activities of eravacycline against clinical bacterial isolates: a multicenter study in Guangdong, China.

Introduction: Eravacycline (ERV), a novel tetracycline derivative, exhibits broad-spectrum antibacterial activity, but data on the bacterial activity against Chinese bacterial isolates are very scarce. This study aims to evaluate the activity of eravacycline against the common Gram-positive and Gram-negative bacteria isolates in Guangdong, China.

Methods: The clinical isolates were collected from four centers between 1 November 2023 and 31 January 2024, and the susceptibility of eravacycline (MIC, MIC, and MIC) was determined using broth microdilution as a reference method and E-TEST strips to evaluate their consistency.

Overcoming the High Error Rate of Composite DNA Letters-Based Digital Storage through Soft-Decision Decoding.

Composite DNA letters, by merging all four DNA nucleotides in specified ratios, offer a pathway to substantially increase the logical density of DNA digital storage (DDS) systems. However, these letters are susceptible to nucleotide errors and sampling bias, leading to a high letter error rate, which complicates precise data retrieval and augments reading expenses. To address this, Derrick-cp is introduced as an innovative soft-decision decoding algorithm tailored for DDS utilizing composite letters.

Enhanced electromagnetic wave absorption properties of SiCN(Ni)/BN ceramics by generated Ni and NiSi.

In this paper, the SiCN(Ni)/BN ceramic with excellent electromagnetic wave (EMW) absorption performance was successfully prepared. The Ni and NiSi were formed by the introduction of nickel acetylacetonate (NA), which effectively improved the impedance matching performance of SiCN(Ni)/BN ceramics. The EMW absorption properties of the SiCN(Ni)/BN ceramics showed a trend of first increasing and then decreasing with the increase in content of NA.

Improving error-correcting capability in DNA digital storage via soft-decision decoding.

Error-correcting codes (ECCs) employed in the state-of-the-art DNA digital storage (DDS) systems suffer from a trade-off between error-correcting capability and the proportion of redundancy. To address this issue, in this study, we introduce soft-decision decoding approach into DDS by proposing a DNA-specific error prediction model and a series of novel strategies. We demonstrate the effectiveness of our approach through a proof-of-concept DDS system based on Reed-Solomon (RS) code, named as Derrick.

The Predictive Value of CD3+/CD8+ Lymphocyte Infiltration and PD-L1 Expression in Colorectal Cancer.

Aim: The immune system plays an important role in tumor development and treatment. In this study, we aimed to determine the relationships among the expressions of PD-L1, CD3, CD8, MMR proteins, clinicopathological features, and prognosis of CRC.

Methods: Immunohistochemistry was used to determine the expression of PD-L1, CD3, and CD8 in 771 patients with CRC.

A Scalable Heat Pump Film with Zero Energy Consumption.

Radiative cooling is an effective technology with zero energy consumption to alleviate climate warming and combat the urban heat island effect. At present, researchers often use foam boxes to isolate non-radiant heat exchange between the cooler and the environment through experiments, so as to achieve maximum cooling power. In practice, however, there are challenges in setting up foam boxes on a large scale, resulting in coolers that can be cooled below ambient only under low convection conditions.

Chromosome-level genome of black cutworm provides novel insights into polyphagy and seasonal migration in insects.

Background: The black cutworm, Agrotis ipsilon, is a serious global underground pest. Its distinct phenotypic traits, especially its polyphagy and ability to migrate long distances, contribute to its widening distribution and increasing difficulty of control. However, knowledge about these traits is still limited.

SNS-023 sensitizes hepatocellular carcinoma to sorafenib by inducing degradation of cancer drivers SIX1 and RPS16.

Hepatocellular carcinoma (HCC) remains challenging due to the lack of efficient therapy. Promoting degradation of certain cancer drivers has become an innovative therapy. The nuclear transcription factor sine oculis homeobox 1 (SIX1) is a key driver for the progression of HCC.

The First High-quality Reference Genome of Sika Deer Provides Insights into High-tannin Adaptation.

Sika deer are known to prefer oak leaves, which are rich in tannins and toxic to most mammals; however, the genetic mechanisms underlying their unique ability to adapt to living in the jungle are still unclear. In identifying the mechanism responsible for the tolerance of a highly toxic diet, we have made a major advancement by explaining the genome of sika deer. We generated the first high-quality, chromosome-level genome assembly of sika deer and measured the correlation between tannin intake and RNA expression in 15 tissues through 180 experiments.

The predictive value and correlation of β-catenin, CMTM6, and PD-L1 expression in colorectal cancer.

CMTM6 is a major regulator of PD-L1 expression. Aberrant Wnt pathway signaling occurs in most sporadic colorectal cancers (CRC). However, the significance and correlation of β-catenin, CMTM6, and PD-L1 immunohistochemical expression in CRC is still unknown and need to be further verified.

The nearly complete genome of Ginkgo biloba illuminates gymnosperm evolution.

Gymnosperms are a unique lineage of plants that currently lack a high-quality reference genome due to their large genome size and high repetitive sequence content. Here, we report a nearly complete genome assembly for Ginkgo biloba with a genome size of 9.87 Gb, an N50 contig size of 1.

SMARTdenovo: a assembler using long noisy reads.

Long-read single-molecule sequencing has revolutionized genome assembly and enabled the automated reconstruction of reference-quality genomes. It has also been widely used to study structural variants, phase haplotypes and more. Here, we introduce the assembler SMARTdenovo, a single-molecule sequencing (SMS) assembler that follows the overlap-layout-consensus (OLC) paradigm.

Recent Advances in the Fabrication and Application of Graphene Microfluidic Sensors.

This review reports the progress of the recent development of graphene-based microfluidic sensors. The introduction of microfluidics technology provides an important possibility for the advance of graphene biosensor devices for a broad series of applications including clinical diagnosis, biological detection, health, and environment monitoring. Compared with traditional (optical, electrochemical, and biological) sensing systems, the combination of graphene and microfluidics produces many advantages, such as achieving miniaturization, decreasing the response time and consumption of chemicals, improving the reproducibility and sensitivity of devices.

From asymmetrical to balanced genomic diversification during rediploidization: Subgenomic evolution in allotetraploid fish.

A persistent enigma is the rarity of polyploidy in animals, compared to its prevalence in plants. Although animal polyploids are thought to experience deleterious genomic chaos during initial polyploidization and subsequent rediploidization processes, this hypothesis has not been tested. We provide an improved reference-quality de novo genome for allotetraploid goldfish whose origin dates to ~15 million years ago.

A genome-wide survey of copy number variations reveals an asymmetric evolution of duplicated genes in rice.

Background: Copy number variations (CNVs) are an important type of structural variations in the genome that usually affect gene expression levels by gene dosage effect. Understanding CNVs as part of genome evolution may provide insights into the genetic basis of important agricultural traits and contribute to the crop breeding in the future. While available methods to detect CNVs utilizing next-generation sequencing technology have helped shed light on prevalence and effects of CNVs, the complexity of crop genomes poses a major challenge and requires development of additional tools.

Understanding divergent domestication traits from the whole-genome sequencing of swamp- and river-buffalo populations.

Domesticated buffaloes have been integral to rice-paddy agro-ecosystems for millennia, yet relatively little is known about the buffalo genomics. Here, we sequenced and assembled reference genomes for both swamp and river buffaloes and we re-sequenced 230 individuals (132 swamp buffaloes and 98 river buffaloes) sampled from across Asia and Europe. Beyond the many actionable insights that our study revealed about the domestication, basic physiology and breeding of buffalo, we made the striking discovery that the divergent domestication traits between swamp and river buffaloes can be explained with recent selections of genes on social behavior, digestion metabolism, strengths and milk production.

LRScaf: improving draft genomes using long noisy reads.

Background: The advent of third-generation sequencing (TGS) technologies opens the door to improve genome assembly. Long reads are promising for enhancing the quality of fragmented draft assemblies constructed from next-generation sequencing (NGS) technologies. To date, a few algorithms that are capable of improving draft assemblies have released.

Comparative profiling between primary colorectal carcinomas and metastases identifies heterogeneity on drug resistance.

Metastases cause recurrence and mortality for patients with colorectal carcinomas (CRC). In present study, we evaluated heterogeneity on drug resistance and its underlying mechanism between metastatic and primary CRC. Immunohistochemical results from clinical tissue microarray (TMA) suggested that the expression concordance rates of cancer stem cells (CSCs) and drug resistance relative proteins between lymph-node metastatic and primary CRC foci were low.

DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies.

The highly anticipated transition from next generation sequencing (NGS) to third generation sequencing (3GS) has been difficult primarily due to high error rates and excessive sequencing cost. The high error rates make the assembly of long erroneous reads of large genomes challenging because existing software solutions are often overwhelmed by error correction tasks. Here we report a hybrid assembly approach that simultaneously utilizes NGS and 3GS data to address both issues.

Unusual combined thymic mucoepidermoid carcinoma and thymoma: a case report and review of literature.

Background: In rare condition, combined thymic epithelial tumors showing either type A or type B thymomas areas combined with thymic carcinoma components may occur in thymus. Mucoepidermoid carcinoma (MEC) of the thymus is rare in thymic carcinoma, and so far there is no report to describe a combined epithelial tumor of thymus with MEC component. We report an unusual case of combined thymic MEC/type B2 thymoma in a middle-aged male occurring in a mass of anterior mediastinum.

Thermodynamic damage mechanism of transparent films caused by a low-power laser.

A new model for analyzing the laser-induced damage process is provided. In many damage pits, the melted residue can been found. This is evidence of the phase change of materials.