Fast Context-Aware Analysis of Genome Annotation Colocalization.

An annotation is a set of genomic intervals sharing a particular function or property. Examples include genes or their exons, sequence repeats, regions with a particular epigenetic state, and copy number variants. A common task is to compare two annotations to determine if one is enriched or depleted in the regions covered by the other.

Efficient Analysis of Annotation Colocalization Accounting for Genomic Contexts.

An annotation is a set of genomic intervals sharing a particular function or property. Examples include genes or their exons, evolutionarily conserved elements, and regions with a particular epigenetic state. A common task is to compare two annotations to determine if one is enriched or depleted in the regions covered by the other.

Reversal in the drought stress response of the Scots pine forest ecosystem: Local soil water regime as a key to improving climate change resilience.

In a changing climate, forest ecosystems have become increasingly vulnerable to continuously exacerbating heat and associated drought conditions. Climate stress resilience is governed by a complex interplay of global, regional, and local factors, with hydrological conditions being among the key players. We studied a Scots pine ( L.

Multi-Geometry Parameters Optimization of Large-Area Roll-to-Roll Nanoimprint Module Using Grey Relational Analysis and Artificial Neural Network.

Micro- and nanofabrication on polymer substrate is integral to the development of flexible electronic devices, including touch screens, transparent conductive electrodes, organic photovoltaics, batteries, and wearable devices. The demand for flexible and wearable devices has spurred interest in large-area, high-throughput production methods. Roll-to-roll (R2R) nanoimprint lithography (NIL) is a promising technique for producing nano-scale patterns rapidly and continuously.

Hybrid Device Fabrication Using Roll-to-Roll Printing for Personal Environmental Monitoring.

Roll-to-roll (R2R) printing methods are well known as additive, cost-effective, and ecologically friendly mass-production methods for processing functional materials and fabricating devices. However, implementing R2R printing to fabricate sophisticated devices is challenging because of the efficiency of material processing, the alignment, and the vulnerability of the polymeric substrate during printing. Therefore, this study proposes the fabrication process of a hybrid device to solve the problems.

Single-nucleotide resolution detection of Topo IV cleavage activity in the genome with Topo-Seq.

Topoisomerase IV (Topo IV) is the main decatenation enzyme in ; it removes catenation links that are formed during DNA replication. Topo IV binding and cleavage sites were previously identified in the genome with ChIP-Seq and NorfIP. Here, we used a more sensitive, single-nucleotide resolution Topo-Seq procedure to identify Topo IV cleavage sites (TCSs) genome-wide.

VirPool: model-based estimation of SARS-CoV-2 variant proportions in wastewater samples.

Background: The genomes of SARS-CoV-2 are classified into variants, some of which are monitored as variants of concern (e.g. the Delta variant B.

Markov chains improve the significance computation of overlapping genome annotations.

Motivation: Genome annotations are a common way to represent genomic features such as genes, regulatory elements or epigenetic modifications. The amount of overlap between two annotations is often used to ascertain if there is an underlying biological connection between them. In order to distinguish between true biological association and overlap by pure chance, a robust measure of significance is required.

AI-assisted reliability assessment for gravure offset printing system.

In printed electronics, flawless printing quality is crucial for electronic device fabrication. While printing defects may reduce the performance or even cause a failure in the electronic device, there is a challenge in quality evaluation using conventional computer vision tools for printing defect recognition. This study proposed the computer vision approach based on artificial intelligence (AI) and deep convolutional neural networks.

Nanopore sequencing of SARS-CoV-2: Comparison of short and long PCR-tiling amplicon protocols.

Surveillance of the SARS-CoV-2 variants including the quickly spreading mutants by rapid and near real-time sequencing of the viral genome provides an important tool for effective health policy decision making in the ongoing COVID-19 pandemic. Here we evaluated PCR-tiling of short (~400-bp) and long (~2 and ~2.5-kb) amplicons combined with nanopore sequencing on a MinION device for analysis of the SARS-CoV-2 genome sequences.

IoT device fabrication using roll-to-roll printing process.

With the development of technology, wireless and IoT devices are increasingly used from daily life to industry, placing demands on rapid and efficient manufacturing processes. This study demonstrates the fabrication of an IoT device using a roll-to-roll printing process, which could shorten the device fabrication time and reduce the cost of mass production. Here, the fabricated IoT device is designed to acquire data through the sensor, process the data, and communicate with end-user devices via Bluetooth communication.

Conserved pan-cancer microenvironment subtypes predict response to immunotherapy.

The clinical use of molecular targeted therapy is rapidly evolving but has primarily focused on genomic alterations. Transcriptomic analysis offers an opportunity to dissect the complexity of tumors, including the tumor microenvironment (TME), a crucial mediator of cancer progression and therapeutic outcome. TME classification by transcriptomic analysis of >10,000 cancer patients identifies four distinct TME subtypes conserved across 20 different cancers.

Isometric gene tree reconciliation revisited.

Background: Isometric gene tree reconciliation is a gene tree/species tree reconciliation problem where both the gene tree and the species tree include branch lengths, and these branch lengths must be respected by the reconciliation. The problem was introduced by Ma et al. in 2008 in the context of reconstructing evolutionary histories of genomes in the infinite sites model.

[External respiratory function in children with bilateral, chronic, nonspecific inflammatory disease of the lungs after surgical treatment].

The results of operative treatment of children with bilateral chronic unspecific inflammatory diseases of the lungs were studied in follow-up periods of up to 17 years. Among the 73 patients studied, 19 had a history of bilateral and the remaining a history of unilateral resections. According to the findings of respiratory function examination, a combined type of ventilation disorders with mild hypoxemia and hypercapnia was characteristic of this group of patients before the operation.

[A trial of Romanomermis iyengari and R. culicivorax mermithids as a means for controlling blood-sucking mosquitoes in the Tadzhik SSR].

Field trials of R. iyengari and R. culicivorax in the biological control for the mosquito larvae were conducted in Parkhar, Kuibyshevsk, Gissar districts and the outskirts of the city of Dushanbe, the Tadjik SSR.