BOAT: Basic Oligonucleotide Alignment Tool

<p>Abstract</p> <p>Background</p> <p>Next-generation DNA sequencing technologies generate tens of millions of sequencing reads in one run. These technologies are now widely used in biology research such as in genome-wide identification of polymorphisms, transcription factor binding sites, methylation states, and transcript expression profiles. Mapping the sequencing reads to reference genomes efficiently and effectively is one of the most critical analysis tasks. Although several tools have been developed, their performance suffers when both multiple substitutions and insertions/deletions (indels) occur together.</p> <p>Results</p> <p>We report a new algorithm, Basic Oligonucleotide Alignment Tool (BOAT) that can accurately and efficiently map sequencing reads back to the reference genome. BOAT can handle several substitutions and indels simultaneously, a useful feature for identifying SNPs and other genomic structural variations in functional genomic studies. For better handling of low-quality reads, BOAT supports a "3'-end Trimming Mode" to build local optimized alignment for sequencing reads, further improving sensitivity. BOAT calculates an E-value for each hit as a quality assessment and provides customizable post-mapping filters for further mapping quality control.</p> <p>Conclusion</p> <p>Evaluations on both real and simulation datasets suggest that BOAT is capable of mapping large volumes of short reads to reference sequences with better sensitivity and lower memory requirement than other currently existing algorithms. The source code and pre-compiled binary packages of BOAT are publicly available for download at <url>http://boat.cbi.pku.edu.cn</url> under GNU Public License (GPL). BOAT can be a useful new tool for functional genomics studies.</p

Learning to Select Bi-Aspect Information for Document-Scale Text Content Manipulation

In this paper, we focus on a new practical task, document-scale text content manipulation, which is the opposite of text style transfer and aims to preserve text styles while altering the content. In detail, the input is a set of structured records and a reference text for describing another recordset. The output is a summary that accurately describes the partial content in the source recordset with the same writing style of the reference. The task is unsupervised due to lack of parallel data, and is challenging to select suitable records and style words from bi-aspect inputs respectively and generate a high-fidelity long document. To tackle those problems, we first build a dataset based on a basketball game report corpus as our testbed, and present an unsupervised neural model with interactive attention mechanism, which is used for learning the semantic relationship between records and reference texts to achieve better content transfer and better style preservation. In addition, we also explore the effectiveness of the back-translation in our task for constructing some pseudo-training pairs. Empirical results show superiority of our approaches over competitive methods, and the models also yield a new state-of-the-art result on a sentence-level dataset.Comment: accepted by AAAI202

Case report: Conversion therapy for advanced intrahepatic cholangiocarcinoma using PD-1 inhibitor plus S-1 and nab-paclitaxel

Intrahepatic cholangiocarcinoma (iCCA) is a highly malignant hepatobiliary tumor with a high rate of advanced disease at initial presentation. Conversion into resectable iCCA is important for improving the prognosis. Immunotherapy-based regimens are being increasingly used for treating advanced iCCA in recent years. However, the use of combined chemotherapy and immunotherapy for conversion has rarely been reported. The aim of this report was to present the outcomes of a 52-year-old female patient with IIIB iCCA. The patient was treated with a programmed cell death protein-1 inhibitor plus S-1 and nab-paclitaxel. The postoperative histopathological results indicated pathologic complete response after six cycles of systematic treatment. The patient is currently disease-free for one year

COVID-19 Epidemic Peer Support and Crisis Intervention Via Social Media

This article is made available for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.This article describes a peer support project developed and carried out by a group of experienced mental health professionals, organized to offer peer psychological support from overseas to healthcare professionals on the frontline of the COVID-19 outbreak in Wuhan, China. This pandemic extremely challenged the existing health care systems and caused severe mental distress to frontline healthcare workers. The authors describe the infrastructure of the team and a novel model of peer support and crisis intervention that utilized a popular social media application on smartphone. Such a model for intervention that can be used elsewhere in the face of current global pandemic, or future disaster response

Basic Research on Rockburst Control Technology for Deep Well Filling of Municipal Solid Waste

AbstractGiven the scarcity of raw materials for rockburst prevention in filling mining and the lack of space for disposal of large amount of municipal waste, the feasibility of preparing filling materials for rockburst mines from stale waste was investigated by laboratory tests and theoretical analysis. On this basis, the process of preparing filling materials from stale garbage was proposed, and corresponding equipment were developed to prepare stale garbage filling mass. According to the characteristics and uses of the stale waste filling materials, two processes of volume filling and strength filling are proposed, and the key technology of stale garbage filling to control rockburst was designed. The following conclusions were drawn: stale garbage can be made into mine filling material because of its composition, strength, and shape. The process of preparing mine filling materials from obsolete waste includes crushing, screening, compression, and packaging. The equipment suitable for the process includes crushing-screening, compression-forming, and sealing-packaging integrated equipment. The equipment has realized effective screening, compression, and bulk packaging of stale garbage, so that the stale garbage filling mass can meet the requirements of environmental protection and strength. Strength filling is a filling method that uses the strength of stale garbage filling mass to protect the overlying strata from or less damage, thereby reducing the stress concentration in the coal face and reducing the risk of rockburst occurring. Volume filling mainly depends on the volume of the filling mass, with the main purpose of reducing the stress concentration in the roadway surrounding rock. The rockburst mine filling technology of stale garbage is support track filling technology and bag filling technology, and the deep well sealing of stale garbage is block stacking technology. The deep well filling mining key technologies provide a new approach to against rockburst and treat large amounts of municipal waste

Representativeness of Two Global Gridded Precipitation Data Sets in the Intensity of Surface Short-Term Precipitation over China

This study evaluates the representativeness of two widely used next-generation global satellite precipitation estimates data for short-term precipitation over China, namely the satellite data from the Climate Prediction Center morphing (CMORPH) and the satellite data from the Global Precipitation Measurement (GPM) mission. These two satellite precipitation data sets were compared with the hourly liquid in-situ precipitation from China national surface stations from 2016 to 2020. The results showed that the GPM precipitation data has better representativeness of surface short-term precipitation than that of the CMORPH data, and these two quantitative precipitation estimate (QPE) data sets underestimated extreme precipitation. Moreover, we analyzed the influence of the error between two QPE data sets and the in-situ precipitation on the classification of short-term precipitation intensity. China uses 8.1–16 mm/h as the definition of heavy precipitation, but the accuracy of the satellite QPE product was different due to the different lowest threshold of heavy rain (more than 8.1 mm/h or more than 16 mm/h). Increasing the threshold value of the QPE data for short-term strong precipitation resulted in lower accuracy for detecting such events, but higher accuracy for detecting moderate intensity rainfall. When studying short-term strong precipitation over China using precipitation grade, selecting an appropriate threshold was important to ensure accurate judgments. Additionally, it is important to account for errors caused by QPE data, which can significantly affect the accuracy of precipitation grading

Effect of Rural Black-Gray Water Treatment by Subsurface Wastewater Infiltration System on Soil Environment of Vegetable Crop Field

A field trial was conducted in Tianjin to assess the impact of “three-compartment septic tank (SPT) + soil wastewater infiltration system (SWIS)” on vegetable crop soil, determine the SPT effluent quality, and establish the consumer safety of vegetables grown above the SWIS. The effluent total nitrogen (TN), total phosphorus (TP), ammonium-N (NH4+-N), chemical oxygen demand (COD), and 5-d biochemical oxygen demand (BOD5) levels all varied largely every month. The average COD failed to meet the criteria of the Standard for Irrigation Water Quality (No. GB5084-2021) but significantly influenced bacterial community distribution. Hierarchical clustering disclosed seasonal variation in SPT effluent. SWIS treatment of rural black-grey water significantly affected both the vegetable soil TN and TP content, and it promoted microbial community diversity and richness in deep soil. The treatment also increased the relative abundances of the beneficial bacterial genera Thiobacillus and Arthrobacter by more than 320% and decreased the relative abundance of the pathogenic bacterial genus Streptomyces in vegetable soil by more than 20.33%. The faecal coliform levels and ascaris egg mortality rates in the vegetable crop soils lay within published human health and safety thresholds both before and after SWIS treatment. All vegetable crops grown above the SWIS were fit for human consumption. The VC level in the vegetables planted in experimental households were higher than those for the vegetables planted in ordinary households. The present work provides reasonable theoretical and empirical bases for optimising the “SPT + SWIS” process and SPT discharge standards in rural areas

Digital Transformation Evaluation for Small- and Medium-Sized Manufacturing Enterprises Using the Fuzzy Synthetic Method DEMATEL-ANP

In view of the characteristics of small- and medium-sized manufacturing enterprises and the status quo of digitalization, it is necessary to develop a more applicable digital transformation maturity model. The decision testing and evaluation laboratory method (DEMATEL) is used to provide the visual impact relationship between digital transformation criteria, and combined with the network analytic hierarchy process (ANP) to determine the mixed weight of indicators, and then fuzzy comprehensive evaluation is used to evaluate the digital maturity of small- and medium-sized manufacturing enterprises. The empirical analysis of small- and medium-sized manufacturing enterprises in Guangdong Province shows that digital strategy and information technology play a key role in the digital transformation of enterprises, and digital process and digital innovation are the main problems faced by small- and medium-sized enterprises. In addition, the digital maturity of enterprises is related to the industrial base, regional policies, industry types, etc. This study provides some guidance for the implementation path selection of small- and medium-sized enterprises’ digital transformation and accelerates the digital transformation and sustainable development of small- and medium-sized manufacturing enterprises

Effect of the plant flavonoid, rhoifolin, on memory and cognition in a rat model of Alzheimer’s disease

Purpose: To investigate the neuroprotective effect of the natural flavonoid rhoifolin in rats with streptozotocin (STZ)-induced (AD). Methods: Morris water-maze and novel object recognition tests were carried out to estimate the effect of rhoifolin on memory and cognition. Histopathological analysis was made to observe thickness of hippocampal CA1 pyramidal layer. Analysis of oxidative stress markers was performed to estimate the effect of rhoifolin on oxidative stress in the hippocampus and frontal cortex. Results: Morris water maze and novel object recognition tests showed a significant improvement in the memory, cognition and spatial learning in rhoifolin treated AD animals (p &lt; 0.05). Moreover, rhoifolin treatment resulted in a significant increase in the CA1 pyramidal layer of AD animals indicating its neuroprotective properties (p &lt; 0.05). The increase in the hippocampal CA1 area further validated the reversal of cognitive dysfunctions caused by STZ treatment. Furthermore, analysis of oxidative stress markers SOD, CAT, GPX, GRX, and MDA showed a significant improvement in the oxidative stress in the hippocampus and frontal cortex (p &lt; 0.05). Conclusion: The present study is the first report to demonstrate the effect of plant flavonoid, rhoifolin on STZ-induced AD in rat model. Rhoifolin improves spatial learning, cognition, and memory in STZ-treated rat model. Therefore, rhoifolin may be a promising therapeutic agent for the management of AD

Research on Mechanism of Rock Burst in Key Working Faces under Thick Magmatite in Deep Mine

The rock burst of key working faces under the thick hard rock in deep mine significantly threatens the mining safety of deep mine. In this study, the key working faces under typical deeply buried thick magmatite were adopted as the engineering background. The mine pressure characteristics during the mining in key working faces under thick magmatite in deep mine were measured and analyzed. Then, the evolution of overburden strata structure under the control of thick magmatite was explored based on the theory of mine pressure to conclude that the horizontal “carrier” load of broken rock beam, the vertical “loader” load, and the shock bump load from thick magmatite fracture are main sources of force behind the burst. Finally, the mechanism of rock burst was studied on the basis of the balanced relationship between loading and bearing. According to the results of research, the burst in key working faces under thick magmatite in deep mine was actually the instability burst of the key working face block. The bearing capacity and load of key working face block were constantly changing during the unstable movement of thick magmatite. The rock burst would occur in the event of any instability during the dynamic confrontation of “loading-bearing”. As per different burst sources, it could be divided into flexural loading burst of thick magmatite and shock bump burst of thick magmatite fracture. The mechanical conditions for each of the two bursts and the width calculation formula for the key working face free from overall instability burst were deduced. The research results were applied to key working face 12310. Meanwhile, the purpose of safe production following the principle of “No disaster in bumps, no harm under burst” was realized by implementing the “Four Keys” comprehensive prevention and control measures of “key monitoring + key speed reduction + key pressure relief + key support”