MoDorado: enhanced detection of tRNA modifications in nanopore sequencing by off-label use of modification callers.

Rapid and accurate identification of transfer RNA (tRNA) modifications is crucial for understanding their role in protein translation and disease. However, their detection on tRNAs is challenging due to high modification density. With the release of the nanopore direct RNA sequencing kit SQK-RNA004, de novo modification calling models became available for pseudouridine (Ψ), m6A, inosine, and m5C, as part of the Dorado basecaller.

Effect and Safety of Finerenone in Patients with IgA Nephropathy.

Purpose: The study aimed to retrospectively evaluate the efficacy and safety of finerenone in patients diagnosed with IgA nephropathy.

Methods: 42 IgA nephropathy patients treated with finerenone combined with renin-angiotensin system inhibitor (RASI) and 42 patients who received RASI monotherapy were included in this study. The follow-up duration was 3 months.

Regulating the N-oxidation selectivity of P450BM3 monooxygenases for N-heterocycles through computer-assisted structure-guided design.

N-oxidation of N-heterocycles is essential in the synthesis of natural products but challenging due to low efficacy and poor regioselectivity. In this study, the N-oxidation selective potential of P450BM3 from Bacillus megaterium for N-heterocyclic compounds is investigated. Here, twelve amino acids located in the active center, including A74, L75, V78, A82, F87, I263, A264, A328, P329, A330, I401, and L437, are investigated by site-saturation mutation.

Polymer Type, Oxidation, Size, and Abundance of Microplastics in Subsoils versus Topsoils with Varying Land Use in Beijing, China.

The occurrence of microplastics (MPs) in topsoil is well documented; however, recent evidence has also shown that MPs can reach the subsoil, which may eventually enter groundwater aquifers posing a potential threat to drinking water. In this study, we examined polymer-type specific, small-sized MPs (20-500 μm) in both topsoil (5 cm) and subsoil (50 and 100 cm) in the megacity of Beijing, China, using Laser Direct Infrared (LDIR) Chemical Imaging Spectroscopy, focusing on variation in abundance, size, polymer type, and oxidation characteristics across 6 land use types. A total of 6085 MP particles with 11 polymer types were identified.

Sacubitril/valsartan affects pulmonary arterial pressure in heart failure with preserved ejection fraction and pulmonary hypertension among PD patients.

Purpose: Pulmonary hypertension is an independent risk factor for all-cause mortality and cardiovascular events in peritoneal dialysis (PD) patients with heart failure with preserved ejection fraction (HFpEF). However, there is still no effective treatment. The aim of this study is to evaluate the efficacy and safety of sacubitril/valsartan in PD patients with HFpEF and pulmonary hypertension.

Thiocyanate degradation by mixed bacterial consortia: Adaptive mechanism in response to thiocyanate stress and metabolic pathway.

Thiocyanate, frequently detected in various industrial wastewater, poses significant risks to organisms. The activated sludge isolate thiocyanate-degrading bacterial consortia (TDBC) efficiently metabolizes thiocyanate. However, the adaptive mechanism in response to thiocyanate stress and metabolic pathway by TDBC have not been elucidated.

Demultiplexing and barcode-specific adaptive sampling for nanopore direct RNA sequencing.

Nanopore direct RNA sequencing (dRNA-seq) enables unique insights into RNA biology. However, applications are currently limited by the lack of accurate and cost-effective sample multiplexing. Here we introduce WarpDemuX, an ultra-fast and highly accurate adapter-barcoding and demultiplexing approach for dRNA-seq with SQK-RNA002 and SQK-RNA004 chemistries.

Global soil pollution by toxic metals threatens agriculture and human health.

Toxic metal pollution is ubiquitous in soils, yet its worldwide distribution is unknown. We analyzed a global database of soil pollution by arsenic, cadmium, cobalt, chromium, copper, nickel, and lead at 796,084 sampling points from 1493 regional studies and used machine learning techniques to map areas with exceedance of agricultural and human health thresholds. We reveal a previously unrecognized high-risk, metal-enriched zone in low-latitude Eurasia, which is attributed to influential climatic, topographic, and anthropogenic conditions.

Nomogram for thromboembolic events in primary membranous nephropathy associated with PLA2R antibody.

Patients with nephrotic syndrome, particularly those with primary membranous nephropathy (pMN), are at a heightened risk of thromboembolic events. The presence of phospholipase A2 receptor (PLA2R) antibody serves as an indicator of active primary membranous nephropathy. Identifying high-risk patients for thromboembolic events is crucial for facilitating effective communication between healthcare providers and patients, evaluating treatment outcomes, and assessing medical costs.

Corrigendum: HIF-1α alleviates high-glucose-induced renal tubular cell injury by promoting Parkin/PINK1-mediated mitophagy.

[This corrects the article DOI: 10.3389/fmed.2021.

When plastisphere and drilosphere meet: Earthworms facilitate microbiome and nutrient turnover to accelerate biodegradation of agricultural plastic films.

Agricultural plastic mulching films have been an environmental concern for decades. The effects of the interactions between the anthropogenic plastisphere and other soil biospheres, particularly that of earthworms, on the fate of plastics remain poorly understood. Here, we investigated the decomposition of buried nonbiodegradable low-density polyethylene (LDPE) versus biodegradable PBTA/PLA copolymers in the presence of earthworms (Amynthas cortices) in dynamic microcosms.

Long-term soil remediation using layered double hydroxides: Field evidence for simultaneous immobilization of both cations and oxyanions.

Layered double hydroxides (LDHs) have great potential for immobilizing potentially toxic elements in soil. Nevertheless, their practical effectiveness under field conditions remains largely unknown. In this study, we conducted a 2.

Tungsten contamination, behavior and remediation in complex environmental settings.

Tungsten (W) is a rare element and present in the earth's crust mainly as iron, aluminium, and calcium minerals including wolframite and scheelite. This review aims to offer an overview on the current knowledge on W pollution in complex environmental settlings, including terrestrial and aquatic ecosystems, linking to its natural and anthropogenic sources, behavior in soil and water, environmental and human health hazards, and remediation strategies. Tungsten is used in many alloys mainly as wafers, which have wide industrial applications, such as incandescent light bulb filaments, X-ray tubes, arc welding electrodes, radiation shielding, and industrial catalysts.

Antioxidative effect of astragalosides on acute pancreatitis in mice.

Introduction: The research examined the antioxidative impact of astragalosides (AST) on experimental acute pancreatitis (AP) in mice. This study aims to assess the correlation between varying doses of astragalosides and superoxide dismutase (SOD) activity in an acute pancreatitis mouse model. By examining the interplay between astragaloside's protective effects and its antioxidant properties, we aim to deepen our understanding of its therapeutic potential in acute pancreatitis.

Layered double hydroxides for simultaneous and long-term immobilization of metal(loid)s in soil under simulated aging.

Soil contamination by toxic metals and metalloids poses a grave threat to food security and human well-being. Immobilization serves as an effective method for the remediation of soils contaminated by metal(loid)s. Nevertheless, the ability of soil amendments for simultaneous immobilization of cations and oxyanions, and the long-term effectiveness of immobilization need substantial improvements.

Exposure Pathways and Toxicity of Microplastics in Terrestrial Insects.

The detrimental effects of plastics on aquatic organisms, including those of macroplastics, microplastics, and nanoplastics, have been well established. However, knowledge on the interaction between plastics and terrestrial insects is limited. To develop effective strategies for mitigating the impact of plastic pollution on terrestrial ecosystems, it is necessary to understand the toxicity effects and influencing factors of plastic ingestion by insects.

Mechanism of clay mineral modified biochar simultaneously immobilizes heavy metals and reduces soil carbon emissions.

Heavy metal pollution in farmland soil has become increasingly severe, and multi-element composite pollution has brought enormous harm to human production and life. Environmental changes in cold regions (such as freeze-thaw cycles and dry-wet alternations) may increase the potential physiological toxicity of heavy metals and exacerbate pollution risks. In order to reveal the effectiveness of sepiolite modified biochar in the remediation of the soil contaminated with lead (Pb), cadmium (Cd), and chromium (Cr), the rice husk biochar pyrolyzed at 500 and 800 °C were selected for remediation treatment (denoted as BC500 and BC800).

Sequencing accuracy and systematic errors of nanopore direct RNA sequencing.

Background: Direct RNA sequencing (dRNA-seq) on the Oxford Nanopore Technologies (ONT) platforms can produce reads covering up to full-length gene transcripts, while containing decipherable information about RNA base modifications and poly-A tail lengths. Although many published studies have been expanding the potential of dRNA-seq, its sequencing accuracy and error patterns remain understudied.

Results: We present the first comprehensive evaluation of sequencing accuracy and characterisation of systematic errors in dRNA-seq data from diverse organisms and synthetic in vitro transcribed RNAs.

Facial Expression Realization of Humanoid Robot Head and Strain-Based Anthropomorphic Evaluation of Robot Facial Expressions.

The facial expressions of humanoid robots play a crucial role in human-computer information interactions. However, there is a lack of quantitative evaluation methods for the anthropomorphism of robot facial expressions. In this study, we designed and manufactured a humanoid robot head that was capable of successfully realizing six basic facial expressions.

Microplastic generation from field-collected plastic gauze: Unveiling the aging processes.

Accumulation of plastic debris in the environment is a matter of global concern. As plastic ages, it generates microplastic (MP) particles with high mobility. Understanding how MPs are generated is crucial to controlling this emerging contaminant.

Predicting Anaerobic Membrane Bioreactor Performance Using Flow-Cytometry-Derived High and Low Nucleic Acid Content Cells.

Having a tool to monitor the microbial abundances rapidly and to utilize the data to predict the reactor performance would facilitate the operation of an anaerobic membrane bioreactor (AnMBR). This study aims to achieve the aforementioned scenario by developing a linear regression model that incorporates a time-lagging mode. The model uses low nucleic acid (LNA) cell numbers and the ratio of high nucleic acid (HNA) to LNA cells as an input data set.

Efficacy and safety of rituximab in elderly patients with membranous nephropathy.

Advancing age is a risk factor for treatment-related side effects and mortality in membranous nephropathy (MN) patients treated with traditional immunosuppressive regimens. This study aimed to determine the efficacy and safety of rituximab (RTX) in the treatment of elderly patients with MN. We performed a single center retrospective review of 37 consecutive MN patients aged 70 and older at the time of RTX infusion.