Bridging the gap between molecular and genomic epidemiology in tuberculosis: inferring MIRU-VNTR patterns from genomic data.

The transition from MIRU-VNTR-based epidemiology studies in tuberculosis (TB) to genomic epidemiology has transformed how we track transmission. However, short-read sequencing is poor at analyzing repetitive regions such as the MIRU-VNTR loci. This causes a gap between the new genomic data and the large amount of information stored in historical databases. Long-read sequencing could bridge this knowledge gap by allowing analysis of repetitive regions. However, the feasibility of extracting MIRU-VNTRs from long reads and linking them to historical data has not been evaluated. In our study, an in silico arm, consisting of inference of MIRU patterns from long-read sequences (using MIRUReader program), was compared with an experimental arm, involving standard amplification and fragment sizing. We analyzed overall performance on 39 isolates from South Africa and confirmed reproducibility in a sample enriched with 62 clustered cases from Spain. Finally, we ran 25 consecutive incident cases, demonstrating the feasibility of correctly assigning new clustered/orphan cases by linking data inferred from genomic analysis to MIRU-VNTR databases. Of the 3,024 loci analyzed, only 11 discrepancies (0.36%) were found between the two arms: three attributed to experimental error and eight to misassigned alleles from long-read sequencing. A second round of analysis of these discrepancies resulted in agreement between the experimental and in silico arms in all but one locus. Adjusting the MIRUReader program code allowed us to flag potential in silico misassignments due to suboptimal coverage or unfixed double alleles. Our study indicates that long-read sequencing could help address potential chronological and geographical gaps arising from the transition from molecular to genomic epidemiology of tuberculosis. IMPORTANCE: The transition from molecular epidemiology in tuberculosis (TB), based on the analysis of repetitive regions (VNTR-based genotyping), to genomic epidemiology transforms in the precision with which we track transmission. However, short-read sequencing, the most common method for performing genomic analysis, is poor at analyzing repetitive regions. This means that we face a gap between the new genomic data and the large amount of information stored in historical databases, which is also an obstacle to cross-national surveillance involving settings where only molecular data are available. Long-read sequencing could help bridge this knowledge gap by allowing analysis of repetitive regions. Our study demonstrates that MIRU-VNTR patterns can be successfully inferred from long-read sequences, allowing the correct assignment of new cases as clustered/orphan by linking new data extracted from genomic analysis to historical MIRU-VNTR databases. Our data may provide a starting point for bridging the knowledge gap between the molecular and genomic eras in tuberculosis epidemiology.

A Low-Order Permutationally Invariant Polynomial Approach to Learning Potential Energy Surfaces Using the Bond-Order Charge-Density Matrix: Application to Cn Clusters for n = 3-10, 20.

A representation for learning potential energy surfaces (PESs) in terms of permutationally invariant polynomials (PIPs) using the Hartree-Fock expression for electronic energy is proposed. Our approach is based on the one-electron core Hamiltonian weighted by the configuration-dependent elements of the bond-order charge density matrix (CDM). While the previously reported model used an s-function Gaussian basis for the CDM, the present formulation is expanded with p-functions, which are crucial for describing chemical bonding. Detailed results are demonstrated on linear and cyclic Cn clusters (n = 3-10) trained on extensive B3LYP/aug-cc-pVTZ data. The described method facilitates PES learning by reducing the root mean squared error (RMSE) by a factor of 5 relative to the s-function formulation and by a factor of 20 relative to the conventional PIP approach. This is equivalent to using CDM and an sp basis with a PIP of order M to achieve the same RMSE as with the conventional method with a PIP of order M + 2. Implications for large-scale problems are discussed using the case of the PES of the C20 fullerene in full permutational symmetry.

Health and sociodemographic factors associated with low muscle strength, muscle mass, and physical performance among people living with HIV.

ABSTRACTThis study examined the factors associated with low muscle strength, muscle mass, and physical performance in 331 people living with HIV. Participants completed handgrip as a strength measure, appendicular skeletal muscle mass using bioimpedance analysis, and chair rise was a physical performance measure. Multivariate logistic regression was used to analyze the association between low values on these measures with sociodemographic, HIV-related factors, and comorbidities. Higher body mass index (BMI) (OR = 0.91; CI = 0.86-0.97) and higher CD4/CD8 ratio (OR = 0.38; 95% CI = 0.18-0.82) were associated with decreased likelihood of low handgrip strength. Being non-employed (OR = 2.08; 95% CI = 1.07-4.06), having hypertension (OR = 2.27; 95% CI = 1.13-4.54) and rheumatism (OR = 5.46; 95% CI = 1.68-17.74) increased the chance of low handgrip strength. Higher BMI (OR = 0.43; 95% CI = 0.34-0.56), CD4/CD8 ratio (OR = 0.29; 95% CI = 0.09-0.93), and bioimpedance phase angle (OR = 0.22; 95% CI = 0.12-0.40) were associated with decreased likelihood of low muscle mass. Lastly, having less than eight years of education (OR = 1.87; 95% CI = 1.02-3.41) and being non-employed (OR = 8.18; 95% CI = 3.09-21.61) increased the chance of low chair stand performance. In addition, higher CD4 + lymphocytes count (OR = 0.99; 95% CI = 0.99-0.99) was associated with a decreased likelihood of low chair stand performance. In conclusion, specific and non-specific HIV-related factors are associated with low handgrip strength, low muscle mass, and/or low chair stand performance.

Current Practices in Airway Stent Management: A National Survey of US Practitioners.

BACKGROUND: Despite a growing number of tracheobronchial stent types and indications, complications remain frequent, and high-quality evidence on practices to prevent stent-related complications is lacking. Understanding current management practice is a first step to designing prospective studies to assess whether specific practices aimed at mitigating stent-related complications improve patient-centered outcomes. OBJECTIVES: In this study, we aimed to understand current management strategies following tracheobronchial stenting. METHOD: We performed a nationwide survey of members of the American Association of Bronchology and Interventional Pulmonology (AABIP) and the General Thoracic Surgical Club (GTSC) who place airway stents. The electronic survey captured data on practitioners' demographics, practice setting, airway stent volume, and standard post-stent practices (if any) including the use of medications, mucus clearance devices, surveillance imaging, and surveillance bronchoscopy. RESULTS: One hundred thirty-eight physicians completed the survey. Respondents were majority male (75.4%) and had diverse training (50.0% completed interventional pulmonary fellowship; 18.1% thoracic surgery; 31.9% other stent training). Post-stent management strategies varied markedly across respondents; 75.4% prescribe at least one medication to prevent post-stent complications, 52.9% perform routine surveillance bronchoscopy in asymptomatic patients, 26.1% prescribe mucus clearance regimens, 16.7% obtain routine computed tomography scans in asymptomatic patients, and 8.3% routinely replace their stents prior to stent failure. CONCLUSIONS: In this national survey of practitioners who place airway stents, there was marked heterogeneity in post-stent management approaches. Further studies are needed to identify which, if any, of these strategies improve patient-centered outcomes.

A One Health approach revealed the long-term role of Mycobacterium caprae as the hidden cause of human tuberculosis in a region of Spain, 2003 to 2022.

IntroductionMycobacterium caprae is a member of the Mycobacterium tuberculosis complex (MTBC) not routinely identified to species level. It lacks specific clinical features of presentation and may therefore not be identified as the causative agent of tuberculosis. Use of whole genome sequencing (WGS) in the investigation of a family microepidemic of tuberculosis in Almería, Spain, unexpectedly identified the involvement of M. caprae.AimWe aimed to evaluate the presence of additional unidentified M. caprae cases and to determine the magnitude of this occurrence.MethodsFirst-line characterisation of the MTBC isolates was done by MIRU-VNTR, followed by WGS. Human and animal M. caprae isolates were integrated in the analysis.ResultsA comprehensive One Health strategy allowed us to (i) detect other 11 M. caprae infections in humans in a period of 18 years, (ii) systematically analyse M. caprae infections on an epidemiologically related goat farm and (iii) geographically expand the study by including 16 M. caprae isolates from other provinces. Integrative genomic analysis of 41 human and animal M. caprae isolates showed a high diversity of strains. The animal isolates' diversity was compatible with long-term infection, and close genomic relationships existed between isolates from goats on the farm and recent cases of M. caprae infection in humans.DiscussionZoonotic circulation of M. caprae strains had gone unnoticed for 18 years. Systematic characterisation of MTBC at species level and/or extended investigation of the possible sources of exposure in all tuberculosis cases would minimise the risk of overlooking similar zoonotic events.

Central ECMO cannulation for severe dihydropyridine calcium channel blocker overdose.

Calcium channel blocker (CCB) toxicity carries a high mortality and is the sixth most fatal drug class reported to US poison centers. Amlodipine overdose is characterized by a life-threatening arterial vasodilation that compromises organ perfusion. The management of CCB intoxication is focused on maintaining adequate organ perfusion. In cases refractory to medical therapies, hemodynamic support with extracorporeal membrane oxygenation (ECMO) is warranted necessitating higher flows than usual to compensate for the vasodilation and requiring central cannulation. We present a case of a 12-year-old with severe dihydropyridine CCB ingestion, refractory to medical management and successfully treated with central ECMO cannulation. The patient was discharged home with no significant disability. Central ECMO cannulation may be helpful to facilitate adequate flows in vasodilatory shock such as CCB overdose.

Candida albicans the main opportunistic pathogenic fungus in humans.

Candida albicans is a commensal of the mammalian microbiome and the primary pathogenic fungus of humans. It becomes a severe health problem in immunocompromised patients and can cause a wide variety of mucosal and systemic infections. The interaction between C. albicans and host cells is characterized by the expression of virulence factors such as adhesins and invasins, the secretion of hydrolytic enzymes, a transition from yeast to filamentous hyphae form, and the ability to form biofilms; these features collectively result in cell adhesion, invasion, and damage. This review describes complex commensal interactions of C. albicans with host cells and the cellular events that it triggers in a pathogenic environment. We also review the host immune response induced by C. albicans antigens and the mechanisms developed by this fungus to avoid the action of antifungal agents.

A cross-sectional study evidences regulations of leukocytes in the colostrum of mothers with obesity.

BACKGROUND: Breastmilk is a dynamic fluid whose initial function is to provide the most adapted nutrition to the neonate. Additional attributes have been recently ascribed to breastmilk, with the evidence of a specific microbiota and the presence of various components of the immune system, such as cytokines and leukocytes. The composition of breastmilk varies through time, according to the health status of mother and child, and altogether contributes to the future health of the infant. Obesity is a rising condition worldwide that creates a state of systemic, chronic inflammation including leukocytosis. Here, we asked whether colostrum, the milk produced within the first 48 h post-partum, would contain a distinct leukocyte composition depending on the body mass index (BMI) of the mother. METHODS: We collected peripheral blood and colostrum paired samples from obese (BMI > 30) and lean (BMI < 25) mothers within 48 h post-partum and applied a panel of 6 antibodies plus a viability marker to characterize 10 major leukocyte subpopulations using flow cytometry. RESULTS: The size, internal complexity, and surface expression of CD45 and CD16 of multiple leukocyte subpopulations were selectively regulated between blood and colostrum irrespective of the study groups, suggesting a generalized cell-specific phenotype alteration. In obesity, the colostrum B lymphocyte compartment was significantly reduced, and CD16+ blood monocytes had an increased CD16 expression compared to the lean group. CONCLUSIONS: This is the first characterization of major leukocyte subsets in colostrum of mothers suffering from obesity and the first report of colostrum leukocyte subpopulations in Latin America. We evidence various significant alterations of most leukocyte populations between blood and colostrum and demonstrate a decreased colostrum B lymphocyte fraction in obesity. This pioneering study is a stepping stone to further investigate active immunity in human breastmilk.

Tracheobronchomalacia and Excessive Dynamic Airway Collapse: Current Concepts and Future Directions.

Tracheobronchomalacia (TBM) and excessive dynamic airway collapse (EDAC) are airway abnormalities that share a common feature of expiratory narrowing but are distinct pathophysiologic entities. Both entities are collectively referred to as expiratory central airway collapse (ECAC). The malacia or weakness of cartilage that supports the tracheobronchial tree may occur only in the trachea (ie, tracheomalacia), in both the trachea and bronchi (TBM), or only in the bronchi (bronchomalacia). On the other hand, EDAC refers to excessive anterior bowing of the posterior membrane into the airway lumen with intact cartilage. Clinical diagnosis is often confounded by comorbidities including asthma, chronic obstructive pulmonary disease, obesity, hypoventilation syndrome, and gastroesophageal reflux disease. Additional challenges include the underrecognition of ECAC at imaging; the interchangeable use of the terms TBM and EDAC in the literature, which leads to confusion; and the lack of clear guidelines for diagnosis and treatment. The use of CT is growing for evaluation of the morphology of the airway, tracheobronchial collapsibility, and extrinsic disease processes that can narrow the trachea. MRI is an alternative tool, although it is not as widely available and is not used as frequently for this indication as is CT. Together, these tools not only enable diagnosis, but also provide a road map to clinicians and surgeons for planning treatment. In addition, CT datasets can be used for 3D printing of personalized medical devices such as stents and splints. An invited commentary by Brixey is available online. Online supplemental material is available for this article. ©RSNA, 2022.

Seminal Studies in Facial Reanimation Surgery: Consensus and Controversies in the Top 50 Most Cited Articles.

ABSTRACT: Facial paralysis can impair one's ability to form facial expressions that are congruent with internal emotion. This hinders communication and the cognitive processing of emotional experience. Facial reanimation surgery, which aims to restore full facial expressivity is a relatively recent undertaking which is still evolving. Due in large part to published techniques, refinements, and clinical outcomes in the scientific literature, consensus on best practice is gradually emerging, whereas controversies still exist.Taking stock of how the discipline reached its current state can help delineate areas of agreement and debate, and more clearly reveal a path forward. To do this, the authors have analyzed the 50 seminal publications pertaining to facial reanimation surgery. In longstanding cases, the free gracilis transfer emerges as a clear muscle of choice but the nerve selection remains controversial with prevailing philosophies advocating cross facial nerve grafts (with or without the support of an ipsilateral motor donor) or an ipsilateral motor donor only, of which the hypoglossal and nerve to masseter predominate. The alternative orthodoxy has refined the approach popularized by Gillies in 1934 and does not require the deployment of microsurgical principles. Although this citation analysis does not tell the whole story, surgeons with an interest in facial reanimation will find that this is a good place to start.

Tracheostomy for COVID-19 Respiratory Failure: Multidisciplinary, Multicenter Data on Timing, Technique, and Outcomes.

OBJECTIVE: The aim of this study was to assess the outcomes of tracheostomy in patients with COVID-19 respiratory failure. SUMMARY BACKGROUND DATA: Tracheostomy has an essential role in managing COVID-19 patients with respiratory failure who require prolonged mechanical ventilation. However, limited data are available on how tracheostomy affects COVID-19 outcomes, and uncertainty surrounding risk of infectious transmission has led to divergent recommendations and practices. METHODS: It is a multicenter, retrospective study; data were collected on all tracheostomies performed in COVID-19 patients at 7 hospitals in 5 tertiary academic medical systems from February 1, 2020 to September 4, 2020. RESULT: Tracheotomy was performed in 118 patients with median time from intubation to tracheostomy of 22 days (Q1-Q3: 18-25). All tracheostomies were performed employing measures to minimize aerosol generation, 78.0% by percutaneous technique, and 95.8% at bedside in negative pressure rooms. Seventy-eight (66.1%) patients were weaned from the ventilator and 18 (15.3%) patients died from causes unrelated to tracheostomy. No major procedural complications occurred. Early tracheostomy (≤14 days) was associated with decreased ventilator days; median ventilator days (Q1-Q3) among patients weaned from the ventilator in the early, middle and late groups were 21 (21-31), 34 (26.5-42), and 37 (32-41) days, respectively with P = 0.030. Compared to surgical tracheostomy, percutaneous technique was associated with faster weaning for patients weaned off the ventilator [median (Q1-Q3): 34 (29-39) vs 39 (34-51) days, P = 0.038]; decreased ventilator-associated pneumonia (58.7% vs 80.8%, P = 0.039); and among patients who were discharged, shorter intensive care unit duration [median (Q1-Q3): 33 (27-42) vs 47 (33-64) days, P = 0.009]; and shorter hospital length of stay [median (Q1-Q3): 46 (33-59) vs 59.5 (48-80) days, P = 0.001]. CONCLUSION: Early, percutaneous tracheostomy was associated with improved outcomes compared to surgical tracheostomy in a multi-institutional series of ventilated patients with COVID-19.

Bronchopleural Fistula in the Mechanically Ventilated Patient: A Concise Review.

OBJECTIVE: To describe the physiology of air leak in bronchopleural fistula in mechanically ventilated patients and how understanding of its physiology drives management of positive-pressure ventilation. To provide guidance of lung isolation, mechanical ventilator, pleural catheter, and endobronchial strategies for the management of bronchopleural fistula on mechanical ventilation. DATA SOURCES: Online search of PubMed and manual review of articles (laboratory and patient studies) was performed. STUDY SELECTION: Articles relevant to bronchopleural fistula, mechanical ventilation in patients with bronchopleural fistula, independent lung ventilation, high-flow ventilatory modes, physiology of persistent air leak, extracorporeal membrane oxygenation, fluid dynamics of bronchopleural fistula airflow, and intrapleural catheter management were selected. Randomized trials, observational studies, case reports, and physiologic studies were included. DATA EXTRACTION: Data from selected studies were qualitatively evaluated for this review. We included data illustrating the physiology of driving pressure across a bronchopleural fistula as well as data, largely from case reports, demonstrating management and outcomes with various ventilator modes, intrapleural catheter techniques, endoscopic placement of occlusion and valve devices, and extracorporeal membrane oxygenation. Themes related to managing persistent air leak with mechanical ventilation were reviewed and extracted. DATA SYNTHESIS: In case reports that demonstrate different approaches to managing patients with bronchopleural fistula requiring mechanical ventilation, common themes emerge. Strategies aimed at decreasing peak inspiratory pressure, using lower tidal volumes, lowering positive end-expiratory pressure, decreasing the inspiratory time, and decreasing the respiratory rate, while minimizing negative intrapleural pressure decreases airflow across the bronchopleural fistula. CONCLUSIONS: Mechanical ventilation and intrapleural catheter management must be individualized and aimed at reducing air leak. Clinicians should emphasize reducing peak inspiratory pressures, reducing positive end-expiratory pressure, and limiting negative intrapleural pressure. In refractory cases, clinicians can consider lung isolation, independent lung ventilation, or extracorporeal membrane oxygenation in appropriate patients as well as definitive management with advanced bronchoscopic placement of valves or occlusion devices.

Toxicity and antitumor activity of novel agents in elderly patients with cancer included in phase 1 studies.

Introduction The number of cancer cases among the elderly continue to increase as the worldwide population ages. This patient subset is underrepresented in clinical trials, partly because of unresolved uncertainties about age-associated tolerabilities and antitumor activities. We reviewed phase 1 trial data to study tolerance and efficacy of novel agents used for treatment of elderly patients with cancer. Methods Data from 773 consecutive evaluable patients in 85 phase 1 clinical trials (2008-2016) at START Madrid-CIOCC were analyzed according to age, with respect to objective response, survival, and toxicity. Results The mean age was 58.7 (range: 18-87) years; 260 (33.6%) patients were >65 y (elderly group). One hundred thirty-seven (17.8%) patients received immunotherapy drugs, 308 (39.8%) received targeted agents, and 328 (42.4%) received chemotherapy. No statistically significant differences in overall survival, objective response, or severe toxicity rates were found according to treatment type. Similar toxicities and clinical activities were found between the two age subgroups; 18.8% of the elderly and 20.7% of the younger patients experienced severe hematological toxicity (p=0.5), and 30.2% and 32.7%, respectively, experienced severe non-hematological toxicity (p=0.4). Regarding antitumor activity, 12.4% of the elderly and 15% of the younger patients achieved objective responses (p=0.41). There were no significant between-group differences in overall survival (9.7 versus 11.5 months, respectively, p=0.1) or progression-free survival (2.3 versus 2.2 months, respectively, p=0.7). Conclusions This retrospective study found that elderly and younger populations had comparable antitumor activities and toxicity profiles. These results support including elderly patients with cancer in early-phase trials.

Variations in hemoglobin measurement and eligibility criteria across blood donation services are associated with differing low-hemoglobin deferral rates: a BEST Collaborative study.

BACKGROUND: Determination of blood donor hemoglobin (Hb) levels is a pre-requisite to ensure donor safety and blood product quality. We aimed to identify Hb measurement practices across blood donation services and to what extent differences associate with low-Hb deferral rates. METHODS: An online survey was performed among Biomedical Excellence for Safer Transfusion (BEST) Collaborative members, extended with published data. Multivariable negative-binomial regression models were built to estimate adjusted associations of minimum donation intervals, Hb cut-offs (high, ≥13.5 g/dL in men or ≥ 12.5 g/dL in women, vs. lower values), iron monitoring (yes/no), providing or prescribing iron supplementation (yes/no), post-versus pre-donation Hb measurement and geographical location (Asian vs. rest), with low-Hb deferral rates. RESULTS: Data were included from 38 blood services. Low-Hb deferral rates varied from 0.11% to 8.81% among men and 0.84% to 31.85% among women. Services with longer minimum donation intervals had significantly lower deferral rates among both women (rate ratio, RR 0.53, 95%CI 0.33-0.84) and men (RR 0.53, 95%CI 0.31-0.90). In women, iron supplementation was associated with lower Hb deferral rates (RR 0.47, 95%CI 0.23-0.94). Finally, being located in Asia was associated with higher low-Hb deferral rates; RR 9.10 (95%CI 3.89-21.27) for women and 6.76 (95%CI 2.45-18.68) for men. CONCLUSION: Differences in Hb measurement and eligibility criteria, particularly longer donation intervals and iron supplementation in women, are associated with variations in low-Hb deferral rates. These insights could help improve both blood donation service efficiency and donor care.

Medium and long-term effects of low doses of Chlorpyrifos during the postnatal, preweaning developmental stage on sociability, dominance, gut microbiota and plasma metabolites.

Autism spectrum disorder (ASD) is a complex neurodevelopmental pathology characterized by altered verbalizations, reduced social interaction behavior, and stereotypies. Environmental factors have been associated with its development. Some researchers have focused on pesticide exposure. Chlorpyrifos (CPF) is the most used Organophosphate. Previous developmental studies with CPF showed decreased, enhanced or no effect on social outcomes eminently in mice. The study of CPF exposure during preweaning stages on social behavior is sparse in mice and non-existent in rats. d stressors could be at the basis of ASD development, and around postnatal day 10 in the rat is equivalent to the human birthday in neurodevelopmental terms. We explored the effects of exposure to low doses (1mg/kg/mL/day) of CPF during this stage regarding: sociability, dominance gut microbiome and plasma metabolomic profile, since alterations in these systems have also been linked to ASD. There was a modest influence of CPF on social behavior in adulthood, with null effects during adolescence. Dominance and hierarchical status were not affected by exposure. Dominance status explained the significant reduction in reaction to social novelty observed on the sociability test. CPF induced a significant gut microbiome dysbiosis and triggered a hyperlipidemic, hypoglycemic/hypogluconeogenesis and a general altered cell energy production in females. These behavioral results in rats extend and complement previous studies with mice and show novel influences on gut metagenomics and plasma lipid profile and metabolomics, but do not stablish a relation between the exposure to CPF and the ASD phenotype. The effects of dominance status on reaction to social novelty have an important methodological meaning for future research on sociability.

Semantic Segmentation of Natural Materials on a Point Cloud Using Spatial and Multispectral Features.

The characterization of natural spaces by the precise observation of their material properties is highly demanded in remote sensing and computer vision. The production of novel sensors enables the collection of heterogeneous data to get a comprehensive knowledge of the living and non-living entities in the ecosystem. The high resolution of consumer-grade RGB cameras is frequently used for the geometric reconstruction of many types of environments. Nevertheless, the understanding of natural spaces is still challenging. The automatic segmentation of homogeneous materials in nature is a complex task because there are many overlapping structures and an indirect illumination, so the object recognition is difficult. In this paper, we propose a method based on fusing spatial and multispectral characteristics for the unsupervised classification of natural materials in a point cloud. A high-resolution camera and a multispectral sensor are mounted on a custom camera rig in order to simultaneously capture RGB and multispectral images. Our method is tested in a controlled scenario, where different natural objects coexist. Initially, the input RGB images are processed to generate a point cloud by applying the structure-from-motion (SfM) algorithm. Then, the multispectral images are mapped on the three-dimensional model to characterize the geometry with the reflectance captured from four narrow bands (green, red, red-edge and near-infrared). The reflectance, the visible colour and the spatial component are combined to extract key differences among all existing materials. For this purpose, a hierarchical cluster analysis is applied to pool the point cloud and identify the feature pattern for every material. As a result, the tree trunk, the leaves, different species of low plants, the ground and rocks can be clearly recognized in the scene. These results demonstrate the feasibility to perform a semantic segmentation by considering multispectral and spatial features with an unknown number of clusters to be detected on the point cloud. Moreover, our solution is compared to other method based on supervised learning in order to test the improvement of the proposed approach.

Frameless radiosurgery for intraocular metastatic tumor: Case report.

AIM: The aim of this case report is to describe the technique and response using frameless radiosurgery technique in intraocular metastases. BACKGROUND: Intraocular metastases are the most common malignant lesion within the eye and its prevalence is probably underestimated. This is of great interest for oncologist as there are new treatment options with high rates of tumor control maintaining patient's quality of life. CASE REPORT: We report a case of a 54-year-old female with intraocular metastases from breast cancer using a frameless radiosurgery technique allowing organ preservation. CONCLUSION: The frameless robotic radiosurgery system is feasible and comfortable option for patients with intraocular metastases. Treatment planning and delivery requires an experienced interdisciplinary team.

Evaluation and optimization of a methodology for the long-term cryogenic storage of Tetradesmus obliquus at - 80 °C.

Cryopreservation is a common methodology for long-term microalgae storage. Current cryopreservation methods are based on using diverse cryoprotectants and two-step cooling protocols, followed by sample storage at the temperature of liquid nitrogen (- 196 °C). However, the use of this methodology requires a continuous liquid N2 supply as well as facilities with dedicated equipment, which is not affordable for every laboratory. In our work, we report on the successful development of a simple and cost-effective method for the long-term cryogenic storage of Tetradesmus obliquus at temperatures (- 80 °C) used in commonly available deep freezers that are more readily accessible to laboratories. Two procedures were evaluated that were originally devised for other microalgae; this was followed by the optimization of critical parameters such as the sample's microalgal concentration and the cryoprotectant reagent's incubation time. Cell viability was monitored using the survival rates obtained by direct agar plating and the growth recovery times in liquid cultures. Viability-related variables were recorded following different storage times of up to 3 years. The main operational factors involved in the process (cell concentration, incubation time, and storage time) were statistically analyzed with regard to their influence on the survival rate. The statistical analysis showed interdependence (a two-factor interaction) between the cellular concentration and the cryoprotectant's incubation time, on the one hand, and between the incubation time and the storage time on the other. Survival rates above 70% were obtained under optimized conditions after 3 months of storage, along with 20-35% viabilities after 3 years. These results open up the possibility of extending this method to other Scenedesmaceae, or even other microalgal species, and for its use in resource-limited laboratories.

Plasmodium genomics: an approach for learning about and ending human malaria.

Malaria causes high levels of morbidity and mortality in human beings worldwide. According to the World Health Organization (WHO), about half a million people die of this disease each year. Malaria is caused by six species of parasites belonging to the Plasmodium genus: P. falciparum, P. knowlesi, P. vivax, P. malariae, P. ovale curtisi, and P. ovale wallikeri. Currently, malaria is being kept under control with varying levels of elimination success in different countries. The development of new molecular tools as well as the use of next-generation sequencing (NGS) technologies and novel bioinformatic approaches has improved our knowledge of malarial epidemiology, diagnosis, treatment, vaccine development, and surveillance strategies. In this work, the genetics and genomics of human malarias have been analyzed. Since the first P. falciparum genome was sequenced in 2002, various population-level genetic and genomic surveys, together with transcriptomic and proteomic studies, have shown the importance of molecular approaches in supporting malaria elimination.

Whole genome sequencing-based analysis of tuberculosis (TB) in migrants: rapid tools for cross-border surveillance and to distinguish between recent transmission in the host country and new importations.

BackgroundThe analysis of transmission of tuberculosis (TB) is challenging in areas with a large migrant population. Standard genotyping may fail to differentiate transmission within the host country from new importations, which is key from an epidemiological perspective.AimTo propose a new strategy to simplify and optimise cross-border surveillance of tuberculosis and to distinguish between recent transmission in the host country and new importationsMethodsWe selected 10 clusters, defined by 24-locus mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR), from a population in Spain rich in migrants from eastern Europe, north Africa and west Africa and reanalysed 66 isolates by whole-genome sequencing (WGS). A multiplex-allele-specific PCR was designed to target strain-specific marker single nucleotide polymorphisms (SNPs), identified from WGS data, to optimise the surveillance of the most complex cluster.ResultsIn five of 10 clusters not all isolates showed the short genetic distances expected for recent transmission and revealed a higher number of SNPs, thus suggesting independent importations of prevalent strains in the country of origin. In the most complex cluster, rich in Moroccan cases, a multiplex allele-specific oligonucleotide-PCR (ASO-PCR) targeting the marker SNPs for the transmission subcluster enabled us to prospectively identify new secondary cases. The ASO-PCR-based strategy was transferred and applied in Morocco, demonstrating that the strain was prevalent in the country.ConclusionWe provide a new model for optimising the analysis of cross-border surveillance of TB transmission in the scenario of global migration.