A generalized method for refining and selecting random crystal structures using graph theory.

Random generation of crystal structures is a key to the success of predicting unknown crystals. In this work, we introduce a general method for refining and selecting random structures that relies on minimal prior information. The method establishes a quotient graph from the random structure using a near-neighbor finding algorithm, which subsequently guides the refinement of the initial structure.

An improved method for phosphate oxygen isotope analysis in water using zirconium-loaded resin enrichment.

The phosphate oxygen isotope (O) tracing analysis method is crucial for identifying the sources of phosphorus pollution in water bodies. However, existing methods face challenges in areas such as presample collection, which demands substantial water volumes, as well as in processing, separation, and purification. This study developed a new O testing method using zirconium (Zr)-loaded resin for enrichment, elution, and purification (ZR-ISEEP).

Detection of sequence-tagged sites to reveal mechanisms of multi-step mutations at multi-copy Y-STRs in father-son pairs.

The case report demonstrates that co-examining various forensic markers with different technologies can strengthen the connection between father-son pairs with multi-step mutations observed at multi-copy Y-chromosomal short tandem repeats (Y-STRs). We detect 33 autosomal STRs and 94 identity-informative single nucleotide polymorphisms (iSNPs) using capillary electrophoresis (CE) and/or next-generation sequencing (NGS) to confirm the relationship within pedigrees. Meanwhile, this study reveals that the mechanisms behind the mutations observed in these cases involve STR slippage (identified using NGS or Sanger sequencing methods) and/or chromosomal structure rearrangement (identified using sequence-tagged site analyses).

Spatial multi-omics reveals the potential involvement of SPP1 fibroblasts in determining metabolic heterogeneity and promoting metastatic growth of colorectal cancer liver metastasis.

This study investigates key microscopic regions involved in colorectal cancer liver metastasis (CRLM), focusing on the crucial role of cancer-associated fibroblasts (CAFs) in promoting tumor progression and providing molecular- and metabolism-level insights for its diagnosis and treatment using multi-omics. We followed 12 fresh surgical samples from 2 untreated CRLM patients. Among these, 4 samples were used for spatial transcriptomics (ST), 4 for spatial metabolomics, and 4 for single-cell RNA sequencing (scRNA-seq).

Mitochondrial genome sequencing with ForenSeq™ mtDNA Whole Genome Kit.

Mitochondrial DNA (mtDNA) possesses unique genetic characteristics and plays a crucial role in forensic DNA analysis. Based on the massively parallel sequencing (MPS) technology alongside the short overlapping amplicon method, the ForenSeq™ mtDNA Whole Genome Kit is specifically designed for mtDNA analysis. In this study, we employ the ForenSeq™ mtDNA Whole Genome Kit on the MiSeq FGx® Sequencing System for mitochondrial genome (mtGenome) sequencing across nine consecutive runs and assess its MPS performance, such as read depth (RD), forward/reverse strand bias (SB), and mtGenome coverage.

Integrated spatial multi-omics profiling of Fusobacterium nucleatum in breast cancer unveils its role in tumour microenvironment modulation and cancer progression.

Tumour-associated microbiota are integral components of the tumour microenvironment (TME). However, previous studies on intratumoral microbiota primarily rely on bulk tissue analysis, which may obscure their spatial distribution and localized effects. In this study, we applied in situ spatial-profiling technology to investigate the spatial distribution of intratumoral microbiota in breast cancer and their interactions with the local TME.

Efficient crystal structure prediction based on the symmetry principle.

Crystal structure prediction (CSP) is an evolving field aimed at discerning crystal structures with minimal prior information. Despite the success of various CSP algorithms, their practical applicability remains circumscribed, particularly for large and complex systems. Here, to address this challenge, we show an evolutionary structure generator within the MAGUS (Machine Learning and Graph Theory Assisted Universal Structure Searcher) framework, inspired by the symmetry principle.

Optimizing nitrogen fertilizer input using fallow season precipitation for dryland winter wheat.

Precipitation is the major cause of yield variation in rainfed agriculture production on the Loess Plateau. Overfertilization is economically and environmentally undesirable. Optimizing nitrogen management based on fallow season precipitation is crucial for enhancing crop water use efficiency and achieving high yields in dryland/rainfed farming systems, considering the economic and environmental drawbacks of overfertilization and the uncertainty of crop yield and N input returns under high rainfall variability.

Metabolites and metabolic pathway reactions links to sensitization of immunotherapy in pan-cancer.

Metabolic features are crucial in tumor immune interactions, but their relationship with antitumor immune responses is not yet fully understood. This study used Mendelian randomization analysis to identify the causal relationships between blood metabolites and immune cells and to evaluate the effects of metabolic pathways and reactions on antitumor immune responses in various cancers. Levels of 156 metabolites exhibited significant associations with selected immune cells.

Prediction on a Missing Ferroelectric Butterfly Phosphorus Allotrope and Its Energy-Favorable Low-Dimensional Forms.

Elemental phosphorus exhibits a remarkable diversity of allotropes, including black, white, and violet phosphorus, each with unique structural and electronic properties. Recently, phosphorus has experienced a renaissance in scientific interest for its potential applications across various fields. Among these, the red phosphorus (RP) possesses a considerable variety of stacking configurations.

The phosphorus export coefficients variability of specific land-use and the threshold response relationship with watershed characteristics in a subtropical hilly region.

The magnitude of land-use phosphorus (P) export in subtropical hilly watersheds is subject to the collective influence of various watershed characteristics. However, the spatiotemporal dynamics of key watershed characteristics and their impacts on P exports remain unclear. Total phosphorus export coefficients (TPECs) can quantify the contribution of different land-use types to P exports.

The heterogeneity of cellular metabolism in the tumour microenvironment of hepatocellular carcinoma with portal vein tumour thrombus.

Given the growing interest in the metabolic heterogeneity of hepatocellular carcinoma (HCC) and portal vein tumour thrombus (PVTT). This study comprehensively analysed the metabolic heterogeneity of HCC, PVTT, and normal liver samples using multi-omics combinations. A single-cell RNA sequencing dataset encompassing six major cell types was obtained for integrated analysis.

Simultaneous sequencing of 102 Y-STRs on Ion Torrent ™ GeneStudio ™ S5 System.

The Precision ID NGS System from Thermo Fisher Scientific is a mainstream next-generation sequencing (NGS) platform used in forensic laboratories to detect almost all commonly used forensic markers, except for Y-chromosomal short tandem repeats (Y-STRs). This study aimed to: 1) develop a Y-STR panel compatible with the automatic workflow of the NGS system using Ion AmpliSeq Technology, 2) evaluate the panel performance following the SWGDAM guidelines, and 3) explore the possibility of using a combination workflow to detect autosomal STRs and Y-STRs (AY-STR NGS workflow). The GrandFiler Y-STR Panel was successfully designed using the 'separating' and 'merging' strategies, including 102 Y-STRs and Amelogenin with an average amplicon length of 133 bp.

Performance and characterization of 94 identity-informative SNPs in Northern Han Chinese using ForenSeq ™ DNA signature prep kit.

Target and flanking region (FR) variation at 94 identity-informative SNPs (iSNPs) are investigated in 635 Northern Han Chinese using the ForenSeq DNA Signature Prep Kit on the MiSeq FGx Forensic Genomics System. The dataset presents the following performance characteristics (average values): ≥60% bases with a quality score of 20 or higher (%≥ Q20); >700 × of depth of coverage (DoC) from both Sample Details Reports and Flanking Region Reports; >80% of effective reads; ≥60% of allele coverage ratio (ACR); and ≥70% of inter-locus balance, while some stable low-performance characteristics are also observed: low DoC at rs1736442, rs1031825, rs7041158, rs338882, rs2920816, rs1493232, rs719366, and rs2342747; high noise at rs891700; and imbalanced ACR at rs6955448 and rs338882. The average amplicon length is 69 bp, suitable for detecting degraded samples.

LOXL1-AS1 inhibits JAK2 ubiquitination and promotes cholangiocarcinoma progression through JAK2/STAT3 signaling.

This study thoroughly investigated the role of the long non-coding RNA LOXL1-AS1 in the pathogenesis of cholangiocarcinoma (CCA). Through bioinformatics analysis and tissue samples validation, the study found that LOXL1-AS1 was significantly elevated in CCA, with its high expression closely tied to clinical pathological features and prognosis. In vitro and in vivo experiments revealed that LOXL1-AS1 was crucial in regulating CCA cell apoptosis, proliferation, migration, and invasion.

Metabolic-suppressed cancer-associated fibroblasts limit the immune environment and survival in colorectal cancer with liver metastasis.

Colorectal cancer liver metastasis is a major risk factor of poor outcomes, necessitating proactive interventions and treatments. Cancer-associated fibroblasts (CAFs) play essential roles in metastasis, with a focus on metabolic reprogramming. However, knowledge about associations between Cancer-associated fibroblasts metabolic phenotypes and immune cell is limited.

Sequence-based mutation patterns at 41 Y chromosomal STRs in 2 548 father-son pairs.

Unlabelled: A total of 2 548 unrelated healthy father-son pairs from a Northern Han Chinese population were genotyped at 41 Y chromosomal short tandem repeat (Y-STRs) including DYS19, DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS444, DYS447, DYS448, DYS449, DYS456, DYS458, DYS460, DYS481, DYS518, DYS522, DYS549, DYS533, DYS557, DYS570, DYS576, DYS593, DYS596, DYS627, DYS635, DYS643, DYS645, Y-GATA-H4, DYF387S1a/b, DYF404S1a/b, DYS385a/b, and DYS527a/b. In 2 548 father samples, 2 387 unique haplotypes were detected with the haplotype diversity and discrimination capacity values of 0.999 956 608 and 0.

Circular RNA nuclear receptor interacting protein 1 promoted biliary tract cancer epithelial-mesenchymal transition and stemness by regulating the miR-515-5p/AKT2 axis and PI3K/AKT/mTOR signaling pathway.

Biliary tract cancer (BTC) is a devastating malignancy that is notoriously difficult to diagnose and is associated with high mortality. Circular RNA (circRNA) is a class of endogenous non-coding RNA which has been regarded as the key regulator of tumor initiation and progression, including BTC. Circular RNA nuclear receptor interacting protein 1 (circ_NRIP1), as a circular RNA, is abnormally expressed in many human tumors and exhibits diverse functions in cancer progression.

A Noninvasive Sweat Glucose Biosensor Based on Glucose Oxidase/Multiwalled Carbon Nanotubes/Ferrocene-Polyaniline Film/Cu Electrodes.

Diabetes remains a great threat to human beings' health and its world prevalence is projected to reach 9.9% by 2045. At present, the detection methods used are often invasive, cumbersome and time-consuming, thus increasing the burden on patients.

Circular RNAs regulate parental gene expression: A new direction for molecular oncology research.

CircRNAs have been the focus of research in recent years. They are differentially expressed in various human tumors and can regulate oncogenes and tumor suppressor genes expression through various mechanisms. The diversity, stability, evolutionary conservatism and cell- or tissue-specific expression patterns of circRNAs also endow them with important regulatory roles in promoting or inhibiting tumor cells malignant biological behaviors progression.

Flexible Two-Dimensional Vanadium Carbide MXene-Based Membranes with Ultra-Rapid Molecular Enrichment for Surface-Enhanced Raman Scattering.

Two-dimensional (2D) MXene materials have attracted broad interest in surface-enhanced Raman scattering (SERS) applications by virtue of their abundant surface terminations and excellent photoelectric properties. Herein, we propose to design highly sensitive MXene-based SERS membranes by integrating a 2D downsizing strategy with molecular enrichment approaches. Two types of 2D vanadium carbide (VC and VC) MXenes are demonstrated for ultrasensitive SERS sensing, and corresponding SERS mechanisms including the effect of 2D vanadium carbide thickness on their electron density states and interfacial photoinduced charge transfer resonance were discussed.

Ion Torrent ™ Genexus ™ Integrated Sequencer and ForeNGS Analysis Software-An automatic NGS-STR workflow from DNA to profile for forensic science.

The Ion Torrent ™ Genexus ™ Sequencer (Genexus) is a highly integrated instrument that can automate library construction, templating, and sequencing in a single-instrument run. By programing the ForeNGS Analysis Software (FNAS), we bridged the gap between sequencing and genotyping without manual intervention. FNAS can automatically transfer sequencing output files from Genexus, analyze the repeat and flanking regions aligned to the GRCh38 assembly, name the alleles according to the ISFG guidelines, and generate user-friendly interactive profiles.