Negative effects of human disturbance and increased aridity on root biomass and nutrients along the regeneration of a tropical dry forest in the context of slash-and-burn agriculture.

Biomass is an important indicator of the ability of tropical forests to deliver ecosystem services, but little attention has been given to belowground biomass and its drivers in human-modified landscapes. Here, we investigated the belowground biomass and nutrient concentration/stocks (C, P, and N) across regenerating forest stands with varying ages (10-76 years old) and old-growth forests in the Caatinga dry forest (northeastern Brazil) in the context of slash-and-burn agriculture. Belowground biomass ranged from 1.89 ± 0.33 Mg ha-1 to 17.53 ± 2.28 Mg ha-1 (mean ± SE) across regenerating forest stands and averaged 8.33 ± 1.59 Mg ha-1, with no differences compared to old-growth stands. However, regenerating stands exhibited a higher root/shoot ratio with biomass concentrated in the superficial soil layer and in large-sized roots, regardless of the successional stage. Root nutrient concentration and stocks were highly variable across forest stands with fine roots supporting a higher concentration of N and P, while regenerating stands supported lower nutrient stocks as compared to old-growth forests. Finally, precipitation and chronic disturbance emerged as the most important drivers of belowground biomass and nutrient concentrations/stocks, while aboveground biomass played a negligible role. Our results indicate that, in human-modified landscapes of tropical dry forests, belowground biomass and nutrients play important roles in ecosystem functions in regenerated forests after slash-and-burn agriculture. Forest resilience and provision of ecosystem services (e.g., nutrient cycling) appear to be very sensitive to increased aridity and exploitation of forest resources.

A preliminary study of fingerprint aging using near infrared hyperspectral imaging (NIR-HSI).

Fingerprinting is one of the most commonly used techniques to obtain pieces of evidence for identification of individuals. An estimation of how long a trace has been left at a crime scene could represent an important improvement for criminal investigations. There is no reliable analytical method, however, to estimate the age of a fingerprint, since this is an uncontrolled process and changes are affected by factors such as environmental conditions. This study aims to better understand the aging process of fingerprints and identify the relevant variables and limitations of the fingerprint aging process using near infrared hyperspectral imaging (NIR-HSI). For this purpose, aging of the fingerprints of 13 volunteers was evaluated using partial least squares - discriminant analysis (PLS-DA) as a preliminary exploratory approach. Four different modelling approaches were evaluated. The percentage of correctly classified pixels varied from 20.92% to 66.67%. An analysis of the associated spectra found that during the first days of aging the degradation of fat-soluble components, as well as the elimination/absorption of water, seemed to follow non-uniform trends and vary in degradation rate from donor to donor. Better classification tended to occur over longer aging times.

People with Primary Progressive Multiple Sclerosis Have a Lower Number of Central Memory T Cells and HLA-DR+ Tregs.

The importance of circulating immune cells to primary progressive multiple sclerosis (PPMS) pathophysiology is still controversial because most immunotherapies were shown to be ineffective in treating people with PPMS (pwPPMS). Yet, although controversial, data exist describing peripheral immune system alterations in pwPPMS. This study aims to investigate which alterations might be present in pwPPMS free of disease-modifying drugs (DMD) in comparison to age- and sex-matched healthy controls. A multicentric cross-sectional study was performed using 23 pwPPMS and 23 healthy controls. The phenotype of conventional CD4+ and CD8+ T cells, regulatory T cells (Tregs), B cells, natural killer (NK) T cells and NK cells was assessed. Lower numbers of central memory CD4+ and CD8+ T cells and activated HLA-DR+ Tregs were observed in pwPPMS. Regarding NK and NKT cells, pwPPMS presented higher percentages of CD56dimCD57+ NK cells expressing NKp46 and of NKT cells expressing KIR2DL2/3 and NKp30. Higher disease severity scores and an increasing time since diagnosis was correlated with lower numbers of inhibitory NK cells subsets. Our findings contribute to reinforcing the hypotheses that alterations in peripheral immune cells are present in pwPPMS and that changes in NK cell populations are the strongest correlate of disease severity.

The pan-genome of the emerging multidrug-resistant pathogen Corynebacterium striatum.

Corynebacterium striatum, a common constituent of the human skin microbiome, is now considered an emerging multidrug-resistant pathogen of immunocompromised and chronically ill patients. However, little is known about the molecular mechanisms in the transition from colonization to the multidrug-resistant (MDR) invasive phenotype in clinical isolates. This study performed a comprehensive pan-genomic analysis of C. striatum, including isolates from "normal skin microbiome" and from MDR infections, to gain insights into genetic factors contributing to pathogenicity and multidrug resistance in this species. For this, three novel genome sequences were obtained from clinical isolates of C. striatum of patients from Brazil, and other 24 complete or draft C. striatum genomes were retrieved from GenBank, including the ATCC6940 isolate from the Human Microbiome Project. Analysis of C. striatum strains demonstrated the presence of an open pan-genome (α = 0.852803) containing 3816 gene families, including 15 antimicrobial resistance (AMR) genes and 32 putative virulence factors. The core and accessory genomes included 1297 and 1307 genes, respectively. The identified AMR genes are primarily associated with resistance to aminoglycosides and tetracyclines. Of these, 66.6% are present in genomic islands, and four AMR genes, including aac(6')-ib7, are located in a class 1-integron. In conclusion, our data indicated that C. striatum possesses genomic characteristics favorable to the invasive phenotype, with high genomic plasticity, a robust genetic arsenal for iron acquisition, and important virulence determinants and AMR genes present in mobile genetic elements.

Low Memory T Cells Blood Counts and High Naïve Regulatory T Cells Percentage at Relapsing Remitting Multiple Sclerosis Diagnosis.

Objective: The aim of this study is to assess the peripheral immune system of newly diagnosed patients with relapsing remitting multiple sclerosis (RRMS) and compare it to healthy controls (HC). Methods: This cross-sectional study involves 30 treatment-naïve newly diagnosed patients with RRMS and 33 sex- and age-matched HC. Peripheral blood mononuclear cells were analyzed regarding: i) thymic function surrogates [T cell receptor excision circles (TRECs) and recent thymic emigrants (RTEs)]; ii) naïve and memory CD4+ and CD8+ T cells subsets; iii) T helper (Th) phenotype and chemokine receptors expression on CD8+ T cells subsets; iv) regulatory T cell (Tregs) phenotype; and exclude expression of activating/inhibitory receptors by natural killer (NK) and NKT cells. Analyses were controlled for age, sex, and human cytomegalovirus (HCMV) IgG seroprevalence. Results: Newly diagnosed patients with RRMS and HC have equivalent thymic function as determined by similar numbers of RTEs and levels of sjTRECs, DJßTRECs, and sj/DJßTREC ratio. In the CD8+ T cells compartment, patients with RRMS have a higher naive to memory ratio and lower memory cell counts in blood, specifically of effector memory and TemRA CD8+ T cells. Interestingly, higher numbers and percentages of central memory CD8+ T cells are associated with increasing time from the relapse. Among CD4+ T cells, lower blood counts of effector memory cells are found in patients upon controlling for sex, age, and anti-HCMV IgG seroprevalence. Higher numbers of CD4+ T cells (both naïve and memory) and of Th2 cells are associated with increasing time from the relapse; lower numbers of Th17 cells are associated with higher MS severity scores (MSSS). Patients with RRMS have a higher percentage of naïve Tregs compared with HC, and lower percentages of these cells are associated with higher MSSS. Percentages of immature CD56bright NK cells expressing the inhibitory receptor KLRG1 and of mature CD56dimCD57+ NK cells expressing NKp30 are higher in patients. No major alterations are observed on NKT cells. Conclusion: Characterization of the peripheral immune system of treatment-naïve newly diagnosed patients with RRMS unveiled immune features present at clinical onset including lower memory T cells blood counts, particularly among CD8+ T cells, higher percentage of naïve Tregs and altered percentages of NK cells subsets expressing inhibitory or activating receptors. These findings might set the basis to better understand disease pathogenesis.

Seropositive Wild Boars Suggesting the Occurrence of a Wild Cycle of Trichinella spp. in Brazil.

Trichinella is a zoonotic nematode traditionally detected worldwide in both domestic and wild animals. In South America, along with the occurrence of this parasite in domestic pigs and wild boars, there are reports of infection in wild carnivores. Brazil is considered free of the domestic cycle of Trichinella, but there is unpublished serological evidence of infection in wild boars, which changed the Brazilian status in OIE regarding the disease after an official communication. We investigated Trichinella spp. infection in wild boars and wild carnivores in the Southeastern region of Brazil. A total of 136 samples were tested, 121 from wild boars and 15 from wild carnivores. Artificial enzymatic digestion (AED) tests were performed on muscle samples from 37 wild boars and 15 wild carnivores, and 115 serum samples from wild boars were tested by iELISA. Seven serum samples from wild boars tested positive (7/115 = 6.1%, 95% CI 3.0-12.0), but no larvae were found in the AED. There was no significant difference between sex, age, and location of the samples. The serological results suggest that a wild cycle of Trichinella spp. may occur in Brazil, but further analyses should be performed to confirm the presence of the parasite.

A novel proposal to investigate the interplay between the spatial and spectral domains in near-infrared spectral imaging data by means of Image Decomposition, Encoding and Localization (IDEL).

The emergence of new spectral imaging applications in many science fields and in industry has not come to be a surprise, considering the immense potential this technique has to map spectral information. In the case of near-infrared spectral imaging, a rapid evolution of the technology has made it more and more appealing in non-destructive analysis of food and materials as well as in process monitoring applications. However, despite its great diffusion, some challenges remain open from the data analysis point of view, with the aim to fully uncover patterns and unveil the interplay between both the spatial and spectral domains. Here we propose a new approach, called Image Decomposition, Encoding and Localization (IDEL), where a spatial perspective is taken for the analysis of spectral images, while maintaining the significant information within the spectral domain. The methodology benefits from wavelet transform to exploit spatial features, encoding the outcoming images into a set of descriptors and utilizing multivariate analysis to isolate and extract the significant spatial-spectral information. A forensic case study of near-infrared images of biological stains on cotton fabrics is used as a benchmark. The stain and fabric have hardly distinguishable spectral signatures due to strong scattering effects that originate from the rough surface of the fabric and the high spectral absorbance of cotton in the near-infrared range. There is no selective information that can isolate signals related to these two components in the spectral images under study, and the complex spatial structure is highly interconnected to the spectral signatures. IDEL was capable of isolating the stains, (spatial) scattering effects, and a possible drying effect from the stains. It was possible to recover, at the same time, specific spectral regions that mostly highlight these isolated spatial structures, which was previously unobtainable.

High Dimensional Immune Profiling Reveals Different Response Patterns in Active and Latent Tuberculosis Following Stimulation With Mycobacterial Glycolipids.

Upon infection with Mycobacterium tuberculosis (Mtb) the host immune response might clear the bacteria, control its growth leading to latent tuberculosis (LTB), or fail to control its growth resulting in active TB (ATB). There is however no clear understanding of the features underlying a more or less effective response. Mtb glycolipids are abundant in the bacterial cell envelope and modulate the immune response to Mtb, but the patterns of response to glycolipids are still underexplored. To identify the CD45+ leukocyte activation landscape induced by Mtb glycolipids in peripheral blood of ATB and LTB, we performed a detailed assessment of the immune response of PBMCs to the Mtb glycolipids lipoarabinomannan (LAM) and its biosynthetic precursor phosphatidyl-inositol mannoside (PIM), and purified-protein derivate (PPD). At 24 h of stimulation, cell profiling and secretome analysis was done using mass cytometry and high-multiplex immunoassay. PIM induced a diverse cytokine response, mainly affecting antigen-presenting cells to produce both pro-inflammatory and anti-inflammatory cytokines, but not IFN-γ, contrasting with PPD that was a strong inducer of IFN-γ. The effect of PIM on the antigen-presenting cells was partly TLR2-dependent. Expansion of monocyte subsets in response to PIM or LAM was reduced primarily in LTB as compared to healthy controls, suggesting a hyporesponsive/tolerance pattern derived from Mtb infection.

Identification of a Zika NS2B epitope as a biomarker for severe clinical phenotypes.

The identification of specific biomarkers for Zika infection and its clinical complications is fundamental to mitigate the infection spread, which has been associated with a broad range of neurological sequelae. We present the characterization of antibody responses in serum samples from individuals infected with Zika, presenting non-severe (classical) and severe (neurological disease) phenotypes, with high-density peptide arrays comprising the Zika NS1 and NS2B proteins. The data pinpoints one strongly IgG-targeted NS2B epitope in non-severe infections, which is absent in Zika patients, where infection progressed to the severe phenotype. This differential IgG profile between the studied groups was confirmed by multivariate data analysis. Molecular dynamics simulations and circular dichroism have shown that the peptide in solution presents itself in a sub-optimal conformation for antibody recognition, which led us to computationally engineer an artificial protein able to stabilize the NS2B epitope structure. The engineered protein was used to interrogate paired samples from mothers and their babies presenting Zika-associated microcephaly and confirmed the absence of NS2B IgG response in those samples. These findings suggest that the assessment of antibody responses to the herein identified NS2B epitope is a strong candidate biomarker for the diagnosis and prognosis of Zika-associated neurological disease.

Amniotic band syndrome with double encephalocele: A case report.

BACKGROUND: Amniotic band syndrome (ABS) is a rare condition of controversial etiology that is associated with varying degrees of anomalies. This study reports a case of a newborn with ABS associated with double encephalocele in the frontal region. CASE DESCRIPTION: A 29-year-old primiparous woman with no history of prenatal infection or consanguineous marriage had a cesarean section at gestational week 38, giving birth to a newborn who was well but had limb anomalies (constriction rings, amputations, and syndactyly) and craniofacial anomalies, mainly double frontal encephalocele. The patient underwent surgical repair and subsequent placement of a ventriculoperitoneal shunt. CONCLUSION: Studies clarifying this uncommon association with double encephalocele are limited. ABS associated with double encephalocele is rare and even more complex when associated with other anomalies. Thus, the conditions in such children are severe and require multidisciplinary monitoring.

Identification of Luminescent Markers for Gunshot Residues: Fluorescence, Raman Spectroscopy, and Chemometrics.

Gunshot residue (GSR) is an evidence of major importance in firearm-related crimes. The recent introduction of nontoxic ammunition has made impossible the characterization of GSR particles by the current methods employed by forensic experts. To overcome this drawback, the introduction of luminescent markers was proposed, allowing on-site visual detection of luminescent gunshot residue (LGSR) at the crime scene. Three different luminescent markers coordinated with europium for specific and selective encoding of ammunition have been proposed. To promote a variety of versatile tools for GSR analysis, spectroscopic techniques combined with chemometric methods can be applied to achieve a reliable, fast, and nondestructive means to identify LGSR and discriminate among the different markers. Luminescence (emission and excitation), normal, and resonance Raman spectroscopies associated with principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were evaluated. The classification model using the complementary information on emission and excitation spectra, a.k.a. data fusion, provided a 100% correct classification for all markers. A comprehensive study has been developed to show that the insertion of luminescent markers enables not only the easy localization of GSR residues but also the possibility of ammunition encoding through the use of multivariate classification methods.

Chemometric approaches for document dating: Handling paper variability.

A non-destructive methodology based on Fourier Transformed Infrared Spectroscopy (FTIR) is proposed in this research to estimate the age of documents of different ages. Due the variability in the samples caused by their different chemical compositions, chemometric approaches were proposed to build one unique regression model able to determine the age of the paper regardless of its composition. PLS models were built employing Generalized Least Squares Weighting (GLSW) and Orthogonal Least Squares (OLS) filters to reduce the variability of samples from the same year. Afterwards, sparse PLS, which is an extension of the PLS model including a variable selection step, was applied to compare its performance with the preprocessing filters. All techniques proposed were compared to the initial PLS models, showing the potential of the chemometric approaches applied to FTIR data to estimate the age of unknown documents.

Microbiological contamination in digital radiography: evaluation at the radiology clinic of an educational institution / Contaminação microbiológica em radiografias digitais: avaliação da clínica de radiologia de uma instituição de ensino

The aim of this study was to evaluate the contamination rate of intraand extraoral digital Xray equipment in a dental radiology clinic at a public educational institution. Samples were collected on three different days, at two times in the day: in the morning, before attending patients, and at the end of the day, after appointment hours and before cleaning and disinfection procedures. Samples were collected from the periapical Xray machine (tube head, positioning device, control panel and activator button), the panoramic Xray machine (temporal support, bite block, control panel and activator button), the intraoral digital system (sensor), and the digital system computers (keyboard and mouse). The samples were seeded in different culture media, incubated, and colonyforming units (CFU/mL) counted. Biochemical tests were performed for suspected colonies of Staphylococcus, Streptococcus and Gramnegative bacilli (GNB). Fungi were visually differentiated into filamentous fungi and yeasts. The results indicated the growth of fungi and Staphylococcus from all sampling locations. GNB growth was observed from all sites sampled from the intraoral Xray equipment. On the panoramic unit, GNB growth was observed in samples from activator button, keyboard and mouse. In general, a higher number of CFU/mL was present before use. It can be concluded that more stringent protocols are needed to control infection and prevent Xray exams from acting as vehicle for cross contamination.

O objetivo neste estudo foi avaliar o índice de contaminação dos equipamentos de radiografias digitais intra e extrabucais da clínica de radiologia odontológica de uma instituição pública de ensino. As amostras foram coletadas em três dias distintos, em dois momentos: pela manhã, antes dos atendimentos clínicos, e ao final do dia, após os atendimentos e antes dos procedimen tos de limpeza e desinfecção. As amostras foram coletadas do aparelho de raios X periapical (cabeçote, braço articular, painel de controle e botão disparador); do aparelho de raios X panorâmico (apoio temporal, bloco de mordida, painel de controle e botão disparador); do sistema digital intrabucal (sensor); dos computadores dos sistemas digitais (teclado emouse). As amostras foram semeadas em diferentes meios de cultura e, após incubação, foram contadas as unidades formadoras de colônia (UFC/mL). Testes bioquímicos foram realizados para colônias suspeitas de Staphylococcus, Streptococcus e bastonetes Gram negativos(BGN). Os fungos foram diferenciados visualmente em fungos filamentosos e leveduras. Os resultados indicaram crescimento de fungos e Staphylococcus em todos os locais amostrados. Em relação aos BGN, houve crescimento em todos os locais coletados do equipamento radiográfico intrabucal. No aparelho panorâmico, houve crescimento de BGN apenas no botão disparador, teclado e mouse. De maneira geral, houve maior número de UFC/mL antes do uso. Pode se concluir que é necessário implantar protocolos mais rigorosos de controle de infecção na prática radiológica, evitando que a obtenção de exames radiográficos seja um veículo para contaminação cruzada na FO/UFJF.

Kinetics of salivary pH after acidic beverage intake by patients undergoing orthodontic treatment.

The saliva of patients undergoing orthodontic treatment with fixed appliances can potentially present a delay in the diluting, clearing, and buffering of dietary acids due to an increased number of retention areas. The aim of this clinical trial was to compare salivary pH kinetics of patients with and without orthodontic treatment, following the intake of an acidic beverage. Twenty participants undergoing orthodontic treatment and 20 control counterparts had their saliva assessed for flow rate, pH, and buffering capacity. There was no significant difference between salivary parameters in participants with or without an orthodontic appliance. Salivary pH recovery following acidic beverage intake was slower in the orthodontic subjects compared to controls. Patients with fixed orthodontic appliances, therefore, seem to be at higher risk of dental erosion, suggesting that dietary advice and preventive care need to be implemented during orthodontic treatment.

Near infrared hyperspectral imaging for forensic analysis of document forgery.

Hyperspectral images in the near infrared range (HSI-NIR) were evaluated as a nondestructive method to detect fraud in documents. Three different types of typical forgeries were simulated by (a) obliterating text, (b) adding text and (c) approaching the crossing lines problem. The simulated samples were imaged in the range of 928-2524 nm with spectral and spatial resolutions of 6.3 nm and 10 µm, respectively. After data pre-processing, different chemometric techniques were evaluated for each type of forgery. Principal component analysis (PCA) was performed to elucidate the first two types of adulteration, (a) and (b). Moreover, Multivariate Curve Resolution-Alternating Least Squares (MCR-ALS) was used in an attempt to improve the results of the type (a) obliteration and type (b) adding text problems. Finally, MCR-ALS and Partial Least Squares-Discriminant Analysis (PLS-DA), employed as a variable selection tool, were used to study the type (c) forgeries, i.e. crossing lines problem. Type (a) forgeries (obliterating text) were successfully identified in 43% of the samples using both the chemometric methods (PCA and MCR-ALS). Type (b) forgeries (adding text) were successfully identified in 82% of the samples using both the methods (PCA and MCR-ALS). Finally, type (c) forgeries (crossing lines) were successfully identified in 85% of the samples. The results demonstrate the potential of HSI-NIR associated with chemometric tools to support document forgery identification.

Strategies and molecular tools to fight antimicrobial resistance: resistome, transcriptome, and antimicrobial peptides.

The increasing number of antibiotic resistant bacteria motivates prospective research toward discovery of new antimicrobial active substances. There are, however, controversies concerning the cost-effectiveness of such research with regards to the description of new substances with novel cellular interactions, or description of new uses of existing substances to overcome resistance. Although examination of bacteria isolated from remote locations with limited exposure to humans has revealed an absence of antibiotic resistance genes, it is accepted that these genes were both abundant and diverse in ancient living organisms, as detected in DNA recovered from Pleistocene deposits (30,000 years ago). Indeed, even before the first clinical use of antibiotics more than 60 years ago, resistant organisms had been isolated. Bacteria can exhibit different strategies for resistance against antibiotics. New genetic information may lead to the modification of protein structure affecting the antibiotic carriage into the cell, enzymatic inactivation of drugs, or even modification of cellular structure interfering in the drug-bacteria interaction. There are still plenty of new genes out there in the environment that can be appropriated by putative pathogenic bacteria to resist antimicrobial agents. On the other hand, there are several natural compounds with antibiotic activity that may be used to oppose them. Antimicrobial peptides (AMPs) are molecules which are wide-spread in all forms of life, from multi-cellular organisms to bacterial cells used to interfere with microbial growth. Several AMPs have been shown to be effective against multi-drug resistant bacteria and have low propensity to resistance development, probably due to their unique mode of action, different from well-known antimicrobial drugs. These substances may interact in different ways with bacterial cell membrane, protein synthesis, protein modulation, and protein folding. The analysis of bacterial transcriptome may contribute to the understanding of microbial strategies under different environmental stresses and allows the understanding of their interaction with novel AMPs.