FLASH X-ray spares intestinal crypts from pyroptosis initiated by cGAS-STING activation upon radioimmunotherapy.

DNA-damaging treatments such as radiotherapy (RT) have become promising to improve the efficacy of immune checkpoint inhibitors by enhancing tumor immunogenicity. However, accompanying treatment-related detrimental events in normal tissues have posed a major obstacle to radioimmunotherapy and present new challenges to the dose delivery mode of clinical RT. In the present study, ultrahigh dose rate FLASH X-ray irradiation was applied to counteract the intestinal toxicity in the radioimmunotherapy. In the context of programmed cell death ligand-1 (PD-L1) blockade, FLASH X-ray minimized mouse enteritis by alleviating CD8+ T cell-mediated deleterious immune response compared with conventional dose rate (CONV) irradiation. Mechanistically, FLASH irradiation was less efficient than CONV X-ray in eliciting cytoplasmic double-stranded DNA (dsDNA) and in activating cyclic GMP-AMP synthase (cGAS) in the intestinal crypts, resulting in the suppression of the cascade feedback consisting of CD8+ T cell chemotaxis and gasdermin E-mediated intestinal pyroptosis in the case of PD-L1 blocking. Meanwhile, FLASH X-ray was as competent as CONV RT in boosting the antitumor immune response initiated by cGAS activation and achieved equal tumor control in metastasis burdens when combined with anti-PD-L1 administration. Together, the present study revealed an encouraging protective effect of FLASH X-ray upon the normal tissue without compromising the systemic antitumor response when combined with immunological checkpoint inhibitors, providing the rationale for testing this combination as a clinical application in radioimmunotherapy.

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm.

Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome. However, existing algorithms either collapse heterozygous alleles into one consensus copy or fail to cleanly separate the haplotypes to produce high-quality phased assemblies. Here we describe hifiasm, a de novo assembler that takes advantage of long high-fidelity sequence reads to faithfully represent the haplotype information in a phased assembly graph. Unlike other graph-based assemblers that only aim to maintain the contiguity of one haplotype, hifiasm strives to preserve the contiguity of all haplotypes. This feature enables the development of a graph trio binning algorithm that greatly advances over standard trio binning. On three human and five nonhuman datasets, including California redwood with a ~30-Gb hexaploid genome, we show that hifiasm frequently delivers better assemblies than existing tools and consistently outperforms others on haplotype-resolved assembly.

Air Quality, Health, and Equity Benefits of Carbon Neutrality and Clean Air Pathways in China.

In the pursuit of carbon neutrality, China's 2060 targets have been largely anchored in reducing greenhouse gas emissions, with less emphasis on the consequential benefits for air quality and public health. This study pivots to this critical nexus, exploring how China's carbon neutrality aligns with the World Health Organization's air quality guidelines (WHO AQG) regarding fine particulate matter (PM2.5) exposure. Coupling a technology-rich integrated assessment model, an emission-concentration response surface model, and exposure and health assessment, we find that decarbonization reduces sulfur dioxide (SO2), nitrogen oxides (NOx), and PM2.5 emissions by more than 90%; reduces nonmethane volatile organic compounds (NMVOCs) by more than 50%; and simultaneously reduces the disparities across regions. Critically, our analysis reveals that further targeted reductions in air pollutants, notably NH3 and non-energy-related NMVOCs, could bring most Chinese cities into attainment of WHO AQG for PM2.5 5 to 10 years earlier than the pathway focused solely on carbon neutrality. Thus, the integration of air pollution control measures into carbon neutrality strategies will present a significant opportunity for China to attain health and environmental equality.

Linker optimization and activity validation of a cell surface vimentin targeted homo-dimeric peptoid antagonist for lung cancer stem cells.

Epithelial-to-mesenchymal transition (EMT) endows epithelia-derived cancer cells with properties of stem cells that govern cancer invasion and metastasis. Vimentin is one of the best studied EMT markers and recent reports indicate that vimentin interestingly translocated onto cell surface under various tumor conditions. We recently reported a cell surface vimentin (CSV) specific peptoid antagonist named JM3A. We now investigated the selective antagonist activity of the optimized homo-dimeric version of JM3A, JM3A-L2D on stem-like cancer cells or cancer stem cells (CSCs) over normal cells in non-small cell lung cancer (NSCLC). Homo-dimerization of JM3A provided the avidity effect and improved the biological activity compared to the monomeric version. We first optimized the central linker length of the dimer by designing seven JM3A derivatives with varying linker lengths/types and evaluated the anti-cancer activity using the standard MTS cell viability assay. The most optimized derivative contains a central lysine linker and two glycines, named JM3A-L2D, which displayed 100 nM vimentin binding affinity (Kd) with an anti-cancer activity (IC50) of 6.7 µM on H1299 NSCLC cells. This is a 190-fold improvement in binding over the original JM3A. JM3A-L2D exhibited better potency on high vimentin-expressing NSCLC cells (H1299 and H460) compared to low vimentin-expressing NSCLC cells (H2122). No activity was observed on normal bronchial HBEC3-KT cells. The anti-CSC activity of JM3A-L2D was evaluated using the standard colony formation assay and JM3A-L2D disrupted the colony formation with IC50 âˆ¼ 400 nM. In addition, JM3A-L2D inhibited cell migration activity at IC50 âˆ¼ 2 µM, assessed via wound healing assay. The underlying mechanism of action seems to be the induction of apoptosis by JM3A-L2D on high-vimentin expressing H1229 and H460 NSCLC cells. Our optimized highly CSV selective peptoid has the potential to be developed as an anti-cancer drug candidate, especially considering the high serum stability and economical synthesis of peptoids.

Tophi and carotid atherosclerosis in gout patients: Role of insulin resistance.

BACKGROUND AND AIM: Gout and cardiovascular disease are closely related, but the mechanism linking them is still unknown. Gout may affect the insulin signaling pathway inducing insulin resistance (IR). The study aims to evaluate the association between tophi and carotid atherosclerosis, considering the potential role of IR. METHODS AND RESULTS: A total of 595 patients with gout aged 18 to 80 were enrolled in this study. Carotid intima-media thickness, plaques and tophi were evaluated by B-mode ultrasonography. IR was assessed by the HOMA index (hepatic IR) and Gutt index (peripheral IR). Multivariable logistic regression and interaction analysis were used to examine the association between tophi and IR and its impact on carotid atherosclerosis. Among these participants, the average age was 55.4 (±12.54) years, and 94.6 % were male. Tophi were associated with increased odds of carotid atherosclerosis and burden after adjustment for confounders (P < 0.05). Tophi and IR synergically interacted for inducing carotid atherosclerosis. The interaction between peripheral IR with tophi was more pronounced than hepatic IR with tophi. CONCLUSIONS: Tophi were independently associated with carotid atherosclerosis risk. IR mediated a significant amount of the effect of tophi on the development of carotid atherosclerosis. Peripheral IR probably plays a more important role than hepatic IR does.

Guanxin V alleviates ventricular remodeling after acute myocardial infarction with circadian disruption by regulating mitochondrial dynamics.

PURPOSE: Circadian disruption has been a common issue due to modern lifestyles. Ventricular remodeling (VR) is a pivotal progressive pathologic change after acute myocardial infarction (AMI) and circadian disruption may have a negative influence on VR according to the latest research. Whether or not Guanxin V (GXV) has a positive effect on VR after AMI with circadian disruption drew our interest. METHODS: Rats were randomly divided into a sham group, an AMI group, an AMI with circadian disruption group, and an AMI with circadian disruption treated with the GXV group according to a random number table. RNA sequencing (RNA-Seq) was utilized to confirm the different expressed genes regulated by circadian disruption. Cardiac function, inflammation factors, pathological evaluation, and mitochondrial dynamics after the intervention were conducted to reveal the mechanism by which GXV regulated VR after AMI with circadian disruption. RESULTS: RNA-Seq demonstrated that NF-κB was up-regulated by circadian disruption in rats with AMI. Functional and pathological evaluation indicated that compared with the AMI group, circadian disruption was associcataed with deteriorated cardiac function, expanded infarcted size, and exacerbated fibrosis and cardiomyocyte apoptosis. Further investigation demonstrated that mitochondrial dynamics imbalance was induced by circadian disruption. GXV intervention reversed the inflammatory status including down-regulation of NF-κB. Reserved cardiac function, limited infarct size, and ameliorated fibrosis and apoptosis were also observed in the GXV treated group. GXV maintained mitochondrial fission/fusion imbalance through suppressed expression of mitochondrial fission-associated proteins. CONCLUSION: The study findings suggest that identified mitochondrial dysfunctions may underlie the link between circadian disruption and VR. GXV may exert cardioprotection after AMI with circadian disruption through regulating mitochondrial dynamics.

Reallocation of time to moderate-to-vigorous physical activity and estimated changes in physical fitness among preschoolers: a compositional data analysis.

BACKGROUND: Previous research has examined the associations of preschoolers' 24-h movement behaviours, including light and moderate-to-vigorous physical activity (LPA and MVPA), sedentary behaviour (SB), sleep, with physical fitness in isolation, ignoring intrinsically compositional nature of movement data while increasing the risk of collinearity. Thus, this study investigated the associations of preschoolers' 24-h Movement behaviours composition with physical fitness, estimated changes in physical fitness when time was reallocated between movement behaviours composition, and determined whether associations differ between different genders, using compositional data analysis. METHODS: In the cross-sectional study, a total of 275 preschoolers (3 ~ 6 y) from China were included. SB, LPA and MVPA times were objectively monitored with an ActiGraph GT9X accelerometer for 7 consecutive days. Sleep duration was obtained using parental reports. Physical fitness parameters, including upper and lower limb strength, static balance, speed-agility, and cardiorespiratory fitness (CRF), were determined with the PREFIT battery. The associations of 24-h movement behaviours composition with each physical fitness parameter were examined employing compositional multivariable linear regression models. The changes following time reallocation among behaviours were estimated employing compositional isotemporal substitution analyses. RESULTS: Greater MVPA, but not LPA, was significantly related to better upper and lower limb strength, speed-agility, and CRF. Reallocating time from LPA or SB to MVPA was related to better physical fitness. The associations were non-symmetrical: the estimated detriments to physical fitness from replacing MVPA with LPA or SB were larger than the estimated benefits associated with adding MVPA of the same magnitude. The aforementioned associations with lower limb strength, CRF, and speed-agility were observed in boys, while associations with upper and lower limb strength were noted in girls. CONCLUSION: Our findings reinforce the importance of physical activity (PA) intensity for the development of physical fitness in preschoolers. Replacing LPA or SB time with MVPA may be an appropriate strategy for enhancing preschoolers' physical fitness.

Possible sarcopenia and risk of chronic kidney disease: a four-year follow-up study and Mendelian randomization analysis.

INTRODUCTION: Chronic kidney disease (CKD) is a common risk factor for sarcopenia. However, whether sarcopenia increases the risk of CKD remains unclear. To investigate the longitudinal and causal associations between possible sarcopenia and CKD, this study was performed. METHODS: Possible sarcopenia was defined according to the Asian Working Group for Sarcopenia in 2019. Participants aged ≥ 40 years were recruited from the baseline survey of the China Health and Retirement Longitudinal Study and followed up for four years. Binary logistic regression was used to evaluate the cross-sectional and longitudinal associations between possible sarcopenia, low muscle strength, low physical performance and CKD. Propensity score matching was used to balance the intergroup differences. Subgroup and interactive analyses were adopted to identify potential interactive effects. Mendelian Randomization analysis was used to assess the causal association between appendicular lean mass (ALM) and CKD. RESULTS: After data cleansing, a total of 7296 participants were included in the baseline survey. In the cross-sectional analyses, the odds ratios (ORs) of prevalent CKD were 1.50 (95% CI = 1.23-1.84, p < 0.001) for possible sarcopenia, 1.37 (95% CI = 1.10-1.70, p < 0.01) for low muscle strength and 1.42 (95% CI = 1.16-1.74, p < 0.001) for low physical performance in the full models. No significant interaction effects of covariates were detected (all P for interaction > 0.05). After four years of follow-up, an increased risk of incident CKD was also observed in participants with possible sarcopenia (OR = 1.66, 95% CI = 1.13-2.44, p = 0.010) and low physical performance (OR = 1.69, 95% CI = 1.16-2.45, p = 0.006), but not in participants with low muscle strength (OR = 1.19, 95% CI = 0.75-1.88, p = 0.469). In the Mendelian Randomization analysis, the inverse variance weighted estimator showed that a 1-standard deviation increase of genetically predicted ALM was associated with a lower risk of CKD (OR = 0.92, 95% CI = 0.85-0.99, p = 0.035). All the sensitivity analyses supported the main findings. CONCLUSIONS: Possible sarcopenia is an independent risk factor for CKD and may serve as a predictor of CKD for early identification and intervention.

Chemoenzymatic Synthesis of 2-Aryl Thiazolines from 4-Hydroxybenzaldehydes Using Vanillyl Alcohol Oxidases.

Nitrogen heterocycles are commonly found in bioactive natural products and drugs. However, the biocatalytic tools for nitrogen heterocycle synthesis are limited. Herein, we report the discovery of vanillyl alcohol oxidases (VAOs) as efficient biocatalysts for the one-pot synthesis of 2-aryl thiazolines from various 4-hydroxybenzaldehydes and aminothiols. The wild-type biocatalyst features a broad scope of 4-hydroxybenzaldehydes. Though the scope of aminothiols is limited, it could be improved via semi-rational protein engineering, generating a variant to produce previously inaccessible cysteine-derived bioactive 2-aryl thiazolines using the wild-type VAO. Benefiting from the derivatizable functional groups in the enzymatic products, we further chemically modified these products to expand the chemical space, offering a new chemoenzymatic strategy for the green and efficient synthesis of structurally diverse 2-aryl-thiazoline derivatives to prompt their use in drug discovery and catalysis.

Schwann cell-specific RhoA knockout accelerates peripheral nerve regeneration via promoting Schwann cell dedifferentiation.

Our previous studies indicated that RhoA knockdown or inhibition could alleviate the proliferation, migration, and differentiation of Schwann cells. However, the role of RhoA in Schwann cells during nerve injury and repair is still unknown. Herein, we developed two lines of Schwann cells conditional RhoA knockout (cKO) mice by breeding RhoAflox / flox mice with PlpCre -ERT2 or DhhCre mice. Our results indicate that RhoA cKO in Schwann cells accelerates axonal regrowth and remyelination after sciatic nerve injury, which enhances the recovery of nerve conduction and hindlimb gait, and alleviates the amyotrophy in gastrocnemius muscle. Mechanistic studies in both in vivo and in vitro models revealed that RhoA cKO could facilitate Schwann cell dedifferentiation via JNK pathway. Schwann cell dedifferentiation subsequently promotes Wallerian degeneration by enhancing phagocytosis and myelinophagy, as well as stimulating the production of neurotrophins (NT-3, NGF, BDNF, and GDNF). These findings shed light on the role of RhoA in Schwann cells during nerve injury and repair, indicating that cell type-specific RhoA targeting could serve as a promising molecular therapeutic strategy for peripheral nerve injury.

Electrocatalytic Biomass Upgrading of Furfural using Transition-Metal Borides via Density Functional Theory Investigation.

Electrocatalytic biomass upgrading has proven to be an effective technique for generating value-added products. Herein, the design and development of furfural upgrading using transition-metal borides (MBenes) with simultaneous production of hydrogen are presented. Using density functional theory, the stabilities, selectivities, and activities of 13 MBene candidates are systematically evaluated for furfural upgrading. This research suggests that Fe2 B2 can serve as a promising electrocatalyst for the formation of furoic acid (FAC), with a limiting potential of -0.15 V, and 5-hydroxy-2(5H)-furanone (HFO), with a limiting potential of -0.93 V. Furthermore, Fe2 B2 and Mn2 Fe2 are shown to exhibit favorable limiting potentials of -1.35 and -1.36 V, respectively, for producing 6-hydroxy-2.3-dihydro-6H-pyrano-3-one (HDPO), indicating that they may also serve as electrocatalysts. Based on Sabatier's principle, a descriptor (φ) of material properties is developed for screening catalysts with high catalytic activity considering the electronegativities and d-electron number of metals. Additionally, surface redox potential, electronic properties, and charge-density differences are determined for Fe2 B2 , which is estimated to exhibit high catalytic activity for the oxidation of furfural to FAC and HFO.

Prognostic value of CT-derived fractional flow reserve and fat attenuation index in patients with suspected coronary artery disease: a sex-disaggregated analyses.

BACKGROUND: There are sex differences in many risk factors associated with coronary artery disease (CAD). CT-derived fractional flow reserve (CT-FFR) and fat attenuation index (FAI) have been shown to independently predict cardiovascular events. We aimed to examine the impact of sex on the prognostic value of CT-FFR and FAI in suspected CAD patients, and to examine the incremental prognostic value of FAI over CT-FFR in both sex. METHODS: A total of 1334 consecutive suspected CAD subjects who underwent coronary computed tomographic angiography (CCTA) were retrospectively collected. We divided the patients into males and females and calculated CT-FFR and FAI data from CCTA images. Kaplan-Meier analysis was used to assess the risk of major adverse cardiovascular events (MACE) stratified by CT-FFR and FAI in both sex. Cox regression models were used to assess the incremental prognostic value of FAI by adding the variable to a model that included CT-FFR and clinical variables. RESULTS: During a median follow-up of 2.08 years, 212 patients had MACE. CT-FFR ≤ 0.80 was significantly associated with MACE in both sex. FAI value of left anterior descending artery (FAI[LAD]) and FAI value of left circumflex (FAI[LCX]) ≥ 70.1 were significantly associated with MACE in females. FAI[LCX] added incremental prognostic value over clinical and CT-FFR variables in females, with hazard ratio (HR) 3.230 (1.982-5.265, P = 0.000), Harrel's C 0.669 (P < 0.001), net reclassification improvement (NRI) 0.161 (0.073-0.260, P < 0.001), and integrated discrimination index (IDI) 0.036 (0.008-0.090, P = 0.010). FAI[LAD] did not enhance risk prediction in females (Harrel's C 0.643, P = 0.054; NRI 0.041, P = 0.189; IDI 0.005, P = 0.259). The decision curve analysis demonstrated that the model including FAI[LCX] resulted in the highest net benefit. CONCLUSIONS: In suspected CAD patients, the prognostic value of CT-FFR is not significantly biased by sex. The prognostic value of FAI[LAD] and FAI[LCX] were significantly associated with MACE in females, but not males. FAI[LCX], not FAI[LAD], added incremental prognostic value over CT-FFR and might enhance CT-FFR risk stratification in females.

NIR Spectral Inversion of Soil Physicochemical Properties in Tea Plantations under Different Particle Size States.

Soil fertility is vital for the growth of tea plants. The physicochemical properties of soil play a key role in the evaluation of soil fertility. Thus, realizing the rapid and accurate detection of soil physicochemical properties is of great significance for promoting the development of precision agriculture in tea plantations. In recent years, spectral data have become an important tool for the non-destructive testing of soil physicochemical properties. In this study, a support vector regression (SVR) model was constructed to model the hydrolyzed nitrogen, available potassium, and effective phosphorus in tea plantation soils of different grain sizes. Then, the successful projections algorithm (SPA) and least-angle regression (LAR) and bootstrapping soft shrinkage (BOSS) variable importance screening methods were used to optimize the variables in the soil physicochemical properties. The findings demonstrated that soil particle sizes of 0.25-0.5 mm produced the best predictions for all three physicochemical properties. After further using the dimensionality reduction approach, the LAR algorithm (R2C = 0.979, R2P = 0.976, RPD = 6.613) performed optimally in the prediction model for hydrolytic nitrogen at a soil particle size of 0.25~0.5. The models using data dimensionality reduction and those that used the BOSS method to estimate available potassium (R2C = 0.977, R2P = 0.981, RPD = 7.222) and effective phosphorus (R2C = 0.969, R2P = 0.964, RPD = 5.163) had the best accuracy. In order to offer a reference for the accurate detection of soil physicochemical properties in tea plantations, this study investigated the modeling effect of each physicochemical property under various soil particle sizes and integrated the regression model with various downscaling strategies.

Research on the Detection Method of Organic Matter in Tea Garden Soil Based on Image Information and Hyperspectral Data Fusion.

Soil organic matter is an important component that reflects soil fertility and promotes plant growth. The soil of typical Chinese tea plantations was used as the research object in this work, and by combining soil hyperspectral data and image texture characteristics, a quantitative prediction model of soil organic matter based on machine vision and hyperspectral imaging technology was built. Three methods, standard normalized variate (SNV), multisource scattering correction (MSC), and smoothing, were first used to preprocess the spectra. After that, random frog (RF), variable combination population analysis (VCPA), and variable combination population analysis and iterative retained information variable (VCPA-IRIV) algorithms were used to extract the characteristic bands. Finally, the quantitative prediction model of nonlinear support vector regression (SVR) and linear partial least squares regression (PLSR) for soil organic matter was established by combining nine color features and five texture features of hyperspectral images. The outcomes demonstrate that, in comparison to single spectral data, fusion data may greatly increase the performance of the prediction model, with MSC + VCPA-IRIV + SVR (R2C = 0.995, R2P = 0.986, RPD = 8.155) being the optimal approach combination. This work offers excellent justification for more investigation into nondestructive methods for determining the amount of organic matter in soil.

Incorporating straw into intensively farmed cropland soil can reduce N2O emission via inhibition of nitrification and denitrification pathways.

Straw incorporation (SI) combined with N fertilizer has been shown to affect soil N2O emission and N-related functional microbes in agriculture. However, the responses of N2O emission, community structure of nitrifiers and denitrifiers and related microbial functional genes to straw management strategies in the winter wheat season in China remain unclear. Here, we conducted a two-season experiment in a winter wheat field in Ningjing County, northern China, to examine four treatments: no fertilizer with (N0S1) and without maize straw (N0S0); N fertilizer with (N1S1) and without maize straw (N1S0), and their effects on N2O emissions, soil chemical parameters, crop yield, as well as the dynamics of nitrifying and denitrifying microbial communities. We found that seasonal N2O emissions decreased by 7.1-11.1% (p < 0.05) in N1S1 as compared to N1S0, without significant difference between N0S1 and N0S0. In combination with N fertilization, SI increased the yield by 2.6-4.3%, altered the microbial community composition, increased Shannon and ACE indexes, and decreased the abundance of AOA (9.2%), AOB (32.2%; p < 0.05), nirS (35.2%; p < 0.05), nirK (21.6%; p < 0.05) and nosZ (19.2%). However, in the absence of N fertilizer, SI promoted the major genera of Nitrosavbrio (AOB), unclassifiied_Gammaproteobacteria, Rhodanobacter (nirS), Sinorhizobium (nirK), which strongly correlated positively with N2O emissions. Thereby, a negative interaction effect between SI and N fertilizer on AOB and nirS emphasized that SI could offset the increase of N2O emission caused by fertilization. Soil moisture and NO3- concentration were the major factors affecting N-related microbial community structure. Our study reveals that SI suppressed N2O emission significantly and simultaneously decreased the abundance of N-related functional genes and altered denitrifying bacterial community composition. We conclude that SI helps to enhance yield and alleviate fertilizer-induced environmental costs in intensively farmed fields in northern China.

Glycosylation Contributes to Thermostability and Proteolytic Resistance of rFIP-nha (Nectria haematococca).

Glycosylation is an important post-translational modification of proteins, contributing to protein function, stability and subcellular localization. Fungal immunomodulatory proteins (FIPs) are a group of small proteins with notable immunomodulatory activity, some of which are glycoproteins. In this study, the impact of glycosylation on the bioactivity and biochemical characteristics of FIP-nha (from Nectria haematococca) is described. Three rFIP-nha glycan mutants (N5A, N39A, N5+39A) were constructed and expressed in Pichia pastoris to study the functionality of the specific N-glycosylation on amino acid N5 and N39. Their protein characteristics, structure, stability and activity were tested. WT and mutants all formed tetramers, with no obvious difference in crystal structures. Their melting temperatures were 82.2 °C (WT), 81.4 °C (N5A), 80.7 °C (N39A) and 80.1 °C (N5+39A), indicating that glycosylation improves thermostability of rFIP-nha. Digestion assays showed that glycosylation on either site improved pepsin resistance, while 39N-glycosylation was important for trypsin resistance. Based on the 3D structure and analysis of enzyme cleavage sites, we conclude that glycosylation might interfere with hydrolysis via increasing steric hindrance. WT and mutants exerted similar bioactivity on tumor cell metabolism and red blood cells hemagglutination. Taken together, these findings indicate that glycosylation of FIP-nha impacts its thermostability and digestion resistance.

Real-time mapping of nanopore raw signals.

MOTIVATION: Oxford Nanopore Technologies sequencing devices support adaptive sequencing, in which undesired reads can be ejected from a pore in real time. This feature allows targeted sequencing aided by computational methods for mapping partial reads, rather than complex library preparation protocols. However, existing mapping methods either require a computationally expensive base-calling procedure before using aligners to map partial reads or work well only on small genomes. RESULTS: In this work, we present a new streaming method that can map nanopore raw signals for real-time selective sequencing. Rather than converting read signals to bases, we propose to convert reference genomes to signals and fully operate in the signal space. Our method features a new way to index reference genomes using k-d trees, a novel seed selection strategy and a seed chaining algorithm tailored toward the current signal characteristics. We implemented the method as a tool Sigmap. Then we evaluated it on both simulated and real data and compared it to the state-of-the-art nanopore raw signal mapper Uncalled. Our results show that Sigmap yields comparable performance on mapping yeast simulated raw signals, and better mapping accuracy on mapping yeast real raw signals with a 4.4× speedup. Moreover, our method performed well on mapping raw signals to genomes of size >100 Mbp and correctly mapped 11.49% more real raw signals of green algae, which leads to a significantly higher F1-score (0.9354 versus 0.8660). AVAILABILITY AND IMPLEMENTATION: Sigmap code is accessible at https://github.com/haowenz/sigmap. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Unbiased peptoid cell screen identifies a peptoid targeting newly appeared cell surface vimentin on tumor transformed early lung cancer cells.

To identify potential new reagents and biomarkers for early lung cancer detection we combined the use of a novel preclinical isogenic model of human lung epithelial cells comparing non-malignant cells with those transformed to full malignancy using defined oncogenic changes and our on-bead two color (red and green stained cells) (OBTC) peptoid combinatorial screening methodology. The preclinical model used normal parent lung epithelial cells (HBEC3-KT, labeled with green dye) and isogenic fully malignant transformed derivatives (labeled with a red dye) via the sequential introduction of key genetic alterations of p53 knockdown, oncogenic KRAS and overexpression of cMYC (HBEC3p53, KRAS, cMYC). Using the unbiased OBTC screening approach, we tested 100,000 different peptoids and identified only one (named JM3A) that bound to the surface of the HBEC3p53, KRAS, cMYC cells (red cells) but not HBEC3-KT cells (green cells). Using the JM3A peptoid and proteomics, we identified the protein bound as vimentin using multiple validation approaches. These all confirmed the cell surface expression of vimentin (CSV) on transformed (HBEC3p53, KRAS, cMYC) but not on untransformed (HBEC3-KT) cells. JM3A coupled with fluorophores was able to detect and stain cell surface vimentin on very early stage lung cancers but not normal lung epithelial cells in a fashion comparable to that using anti-vimentin antibodies. We conclude: using a combined isogenic preclinical model of lung cancer and two color screening of a large peptoid library, we have identified differential expression of cell surface vimentin (CSV) after malignant transformation of lung epithelial cells, and developed a new peptoid reagent (JM3A) for detection of CSV which works well in staining of early stage NSCLCs. This new, highly specific, easy to prepare, CSV detecting JM3A peptoid provides an important new reagent for identifying cancer cells in early stage tumors as well as a resource for detection and isolating of CSV expressing circulating tumor cells.

Optimization of a cell surface vimentin binding peptoid to extract antagonist effect on lung cancer cells.

Targeting cytoskeletal proteins that are uniquely translocated to cancer cell surface may provide an alternative path for conventional drug discovery. Vimentin is such a cell surface-translocated cytoskeletal protein (CSV) found in non small cell lung cancer (NSCLC). We previously reported the identification of CSV-binding peptoid, named JM3A. While JM3A had no antagonist effect, here we used multiple strategies to optimize the binding of JM3A on CSV and extract the antagonistic effect. We first performed minimum pharmacophore identification studies using alanine/sarcosine scans. These studies revealed that residues 1-4 and 8 (from the C-terminus) are not important and those residues 5-7 are important for JM3A binding to CSV. We then found that our previous N-terminal benzophenone (BP)-coupled JM3A (JM3A-BP), which was used for pull-down and target identification studies, displayed 3-fold binding enhancement. The molecular docking studies indicated that the BP moiety binds to a new binding pocket on the vimentin coil 2 fragment, and further studies using 12 benzophenone-like moieties indicated that at least two phenyl groups are needed to occupy this new binding site. Interestingly, the binding was improved when non-important and bulky residues at the 4th and 8th positions were replaced with methyl groups (JM3A-4,8-BP). We next dimerized JM3A-4,8-BP to enhance the binding via the "avidity effect," using a central lysine linker to develop JM3A-4,8-BPD1 (EC50 = 300 nM). This showed 27- and 63-fold-improvement in binding over JM3A-4,8-BP and JM3A monomers, respectively. JM3A4,8BPD1 also displayed binding comparable to vimentin antibody. Finally, we observed an antagonist effect on H1299 NSCLC cell proliferation and viability from this most improved dimeric JM3A-4,8BPD1, which was not shown by the monomeric versions.

Various quantification methods for estimating ammonia volatilization from wheat-maize cropping system.

Ammonia volatilization (AV) dominates the pathway of nitrogen (N) fertilizer losses in crops throughout the world. However, different methods are highly responsible for the different measurements of AV. The existing techniques were separated into static chamber methods (SCM), dynamic chamber methods (DCM), calibrated Dräger-tube method (DTM) and micrometeorological methods (MMM), which were analyzed by a meta-study of 595 observations from 33 published studies. An exponential relationship (P < 0.01) was found between AV and the N fertilizer applied to wheat and maize using all the methods. The amount of AV using SCM was the lowest. The AV monitored by DCM was 24.5%-55.0% (wheat) and 46.9%-65.0% (maize) lower than that for the DTM. Additionally, the AV measured by DTM did not differ significantly in the wheat season but was 58.9% lower (P < 0.05) in the maize season than that in the MMM. To reveal the influencing factors responsible that were for DCM and DTM, a field experiment was conducted during the period of Oct. 2016 to Oct. 2017. The study indicated that the AV was 15.8%-28.3% (wheat, P < 0.05) and 36.7%-44.2% (maize, P < 0.05) lower when monitored by the DCM than when estimated by DTM. The concentration of soil NH4+-N, air temperature, and wind speed positively correlated with the NH3 fluxes. In addition, there was a significant linear correlation (P < 0.01) between the AV measured by DCM and DTM when the wind speed was <1.5 m s-1. This study highlighted the fact that wind speed was the main factor that caused the large difference between DCM and DTM. Herein, DTM or MMM was first recommended, and DCM was accepted when wind speed was <1.5 m s-1 for quantitative estimates of AV. However, only a straight comparison between DCM and DTM under the same field experiment was done, the other comparisons only being based on similar fertilization and environmental conditions. Consequently, the differences between methods have to be treated carefully.