piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing

MOTIVATION: PIWI-interacting RNAs (piRNAs), 23-36 nt small silencing RNAs, repress transposon expression in the metazoan germ line, thereby protecting the genome. Although high-throughput sequencing has made it possible to examine the genome and transcriptome at unprecedented resolution, extracting useful information from gigabytes of sequencing data still requires substantial computational skills. Additionally, researchers may analyze and interpret the same data differently, generating results that are difficult to reconcile. To address these issues, we developed a coordinated set of pipelines, \u27piPipes\u27, to analyze piRNA and transposon-derived RNAs from a variety of high-throughput sequencing libraries, including small RNA, RNA, degradome or 7-methyl guanosine cap analysis of gene expression (CAGE), chromatin immunoprecipitation (ChIP) and genomic DNA-seq. piPipes can also produce figures and tables suitable for publication. By facilitating data analysis, piPipes provides an opportunity to standardize computational methods in the piRNA field. SUPPLEMENTARY INFORMATION: Supplementary information, including flowcharts and example figures for each pipeline, are available at Bioinformatics online. AVAILABILITY AND IMPLEMENTATION: piPipes is implemented in Bash, C++, Python, Perl and R. piPipes is free, open-source software distributed under the GPLv3 license and is available at http://bowhan.github.io/piPipes/. CONTACT: [email protected] or [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Potentiometric titration curves of aluminium salt solutions and its species conversion in the hydrolysis-polymerization course

A new concept of critical point is expounded by analysing the potentiometric titration curves of aluminium salt solutions under the moderate slow rate of base injection. The critical point is defined as the characteristic spot of the Al3+ salt solutions potentiometric titration curve, which is related to the experiment conditions. In addition, the changes of critical points reflect the influence of experiment conditions on the course of the hydrolysis-polymerization and the conversion of hydroxyl polynuclear aluminum species. According to the OH/Al mole ratio, the Al species can be divided into four regions quantitatively by three characteristic points on the titration curves: Part I, Al3+/Ala region, consist chiefly of Al3+ and mononuclear Al; Part II, the small/middle polynuclear Al region, including Al2-Al12; Part III, the large-size polynuclear aluminum region, consistent with predominantly Al13-Al54 and a little sol/gel Al(OH)3; Part IV, the dissolving region of sol/gel Alc, only Al(OH)3 (aq or am) and Al(OH)4- species, which set up a base to study on the hydrolysis-polymerization of Al3+. At the same time, significant effects of total aluminum concentration, temperature, halide ion, silicate radical, and organic acid radical on the titration curves and its critical points were observed. Given the three critical points which demarcating the aluminum forms, we carry out a through investigation into the fundamental regulations of these factors’ influence, and offer a fresh train of thought to study the hydrolysis-polymerization of Al3+ in soil solutions. KEY WORDS: Potentiometric titration, Hydroxyl polynuclear aluminum species, Hydrolysis-polymerization, Critical point, Factors affecting titration curves  Bull. Chem. Soc. Ethiop. 2008, 22(2), 155-164

Effect of Nb Additive on the Dynamic Compression Property of a Zr-Ta Alloy

In this paper, Ta50-Zr50 and Ta45-Zr45-Nb10 alloys were compounded by casting. Quasi-static and dynamic compression tests were applied for both alloys, and also the role of Nb additive on the mechanical property of Zr-Ta alloy, was studied. The microstructure characterization demonstrated that both alloys had relative homogeneous structure with micro-laminate structure inside grains. The Nb additives increased the strength of the alloy by various strain rates, while the ductility of the alloys was decreased. The various parameters of constitutive equations for both alloys were obtained by fitting data. The constitutive equations are applied in theoretical models, the simulation software helps to predict the strength of alloy through various strain rates

Well pattern optimization based on StoSAG algorithm

The well pattern optimization in the oilfield is challenging and intricate work due to the heterogeneity of the permeability and viscosity. Traditionally, the well pattern optimization is conducted by comparing the results of several plans manually designed by the reservoir engineer, which is difficult to obtain the optimal well pattern. To address these challenges, a framework that integrates a reservoir simulator into the StoSAG algorithm is proposed. The well pattern operators proposed by Onwunalu and Durlofsy are applied to obtain the variations of the well pattern and used as the optimization variables. During the framework, the optimization variables are continuously adjusted by the StoSAG algorithm in order to obtain the optimal one which maximize the objective function value. The framework is applied to a synthetic reservoir. The results show that the StoSAG algorithm can be successfully applied in the well pattern optimization and remarkably improve the development effect. This method can be widely used in new oilfield development plan and offer reference for well pattern deployment.Cited as: Wang, S., Li, Z., Wang, S., Han, X. Well pattern optimization based on StoSAG algorithm. Advances in Geo-energy Research, 2018, 2(1): 103-112, doi: 10.26804/ager.2018.01.0

Twins:Device-free Object Tracking using Passive Tags

Without requiring objects to carry any transceiver, device-free based object tracking provides a promising solution for many localization and tracking systems to monitor non-cooperative objects such as intruders. However, existing device-free solutions mainly use sensors and active RFID tags, which are much more expensive compared to passive tags. In this paper, we propose a novel motion detection and tracking method using passive RFID tags, named Twins. The method leverages a newly observed phenomenon called critical state caused by interference among passive tags. We contribute to both theory and practice of such phenomenon by presenting a new interference model that perfectly explains this phenomenon and using extensive experiments to validate it. We design a practical Twins based intrusion detection scheme and implement a real prototype with commercial off-the-shelf reader and tags. The results show that Twins is effective in detecting the moving object, with low location error of 0.75m in average

Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs

Small silencing RNAs, including microRNAs, endogenous small interfering RNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs), have been shown to play important roles in fine-tuning gene expression, defending virus and controlling transposons. Loss of small silencing RNAs or components in their pathways often leads to severe developmental defects, including lethality and sterility. Recently, non-templated addition of nucleotides to the 3\u27 end, namely tailing, was found to associate with the processing and stability of small silencing RNAs. Next Generation Sequencing has made it possible to detect such modifications at nucleotide resolution in an unprecedented throughput. Unfortunately, detecting such events from millions of short reads confounded by sequencing errors and RNA editing is still a tricky problem. Here, we developed a computational framework, Tailor, driven by an efficient and accurate aligner specifically designed for capturing the tailing events directly from the alignments without extensive post-processing. The performance of Tailor was fully tested and compared favorably with other general-purpose aligners using both simulated and real datasets for tailing analysis. Moreover, to show the broad utility of Tailor, we used Tailor to reanalyze published datasets and revealed novel findings worth further experimental validation. The source code and the executable binaries are freely available at https://github.com/jhhung/Tailor

The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology

We report a draft assembly of the genome of Hi5 cells from the lepidopteran insect pest, Trichoplusia ni, assigning 90.6% of bases to one of 28 chromosomes and predicting 14,037 protein-coding genes. Chemoreception and detoxification gene families reveal T. ni-specific gene expansions that may explain its widespread distribution and rapid adaptation to insecticides. Transcriptome and small RNA data from thorax, ovary, testis, and the germline-derived Hi5 cell line show distinct expression profiles for 295 microRNA- and \u3e 393 piRNA-producing loci, as well as 39 genes encoding small RNA pathway proteins. Nearly all of the W chromosome is devoted to piRNA production, and T. ni siRNAs are not 2 -O-methylated. To enable use of Hi5 cells as a model system, we have established genome editing and single-cell cloning protocols. The T. ni genome provides insights into pest control and allows Hi5 cells to become a new tool for studying small RNAs ex vivo

Investigating the mechanism of rough phenotype in a naturally attenuated Brucella strain: insights from whole genome sequencing

ObjectiveBrucellosis, a significant zoonotic disease, not only impacts animal health but also profoundly influences the host immune responses through gut microbiome. Our research focuses on whole genome sequencing and comparative genomic analysis of these Brucella strains to understand the mechanisms of their virulence changes that may deepen our comprehension of the host immune dysregulation.MethodsThe Brucella melitensis strain CMCC55210 and its naturally attenuated variant CMCC55210a were used as models. Biochemical identification tests and in vivo experiments in mice verified the characteristics of the strain. To understand the mechanism of attenuation, we then performed de novo sequencing of these two strains.ResultsWe discovered notable genomic differences between the two strains, with a key single nucleotide polymorphism (SNP) mutation in the manB gene potentially altering lipopolysaccharide (LPS) structure and influencing host immunity to the pathogen. This mutation might contribute to the attenuated strain's altered impact on the host's macrophage immune response, overing insights into the mechanisms of immune dysregulation linked to intracellular survival. Furthermore, we explore that manipulating the Type I restriction-modification system in Brucella can significantly impact its genome stability with the DNA damage response, consequently affecting the host's immune system.ConclusionThis study not only contributes to understanding the complex relationship between pathogens, and the immune system but also opens avenues for innovative therapeutic interventions in inflammatory diseases driven by microbial and immune dysregulation

A Large Portal Vein: A Rare Finding of Recent Portal Vein Thrombosis

Acute portal vein thrombosis (PVT) is rarely encountered by clinicians. The most common manifestation of acute PVT is sudden onset of abdominal pain. A computed tomography scan without contrast often shows a high-density material in the portal vein. After injection of contrast agents, absence of luminal enhancement and enlargement of the obstructed portal vein are shown. In this case report, we demonstrated a rare computed tomography finding in which the diameter of the main portal vein was enormously distended to 3-fold that of the aorta in a patient with recent PVT. Despite thrombolysis and anticoagulation were immediately given, portal venous recanalization was not achieved in the patient. After 5 years, variceal bleeding and ascites occurred and liver function had persistently deteriorated. Finally, he died of progressive liver failure. Considering this case, we suggest that an early decision for invasive interventional treatment might be necessary to both increase the rate of portal venous recanalization and improve prognosis, as anticoagulation and thrombolysis therapy failed to recanalize recent PVT