Insight into spatial variations of DOM fractions and its interactions with microbial communities of shallow groundwater in a mesoscale lowland river watershed.

Dissolved organic matter (DOM) plays a crucial role in driving biogeochemical processes and determining water quality in shallow groundwater systems, where DOM could be susceptible to dynamic influences of surface water influx. This study employed fluorescence excitation-emission matrix (EEM) spectroscopy combined with principal component coefficients, parallel factor analysis (PARAFAC), co-occurrence network analysis and structural equation modeling (SEM) to examine changes of DOM fractions from surface water to shallow groundwater in a mesoscale lowland river basin. Combining stable isotope and hydrochemical parameters, except for surface water (SW), two groups of groundwater samples were defined, namely, deeply influenced by surface water (IGW) and groundwater nearly non-influenced by surface water (UGW), which were 50.34 % and 19.39 % recharged by surface water, respectively. According to principal component coefficients, reassembled EEM data of these categories highlighted variations of the tyrosine-like peak in DOM. EEMs coupled with PARAFAC extracted five components (C1-C5), i.e. C1, protein-like substances, C2 and C4, humic-like substances, and C3 and C5, microbial-related substances. The abundance of the protein-like was SW > IGW > UGW, while the order of the humic-like was opposite. The bacterial communities exhibited an obvious cluster across three regions, which hinted their sensitivity to variations in environmental conditions. Based on co-occurrence, SW represented the highest connectivity between bacterial OTUs and DOM fractions, followed by IGW and UGW. SEM revealed that microbial activities increased bioavailability of the humic-like in the SW and IGW, whereas microbial compositions promoted the evolution of humic-like substances in the UGW. Generally, these results could be conducive to discern dissimilarity in DOM fractions across surface water and shallow groundwater, and further trace their interactions in the river watershed.

Spectral and molecular insights into the characteristics of dissolved organic matter in nitrate-contaminated groundwater.

The characteristics of dissolved organic matter (DOM) serve as indicators of nitrate pollution in groundwater. However, the specific DOM components associated with nitrate in groundwater systems remain unclear. In this study, dual isotopes of nitrate, three-dimensional Excitation emission matrices (EEMs) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) were utilized to uncover the sources of nitrate and their associations with DOM characteristics. The predominant nitrate in the targeted aquifer was derived from soil organic nitrogen (mean 46.0%) and manure &sewage (mean 34.3%). The DOM in nitrate-contaminated groundwater (nitrate-nitrogen >20 mg/L) exhibited evident exogenous characteristics, with a bioavailable content 2.58 times greater than that of uncontaminated groundwater. Regarding the molecular characteristics, DOM molecules characterized by CHO + 3N, featuring lower molecular weights and H/C ratios, indicated potential for mineralization, while CHONS formulas indicated the exogenous features, providing the potential for accurate traceability. These findings provided insights at the molecular level into the characterization of DOM in nitrate-contaminated groundwater and offer scientific guidance for decision-making regarding the remediation of groundwater nitrate pollution.

Glutamine antagonist DRP-104 suppresses tumor growth and enhances response to checkpoint blockade in KEAP1 mutant lung cancer.

Loss-of-function mutations in KEAP1 frequently occur in lung cancer and are associated with poor prognosis and resistance to standard of care treatment, highlighting the need for the development of targeted therapies. We previously showed that KEAP1 mutant tumors consume glutamine to support the metabolic rewiring associated with NRF2-dependent antioxidant production. Here, using preclinical patient-derived xenograft models and antigenic orthotopic lung cancer models, we show that the glutamine antagonist prodrug DRP-104 impairs the growth of KEAP1 mutant tumors. We find that DRP-104 suppresses KEAP1 mutant tumors by inhibiting glutamine-dependent nucleotide synthesis and promoting antitumor T cell responses. Using multimodal single-cell sequencing and ex vivo functional assays, we demonstrate that DRP-104 reverses T cell exhaustion, decreases Tregs, and enhances the function of CD4 and CD8 T cells, culminating in an improved response to anti-PD1 therapy. Our preclinical findings provide compelling evidence that DRP-104, currently in clinical trials, offers a promising therapeutic approach for treating patients with KEAP1 mutant lung cancer.

Visible-Light-Promoted Cascade Coupling of 2-Isocyanonaphthalenes with Elemental Sulfur and Amines to Construct Naphtho[2,1-d]thiazol-2-Amines.

A visible-light-induced strategy has been explored for the synthesis of naphtho[2,1-d]thiazol-2-amines through ortho-C-H sulfuration of 2-isocyanonaphthalenes with elemental sulfur and amines under external photocatalyst-free conditions. This three-component reaction, which utilizes elemental sulfur as the odorless sulfur source, molecular oxygen as the clean oxidant, and visible light as the clean energy source, provides a mild and efficient approach to construct a series of naphtho[2,1-d]thiazol-2-amines. Preliminary mechanistic studies indicated that visible-light-promoted photoexcitation of reaction intermediates consisting of thioureas and DBU might be involved in this transformation.

Revisiting an old relationship: the causal associations of the ApoB/ApoA1 ratio with cardiometabolic diseases and relative risk factors-a mendelian randomization analysis.

BACKGROUND: It has been confirmed that the ApoB/ApoA1 ratio is closely associated with the incidence of cardiometabolic diseases (CMD). However, due to uncontrolled confounding factors in observational studies, the causal relationship of this association remains unclear. METHODS: In this study, we extracted the ApoB/ApoA1 ratio and data on CMD and its associated risk factors from the largest European Genome-Wide Association Study. The purpose was to conduct Mendelian Randomization (MR) analysis. The causal relationship between the ApoB/ApoA1 ratio and CMD was evaluated using both univariable and multivariable MR analyses. Furthermore, bidirectional MR analysis was performed to estimate the causal relationship between the ApoB/ApoA1 ratio and risk factors for CMD. The final verification confirmed whether the ApoB/ApoA1 ratio exhibits a mediating effect in CMD and related risk factors. RESULTS: In terms of CMD, a noteworthy correlation was observed between the increase in the ApoB/ApoA1 ratio and various CMD, including ischemic heart disease, major adverse cardiovascular events, aortic aneurysm, cerebral ischemic disease and so on (all PFDR<0.05). Meanwhile, the ApoB/ApoA1 ratio was significantly associated with CMD risk factors, such as hemoglobin A1c, fasting insulin levels, waist-to-hip ratio, sedentary behavior, and various others, demonstrating a notable causal relationship (all PFDR<0.05). Additionally, the ApoB/ApoA1 ratio played a mediating role in CMD and relative risk factors. CONCLUSIONS: This MR study provides evidence supporting the significant causal relationship between the ApoB/ApoA1 ratio and CMD and its risk factors. Moreover, it demonstrates the mediating effect of the ApoB/ApoA1 ratio in CMD and its risk factors. These findings suggest that the ApoB/ApoA1 ratio may serve as a potential indicator for identifying the risk of developing CMD in participants.

Composition Design Strategy for High Entropy Amorphous Alloys.

High entropy amorphous alloys (HEAAs) are materials that have received much attention in recent years. They exhibit many unique properties; however, research on their composition design method has not been deep enough. In this paper, we summarized some effective composition design strategies for HEAAs. By adjusting the atomic ratio from quinary bulk metallic glasses, Ti20Zr20Cu20Ni20Be20 HEAA with a high fracture strength of 2315 MPa was designed. By similar element addition/substitution, a series of Ti-(Zr, Hf, Nb)-Cu-Ni-Be HEAAs was developed. They possess good glass-forming ability with a maximum critical diameter of 30 mm. Combining elements from those ternary/quaternary bulk metallic glasses has also proved to be an effective method for designing new HEAAs. The effect of high entropy on the property of the alloy, possible composition design methods, and potential applications were also discussed. This paper may provide helpful inspiration for future development of HEAAs.

Glutamine antagonist DRP-104 suppresses tumor growth and enhances response to checkpoint blockade in KEAP1 mutant lung cancer.

Loss-of-function mutations in KEAP1 frequently occur in lung cancer and are associated with resistance to standard of care treatment, highlighting the need for the development of targeted therapies. We have previously shown that KEAP1 mutant tumors have increased glutamine consumption to support the metabolic rewiring associated with NRF2 activation. Here, using patient-derived xenograft models and antigenic orthotopic lung cancer models, we show that the novel glutamine antagonist DRP-104 impairs the growth of KEAP1 mutant tumors. We find that DRP-104 suppresses KEAP1 mutant tumor growth by inhibiting glutamine-dependent nucleotide synthesis and promoting anti-tumor CD4 and CD8 T cell responses. Using multimodal single-cell sequencing and ex vivo functional assays, we discover that DRP-104 reverses T cell exhaustion and enhances the function of CD4 and CD8 T cells culminating in an improved response to anti-PD1 therapy. Our pre-clinical findings provide compelling evidence that DRP-104, currently in phase 1 clinical trials, offers a promising therapeutic approach for treating patients with KEAP1 mutant lung cancer. Furthermore, we demonstrate that by combining DRP-104 with checkpoint inhibition, we can achieve suppression of tumor intrinsic metabolism and augmentation of anti-tumor T cell responses.

INSnet: a method for detecting insertions based on deep learning network.

BACKGROUND: Many studies have shown that structural variations (SVs) strongly impact human disease. As a common type of SV, insertions are usually associated with genetic diseases. Therefore, accurately detecting insertions is of great significance. Although many methods for detecting insertions have been proposed, these methods often generate some errors and miss some variants. Hence, accurately detecting insertions remains a challenging task. RESULTS: In this paper, we propose a method named INSnet to detect insertions using a deep learning network. First, INSnet divides the reference genome into continuous sub-regions and takes five features for each locus through alignments between long reads and the reference genome. Next, INSnet uses a depthwise separable convolutional network. The convolution operation extracts informative features through spatial information and channel information. INSnet uses two attention mechanisms, the convolutional block attention module (CBAM) and efficient channel attention (ECA) to extract key alignment features in each sub-region. In order to capture the relationship between adjacent subregions, INSnet uses a gated recurrent unit (GRU) network to further extract more important SV signatures. After predicting whether a sub-region contains an insertion through the previous steps, INSnet determines the precise site and length of the insertion. The source code is available from GitHub at https://github.com/eioyuou/INSnet . CONCLUSION: Experimental results show that INSnet can achieve better performance than other methods in terms of F1 score on real datasets.

Visible-Light-Initiated Multicomponent Reactions of α-Diazoesters to Access Organophosphorus Compounds.

A simple visible-light-initiated strategy has been established for the construction of organophosphorus compounds via aerobic multicomponent reaction of α-diazoesters, cyclic ethers, and P(O)H compounds under air. A number of phosphonates and phosphinates could be efficiently isolated in moderate to good yields without the use of photosensitizers and metal reagents. This multicomponent reaction has advantages of mild condition, simple operation, eco-friendly energy, good functional-group tolerance, and gram-scale synthesis.

MAMnet: detecting and genotyping deletions and insertions based on long reads and a deep learning approach.

Structural variations (SVs) play important roles in human genetic diversity; deletions and insertions are two common types of SVs that have been proven to be associated with genetic diseases. Hence, accurately detecting and genotyping SVs is significant for disease research. Despite the fact that long-read sequencing technologies have improved the field of SV detection and genotyping, there are still some challenges that prevent satisfactory results from being obtained. In this paper, we propose MAMnet, a fast and scalable SV detection and genotyping method based on long reads and a combination of convolutional neural network and long short-term network. MAMnet uses a deep neural network to implement sensitive SV detection with a novel prediction strategy. On real long-read sequencing datasets, we demonstrate that MAMnet outperforms Sniffles, SVIM, cuteSV and PBSV in terms of their F1 scores while achieving better scaling performance. The source code is available from https://github.com/micahvista/MAMnet.

High-entropy induced a glass-to-glass transition in a metallic glass.

Glass-to-glass transitions are useful for us to understand the glass nature, but it remains difficult to tune the metallic glass into significantly different glass states. Here, we have demonstrated that the high-entropy can enhance the degree of disorder in an equiatomic high-entropy metallic glass NbNiZrTiCo and elevate it to a high-energy glass state. An unusual glass-to-glass phase transition is discovered during heating with an enormous heat release even larger than that of the following crystallization at higher temperatures. Dramatic atomic rearrangement with a short- and medium-range ordering is revealed by in-situ synchrotron X-ray diffraction analyses. This glass-to-glass transition leads to a significant improvement in the modulus, hardness, and thermal stability, all of which could promote their applications. Based on the proposed high-entropy effect, two high-entropy metallic glasses are developed and they show similar glass-to-glass transitions. These findings uncover a high-entropy effect in metallic glasses and create a pathway for tuning the glass states and properties.

Designing High Entropy Bulk Metallic Glass (HE-BMG) by Similar Element Substitution/Addition.

In this paper, we report that two newly designed high entropy bulk metallic glasses (HE-BMGs), Ti20Hf20Cu20Ni20Be20 with a critical diameter of 2 mm, and Ti16.7Zr16.7Nb16.7Cu16.7Ni16.7Be16.7 with a critical diameter of 1.5 mm, can be fabricated by copper mold casting method. These newly developed HE-BMGs exhibited a high fracture strength over 2300 MPa. The glass forming ability and atomic size distribution characteristics of the HE-BMGs are discussed in detail. Moreover, a parameter δ' was proposed to evaluate the atomic size distribution characteristics in different HEAs. It showed that this new parameter is closely related to the degree of lattice distortion and phase selection of high-entropy alloys. Adjusting the value of δ' parameter by similar element substitution/addition would be beneficial for designing high entropy bulk metallic glasses.

Factors related to the absorption rate of benign thyroid nodules after image-guided microwave ablation: a 3-year follow-up.

PURPOSE: To assess the absorption rate and factors related to the development of benign thyroid nodules (BTNs) following image-guided microwave ablation (MWA). MATERIALS AND METHODS: This retrospective study reviewed nodule efficacy in patients who underwent MWA of BTNs between January 2016 and January 2018. The endpoint was a third-year follow-up. Nodules were categorized into those showing complete absorption (volumes with less than 100% volume reduction ratio (VRR) and those showing partial absorption (100% VRR)). Univariable and multivariable regression analyses were carried out to identify variables that were associated with nodule absorption rates. RESULTS: A total of 173 BTNs (median volume= 4.23 ml; 25-75 percentiles= 2.27-9.00 ml) from 173 patients were evaluated. 49.7% (86/173) of patients had nodules that became completely absorbed. The mean VRRs of all BTNs were 18.0%, 78.7%, 89.0%, 94.5%, and 97.1% at the 1-, 6-,12-, 24- and 36- month follow-ups. At the 3-year follow-up time point, nodule characteristics related to nodule VRR included nodule volume (adjusted odds ratio [AOR], 1.1 [95% CI: 1.0, 1.2]; p = 0.03) and nodule margin (AOR, 5.3 [95% CI: 1.8, 16.0]; p < 0.01). Treatment-related characteristics included energy per ml in nodular volume (AOR, 1.0 [95% CI: 1.0, 1.0]; p < 0.01) and blockage of peripheral flow (AOR, 3.3 [95% CI: 1.3 8.3]; p = 0.01). CONCLUSIONS: US-guided image-guided MWA results in satisfactory long-term outcomes for the patients with BTNs. Factors related to nodule absorption rate were the volume and margin of the nodule, energy per ml in nodular volume and blockage of peripheral flow.

BreakNet: detecting deletions using long reads and a deep learning approach.

BACKGROUND: Structural variations (SVs) occupy a prominent position in human genetic diversity, and deletions form an important type of SV that has been suggested to be associated with genetic diseases. Although various deletion calling methods based on long reads have been proposed, a new approach is still needed to mine features in long-read alignment information. Recently, deep learning has attracted much attention in genome analysis, and it is a promising technique for calling SVs. RESULTS: In this paper, we propose BreakNet, a deep learning method that detects deletions by using long reads. BreakNet first extracts feature matrices from long-read alignments. Second, it uses a time-distributed convolutional neural network (CNN) to integrate and map the feature matrices to feature vectors. Third, BreakNet employs a bidirectional long short-term memory (BLSTM) model to analyse the produced set of continuous feature vectors in both the forward and backward directions. Finally, a classification module determines whether a region refers to a deletion. On real long-read sequencing datasets, we demonstrate that BreakNet outperforms Sniffles, SVIM and cuteSV in terms of their F1 scores. The source code for the proposed method is available from GitHub at https://github.com/luojunwei/BreakNet . CONCLUSIONS: Our work shows that deep learning can be combined with long reads to call deletions more effectively than existing methods.

Activation of the NRF2 antioxidant program sensitizes tumors to G6PD inhibition.

The KEAP1/NRF2 pathway promotes metabolic rewiring to support redox homeostasis. Activation of NRF2 occurs in many cancers, often due to KEAP1 mutations, and is associated with more aggressive disease and treatment resistance. To identify metabolic dependencies in cancers with NRF2 activation, we performed a metabolism-focused CRISPR screen. Glucose-6-phosphate dehydrogenase (G6PD), which was recently shown to be dispensable in Ras-driven tumors, was a top dependency. G6PD catalyzes the committed step of the oxidative pentose phosphate pathway that produces NADPH and nucleotide precursors, but neither antioxidants nor nucleosides rescued. Instead, G6PD loss triggered tricarboxylic acid (TCA) intermediate depletion because of up-regulation of the alternative NADPH-producing enzymes malic enzyme and isocitrate dehydrogenase. In vivo, G6PD impairment markedly suppressed KEAP1 mutant tumor growth, and this suppression was further augmented by TCA depletion by glutaminase inhibition. Thus, G6PD inhibition­induced TCA depletion is a therapeutic vulnerability of NRF2-activated cancer.

UBQLN4 is an ATM substrate that stabilizes the anti-apoptotic proteins BCL2A1 and BCL2L10 in mesothelioma.

ATM serine/threonine kinase (ATM; previously known as ataxia-telangiectasia mutated) plays a critical role in maintaining genomic stability and regulates multiple downstream pathways, such as DNA repair, cell cycle arrest, and apoptosis. As a serine/threonine kinase, ATM has an array of downstream phosphorylation substrates, including checkpoint effector checkpoint kinase 2 (CHK2). ATM inhibits cell cycle progression by phosphorylating and activating CHK2, which plays an important role in the formation and development of tumors and participates in DNA repair responses after double-stranded DNA breaks. In this study, we used a recently developed mammalian functional genetic screening system to explore a series of ATM substrates and their role in DNA damage to enhance our understanding of the DNA damage response. Ubiquilin 4 (UBQLN4), which belongs to the ubiquilin family characterized by its ubiquitin-like (UBL) and ubiquitin-associated (UBA) domains, was identified as a new substrate for ATM. UBQLN4 is involved in various intracellular processes, such as autophagosome maturation, p21 regulation, and motor axon morphogenesis. However, the biological function of UBQLN4 remains to be elucidated. In this study, we not only identified UBQLN4 as a substrate for ATM, but also found that UBQLN4 interacts with and stabilizes the anti-apoptotic proteins Bcl-2-related protein A1 (BCL2A1) and Bcl-2-like protein 10 (BCL2L10) and prevents mesothelioma cell apoptosis in response to DNA damage. These findings expand our understanding of the role of UBQLN4 in mesothelioma and provide new insights into potential mesothelioma treatments targeting substrates for ATM.

SHANK2 is a frequently amplified oncogene with evolutionarily conserved roles in regulating Hippo signaling.

Dysfunction of the Hippo pathway enables cells to evade contact inhibition and provides advantages for cancerous overgrowth. However, for a significant portion of human cancer, how Hippo signaling is perturbed remains unknown. To answer this question, we performed a genome-wide screening for genes that affect the Hippo pathway in Drosophila and cross-referenced the hit genes with human cancer genome. In our screen, Prosap was identified as a novel regulator of the Hippo pathway that potently affects tissue growth. Interestingly, a mammalian homolog of Prosap, SHANK2, is the most frequently amplified gene on 11q13, a major tumor amplicon in human cancer. Gene amplification profile in this 11q13 amplicon clearly indicates selective pressure for SHANK2 amplification. More importantly, across the human cancer genome, SHANK2 is the most frequently amplified gene that is not located within the Myc amplicon. Further studies in multiple human cell lines confirmed that SHANK2 overexpression causes deregulation of Hippo signaling through competitive binding for a LATS1 activator, and as a potential oncogene, SHANK2 promotes cellular transformation and tumor formation in vivo. In cancer cell lines with deregulated Hippo pathway, depletion of SHANK2 restores Hippo signaling and ceases cellular proliferation. Taken together, these results suggest that SHANK2 is an evolutionarily conserved Hippo pathway regulator, commonly amplified in human cancer and potently promotes cancer. Our study for the first time illustrated oncogenic function of SHANK2, one of the most frequently amplified gene in human cancer. Furthermore, given that in normal adult tissues, SHANK2's expression is largely restricted to the nervous system, SHANK2 may represent an interesting target for anticancer therapy.

Gender-related differences in concomitant articular injuries after acute lateral patellar dislocation.

OBJECTIVES: To explore the gender differences in the concomitant articular injuries after acute lateral patellar dislocation (LPD). METHODS: Magnetic resonance images were prospectively analyzed in 166 patients after an acute LPD. Concomitant articular injuries included bone contusion, medial patellofemoral ligament (MPFL) injury, articular cartilage lesion, and vastus medialis obliquus (VMO) lesion. Statistical analyses were performed between the patient's gender and the incidence of concomitant articular injuries in adolescent and adult subgroups. RESULTS: The incidence of partial and complete MPFL tear in adolescent males and females were (45%, 50%) and (63.2%, 29.8%), respectively. Compared with adolescent females, adolescent males showed higher incidence of complete MPFL tear (P = 0.049). The incidence of articular cartilage lesion of patella in adolescent males and females were 40% and 21.1%, respectively. Compared with adolescent females, adolescent males showed higher incidence of articular cartilage lesion of the patella (P = 0.043). No correlations were identified in other injuries in the adolescent group. The incidence of partial and complete MPFL tear in adult males and females were (34.4%, 65.6%) and (56.8%, 37.8%), respectively. Compared with adult females, adult males showed higher incidence of complete MPFL tear (P = 0.036). The incidence of articular cartilage lesion of patella in adult males and females were 56.3% and 32.4%, respectively. Compared with adult females, adult males showed higher incidence of articular cartilage lesion of patella (P = 0.047). The incidence of VMO injury in adult males and females were 59.4% and 35.1%, respectively. Compared with adult females, adult males showed higher incidence of VMO injury (P = 0.044). No correlations were identified in other injuries in the adult group. CONCLUSIONS: Compared with females, males predispose to complete MPFL tear and articular cartilage lesion of patella after acute LPD. Compared with female adults, male adults predispose to VMO injury.