Routine screening and rates of metabolic syndrome in patients treated with clozapine and long-acting injectable antipsychotic medications: a cross-sectional study.

OBJECTIVES: To examine the rate of monitoring of metabolic syndrome and actual rates of metabolic syndrome in two patient cohorts [clozapine treatment and long-acting injectable (LAI) antipsychotic] who are reviewed on an equally regular basis (1-4 weekly) for administration of treatment. METHODS: Clinical and laboratory data are examined on 119 patients treated with clozapine and 116 patients treated with LAI antipsychotic medications to determine the rates of metabolic syndrome and evidence of monitoring for metabolic syndrome in the previous 6 months. Individuals with insufficient data from these cohorts were invited to attend for metabolic screening to determine actual rates of metabolic syndrome in these two cohorts of patients. RESULTS: All metabolic parameters were monitored to a significantly greater extent in the clozapine cohort (>90%), compared to those treated with LAI antipsychotic medications (<50%) (blood pressure, weight, lipid and glucose levels; p < 0.001). Metabolic syndrome was present in 38.9% of those treated with clozapine compared to 31.1% of patients treated with LAI antipsychotic medications (X2 = 0.54, p = 0.46). CONCLUSIONS: These findings suggest that a robust screening plan should be in place to monitor for metabolic syndrome in individuals treated with LAI antipsychotic medications. This screening should include measurement of body weight, waist circumference, fasting glucose, lipids and fasting insulin levels. Early recognition of abnormal metabolic parameters allows early intervention, therefore, improving long-term cardiovascular outcomes.

Skin Toxicity in Early Breast Cancer Patients Treated with Field-In-Field Breast Intensity-Modulated Radiotherapy versus Helical Inverse Breast Intensity-Modulated Radiotherapy: Results of a Phase III Randomised Controlled Trial.

AIMS: Skin toxicity is a common adverse effect of breast radiotherapy. We investigated whether inverse-planned intensity-modulated radiotherapy (IMRT) would reduce the incidence of skin toxicity compared with forward field-in-field breast IMRT (FiF-IMRT) in early stage breast cancer. MATERIALS AND METHODS: This phase III randomised controlled trial compared whole-breast irradiation with either FiF-IMRT or helical tomotherapy IMRT (HT-IMRT), with skin toxicity as the primary end point. Patients received 50 Gy in 25 fractions and were assessed to compare skin toxicity between treatment arms. RESULTS: In total, 177 patients were available for assessment and the median follow-up was 73.1 months. Inverse IMRT achieved more homogeneous coverage than FiF-IMRT; erythema and moist desquamation were higher with FiF-IMRT compared with HT-IMRT (61% versus 34%; P < 0.001; 33% versus 11%; P < 0.001, respectively). Multivariate analysis showed large breast volume, FiF-IMRT and chemotherapy were independent factors associated with worse acute toxicity. There was no difference between treatment arms in the incidence of late toxicities. The 5-year recurrence-free survival was 96.3% for both FiF-IMRT and HT-IMRT and the 5-year overall survival was 96.3% for FiF-IMRT and 97.4% for HT-IMRT. CONCLUSIONS: Our study showed significant reduction in acute skin toxicity using HT-IMRT compared with FiF-IMRT, without significant reduction in late skin toxicities. On the basis of these findings, inverse-planned IMRT could be used in routine practice for whole-breast irradiation with careful plan optimisation to achieve the required dose constraints for organs at risk.

How Alfvén waves induce compressive flows in the neighborhood of a 2.5D magnetic null-point.

The aim of the present study is to provide insight on the induced compressive perturbations together with the modifications of the environmental parameters in the course of Alfvén wave interaction with a solar magnetic null-point. The shock-capturing Godunov-type code PLUTO is used to solve the set of ideal magnetohydrodynamic equations. The nonlinear effects connected with an initial Alfvén pulse nearing a magnetic null point induces fast and slow magnetoacoustic waves with anti phase conduct. The induced current density and flows are independent of the local plasma-[Formula: see text] at the reconnection site. The induced inflows and outflows highly depend on the polarization. The inflows have a stronger effect compared to the outflows in both the x and y directions showing its peak in the x-direction. The dominant wave that couples to flows is the fast wave due to the in-phase harmony between perturbations of the compressive parameters and the fast wave. The induced current density possesses a steady orientation at the reconnection site which governs the diffusion or propagation of the waves. Induced perturbations by the nonlinear forces together with their back reaction on the Alfvén wave have a significant role in the current density excitation being responsible for the creation of inflows and outflows that are possible candidates for the creation of solar jets which has a significant contribution towards coronal seismology.

Rabies virus diversification in aerial and terrestrial mammals.

Rabies is a fatal zoonotic infection of the central nervous system of mammals and has been known to humans for millennia. The etiological agent, is a neurotropic RNA virus in the order Mononegavirales, family Rhabdoviridae, genus Lyssavirus. There are currently accepted to be two cycles for rabies transmission: the urban cycle and the sylvatic cycle. The fact that both cycles originated from a common RABV or lyssavirus ancestor and the adaptive divergence that occurred since then as this ancestor virus adapted to a wide range of fitness landscapes represented by reservoir species in the orders Carnivora and Chiroptera led to the emergence of the diverse RABV lineages currently found in the sylvatic and urban cycles. Here we study full genome phylogenies and the time to the most recent common ancestor (TMRCA) of the RABVs in the sylvatic and urban cycles. Results show that there were differences between the nucleotide substitution rates per site per year for the same RABV genes maintained independently in the urban and sylvatic cycles. The results identify the most suitable gene for phylogenetic analysis, heterotachy among RABV genes and the TMRCA for the two cycles.

Zika Virus Amplification Using Strand Displacement Isothermal Method and Sequencing Using Nanopore Technology.

Development of novel point of care diagnostic methods in order to help in implementing disease control program and identifying the causative agent of an outbreak is crucial. Classical diagnostic techniques, e.g., real-time polymerase chain reaction (PCR), rely on the presence of the nucleic acid sequence of the target in GenBank. In the case of an emerging new strain of a known or novel pathogen, false-negative results will be recorded by PCR. On the other hand, next-generation sequencing technologies allow rapid whole genome sequencing without previous knowledge of the target. One of these methods is the Oxford Nanopore sequencing technique, which utilizes a portable device named MinION and has a short run time. In this protocol, we describe the development of a novel nanopore sequencing protocol by combining random isothermal amplification technology and nanopore sequencing. The established protocol is rapid (<7 h) and sensitive as less than 4% of the sequenced RNA belonged to the target virus, Zika. Interestingly, we have established an offline BLAST search for the data analysis that facilitates the use of the whole protocol at remote settings without the need of an Internet connection.

The Vaginal Microbiome as a Tool to Predict rASRM Stage of Disease in Endometriosis: a Pilot Study.

Endometriosis remains a challenge to understand and to diagnose. This is an observational cross-sectional pilot study to characterize the gut and vaginal microbiome profiles among endometriosis patients and control subjects without the disease and to explore their potential use as a less-invasive diagnostic tool for endometriosis. Overall, 59 women were included, n = 35 with endometriosis and n = 24 controls. Rectal and vaginal samples were collected in two different periods of the menstrual cycle from all subjects. Gut and vaginal microbiomes from patients with different rASRM (revised American Society for Reproductive Medicine) endometriosis stages and controls were analyzed. Illumina sequencing libraries were constructed using a two-step 16S rRNA gene PCR amplicon approach. Correlations of 16S rRNA gene amplicon data with clinical metadata were conducted using a random forest-based machine-learning classification analysis. Distribution of vaginal CSTs (community state types) significantly differed between follicular and menstrual phases of the menstrual cycle (p = 0.021, Fisher's exact test). Vaginal and rectal microbiome profiles and their association to severity of endometriosis (according to rASRM stages) were evaluated. Classification models built with machine-learning methods on the microbiota composition during follicular and menstrual phases of the cycle were built, and it was possible to accurately predict rASRM stages 1-2 verses rASRM stages 3-4 endometriosis. The feature contributing the most to this prediction was an OTU (operational taxonomic unit) from the genus Anaerococcus. Gut and vaginal microbiomes of women with endometriosis have been investigated. Our findings suggest for the first time that vaginal microbiome may predict stage of disease when endometriosis is present.

Asaia (Rhodospirillales: Acetobacteraceae) and Serratia (Enterobacterales: Yersiniaceae) associated with Nyssorhynchus braziliensis and Nyssorhynchus darlingi (Diptera: Culicidae)

Abstract Midgut transgenic bacteria can be used to express and deliver anti-parasite molecules in malaria vector mosquitoes to reduce transmission. Hence, it is necessary to know the symbiotic bacteria of the microbiota of the midgut to identify those that can be used to interfering in the vector competence of a target mosquito population. The bacterial communities associated with the abdomen of Nyssorhynchus braziliensis (Chagas) (Diptera: Culicidae) and Nyssorhynchus darlingi (Root) (Diptera: Culicidae) were identified using Illumina NGS sequencing of the V4 region of the 16S rRNA gene. Wild females were collected in rural and periurban communities in the Brazilian Amazon. Proteobacteria was the most abundant group identified in both species. Asaia (Rhodospirillales: Acetobacteraceae) and Serratia (Enterobacterales: Yersiniaceae) were detected in Ny. braziliensis for the first time and its presence was confirmed in Ny. darlingi.

Dataset of the microbiome composition in skin lesions caused by lumpy skin disease virus via 16s rRNA massive parallel sequencing.

Lumpy Skin Disease (LSD) is a highly contagious viral disease affecting cattle mainly and induced by the Lumpy Skin Virus within the Capripoxvirus genus of the family Poxviridae. LSD infected animals exhibit pyrexia and sudden appearance of localized or generalized skin nodules that may slough leaving ulcers. The disease has negative economic impacts as a result of hide damage, mastitis, infertility and losses in milk production. Secondary bacterial infection in the affected skin lesions can increase the severity and prolong the course of the disease. Little is known about the microbiome in the ulcerated skin sites. Therefore, the present study was directed to identify the prevalent bacterial communities in affected lesion via the 16s rRNA gene sequencing. Up to 98 species were found in the samples, most of them belonging to the phyla of Proteobacteria, followed by Firmicutes, Actinobacteria, and Bacteroidetes. All found bacterial species are known as opportunistic pathogens, but can withstand the inflammatory reaction.

Diagnosing Zika virus infection against a background of other flaviviruses: Studies in high resolution serological analysis.

Zika virus (ZIKV) is a mosquito-borne flavivirus. Homologous proteins of different flaviviruses display high degrees of sequence identity, especially within subgroups. This leads to extensive immunological cross-reactivity and corresponding problems for developing a ZIKV-specific serological assay. In this study, peptide microarrays were employed to identify individual ZIKV antibody targets with promise in differential diagnosis. A total of 1643 overlapping oligopeptides were synthesized and printed onto glass slides. Together, they encompass the full amino acid sequences of ZIKV proteomes of African, Brazilian, USA, and French Polynesian origins. The resulting ZIKV scanning microarray chips were used to screen three pools of sera from recent Zika outbreaks in Senegal and Cape Verde, in Brazil, and from overseas travelers returning to the EU. Together with a mixed pool of well characterized, archived sera of patients suffering from infections by dengue, yellow fever, tick-borne encephalitis, and West Nile viruses, a total of 42 sera went into the study. Sixty-eight antibody target regions were identified. Most of which were hitherto unknown. Alignments and sequence comparisons revealed 13 of which could be classified as bona fide ZIKV-specific. These identified antibody target regions constitute a founding set of analytical tools for serological discrimination of ZIKV from other flaviviruses.

Shifts in intestinal microbiota after duodenal exclusion favor glycemic control and weight loss: a randomized controlled trial.

BACKGROUND: In recent years, studies indicate gut microbiota as an important modulator in the pathophysiology of type 2 diabetes. Environmental and genetic factors interact to control the host's intestinal microbiota, triggering metabolic disorders such as obesity and insulin resistance. OBJECTIVES: The objective of this study was to identify the fecal microbiota in adult type 2 diabetes patients and to assess changes in composition after metabolic surgery. SETTING: University Hospital of the University of São Paulo. METHODS: Twenty-one patients were enrolled in a randomized controlled study divided into 2 arms. One group underwent duodenal-jejunal bypass surgery with minimal gastric resection, and fecal samples were collected before the operation and after 6 and 12 months. The other group received medical care (standard care group) and was followed for 12 months. Fecal samples were collected at baseline and after 6 and 12 months. Fecal microbiota was analyzed using high-throughput sequencing with V4 16 S rRNA primers. RESULTS: The fecal microbiota in duodenal-jejunal bypass surgery with minimal gastric resection group (Bacteroides, Akkermansia, and Dialister) exhibited increased abundance and diversity compared with that in the standard care group; however, the increase in A. muciniphila was only statistically significant in the surgical group, probably due to the study's small sample size. CONCLUSIONS: The data presented suggest that duodenal-jejunal bypass surgery with minimal gastric resection increases microbial richness and abundancy, mainly for those bacteria related to weight loss and metabolic control (Akkermansia), providing a better understanding of the role of microbiota in type 2 diabetes regulation and its changes after metabolic surgery.

Combination random isothermal amplification and nanopore sequencing for rapid identification of the causative agent of an outbreak.

BACKGROUND: Outbreaks of fever of unknown origin start with nonspecific symptoms and case definition is only slowly developed and adapted, therefore, identifying the causative agent is crucial to ensure suitable treatment and control measures. As an alternative method for Polymerase Chain Reaction in molecular diagnostics diagnostic, metagenomics can be applied to identify the pathogen responsible for the outbreak through sequencing all nucleic acids present in a sample extract. Sequencing data obtained can identify new or variants of known agents. OBJECTIVES: To develop a rapid and field applicable protocol to allow the identification of the causative agent of an outbreak. STUDY DESIGN: We explored a sequencing protocol relying on multiple displacement isothermal amplification and nanopore sequencing in order to allow the identification of the causative agent in a sample. To develop the procedure, a mock sample consisting of supernatant from Zika virus tissue culture was used. RESULTS: The procedure took under seven hours including sample preparation and data analysis using an offline BLAST search. In total, 63,678 sequence files covering around 10,000 bases were extracted. BLAST search revealed the presence of Zika virus. CONCLUSION: In conclusion, the protocol has potential for point of need sequencing to identify RNA viruses. The whole procedure was operated in a suitcase laboratory. However, the procedure is cooling chain dependent and the cost per sequencing run is still high.

High prevalence of HIV-1 transmitted drug-resistance mutations from proviral DNA massively parallel sequencing data of therapy-naïve chronically infected Brazilian blood donors.

BACKGROUND: An improved understanding of the prevalence of low-abundance transmitted drug-resistance mutations (TDRM) in therapy-naïve HIV-1-infected patients may help determine which patients are the best candidates for therapy. In this study, we aimed to obtain a comprehensive picture of the evolving HIV-1 TDRM across the massive parallel sequences (MPS) of the viral entire proviral genome in a well-characterized Brazilian blood donor naïve to antiretroviral drugs. MATERIALS AND METHODS: The MPS data from 128 samples used in the analysis were sourced from Brazilian blood donors and were previously classified by less-sensitive (LS) or "detuned" enzyme immunoassay as non-recent or longstanding HIV-1 infections. The Stanford HIV Resistance Database (HIVDBv 6.2) and IAS-USA mutation lists were used to interpret the pattern of drug resistance. The minority variants with TDRM were identified using a threshold of ≥ 1.0% and ≤ 20% of the reads sequenced. The rate of TDRM in the MPS data of the proviral genome were compared with the corresponding published consensus sequences of their plasma viruses. RESULTS: No TDRM were detected in the integrase or envelope regions. The overall prevalence of TDRM in the protease (PR) and reverse transcriptase (RT) regions of the HIV-1 pol gene was 44.5% (57/128), including any mutations to the nucleoside analogue reverse transcriptase inhibitors (NRTI) and non-nucleoside analogue reverse transcriptase inhibitors (NNRTI). Of the 57 subjects, 43 (75.4%) harbored a minority variant containing at least one clinically relevant TDRM. Among the 43 subjects, 33 (76.7%) had detectable minority resistant variants to NRTIs, 6 (13.9%) to NNRTIs, and 16 (37.2%) to PR inhibitors. The comparison of viral sequences in both sources, plasma and cells, would have detected 48 DNA provirus disclosed TDRM by MPS previously missed by plasma bulk analysis. CONCLUSION: Our findings revealed a high prevalence of TDRM found in this group, as the use of MPS drastically increased the detection of these mutations. Sequencing proviral DNA provided additional information about TDRM, which may impact treatment decisions. The overall results emphasize the importance of continuous monitoring.

Serum sonic hedgehog (SHH) and interleukin-(IL-6) as dual prognostic biomarkers in progressive metastatic breast cancer.

Serum from one hundred and ten breast cancer patients and thirty healthy female volunteers, were prospectively collected and evaluated for serum levels of Shh and IL-6 using human Shh and IL-6 specific enzyme-linked immunoassays. All patients were regularly monitored for event free survival (EFS) and overall survival (OS). Overall outcome analysis was based on serum Shh and IL-6 levels. In patients with progressive metastatic BC, both serum Shh and IL-6 concentrations were elevated in 44% (29 of 65) and 63% (41 of 65) of patients, respectively, at a statistically significant level [Shh (p = 0.0001) and IL-6 (p = 0.0001)] compared to the low levels in healthy volunteers. Serum levels tended to increase with metastatic progression and lymph node positivity. High serum Shh and IL-6 levels were associated with poor EFS and OS opposite to the negative or lower levels in serum Shh and IL-6. The elevated levels of both serum Shh and IL-6 were mainly observed in BC patients who had a significantly higher risk of early recurrence and bone metastasis, and associated with a worse survival for patients with progressive metastatic BC. Further studies are warranted for validating these biomarkers as prognostic tools in a larger patient cohort and in a longer follow-up study.

A modification of endoscopic endonasal approach for management of encephaloceles in sphenoid sinus lateral recess.

Spontaneous cerebrospinal fluid leak with meningoencephaloceles in sphenoid sinus lateral recess is challenging. Transnasal visualization of this area is difficult, especially when large pneumatization is present. External approaches to this region involve aggressive surgery and are often associated with significant morbidity. The aim of this study is to assess the real effectiveness of a modification of the endoscopic endonasal approach for their management. This is a prospective case series study and was conducted at Otolaryngology department, Ain Shams University Hospitals, Cairo, Egypt. Seven patients with spontaneous cerebrospinal fluid leak with meningoencephaloceles in the sphenoid sinus lateral recess were included. Diagnosis was confirmed by: analysis for beta-2 transferrin and imaging. They were managed with endoscopic endonasal retrograde trans-sphenoid approach described in this study with multilayered reconstruction of the defect. Mean age of our patients was 40.14 ± 8.35 years; mean BMI was 36.37 ± 2.59 kg/m2. Primary empty sella was present and osteodural defect was identified in superior wall of sphenoid sinus lateral recess with punched out and regular smooth edges. Mean intra-cranial pressure was (26.42 ± 3.87 mmH2O) and size of defect was less than 10 mm, mean 7.85 ± 1.34. Mean-operative time was 169.28 ± 21.87 min. The mean hospital stay was 7.42 ± 1.39 days. No cerebrospinal fluid leak recurrences were observed during follow-up period that ranged from 37 to 48 months. Endoscopic endonasal retrograde trans-sphenoid approach provides a wide, safe, and direct route to the management of sphenoid sinus lateral recess cerebrospinal fluid leak.

Ultra-Deep Sequencing of HIV-1 near Full-Length and Partial Proviral Genomes Reveals High Genetic Diversity among Brazilian Blood Donors.

BACKGROUND: Here, we aimed to gain a comprehensive picture of the HIV-1 diversity in the northeast and southeast part of Brazil. To this end, a high-throughput sequencing-by-synthesis protocol and instrument were used to characterize the near full length (NFLG) and partial HIV-1 proviral genome in 259 HIV-1 infected blood donors at four major blood centers in Brazil: Pro-Sangue foundation (São Paulo state (SP), n 51), Hemominas foundation (Minas Gerais state (MG), n 41), Hemope foundation (Recife state (PE), n 96) and Hemorio blood bank (Rio de Janeiro (RJ), n 70). MATERIALS AND METHODS: A total of 259 blood samples were obtained from 195 donors with long-standing infections and 64 donors with a lack of stage information. DNA was extracted from the peripheral blood mononuclear cells (PBMCs) to amplify the HIV-1 NFLGs from five overlapping fragments. The amplicons were molecularly bar-coded, pooled, and sequenced by Illumina paired-end protocol. RESULTS: Of the 259 samples studied, 208 (80%) NFLGs and 49 (18.8%) partial fragments were de novo assembled into contiguous sequences and successfully subtyped. Of these 257 samples, 183 (71.2%) were pure subtypes consisting of clade B (n = 167, 65%), C (n = 10, 3.9%), F1 (n = 4, 1.5%), and D (n = 2, 0.7%). Recombinant viruses were detected in 74 (28.8%) samples and consist of unique BF1 (n = 41, 15.9%), BC (n = 7, 2.7%), BCF1 (n = 4, 1.5%), CF1 and CDK (n = 1, 0.4%, each), CRF70_BF1 (n = 4, 1.5%), CRF71_BF1 (n = 12, 4.7%), and CRF72_BF1 (n = 4, 1.5%). Evidence of dual infection was detected in four patients coinfected with the same subtype (n = 3) and distinct subtype (n = 1). CONCLUSION: Based on this work, subtype B appears to be the prevalent subtype followed by a high proportion of intersubtype recombinants that appeared to be arising continually in this country. Our study represents the largest analysis of the viral NFLG ever undertaken worldwide and provides insights into the understanding the genesis of the HIV-1 epidemic in this particular area of South America and informs vaccine design and clinical trials.