Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of the Biofire Filmarray Pneumonia panel plus for lower respiratory tract infections

Abstract Background: Standard diagnostic methods for lower respiratory tract infections are currently too slow and insensitive to guide early clinical decisions concerning treatment and isolation. Syndrome-specific, diagnostic panels have potential to provide information about aetiology quickly. Available panels have been of limited use in lower respiratory tract infections due to slow turn-around-time, lack of quantification of important pathogens and lack of detection of resistance genes. Materials/methods: We evaluated the newly developed Biofire® Filmarray® Pneumonia Panel plus (Biomérieux). Eighty-eight consecutive lower respiratory tract samples were analyzed by both standard microbiological methods, as requested by the referring clinician, and by the panel. The agreement with standard methods, empirical treatment coverage and possible impact on isolation practices were assessed by comparing the results from standard diagnostic methods with the panel results in relation to clinical data and information of antimicrobial therapy. Results: Both qualitative and semi-quantitative results from the panel generally displayed good agreement with standard methods and by combining methods, a possible aetiology was detected in 73% of patients. Due to the panel approach, the panel detected viruses more frequently. In 25% of the 60 patients assessed for empirical treatment coverage, a pathogen not covered by current therapy was detected and in 30% of in-house patients the panel results were found to potentially influence clinical decisions related to isolation care. Conclusions: The new diagnostic panel shows promise in improving aetiological diagnostics of lower respiratory tract infections. Correctly applied it has potential to offer support in clinical decision-making within hours of sampling.
BayesENproteomics: Bayesian elastic nets for quantification of peptidoforms in complex samples.

Multivariate regression modelling provides a statistically powerful means of quantifying the effects of a given treatment while compensating for sources of variation and noise, such as variability between human donors and the behaviour of different peptides during mass spectrometry. However, methods to quantify endogenous post-translational modifications (PTMs) are typically reliant on summary statistical methods that fail to consider sources of variability such as changes in levels of the parent protein. Here, we compare three multivariate regression methods, including a novel Bayesian elastic net algorithm (BayesENproteomics) that enables assessment of relative protein abundances while also quantifying identified PTMs for each protein. We tested the ability of these methods to accurately quantify expression of proteins in a mixed-species benchmark experiment, and to quantify synthetic PTMs induced by stable isotope labelling. Finally, we extended our regression pipeline to calculate fold changes at the pathway level, providing a complement to commonly used enrichment analysis. Our results show that BayesENproteomics can quantify changes to protein levels across a broad dynamic range while also accurately quantifying PTM and pathway-level fold changes.
Cost analysis of materials used in the endovascular treatment of unruptured intracranial aneurysms in Mexico

Background To prevent the potentially fatal consequences of intracranial aneurysmal rupture, exclusion from the circulation can be achieved through an endovascular approach. However, the elevated cost of such procedures can be prohibitive for patients in low resource settings. The objective of this study is to identify the factors that modify the cost of the materials used for endovascular treatment of unruptured intracranial aneurysms. Methods Medical records of patients who underwent an endovascular treatment for unruptured intracranial aneurysms between June 2013 and June 2019 in a hospital located in Northeast Mexico were reviewed. Descriptive statistics of the cost of consumable materials used during the procedure was performed, and a regression model was undertaken to examine potential associations between the studied variables and total cost of the intervention. Results A total of 128 patients were included in this analysis. The average intervention cost was $21,687.22 USD. The variables associated with increased material cost were aneurysm size (p = 0.03), aneurysm neck size (p < 0.001), and aneurysm localization in the cavernous segment of the internal carotid artery (p = 0.01). Other variables such as patient age and sex, other aneurysm localizations, laterality of the aneurysm, performing neurointerventionalist, and presence of intervention complications were not statistically significant. Conclusions To our knowledge, this is the first study that examines the variables associated with the material cost of endovascular treatment of unruptured intracranial aneurysms. Awareness of which elements are important drivers of materials’ costs provides a strategic advantage when making hospital administrative decisions and attempting to improve access to endovascular treatment in countries of low income.
Prostate cancer visibility on multiparametric magnetic resonance imaging: high Gleason grade and increased tumour volume are not the only important histopathological features

Multiparametric magnetic resonance imaging (mpMRI) has excellent pre-biopsy sensitivity for detection of clinically significant prostate cancer, and this now places mpMRI at the forefront of our risk stratification process. Despite this, it appears that not all significant cancers are detected by mpMRI. We know that Gleason grade and tumour volume are strong determinants of conspicuity on mpMRI, which works to our benefit, as it means that small, low-grade cancers can be avoided, whilst high-risk tumours can be detected [1]. However, beyond this, there are likely additional factors that influence tumour visibility on mpMRI. Here, we explore histopathological features (beyond grade and volume) associated with tumour conspicuity on mpMRI.
The effect of diet and sociopolitical change on physiological stress and behavior in late Roman-Early Byzantine (300-700 AD) and Islamic (902-1,235 AD) populations from Ibiza, Spain.

OBJECTIVES This study evaluated chronological changes in physiological stress and levels of habitual loading of Ibizan populations from the Late Roman-Early Byzantine (LREB) to the Islamic period (300-1,235 AD) using measures of body size and bone cross-sectional properties to compare Urban LREB, Urban Medieval Islamic, and Rural Medieval Islamic groups. It also explored the effect of diet, modeled using stable isotopes, on physiological stress levels and behavior. MATERIALS AND METHODS The sample comprised individuals from three archeological populations: Urban Late Roman- Early Byzantine (LREB) (300-700 AD), Medieval Urban Islamic (902-1,235 AD), and Medieval Rural Islamic. Bone lengths, femoral head dimensions, and cross-sectional properties, diaphyseal products and circumferences, were compared to assess differences in body size and habitual loading in 222 adult individuals. Ordinary least squares regression evaluated the correlations between these measures and carbon (δ13 C) and nitrogen (δ15 N) stable isotope ratios in 115 individuals for whom both isotope values and osteological measures are available. RESULTS The Medieval Rural Islamic group had shorter stature and reduced lower limb cross-sectional properties compared to the two urban groups. Limb shape differs between Urban LREB and Urban Medieval Islamic groups. Measures of body size length were positively correlated with δ13 C values in all individuals and separately in the Urban LREB and Rural Medieval Islamic groups. δ15 N showed a positive correlation with left humerus shape in the Urban LREB sample. CONCLUSIONS The low stature and cross-sectional properties of the Medieval Rural Islamic group may be an indicator of greater physiological stress, potentially due to poorer diet. Positive correlations between measures of body size and δ13 C values further suggest that greater access to C4 resources improved diet quality. Alternatively, this relationship could indicate greater body size among migrants from areas where individuals consumed more C4 resources.
The Importance of Porins and β-Lactamase in Outer Membrane Vesicles on the Hydrolysis of β-Lactam Antibiotics

Gram-negative bacteria have an outer membrane inhibiting the entry of antibiotics. Porins, found within the outer membrane, are involved in regulating the permeability of β-lactam antibiotics. β-lactamases are enzymes that are able to inactivate the antibacterial properties of β-lactam antibiotics. Interestingly, porins and β-lactamase are found in outer membrane vesicles (OMVs) of β-lactam-resistant Escherichia coli and may be involved in the survival of susceptible strains of E. coli in the presence of antibiotics, through the hydrolysis of the β-lactam antibiotic. In this study, OMVs isolated from β-lactam-resistant E. coli and from mutants, lacking porin or β-lactamase, were evaluated to establish if the porins or β-lactamase in OMVs were involved in the degradation of β-lactam antibiotics. OMVs isolated from E. coli deficient in β-lactamase did not show any degradation ability against β-lactam antibiotics, while OMVs lacking OmpC or OmpF showed significantly lower levels of hydrolyzing activity than OMVs from parent E. coli. These data reveal an important role of OMVs in bacterial defense mechanisms demonstrating that the OmpC and OmpF proteins allow permeation of β-lactam antibiotics into the lumen of OMVs, and antibiotics that enter the OMVs can be degraded by β-lactamase.
The genome of a Bacteroidetes inhabitant of the human gut encodes a structurally distinct enoyl-acyl carrier protein reductase (FabI)

Enoyl-acyl carrier protein reductase (FabI) catalyzes a rate-controlling step in bacterial fatty-acid synthesis and is a target for antibacterial drug development. A phylogenetic analysis shows that FabIs fall into four divergent clades. Members of clades 1–3 have been structurally and biochemically characterized, but the fourth clade, found in members of phylum Bacteroidetes, is uncharacterized. Here, we identified the unique structure and conformational changes that distinguish clade 4 FabIs. Alistipes finegoldii is a prototypical Bacteroidetes inhabitant of the gut microbiome. We found that A. finegoldii FabI (AfFabI) displays cooperative kinetics and uses NADH as a cofactor, and its crystal structure at 1.72 Å resolution showed that it adopts a Rossmann fold as do other characterized FabIs. It also disclosed a carboxyl-terminal extension that forms a helix–helix interaction that links the protomers as a unique feature of AfFabI. An AfFabI·NADH crystal structure at 1.86 Å resolution revealed that this feature undergoes a large conformational change to participate in covering the NADH-binding pocket and establishing the water channels that connect the active site to the central water well. Progressive deletion of these interactions led to catalytically compromised proteins that fail to bind NADH. This unique conformational change imparted a distinct shape to the AfFabI active site that renders it refractory to a FabI drug that targets clade 1 and 3 pathogens. We conclude that the clade 4 FabI, found in the Bacteroidetes inhabitants of the gut, have several structural features and conformational transitions that distinguish them from other bacterial FabIs.
PRIORI-T: A tool for rare disease gene prioritization using MEDLINE

Introduction Phenotype-driven rare disease gene prioritization relies on high quality curated resources containing disease, gene and phenotype annotations. However, the effectiveness of gene prioritization tools is constrained by the incomplete coverage of rare disease, phenotype and gene annotations in such curated resources. Methods We extracted rare disease correlation pairs involving diseases, phenotypes and genes from MEDLINE abstracts and used the information propagation algorithm GCAS to build an association network. We built a tool called PRIORI-T for rare disease gene prioritization that uses this network for phenotype-driven rare disease gene prioritization. The quality of disease-gene associations in PRIORI-T was compared with resources such as DisGeNET and Open Targets in the context of rare diseases. The gene prioritization performance of PRIORI-T was evaluated using phenotype descriptions of 230 real-world rare disease clinical cases collated from recent publications, as well as compared to other gene prioritization tools such as HANRD and Orphamizer. Results PRIORI-T contains qualitatively better associations than DisGeNET and Open Targets. Furthermore, the causal genes were captured within Top-50 for more than 40% of the real-world clinical cases and within Top-300 for more than 72% of the cases when PRIORI-T was used for gene prioritization. It outperformed other gene prioritization tools such as HANRD and Orphamizer that primarily rely on curated resources. Conclusions PRIORI-T exhibited improved gene prioritization performance without requiring high quality curated data. Thus, it holds great promise in phenotype-driven gene prioritization for rare disease studies.
Characterization of Thermal Damage Due to Two-Temperature High-Order Thermal Lagging in a Three-Dimensional Biological Tissue Subjected to a Rectangular Laser Pulse

The use of lasers and thermal transfers on the skin is fundamental in medical and clinical treatments. In this paper, we constructed and applied bioheat transfer equations in the context of a two-temperature heat conduction model in order to discuss the three-dimensional variation in the temperature of laser-irradiated biological tissue. The amount of thermal damage in the tissue was calculated using the Arrhenius integral. Mathematical difficulties were encountered in applying the equations. As a result, the Laplace and Fourier transform technique was employed, and solutions for the conductive temperature and dynamical temperature were obtained in the Fourier transform domain.
Virus Like Particles (VLPs) as a Platform for Hierarchical Compartmentalization.

Hierarchically self-assembled structures are common in biology but it is often challenging to design and fabricate synthetic analogs. The archetypal cell is defined by hierarchically organized multicompartmentalized structures with boundaries that delineate interior from exterior environments and is an inspiration for complex functional materials. Here we have demonstrated an approach to the design and construction of a nested protein cage system that can additionally incorporate the packing of other functional macromolecules and exhibits some of the features of a minimal synthetic cell-like material. We have demonstrated a strategy for controlled co-packaging of sub-compartments, ferritin (Fn) cages, together with active cellobiose-hydrolyzing enzyme -glycosidase enzyme macromolecules, CelB, inside the sequestered volume of the bacteriophage P22 capsid. Using controlled in vitro assembly, we were able to modulate the stoichiometry of Fn cages and CelB encapsulated inside the P22 to control the degree of compartmentalization. The co-encapsulated enzyme CelB showed catalytic activity even when packaged at high total macromolecular concentrations comparable to an intracellular environment. This approach could be used as a model to create synthetic protein-based protocells that can confine smaller functionalized proto-organelles and additional macromolecules to support a range of biochemical reactions.
Detection of the United States Neisseria meningitidis urethritis clade in the United Kingdom, August and December 2019 – emergence of multiple antibiotic resistance calls for vigilance

Since 2015 in the United States (US), the US Neisseria meningitidis urethritis clade (US_NmUC) has caused a large multistate outbreak of urethritis among heterosexual males. Its ‘parent’ strain caused numerous outbreaks of invasive meningococcal disease among men who have sex with men in Europe and North America. We highlight the arrival and dissemination of US_NmUC in the United Kingdom and the emergence of multiple antibiotic resistance. Surveillance systems should be developed that include anogenital meningococci.
Computer-assisted interpretation of chest radiographs: signs of hope for silicosis and tuberculosis.

Although silicosis, tuberculosis (TB) and the comorbid condition of silicotuberculosis are diseases of antiquity, accurate and consistent diagnostic technologies for such conditions have only relatively recently been developed. Autopsies of Egyptian mummies have revealed that silicosis and TB have been accompanying mankind for at least 2500 years, and osteological evidence of TB dates to over 7000 years ago. 1,2 However, widespread use of chest radiography as a diagnostic tool for silicosis and TB were not available until the early 1900 s , and consistent and accurate diagnosis remained a challenge through the mid-20 th century, particularly in resource-poor regions. Since that time, medical technology and standards have improved at a remarkable pace and experts can now—within minutes— accurately and non-invasively identify likely cases of silicosis and pulmonary TB. For population-based medical monitoring programs, using expert readers who are proficient in classifying radiographs using established systems such as the one specified in the International Labour Office Guidelines for the Classification of Radiographs of Pneumoconioses
Listeria monocytogenes Wall Teichoic Acid Glycosylation Promotes Surface Anchoring of Virulence Factors, Resistance to Antimicrobial Peptides, and Decreased Susceptibility to Antibiotics

The cell wall of Listeria monocytogenes (Lm), a major intracellular foodborne bacterial pathogen, comprises a thick peptidoglycan layer that serves as a scaffold for glycopolymers such as wall teichoic acids (WTAs). WTAs contain non-essential sugar substituents whose absence prevents bacteriophage binding and impacts antigenicity, sensitivity to antimicrobials, and virulence. Here, we demonstrated, for the first time, the triple function of Lm WTA glycosylations in the following: (1) supporting the correct anchoring of major Lm virulence factors at the bacterial surface, namely Ami and InlB; (2) promoting Lm resistance to antimicrobial peptides (AMPs); and (3) decreasing Lm sensitivity to some antibiotics. We showed that while the decoration of WTAs by rhamnose in Lm serovar 1/2a and by galactose in serovar 4b are important for the surface anchoring of Ami and InlB, N-acetylglucosamine in serovar 1/2a and glucose in serovar 4b are dispensable for the surface association of InlB or InlB/Ami. We found that the absence of a single glycosylation only had a slight impact on the sensibility of Lm to AMPs and antibiotics, however the concomitant deficiency of both glycosylations (rhamnose and N-acetylglucosamine in serovar 1/2a, and galactose and glucose in serovar 4b) significantly impaired the Lm capacity to overcome the action of antimicrobials. We propose WTA glycosylation as a broad mechanism used by Lm, not only to properly anchor surface virulence factors, but also to resist AMPs and antibiotics. WTA glycosyltransferases thus emerge as promising drug targets to attenuate the virulence of bacterial pathogens, while increasing their susceptibility to host immune defenses and potentiating the action of antibiotics.
A Novel Loop Closure Detection Approach Using Simplified Structure for Low-Cost LiDAR

Reducing the cumulative error is a crucial task in simultaneous localization and mapping (SLAM). Usually, Loop Closure Detection (LCD) is exploited to accomplish this work for SLAM and robot navigation. With a fast and accurate loop detection, it can significantly improve global localization stability and reduce mapping errors. However, the LCD task based on point cloud still has some problems, such as over-reliance on high-resolution sensors, and poor detection efficiency and accuracy. Therefore, in this paper, we propose a novel and fast global LCD method using a low-cost 16 beam Lidar based on “Simplified Structure”. Firstly, we extract the “Simplified Structure” from the indoor point cloud, classify them into two levels, and manage the “Simplified Structure” hierarchically according to its structure salience. The “Simplified Structure” has simple feature geometry and can be exploited to capture the indoor stable structures. Secondly, we analyze the point cloud registration suitability with a pre-match, and present a hierarchical matching strategy with multiple geometric constraints in Euclidean Space to match two scans. Finally, we construct a multi-state loop evaluation model for a multi-level structure to determine whether the two candidate scans are a loop. In fact, our method also provides a transformation for point cloud registration with “Simplified Structure” when a loop is detected successfully. Experiments are carried out on three types of indoor environment. A 16 beam Lidar is used to collect data. The experimental results demonstrate that our method can detect global loop closures efficiently and accurately. The average global LCD precision, accuracy and negative are approximately 0.90, 0.96, and 0.97, respectively.
Heat Shock Affects Mitotic Segregation of Human Chromosomes Bound to Stress-Induced Satellite III RNAs

Heat shock activates the transcription of arrays of Satellite III (SatIII) DNA repeats in the pericentromeric heterochromatic domains of specific human chromosomes, the longest of which is on chromosome 9. Long non-coding SatIII RNAs remain associated with transcription sites where they form nuclear stress bodies or nSBs. The biology of SatIII RNAs is still poorly understood. Here, we show that SatIII RNAs and nSBs are detectable up to four days after thermal stress and are linked to defects in chromosome behavior during mitosis. Heat shock perturbs the execution of mitosis. Cells reaching mitosis during the first 3 h of recovery accumulate in pro-metaphase. During the ensuing 48 h, this block is no longer detectable; however, a significant fraction of mitoses shows chromosome segregation defects. Notably, most of lagging chromosomes and chromosomal bridges are bound to nSBs and contain arrays of SatIII DNA. Disappearance of mitotic defects at the end of day 2 coincides with the processing of long non-coding SatIII RNAs into a ladder of small RNAs associated with chromatin and ranging in size from 25 to 75 nt. The production of these molecules does not rely on DICER and Argonaute 2 components of the RNA interference apparatus. Thus, massive transcription of SatIII DNA may contribute to chromosomal instability.
Silica Gel Impregnated by Deep Eutectic Solvents for Adsorptive Removal of BTEX from Gas Streams

The paper presents the preparation of new adsorbents based on silica gel (SiO2) impregnated with deep eutectic solvents (DESs) to increase benzene, toluene, ethylbenzene, and p-xylene (BTEX) adsorption efficiency from gas streams. The DESs were synthesized by means of choline chloride, tetrapropylammonium bromide, levulinic acid, lactic acid, and phenol. The physico-chemical properties of new sorbent materials, including surface morphology and structures, as well as porosity, were studied by means of thermogravimetric analysis, Fourier transform infrared spectroscopy, scanning electron microscopy, X-ray diffraction, and Brunauer–Emmett–Teller analysis. The effect of DESs type, flow rate, and initial concentration of BTEX were also investigated followed by regeneration and reusability of adsorbents. The results indicate that SiO2 impregnated with tetrapropylammonium bromide and lactic acid in a 1:2 molar ratio have great potential for the removal of BTEX from gas streams. Its adsorption capacity was higher than the pure SiO2 and other developed SiO2-DES adsorbents. This result can be explained by the specific interaction between DESs and BTEX, i.e., hydrogen bonds interaction.