Miracle-dz/UniFAR-FTUs huggingface dataset:
Adhesion of Staphylococcus aureus to Candida albicans During Co-Infection Promotes Bacterial Dissemination Through the Host Immune Response

Interspecies interactions greatly influence the virulence, drug tolerance and ultimately the outcome of polymicrobial biofilm infections. A synergistic interaction is observed between the fungus Candida albicans and the bacterium Staphylococcus aureus. These species are both normal commensals of most healthy humans and co-exist in several niches of the host. However, under certain circumstances, they can cause hospital-acquired infections with high morbidity and mortality rates. Using a mouse model of oral co-infection, we previously showed that an oral infection with C. albicans predisposes to a secondary systemic infection with S. aureus. Here, we unraveled this intriguing mechanism of bacterial dissemination. Using static and dynamic adhesion assays in combination with single-cell force spectroscopy, we identified C. albicans Als1 and Als3 adhesins as the molecular players involved in the interaction with S. aureus and in subsequent bacterial dissemination. Remarkably, we identified the host immune response as a key element required for bacterial dissemination. We found that the level of immunosuppression of the host plays a critical yet paradoxical role in this process. In addition, secretion of candidalysin, the C. albicans peptide responsible for immune activation and cell damage, is required for C. albicans colonization and subsequent bacterial dissemination. The physical interaction with C. albicans enhances bacterial uptake by phagocytic immune cells, thereby enabling an opportunity to disseminate.
Novel sample preparation technique for protein crystal X-ray crystallographic analysis combining microfluidics and acoustic manipulation

In order to perform X-ray crystallographic analysis, protein crystals are removed from their growing solution by means of a nylon loop, which is then mounted on a goniometer. As this process is repeated for a large number of crystals, there is a need for automation, especially with regard to the placement on the nylon loop. A novel technique involving the use of acoustic radiation forces and a micro-machined fluidic device is introduced here. After insertion into the micro-machined channel, the crystals are positioned in a row along its centre-line by excitation of a high-frequency standing pressure field, and then moved towards an orifice by applying a flow along the channel, which also ensures spatial separation. Once located in a defined orifice, the single crystals can be removed using a nylon loop. X-ray crystallographic analysis showed that application of ultrasound does not influence the diffraction properties of the crystals.
Probiotics, Anticipation Stress, and the Acute Immune Response to Night Shift

Introduction Sleep disturbance and sleep disruption are associated with chronic, low grade inflammation and may underpin a range of chronic diseases in night shift workers. Through modulation of the intestinal microbiota, probiotic supplements may moderate the effects of sleep disruption on the immune system. The aim of this study was to examine 14 days of daily probiotic supplementation on the acute response of acute phase proteins and immune markers to sleep disruption associated with night shift work (Australia and New Zealand Clinical Trials Registry: 12617001552370). Methods Individuals (mean age 41 ± 11 yrs; 74% female) performing routine night shift were randomly assigned to a probiotic group (1 × 1010 colony forming units (CFU) Lactobacillus acidophilus DDS-1 or 1 × 1010 CFU Bifidobacterium animalis subsp. lactis UABla-12) or placebo (n= 29 per group). Participants undertook a 14-day supplementation period that coincided with a period of no night shifts followed by two consecutive night shifts. Blood samples were collected prior to the start of supplementation (V1), prior to commencing the first night shift (V2), after the first night shift (V3) and after the second night shift (V4). Serum was assessed for markers of stress (cortisol), acute phase response (C reactive protein (CRP), erythrocyte sedimentation rate, pentraxin), adhesion markers (serum E-selectin, mucosal vascular addressin cell adhesion molecule 1 (MAdCAM-1), and serum cytokines (interleukin (IL)-1ra, IL-1β, IL-6, tumor necrosis factor (TNF)-α, IL-10). Sleep quality was assessed with the Pittsburgh Sleep Quality Index (PSQI) and a Fitbit activity tracker. Results The groups were well balanced on key markers and the probiotic strains were well tolerated. The 14-day supplementation period that coincided with typical night-day sleep-wake cycles leading up to night shift (V1 to V2) was associated with significant changes in the placebo group in the concentration of serum cortisol (p = 0.01), pentraxin (p = 0.001), MAdCAM-1 (p = 0.001), and IL-1ra (p=0.03). In contrast, probiotic supplementation moderated changes in these serum markers from V1 to V2. No significant interaction effects (time by group) were observed for the serum markers prior to and after night shift work following probiotic supplementation due to the substantial changes in the serum markers that occurred during the normal sleep period from V1 to V2. Conclusions Probiotics may moderate the effects of anticipatory stress on the immune system in the lead up to night shift.
Microbial Metabolic Genes Crucial for S. aureus Biofilms: An Insight From Re-analysis of Publicly Available Microarray Datasets

Bacterial biofilms are microbial lifestyles found in all environments. Up to 80% of human infections and 60–70% of hospital-acquired infections have a biofilm origin, with Staphylococcus aureus one of the leading causes of these infections. Microorganisms in biofilms exhibit significant antimicrobial resistance which poses important treatment challenges, hence the urgent need to identify novel antibiofilm strategies. Microbes form biofilms in response to various factors, and once these 3-dimentional structures form they are highly recalcitrant to removal. The switch from planktonic lifestyle to the biofilm protected mode of growth results in a phenotypic shift in the behavior of the microorganisms in terms of growth rate and gene expression. Given these changes, investigation of microbial gene expression and their modulation at different stages of biofilm maturation is needed to provide vital insight into the behavior of biofilm cells. In this study, we analyzed publicly available transcriptomic dataset of S. aureus biofilms at different stages of maturation to identify consistently upregulated genes irrespective of the biofilm maturation stage. Our reanalysis identified a total of 6 differentially expressed genes upregulated in both 48 and 144-h old S. aureus biofilms. Functional analysis revealed that these genes encode for proteins which play a role in key microbial metabolic pathways. However, these genes, as yet, are unrelated or fully studied in the context of biofilm. Moreover, the findings of this in silico work, suggest that these genes may represent potential novel targets for the development of more effective antibiofilm strategies against S. aureus biofilm-associated infections.
Practical Volcano-Independent Recognition of Seismic Events: VULCAN.ears Project

Recognizing the mechanisms underlying seismic activity and tracking temporal and spatial patterns of earthquakes represent primary inputs to monitor active volcanoes and forecast eruptions. To quantify this seismicity, catalogs are established to summarize the history of the observed types and number of volcano-seismic events. In volcano observatories the detection and posterior classification or labeling of the events is manually performed by technicians, often suffering a lack of unified criteria and eventually resulting in poorly reliable labeled databases. State-of-the-art automatic Volcano-Seismic Recognition (VSR) systems allow real-time monitoring and consistent catalogs. VSR systems are generally designed to monitor one station of one volcano, decreasing their efficiency when used to recognize events from another station, in a different eruptive scenario or at different volcanoes. We propose a Volcano-Independent VSR (VI.VSR) solution for creating an exportable VSR system, whose aim is to generate labeled catalogs for observatories which do not have the resources for deploying their own systems. VI.VSR trains universal recognition models with data of several volcanoes to obtain portable and robust characteristics. We have designed the VULCAN.ears ecosystem to facilitate the VI.VSR application in observatories, including the pyVERSO tool to perform VSR tasks in an intuitive way, its graphical interface, geoStudio, and liveVSR for real-time monitoring. Case studies are presented at Deception, Colima, Popocatépetl and Arenal volcanoes testing VI.VSR models in challenging scenarios, obtaining encouraging recognition results in the 70–80% accuracy range. VI.VSR technology represents a major breakthrough to monitor volcanoes with minimal effort, providing reliable seismic catalogs to characterise real-time changes.
Low Soluble Receptor for Advanced Glycation End Products Precedes and Predicts Cardiometabolic Events in Women With Rheumatoid Arthritis

Background: Cardiovascular disease (CVD) causes premature mortality in rheumatoid arthritis (RA). Levels of soluble (s)RAGE change with aging, hypertension and hypercholesterolemia. We assessed whether sRAGE was associated with increased risk of CVD in RA patients. Methods: Serum sRAGE was measured in 184 female RA patients and analyzed with respect to CVD risk estimated by the Framingham algorithm (eCVR), metabolic profile and inflammation. Levels of sRAGE in 13 patients with known cardio-metabolic morbidity defined the cut-off for low sRAGE. Prospective 5-year follow-up of new CV and metabolic events was completed. Results: Low sRAGE was significantly associated with previous history and with new imminent cardiometabolic events in the prospective follow-up of RA patients. In both cases, low sRAGE reflected higher estimation of CVR in those patients. Low sRAGE was attributed to adverse metabolic parameters including high fasting plasma glucose and body fat content rather than inflammation. The association of sRAGE and poor metabolic profile was prominent in patients younger than 50 years. Conclusions: This study points at low sRAGE as a marker of metabolic failure developed during chronic inflammation. It highlights the importance for monitoring metabolic health in female RA patients for timely prevention of CVD. Trial registration: ClinicalTrials.gov with ID NCT03449589. Registered 28, February 2018.
First Molecular Evidence and Genetic Characterization of Ovine Herpesvirus 2 in Multiple Animal Species in India

Ovine herpesvirus 2 (OvHV-2) is the causative agent of sheep-associated malignant catarrhal fever (SA-MCF), a highly fatal disease syndrome that predominantly affects susceptible hosts of the order Artiodactyla. In this study, an in-depth clinico-molecular investigation of SA-MCF disease in a morbid 50-days-old cattle calf (Bos taurus indicus) and asymptomatic infection in the in-contact reservoir hosts, sheep (Ovis aries), and goat (Capra hircus) housed on a farm located in the Southern India is reported. An OIE recommended SA-MCF type-specific PCR confirmed the etiological agent as OvHV-2. The genetic characterization and phylogenetic analyses based on the glycoprotein B (gB) gene indicate that three genetic variants of OvHV-2 had infected the animal cluster of this study. As the OvHV-2 infection eventually lead to the death of the cattle calf, and the fact that its gB sequence carried four unique amino acid substitutions (N169S, L594P, I645V, and V730A), an investigation of these substitutions impact on its stability and molecular flexibility was carried out. The mapping of these amino acid substitutions on the three-dimensional structure of gB coupled with supplementary investigations showed that these substitutions conveyed the molecular flexibility to the gB, at the cost of its stability. Future studies would be to investigate whether these gB substitutions have any impact on membrane fusion activity using a virus-free cell-to-cell membrane fusion assay. The study also highlights the importance of adopting stringent biosecurity measures where mixed animal farming is a common practice.
Use of Contemporary Groups in the Construction of Multi-Environment Trial Datasets for Selection in Plant Breeding Programs

Plant breeding programs use multi-environment trial (MET) data to select superior lines, with the ultimate aim of increasing genetic gain. Selection accuracy can be improved with the use of advanced statistical analysis methods that employ informative models for genotype by environment interaction, include information on genetic relatedness and appropriately accommodate within-trial error variation. The gains will only be achieved, however, if the methods are applied to suitable MET datasets. In this paper we present an approach for constructing MET datasets that optimizes the information available for selection decisions. This is based on two new concepts that characterize the structure of a breeding program. The first is that of “contemporary groups,” which are defined to be groups of lines that enter the initial testing stage of the breeding program in the same year. The second is that of “data bands,” which are sequences of trials that correspond to the progression through stages of testing from year to year. MET datasets are then formed by combining bands of data in such a way as to trace the selection histories of lines within contemporary groups. Given a specified dataset, we use the A-optimality criterion from the model-based design literature to quantify the information for any given selection decision. We demonstrate the methods using two motivating examples from a durum and chickpea breeding program. Datasets constructed using contemporary groups and data bands are shown to be superior to other forms, in particular those that relate to a single year alone.
Signaling Toward Reactive Oxygen Species-Scavenging Enzymes in Plants

Reactive oxygen species (ROS) are signaling molecules essential for plant responses to abiotic and biotic stimuli as well as for multiple developmental processes. They are produced as byproducts of aerobic metabolism and are affected by adverse environmental conditions. The ROS content is controlled on the side of their production but also by scavenging machinery. Antioxidant enzymes represent a major ROS-scavenging force and are crucial for stress tolerance in plants. Enzymatic antioxidant defense occurs as a series of redox reactions for ROS elimination. Therefore, the deregulation of the antioxidant machinery may lead to the overaccumulation of ROS in plants, with negative consequences both in terms of plant development and resistance to environmental challenges. The transcriptional activation of antioxidant enzymes accompanies the long-term exposure of plants to unfavorable environmental conditions. Fast ROS production requires the immediate mobilization of the antioxidant defense system, which may occur via retrograde signaling, redox-based modifications, and the phosphorylation of ROS detoxifying enzymes. This review aimed to summarize the current knowledge on signaling processes regulating the enzymatic antioxidant capacity of plants.
Model-Based Control and External Load Estimation of an Extensible Soft Robotic Arm

Soft robotics has widely been known for its compliant characteristics when dealing with contraction or manipulation. These soft behavior patterns provide safe and adaptive interactions, greatly relieving the complexity of active control policies. However, another promising aspect of soft robotics, which is to achieve useful information from compliant behavior, is not widely studied. This characteristic could help to reduce the dependence of sensors, gain a better knowledge of the environment, and enrich high-level control strategies. In this paper, we have developed a state-change model of a soft robotic arm, and we demonstrate how compliant behavior could be used to estimate external load based on this model. Moreover, we propose an improved version of the estimation procedure, further reducing the estimation error by compensating the influcence of pressure deadzone. Experiments of both methods are compared, displaying the potential effectiveness of applying these methods.
The properties of silicon dioxide films on silicon as diffusion masks for boron

Measurements of the diffusion constant and segregation coefficient have been made for silicon dioxide films on silicon, using six different methods of preparing the oxide films. The results show that the thermally grown oxides give the best masking properties against the diffusion of boron, but that other oxides, notably reactively sputtered oxide and oxide formed by decomposition of tetraethoxysilane, can be almost as good. It is also shown that the exact method of preparation of the latter two oxides is important; for example, an argon-oxygen mixture gives much better oxide than pure oxygen.
Pan-Cancer Molecular Characterization of m6A Regulators and Immunogenomic Perspective on the Tumor Microenvironment

Purpose N6-methyladenosine (m6A) methylation plays a critical role in diverse biological processes. However, knowledge regarding the constitution of m6A on tumor microenvironment (TME) and tumor-infiltrating lymphocytes (TILs) across cancer types is still lacking. We performed comprehensive immuno-genomic analyses to reveal molecular characterization of the m6A regulators and immune-related genes (IRGs) across TME and TIL heterogeneity. Methods We comprehensively analyzed the properties of m6A regulators in genomic profiles from The Cancer Genome Atlas (TCGA) according to expression perturbations of crucial IRGs, CD274, CD8A, GZMA, and PRF1. The four IRGs were proved to be reliable biomarkers of TILs and TME via CIBERSORT and ESTIMATE analyses, and their co-expression relationship was certified by TIMER analysis. Based on their median values, the samples from the pan-cancer tissues (N = 11,057) were classified into eight TME types. The RNA expression levels of 13 m6A regulators were compared across TME subtypes. Single-sample Gene Set Enrichment Analysis (ssGSEA) was also used to classify TME clusters, expression variants of IRGs and m6A regulators were verified among TME clusters. Meanwhile, the correlation between m6A regulators and tumor mutational burden (TMB) were tested. Finally, the impacts of IRGs and TME clusters in clinical characteristics and outcomes were revealed. Results CD274, CD8A, GZMA, and PRF1 showed similar TILs’ characteristics, of which the level of T cells CD8 and T cells CD4 memory activated are consistent with the expression levels of the four IRGs and higher immune infiltration. Besides, CD274, CD8A, GZMA, and PRF1 were positively correlated with the stromal score or immune score in almost all 33 tumor types. All of four IRGs showed impact between tumor pathological stages or clinical outcomes. Among TME type I to type IV, m6A regulators’ expression drift changed from high-level to low-level in ESCA, BLCA, HNSC, CESC, BRCA, and GBM. However among TME type V to type VIII, m6A regulators drew a shift from low-level to high-level expression in CESC, BLCA, ESCA, KIRP, HNSC, BRCA, KIRC, COAD, LAML, GBM, and KICH. In ssGSEA analyses, IRGs’ expression levels were elevated with the immune infiltration degree and m6A regulators’ expression level varied among three TIL subgroups. With different TMB levels, expression differences of m6A regulators were observed in BLCA, BRCA, COAD, LGG, LUAD, LUSC, STAD, THCA, and UCEC. Conclusion We identified four crucial IRGs affecting TILs, TME characteristics and clinical parameters. Expression variants of m6A regulators among the subgroups of TME types and ssGSEA clusters suggested that m6A regulators may be essential factors for phenotypic modifications of IRGs and thus affecting TME characteristics across multiple tumor types.
The Relationship Between Retinal Nerve Fiber Layer Thickness and Clinical Symptoms of Alzheimer's Disease

Background/Aim: Retinal nerve fiber layer (RNFL) thickness (RT), which can reflect the status of the retinal optic nerve cells, may be affected in patients with Alzheimer's disease (AD). There are few studies on the correlation of RT of patients with AD (AD-RT) with clinical symptoms of various cognitive domains, neuropsychiatric symptoms, and activities of daily living (ADL). This study is to investigate the relationships between RT and the abovementioned clinical symptoms of AD. Methods: A total of 96 patients with AD were included in this study. RT was measured in these patients using optical coherence tomography (OCT). Demographic variables, RT, and clinical symptoms were compared between the normal and the abnormal AD-RT groups. Clinical symptoms, including cognitive symptoms, neuropsychiatric symptoms, and ADL, were evaluated using a series of rating scales. Results: The relationships between RT and cognitive symptoms scores were analyzed in patients with AD. Reduced RT was found in 54.4% of patients with AD. The average RT, RT of the superior 1/2 quadrant, and RT of the inferior 1/2 quadrant of both eyes were all significantly decreased in the abnormal AD-RT group (p < 0.001). Overall cognitive function and performance in multiple cognitive domains, including memory, language, attention, and executive function, were also significantly impaired in the abnormal AD-RT group (p < 0.05). For lower RT value, the global cognitive function and the performance in multiple cognitive domains were worse. ADL was significantly compromised in patients with AD having lower RT values (p < 0.05). Conclusions: Lower RT value appear to be correlated with cognitive impairment, and RT may be an indicator of cognitive decline in patients with AD. Further studies are required to confirm our findings.
Remote Actuation Systems for Fully Wearable Assistive Devices: Requirements, Selection, and Optimization for Out-of-the-Lab Application of a Hand Exoskeleton

Wearable robots assist individuals with sensorimotor impairment in daily life, or support industrial workers in physically demanding tasks. In such scenarios, low mass and compact design are crucial factors for device acceptance. Remote actuation systems (RAS) have emerged as a popular approach in wearable robots to reduce perceived weight and increase usability. Different RAS have been presented in the literature to accommodate for a wide range of applications and related design requirements. The push toward use of wearable robotics in out-of-the-lab applications in clinics, home environments, or industry created a shift in requirements for RAS. In this context, high durability, ergonomics, and simple maintenance gain in importance. However, these are only rarely considered and evaluated in research publications, despite being drivers for device abandonment by end-users. In this paper, we summarize existing approaches of RAS for wearable assistive technology in a literature review and compare advantages and disadvantages, focusing on specific evaluation criteria for out-of-the-lab applications to provide guidelines for the selection of RAS. Based on the gained insights, we present the development, optimization, and evaluation of a cable-based RAS for out-of-the-lab applications in a wearable assistive soft hand exoskeleton. The presented RAS features full wearability, high durability, high efficiency, and appealing design while fulfilling ergonomic criteria such as low mass and high wearing comfort. This work aims to support the transfer of RAS for wearable robotics from controlled lab environments to out-of-the-lab applications.