LNDb v4: pulmonary nodule annotation from medical reports.

Given the high prevalence of lung cancer, an accurate diagnosis is crucial. In the diagnosis process, radiologists play an important role by examining numerous radiology exams to identify different types of nodules. To aid the clinicians' analytical efforts, computer-aided diagnosis can streamline the process of identifying pulmonary nodules. For this purpose, medical reports can serve as valuable sources for automatically retrieving image annotations. Our study focused on converting medical reports into nodule annotations, matching textual information with manually annotated data from the Lung Nodule Database (LNDb)-a comprehensive repository of lung scans and nodule annotations. As a result of this study, we have released a tabular data file containing information from 292 medical reports in the LNDb, along with files detailing nodule characteristics and corresponding matches to the manually annotated data. The objective is to enable further research studies in lung cancer by bridging the gap between existing reports and additional manual annotations that may be collected, thereby fostering discussions about the advantages and disadvantages between these two data types.

Safety and Efficacy of Endovascular Coils and Non-Flow-Diverting Stents for Management of Unruptured Intracranial Aneurysms: A Location-Specific Outcomes Analysis.

INTRODUCTION: The relationship between the anatomical location of an unruptured saccular aneurysm, the efficacy, and the potential complications associated with coil and non-flow-diverting stents remains poorly documented. Therefore, the aim of this study is to evaluate the efficacy and safety of endovascular treatment based on the anatomical position of the unruptured intracranial aneurysm (UIA). METHODS: A retrospective cohort study was conducted using an anonymized database of patients who underwent endovascular therapy for UIAs between 2014 and 2021. RESULTS: A total of 138 patients with 147 UIAs were included. Immediate Raymond-Roy occlusion class I or II was achieved in 99.2% of patients in all anatomical locations, with a 96.2% occlusion rate at the 12-month follow-up. Complications occurred more frequently in the anterior cerebral artery (35%) and internal carotid artery in its ophthalmic segment (25%). However, the difference was not statistically significant. CONCLUSIONS: Our study shows that endovascular treatment with stents and coils is effective and safe for managing UIAs in various anatomical locations. The incidence of thromboembolic complications was significantly higher for UIAs located in the anterior cerebral artery.

Clinical perspective in relation to age in patients treated with thrombectomy for anterior circulation stroke in a stroke center in Colombia.

BACKGROUND AND AIMS: Endovascular treatment for cerebrovascular disease is accepted as a first-line option with level I evidence in patients with an early and late time of window of onset symptoms, and an additional option in patients who do not respond or with contraindications to systemic thrombolysis; nevertheless the efficacy and outcomes of some groups were not clear, one of them are patients aged 80 years and older, because they were excluded of the trials, so the evidence is controversial with significant heterogeneity, for that reason in our study, we decided to analyze the age in the patients treated in our stroke center, as a predictor of prognosis, and to provide a baseline for the establishment of personalized treatment plans. METHODS: Observational, retrospective study of patients that received endovascular treatment for cerebrovascular disease in a Colombian stroke center between 2016 and 2020, continuous and categorical variables were compared using the Student's t test and Chi-Square. To determine cut-off points in the variable against death and Rankin score variable on 90th day. RESULTS: In total, 108 patients were recruited, 35 of them were of 80 or more years, and the mean age was 72.7 years, we found age as a significant variable to predict the risk in the population over 80 years of age [RR 3.37 CI (95% 1.14-103) p = 0.029]. CONCLUSIONS: Age younger than 80 is a significant predictor for results and long-term outcomes in patients suffering from stroke, and in patients older than 80 years old a Thrombolysis in Cerebral Infarction score 2b-3 is a predictor of good outcomes. Further studies are needed to evaluate the relationship between intrahospital complications and long-term outcomes.

Comparative Genome Analysis of Bacillus sporothermodurans with Its Closest Phylogenetic Neighbor, Bacillus oleronius, and Bacillus cereus and Bacillus subtilis Groups.

Bacillus sporothermodurans currently possesses one of the most highly heat-resistant spores (HRS), which can withstand ultra-high temperature (UHT) processing. Determination of multiple whole genome sequences of B. sporothermodurans provided an opportunity to perform the first comparative genome analysis between strains and with B. oleronius, B. cereus, and B. subtilis groups. In this study, five whole genome sequences of B. sporothermodurans strains, including those belonging to the HRS clone (SAD and BR12) normally isolated from UHT milk, were compared with the aforementioned Bacillus species for gene clusters responsible for heat resistance. In the phylogenomic analysis, B. sporothermodurans, with its closest phylogenetic neighbor, B. oleronius, clustered with B. thermoamylovorans and B. thermotolerans. Heat shock proteins GrpE, GroES, GroEL, and DnaK presented identical sequences for all B. sporothermodurans strains, indicating that differences in functional efficiency are not involved in the thermal resistance variations. However, comparing all species evaluated, B. sporothermodurans exhibited a different gene configuration in the chromosomal region of the heat shock protein GrpE. Furthermore, only B. sporothermodurans strains presented the stage II sporulation protein P gene located in this region. Multisequence alignment and phylogenetic analysis of the ClpB protein showed differences for HRS and non-HRS strains. The study identified ClpC, ClpE, and ClpX as the three ATPases putatively involved in protein disaggregation in B. sporothermodurans. Bacillussporothermodurans exhibits high homology with other Bacillus species in the DnaK, DnaJ, GroEL, and GroES cluster of genes involved in heat resistance. The data presented here pave the way to select and evaluate the phenotypic effects of genes putatively involved in heat resistance.

White sand vegetation in an Amazonian lowland under the perspective of a young geological history.

What controls the formation of patchy substrates of white sand vegetation in the Amazonian lowlands is still unclear. This research integrated the geological history and plant inventories of a white sand vegetation patch confined to one large fan-shaped sandy substrate of northern Amazonia, which is related to a megafan environment. We examined floristic patterns to determine whether abundant species are more often generalists than the rarer one, by comparing the megafan environments and older basement rocks. We also investigated the pattern of species accumulation as a function of increasing sampling effort. All plant groups recorded a high proportion of generalist species on the megafan sediments compared to older basement rocks. The vegetation structure is controlled by topographic gradients resulting from the smooth slope of the megafan morphology and microreliefs imposed by various megafan subenvironments. Late Pleistocene-Holocene environmental disturbances caused by megafan sedimentary processes controlled the distribution of white sand vegetation over a large area of the Amazonian lowlands, and may have also been an important factor in species diversification during this period. The integration of geological and biological data may shed new light on the existence of many patches of white sand vegetation from the plains of northern Amazonia.

Electrospun Conducting and Biocompatible Uniaxial and Core-Shell Fibers Having Poly(lactic acid), Poly(ethylene glycol), and Polyaniline for Cardiac Tissue Engineering.

Electroactive and biocompatible fibrous scaffolds have been prepared and characterized using polyaniline (PAni) doped with dodecylbenzenesulfonic acid (DBSA) combined with poly(lactic acid) (PLA) and PLA/poly(ethylene glycol) (PEG) mixtures. The composition of simple and core-shell fibers, which have been obtained by both uniaxial and coaxial electrospinning, respectively, has been corroborated by Fourier-transform infrared and micro-Raman spectroscopies. Morphological studies suggest that the incorporation of PEG enhances the packing of PLA and PAni chains, allowing the regulation of the thickness of the fibers. PAni and PEG affect the thermal and electrical properties of the fibers, both decreasing the glass transition temperature and increasing the electrical conductivity. Interestingly, the incorporation of PEG improves the PAni-containing paths associated with the conduction properties. Although dose response curves evidence the high cytotoxicity of PAni/DBSA, cell adhesion and cell proliferation studies on PLA/PAni fibers show a reduction of such harmful effects as the conducting polymer is mainly retained inside the fibers through favorable PAni···PLA interactions. The incorporation of PEG into uniaxial fibers resulted in an increment of the cell mortality, which has been attributed to its rapid dissolution into the culture medium and the consequent enhancement of PAni release. In opposition, the delivery of PAni decreases and, therefore, the biocompatibility of the fibers increases when a shell coating the PAni-containing system is incorporated through coaxial electrospinning. Finally, morphological and functional studies using cardiac cells indicated that these fibrous scaffolds are suitable for cardiac tissue engineering applications.

Genome Sequences of Bacillus sporothermodurans Strains Isolated from Ultra-High-Temperature Milk.

Here, we report the draft genome sequences of 3 Bacillus sporothermodurans strains isolated from ultra-high-temperature milk products in South Africa and Brazil and the type strain MB 581 (DSM 10599). The genomes will provide valuable information on the molecular dynamics of heat resistance in B sporothermodurans.

A molecular dynamics study on glucose molecular recognition by a non-enzymatic selective sensor based on a conducting polymer.

Poly(hydroxymethyl-3,4-ethylendioxythiophene) (PHMeDOT), a very electroactive polythiophene derivative bearing a dioxane ring fused onto the thiophene ring and an exocyclic hydroxymethyl substituent, is able to electrocatalyze the oxidation of glucose in the presence of interferents (e.g. dopamine, uric acid and ascorbic acid) without the assistance of an enzymatic catalyst. In this work, after demonstrating that the chronoamperometric response of such polythiophene derivatives allows discrimination of glucose from fructose, the PHMeDOTsugar recognition mechanism has been investigated using atomistic computer simulations. More specifically, molecular dynamics simulations were conducted on model systems formed by a steel surface covered with a nanometric film of PHMeDOT, which was immersed in an aqueous environment with a few explicit sugar molecules (i.e. glucose or fructose). Analyses of the trajectories indicate that glucose interacts with PHMeDOT forming a well-defined network of specific hydrogen bonds. More specifically, glucose prefers to interact as a hydrogen bonding donor using the hydroxyl group tether to the main sugar ring, while PHMeDOT acts as the hydrogen bonding acceptor. Interestingly, (glucose)O-HO(PHMeDOT) interactions involve, as hydrogen bonding acceptors, not only the oxygen atoms of the dioxane ring but also the oxygen atom of the exocyclic hydroxymethyl substituent, which is a differential trend with respect to the other polythiophene derivatives that do not exhibit sensing ability. In contrast, fructose does not present such well-defined patterns of specific interactions, especially those that are distinctive because of the exocyclic hydroxymethyl substituent, making the experimental observations understandable.

Impedance Analysis of Polyaniline in Comparison with Some Conventional Solid Electrolytes.

Doped polyaniline (PANI) is well-known as an electronic (polaronic) conductor and mostly is used as semiconductor in various applications. However, in the literature there are examples of employment of the acid doped form of PANI as electrolytic filler in proton exchange membranes. In order to distinguish between two types of conduction, in the present study powdered samples of polyaniline, either in the form of emeraldine base (PANI-EB) or in the form doped with camphorsulfonic acid (PANI-CSA), were investigated using impedance spectroscopy both in the dry state and in contact with liquid water. The obtained spectra were compared with the spectra of such conventional solid electrolytes, as zeolites X and ZSM5 and a strong electrolyte boron orthophosphate, acquired in identical conditions. The most important dissimilarity between conventional electrolytes and PANI was that ion diffusion dominates in the impedance response of the formers, whereas the behavior of PANI is under control of electron/hole displacement and the diffusion part is quite inessential. This corroborates the results of analysis of temperature dependence of PANI conductivity, which revealed values of activation energy twice as large as typical solid electrolytes. Equivalent circuits, simulating the impedance responses of all materials, were built up and used to estimate a possible diffusion coefficient of cations in the comparable solids. It was found that the diffusion in a strong electrolyte such as BPO4 is ∼2 orders of magnitude faster than evaluated for zeolites and ∼4 orders higher than what was PANI estimation. A conclusion was made that the slow cation diffusion both in protonated and in base form of PANI makes them less efficient solid electrolytes than conventional materials.

Absorption Refrigeration Cycles with Ammonia-Ionic Liquid Working Pairs Studied by Molecular Simulation.

For absorption refrigeration, it has been shown that ionic liquids have the potential to replace conventional working pairs. Due to the huge number of possibilities, conducting lab experiments to find the optimal ionic liquid is infeasible. Here, we provide a proof-of-principle study of an alternative computational approach. The required thermodynamic properties, i.e., solubility, heat capacity, and heat of absorption, are determined via molecular simulations. These properties are used in a model of the absorption refrigeration cycle to estimate the circulation ratio and the coefficient of performance. We selected two ionic liquids as absorbents: [emim][Tf2N], and [emim][SCN]. As refrigerant NH3 was chosen due to its favorable operating range. The results are compared to the traditional approach in which parameters of a thermodynamic model are fitted to reproduce experimental data. The work shows that simulations can be used to predict the required thermodynamic properties to estimate the performance of absorption refrigeration cycles. However, high-quality force fields are required to accurately predict the cycle performance.

Isolation and Characterization of Stenotrophomonas maltophilia Isolates from a Brazilian Hospital.

Stenotrophomonas maltophilia is an emerging nosocomial pathogen responsible for several infections in immunocompromised patients. To characterize the antimicrobial resistance and virulence potential of this microorganism in a Brazilian hospital, a total of 936 samples were collected from a nosocomial environment and medical devices, and 100 isolates from clinical specimens were obtained in the same hospital. S. maltophilia was found in 3% of the samples collected, especially in bed rails from hospital rooms. The smf-1 gene was detected in 23% and 42% of the clinical and hospital environment isolates, respectively, and almost all (96.8%) isolates that harbored smf-1 were able to form biofilm. All isolates were susceptible to minocycline and chloramphenicol, and the majority of isolates were susceptible to levofloxacin. High resistance to ceftazidime was detected in both groups of isolates. Resistance to trimethoprim-sulfamethoxazole (TMP/SMX) was found in 14.8% of the isolates. All TMP/SMX-resistant isolates presented class 1 integron and sul1 gene, and 47.4% of them also harbored the sul2 gene, which was inserted into a 7.3 kb plasmid. Genetic relatedness among the isolates was evaluated by enterobacterial repetitive intergenic consensus-PCR, and eight genetic patterns were identified. One pattern comprised 54.7% of isolates and was spread among clinical and environmental (furniture and medical devices) sources. The presence of S. maltophilia in the hospital environment indicates that it can act as a reservoir of this microorganism. In addition, hospital isolates resistant to TMP/SMX showed that the genetic determinants were present in mobile elements, which can constitute great concern, as it may indicate a tendency to spread.

Detection and quantification of viable Bacillus cereus group species in milk by propidium monoazide quantitative real-time PCR.

The Bacillus cereus group includes important spore-forming bacteria that present spoilage capability and may cause foodborne diseases. These microorganisms are traditionally evaluated in food using culturing methods, which can be laborious and time-consuming, and may also fail to detect bacteria in a viable but nonculturable state. The purpose of this study was to develop a quantitative real-time PCR (qPCR) combined with a propidium monoazide (PMA) treatment to analyze the contamination of UHT milk by B. cereus group species viable cells. Thirty micrograms per milliliter of PMA was shown to be the most effective concentration for reducing the PCR amplification of extracellular DNA and DNA from dead cells. The quantification limit of the PMA-qPCR assay was 7.5 × 10(2) cfu/mL of milk. One hundred thirty-five UHT milk samples were analyzed to evaluate the association of PMA to qPCR to selectively detect viable cells. The PMA-qPCR was able to detect B. cereus group species in 44 samples (32.6%), whereas qPCR without PMA detected 78 positive samples (57.8%). Therefore, the PMA probably inhibited the amplification of DNA from cells that were killed during UHT processing, which avoided an overestimation of bacterial cells when using qPCR and, thus, did not overvalue potential health risks. A culture-based method was also used to detect and quantify B. cereus sensu stricto in the same samples and showed positive results in 15 (11.1%) samples. The culture method and PMA-qPCR allowed the detection of B. cereus sensu stricto in quantities compatible with the infective dose required to cause foodborne disease in 3 samples, indicating that, depending on the storage conditions, even after UHT treatment, infective doses may be reached in ready-to-consume products.

Characterization of antimicrobial resistance in Salmonella enterica strains isolated from Brazilian poultry production.

Antimicrobial resistance profiles and presence of resistance determinants and integrons were evaluated in Salmonella enterica strains from Brazilian poultry. The analysis of 203 isolates showed that those from the poultry environment (88 isolates) were significantly more resistant to antimicrobials than isolates from other sources, particularly those isolated from poultry by-product meal (106 isolates). Thirty-seven isolates were resistant to at least three antimicrobial classes. Class 1 integrons were detected in 26 isolates, and the analysis of the variable region between the 5' conserved segment (CS) and 3' CS of each class 1 integron-positive isolate showed that 13 contained a typical 3' CS and 14 contained an atypical 3' CS. One Salmonella Senftenberg isolate harbored two class 1 integrons, showing both typical and atypical 3' CSs. The highest percentage of resistance was found to sulfonamides, and sul genes were detected in the majority of the resistant isolates. Aminoglycoside resistance was detected in 50 isolates, and aadA and aadB were present in 28 and 32 isolates, respectively. In addition, strA and strB were detected in 78.1 and 65.6% isolates resistant to streptomycin, respectively. Twenty-one isolates presented reduced susceptibility to ß-lactams and harbored bla(TEM), bla(CMY), and/or bla(CTX-M). Forty isolates showed reduced susceptibility to tetracycline, and most presented tet genes. These results highlight the importance of the environment as a reservoir of resistant Salmonella, which may enable the persistence of resistance determinants in the poultry production chain, contributing, therefore, to the debate regarding the impacts that antimicrobial use in animal production may exert in human health.

Measuring the proton conductivity of ion-exchange membranes using electrochemical impedance spectroscopy and through-plane cell.

The role of the incorporation of conducting polymer (CP), doped with different sulfonic acid organic molecules, in polystyrene (PS) and high-impact polystyrene (HIPS) with poly(styrene-ethylene-butylene) (SEBS) triblock copolymer has been investigated. Two factors associated with this model membrane system are addressed: (i) the influence of the presence of a low concentration of doped conducting polymer and (ii) the influence of the membrane preparation method. Membrane characterization and bulk conductivity measurements allowed the conclusion that proton conductivity has been promoted by the addition of CP; the best results were achieved for PAni-CSA, in either PS/SEBS or HIPS/SEBS blends. Additionally, the water uptake only decreased with the addition of PAni-doped molecules compared to the pure copolymer, without loss of ion-exchange capacity (IEC). Electrodialysis efficiency for HIPS/SEBS (before annealing) is higher than that for HIPS/SEBS (after annealing), indicating that membrane preparation method is crucial. Finally, through-plane cell arrangement proved to be an effective, quick, and time-saving tool for studying the main resistance parameters of isolating polymers, which is useful for application in industry and research laboratories working with membranes for electrodialysis or fuel cells.

Tissue expression and the host's immunological recognition of a Rhipicephalus microplus paramyosin.

Rhipicephalus microplus is a parasite that causes economic losses in cattle herds, and immunological control is the most promising alternative to replace chemical control. The muscular protein paramyosin has been additionally found in non-muscle tissues and characterized as presenting activities that enable the evasion of the host's immune system in various parasites. This report investigated the recognition level of paramyosin by sera of infested bovines, its expression in tissues, organs and different life stages of R. microplus. ELISA analyses showed that paramyosin and salivary gland extract were recognized by infested Bos taurus and B. indicus sera. Paramyosin gene expression was evaluated in egg, larvae, adult male, and several tissues of partially- and fully-engorged females by qRT-PCR, showing the highest expression levels in fat body. These results show that R. microplus paramyosin is immunologically recognized during the tick infestation and together with the high transcription rate found in organs that do not present a highly developed musculature, further suggests that it may possess additional, non-muscle functions in the tick-bovine relationship.

New sulfonated polystyrene and styrene-ethylene/butylene-styrene block copolymers for applications in electrodialysis.

In this study we prepared blends of polystyrene (PS) and high-impact polystyrene (HIPS) with poly(styrene-ethylene-butylene) (SEBS) triblock copolymer. After sulfonation, blends were used to fabricate ion-exchange membranes by solvent-casting and subsequent thermal treatment to obtain homogeneous packing densities. The morphology and structure of the blends were investigated by scanning electron microscopy, atomic force microscopy, and FTIR spectroscopy. Furthermore, the thermal transitions and stability of all the blends were characterized using calorimetric techniques and compared with those of the individual polymers. Analyses of the physical properties (i.e., ionic conductivity, ion-exchange capacity, water uptake, dimensional stability, mechanical properties, etc.) showed that the performance of the PS-containing membranes is, in general, higher than that of the HIPS containing one. Furthermore, the highest sulfonation degree was also found for the PS/SEBS membranes. The capabilities of the membranes were tested by investigating the extraction of Na(+) by electrodyalisis. Comparison of the percentage of extracted ions indicates that the incorporation of SEBS results in a significant improvement with respect to membranes made of individual polymers.

Sodium chloride affects propidium monoazide action to distinguish viable cells.

Propidium monoazide (PMA) is a DNA-intercalating agent used to selectively detect DNA from viable cells by polymerase chain reaction (PCR). Here, we report that high concentrations (>5%) of sodium chloride (NaCl) prevents PMA from inhibiting DNA amplification from dead cells. Moreover, Halobacterium salinarum was unable to maintain cell integrity in solutions containing less than 15% NaCl, indicating that extreme halophilic microorganisms may not resist the concentration range in which PMA fully acts. We conclude that NaCl, but not pH, directly affects the efficiency of PMA treatment, limiting its use for cell viability assessment of halophiles and in hypersaline samples.

A first principle analysis of the structure of oligoanilines doped with alkylsulfonic acids.

The interaction of polyaniline with alkylsulfonate dopants have been investigated at the atomic level using quantum mechanical methods. Calculations have been performed on complexes formed by dopant molecules with an alkyl group ranging from methyl to nonyl and model oligoanilines of different sizes. The stabilization provided by the formation of the alkylsulfonate...oligoaniline complexes (70-90 kcal/mol) is significantly higher than that found for conventional hydrogen bonds (5-12 kcal/mol) but lower than that obtained for methylsulfate...alkylammonium and methylsulfate...Na(+) systems (120-135 kcal/mol). On the other hand, the influence of size of the alkyl group contained in the dopant on the interaction is practically negligible, whereas, in opposition, the number of aniline units used to represent polyaniline significantly affects the energetics of the interaction. Specifically, the interaction energy of an alkyl-dopant molecule and an infinite polyaniline chain has been predicted to be around -65 kcal/mol. The overall results allow the conclusion that the interaction between alkylsulfonate dopants and polyaniline is a very local phenomenon.

Vaccination of bovines with recombinant Boophilus Yolk pro-Cathepsin.

Boophilus Yolk pro-Cathepsin (BYC) is an aspartic proteinase found in Boophilus microplus eggs that is involved in the embryogenesis and has been tested as antigen to compose an anti-tick vaccine. The vaccine potential of a recombinant BYC expressed in Escherichia coli (rBYC) was investigated. rBYC was purified and used to immunize Hereford cattle. The sera of bovines immunized with rBYC recognized the native BYC with a titer ranging from 125 to 4000. Furthermore, immunized bovines challenged with 20,000 larvae presented an overall protection of 25.24%. The partial protection obtained against B. microplus infestation with the recombinant protein immunization was similar to the already described for native BYC immunization.

Purification and antigenicity of two recombinant forms of Boophilus microplus yolk pro-cathepsin expressed in inclusion bodies.

The tick Boophilus microplus is a bovine ectoparasite present in tropical and subtropical areas of the world and the use of vaccines is a promising method for tick control. BYC is an aspartic proteinase found in eggs that is involved in the embryogenesis of B. microplus and was proposed as an important antigen in the development of an anti-tick vaccine. The cDNA of BYC was amplified by PCR and cloned for expression in two forms with and without thioredoxin fusion protein (Trx), coding recombinant proteins named rBYC-Trx and rBYC, respectively. Expression, solubility, and yields of the two forms were analyzed. The recombinant proteins were expressed in inclusion bodies (IBs) and three denaturant agents (N-lauroyl sarcosine, guanidine hydrochloride, and urea) were tested for IBs solubilization. The N-lauroyl sarcosine solubilized 90.4 and 92.4% of rBYC-Trx and rBYC IBs, respectively, and was the most efficient denaturant. Two recombinant forms were affinity-purified by Ni2+-Sepharose under denaturing conditions. After dialysis, the yield of soluble protein was 84.1% for r-BYC-Trx and 5.9% for rBYC. These proteins were immune-reactive against sera from rabbit, mouse, and bovine previously immunized with native BYC, which confirms the antigenicity of the recombinant BYCs expressed in the Escherichia coli system.