UMRFormer-net: a three-dimensional U-shaped pancreas segmentation method based on a double-layer bridged transformer network.

Background: Methods based on the combination of transformer and convolutional neural networks (CNNs) have achieved impressive results in the field of medical image segmentation. However, most of the recently proposed combination segmentation approaches simply treat transformers as auxiliary modules which help to extract long-range information and encode global context into convolutional representations, and there is a lack of investigation on how to optimally combine self-attention with convolution. Methods: We designed a novel transformer block (MRFormer) that combines a multi-head self-attention layer and a residual depthwise convolutional block as the basic unit to deeply integrate both long-range and local spatial information. The MRFormer block was embedded between the encoder and decoder in U-Net at the last two layers. This framework (UMRFormer-Net) was applied to the segmentation of three-dimensional (3D) pancreas, and its ability to effectively capture the characteristic contextual information of the pancreas and surrounding tissues was investigated. Results: Experimental results show that the proposed UMRFormer-Net achieved accuracy in pancreas segmentation that was comparable or superior to that of existing state-of-the-art 3D methods in both the Clinical Proteomic Tumor Analysis Consortium Pancreatic Ductal Adenocarcinoma (CPTAC-PDA) dataset and the public Medical Segmentation Decathlon dataset (self-division). UMRFormer-Net statistically significantly outperformed existing transformer-related methods and state-of-the-art 3D methods (P<0.05, P<0.01, or P<0.001), with a higher Dice coefficient (85.54% and 77.36%, respectively) or a lower 95% Hausdorff distance (4.05 and 8.34 mm, respectively). Conclusions: UMRFormer-Net can obtain more matched and accurate segmentation boundary and region information in pancreas segmentation, thus improving the accuracy of pancreas segmentation. The code is available at https://github.com/supersunshinefk/UMRFormer-Net.

Insights into the conversion of dissolved organic phosphorus favors algal bloom, arsenate biotransformation and microcystins release of Microcystis aeruginosa.

Little information is available on influences of the conversion of dissolved organic phosphorus (DOP) to inorganic phosphorus (IP) on algal growth and subsequent behaviors of arsenate (As(V)) in Microcystis aeruginosa (M. aeruginosa). In this study, the influences factors on the conversion of three typical DOP types including adenosine-5-triphosphate disodium salt (ATP), ß-glycerophosphate sodium (ßP) and D-glucose-6-phosphate disodium salt (GP) were investigated under different extracellular polymeric secretions (EPS) ratios from M. aeruginosa, and As(V) levels. Thus, algal growth, As(V) biotransformation and microcystins (MCs) release of M. aeruginosa were explored in the different converted DOP conditions compared with IP. Results showed that the three DOP to IP without EPS addition became in favor of algal growth during their conversion. Compared with IP, M. aeruginosa growth was thus facilitated in the three converted DOP conditions, subsequently resulting in potential algal bloom particularly at arsenic (As) contaminated water environment. Additionally, DOP after conversion could inhibit As accumulation in M. aeruginosa, thus intracellular As accumulation was lower in the converted DOP conditions than that in IP condition. As(V) biotransformation and MCs release in M. aeruginosa was impacted by different converted DOP with their different types. Specifically, DMA concentrations in media and As(III) ratios in algal cells were promoted in converted ßP condition, indicating that the observed dissolved organic compositions from ßP conversion could enhance As(V) reduction in M. aeruginosa and then accelerate DMA release. The obtained findings can provide better understanding of cyanobacteria blooms and As biotransformation in different DOP as the main phosphorus source.

Photodegradation Kinetics and Deep Learning-Based Intelligent Colorimetric Method for Bioavailability-Based Dissolved Iron Speciation.

Via the photodegradation of dissolved iron (dFe) complexes in the euphotic zone, released free Fe(III) is the most important source of bioavailable iron for eukaryotic phytoplankton. There is an urgent need to establish bioavailability-based dissolved iron speciation (BDIS) methods. Herein, an intelligent system with dFe pretreatment and a colorimetric sensor is developed for real-time monitoring of newly generated Fe(III) ions. According to the photodegradation kinetics of dFe, including kinetic constant and photogenerated time of free Fe(III) ions, 3 sources, 6 kinds, and 12 species of dFe are determined by our photocatalytic-assisted colorimetric sensor and deep learning model within 20.0 min. The algal dFe-uptake for 4 days can be predicted by BDIS with correlation coefficient 0.85, which could be explained by the hard and soft acids and bases theory (HSAB) and density functional theory (DFT). These results successfully demonstrate the proof-of-concept for photodegradation kinetics-based speciation and bioavailability assessments of dissolved metals.

Responses of nickel bioavailability and toxicity of Prorocentrum Donghaienses to dissolved organic matter (DOM) fractions incubated in urea.

Urea, nickel (Ni) and dissolved organic matter (DOM) from land varied with different sources have a great impact on the offshore ecosystem. The heterogeneity of Ni bioavailability and toxicity of Prorocentrum donghaiense influenced by DOM fractions incubated in urea was investigated in this study. On the occasion, chlorophyll (Chl a) concentration, growth rate, and photosynthesis parameters were monitored to track changes occurring in the test organism. Chl a concentration and photosynthesis parameters in the treatment of hydrophilic DOM (HPI) with Ni-free was significantly higher than that in the control treatment, and similar data were shown in the treatment of hydrophobic DOM（HPO）with the low Ni environment (0.17µmol L-1). However, the opposite phenomena were observed in the treatments of HPO with the higher Ni environment (over 170µmol L-1). Moreover, the EC50 of Ni for P.donghaiense incubated in HPO was relatively lower than that in HPI and control treatment, which implied that HPO elevated the toxicity of Ni. Therefore, the varied DOM compositions because of different origins, as a chelating agent and potential nutrient source in coastal waters, shows the significantly different bioavailability and toxicity of Ni with the increasing inputs of urea, which in turn influences the dynamics of phytoplankton.

Low-toxic, fluorescent labeled and size-controlled graphene oxide quantum dots@polystyrene nanospheres as reference material for quantitative determination and in vivo tracing.

Polystyrene (PS) is selected as a representative nanoplastic and persistent pollutant for its difficult degradation and wide application. The environmental risk assessment of PS is obstructed by the toxic dye-based fluorescent PS, which false positives could be induced by the leakage of dye. For high biocompatibility, low toxicity, hydrophilicity, good water dispersibility, strong fluorescent stability, graphene oxide quantum dots (o-CQDs) are selected and embedded into PS microspheres, i.e., o-CQDs@PS, by microemulsion polymerization and denoted as CPS. Meanwhile, the sizes of CPS, e.g., 100, 150, and 200 nm, could be controlled by optimizing the type and number of water-soluble initiators. The anti-interference, low toxicity, and in vivo fluorescent tracing of CPS are proven by the coexistence of metals (including Fe2+, Fe3+, K+, Ba2+, Al3+, Zn2+, Mg2+, Ca2+, and Na+) on the fluorescence intensity of CPS, the growth of Chlorella pyrenoidosa and Artemia cysts as aquatic phytoplankton and zooplankton cultured with CPS, and the transfer of CPS from water into brine shrimp. In the concentration range of 0.1-100 mg/L, CPS can be quantitatively determined, which is suitable for coastal water and wastewater treatment plants. Therefore, CPS with standard size is suitable as reference material of PS.

Benefit-Risk Assessment of Dietary Patterns by Bioavailable Metals, Gut Microbes, and Their Interaction for Human Health.

The high-carbohydrate, low-fat, low-protein (HC-LFP) and low-carbohydrate, high-fat, high-protein (LC-HFP) diets are the main dietary patterns worldwide. The influence of dietary patterns on bioavailable metals, gut microbes, and their interaction is still unknown. A biomimetic digestive tract with full functions is constructed to transform the diets into chyme, and the gut microbes are cultured with the corresponding chyme. The diet species-specificity in bioavailable metal content and the positive and negative correlations between bioavailable metals and microbial reproductions are disclosed. The safe dosage and maximum consumption are 369.5 and 858.6 g/d and 268.6 and 3119.0 g/d for LC-HFP and HC-LFP, respectively. When replacing HC-LFP with LC-HFP for 21 days, the bioavailability of Fe and Cr is increased 83.2% and 268.4%, respectively; the reproductions of harmful and benefical microbes are significantly increased and decreased. The prevalences of obesity, inflammation, septicemia, and cancer are increased, and then the risk of dietary pattern shift is disclosed.

Long-term stable, high accuracy, and visual detection platform for In-field analysis of nitrite in food based on colorimetric test paper and deep convolutional neural networks.

Nitrite is one of the most common carcinogens in daily food. Its simple, rapid, inexpensive, and in-field measurement is important for food safety, based on the requirements of the standard from Codex Alimentarius Commission and China. Using polyacrylonitrile (PAN) and thin layer silica gel (SG), p-aminophenylcyclic acid (SA) and naphthalene ethylenediamine hydrochloride (NEH), as carriers and chromogenic agents, respectively, PAN-NSS as nitrite color sensor is proposed. After fixing and protecting of SA and NEH with layer-upon-layer PAN, the validity period of the test paper can be prolonged from 7 days to more than 30 days. The reproducibility of PAN-NSS preparation is ensured by electrospinning. Combined with PAN-NSS, deep convolutional neural network (DCNN) and APP as a visual monitoring platform, which has the functions of rapid sampling, data processing and transmission, intuitive feedback, etc., and provides a fully integrated detection system for field detection.

Transition Radiation as a Probe of the Chiral Anomaly.

A fast charged particle crossing the boundary between chiral matter and vacuum radiates transition radiation. Its most remarkable features-the resonant behavior at a certain emission angle and the circular polarization of the spectrum-depend on the parameters of the chiral anomaly in a particular material or matter. Chiral transition radiation can be used to investigate the chiral anomaly in such diverse media as the quark-gluon plasma, Weyl semimetals, and axionic dark matter.

Regulated effects of Prorocentrum donghaiense Lu exudate on nickel bioavailability when cultured with different nitrogen sources.

Exudates by marine phytoplankton and metals coexist in the seawater, but little is known about their interaction. In this study, cultures of Prorocentrum donghaiense Lu were grown in urea and ammonium, and then exposed to different Ni ion levels in order to study the effects of Ni ions on algal growth. The regulatory mechanisms of P. donghaiense Lu for coping with different Ni ion levels was investigating by characterizing dissolved organic carbon (DOC), carbohydrate and protein content released per cell, hydropathy properties (hydrophilic and hydrophobic fractions) and thiol compounds (cysteine-like or glutathione-like). Lower levels of Ni ions (pNi>10.0) significantly promoted the growth of P. donghaiense Lu when incubated in urea; however, the same was not true for P. donghaiense Lu cultivated in ammonium. An increased presence of hydrophobic fractions and thiol compounds (cysteine-like or glutathione-like compounds) induced by low Ni ions (pNi>10.0) in urea cultures suggest that the activation of cellular mechanisms in response to insufficient Ni ion stress enhances Ni bioavailability. Furthermore, the abundance of carbohydrates and proteins released by cells when exposed to higher Ni ions levels (from pNi = 10.0 to pNi = 8.0) both in urea and ammonium cultures suggests that algal cells may utilize exudate to complex Ni cations and reduce their toxicity. Therefore, it can be speculated that phytoplankton can produce large amounts of specific exudate, which may accelerate the metal bioavailability (insufficient levels) and reduce metal toxicity (excess levels) to maintain an equilibrium with metals in the environment.

The influence of urea and nitrate nutrients on the bioavailability and toxicity of nickel to Prorocentrum donghaiense (Dinophyta) and Skeletonema costatum (Bacillariophyta).

Nitrogen nutrients and nickel(Ni) are ubiquitous in aquatic environments, and they are important for primary production of ocean ecosystem. This study examined the interaction of nitrogen nutrients (specifically urea and nitrate) and Ni on chlorophyll (Chl a) concentration and photosynthesis parameters values of Prorocentrum donghaiense and Skeletonema costatum. The data presented here indicate that low concentration of Ni for P. donghaiense and S. costatum can enhance both Chl a concentration and photosynthesis parameters values when grown in urea containing environment. Despite this increase there was also an observed depression in both species tested when incubated in high concentration of Ni for P. donghaiense and S. costatum regardless of incubating in urea or nitrate. Additionally, EC50 values of Chl a and Fv/Fm for Ni at different time intervals were calculated in this study. These observations indicated that the Ni tolerance was higher in P. donghaiense as compared to S. costatum. The Ni tolerance of P. donghaiense incubated in urea was higher than that incubating in nitrate. The same phenomenon was not observed in S. costatum, which indicated that the influence of urea was dependent on the species investigated. Thus, urea input could impact Ni bioavailability and toxicity, and then affect the biodynamics thereafter.

Electromagnetic fields and anomalous transports in heavy-ion collisions-a pedagogical review.

The hot and dense matter generated in heavy-ion collisions may contain domains which are not invariant under P and CP transformations. Moreover, heavy-ion collisions can generate extremely strong magnetic fields as well as electric fields. The interplay between the electromagnetic field and triangle anomaly leads to a number of macroscopic quantum phenomena in these P- and CP-odd domains known as anomalous transports. The purpose of this article is to give a pedagogical review of various properties of the electromagnetic fields, the anomalous transport phenomena, and their experimental signatures in heavy-ion collisions.

Effects of nitrate addition and iron speciation on trace element transfer in coastal food webs under phosphate and iron enrichment.

Coastal organisms are often exposed to both iron enrichment and eutrophication. Trace elements transfer in coastal food webs are critical for marine life and therefore influence coastal ecosystem function and the global carbon cycle. However, how these exposures affect algal element uptake and the subsequent element transfer to marine copepods (Tigriopus japonicus) is unknown. Here we investigated the effects of nitrate addition and iron speciation (Fe (OH)3 or EDTA-Fe) on the biological uptake of Cu, Zn, and Se under phosphate and iron enrichment, using Thalassiosira weissflogii, Skeletonema costatum, and Chlorella vulgaris as model marine algae. Algal element adsorption/absorption generally increased with increasing macronutrient concentrations. Algal element assimilation efficiencies depended on iron speciation and marine algae species. Element assimilation efficiencies of copepods were significantly correlated to the intracellular element concentrations in algal cells. Element uptake and transfer were controlled by eutrophication, iron speciation, and algal species in coastal food webs.

Effects of macronutrient additions on nickel uptake and distribution in the dinoflagellate Prorocentrum donghaiense Lu.

The influences of macronutrient additions on nickel (Ni) uptake and distribution in the subcellular structures and macromolecular components of the dinoflagellate Prorocentrum donghaiense Lu were examined using a radioisotope tracer method. The results showed that nitrate addition enhanced the uptake of Ni by P. donghaiense, whereas phosphate addition inhibited Ni uptake at high-Ni concentration. Nitrate or phosphate addition significantly affected Ni distribution in the subcellular structures and components. The majority of Ni was found in the soluble substances (>70%) and in the proteins (55.0-79.6%) of the algal cells. Urea reduced the Ni content in the amino acid-carbohydrate but elevated its content in proteins, and shown significantly correlated with the protein content of the algal cells. Thus, nutrient enrichment could influence both metal uptake and its distribution in the subcellular structures and components of the phytoplankton, as well as its subsequent transfer in marine food chains.

Influence of N, P additions on the transfer of nickel from phytoplankton to copepods.

We examined the influence of macronutrient (nitrate and phosphate) additions on Ni uptake by phytoplankton (Prorocentrum donghaiense and Skeletonema costatum) and its subsequent transfer to marine copepods (Calanus sinicus and Labidocera euchaeta). Ni uptake by phytoplankton after 24h of exposure was markedly dependent on nutrient conditions, with a higher nutrient quota facilitating Ni accumulation in the algae. Trophic transfer was quantified by measurements of the Ni assimilation efficiency in C. sinicus and L. euchaeta, feeding on the algae under different nutrient treatments. Ni assimilation efficiency generally increased with an increase of nutrient concentration in the algae. A significant positive-correlation was found between the Ni assimilation efficiencies of the copepods and the %intracellular Ni in the algal cells. However, ambient nutritional conditions had little effect on the physiological turnover rate constant of Ni by copepods. Thus, nutrient enrichment may lead to an increase in Ni uptake and transfer in marine plankton.