in NSCLC cells. FAS-AS1 inhibited cell proliferation, migration, and invasion in NSCLC cells. Additionally, FAS-AS1 directly targeted miR-19a-5p and negatively regulated the expression of miR-19a-5p in NSCLC cells. Furthermore, FAS-AS1 overexpression restored the promotion of miR-19a-5p overexpression on proliferation, migration, and invasion of NSCLC cells. Additionally, suppression of FAS-AS1 abrogated the inhibitory effects of miR-19a-5p knockdown on the progression of NSCLC. FAS-AS1 suppressed the tumor growth in vivo. CONCLUSIONS FAS-AS1 suppressed cell proliferation, migration, and invasion by sponging miR-19a-5p in NSCLC, indicating that FAS-AS1 might be a potential biomarker and therapeutic target for NSCLC.
Dynamics of Different Buffer Systems in Slurries Based on Time and Temperature of Storage and Their Visualization by a New Mathematical Tool

Simple Summary Efficient slurry management is a key strategy to reduce the release of environmentally harmful gases produced by farm animals. Slurry treatments such as acidification and alkalization have proven to be promising solutions to reduce these emissions. In this context, it is crucial to understand how buffer capacities behave and may influence each other during storage under the influence of different temperatures. To realize this, we have developed and successfully verified a new mathematical tool. It allows an exact calculation and detailed visualization of the most important buffer systems found in the analyzed slurries. This knowledge can be used to optimize slurry treatments, as it allows faster, more precise and efficient timing of pH adjustment, thus, reducing the use of resources. Abstract Slurry treatments such as acidification and alkalization have proven to be promising solutions to reduce gaseous emission produced by farm animals. The optimization of these technologies requires detailed knowledge of how and to what extent the buffer capacities in slurries will change during storage under the influence of different temperatures, as this may save resources needed to adjust a targeted pH value. Fresh slurries from dairy cows, fattening pigs and sows were collected and stored for 12 weeks under either cold (4.7 ± 1.1 °C) or warm (23.6 ± 2.1 °C) conditions to perform titrations in acidic and alkaline milieu at regular intervals. Based on these results, we successfully verified a new mathematical tool that we have developed to be able to calculate and visualize the most important buffer systems found in the analyzed slurries. Our experimental results showed a strong correlation between the degradation of the volatile fatty acid (VFA) buffer and the emergence of the carbonate buffers, i.e., the HCO3− and the CO32− buffer. Furthermore, a drop in the pH value caused by enhanced microbial production of VFAs can be mitigated by the presence of the NH3 buffer. In conclusion, we demonstrated that the buffers cannot be considered individually but must be interpreted as a complex and interacting system.
Correlation of heart rate and blood pressure variability as well as hs-CRP with the burden of stable coronary artery disease.

OBJECTIVE The aim is to investigate the predictive value of heart rate variability (HRV), blood pressure variability (BPV), and high-sensitivity C-reactive protein (hs-CRP) levels in patients with stable coronary artery disease (SCAD) to assess whether these variables predict the Gensini score. METHODS 588 patients with SCAD were enrolled. Normal coronary angiography (102 patients) and healthy physical examination patients (104 patients) as control group for HRV. Dynamic electrocardiogram, ambulatory blood pressure, and hs-CRP were measured in SCHD, and Gensini scores were calculated. The relationship between the level of Gensini scores and HRV, BPV and hs-CRP in SCAD was analyzed. Assess the predictive value of non-invasive markers for the degree of coronary artery disease in SCAD. RESULTS HRV was negatively correlated with coronary lesions Gensini scores, and BPV was positively correlated with them. The correlation coefficients of SDNN, PNN50, SDANN, RMSSD, and TRIA in HRV are -0.327, -0.489, -0.153 -0.206, -0.292, respectively (P<0.01); while 24hSBPV, 24hDBPV, dSBPV, dDBPV, nSBPV and nSBPdrinBPV are 0.286, 0.233, 0.141, 0.139, 0.218, 0.113, respectively (P<0.01); hs-CRP was positively correlated with the Gensini scores of coronary lesions (0.325, P<0.01); HRV decreased (PNN50<14.97, TRIA<160.86) and BPV increased (24hSBPV>20%, nSBPV>20%) combined with hs-CRP positive (hs-CR>3.0 mg/L) performance can effectively predict coronary lesions in SCAD. CONCLUSIONS HRV, BPV and hs-CRP are all significantly associated with coronary lesions. And these variables can predict the Gensini score in SCAD.
Proteomic and Bioinformatic Analysis of Streptococcus suis Human Isolates: Combined Prediction of Potential Vaccine Candidates

Streptococcus suis is a Gram-positive bacterium responsible for major infections in pigs and economic losses in the livestock industry, but also an emerging zoonotic pathogen causing serious diseases in humans. No vaccine is available so far against this microorganism. Conserved surface proteins are among the most promising candidates for new and effective vaccines. Until now, research on this pathogen has focused on swine isolates, but there is a lack of studies to identify and characterize surface proteins from human clinical isolates. In this work, we performed a comparative proteomic analysis of six clinical isolates from human patients, all belonging to the major serotype 2, by “shaving” the live bacterial cells with trypsin, followed by LC-MS/MS analysis. We identified 131 predicted surface proteins and carried out a label-free semi-quantitative analysis of protein abundances within the six strains. Then, we combined our proteomics results with bioinformatic tools to help improving the selection of novel antigens that can enter the pipeline of vaccine candidate testing. Our work is then a complement to the reverse vaccinology concept.
The Osteosarcoma Microenvironment: A Complex but Targetable Ecosystem

Osteosarcomas are the most frequent primary bone sarcomas, affecting mainly children, adolescents, and young adults, and with a second peak of incidence in elderly individuals. The current therapeutic management, a combined regimen of poly-chemotherapy and surgery, still remains largely insufficient, as patient survival has not improved in recent decades. Osteosarcomas are very heterogeneous tumors, both at the intra- and inter-tumor level, with no identified driver mutation. Consequently, efforts to improve treatments using targeted therapies have faced this lack of specific osteosarcoma targets. Nevertheless, these tumors are inextricably linked to their local microenvironment, composed of bone, stromal, vascular and immune cells and the osteosarcoma microenvironment is now considered to be essential and supportive for growth and dissemination. This review describes the different actors of the osteosarcoma microenvironment and gives an overview of the past, current, and future strategies of therapy targeting this complex ecosystem, with a focus on the role of extracellular vesicles and on the emergence of multi-kinase inhibitors.
Epidemiology and Genetic Variability of Circulating Influenza B Viruses in Uruguay, 2012–2019

Influenza B viruses (IBV) are an important cause of morbidity and mortality during interpandemic periods in the human population. Two phylogenetically distinct IBV lineages, B/Yamagata and B/Victoria, co-circulate worldwide and they present challenges for vaccine strain selection. Until the present study, there was little information regarding the pattern of the circulating strains of IBV in Uruguay. A subset of positive influenza B samples from influenza-like illness (ILI) outpatients and severe acute respiratory illness (SARI) inpatients detected in sentinel hospitals in Uruguay during 2012–2019 were selected. The sequencing of the hemagglutinin (HA) and neuraminidase (NA) genes showed substitutions at the amino acid level. Phylogenetic analysis reveals the co-circulation of both lineages in almost all seasonal epidemics in Uruguay, and allows recognizing a lineage-level vaccine mismatch in approximately one-third of the seasons studied. The epidemiological results show that the proportion of IBV found in ILI was significantly higher than the observed in SARI cases across different groups of age (9.7% ILI, 3.2% SARI) and patients between 5–14 years constituted the majority (33%) of all influenza B infection (p < 0.05). Interestingly, we found that individuals >25 years were particularly vulnerable to Yamagata lineage infections.
Tea extracts differentially inhibit Streptococcus mutans and Streptococcus sobrinus biofilm colonization depending on the steeping temperature

Abstract This study aimed to evaluate the effects of tea extracts on oral biofilm colonization depending on steeping temperature. S. mutans and S. sobrinus were cultured and treated with green or black tea extracts prepared under different steeping conditions. Biofilm formation, glucosyltransferase (GTF) levels, bacterial growth, and acidogenicity were evaluated. Biofilms were also assessed by gas chromatography-mass spectrometry and confocal laser scanning microscopy. All extracts with hot steeping showed higher inhibitory effects on biofilm formation and cell viability and lower GTF levels compared with those with cold steeping (p < 0.05). Hot steeping significantly reduced bacterial growth (p < 0.05) and maintained the pH. Catechins were only identified from hot steeping extracts. Within the limits of this study, extracts with cold steeping showed lower inhibitory effects on oral biofilms. The different effects between steeping extracts may be attributed to the difference in catechins released from tea extracts under the different steep conditions.
Molecular polymorphisms for phylogeny, pedigree and population structure studies

A number of types of molecular polymorphisms can be used for studying genetic relationship and evolutionary history. Microsatellites are hypervariable and can be very useful tools to determine population structure, distinguish sibling species, as well as verifying parental relationships and pedigrees. However, while microsatellite polymorphisms are useful for solving relationships between populations within a species, relations among species or genera will probably be obscured due to a high degree of homoplasy —identity arising from evolutionary convergence not by descent. For long range evolutionary history, such as phylogeny from old world monkey to human, mtDNA markers may be better candidates. The aim of this thesis is to assess molecular polymorphisms of different types and their optimal use in different situations. Two widely separated taxa were used for testing –the green monkey Chlorocebus sabaeus, and the sibling dipteran flies Bactrocera tryoni and B. neohumeralis, known collectively as the Queensland fruit fly. In the present study a complete 16,550 bp mtDNA sequence of the green monkey Chlorocebus sabaeus is reported for the fist time and has been annotated (Chapter 2). Knowledge of the mtDNA genome contributes not only to identification of large scale single nucleotide polymorphisms (SNPs) (Chapter 4) or other mtDNA polymorphisms development, but also to primate phylogenetic and evolutionary study (Chapter 3). Microsatellites used for the green monkey paternity and pedigree studies were developed by cross-amplification using human primers (Chapter 5). For studies of population
Metagenomic analysis of the human microbiome reveals the association between the abundance of gut bile salt hydrolases and host health

ABSTRACT Bile acid metabolism by the gut microbiome exerts both beneficial and harmful effects on host health. Microbial bile salt hydrolases (BSHs), which initiate bile acid metabolism, exhibit both positive and negative effects on host physiology. In this study, 5,790 BSH homologs were collected and classified into seven clusters based on a sequence similarity network. Next, the abundance and distribution of BSH in 380 metagenomes from healthy participants were analyzed. It was observed that different clusters occupied diverse ecological niches in the human microbiome and that the clusters with signal peptides were relatively abundant in the gut. Then, the association between BSH clusters and 12 human diseases was analyzed by comparing the abundances of BSH genes in patients (n = 1,605) and healthy controls (n = 1,540). The analysis identified a significant association between BSH gene abundance and 10 human diseases, including gastrointestinal diseases, obesity, type 2 diabetes, liver diseases, cardiovascular diseases, and neurological diseases. The associations were further validated by separate cohorts with inflammatory bowel diseases and colorectal cancer. These large-scale studies of enzyme sequences combined with metagenomic data provide a reproducible assessment of the association between gut BSHs and human diseases. This information can contribute to future diagnostic and therapeutic applications of BSH-active bacteria for improving human health.
Necroptosis in Cholangiocarcinoma

Necroptosis is a type of regulated cell death that is increasingly being recognized as a relevant pathway in different pathological conditions. Necroptosis can occur in response to multiple stimuli, is triggered by the activation of death receptors, and is regulated by receptor-interacting protein kinases 1 and 3 and mixed-lineage kinase domain-like, which form a regulatory complex called the necrosome. Accumulating evidence suggests that necroptosis plays a complex role in cancer, which is likely context-dependent and can vary among different types of neoplasms. Necroptosis serves as an alternative mode of programmed cell death overcoming apoptosis and, as a pro-inflammatory death type, it may inhibit tumor progression by releasing damage-associated molecular patterns to elicit robust cross-priming of anti-tumor CD8+ T cells. The development of therapeutic strategies triggering necroptosis shows great potential for anti-cancer therapy. In this review, we summarize the current knowledge on necroptosis and its role in liver biliary neoplasms, underlying the potential of targeting necroptosis components for cancer treatment.
Is forest fecundity resistant to drought? Results from an 18‐yr rainfall‐reduction experiment

Summary Recruitment is a primary determinant of the long‐term dynamics of plant populations in changing environments. However, little information is known about the effects of anthropogenic environmental changes on reproductive ecology of trees. We evaluated the impact of experimentally induced 18 yr of drought on reproduction of three contrasting forest trees: Quercus ilex, Phillyrea latifolia and Arbutus unedo. Rainfall reduction did not decrease tree fecundity. Drought, however, affected the allocation of resources in Q. ilex and A. unedo but not the more drought tolerant P. latifolia. Larger crop production by Q. ilex and A. unedo was associated with a stronger decrease in growth in the rainfall‐reduction plots compared with the control plots, suggesting that these species were able to maintain their fecundity by shifting their allocation of resources away from growth. Our results indicated resistance to change in tree fecundity in Mediterranean‐type forest subjected to an average 15% decrease in the amount of soil moisture, suggesting that these ecosystems may adapt to a progressive increase in arid conditions. However, the species‐specific reductions in growth may indirectly affect future fecundity and ultimately shift community composition, even without immediate direct effects of drought on tree fecundity.
Partitioning heritability analyses unveil the genetic architecture of human brain multidimensional functional connectivity patterns

Resting‐state functional connectivity profiles have been increasingly shown to be important endophenotypes that are tightly linked to human cognitive functions and psychiatric diseases, yet the genetic architecture of this multidimensional trait is barely understood. Using a unique sample of 1,704 unrelated, young and healthy Chinese Han individuals, we revealed a significant heritability of functional connectivity patterns in the whole brain and several subnetworks. We further proposed a partitioned heritability analysis for multidimensional functional connectivity patterns, which revealed the common and unique enrichment patterns of the genetic contributions to brain connectivity patterns for several gene sets linked to brain functions, including the genes expressed preferentially in the central nervous system and those associated with intelligence, educational attainment, attention‐deficit/hyperactivity disorder, and schizophrenia. These results for the first time reveal the genetic architecture of multidimensional brain connectivity patterns across different networks and advance our understanding of the complex relationship between gene sets, neural networks, and behaviors.
Sphingomyelins Prevent Propagation of Lipid Peroxidation—LC-MS/MS Evaluation of Inhibition Mechanisms

Free radical driven lipid peroxidation is a chain reaction which can lead to oxidative degradation of biological membranes. Propagation vs. termination rates of peroxidation in biological membranes are determined by a variety of factors including fatty acyl chain composition, presence of antioxidants, as well as biophysical properties of mono- or bilayers. Sphingomyelins (SMs), a class of sphingophospholipids, were previously described to inhibit lipid oxidation most probably via the formation of H-bond network within membranes. To address the “antioxidant” potential of SMs, we performed LC-MS/MS analysis of model SM/glycerophosphatidylcholine (PC) liposomes with different SM fraction after induction of radical driven lipid peroxidation. Increasing SM fraction led to a strong suppression of lipid peroxidation. Electrochemical oxidation of non-liposomal SMs eliminated the observed effect, indicating the importance of membrane structure for inhibition of peroxidation propagation. High resolution MS analysis of lipid peroxidation products (LPPs) observed in in vitro oxidized SM/PC liposomes allowed to identify and relatively quantify SM- and PC-derived LPPs. Moreover, mapping quantified LPPs to the known pathways of lipid peroxidation allowed to demonstrate significant decrease in mono-hydroxy(epoxy) LPPs relative to mono-keto derivatives in SM-rich liposomes. The results presented here illustrate an important property of SMs in biological membranes, acting as “biophysical antioxidant”. Furthermore, a ratio between mono-keto/mono-hydroxy(epoxy) oxidized species can be used as a marker of lipid peroxidation propagation in the presence of different antioxidants.
Investigating Various Permutations of Copper Iodide/FeCu Tandem Materials as Electrodes for Dye-Sensitized Solar Cells with a Natural Dye

This work presents the synthesis and deposition of CuI and FeCu materials on copper substrates for dye-sensitized solar cell applications. FeCu is a metastable alloy of iron and copper powders and possesses good optical and intrinsic magnetic properties. Coupled with copper iodide as tandem layers, the deposition of these two materials was permutated over a pure copper substrate, characterized and then tested within a solar cell. The cell was sensitized with a natural dye extracted from a local desert plant (Calotropis gigantea) and operated with an iodine/triiodide electrolyte. The results show that the best layer arrangement was Cu/FeCu/CuI, which gave an efficiency of around 0.763% (compared to 0.196% from reported cells in the literature using a natural sensitizer).
Sepsis: the silent killer we should be stopping

The UK Sepsis Trust estimates that sepsis may kill as many as six million people globally each year. We know that sepsis goes unrecognised by members of the public, and that often victims present to healthcare too late as a result. We also know that healthcare professionals could be better educated, so that sepsis diagnoses can be made more quickly, and treatment administered as fast as possible. Earlier identification and treatment could prevent many of the millions of unnecessary deaths every year. First Aid providers can help by equipping themselves with the information they need to recognise the signs of sepsis and seek medical attention urgently, thereby starting the Chain of Survival Behaviour (IFRC, 2016) as early as possible.