Scalable Unsupervised Domain Adaptation for Electron Microscopy

While Machine Learning algorithms are key to automating organelle segmentation in large EM stacks, they require annotated data, which is hard to come by in sufficient quantities. Furthermore, images acquired from one part of the brain are not always representative of another due to the variability in the acquisition and staining processes. Therefore, a classifier trained on the first may perform poorly on the second and additional annotations may be required. To remove this cumbersome requirement, we introduce an Unsupervised Domain Adaptation approach that can leverage annotated data from one brain area to train a classifier that applies to another for which no labeled data is available. To this end, we establish noisy visual correspondences between the two areas and develop a Multiple Instance Learning approach to exploiting them. We demonstrate the benefits of our approach over several baselines for the purpose of synapse and mitochondria segmentation in EM stacks of different parts of mouse brains

A young infant with transient severe hypertriglyceridemia temporarily associated with meropenem administration : A case report and review of the literature

Background: Slight changes in the lipid profile can be observed over the acute phase of infectious diseases. Moreover, some antiinfective drugs can modify serum lipid concentrations, although antibiotics do not seem to have a relevant, direct, or acute effect on the lipid profile. Methods:A 75-day-old breastfed Caucasian female, born at term after a regular pregnancy, was hospitalized for osteomyelitis. She was immediately treated with intravenous meropenem and vancomycin. Therapy was effective, but after 22 days of treatment, her blood was found to be viscous with a purple shade. Results: A fasting blood sample showed serum triglycerides of 966mg/dL, total cholesterol of 258mg/dL, and high-density lipoprotein cholesterol of 15mg/dL. Secondary causes of hyperlipidemia and primary hereditary disorders were ruled out. Thereafter, the possibility that antibiotics may have had a role in the hypertriglyceridemia was considered, and meropenem was discontinued. After 72 hours of meropenem discontinuation, a sharp modification of lipid variables was observed, and further testing showed a complete normalization of the lipid profile. Conclusion: In this child with osteomyelitis, the increase in serum triglycerides appeared suddenly after 3 weeks of meropenem treatment and resolved quickly after meropenem discontinuation, thus highlighting the possible association between meropenem and lipid profile alterations. Monitoring the lipid profile should be considered in cases of long-term treatment with meropenem, and further studies on meropenem safety should include evaluation of the lipid profile

Cultivar-specific transcriptome prediction and annotation in Ficus carica L.

The availability of transcriptomic data sequence is a key step for functional genomics studies. Recently, a repertoire of predicted genes of a Japanese cultivar of fig (Ficus carica L.) was released. Because of the great phenotypic variability that can be found in this species, we decided to study another fig genotype, the Italian cv. Dottato, in order to perform comparative studies between the two cultivars and extend the pan genome of this species. We isolated, sequenced and assembled fig genomic DNA from young fruits of cv. Dottato. Then, putative gene sequences were predicted and annotated. Finally, a comparison was performed between cvs. Dottato and Horaishi predicted transcriptomes. Our data provide a resource (available at the Sequence Read Archive database under SRP109082) to be used for functional genomics of fig, in order to fill the gap of knowledge still existing in this species concerning plant development, defense and adaptation to the environment

Rapid and sensitive detection of mycobacterium ulcerans by use of a loop-mediated isothermal amplification test

This work reports the design and evaluation of a rapid loop-mediated isothermal amplification test for detecting Mycobacterium ulcerans DNA based on the multicopy insertion sequence IS2404. The test is robust and specific with a detection limit equivalent to 20 copies of the target sequence (0.01 to 0.1 genome). The test has potential for the diagnosis of Buruli ulcer under field conditions

Area-wide eradication of the invasive European grapevine moth Lobesia botrana in California, USA

17openBothIn the fall of 2009, the first confirmed North American detection of the European grapevine moth (EGVM) Lobesia botrana (Denis & Schiffermüller) occurred in Napa County, California, USA. Based on its status as a significant grape pest in other parts of the world, the establishment of EGVM in California presented significant production and export issues for grapes, as well as for other fresh market agricultural commodities. Over the following seven years, an intensive California state-wide survey and area-wide eradication campaign was undertaken in partnership with agricultural officials at local, state and federal levels, university scientists and the wine, table grape and raisin industries. These efforts resulted in a dramatic decline in moth captures in pheromone traps from over 100 000 moths in 2010, to one in 2014, and none in 2015. In August of 2016, eradication was declared for all previously infested areas in California. The decision to pursue the eradication effort was based on the limited host range and geographic area of the EGVM infestation, the availability of effective tools for monitoring and control, and the strong support of the affected grape production and export industries. The eradication campaign employed coordinated logistical, regulatory, and technical efforts that included: 1) state-wide-monitoring using a network of pheromone-baited traps and in field monitoring; these findings were recorded in a geographic information system that was used to regularly communicate survey results to programme officials; 2) an area-wide application of mating disruption dispensers to infested vineyards, including use in urban environments within infested zones; 3) implementation by coordinators of area-wide insecticide treatments with application timing determined by degree-day modelling for each infested region; 4) a robust regulatory programme that initiated and maintained a quarantine of infested areas that regulated movement of fruit, farming equipment and winery processing waste; 5) an extensive outreach programme to grape growers, wineries, pest control specialists and the public; 6) formation of a technical working group that provided recommendations to the operational programme. An extensive methods development effort supported the programme. This included developing enhanced detection methods for vineyards under mating disruption, testing efficacy and residual control of insecticides, testing mating disruption formulations, evaluating the impacts of winery processing methods on EGVM mortality, developing methods to determine the timing of the development of successive EGVM generations (or biofix) under California conditions to improve degree-day models, developing EGVM rearing methods, testing the quality of pheromone lures and trap monitoring; and a spatial analysis of trapping data to determine programme effectiveness and to analyse invasion pathwaysopenSimmons, G.S.; Varela, L.; Daugherty, M.; Cooper, M.; Lance, D.; Mastro, V.; Carde, R.T.; Lucchi, A.; Ioriatti, C.; Bagnoli, B.; Steinhauer, R.; Broadway, R.; Stone Smith, B.; Hoffman, K.; Clark, G.; Whitmer, D.; Johnson, R.Simmons, G.S.; Varela, L.; Daugherty, M.; Cooper, M.; Lance, D.; Mastro, V.; Carde, R.T.; Lucchi, A.; Ioriatti, C.; Bagnoli, B.; Steinhauer, R.; Broadway, R.; Stone Smith, B.; Hoffman, K.; Clark, G.; Whitmer, D.; Johnson, R

The International Thymic Malignancy Interest Group Classification of Thymoma Recurrence: Survival Analysis and Perspectives

Introduction: The International Thymic Malignancy Interest Group (ITMIG) classifies thymoma recurrences on the basis of the topographic location, but its effectiveness in prognosis prediction has not been well investigated yet. Aims of this study are to analyze survival outcome of patients surgically treated for thymoma recurrence according to the ITMIG recurrence classification and to investigate possible alternatives. Methods: From January 1, 1990, to January 7, 2017, data on 135 surgically treated patients for thymoma recurrence from three high-volume centers were collected and retrospectively analyzed. Patients were classified according to the ITMIG classification as local, regional, and distant. The ITMIG classification and alternative classifications were correlated to overall survival (OS). Results: According to the ITMIG classification, recurrence was local in 17 (12.5%), regional in 97 (71.8%), and distant in 21 (15.7%) patients, with single localization in 38 (28.2%) and multiple localizations in 97 (71.8%). The 5- and 10-year OS were 79.9% and 49.7% in local, 68.3% and 52.6% in regional, and 66.3% and 35.4% in distant recurrences, respectively, but differences were not statistically significant (p = 0.625). A significant difference in survival was present considering single versus multiple localizations: 5- and 10-year OS of 86.2% and 81.2% versus 61.3% and 31.5% (p = 0.005, hazard ratio = 7.22, 95% confidence interval: 0.147–0.740), respectively. Combining the localization number with the recurrence site, ITMIG locoregional single recurrence had a statistically significant better survival compared with patients with ITMIG locoregional multiple recurrence or ITMIG distant recurrence (p = 0.028). Similarly, a significant difference was present considering intrathoracic single versus intrathoracic multiple versus distant recurrence (p = 0.024). Conclusions: The ITMIG classification for thymoma recurrence did not have significant survival differences comparing local, regional, and distant recurrences. Integrating this classification with the number of the localizations may improve its effectiveness in prognosis prediction

Real-Time Fluorescence Loop Mediated Isothermal Amplification for the Diagnosis of Malaria

BACKGROUND: Molecular diagnostic methods can complement existing tools to improve the diagnosis of malaria. However, they require good laboratory infrastructure thereby restricting their use to reference laboratories and research studies. Therefore, adopting molecular tools for routine use in malaria endemic countries will require simpler molecular platforms. The recently developed loop-mediated isothermal amplification (LAMP) method is relatively simple and can be improved for better use in endemic countries. In this study, we attempted to improve this method for malaria diagnosis by using a simple and portable device capable of performing both the amplification and detection (by fluorescence) of LAMP in one platform. We refer to this as the RealAmp method. METHODOLOGY AND SIGNIFICANT FINDINGS: Published genus-specific primers were used to test the utility of this method. DNA derived from different species of malaria parasites was used for the initial characterization. Clinical samples of P. falciparum were used to determine the sensitivity and specificity of this system compared to microscopy and a nested PCR method. Additionally, directly boiled parasite preparations were compared with a conventional DNA isolation method. The RealAmp method was found to be simple and allowed real-time detection of DNA amplification. The time to amplification varied but was generally less than 60 minutes. All human-infecting Plasmodium species were detected. The sensitivity and specificity of RealAmp in detecting P. falciparum was 96.7% and 91.7% respectively, compared to microscopy and 98.9% and 100% respectively, compared to a standard nested PCR method. In addition, this method consistently detected P. falciparum from directly boiled blood samples. CONCLUSION: This RealAmp method has great potential as a field usable molecular tool for diagnosis of malaria. This tool can provide an alternative to conventional PCR based diagnostic methods for field use in clinical and operational programs