Notes

Very first total chloroplast genome with the uncommon healing seed Schnabelia tetrodonta.
We implemented the Self-Organizing Maps (SOMs) algorithm running efficiently on GPUs, and also provide several clustering methods of the resulting maps. We provide scripts and a use case to cluster macro-molecular conformations generated by molecular dynamics (MD) simulations.

The method is available on GitHub and distributed as a pip package.

[email protected].
[email protected].
Assessing the effect of statin therapy at hospital admission for COVID-19 on in-hospital mortality.

Retrospective observational study. Patients taking statins were 11 years older and had significantly more comorbidities than patients who were not taking statins. A genetic matching (GM) procedure was performed prior to analysis of the mortality risk. A Cox proportional hazards model was used for the cause-specific hazard (CSH) function, and a competing-risks Fine and Gray (FG) model was also used to study the direct effects of statins on risk.Data from reverse transcription-polymerase chain reaction-confirmed 2157 SARS-CoV-2-infected patients (1234 men, 923 women; age 67 y/o (IQR 54-78)) admitted to the hospital were retrieved from the clinical records in anonymized manner. 353 deaths occurred. 581 patients were taking statins. Univariate test after GM showed a significantly lower mortality rate in patients on statin therapy than the matched non-statin group (19.8% vs. 25.4%, χ2 with Yates continuity correction p = 0.027). The mortality rate was even lower in patients (n = 336) who maintained their statin treatments during hospitalization compared to the GM non-statin group (17.4%; p = 0.045). The Cox model applied to the CSH function (HR = 0.58(CI 0.39-0.89); p = 0.01) and the competing risks FG model (HR = 0.60(CI 0.39-0.92); p = 0.02) suggest that statins are associated with reduced COVID-19-related mortality.

A lower SARS-CoV-2 infection-related mortality was observed in patients treated with statin therapy prior to hospitalization. Statin therapy should not be discontinued due to the global concern of the pandemic or in patients hospitalized for COVID-19.
A lower SARS-CoV-2 infection-related mortality was observed in patients treated with statin therapy prior to hospitalization. Statin therapy should not be discontinued due to the global concern of the pandemic or in patients hospitalized for COVID-19.
The distribution of biological features strongly indicates their functional relevance. Compared to DNA-related features, deciphering the distribution of mRNA-related features is non-trivial due to the existence of isoform ambiguity and compositional diversity of mRNAs.

We propose here a rigorous statistical framework, MetaTX, for deciphering the distribution of mRNA-related features. Through a standardized mRNA model, MetaTX firstly unifies various mRNA transcripts of diverse compositions, and then corrects the isoform ambiguity by incorporating the overall distribution pattern of the features through an EM algorithm. MetaTX was tested on both simulated and real data. Results suggested that MetaTX substantially outperformed existing direct methods on simulated datasets, and that a more informative distribution pattern was produced for all the three datasets tested, which contain N 6-Methyladenosine sites generated by different technologies. MetaTX should make a useful tool for studying the distribution and functions of mRNA-related biological features, especially for mRNA modifications such as N 6-Methyladenosine.

The MetaTX R package is freely available at GitHub https//github.com/yue-wang-biomath/MetaTX.1.0.
The MetaTX R package is freely available at GitHub https//github.com/yue-wang-biomath/MetaTX.1.0.The neocortex is composed of layers. Whether layers constitute an essential framework for the formation of functional circuits is not well understood. We investigated the brain-wide input connectivity of vasoactive intestinal polypeptide (VIP) expressing neurons in the reeler mouse. This mutant is characterized by a migration deficit of cortical neurons so that no layers are formed. Still, neurons retain their properties and reeler mice show little cognitive impairment. We focused on VIP neurons because they are known to receive strong long-range inputs and have a typical laminar bias toward upper layers. In reeler, these neurons are more dispersed across the cortex. We mapped the brain-wide inputs of VIP neurons in barrel cortex of wild-type and reeler mice with rabies virus tracing. Innervation by subcortical inputs was not altered in reeler, in contrast to the cortical circuitry. Numbers of long-range ipsilateral cortical inputs were reduced in reeler, while contralateral inputs were strongly increased. Reeler mice had more callosal projection neurons. Hence, the corpus callosum was larger in reeler as shown by structural imaging. We argue that, in the absence of cortical layers, circuits with subcortical structures are maintained but cortical neurons establish a different network that largely preserves cognitive functions.
Applied research in machine learning progresses faster when a clean dataset is available and ready to use. Several datasets have been proposed and released over the years for specific tasks such as image classification, speech-recognition, and more recently for protein structure prediction. However, for the fundamental problem of RNA structure prediction, information is spread between several databases depending on the level we are interested in sequence, secondary structure, 3 D structure, or interactions with other macromolecules. In order to speed-up advances in machine-learning based approaches for RNA secondary and/or 3 D structure prediction, a dataset integrating all this information is required, to avoid spending time on data gathering and cleaning.

Here we propose the first attempt of a standardized and automatically generated dataset dedicated to RNA combining together RNA sequences, homology information (under the form of position-specific scoring matrices), and information derived by annotation of available 3 D structures (including secondary structure, canonical and non-canonical interactions, and backbone torsion angles). PF-3758309 manufacturer The data is retrieved from public databases PDB, Rfam and SILVA. The paper describes the procedure to build such dataset and the RNA structure descriptors we provide. Some statistical descriptions of the resulting dataset are also provided.

The dataset is updated every month and available online (in flat-text file format) on the EvryRNA software platform (https//evryrna.ibisc.univ-evry.fr/evryrna/rnanet). An efficient parallel pipeline to build the dataset is also provided for easy reproduction or modification.

[email protected], [email protected].
[email protected], [email protected].
Here's my website: https://www.selleckchem.com/products/pf-3758309.html