TULIP: An RNA-seq-based Primary Tumor Type Prediction Tool Using Convolutional Neural Networks.

Background: With cancer as one of the leading causes of death worldwide, accurate primary tumor type prediction is critical in identifying genetic factors that can inhibit or slow tumor progression. There have been efforts to categorize primary tumor types with gene expression data using machine learning, and more recently with deep learning, in the last several years. Methods: In this paper, we developed four 1-dimensional (1D) Convolutional Neural Network (CNN) models to classify RNA-seq count data as one of 17 highly represented primary tumor types or 32 primary tumor types regardless of imbalanced representation. Additionally, we adapted the models to take as input either all Ensembl genes (60,483) or protein coding genes only (19,758). Unlike previous work, we avoided selection bias by not filtering genes based on expression values. RNA-seq count data expressed as FPKM-UQ of 9,025 and 10,940 samples from The Cancer Genome Atlas (TCGA) were downloaded from the Genomic Data Commons (GDC) corresponding to 17 and 32 primary tumor types respectively for training and validating the models. Results: All 4 1D-CNN models had an overall accuracy of 94.7% to 97.6% on the test dataset. Further evaluation indicates that the models with protein coding genes only as features performed with better accuracy compared to the models with all Ensembl genes for both 17 and 32 primary tumor types. For all models, the accuracy by primary tumor type was above 80% for most primary tumor types. Conclusions: We packaged all 4 models as a Python-based deep learning classification tool called TULIP (TUmor CLassIfication Predictor) for performing quality control on primary tumor samples and characterizing cancer samples of unknown tumor type. Further optimization of the models is needed to improve the accuracy of certain primary tumor types.

Genomic mapping in outbred mice reveals overlap in genetic susceptibility for HZE ion- and γ-ray-induced tumors.

Cancer risk from galactic cosmic radiation exposure is considered a potential "showstopper" for a manned mission to Mars. Calculating the actual risks confronted by spaceflight crews is complicated by our limited understanding of the carcinogenic effects of high-charge, high-energy (HZE) ions, a radiation type for which no human exposure data exist. Using a mouse model of genetic diversity, we find that the histotype spectrum of HZE ion-induced tumors is similar to the spectra of spontaneous and γ-ray-induced tumors and that the genomic loci controlling susceptibilities overlap between groups for some tumor types. Where it occurs, this overlap indicates shared tumorigenesis mechanisms regardless of the type of radiation exposure and supports the use of human epidemiological data from γ-ray exposures to predict cancer risks from galactic cosmic rays.

Treatment of hereditary hypotrichosis simplex of the scalp with topical gentamicin.

BACKGROUND: Hypotrichosis simplex of the scalp (HSS) is characterized by progressive loss of scalp hair that results in almost complete baldness at a young age. HSS is often caused by dominant nonsense mutations in CDSN encoding corneodesmosin, leading to the formation of an amyloid-like material, which interferes with normal hair follicle cycle. OBJECTIVES: As gentamicin has been shown to mediate ribosomal read-through, we aimed to ascertain its therapeutic efficacy in a small series of patients carrying a recurrent mutation in CDSN . METHODS: We used a green fluorescence reporter assay system, confocal microscopy and Western blot analysis to ascertain in vitro the ability of gentamicin to induce translational read-through across a causative CDSN mutation. RESULTS: Using a reporter assay, we initially showed that gentamicin induces read-through activity across an HSS-causing nonsense mutation. Gentamicin was further shown to rescue corneodesmosin translation in primary keratinocytes obtained from a patient with HSS. To validate the in vitro data, we conducted a pilot clinical trial where the scalp of four patients was treated topically with gentamicin for 6 months, demonstrating significant improvement as ascertained by the Severity of Alopecia Tool score. CONCLUSIONS: Our findings indicate that topical gentamicin should be considered as a potential therapeutic modality in HSS. What's already known about this topic? Hypotrichosis simplex of the scalp (HSS) is caused by nonsense mutations in CDSN encoding corneodesmosin. The mutant corneodesmosin has been hypothesized to be toxic to the hair follicles, leading to hypotrichosis. Disorders caused by nonsense mutations are amenable to ribosomal read-through using gentamicin. What does this study add? Gentamicin enhanced read-through activity and promoted full-length corneodesmosin synthesis in primary keratinocytes derived from patients carrying a nonsense mutation in CDSN. Topical treatment with gentamicin was found to rescue the hypotrichosis phenotype partially in four patients with HSS. What is the translational message? Topical gentamicin should be considered as a potential treatment for HSS.

Publisher Correction: Magnetoelectric inversion of domain patterns.

Four incorrect figure citations in this Letter have been corrected online.

Magnetoelectric inversion of domain patterns.

The inversion of inhomogeneous physical states has great technological importance; for example, active noise reduction relies on the emission of an inverted sound wave that interferes destructively with the noise of the emitter1, and inverting the evolution of a spin system by using a magnetic-field pulse enables magnetic resonance tomography2. In contrast to these examples, inversion of a distribution of ferromagnetic or ferroelectric domains within a material is surprisingly difficult: field poling creates a single-domain state, and piece-by-piece inversion using a scanning tip is impractical. Here we report inversion of entire ferromagnetic and ferroelectric domain patterns in the magnetoelectric material Co3TeO6 and the multiferroic material Mn2GeO4, respectively. In these materials, an applied magnetic field reverses the magnetization or polarization, respectively, of each domain, but leaves the domain pattern intact. Landau theory indicates that this type of magnetoelectric inversion is universal across materials that exhibit complex ordering, with one order parameter holding the memory of the domain structure and another setting its overall sign. Domain-pattern inversion is only one example of a previously unnoticed effect in systems such as multiferroics, in which several order parameters are available for combination. Exploring these effects could therefore advance multiferroics towards new levels of functionality.

[Outcome of in utero transfusion in case of fœtomaternal red blood cell incompatibility]. / Devenir obstétrical après transfusion in utero pour allo-immunisation fœto-maternelle.

OBJECTIVE: Erythrocyte allo-immunization's rate has decreased but without adapted treatment the prognosis is still poor. The aim of our study was to evaluate the fetal prognosis, the complication's rate and the risk factors of complications of the intrauterine transfusion. METHODS: Retrospective study about 37 fetus and 86 intrauterine transfusions between 2001 and 2017. Our main criterion in judging was the occurrence of procedure related complications: premature membrane rupture or premature delivery within seven days from the procedure, chorioamnionitis, abnormal fetal heart rate indicating an emergency ceasarean section within the 24hours from the procedure, in utero death or neonatal death related to the procedure. RESULTS: The survival rate was about 88.9% with a severe complication's rate of 5.8% per intrauterine transfusion and 13.5% per pregnancy. Intrauterine transfusions before 18 weeks of pregnancies was a complication risk factor: 50% of complications before 18 weeks vs. 1.3%, P=0.8×10-3. On the contrary, hydrops did not seem to be a complication risk factor (16.7% of complication with hydrops vs. 3.9%, P=0.27). The localisation of the needle insertion, intra-abdominal or placental insertion, had no effect on the fetal prognosis. CONCLUSION: Intrauterine transfusion complications are rare and it enhances the fetal prognosis. However, an early procedure is related to a higher rate of complications.

Prevalence of anti-hepatitis B surface antibodies among children and adolescents vaccinated in infancy and effect of booster dose administered within a pilot study.

We determined the prevalence of anti-hepatitis B surface antibodies (anti-HBs) among children and adolescents vaccinated for hepatitis B virus in infancy as part of the routine vaccination programme. A representative serum sample of the Israeli population age 0-19 was tested. In a separate pilot study, a booster dose of hepatitis B vaccine was administered to 31 candidates for national service, who were fully vaccinated in infancy and tested negative for hepatitis B surface antibodies at age 17-19 years and anti-HBs antibodies were assessed 8 weeks later. Of the 1273 samples tested, 631 (49·6%) were positive to anti-HBs antibodies. Seropositivity rates were 89·5% among infants aged 6-12 months and declined significantly with age to 20·7% at age 19 years. No differences in seropositivity rates were observed between Jews and Arabs, males and females and those born in Israel and in other countries. Seroconversion rate among the 31 individuals who received a booster dose was 90·3% (95% CI: 75·1-96·6%). We recommend a booster dose for healthcare personnel before starting to work at the health care facility.

Draft sequencing and assembly of the genome of the world's largest fish, the whale shark: Rhincodon typus Smith 1828.

BACKGROUND: The whale shark (Rhincodon typus) has by far the largest body size of any elasmobranch (shark or ray) species. Therefore, it is also the largest extant species of the paraphyletic assemblage commonly referred to as fishes. As both a phenotypic extreme and a member of the group Chondrichthyes - the sister group to the remaining gnathostomes, which includes all tetrapods and therefore also humans - its genome is of substantial comparative interest. Whale sharks are also listed as an endangered species on the International Union for Conservation of Nature's Red List of threatened species and are of growing popularity as both a target of ecotourism and as a charismatic conservation ambassador for the pelagic ecosystem. A genome map for this species would aid in defining effective conservation units and understanding global population structure. RESULTS: We characterised the nuclear genome of the whale shark using next generation sequencing (454, Illumina) and de novo assembly and annotation methods, based on material collected from the Georgia Aquarium. The data set consisted of 878,654,233 reads, which yielded a draft assembly of 1,213,200 contigs and 997,976 scaffolds. The estimated genome size was 3.44Gb. As expected, the proteome of the whale shark was most closely related to the only other complete genome of a cartilaginous fish, the holocephalan elephant shark. The whale shark contained a novel Toll-like-receptor (TLR) protein with sequence similarity to both the TLR4 and TLR13 proteins of mammals and TLR21 of teleosts. The data are publicly available on GenBank, FigShare, and from the NCBI Short Read Archive under accession number SRP044374. CONCLUSIONS: This represents the first shotgun elasmobranch genome and will aid studies of molecular systematics, biogeography, genetic differentiation, and conservation genetics in this and other shark species, as well as providing comparative data for studies of evolutionary biology and immunology across the jawed vertebrate lineages.

Impact of blanching, sweating and drying operations on pungency, aroma and color of Piper borbonense.

Low pungency, high aromatic potential and red color, give to Piper borbonense its originality when compared to Piper nigrum. Effects of blanching, sweating and drying on these characteristics were assessed. The three operations had no impact on the concentration of piperine and essential oil but affected the composition of essential oil slightly and considerably affected the color of the pepper. The "wet process", including blanching, sweating and drying, had the largest impact on the composition of aroma, increasing para-cymene content by 89% and reducing safrole content by 33% in dried pepper compared to fresh. Blanching increased the drying rate thus reducing drying time. Drying had a major impact on color, which changed from red to brown. The biggest differences observed led to reductions of 2.2, 7.9 and 8.4units in L∗, a∗ and b∗ values, when chromatic values measured in fresh pepper were compared to those of dried pepper.

Modeling the spread of polio in an IPV-vaccinated population: lessons learned from the 2013 silent outbreak in southern Israel.

BACKGROUND: Polio eradication is an extraordinary globally coordinated health program in terms of its magnitude and reach, leading to the elimination of wild poliovirus (WPV) in most parts of the world. In 2013, a silent outbreak of WPV was detected in Israel, a country using an inactivated polio vaccine (IPV) exclusively since 2005. The outbreak was detected using environmental surveillance (ES) of sewage reservoirs. Stool surveys indicated the outbreak to be restricted mainly to children under the age of 10 in the Bedouin population of southern Israel. In order to curtail the outbreak, a nationwide vaccination campaign using oral polio vaccine (OPV) was conducted, targeting all children under 10. METHODS: A transmission model, fitted to the results of the stool surveys, with additional conditions set by the ES measurements, was used to evaluate the prevalence of WPV in Bedouin children and the effectiveness of the vaccination campaign. Employing the parameter estimates of the model fitting, the model was used to investigate the effect of alternative timings, coverages and dosages of the OPV campaign on the outcome of the outbreak. RESULTS: The mean estimate for the mean reproductive number was 1.77 (95 % credible interval, 1.46-2.30). With seasonal variation, the reproductive number maximum range was between zero and six. The mean estimate for the mean infectious periods was 16.8 (8.6-24.9) days. The modeling indicates the OPV campaign was effective in curtailing the outbreak. The mean estimate for the attack rate in Bedouin children under 10 at the end of 2014 was 42 % (22-65 %), whereas without the campaign the mean projected attack rate was 57 % (35-74 %). The campaign also likely shortened the duration of the outbreak by a mean estimate of 309 (2-846) days. A faster initiation of the OPV campaign could have reduced the incidence of WPV even if a lower coverage was reached, at the risk of prolonging the outbreak. CONCLUSIONS: OPV campaigns are essential for interrupting WPV transmission, even in a developed country setting with a high coverage of IPV. In this setting, establishing ES of WPV circulation is particularly crucial for early detection and containment of an outbreak.

Chlamydia psittaci comparative genomics reveals intraspecies variations in the putative outer membrane and type III secretion system genes.

Chlamydia psittaci is an obligate intracellular bacterium that can cause significant disease among a broad range of hosts. In humans, this organism may cause psittacosis, a respiratory disease that can spread to involve multiple organs, and in rare untreated cases may be fatal. There are ten known genotypes based on sequencing the major outer-membrane protein gene, ompA, of C. psittaci. Each genotype has overlapping host preferences and virulence characteristics. Recent studies have compared C. psittaci among other members of the Chlamydiaceae family and showed that this species frequently switches hosts and has undergone multiple genomic rearrangements. In this study, we sequenced five genomes of C. psittaci strains representing four genotypes, A, B, D and E. Due to the known association of the type III secretion system (T3SS) and polymorphic outer-membrane proteins (Pmps) with host tropism and virulence potential, we performed a comparative analysis of these elements among these five strains along with a representative genome from each of the remaining six genotypes previously sequenced. We found significant genetic variation in the Pmps and tbl3SS genes that may partially explain differences noted in C. psittaci host infection and disease.

Whole-genome analysis of Exserohilum rostratum from an outbreak of fungal meningitis and other infections.

Exserohilum rostratum was the cause of most cases of fungal meningitis and other infections associated with the injection of contaminated methylprednisolone acetate produced by the New England Compounding Center (NECC). Until this outbreak, very few human cases of Exserohilum infection had been reported, and very little was known about this dematiaceous fungus, which usually infects plants. Here, we report using whole-genome sequencing (WGS) for the detection of single nucleotide polymorphisms (SNPs) and phylogenetic analysis to investigate the molecular origin of the outbreak using 22 isolates of E. rostratum retrieved from 19 case patients with meningitis or epidural/spinal abscesses, 6 isolates from contaminated NECC vials, and 7 isolates unrelated to the outbreak. Our analysis indicates that all 28 isolates associated with the outbreak had nearly identical genomes of 33.8 Mb. A total of 8 SNPs were detected among the outbreak genomes, with no more than 2 SNPs separating any 2 of the 28 genomes. The outbreak genomes were separated from the next most closely related control strain by ∼136,000 SNPs. We also observed significant genomic variability among strains unrelated to the outbreak, which may suggest the possibility of cryptic speciation in E. rostratum.

Microbial biofilms on needleless connectors for central venous catheters: comparison of standard and silver-coated devices collected from patients in an acute care hospital.

Microorganisms may colonize needleless connectors (NCs) on intravascular catheters, forming biofilms and predisposing patients to catheter-associated infection (CAI). Standard and silver-coated NCs were collected from catheterized intensive care unit patients to characterize biofilm formation using culture-dependent and culture-independent methods and to investigate the associations between NC usage and biofilm characteristics. Viable microorganisms were detected by plate counts from 46% of standard NCs and 59% of silver-coated NCs (P=0.11). There were no significant associations (P>0.05, chi-square test) between catheter type, side of catheter placement, number of catheter lumens, site of catheter placement, or NC placement duration and positive NC findings. There was an association (P=0.04, chi-square test) between infusion type and positive findings for standard NCs. Viable microorganisms exhibiting intracellular esterase activity were detected on >90% of both NC types (P=0.751), suggesting that a large percentage of organisms were not culturable using the conditions provided in this study. Amplification of the 16S rRNA gene from selected NCs provided a substantially larger number of operational taxonomic units per NC than did plate counts (26 to 43 versus 1 to 4 operational taxonomic units/NC, respectively), suggesting that culture-dependent methods may substantially underestimate microbial diversity on NCs. NC bacterial communities were clustered by patient and venous access type and may reflect the composition of the patient's local microbiome but also may contain organisms from the health care environment. NCs provide a portal of entry for a wide diversity of opportunistic pathogens to colonize the catheter lumen, forming a biofilm and increasing the potential for CAI, highlighting the importance of catheter maintenance practices to reduce microbial contamination.

Isolation and molecular characterization of Fikirini rhabdovirus, a novel virus from a Kenyan bat.

Zoonotic and vector-borne pathogens have comprised a significant component of emerging human infections in recent decades, and bats are increasingly recognized as reservoirs for many of these disease agents. To identify novel pathogens associated with bats, we screened tissues of bats collected in Kenya. Virus isolates were identified by next generation sequencing of viral nucleic acid preparations from the infected cell culture supernatant and characterized. Here we report the identification of Fikirini rhabdovirus, a novel rhabdovirus isolated from a bat, Hipposideros vittatus, captured along the Kenyan coast.

Electrical monitoring of polyelectrolyte multilayer formation by means of capacitive field-effect devices.

The semiconductor field-effect platform represents a powerful tool for detecting the adsorption and binding of charged macromolecules with direct electrical readout. In this work, a capacitive electrolyte-insulator-semiconductor (EIS) field-effect sensor consisting of an Al-p-Si-SiO2 structure has been applied for real-time in situ electrical monitoring of the layer-by-layer formation of polyelectrolyte (PE) multilayers (PEM). The PEMs were deposited directly onto the SiO2 surface without any precursor layer or drying procedures. Anionic poly(sodium 4-styrene sulfonate) and cationic weak polyelectrolyte poly(allylamine hydrochloride) have been chosen as a model system. The effect of the ionic strength of the solution, polyelectrolyte concentration, number and polarity of the PE layers on the characteristics of the PEM-modified EIS sensors have been studied by means of capacitance-voltage and constant-capacitance methods. In addition, the thickness, surface morphology, roughness and wettabilityof the PE mono- and multilayers have been characterised by ellipsometry, atomic force microscopy and water contact-angle methods, respectively. To explain potential oscillations on the gate surface and signal behaviour of the capacitive field-effect EIS sensor modified with a PEM, a simplified electrostatic model that takes into account the reduced electrostatic screening of PE charges by mobile ions within the PEM has been proposed and discussed.

Impedance spectroscopy with field-effect transistor arrays for the analysis of anti-cancer drug action on individual cells.

In this study, impedance spectroscopy measurements of silicon-based open-gate field-effect transistor (FET) devices were utilized to study the adhesion status of cancer cells at a single cell level. We developed a trans-impedance amplifier circuit for the FETs with a higher bandwidth compared to a previously described system. The new system was characterized with a fast lock-in amplifier, which enabled measuring of impedance spectra up to 50 MHz. We studied cellular activities, including cell adhesion and anti-cancer drug induced apoptosis of human embryonic kidney (HEK293) and human lung adenocarcinoma epithelial (H441) cells. A well-known chemotherapeutic drug, topotecan hydrochloride, was used to investigate the effect of this drug to tumor cells cultured on the FET devices. The presence of the drug resulted in a 20% change in the amplitude of the impedance spectra at 200 kHz as a result of the induced apoptosis process. Real-time impedance measurements were performed inside an incubator at a constant frequency. The experimental results can be interpreted with an equivalent electronic circuit to resolve the influence of the system parameters. The developed method could be applied for the analysis of the specificity and efficacy of novel anti-cancer drugs in cancer therapy research on a single cell level in parallelized measurements.

Monte Carlo model of the scanning beam digital x-ray (SBDX) source.

The scanning-beam digital x-ray (SBDX) system has been developed for fluoroscopic imaging using an inverse x-ray imaging geometry. The SBDX system consists of a large-area x-ray source with a multihole collimator and a small detector. The goal of this study was to build a Monte Carlo (MC) model of the SBDX source as a useful tool for optimization of the SBDX imaging system in terms of its hardware components and imaging parameters. The MC model of the source was built in the EGSnrc/BEAMnrc code and validated using the DOSXYZnrc code and Gafchromic film measurements for 80, 100, and 120 kV x-ray source voltages. The MC simulated depth dose curves agreed with measurements to within 5%, and beam profiles at three selected depths generally agreed within 5%. Exposure rates and half-value layers for three voltages were also calculated from the MC simulations. Patient skin-dose per unit detector-dose was quantified as a function of patient size for all three x-ray source voltages. The skin-dose to detector-dose ratio ranged from 5-10 for a 20 cm thick patient to 1 × 10(3)-1 × 10(5) for a 50 cm patient for the 120 and 80 kV beams, respectively. Simulations of imaging dose for a prostate patient using common imaging parameters revealed that skin-dose per frame was as low as 0.2 mGy.

Investigation of the first laboratory-acquired human cowpox virus infection in the United States.

BACKGROUND: Cowpox virus is an Orthopoxvirus that can cause infections in humans and a variety of animals. Infections occur in Eurasia; infections in humans and animals have not been reported in the United States. This report describes the occurrence of the first known human case of laboratory-acquired cowpox virus infection in the United States and the ensuing investigation. METHODS: The patient and laboratory personnel were interviewed, and laboratory activities were reviewed. Real-time polymerase chain reaction (PCR) and serologic assays were used to test the patient's specimens. PCR assays were used to test specimens obtained during the investigation. RESULTS: A specimen from the patient's lesion tested positive for cowpox virus DNA. Genome sequencing revealed a recombinant region consistent with a strain of cowpox virus stored in the research laboratory's freezer. Cowpox virus contamination was detected in 6 additional laboratory stocks of viruses. Orthopoxvirus DNA was present in 3 of 20 environmental swabs taken from laboratory surfaces. CONCLUSIONS: The handling of contaminated reagents or contact with contaminated surfaces was likely the mode of transmission. Delays in recognition and diagnosis of this infection in a laboratory researcher underscore the importance of a thorough patient history-including occupational information-and laboratory testing in facilitating a prompt investigation and application of control and remediation measures.