SAMMate: a GUI tool for processing short read alignments in SAM/BAM format

<p>Abstract</p> <p>Background</p> <p>Next Generation Sequencing (NGS) technology generates tens of millions of short reads for each DNA/RNA sample. A key step in NGS data analysis is the short read alignment of the generated sequences to a reference genome. Although storing alignment information in the Sequence Alignment/Map (SAM) or Binary SAM (BAM) format is now standard, biomedical researchers still have difficulty accessing this information.</p> <p>Results</p> <p>We have developed a Graphical User Interface (GUI) software tool named SAMMate. SAMMate allows biomedical researchers to quickly process SAM/BAM files and is compatible with both single-end and paired-end sequencing technologies. SAMMate also automates some standard procedures in DNA-seq and RNA-seq data analysis. Using either standard or customized annotation files, SAMMate allows users to accurately calculate the short read coverage of genomic intervals. In particular, for RNA-seq data SAMMate can accurately calculate the gene expression abundance scores for customized genomic intervals using short reads originating from both exons and exon-exon junctions. Furthermore, SAMMate can quickly calculate a whole-genome signal map at base-wise resolution allowing researchers to solve an array of bioinformatics problems. Finally, SAMMate can export both a wiggle file for alignment visualization in the UCSC genome browser and an alignment statistics report. The biological impact of these features is demonstrated via several case studies that predict miRNA targets using short read alignment information files.</p> <p>Conclusions</p> <p>With just a few mouse clicks, SAMMate will provide biomedical researchers easy access to important alignment information stored in SAM/BAM files. Our software is constantly updated and will greatly facilitate the downstream analysis of NGS data. Both the source code and the GUI executable are freely available under the GNU General Public License at <url>http://sammate.sourceforge.net</url>.</p

Failure Behaviours of Steel Projectiles with Localised Melting Against Armour Plates

The surface remelting technology of high energy beam can locally weaken the case for controlled fragmentation,&nbsp;which may affect the survivability of the impacting projectiles. Failure behaviours of steel projectiles with melted&nbsp;layers grid normally perforating armour plates was investigated. The results reveal that shear fracture mainly occurs&nbsp;in the nose region of projectiles due to high loading, and the melting zone of projectiles can keep integrity with no&nbsp;damage, which means the survivability of projectile can be assured. Furthermore, an analytical model was proposed&nbsp;to the structural analysis of projectile, which is in accordance with the test results

Interrogating the superconductor Ca10(Pt4As8)(Fe2-xPtxAs2)5 Layer-by-layer

Ever since the discovery of high-Tc superconductivity in layered cuprates, the roles that individual layers play have been debated, due to difficulty in layer-by-layer characterization. While there is similar challenge in many Fe-based layered superconductors, the newly-discovered Ca10(Pt4As8)(Fe2As2)5 provides opportunities to explore superconductivity layer by layer, because it contains both superconducting building blocks (Fe2As2 layers) and intermediate Pt4As8 layers. Cleaving a single crystal under ultra-high vacuum results in multiple terminations: an ordered Pt4As8 layer, two reconstructed Ca layers on the top of a Pt4As8 layer, and disordered Ca layer on the top of Fe2As2 layer. The electronic properties of individual layers are studied using scanning tunneling microscopy/spectroscopy (STM/S), which reveals different spectra for each surface. Remarkably superconducting coherence peaks are seen only on the ordered Ca/Pt4As8 layer. Our results indicate that an ordered structure with proper charge balance is required in order to preserve superconductivity

Study on adaptive cycle life extension method of li-ion battery based on differential thermal voltammetry parameter decoupling

Battery aging leads to reduction in a battery’s cycle life, which restricts the development of energy storage technology. At present, the state of health (SOH) assessment technology, which is used to indicate the battery cycle life, has been widely studied. This paper tries to find a way to adjust the battery management system adaptively in order to prolong the battery cycle life with the change of SOH. In this paper, an improved Galvanostatic Intermittent Titration Technique (GITT) method is proposed to decouple the terminal voltage into overpotential (induced by total internal resistance) and stoichiometric drift (caused by battery aging, indicated by OCV). Based on improved GITT, the open circuit voltage-temperature change (OCV-dT/dV) characteristics of SOH are described more accurately. With such an accurate description of SOH change, the adaptive method to change the discharge and charge cut-off voltage is obtained, whose application can prolong battery cycle life. Experiments verify that, in the middle of a battery’s life-cycle, the adaptive method to change the discharge and charge cut-off voltage can effectively improve the cycle life of the battery. This method can be applied during the period of preventive maintenance in battery storage systems

Lifetime Prediction of DC-link Capacitors in Multiple Drives System Based on Simplified Analytical Modeling

Lifetime prediction of dc-link capacitors in a single drive has been discussed before, which indicates that the capacitor in a standard drive meets serious reliability challenges and in a slim drive does not. However, in most of the applications, drives are connected in parallel with the power grid. The large amount of harmonic distortion produced by nonlinearity drives may transmit and couple between grid and drives, which changes the stresses of devices as well as the dc-link filters. Therefore, the estimated results in a single drive cannot be extended to multiple drives any more. This article investigates the lifetime of dc-link capacitors in multiple drives system. First, by decoupling the interactions among grid-connected drives, a simplified equivalent circuit model and its analytical model to obtain the dc-link continuous current in multiple drives is proposed, which releases the designers from configuring the large simulation for multiple drives. Then, applying the lifetime prediction method, the lifetime of dc-link capacitors in multiple drives is investigated, in terms of types of drives, numbers of drives, and grid conditions. The results show that the lifetime of the standard drives extends in the multidrive systems and the lifetime of the slim drives decreases in the multidrive systems, which break the previous mind. Finally, based on the proposed analytical model and lifetime estimation method, the capacitor sizing from reliability aspect for multiple slim drives is given. The outcomes of the lifetime investigation could be a guideline for the design of the capacitive dc link in multidrive systems

Influence of Different Phenolic Fractions on Red Wine Astringency Based on Polyphenol/Protein Binding

The presence of phenolic compounds can make a great contribution to the perception of astringency in red wines based on their interactions with proteins. Human salivary protein and bovine serum albumin were used in this study to investigate the relationship between astringency and polyphenol composition.  The interactions between polyphenols and proteins were analysed by means of electrophoresis and fluorescence spectra, and they were further confirmed by sensory analysis. The results indicate that a positive correlation existed among the percentage of polymeric proanthocyanidins and the total phenols.  Additionally, astringent wine was generally identified as having a high percentage of polymeric fragments.  In comparison with other fractions, polymeric fractions exhibited the highest affinity for protein, and thus the highest astringency

A mouse model to distinguish NLRP6-mediated inflammasome-dependent and -independent functions

The NOD-like receptor (NLR) family pyrin domain containing 6 (NLRP6) serves as a sensor for microbial dsRNA or lipoteichoic acid (LTA) in intestinal epithelial cells (IECs), and initiating multiple pathways including inflammasome pathway and type I interferon (IFN) pathway, or regulating nuclear factor-κB (NF-κB) and mitogen-activated protein kinase (MAPK) pathways. NLRP6 can exert its function in both inflammasome-dependent and inflammasome-independent manners. However, there is no tool to distinguish the contribution of individual NLRP6-mediated pathway to the physiology and pathology in vivo. Here, we validated that Arg39 and Trp50 residues in the pyrin domain (PYD) of murine NLRP6 are required for ASC recruitment and inflammasome activation, but are not important for the RNA binding and PYD-independent NLRP6 oligomerization. We further generated th

Amino acid Formula induces Microbiota Dysbiosis and Depressive-Like Behavior in Mice

Amino acid formula (AAF) is increasingly consumed in infants with cow\u27s milk protein allergy; however, the long-term influences on health are less described. In this study, we established a mouse model by subjecting neonatal mice to an amino acid diet (AAD) to mimic the feeding regimen of infants on AAF. Surprisingly, AAD-fed mice exhibited dysbiotic microbiota and increased neuronal activity in both the intestine and brain, as well as gastrointestinal peristalsis disorders and depressive-like behavior. Furthermore, fecal microbiota transplantation from AAD-fed mice or AAF-fed infants to recipient mice led to elevated neuronal activations and exacerbated depressive-like behaviors compared to that from normal chow-fed mice or cow\u27s-milk-formula-fed infants, respectively. Our findings highlight the necessity to avoid the excessive use of AAF, which may influence the neuronal development and mental health of children