EnGens: a computational framework for generation and analysis of representative protein conformational ensembles.

Proteins are dynamic macromolecules that perform vital functions in cells. A protein structure determines its function, but this structure is not static, as proteins change their conformation to achieve various functions. Understanding the conformational landscapes of proteins is essential to understand their mechanism of action. Sets of carefully chosen conformations can summarize such complex landscapes and provide better insights into protein function than single conformations. We refer to these sets as representative conformational ensembles. Recent advances in computational methods have led to an increase in the number of available structural datasets spanning conformational landscapes. However, extracting representative conformational ensembles from such datasets is not an easy task and many methods have been developed to tackle it. Our new approach, EnGens (short for ensemble generation), collects these methods into a unified framework for generating and analyzing representative protein conformational ensembles. In this work, we: (1) provide an overview of existing methods and tools for representative protein structural ensemble generation and analysis; (2) unify existing approaches in an open-source Python package, and a portable Docker image, providing interactive visualizations within a Jupyter Notebook pipeline; (3) test our pipeline on a few canonical examples from the literature. Representative ensembles produced by EnGens can be used for many downstream tasks such as protein-ligand ensemble docking, Markov state modeling of protein dynamics and analysis of the effect of single-point mutations.

Mathematical kinetic modelling followed by in vitro and in vivo assays reveal the bifunctional rice GTPCHII/DHBPS enzymes and demonstrate the key roles of OsRibA proteins in the vitamin B2 pathway.

BACKGROUND: Riboflavin is the precursor of several cofactors essential for normal physical and cognitive development, but only plants and some microorganisms can produce it. Humans thus rely on their dietary intake, which at a global level is mainly constituted by cereals (> 50%). Understanding the riboflavin biosynthesis players is key for advancing our knowledge on this essential pathway and can hold promise for biofortification strategies in major crop species. In some bacteria and in Arabidopsis, it is known that RibA1 is a bifunctional protein with distinct GTP cyclohydrolase II (GTPCHII) and 3,4-dihydroxy-2-butanone-4-phosphate synthase (DHBPS) domains. Arabidopsis harbors three RibA isoforms, but only one retained its bifunctionality. In rice, however, the identification and characterization of RibA has not yet been described. RESULTS: Through mathematical kinetic modeling, we identified RibA as the rate-limiting step of riboflavin pathway and by bioinformatic analysis we confirmed that rice RibA proteins carry both domains, DHBPS and GTPCHII. Phylogenetic analysis revealed that OsRibA isoforms 1 and 2 are similar to Arabidopsis bifunctional RibA1. Heterologous expression of OsRibA1 completely restored the growth of the rib3∆ yeast mutant, lacking DHBPS expression, while causing a 60% growth improvement of the rib1∆ mutant, lacking GTPCHII activity. Regarding OsRibA2, its heterologous expression fully complemented GTPCHII activity, and improved rib3∆ growth by 30%. In vitro activity assays confirmed that both OsRibA1 and OsRibA2 proteins carry GTPCHII/DHBPS activities, but that OsRibA1 has higher DHBPS activity. The overexpression of OsRibA1 in rice callus resulted in a 28% increase in riboflavin content. CONCLUSIONS: Our study elucidates the critical role of RibA in rice riboflavin biosynthesis pathway, establishing it as the rate-limiting step in the pathway. By identifying and characterizing OsRibA1 and OsRibA2, showcasing their GTPCHII and DHBPS activities, we have advanced the understanding of riboflavin biosynthesis in this staple crop. We further demonstrated that OsRibA1 overexpression in rice callus increases its riboflavin content, providing supporting information for bioengineering efforts.

Retrograde distal access versus femoral access for below the knee angioplasty.

BACKGROUND: The prevalence of peripheral artery disease (PAD) in the general population is about 12% to 14% and it increases with age. PAD increased from 164 million people in 2000 to 202 million people in 2010. More than two-thirds of people with PAD are based in low- or middle-income countries. Critical limb ischaemia (CLI) occurs in 1% to 2% of people with intermittent claudication over five years. One third of people with CLI have isolated below the knee (BTK) lesions. CLI and isolated BTK lesions are associated with a higher incidence of limb loss when compared with people with multilevel arterial disease. Endovascular procedures such as angioplasty (with or without stenting) are widely used to treat isolated BTK lesions, aiming to improve blood flow and limb salvage. The technical success of any angioplasty procedure depends on the ability to cross the target lesion. Failed attempts are underestimated in the literature and failures in the real world appear to be higher than reported. People with isolated BTK lesions undergoing angioplasty by conventional femoral access present a high failure rate to cross these lesions. Retrograde distal access may provide some advantages that can lead to successful crossing of the target lesion. OBJECTIVES: To evaluate the benefits and harms of retrograde distal access versus conventional femoral access for people undergoing below the knee angioplasty. SEARCH METHODS: The Cochrane Vascular Information Specialist searched the Cochrane Vascular Specialised Register, CENTRAL, MEDLINE, Embase and CINAHL databases, and World Health Organization International Clinical Trials Registry Platform and ClinicalTrials.gov trials registers to 26 September 2022. SELECTION CRITERIA: We planned to include randomised or quasi-randomised controlled trials comparing people undergoing retrograde distal access versus people undergoing conventional femoral access (ipsilateral antegrade or contralateral retrograde) for BTK angioplasty. DATA COLLECTION AND ANALYSIS: Two review authors independently assessed identified studies for potential inclusion in the review. We used standard methodological procedures in accordance with the Cochrane Handbook for Systematic Review of Interventions. Our primary outcomes were technical success of angioplasty procedure and major procedural complications. Our secondary outcomes were mortality rate, amputation-free survival, primary patency, minor procedural complications and wound healing. We planned to use GRADE to assess the certainty of the evidence for each outcome. MAIN RESULTS: We identified no randomised or quasi-randomised controlled trials that met the inclusion criteria. AUTHORS' CONCLUSIONS: We identified no randomised or quasi-randomised controlled trials that compared retrograde distal access versus femoral access for BTK angioplasty. High-quality studies that compare retrograde distal access versus conventional femoral access for BTK angioplasty are needed.

Interventions for thrombosed haemodialysis arteriovenous fistulas and grafts.

BACKGROUND: Patients who present with problems with definitive dialysis access (arteriovenous fistula (AVF) or arteriovenous graft (AVG)) become catheter dependent (temporary access), a condition that often carries a higher risk of infections, central venous occlusions and recurrent hospitalisations. For AVG, primary patency rates are reported to be 30% to 90% in patients undergoing thrombectomy or thrombolysis. According to the National Kidney Foundation-Kidney Disease Outcomes Quality Initiative (NKF-KDOQI) guidelines, surgery is preferred when the cause of the thrombosis is a stenosis at the site of the anastomosis in thrombosed AVF. The European Best Practice Guidelines (EBPG) reported that thrombosed AVF may be preferably treated with endovascular techniques, but when the cause of thrombosis is in the anastomosis, surgery provides better results with re-anastomosis. Therefore, there is a need to carry out a systematic review to determine the effectiveness and safety of the intervention for thrombosed fistulae. OBJECTIVES: This review aims to establish the efficacy and safety of interventions for failed AVF and AVG in patients receiving haemodialysis (HD). SEARCH METHODS: We searched the Cochrane Kidney and Transplant Register of Studies up to 28 January 2024 through contact with the Information Specialist using search terms relevant to this review. Studies in the Register are identified through searches of CENTRAL, MEDLINE, EMBASE, conference proceedings, the International Clinical Trials Registry Portal (ICTRP) Search Portal and ClinicalTrials.gov. SELECTION CRITERIA: The review included randomised controlled trials (RCTs) and quasi-RCTs in people undergoing HD treatment using AVF or AVG presenting with clinical or haemodynamic evidence of thrombosis. Patients had to have used an AVF or AVG at least once. DATA COLLECTION AND ANALYSIS: Summary estimates of effect were obtained using a random-effects model, and results were expressed as risk ratios (RR) and their 95% confidence intervals (CI) for dichotomous outcomes. Confidence in the evidence was assessed using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach. MAIN RESULTS: Our search strategy identified 14 eligible studies (1176 randomised participants) for inclusion in this review. We included three types of interventions for the treatment of thrombosed AVF and AVG: (1) types of thrombectomy, (2) types of thrombolysis and (3) surgical procedures. Most of the included studies had a high risk of bias due to a poor study design, a low number of patients and industry involvement. Overall, there was insufficient evidence to suggest that a specific intervention was better than another for the outcomes of failure, primary patency at 30 days, technical success and adverse events (both major and minor). Primary patency at 30 days may improve with surgical compared to mechanical thrombectomy (3 studies, 404 participants: RR 1.36, 95% CI 1.07 to 1.67); however, the evidence is very uncertain. Death, access dysfunction, successful dialysis, and SONG (Standards Outcomes in Nephrology) outcomes were rarely reported. The current review is limited by the small number of available studies with a limited number of patients enrolled. Most of the studies included in this review have a high risk of bias and a low or very low certainty of evidence. Further research is required to define the most effective and clinically appropriate technique for access dysfunction. AUTHORS' CONCLUSIONS: It remains unclear whether any intervention therapy affects the patency at 30 days or failure in any thrombosed HD AV access (very low certainty of evidence). Future research will very likely change the evidence base. Based on the importance of HD access to these patients, future studies of these interventions among people receiving HD should be a priority.

Nutrient-efficient catfish-based aquaponics for producing lamb's lettuce at two light intensities.

BACKGROUND: Aquaponic systems are sustainable processes of managing water and nutrients for food production. An innovate nutrient-efficient catfish-based (Clarias gariepinus) aquaponics system was implemented for producing two cultivars of two leafy vegetables largely consumed worldwide: lamb's lettuce (Valerianella locusta var. Favor and Valerianella locusta var. de Hollande) and arugula (Eruca vesicaria var. sativa and Eruca sativa). Different growing treatments (4 × 2 factorial design) were applied to plants of each cultivar, grown at two light intensities (120 and 400 µmol m-2 s-1). During growth, several morphological characteristics (root length, plant height, leaf number, foliage diameter and biggest leaf length) were measured. At harvest, plants were weighed and examined qualitatively in terms of greenness and health status. Additionally, leaf extracts were obtained and used to determine total phenolic contents, antioxidant capacities, and levels of cytotoxicity to Caco-2 intestinal model cells. RESULTS: After a 5-week growth period, both lamb's lettuce cultivars presented high levels of greenness and health status, at both light intensities, particularly the var. de Hollande that also showed higher average performance in terms of plant morphology. In turn, arugula cultivars showed lower levels of greenness and health status, especially the cultivar E. vesicaria var. sativa submitted to direct sunlight during growth. In addition, plant specimens submitted to higher levels of light intensity showed higher contents in antioxidants/polyphenols. Cultivars with a higher content in antioxidants/polyphenols led to higher Caco-2 cell viability. CONCLUSION: For successful industrial implementation of the aquaponics technology, different and optimized acclimatizing conditions must be applied to different plant species and cultivars. © 2024 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

IgG Antibody Responses to Epstein-Barr Virus in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: Their Effective Potential for Disease Diagnosis and Pathological Antigenic Mimicry.

Background and Objectives: The diagnosis and pathology of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) remain under debate. However, there is a growing body of evidence for an autoimmune component in ME/CFS caused by the Epstein-Barr virus (EBV) and other viral infections. Materials and Methods: In this work, we analyzed a large public dataset on the IgG antibodies to 3054 EBV peptides to understand whether these immune responses could help diagnose patients and trigger pathological autoimmunity; we used healthy controls (HCs) as a comparator cohort. Subsequently, we aimed at predicting the disease status of the study participants using a super learner algorithm targeting an accuracy of 85% when splitting data into train and test datasets. Results: When we compared the data of all ME/CFS patients or the data of a subgroup of those patients with non-infectious or unknown disease triggers to the data of the HC, we could not find an antibody-based classifier that would meet the desired accuracy in the test dataset. However, we could identify a 26-antibody classifier that could distinguish ME/CFS patients with an infectious disease trigger from the HCs with 100% and 90% accuracies in the train and test sets, respectively. We finally performed a bioinformatic analysis of the EBV peptides associated with these 26 antibodies. We found no correlation between the importance metric of the selected antibodies in the classifier and the maximal sequence homology between human proteins and each EBV peptide recognized by these antibodies. Conclusions: In conclusion, these 26 antibodies against EBV have an effective potential for disease diagnosis in a subset of patients. However, the peptides associated with these antibodies are less likely to induce autoimmune B-cell responses that could explain the pathogenesis of ME/CFS.

Lead-Free Metal Halide Perovskite Nanocrystals: From Fundamentals to Applications.

Lead (Pb) halide perovskite nanocrystals, with the general formula APbX3 , where A=CH3 NH3+ , CH(NH2 )2+ , or Cs+ and X=Cl- , Br- , or I- , have emerged as a class of materials with promising properties due to their remarkable optical properties and solar cell performance. However, important issues still need to be addressed to enable practical applications of these materials, such as instability, mass production, and Pb toxicity. Recent studies have carried out the replacement of Pb by various less-toxic cations as Sn, Ge, Sb, and Bi. This variety of chemical compositions provide Pb-free perovskite and metal halide nanostructures with a wide spectral range, in addition to being considered less toxic, therefore having greater practical applicability. Highlighting the necessity to address and solve the toxicity problems related to Pb-containing perovskite, this review considers the prospects of the Pb-free perovskite, involving synthesis methods, and properties of them, including advantages, disadvantages, and applications.

Machine learning predicted emission of water-stable CdTe quantum dots.

Quantum dots (QDs) have attracted much attention and exhibit many attractive properties, including high absorption coefficient, adjustable bandgap, high brightness, long-term stability, and size-dependent emission. It is known that to obtain high-quality luminescent properties (i.e. emission color, color purity, quantum yield, and stability), the synthesis parameters must be precisely controlled. In this work, we have constructed a database with CdTe aqueous synthesis parameters and spectroscopic results and applied machine learning algorithms to better understand the influence of the main synthesis parameters of CdTe QDs on their final emission properties. A strong dependence of the final emission wavelength with the reaction time and surface ligands and precursors concentrations was demonstrated. These parameters adjusted synchronously were shown to be very useful for provide ideal synthesis conditions for the preparation of CdTe QDs with desirable emission wavelengths. Moreover, applying the algorithms correctly allows for obtaining information and insights into the growth kinetics of QDs under different synthetic conditions.

Classification of Parkinson's disease motor phenotype: a machine learning approach.

To assess the cortical activity in people with Parkinson's disease (PwP) with different motor phenotype (tremor-dominant-TD and postural instability and gait difficulty-PIGD) and to compare with controls. Twenty-four PwP (during OFF and ON medication) and twelve age-/sex-/handedness-matched healthy controls underwent electrophysiological assessment of spectral ratio analysis through electroencephalography (EEG) at resting state and during the hand movement. We performed a machine learning method with 35 attributes extracted from EEG. To verify the efficiency of the proposed phenotype-based EEG classification the random forest and random tree were tested (performed 30 times, using a tenfolds cross validation in Weka environment). The analyses based on phenotypes indicated a slowing down of cortical activity during OFF medication state in PwP. PD with TD phenotype presented this characteristic at resting and the individuals with PIGD presented during the hand movement. During the ON state, there is no difference between phenotypes at resting nor during the hand movement. PD phenotypes may influence spectral activity measured by EEG. Random forest machine learning provides a slightly more accurate, sensible and specific approach to distinguish different PD phenotypes. The phenotype of PD might be a clinical characteristic that could influence cortical activity.

Recent Evolution and Genomic Profile of Salmonella enterica Serovar Heidelberg Isolates from Poultry Flocks in Brazil.

Salmonella enterica serovar Heidelberg is isolated from poultry-producing regions around the world. In Brazil, S. Heidelberg has been frequently detected in poultry flocks, slaughterhouses, and chicken meat. The goal of the present study was to assess the population structure, recent temporal evolution, and some important genetic characteristics of S. Heidelberg isolated from Brazilian poultry farms. Phylogenetic analysis of 68 S. Heidelberg genomes sequenced here and additional whole-genome data from NCBI demonstrated that all isolates from the Brazilian poultry production chain clustered into a monophyletic group, here called S. Heidelberg Brazilian poultry lineage (SH-BPL). Bayesian analysis defined the time of the most recent common ancestor (tMRCA) as 2004, and the overall population size (Ne) was constant until 2008, when an ∼10-fold Ne increase was observed until circa 2013. SH-BPL presented at least two plasmids with replicons ColpVC (n = 68; 100%), IncX1 (n = 66; 97%), IncA/C2 (n = 65; 95.5%), ColRNAI (n = 43; 63.2%), IncI1 (n = 32; 47%), ColMG828, Col156, IncHI2A, IncHI2, IncQ1, IncX4, IncY, and TrfA (each with n < 4; <4% each). Antibiotic resistance genes were found, with high frequencies of fosA7 (n = 68; 100%), mdf(A) (n = 68; 100%), tet(34) (n = 68; 100%), sul2 (n = 64; 94.1%), and blaCMY-2 (n = 56; 82.3%), along with an overall multidrug resistance (MDR) profile. Ten Salmonella pathogenicity islands (SPI1 to SPI5, SPI9, and SPI11 to SPI14) and 139 virulence genes were also detected. The SH-BPL profile was like those of other previous S. Heidelberg isolates from poultry around the world in the 1990s. In conclusion, the present study demonstrates the recent introduction (2004) and high level of dissemination of an MDR S. Heidelberg lineage in Brazilian poultry operations. IMPORTANCES. Heidelberg is the most frequent serovar in several broiler farms from the main Brazilian poultry-producing regions. Therefore, avian-source foods (mainly chicken carcasses) commercialized in the country and exported to other continents are contaminated with this foodborne pathogen, generating several national and international economic losses. In addition, isolates of this serovar are usually resistant to antibiotics and can cause human invasive and septicemic infection, representing a public health concern. This study demonstrates the use of whole-genome sequencing (WGS) to obtain epidemiological information for one S. Heidelberg lineage highly spread among Brazilian poultry farms. This information will help to define biosecurity measures to control this important Salmonella serovar in Brazilian and worldwide poultry operations.

Dissemination and evolution of SARS-CoV-2 in the early pandemic phase in South America.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic spread rapidly and this scenario is concerning in South America, mainly in Brazil with more than seven million cases of infection. Three major pandemic lineages/clades could be identified along with SARS-CoV-2 dissemination (G, GR, and GH) in the Americas. These clades differ according to their genomic characteristics, virulence, and spreading times. The present study describes the main clades and the respective temporal spreading analyses based on SARS-CoV-2 whole-genome sequences (WGS) from South America, obtained in the early pandemic phase (from March 1 to May 31 in 2020). SARS-CoV-2 WGSs with available information from country and year of sampling were obtained from different countries and the main clades were identified and analyzed independently with a Bayesian approach. The results demonstrated the prevalence of clades GR (n = 842; 54.6%), G (n = 529; 34.3%), and GH (n = 171; 11.1%). The frequencies of the clades were significantly different between South American countries. Clade G was the most prevalent in Ecuador, Suriname, and Uruguay, clade GR in Argentina, Brazil, and Peru, and clade GH in Colombia. The phylodynamic analysis indicated that all these main lineages increased viral spreading from February to early March and after an evolutionary stationary phase was observed. The decrease observed in the virus dissemination was directly associated to the reduction of social movement after March. In conclusion, these data demonstrated the current predominance of clades G, GR, and GH in South America because of the early dissemination of them in the first pandemic phase in South America.

Intrahemispheric EEG: A New Perspective for Quantitative EEG Assessment in Poststroke Individuals.

The ratio between slower and faster frequencies of brain activity may change after stroke. However, few studies have used quantitative electroencephalography (qEEG) index of ratios between slower and faster frequencies such as the delta/alpha ratio (DAR) and the power ratio index (PRI; delta + theta/alpha + beta) for investigating the difference between the affected and unaffected hemisphere poststroke. Here, we proposed a new perspective for analyzing DAR and PRI within each hemisphere and investigated the motor impairment-related interhemispheric frequency oscillations. Forty-seven poststroke subjects and twelve healthy controls were included in the study. Severity of upper limb motor impairment was classified according to the Fugl-Meyer assessment in mild/moderate (n = 25) and severe (n = 22). The qEEG indexes (PRI and DAR) were computed for each hemisphere (intrahemispheric index) and for both hemispheres (cerebral index). Considering the cerebral index (DAR and PRI), our results showed a slowing in brain activity in poststroke patients when compared to healthy controls. Only the intrahemispheric PRI index was able to find significant interhemispheric differences of frequency oscillations. Despite being unable to detect interhemispheric differences, the DAR index seems to be more sensitive to detect motor impairment-related frequency oscillations. The intrahemispheric PRI index may provide insights into therapeutic approaches for interhemispheric asymmetry after stroke.

An integrated approach to identify bimodal genes associated with prognosis in câncer.

Bimodal gene expression (where a gene expression distribution has two maxima) is associated with phenotypic diversity in different biological systems. A critical issue, thus, is the integration of expression and phenotype data to identify genuine associations. Here, we developed tools that allow both: i) the identification of genes with bimodal gene expression and ii) their association with prognosis in cancer patients from The Cancer Genome Atlas (TCGA). Bimodality was observed for 554 genes in expression data from 25 tumor types. Furthermore, 96 of these genes presented different prognosis when patients belonging to the two expression peaks were compared. The software to execute the method and the corresponding documentation are available at the Data access section.

Genotypic characterization and molecular evolution of avian reovirus in poultry flocks from Brazil.

Avian reovirus (ARV) is one of the main causes of infectious arthritis/tenosynovitis and malabsorption syndrome (MAS) in poultry. ARVs have been disseminated in Brazilian poultry flocks in the last years. This study aimed to genotype ARVs and to evaluate the molecular evolution of the more frequent ARV lineages detected in Brazilian poultry-producing farms. A total of 100 poultry flocks with clinical signs of tenosynovitis/MAS, from all Brazilian poultry-producing regions were positive for ARV by PCR. Seventeen bird tissues were submitted to cell culture and ARV RNA detection/genotyping by two PCRs. The phylogenetic classification was based on σC gene alignment using a dataset with other Brazilian and worldwide ARVs sequences. ARVs were specifically detected by both PCRs from the 17 cell cultures, and σC gene partial fragments were sequenced. All these sequences were aligned with a total of 451 ARV σC gene data available in GenBank. Phylogenetic analysis demonstrated five well-defined clusters that were classified into lineages I, II, III, IV, and V. Three lineages could be further divided into sub-lineages: I (I vaccine, Ia, Ib), II (IIa, IIb, IIc) and IV (IVa and IVb). Brazilian ARVs were from four lineages/sub-lineages: Ib (48.2%), IIb (22.2%), III (3.7%) and V (25.9%). The Bayesian analysis demonstrated that the most frequent sub-lineage Ib emerged in the world around 1968 and it was introduced into Brazil in 2010, with increasing spread soon after. In conclusion, four different ARV lineages are circulating in Brazilian poultry flocks, all associated with clinical diseases. RESEARCH HIGHLIGHTS One-hundred ARV-positive flocks were detected in all main poultry-producing regions from Brazil. A large dataset of 468 S1 sequences was constructed and divided ARVs into five lineages. Four lineages/sub-lineages (Ib, IIb, III and V) were detected in commercial poultry flocks from Brazil. Brazilian lineages shared a low identity with the commercial vaccine lineage (I vaccine). Sub-lineage Ib emerged around 1968 and was introduced into Brazil in 2010.

Beyond the target area: an integrative view of tDCS-induced motor cortex modulation in patients and athletes.

Transcranial Direct Current Stimulation (tDCS) is a non-invasive technique used to modulate neural tissue. Neuromodulation apparently improves cognitive functions in several neurologic diseases treatment and sports performance. In this study, we present a comprehensive, integrative review of tDCS for motor rehabilitation and motor learning in healthy individuals, athletes and multiple neurologic and neuropsychiatric conditions. We also report on neuromodulation mechanisms, main applications, current knowledge including areas such as language, embodied cognition, functional and social aspects, and future directions. We present the use and perspectives of new developments in tDCS technology, namely high-definition tDCS (HD-tDCS) which promises to overcome one of the main tDCS limitation (i.e., low focality) and its application for neurological disease, pain relief, and motor learning/rehabilitation. Finally, we provided information regarding the Transcutaneous Spinal Direct Current Stimulation (tsDCS) in clinical applications, Cerebellar tDCS (ctDCS) and its influence on motor learning, and TMS combined with electroencephalography (EEG) as a tool to evaluate tDCS effects on brain function.

Virulence gene content in Escherichia coli isolates from poultry flocks with clinical signs of colibacillosis in Brazil.

Escherichia coli is a commensal bacterium of the bird's intestinal tract, but it can invade different tissues resulting in systemic symptoms (colibacillosis). This disease occurs only when the E. coli infecting strain presents virulence factors (encoded by specific genes) that enable the adhesion and proliferation in the host organism. Thus, it is important to differentiate pathogenic (APEC, avian pathogenic E. coli) and non-pathogenic or fecal (AFEC, avian fecal E. coli) isolates. Previous studies analyzed the occurrence of virulence factors in E. coli strains isolated from birds with colibacillosis, demonstrating a high frequency of the bacterial genes cvaC, iroN, iss, iutA, sitA, tsh, fyuA, irp-2, ompT and hlyF in pathogenic strains. The aim of the present study was to evaluate the occurrence and frequency of these virulence genes in E. coli isolated from poultry flocks in Brazil. A total of 138 isolates of E. coli was obtained from samples of different tissues and/or organs (spleen, liver, kidney, trachea, lungs, skin, ovary, oviduct, intestine, cloaca) and environmental swabs collected from chicken and turkey flocks suspected to have colibacillosis in farms from the main Brazilian producing regions. Total DNA was extracted and the 10 virulence genes were detected by traditional and/or real-time PCR. At least 11 samples of each gene were sequenced and compared to reference strains. All 10 virulence factors were detected in Brazilian E. coli isolates, with frequencies ranging from 39.9% (irp-2) to 68.8% (hlyF and sitA). Moreover, a high nucleotide similarity (over 99%) was observed between gene sequences of Brazilian isolates and reference strains. Seventy-nine isolates were defined as pathogenic (APEC) and 59 as fecal (AFEC) based on previously described criteria. In conclusion, the main virulence genes of the reference E. coli strains are also present in isolates associated with colibacillosis in Brazil. The analysis of this set of virulence factors can be used to differentiate between APEC and AFEC isolates in Brazil.

Endovascular treatment of a giant hepatic artery aneurysm with Amplatzer vascular plug.

Hepatic artery aneurysms are uncommon and account for 20% of visceral aneurysms. Some authors consider endovascular procedures as the first line treatment for most hepatic artery aneurysms, being the conventional surgery reserved for unstable ruptured aneurysms or if the anatomy is unsuitable for endovascular repair. In this report, we describe the endovascular treatment of a giant common hepatic artery aneurysm with an Amplatzer vascular plug.

Taqman real-time PCR assays for rapid detection of avian pathogenic Escherichia coli isolates.

Avian pathogenic Escherichia coli (APEC) isolates are currently differentiated from nonpathogenic strains by classical PCR of virulence genes. This study improves the detection of the five main virulence genes used for APEC detection with the development of duplex and single Taqman real-time PCR to these targets. Primers and probes targeted to ompT, hlyF, iroN, iutA, and iss genes were designed and used in the implementation of single (iss) and duplex (hlyF/ompT and iroN/iutA) Taqman PCR assays. All five virulence genes of E coli strains were successfully detected by classical and Taqman real-time (single and duplex) PCR. A panel of 111 E coli isolates, obtained from avian samples collected in different Brazilian regions between 2010 and 2011, were further tested by both assays. Complete agreement was observed in the detection of four genes, ompT, hlyF, iron, iutA, but not for iss. This issue was addressed by combining the forward primer of the classical PCR to the new iss reverse primer and probe, resulting in complete agreement for all five genes. In total, 61 (55%) Brazilian E. coli isolates were detected as APEC, and the remaining 50 (45%) as avian fecal E. coli (AFEC). In conclusion, classical and Taqman real-time PCR presented exactly the same analytical performance for the differentiation of APEC and AFEC isolates. The developed real-time Taqman PCR assays could be used for the detection and differentiation of APEC isolates.

Infectious bronchitis virus in different avian physiological systems-a field study in Brazilian poultry flocks.

Avian infectious bronchitis is a highly contagious viral disease with economic effects on poultry agribusiness. The disease presents multi-systemic clinical signs (respiratory, renal, enteric, and reproductive) and is caused by one coronavirus (infectious bronchitis virus, IBV). Infectious bronchitis virus is classified into different serotypes and genotypes (vaccine strains and field variants). This study aimed to evaluate the occurrence of IBV in commercial poultry flocks from 3 important producing regions in Brazil and to determine the tropism of the main circulating genotypes to 3 different avian physiological systems (respiratory, digestive, urinary/reproductive). Clinical samples with suggestive signs of IBV infection were collected from 432 different poultry commercial flocks (198 from broilers and 234 from breeders). The total number of biological samples consisted of organ pools from the 3 above physiological systems obtained of farms from 3 important producing regions: midwest, northeast, and south. Infectious bronchitis virus was detected by reverse-transcription, real-time PCR of the 5' untranslated region. The results showed 179 IBV-positive flocks (41.4% of the flocks), with 107 (24.8%) from broilers and 72 (16.8%) from breeders. There were similar frequencies of IBV-positive flocks in farms from different regions of the country, most often in broilers (average 54%) compared with breeders (average 30.8%). reverse-transcription was more frequently detected in the digestive system of breeders (40%), and in the digestive (43.5%) and respiratory (37.7%) systems of broilers. Infectious bronchitis virus genotyping was performed by a reverse-transcription nested PCR and sequencing of the S1 gene from a selection of 79 IBV-positive flocks (45 from broilers and 34 from breeders). The majority of the flocks were infected with Brazilian variant genotype than with Massachusetts vaccine genotype. These results demonstrate the predominance of the Brazilian variant (mainly in the enteric tract) in commercial poultry flocks from 3 important producing regions in Brazil.

Antibody selection strategies and their impact in predicting clinical malaria based on multi-sera data.

BACKGROUND: Nowadays, the chance of discovering the best antibody candidates for predicting clinical malaria has notably increased due to the availability of multi-sera data. The analysis of these data is typically divided into a feature selection phase followed by a predictive one where several models are constructed for predicting the outcome of interest. A key question in the analysis is to determine which antibodies  should be included in the predictive stage and whether they should be included in the original or a transformed scale (i.e. binary/dichotomized). METHODS: To answer this question, we developed three approaches for antibody selection in the context of predicting clinical malaria: (i) a basic and simple approach based on selecting antibodies via the nonparametric Mann-Whitney-Wilcoxon test; (ii) an optimal dychotomizationdichotomization approach where each antibody was selected according to the optimal cut-off via maximization of the chi-squared (χ2) statistic for two-way tables; (iii) a hybrid parametric/non-parametric approach that integrates Box-Cox transformation followed by a t-test, together with the use of finite mixture models and the Mann-Whitney-Wilcoxon test as a last resort. We illustrated the application of these three approaches with published serological data of 36 Plasmodium falciparum antigens for predicting clinical malaria in 121 Kenyan children. The predictive analysis was based on a Super Learner where predictions from multiple classifiers including the Random Forest were pooled together. RESULTS: Our results led to almost similar areas under the Receiver Operating Characteristic curves of 0.72 (95% CI = [0.62, 0.82]), 0.80 (95% CI = [0.71, 0.89]), 0.79 (95% CI = [0.7, 0.88]) for the simple, dichotomization and hybrid approaches, respectively. These approaches were based on 6, 20, and 16 antibodies, respectively. CONCLUSIONS: The three feature selection strategies provided a better predictive performance of the outcome when compared to the previous results relying on Random Forest including all the 36 antibodies (AUC = 0.68, 95% CI = [0.57;0.79]). Given the similar predictive performance, we recommended that the three strategies should be used in conjunction in the same data set and selected according to their complexity.