RevelsMD: Reduced Variance Estimators of the Local Structure in Molecular Dynamics

RevelsMD is a new open source Python library, which uses reduced variance force sampling based estimators to calculate 3D particle densities and radial distribution functions from molecular dynamics simulations. This short note describes the scientific background of the code, its utility and how it fits within the current zeitgeist in computational chemistry and materials science.Comment: 3 page note describing an open source cod

Hamartomas, teratomas and teratocarcinosarcomas of the head and neck: Report of 3 new cases with clinico-pathologic correlation, cytogenetic analysis, and review of the literature

<p>Abstract</p> <p>Background</p> <p>Germ-cell tumors (GCT) are a histologically and biologically diverse group of neoplasms which primarily occur in the gonads but also develop at different extragonadal sites in the midline of the body. The head and neck region including the upper respiratory tract is a very rare location for such tumors in both children and adults, which can cause diagnostic and therapeutic difficulties.</p> <p>Methods</p> <p>We describe here two new cases of multilineage tumors including sinonasal teratocarcinosarcoma [SNTCS], and congenital oronasopharyngeal teratoma (epignathus) and compare their features with those of a new case of a rare salivary gland anlage tumor [SGAT], an entity for which the pathogenesis is unclear (i.e. hamartoma versus neoplasm). We correlate their presenting clinico-pathological features and compare histologic and cytogenetic features in an attempt to elucidate their pathogenesis and biologic potentials.</p> <p>Results and discussion</p> <p>Cytogenetic analysis revealed chromosomal abnormalities only in the case of SNTCS that showed trisomy 12 and 1p deletion. Both cytogenetic abnormalities are characteristically present in malignant germ cell tumors providing for the first time evidence that this rare tumor type indeed might represent a variant of a germ cell neoplasm. The SGAT and epignathus carried no such cytogenetic abnormalities, in keeping with their limited and benign biologic potential.</p> <p>Conclusion</p> <p>The comparison of these three cases should serve to emphasize the diversity of multilineage tumors (hamartomas and GCT) of the upper respiratory tract in regards to their biology, age of presentation and clinical outcomes. Malignant tumors of germ cell origins are more likely to affect adults with insidious symptom development, while benign tumors can nevertheless cause dramatic clinical symptoms which, under certain circumstances, can be fatal.</p

Genome-enabled insights into the biology of thrips as crop pests

Background The western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber, and ornamental crops. The underlying genetic mechanisms of the processes governing thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance are largely unknown. To address this gap, we present the F. occidentalis draft genome assembly and official gene set. Results We report on the first genome sequence for any member of the insect order Thysanoptera. Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size = 415.8 Mb, scaffold N50 = 948.9 kb) revealed a relatively complete and well-annotated assembly in comparison to other insect genomes. The genome is unusually GC-rich (50%) compared to other insect genomes to date. The official gene set (OGS v1.0) contains 16,859 genes, of which ~ 10% were manually verified and corrected by our consortium. We focused on manual annotation, phylogenetic, and expression evidence analyses for gene sets centered on primary themes in the life histories and activities of plant-colonizing insects. Highlights include the following: (1) divergent clades and large expansions in genes associated with environmental sensing (chemosensory receptors) and detoxification (CYP4, CYP6, and CCE enzymes) of substances encountered in agricultural environments; (2) a comprehensive set of salivary gland genes supported by enriched expression; (3) apparent absence of members of the IMD innate immune defense pathway; and (4) developmental- and sex-specific expression analyses of genes associated with progression from larvae to adulthood through neometaboly, a distinct form of maturation differing from either incomplete or complete metamorphosis in the Insecta. Conclusions Analysis of the F. occidentalis genome offers insights into the polyphagous behavior of this insect pest that finds, colonizes, and survives on a widely diverse array of plants. The genomic resources presented here enable a more complete analysis of insect evolution and biology, providing a missing taxon for contemporary insect genomics-based analyses. Our study also offers a genomic benchmark for molecular and evolutionary investigations of other Thysanoptera species

Homéogènes et troubles psychiatriques d origine neurodéveloppementale (caractérisation comportementale d un modèle de souris haplo-insuffisante pour Otx2)

Le spectre des troubles neurodéveloppementaux regroupe l ensemble des pathologies dont l origine est en rapport avec une anomalie du développement cérébral.L existence d un important recouvrement épidémiologique, clinique et génétique est en faveur d un continuum entre ces pathologies qui pourraient partager des étiologies communes aussi bien génétiques qu environnementales.Les homéogènes codent pour des facteurs de transcription. Ils sont exprimés précocement pendant l embryogénèse et coordonnent le développement cérébral. Le résultat le plus robuste de la revue de la littérature, que nous avons réalisé, entre les pathologies neurodéveloppementales et les mutations des homéogènes est l association entre deux polymorphismes d Engrailed 2 et l autisme.L homéogène Otx2 est impliqué dans l organisation et la différenciation de structures cérébrales et de systèmes de neurotransmission pour lesquels des anomalies ont été décrites dans plusieurs pathologies psychiatriques. Nous avons évalué dans le modèle murin Otx2GFP/+, où un allèle du gène a été inactivé, l apparition de traits comportementaux en rapport avec la cognition, l anxiété, la dépression, la psychose ainsi que les capacités motrices et sociales. Nous avons mis en évidence au cours de ces tests que les souris hétérozygotes présentaient un niveau d anxiété plus faible que les sauvages ainsi qu une vulnérabilité pour les troubles psychotiques. Ces résultats permettent de progresser dans la connaissance de l implication des homéogènes dans la physiopathologie de ces troubles et ouvrent de nouvelles perspectives de recherchePARIS6-Bibl.Pitié-Salpêtrie (751132101) / SudocSudocFranceF

Bandwidth Manipulated Leaky-Wave Antenna using a Sinusoidal Ridge in Folded Substrate Integrated Waveguide

The impedance bandwidth for leaky-wave antennas (LWAs) is usually very broad, leading to wide signal interference from unwanted spectrums. For instance, the uplink signals will cause jamming effect to the downlink for Satellite communication systems. Hence, an integrated LWA with a bandpass filter is proposed in this paper. A folded substrate integrated waveguide (FSIW) LWA is utilized to reduce the SIW width to build a 2D LWA array with low side lobes. Periodic fan-shaped slots are etched on the top of the FSIW for circular polarization in a band centered at 11.5 GHz. A bandpass filter is investigated by elaborating a sinusoidal ridge in the FSIW LWA. It has been successfully validated through full-wave simulation that the bandpass filtering can be manipulated by varying the amplitude of the sine curve, whereas the circular polarization is well maintained. The proposed antenna is a very promising candidate for next-generation satellite communication systems