Universidade Federal do Estado do Rio de Janeiro

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is thatthere is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the completeprocess including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increasedautophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in manycases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as forreviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multipleassays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagyrelated protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.

Inland waters (lakes, reservoirs, streams, and rivers) are often substantial methane (CH(4)) sources in the terrestrial landscape. They are, however, not yet well integrated in global greenhouse gas (GHG) budgets. Data from 474 freshwater ecosystems and the most recent global water area estimates indicate that freshwaters emit at least 103 teragrams of CH(4) year(-1), corresponding to 0.65 petagrams of C as carbon dioxide (CO(2)) equivalents year(-1), offsetting 25% of the estimated land carbon sink. Thus, the continental GHG sink may be considerably overestimated, and freshwaters need to be recognized as important in the global carbon cycle.

Drug concentrations associated with protection from HIV-1 acquisition have not been determined. We evaluated drug concentrations among men who have sex with men in a substudy of the iPrEx trial (1). In this randomized placebo-controlled trial, daily oral doses of emtricitabine/tenofovir disoproxil fumarate were used as pre-exposure prophylaxis (PrEP) in men who have sex with men. Drug was detected less frequently in blood plasma and in viable cryopreserved peripheral blood mononuclear cells (PBMCs) in HIV-infected cases at the visit when HIV was first discovered compared with controls at the matched time point of the study (8% versus 44%; P < 0.001) and in the 90 days before that visit (11% versus 51%; P < 0.001). An intracellular concentration of the active form of tenofovir, tenofovir-diphosphate (TFV-DP), of 16 fmol per million PBMCs was associated with a 90% reduction in HIV acquisition relative to the placebo arm. Directly observed dosing in a separate study, the STRAND trial, yielded TFV-DP concentrations that, when analyzed according to the iPrEx model, corresponded to an HIV-1 risk reduction of 76% for two doses per week, 96% for four doses per week, and 99% for seven doses per week. Prophylactic benefits were observed over a range of doses and drug concentrations, suggesting ways to optimize PrEP regimens for this population.

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Systematic literature review (SLR) is a well-known research method. However, there is a paucity of detailed SLR guidelines in operations management (OM). The recent interest in SLR in OM has not been followed by the same rigour observed in disciplines as medical sciences and public policy. There are no OM-specific SLR protocols, detailed step-by-step methods and reporting procedures. Therefore, this paper provides a step-by-step approach to SLR for OM scholars and an overview of SLR’s evolution as a research method in OM and the resulting progression of themes. The step-by-step approach aims to serve as a guideline sufficiently broad to avoid skipping any significant step, but still being easy to be understood and applied. The paper describes procedures for rigourous SLR, reveals a growing use of literature review in OM, specially for qualitative SLR and traditional narrative reviews, assesses contemporary and emerging themes in OM, and provides a research agenda.

Department of Economics and Statistics, University of Naples Federico II, Italy. info@bibliometrix.org; https://www.bibliometrix.org/; free, donations accepted.

Is active restoration the best approach to achieve ecological restoration success (the return to a reference condition, that is, old-growth forest) when compared to natural regeneration in tropical forests? Our meta-analysis of 133 studies demonstrated that natural regeneration surpasses active restoration in achieving tropical forest restoration success for all three biodiversity groups (plants, birds, and invertebrates) and five measures of vegetation structure (cover, density, litter, biomass, and height) tested. Restoration success for biodiversity and vegetation structure was 34 to 56% and 19 to 56% higher in natural regeneration than in active restoration systems, respectively, after controlling for key biotic and abiotic factors (forest cover, precipitation, time elapsed since restoration started, and past disturbance). Biodiversity responses were based primarily on ecological metrics of abundance and species richness (74%), both of which take far less time to achieve restoration success than similarity and composition. This finding challenges the widely held notion that natural forest regeneration has limited conservation value and that active restoration should be the default ecological restoration strategy. The proposition that active restoration achieves greater restoration success than natural regeneration may have arisen because previous comparisons lacked controls for biotic and abiotic factors; we also did not find any difference between active restoration and natural regeneration outcomes for vegetation structure when we did not control for these factors. Future policy priorities should align the identified patterns of biophysical and ecological conditions where each or both restoration approaches are more successful, cost-effective, and compatible with socioeconomic incentives for tropical forest restoration.

Two billion ha have been identified globally for forest restoration. Our meta-analysis encompassing 221 study landscapes worldwide reveals forest restoration enhances biodiversity by 15-84% and vegetation structure by 36-77%, compared with degraded ecosystems. For the first time, we identify the main ecological drivers of forest restoration success (defined as a return to a reference condition, that is, old-growth forest) at both the local and landscape scale. These are as follows: the time elapsed since restoration began, disturbance type and landscape context. The time elapsed since restoration began strongly drives restoration success in secondary forests, but not in selectively logged forests (which are more ecologically similar to reference systems). Landscape restoration will be most successful when previous disturbance is less intensive and habitat is less fragmented in the landscape. Restoration does not result in full recovery of biodiversity and vegetation structure, but can complement old-growth forests if there is sufficient time for ecological succession.

Roads fragment landscapes and trigger human colonization and degradation of ecosystems, to the detriment of biodiversity and ecosystem functions. The planet's remaining large and ecologically important tracts of roadless areas sustain key refugia for biodiversity and provide globally relevant ecosystem services. Applying a 1-kilometer buffer to all roads, we present a global map of roadless areas and an assessment of their status, quality, and extent of coverage by protected areas. About 80% of Earth's terrestrial surface remains roadless, but this area is fragmented into ~600,000 patches, more than half of which are <1 square kilometer and only 7% of which are larger than 100 square kilometers. Global protection of ecologically valuable roadless areas is inadequate. International recognition and protection of roadless areas is urgently needed to halt their continued loss.

Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy and middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellite blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. Further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads.

OBJECTIVE To assess the impact of consuming ultra-processed foods on the nutritional dietary profile in Brazil. METHODS Cross-sectional study conducted with data from the module on individual food consumption from the 2008-2009 Pesquisa de Orçamentos Familiares (POF - Brazilian Family Budgets Survey). The sample, which represented the section of the Brazilian population aged 10 years or over, involved 32,898 individuals. Food consumption was evaluated by two 24-hour food records. The consumed food items were classified into three groups: natural or minimally processed, including culinary preparations with these foods used as a base; processed; and ultra-processed. RESULTS The average daily energy consumption per capita was 1,866 kcal, with 69.5% being provided by natural or minimally processed foods, 9.0% by processed foods and 21.5% by ultra-processed food. The nutritional profile of the fraction of ultra-processed food consumption showed higher energy density, higher overall fat content, higher saturated and trans fat, higher levels of free sugar and less fiber, protein, sodium and potassium, when compared to the fraction of consumption related to natural or minimally processed foods. Ultra-processed foods presented generally unfavorable characteristics when compared to processed foods. Greater inclusion of ultra-processed foods in the diet resulted in a general deterioration in the dietary nutritional profile. The indicators of the nutritional dietary profile of Brazilians who consumed less ultra-processed foods, with the exception of sodium, are the stratum of the population closer to international recommendations for a healthy diet. CONCLUSIONS The results from this study highlight the damage to health that is arising based on the observed trend in Brazil of replacing traditional meals, based on natural or minimally processed foods, with ultra-processed foods. These results also support the recommendation of avoiding the consumption of these kinds of foods.

The current standard of care for newly diagnosed cases of high-grade glioma is surgical resection followed by RT with concurrent chemotherapy. The most widely used criteria for assessing treatment response are based on a 2D measurement of the enhancing area on MR imaging known as the Macdonald Criteria. Recently, nontumoral increases (pseudoprogression) and decreases (pseudoresponse) in enhancement have been found, and these can confuse outcome evaluation. Here we review pseudoprogression and pseudoresponse and describe how better understanding of these phenomena can aid interpretation.

In this international study, we examined the incidence of hip fractures, postfracture treatment, and all-cause mortality following hip fractures, based on demographics, geography, and calendar year. We used patient-level healthcare data from 19 countries and regions to identify patients aged 50 years and older hospitalized with a hip fracture from 2005 to 2018. The age- and sex-standardized incidence rates of hip fractures, post-hip fracture treatment (defined as the proportion of patients receiving anti-osteoporosis medication with various mechanisms of action [bisphosphonates, denosumab, raloxifene, strontium ranelate, or teriparatide] following a hip fracture), and the all-cause mortality rates after hip fractures were estimated using a standardized protocol and common data model. The number of hip fractures in 2050 was projected based on trends in the incidence and estimated future population demographics. In total, 4,115,046 hip fractures were identified from 20 databases. The reported age- and sex-standardized incidence rates of hip fractures ranged from 95.1 (95% confidence interval [CI] 94.8-95.4) in Brazil to 315.9 (95% CI 314.0-317.7) in Denmark per 100,000 population. Incidence rates decreased over the study period in most countries; however, the estimated total annual number of hip fractures nearly doubled from 2018 to 2050. Within 1 year following a hip fracture, post-hip fracture treatment ranged from 11.5% (95% CI 11.1% to 11.9%) in Germany to 50.3% (95% CI 50.0% to 50.7%) in the United Kingdom, and all-cause mortality rates ranged from 14.4% (95% CI 14.0% to 14.8%) in Singapore to 28.3% (95% CI 28.0% to 28.6%) in the United Kingdom. Males had lower use of anti-osteoporosis medication than females, higher rates of all-cause mortality, and a larger increase in the projected number of hip fractures by 2050. Substantial variations exist in the global epidemiology of hip fractures and postfracture outcomes. Our findings inform possible actions to reduce the projected public health burden of osteoporotic fractures among the aging population. © 2023 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).

Given the importance of bacteria in the development of periradicular lesions, the eradication of the root canal infection is paramount in endodontic treatment. This study evaluated the in vitro intracanal bacterial reduction produced by instrumentation and irrigation with 1%, 2.5%, and 5.25% sodium hypochlorite (NaOCl) or saline solution. Root canals inoculated with Enterococcus faecalis were instrumented and irrigated with the solutions tested. Canals were sampled before and after preparation. After serial dilution, samples were plated onto Mitis salivarius agar, and the colony-forming units grown were counted. Inhibitory effects of the three NaOCl solutions on E. faecalis were also evaluated by means of the agar diffusion test. All test solutions significantly reduced the number of bacterial cells in the root canal (p < 0.05). There was no significant difference between the three NaOCl solutions tested (p > 0.05). Nonetheless, all NaOCl solutions were significantly more effective than saline solution in reducing the number of bacterial cells within the root canal (p < 0.05). The three NaOCl concentrations showed large zones of inhibition against E. faecalis. The results of this study suggest that regular exchange and the use of large amounts of irrigant should maintain the antibacterial effectiveness of the NaOCl solution, compensating for the effects of concentration.

Myiasis is defined as the infestation of live vertebrates (humans and/or animals) with dipterous larvae. In mammals (including humans), dipterous larvae can feed on the host's living or dead tissue, liquid body substance, or ingested food and cause a broad range of infestations depending on the body location and the relationship of the larvae with the host. In this review, we deeply discuss myiasis as a worldwide infestation with different agents and with its broad scenario of clinical manifestations as well as diagnosis techniques and treatment.

PURPOSE: The GEANT4 general-purpose Monte Carlo simulation toolkit is able to simulate physical interaction processes of electrons, hydrogen and helium atoms with charge states (H0, H+) and (He0, He+, He2+), respectively, in liquid water, the main component of biological systems, down to the electron volt regime and the submicrometer scale, providing GEANT4 users with the so-called "GEANT4-DNA" physics models suitable for microdosimetry simulation applications. The corresponding software has been recently re-engineered in order to provide GEANT4 users with a coherent and unique approach to the simulation of electromagnetic interactions within the GEANT4 toolkit framework (since GEANT4 version 9.3 beta). This work presents a quantitative comparison of these physics models with a collection of experimental data in water collected from the literature. METHODS: An evaluation of the closeness between the total and differential cross section models available in the GEANT4 toolkit for microdosimetry and experimental reference data is performed using a dedicated statistical toolkit that includes the Kolmogorov-Smirnov statistical test. The authors used experimental data acquired in water vapor as direct measurements in the liquid phase are not yet available in the literature. Comparisons with several recommendations are also presented. RESULTS: The authors have assessed the compatibility of experimental data with GEANT4 microdosimetry models by means of quantitative methods. The results show that microdosimetric measurements in liquid water are necessary to assess quantitatively the validity of the software implementation for the liquid water phase. Nevertheless, a comparison with existing experimental data in water vapor provides a qualitative appreciation of the plausibility of the simulation models. The existing reference data themselves should undergo a critical interpretation and selection, as some of the series exhibit significant deviations from each other. CONCLUSIONS: The GEANT4-DNA physics models available in the GEANT4 toolkit have been compared in this article to available experimental data in the water vapor phase as well as to several published recommendations on the mass stopping power. These models represent a first step in the extension of the GEANT4 Monte Carlo toolkit to the simulation of biological effects of ionizing radiation.

Archaeology and indigenous history of Native Amazonian peoples in the Upper Xingu region of Brazil reveal unexpectedly complex regional settlement patterns and large-scale transformations of local landscapes over the past millennium. Mapping and excavation of archaeological structures document pronounced human-induced alteration of the forest cover, particularly in relation to large, dense late-prehistoric settlements (circa 1200 to 1600 A.D.). The findings contribute to debates on human carrying capacity, population size and settlement patterns, anthropogenic impacts on the environment, and the importance of indigenous knowledge, as well as contributing to the pride of place of the native peoples in this part of the Amazon.

Factors influencing the morbidity and mortality associated with viremic hepatitis C virus (HCV) infection change over time and place, making it difficult to compare reported estimates. Models were developed for 17 countries (Bahrain, Bulgaria, Cameroon, Colombia, Croatia, Dominican Republic, Ethiopia, Ghana, Hong Kong, Jordan, Kazakhstan, Malaysia, Morocco, Nigeria, Qatar and Taiwan) to quantify and characterize the viremic population as well as forecast the changes in the infected population and the corresponding disease burden from 2015 to 2030. Model inputs were agreed upon through expert consensus, and a standardized methodology was followed to allow for comparison across countries. The viremic prevalence is expected to remain constant or decline in all but four countries (Ethiopia, Ghana, Jordan and Oman); however, HCV-related morbidity and mortality will increase in all countries except Qatar and Taiwan. In Qatar, the high-treatment rate will contribute to a reduction in total cases and HCV-related morbidity by 2030. In the remaining countries, however, the current treatment paradigm will be insufficient to achieve large reductions in HCV-related morbidity and mortality.

Objective To develop new antiphospholipid syndrome (APS) classification criteria with high specificity for use in observational studies and trials, jointly supported by the American College of Rheumatology (ACR) and EULAR. Methods This international multidisciplinary initiative included 4 phases: 1) Phase I, criteria generation by surveys and literature review; 2) Phase II, criteria reduction by modified Delphi and nominal group technique exercises; 3) Phase III, criteria definition, further reduction with the guidance of real‐world patient scenarios, and weighting via consensus‐based multicriteria decision analysis, and threshold identification; and 4) Phase IV, validation using independent adjudicators’ consensus as the gold standard. Results The 2023 ACR/EULAR APS classification criteria include an entry criterion of at least one positive antiphospholipid antibody (aPL) test within 3 years of identification of an aPL‐associated clinical criterion, followed by additive weighted criteria (score range 1–7 points each) clustered into 6 clinical domains (macrovascular venous thromboembolism, macrovascular arterial thrombosis, microvascular, obstetric, cardiac valve, and hematologic) and 2 laboratory domains (lupus anticoagulant functional coagulation assays, and solid‐phase enzyme‐linked immunosorbent assays for IgG/IgM anticardiolipin and/or IgG/IgM anti–β 2 ‐glycoprotein I antibodies). Patients accumulating at least 3 points each from the clinical and laboratory domains are classified as having APS. In the validation cohort, the new APS criteria versus the 2006 revised Sapporo classification criteria had a specificity of 99% versu s 86%, and a sensitivity of 84% versus 99%. Conclusion These new ACR/EULAR APS classification criteria were developed using rigorous methodology with multidisciplinary international input. Hierarchically clustered, weighted, and risk‐stratified criteria reflect the current thinking about APS, providing high specificity and a strong foundation for future APS research.

Plant preparations have been used to treat various diseases and discussed for centuries. Research has advanced to discover and identify the plant components with beneficial effects and reveal their underlying mechanisms. Flavonoids are phytoconstituents with anti‐inflammatory, antimutagenic, anticarcinogenic, and antimicrobial properties. Herein, we listed and contextualized various aspects of the protective effects of the flavonols quercetin, isoquercetin, kaempferol, and myricetin and the flavones luteolin, apigenin, 3′,4′‐dihydroxyflavone, baicalein, scutellarein, lucenin‐2, vicenin‐2, diosmetin, nobiletin, tangeretin, and 5‐O‐methyl‐scutellarein. We presented their structural characteristics and subclasses, importance, occurrence, and food sources. The bioactive compounds present in our diet, such as fruits and vegetables, may affect the health and disease state. Therefore, we discussed the role of these compounds in inflammation, oxidative mechanisms, and bacterial metabolism; moreover, we discussed their synergism with antibiotics for better disease outcomes. Indiscriminate use of antibiotics allows the emergence of multidrug‐resistant bacterial strains; thus, bioactive compounds may be used for adjuvant treatment of infectious diseases caused by resistant and opportunistic bacteria via direct and indirect mechanisms. We also focused on the reported mechanisms and intracellular targets of flavonols and flavones, which support their therapeutic role in inflammatory and infectious diseases.