PathologyGAN: Learning deep representations of cancer tissue

We apply Generative Adversarial Networks (GANs) to the domain of digital pathology. Current machine learning research for digital pathology focuses on diagnosis, but we suggest a different approach and advocate that generative models could drive forward the understanding of morphological characteristics of cancer tissue. In this paper, we develop a framework which allows GANs to capture key tissue features and uses these characteristics to give structure to its latent space. To this end, we trained our model on 249K H&E breast cancer tissue images, extracted from 576 TMA images of patients from the Netherlands Cancer Institute (NKI) and Vancouver General Hospital (VGH) cohorts. We show that our model generates high quality images, with a Frechet Inception Distance (FID) of 16.65. We further assess the quality of the images with cancer tissue characteristics (e.g. count of cancer, lymphocytes, or stromal cells), using quantitative information to calculate the FID and showing consistent performance of 9.86. Additionally, the latent space of our model shows an interpretable structure and allows semantic vector operations that translate into tissue feature transformations. Furthermore, ratings from two expert pathologists found no significant difference between our generated tissue images from real ones. The code, generated images, and pretrained model are available at https://github.com/AdalbertoCq/Pathology-GANComment: MIDL 2020 final versio

A novel polymer of tubulin forms the conoid of Toxoplasma gondii

Toxoplasma gondii is an obligatory intracellular parasite, an important human pathogen, and a convenient laboratory model for many other human and veterinary pathogens in the phylum Apicomplexa, such as Plasmodium, Eimeria, and Cryptosporidia. 22 subpellicular microtubules form a scaffold that defines the cell shape of T. gondii. Its cytoskeleton also includes an intricate apical structure consisting of the conoid, two intraconoid microtubules, and two polar rings. The conoid is a 380-nm diameter motile organelle, consisting of fibers wound into a spiral like a compressed spring. FRAP analysis of transgenic T. gondii expressing YFP-α-tubulin reveals that the conoid fibers are assembled by rapid incorporation of tubulin subunits during early, but not late, stages of cell division. Electron microscopic analysis shows that in the mature conoid, tubulin is arranged into a novel polymer form that is quite different from typical microtubules

Influence of geography on language competition

Competition between languages or cultural traits diffusing in the same geographical area is studied combining the language competition model of Abrams and Strogatz and a human dispersal model on an inhomogeneous substrate. Also, the effect of population growth is discussed. It is shown through numerical experiments that the final configuration of the surviving language can be strongly affected by geographical and historical factors. These factors are not related to the dynamics of culture transmission, but rather to initial population distributions as well as geographical boundaries and inhomogeneities, which modulate the diffusion process.Comment: typos in contact information have been corrected - text/figures not change

Evidence for Circumpolar Distribution of Planktonic Archaea in the Southern Ocean

Surveys using rRNA-targeted probes specific for the 3 domains of life (Eucarya, Archaea, and Bacteria) indicated the presence, and at times high abundance, of archaeal rRNA in a variety of water masses surrounding Antarctica. Hybridization signals of archaeal rRNA contributed significantly to that of total picoplankton rRNA both north and south of the Polar Front in Drake Passage. Late winter surface water populations collected around the South Shetland Islands also yielded relatively high archaeal rRNA hybridization signals, approaching 10% or greater of the total rRNA. Summer samples collected in the western region of the Antarctic Peninsula and at McMurdo Sound in the Ross Sea region of Antarctica yielded lower amounts of archaeal rRNA in the surface waters, and higher levels of archaeal rRNA at depth (150 to 500 m). The hybridization data were compared to biological, chemical, and hydrographic information when possible. In surface waters, archaeal rRNA and chlorophyll a varied inversely. The data presented here further supports the hypothesis that planktonic archaea are a common, widespread and likely ecologically important component of Antarctic picoplankton assemblages. The presence of these archaea in circumpolar deep water suggests a conduit for their circumpolar transport around Antarctica via the Antarctic Circumpolar Current, as well as their export to the deep sea, or to intermediate waters of the South Atlantic via mixing at the polar front

Retropharyngeal Lymph Node Involvement in Oropharyngeal Carcinoma: Impact upon Risk of Distant Metastases and Survival Outcomes

The influence of retropharyngeal lymph node (RPLN) involvement on prognosis in oropharyngeal carcinoma remains poorly defined. The aim of this study was to assess the impact of RPLN involvement upon outcomes. A single-centre retrospective analysis of 402 patients with oropharyngeal carcinoma treated nonsurgically between 2010 and 2017 was performed. All had a baseline 2-[fluorine-18]-fluoro-2-deoxy-d-glucose (FDG) PET-CT and contrast-enhanced MRI and/or CT. RPLN status was determined by radiology review of cases with reported abnormal RPLN. Multivariate backwards logistic regression was used to examine impact on outcomes of factors. Abnormal RPLNs were identified in 40/402 (10%) of patients. Median follow up was 42.9 months. RPLN involvement was associated with inferior 3 year outcomes for overall survival (OS) (67.1% vs. 79.1%, p = 0.006) and distant metastases-free survival (DMFS) (73.9% versus 88.0%, p = 0.011), with no significant difference in local control (81.6% vs. 87.7%, p = 0.154) or regional control (80.7% vs. 85.4%, p = 0.252). On multivariate analysis abnormal RPLN, no concurrent chemotherapy and ongoing smoking were associated with inferior DMFS and OS, while advanced T stage was also associated with inferior OS. In summary, RPLN involvement, present in 10% of patients, was an independent prognostic factor for the development of distant disease failure translating into inferior OS. These findings need confirmation in future studies

An ensemble of specifically targeted proteins stabilizes cortical microtubules in the human parasite Toxoplasma gondii

Although all microtubules within a single cell are polymerized from virtually identical subunits, different microtubule populations carry out specialized and diverse functions, including directional transport, force generation, and cellular morphogenesis. Functional differentiation requires specific targeting of associated proteins to subsets or even subregions of these polymers. The cytoskeleton of Toxoplasma gondii, an important human parasite, contains at least five distinct tubulin-based structures. In this work, we define the differential localization of proteins along the cortical microtubules of T. gondii, established during daughter biogenesis and regulated by protein expression and exchange. These proteins distinguish cortical from mitotic spindle microtubules, even though the assembly of these subsets is contemporaneous during cell division. Finally, proteins associated with cortical microtubules collectively protect the stability of the polymers with a remarkable degree of functional redundancy

On Hilbert-Schmidt operator formulation of noncommutative quantum mechanics

This work gives value to the importance of Hilbert-Schmidt operators in the formulation of a noncommutative quantum theory. A system of charged particle in a constant magnetic field is investigated in this framework

Infectious Disease in a Warming World: How Weather Influenced West Nile Virus in the United States (2001–2005)

Background: The effects of weather on West Nile virus (WNV) mosquito populations in the United States have been widely reported, but few studies assess their overall impact on transmission to humans. Objectives: We investigated meteorologic conditions associated with reported human WNV cases in the United States. Methods: We conducted a case–crossover study to assess 16,298 human WNV cases reported to the Centers for Disease Control and Prevention from 2001 to 2005. The primary outcome measures were the incidence rate ratio of disease occurrence associated with mean weekly maximum temperature, cumulative weekly temperature, mean weekly dew point temperature, cumulative weekly precipitation, and the presence of ≥ 1 day of heavy rainfall (≥ 50 mm) during the month prior to symptom onset. Results: Increasing weekly maximum temperature and weekly cumulative temperature were similarly and significantly associated with a 35–83% higher incidence of reported WNV infection over the next month. An increase in mean weekly dew point temperature was significantly associated with a 9–38% higher incidence over the subsequent 3 weeks. The presence of at least 1 day of heavy rainfall within a week was associated with a 29–66% higher incidence during the same week and over the subsequent 2 weeks. A 20-mm increase in cumulative weekly precipitation was significantly associated with a 4–8% increase in incidence of reported WNV infection over the subsequent 2 weeks. Conclusions: Warmer temperatures, elevated humidity, and heavy precipitation increased the rate of human WNV infection in the United States independent of season and each others’ effects

Energy savings and economic benefits of transition towards efficient lighting in residential buildings in Cameroon

Lighting accounts for over 20% of electricity use in the residential sector of Cameroon. Due to the unreliable and inadequate energy supply in the country, there is a need for the efficient utilization of the available energy. This paper presents the current different technologies used for artificial lighting including the economic and environmental benefits associated with a switch from incandescent lighting to compact fluorescent lamp (CFL) and light emitting diode (LED) in residential dwellings in Buea, Cameroon. The study employed a survey of 100 residential dwellings in Buea. Results of the survey revealed that artificial lighting in dwellings is achieved through the use of the following technologies: incandescent lamps, CFLs and fluorescent tubes. The economic assessment for the substitution of incandescent lamps with CFL and LED considering an average daily lighting duration of six hours was also conducted using the net present value (NPV), benefit cost ratio (BCR), the simple payback period (PBP) and a life cycle cost analysis (LCC). The economic assessment revealed an NPV that ranges from $47 to$282.02, a BCR of 1.84 and a PBP of 0.17 year for the substitution of current incandescent lamps in dwellings with CFL while the substitution of incandescent lamps with LED revealed an NPV of the range $89.14 to$370, a BCR of 3.18 and a PBP of 1.92 years. The LED and incandescent technologies emerged with the lowest and highest LCC respectively. Substituting incandescent lamps with CFL and LED results in a reduction in lighting related greenhouse gas (GHG) emissions from dwellings by 66.6% and 83.3% respectively. From the results, a transition towards efficient lighting in the residential sector of Cameroon possesses great economic and environmental benefits. There is need for the government of Cameroon to expedite the uptake of LED through the formulation and implementation of favourable policies