Quadruple primary tumors in a lynch syndrome patient surviving more than 26 years with genetic analysis: a case report and literature review.

The incidence of multiple primary tumors(MPTs) is on the rise in recent years, but patients having four or more primary tumors is still rare. Lynch syndrome (LS) patients have a high risk of developing MPTs. NGS sequencing could identify the genetic alterations in different tumors to make a definite diagnosis of uncommon cases in clinical practice. Here, we report the case of a 66-year-old female patient who develops four MPTS between the ages of 41 and 66, that is sigmoid colon cancer, acute non-lymphocytic leukemia, urothelial carcinoma and ascending colon cancer. She has survived for more than 26 years since the first discovery of tumor. Targeted sequencing indicates that she has a pathogenic germline mutation in the exon 13 of MSH2, and her 2020 ureteral cancer sample and 2023 colon cancer sample have completely different mutation profiles. To the best of our knowledge, this is the first case of multiple primary tumors with an acute non-lymphocytic leukemia in LS patients.

Synergistic effect of adsorption-photocatalytic reduction of Cr(VI) in wastewater with biochar/TiO2 composite under simulated sunlight illumination.

Photocatalysis, which is an alternative technology to conventional methods, utilizes solar energy as the driving force to address environmental concerns and has attracted widespread attention from chemists worldwide. In this study, a series of photocatalytic materials composed of agricultural waste and titanium dioxide (TiO2) nanomaterial was prepared for the synergistic adsorption-photocatalytic reduction of hexavalent chromium in wastewater under mild conditions. The results showed that the TiO2 nanomaterial exhibited a higher photogenerated carrier separation efficiency and performance for the adsorption-photocatalytic reduction of Cr(VI) after loading straw biochar (BC). When the loading amount of BC was 0.025 g (i.e., TBC-3), the removal efficiency of Cr(VI) was as high as 99.9% under sunlight irradiation for 25 min, which was 2.9 and 3.5 times higher than that of pure TiO2 and BC samples, respectively. Additionally, after four cycles of experiments, the removal efficiency of Cr(VI) by TBC-3 remained at about 93.0%, proving its good chemical ability in our reaction system. Its excellent adsorption-photocatalytic performance is mainly attributed to the synergistic effect of the strong adsorption of BC and the outstanding photocatalytic performance of TiO2. Finally, the possible mechanism for the synergistic adsorption-photocatalytic reduction on BC/TiO2 to remove the highly toxic Cr(VI) in wastewater was proposed.

Personalized therapy guided by longitudinal liquid biopsies for treatment of leptomeningeal disease from lung adenocarcinoma: A case report.

Molecular-based targeted therapies have significantly benefited certain patients with cancer; however, those with leptomeningeal disease (LMD) persistently exhibit a poor prognosis and are often excluded from clinical trials. Tumor-derived cell-free (cf)DNA, found in the cerebrospinal fluid (CSF) of patients with LMD, can assist in diagnosis and tracking of disease progression. However, the utilization of CSF to direct targeted cancer therapy has yet to be extensively explored. The present study reported the case of a patient with lung adenocarcinoma and LMD who was monitored by performing a series of liquid biopsies of CSF and blood. Targeted sequencing was performed on cfDNA from the CSF and plasma, and the variant allele frequencies (VAFs) of BRAF and NRAS mutations were assessed and analyzed in conjunction with the clinical presentation of the patient. The patient then underwent serial chemotherapy, radiation therapy, immunotherapy and targeted treatment based on the results of the liquid biopsies. Upon the LMD diagnosis, a BRAF p.V600E mutation was detected in plasma cfDNA. Consequently, the patient was treated with vemurafenib and responded favorably to this consolidation treatment for 13 months. After a relapse in July 2018, both BRAF p.V600E and NRAS p.Q61K mutations were detected in CSF supernatant and sediment cell samples, suggesting drug resistance. Therefore, the treatment strategy for the patient changed to cobimetnib plus vemurafenib. Notably, the changes of VAF in the CSF supernatant samples were associated with the clinical status of the patient. The patient survived for 33 months post-LMD diagnosis. The present case report highlights the potential use of liquid biopsy in personalized therapy, as it was instrumental in informing the combinational treatment plan of the patient, which ultimately proved beneficial.

Design of p-n heterojunction between CoWO4 and Zn-defective Zn0.3Cd0.7S for efficient photocatalytic H2 evolution.

To enhance the efficiency of photocatalytic H2 evolution, numerous methods are employed by increasing the utilization of photogenerated charge carriers (PCCs), including catalyst design, defect regulation, and selection of suitable H+ resources. Using self-assembly method, CoWO4/ZnxCd1-xS with p-n heterojunction was synthesized. Although CoWO4 (CW) cannot produce H2 under visible light irradiation, it can provide photogenerated electrons (e-) to Zn0.3Cd0.7S (ZCS), and largely increase the photocatalytic activity of ZCS. The optimal CW/ZCS composite can reach 15.58 mmol·g-1·h-1, which is 45.8 and 24.3 times higher than the values of the pure CdS and ZCS, respectively. The largely enhanced photocatalytic H2 production is attributed to the Zn vacancies (VZn), p-n heterojunction, and p-chlorobenzyl alcohol (Cl-PhCH2OH) as the H+ source of H2 production. VZn on the ZCS surface as the capture center of photogenerated holes (h+), can regulate the carrier distribution, which results in more photogenerated e- and less generated h+. The combination of p-n heterojunction and VZn can enhance the separation and transfer efficiency of PCCs, and effectively inhibit the recombination of charge carriers. To further improve the utilization rate of PCCs, the photocatalytic H2 evolution is proceeded by Cl-PhCH2OH oxidation in N,N-dimethylformamide solution, with 4-chlorobenzaldehyde (Cl-PhCHO) generated. The separated photogenerated e- and h+ both participated in the redox reaction of H+ reduction and Cl-PhCH2OH oxidation, considering that the amount of H2 and Cl-PhCHO products are close to 1:1. This work not only facilitates the separation and transfer of PCCs, but also provides directions for the design of efficient photocatalysts and H2 evolution in the organic phase.

Metal Sulfide S-Scheme Homojunction for Photocatalytic Selective Phenylcarbinol Oxidation.

Metal sulfide-based homojunction photocatalysts are extensively explored with improved photocatalytic performance. However, the construction of metal sulfide-based S-scheme homojunction remains a challenge. Herein, the fabrication of 2D CdIn2S4 nanosheets coated 3D CdIn2S4 octahedra (referred to as 2D/3D n-CIS/o-CIS) S-scheme homojunction photocatalyst is reported by simply adjustment of polyvinyl pyrrolidone amount during the solvothermal synthesis. The formation of S-scheme homojunction within n-CIS/o-CIS is systematically investigated via a series of characterizations, which can generate an internal electric field to facilitate the separation and migration of photogenerated electron-hole pairs. The 2D/3D n-CIS/o-CIS composite exhibits significantly improved photocatalytic activity and stability in the selective oxidation of phenylcarbinol (PhCH2OH) to benzaldehyde (PhCHO) when compared to pure n-CIS and o-CIS samples under visible light irradiation. It is hoped that this work can contribute novel insights into the development of metal sulfides S-scheme homojunction photocatalysts for solar energy conversion.

Designable Synthesis of Layered Silicates and Tunable Interlayer Expanded to Zeolites.

Layered zeolitic silicates and corresponding interlayer-expanded porous materials exhibit attractive application potential in wide fields. Nonetheless, designable synthesis and structure analysis of layered silicates remain challenging. Herein, two kinds of layered silicates are synthesized using different di-quaternary ammonium-type organic structure-directing agents (OSDAs). Their crystal structures are analyzed and verified by 3D electron diffraction (3D ED) and high-resolution TEM imaging. The suitable configurations of OSDA can lead to desirable interlayer states. Additionally, two new zeolite structures both with 12-membered ring (MR) channels intersected by 8 MR channels and larger interlayer spaces are constructed from layered silicate precursors by interlayer silylation. The new zeolitic material exhibits potential application in adsorption of organic pollution and catalytic reaction. This study is expected to develop versatile ways for the design and synthesis of layered silicates even zeolites and provide references in characterizing layered materials and zeolites as well.

Superhydrophilic Dendritic FeP/Cu3P Electrocatalyst for Urea Splitting via the Intramolecular Mechanism.

The electrocatalytic overall urea splitting can achieve the dual goals of urea treatment and hydrogen energy acquisition. Herein, we exploited the principle of precipitation dissolution equilibrium to obtain bimetallic phosphide FeP/Cu3P/CF for the simultaneous oxidation of urea and reduction of water and comprehensively reveal the inherent molecular thermodynamic mechanisms on the surface of catalysts. The excellent electrochemical performance can be derived from the super water affinity and synergistic effect. Especially, the theoretical calculation unveils that the synergistic effect between FeP and Cu3P can lower the activation energy required for urea electrooxidation, thereby promoting urea splitting. In situ differential electrochemical mass spectrometry (in situ DEMS) measurements further demonstrated that urea oxidation on FeP/Cu3P/CF proceeded according to the intramolecular mechanism. This work has laid the foundation for constructing highly efficient superhydrophilic bifunctional electrocatalysts.

Oxygen vacancies synergistic cobalt phosphide electron bridge modulated bismuth oxychloride/carbon nitride Z-scheme junction for efficient carbon dioxide reduction coupled with tetracycline oxidation.

Although great progress has been made with respect to electron bridges, the electron mobility of the state-of-the-art electron bridges is far from satisfactory because of weak electrical conductivity. To overcome the above issue, cobalt phosphide (CoP), as a model electron bridge, was modified by superficial oxygen vacancies (OVs) and embedded into a defective bismuth oxychloride/carbon nitride (BiO1-xCl/g-C3N4) Z-scheme heterojunction to obtain atomic-level insights into the effect of surface OVs on CoP electron bridges. Compared to BiO1-xCl/g-C3N4 and bismuth oxychloride/cobalt phosphide/carbon nitride (BiOCl/CoP/g-C3N4) composites, the defective bismuth oxychloride/cobalt phosphide/carbon nitride (BiO1-xCl/CoP/g-C3N4) heterojunction exhibited remarkable photocatalytic redox performance, indicating that the surface OVs-assisted CoP electron bridge effectively boosted electrical conductivity and yielded ultrafast electron transfer rates. The theoretical and experimental results demonstrate that the surface OVs play a critical role in improving the electrical conductivity of the CoP electron bridge, thereby accelerating electron mobility. This research provides insights into interfacial OVs-modified transition metal phosphide (TMP) electron bridges and their potential application in heterojunctions for energy crisis mitigation and environmental remediation.

Visualizing Large-Scale Spatial Time Series with GeoChron.

In geo-related fields such as urban informatics, atmospheric science, and geography, large-scale spatial time (ST) series (i.e., geo-referred time series) are collected for monitoring and understanding important spatiotemporal phenomena. ST series visualization is an effective means of understanding the data and reviewing spatiotemporal phenomena, which is a prerequisite for in-depth data analysis. However, visualizing these series is challenging due to their large scales, inherent dynamics, and spatiotemporal nature. In this study, we introduce the notion of patterns of evolution in ST series. Each evolution pattern is characterized by 1) a set of ST series that are close in space and 2) a time period when the trends of these ST series are correlated. We then leverage Storyline techniques by considering an analogy between evolution patterns and sessions, and finally design a novel visualization called GeoChron, which is capable of visualizing large-scale ST series in an evolution pattern-aware and narrative-preserving manner. GeoChron includes a mining framework to extract evolution patterns and two-level visualizations to enhance its visual scalability. We evaluate GeoChron with two case studies, an informal user study, an ablation study, parameter analysis, and running time analysis.

Comparison of the somatic genomic landscape between central- and peripheral-type non-small cell lung cancer.

OBJECTIVE: Lung cancer is classified into central and peripheral types based on the anatomic location. The present study aimed to explore the distinct patterns of genomic alterations between central- and peripheral-type non-small cell lung cancers (NSCLCs) with negative driver genes and identify potential driver genes and biomarkers to improve therapy strategies for NSCLC. METHODS: Whole-exome sequencing (WES) was performed with 182 tumor/control pairs of samples from 145 Chinese NSCLC patients without EGFR, ALK, or ROS1 alterations. Significantly mutated genes (SMGs) and somatic copy number alterations (SCNAs) were identified. Subsequently, tumor mutation burden (TMB), weighted genome integrity index (wGII), copy number alteration (CNA) burden, Shannon diversity index (SDI), intratumor heterogeneity (ITH), neoantigen load (NAL), and clonal variations were evaluated in central- and peripheral-type NSCLCs. Furthermore, mutational signature analysis and survival analysis were performed. RESULTS: TP53 was the most frequently mutated gene in NSCLC and more frequently mutated in central-type NSCLC. Higher wGII, ITH, and SDI were found in central-type lung adenocarcinoma (LUAD) than in peripheral-type LUAD. The NAL of central-type lung squamous cell carcinoma (LUSC) with stage III/IV was significantly higher than that of peripheral-type LUSC. Mutational signature analysis revealed that SBS10b, SBS24, and ID7 were significantly different in central- and peripheral-type NSCLCs. Furthermore, central-type NSCLC was found to evolve at a higher level with fewer clones and more subclones, particularly in central-type LUSC. Survival analysis revealed that TMB, CNA burden, NAL, subclonal driver mutations, and subclonal mutations were negatively related to the overall survival (OS) and the progression-free survival (PFS) of central-type LUAD. CONCLUSIONS: Central-type NSCLC tended to evolve at a higher level and might suggest a favorable response to immunotherapy. Our study also identified several potential driver genes and promising biomarkers for the prognosis and prediction of chemotherapy responses in NSCLC.

The Mars-Van Krevelen cycle and non-noble metal Ni jointly promoting Z-scheme charge transfer: a study on the photothermal synergy effect applied in selectively oxidizing aromatic alcohols.

Photothermal catalysis is a promising method for selectively oxidizing organic compounds, effectively addressing the energy-intensive and low-selective processes of thermal catalysis, as well as the slow reaction rates of photocatalysis. In this study, a ternary photothermal catalyst, Ni/CeO2/CdS, was synthesized using a simple calcination and solvothermal method. The catalyst demonstrated remarkable improvement in reaction rates and achieved nearly 100% selectivity in converting benzyl alcohol to benzaldehyde through photothermal catalysis at normal pressure. The reaction rates were 5.9 times and 63 times higher than those of CdS and Ni/CeO2 individually. XPS analysis confirmed that the thermal catalysis followed the Mars-Van Krevelen (MVK) mechanism and also proved that photocatalysis facilitated the MVK cycle. Additionally, DFT calculations showed that Ni acted as an electron transfer channel, facilitating efficient Z-scheme charge transfer. The in situ infrared technique was used to dynamically monitor the reaction process and explain the high selectivity of the product. Furthermore, detailed explanations of photocatalysis, thermocatalysis, and photothermal synergistic catalysis were proposed based on the aforementioned characterization and theoretical calculations. This approach establishes a theoretical foundation for the development of efficient photothermal catalysts.

Efficient sequencing data compression and FPGA acceleration based on a two-step framework.

With the increasing throughput of modern sequencing instruments, the cost of storing and transmitting sequencing data has also increased dramatically. Although many tools have been developed to compress sequencing data, there is still a need to develop a compressor with a higher compression ratio. We present a two-step framework for compressing sequencing data in this paper. The first step is to repack original data into a binary stream, while the second step is to compress the stream with a LZMA encoder. We develop a new strategy to encode the original file into a LZMA highly compressed stream. In addition an FPGA-accelerated of LZMA was implemented to speedup the second step. As a demonstration, we present repaq as a lossless non-reference compressor of FASTQ format files. We introduced a multifile redundancy elimination method, which is very useful for compressing paired-end sequencing data. According to our test results, the compression ratio of repaq is much higher than other FASTQ compressors. For some deep sequencing data, the compression ratio of repaq can be higher than 25, almost four times of Gzip. The framework presented in this paper can also be applied to develop new tools for compressing other sequencing data. The open-source code of repaq is available at: https://github.com/OpenGene/repaq.

Photoredox Coupling of CO2 Reduction with Benzyl Alcohol Oxidation over Ternary Metal Chalcogenides (ZnmIn2S3+m, m = 1-5) with Regulable Products Selectivity.

Integrating photocatalytic CO2 reduction with selective benzyl alcohol (BA) oxidation in one photoredox reaction system is a promising way for the simultaneous utilization of photogenerated electrons and holes. Herein, ZnmIn2S3+m (m = 1-5) semiconductors (ZnIn2S4, Zn2In2S5, Zn3In2S6, Zn4In2S7, and Zn5In2S8) with various composition faults were synthesized via a simple hydrothermal method and used for effective selective dehydrocoupling of benzyl alcohol into high-value C-C coupling products and reduction of CO2 into syngas under visible light. The absorption edge of ZnmIn2S3+m samples shifted to shorter wavelengths as the atomic ratio of Zn/In was increased. The conduction band and valence band position can be adjusted by changing the Zn/In ratio, resulting in controllable photoredox ability for selective BA oxidation and CO2 reduction. For example, the selectivity of benzaldehyde (BAD) product was reduced from 76% (ZnIn2S4, ZIS1) to 27% (Zn4In2S7, ZIS4), while the selectivity of hydrobenzoin (HB) was increased from 22% to 56%. Additionally, the H2 formation rate on ZIS1 (1.6 mmol/g/h) was 1.6 times higher than that of ZIS4 (1.0 mmol/g/h), and the CO formation rate on ZIS4 (0.32 mmol/g/h) was three times higher than that of ZIS1 (0.13 mmol/g/h), demonstrating that syngas with different H2/CO ratios can be obtained by controlling the Zn/In ratio in ZnmIn2S3+m. This study provides new insights into unveiling the relationship of structure-property of ZnmIn2S3+m layered crystals, which are valuable for implementation in a wide range of environment and energy applications.

Single-cell RNA-seq Revealed that Altered Tumor Infiltrating Lymphocytes in Cirrhotic Liver Indicate Development of Hepatocellular Carcinoma.

Background and Aims: Cirrhosis is the precursor lesion for most hepatocellular carcinoma (HCC) cases. However, no biomarker effectively predicted HCC initiation before diagnosis by imaging. We aimed to investigate the hallmarks of immune microenvironments in healthy, cirrhotic livers and HCC tumor tissues and to identify immune biomarkers of cirrhosis-HCC transition. Methods: Expression matrices of single-cell RNA sequencing studies were downloaded and integrated with Seurat package vignettes. Clustering was performed to analyze the immune cell compositions of different sample types. Results: The cirrhotic liver and HCC tumors had distinct immune microenvironments, but the immune landscape of cirrhotic livers was not markedly modified compared with healthy livers. Two subsets of B cells and three subsets of T cells were identified in the samples. Among the T cells, naïve T cells were more prominent in the cirrhotic and healthy liver samples than in the HCC samples. In contrast, the neutrophil count was lower in cirrhotic livers. Two macrophage clusters were identified, one that actively interacted with T cells and B cells and was enriched in cirrhotic blood compared with HCC blood samples. Conclusions: Decreased naïve T cell infiltration and increased neutrophil infiltration in the liver may indicate the development of HCC in cirrhotic patients. Alterations in blood-resident immune cells may also be a sign of HCC development in cirrhotic patients. The dynamics of the immune cell subsets may serve as novel biomarkers to predict the transition from cirrhosis to HCC.

Two-Way PBM-Euler Model for Gas and Liquid Flow in the Ladle.

Ladle metallurgy is an important steelmaking technology in high-quality steel production. The blowing of argon at the ladle bottom has been applied in ladle metallurgy for several decades. Until now, the issue of breakage and coalescence among bubbles was still far from being solved. In order to have a deep insight into the complex process of fluid flow in the gas-stirred ladle, the Euler-Euler model and population balance model (PBM) are coupled to investigate the complex fluid flow in the gas-stirred ladle. Here, the Euler-Euler model is applied to predict the two-phase flow, and PBM is applied to predict the bubble and size distribution. The coalescence model, which considers turbulent eddy and bubble wake entrainment, is taken into account to determine the evolution of the bubble size. The numerical results show that if the mathematical model ignores the breakage of bubbles, the mathematical model gives the wrong bubble distribution. For bubble coalescence in the ladle, turbulent eddy coalescence is the main mode, and wake entrainment coalescence is the minor mode. Additionally, the number of the bubble-size group is a key parameter for describing the bubble behavior. The size group number 10 is recommended to predict the bubble-size distribution.

High activity of bifunctional Ni2P electrocatalyst for benzyl alcohol oxidation coupled with hydrogen evolution.

Considering the high costs of producing catalysts, designing a bifunctional catalyst is one of the favorable ways through which the best result can be achieved with less effort. Herein, we use a one-step calcination method to obtain a bifunctional catalyst Ni2P/NF for the simultaneous oxidation of benzyl alcohol (BA) and reduction of water. A series of electrochemical tests have shown that this catalyst has a low catalytic voltage, long-term stability and high conversion rates. The theoretical calculation unveils the essential reason for its excellent activity. The synergistic effect of Ni and P optimizes the adsorption and desorption energy of the intermediate species, thus reducing the energy barrier of the rate-determining step during BA electrooxidation. Thus, this work has laid the foundation for designing a highly efficient bifunctional electrocatalyst for BA oxidation and the hydrogen revolution.

The genomic characteristics of RET fusion positive tumors in Chinese non-small cell lung cancer (NSCLC) patients.

BACKGROUND: Approximately 1-2% of non-small cell lung cancer (NSCLC) patients harbor RET (rearranged during transfection) fusions. The oncogenic RET fusions could lead to constitutive kinase activation and oncogenesis. METHODS: 1746 Chinese NSCLC patients were analyzed in this study. Tumor tissues were collected, and were formalin fixed, paraffin-embedded (FFPE) and archived. Peripheral blood (PB) samples were also collected from each patient as control. In addition, we selected 17 of them for cfDNA NGS testing and 14 tumor samples for immunohistochemistry testing using PD-L1 rabbit monoclonal antibody, clones 28-8 (Abcam, Cambridge, UK). RESULTS: Of the 1746 NSCLC cases, RET rearrangements were identified in 25 cases (1.43%) with locally advanced or metastatic NSCLC, of which 20 (80%) were female. We found that 14 out of 25 patients had an KIF5B-RET fusion, with KIF5B exon15-RET exon12, KIF5B exon23-RET exon12, and KIF5B exon24-RET exon11 detected in 14, 3, and 1 patients, respectively. We also identified one novel RET fusion partner PLCE1 and 4 intergenic-breakpoint fusions. CONCLUSION: In this study, using the hybrid capture based next generation sequencing (NGS) techniques, we revealed the genomic profiling for the patients with RET fusion-positive NSCLC. To the best of our knowledge, this is the first study that exhibited the detailed breakpoints of Chinese NSCLC patients with RET rearrangement, and we found a novel new partner PLCE1. The results provided genomic information for patients with RET fusion which is significant for personalized clinical management in the era of precision medicine.

Image-based deep learning identifies glioblastoma risk groups with genomic and transcriptomic heterogeneity: a multi-center study.

OBJECTIVES: To develop and validate a deep learning imaging signature (DLIS) for risk stratification in patients with multiforme (GBM), and to investigate the biological pathways and genetic alterations underlying the DLIS. METHODS: The DLIS was developed from multi-parametric MRI based on a training set (n = 600) and validated on an internal validation set (n = 164), an external test set 1 (n = 100), an external test set 2 (n = 161), and a public TCIA set (n = 88). A co-profiling framework based on a radiogenomics analysis dataset (n = 127) using multiscale high-dimensional data, including imaging, transcriptome, and genome, was established to uncover the biological pathways and genetic alterations underpinning the DLIS. RESULTS: The DLIS was associated with survival (log-rank p < 0.001) and was an independent predictor (p < 0.001). The integrated nomogram incorporating the DLIS achieved improved C indices than the clinicomolecular nomogram (net reclassification improvement 0.39, p < 0.001). DLIS significantly correlated with core pathways of GBM (apoptosis and cell cycle-related P53 and RB pathways, and cell proliferation-related RTK pathway), as well as key genetic alterations (del_CDNK2A). The prognostic value of DLIS-correlated genes was externally confirmed on TCGA/CGGA sets (p < 0.01). CONCLUSIONS: Our study offers a biologically interpretable deep learning predictor of survival outcomes in patients with GBM, which is crucial for better understanding GBM patient's prognosis and guiding individualized treatment. KEY POINTS: • MRI-based deep learning imaging signature (DLIS) stratifies GBM into risk groups with distinct molecular characteristics. • DLIS is associated with P53, RB, and RTK pathways and del_CDNK2A mutation. • The prognostic value of DLIS-correlated pathway genes is externally demonstrated.

Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp.

A large amount of sequencing data is generated and processed every day with the continuous evolution of sequencing technology and the expansion of sequencing applications. One consequence of such sequencing data explosion is the increasing cost and complexity of data processing. The preprocessing of FASTQ data, which means removing adapter contamination, filtering low-quality reads, and correcting wrongly represented bases, is an indispensable but resource intensive part of sequencing data analysis. Therefore, although a lot of software applications have been developed to solve this problem, bioinformatics scientists and engineers are still pursuing faster, simpler, and more energy-efficient software. Several years ago, the author developed fastp, which is an ultrafast all-in-one FASTQ data preprocessor with many modern features. This software has been approved by many bioinformatics users and has been continuously maintained and updated. Since the first publication on fastp, it has been greatly improved, making it even faster and more powerful. For instance, the duplication evaluation module has been improved, and a new deduplication module has been added. This study aimed to introduce the new features of fastp and demonstrate how it was designed and implemented.

ScRNAPip: A systematic and dynamic pipeline for single-cell RNA sequencing analysis.

With the advancement of sequencing technology, cell separation, and whole-genome amplification techniques, single cell technology for genome sequencing is emerging gradually. In comparison to traditional genome sequencing at the multi-cellular level, single-cell sequencing can not only measure the gene expression level more accurately but also can detect a small amount of gene expression or rare noncoding RNA. This technology has garnered increasing interest among researchers engaged in single-cell studies in recent years. Here, we developed a reproducible computational workflow for scRNA-seq data analysis which including tasks like quality control, normalization, data correction, pseudotime analysis, copy number analysis, etc. We illustrate the application of these steps using publicly available datasets and provide practical recommendations for their implementation. This study serves as a comprehensive tutorial for researchers keen on single-cell data analysis, aiding users in constructing and refining their own analysis pipelines.