Large-scale multiplexed mosaic CRISPR perturbation in the whole organism.

Here, we report inducible mosaic animal for perturbation (iMAP), a transgenic platform enabling in situ CRISPR targeting of at least 100 genes in parallel throughout the mouse body. iMAP combines Cre-loxP and CRISPR-Cas9 technologies and utilizes a germline-transmitted transgene carrying a large array of individually floxed, tandemly linked gRNA-coding units. Cre-mediated recombination triggers expression of all the gRNAs in the array but only one of them per cell, converting the mice to mosaic organisms suitable for phenotypic characterization and also for high-throughput derivation of conventional single-gene perturbation lines via breeding. Using gRNA representation as a readout, we mapped a miniature Perturb-Atlas cataloging the perturbations of 90 genes across 39 tissues, which yields rich insights into context-dependent gene functions and provides a glimpse of the potential of iMAP in genome decoding.

Synergistic removal of total petroleum hydrocarbons and antibiotic resistance genes in Yellow River Delta wetlands contaminated soil composting regulated by biogas slurry addition.

The interactive effects between the emerging contaminant antibiotic resistance genes (ARGs) and the traditional pollutant total petroleum hydrocarbons (TPHs) in contaminated soils remain unclear. The synergistic removal of TPHs and ARGs from composted contaminated soil, along with the microbial mechanisms driven by the addition of biogas slurry, have not yet been investigated. This study explored the impact of biogas slurry on the synergistic degradation mechanisms and bacterial community dynamics of ARGs and TPHs in compost derived from contaminated soil. The addition of biogas slurry resulted in a reduction of targeted ARGs and mobile genetic elements (MGEs) by 9.96%-95.70% and 13.32%-97.66%, respectively. Biogas slurry changed the succession of bacterial communities during composting, thereby reducing the transmission risk of ARGs. Pseudomonas, Cellvibrio, and Devosia were identified as core microorganisms in the synergistic degradation of ARGs and TPHs. According to the partial least squares path model, temperature and NO3- indirectly influenced the removal of ARGs and TPHs by directly regulating the abundance and composition of host microbes and MGEs. In summary, the results of this study contribute to the high-value utilization of biogas slurry and provide methodological support for the low-cost remediation of contaminated soils.

Self-regulation and comprehension in shared reading: The moderating effects of verbal interactions and E-book discussion prompts.

The study examined how children's self-regulation skills measured by the strengths and weaknesses of ADHD symptoms and normal behavior rating are associated with story comprehension and how verbal engagement and e-book discussion prompts moderate this relation. Children aged 3-7 (N = 111, 50% female, Chinese as first language) read an interactive Chinese-English bilingual story e-book with or without discussion prompts twice with their parents (2020-2021). Results demonstrated that the lower children's self-regulation skills, the more they struggled with story comprehension. Critically, our data suggest that embedding e-book discussion prompts and more verbalization in English can mitigate this negative association for children with inattention/hyperactivity. These findings have critical implications for future e-book design, interventions, and home reading practice for children with inattention/hyperactivity and those at risk for attention deficit/hyperactivity disorder.

Development and Validation of a Patient Discharge Readiness Scale for Daytime Cataract Surgery (DRS-CAT).

PURPOSE: To ensure the safety of patients discharged from the hospital, a nurse-assessed scale for outpatient cataract surgery patients was constructed to provide a special tool for cataract patients' discharge readiness evaluation. DESIGN: This is a methodological study. METHODS: The development of the tool was completed between 2021 and 2022. Based on the literature review and qualitative interviews, the initial entry pool of the discharge readiness scale was established. After consultation with Delphi experts, the preliminary scale was tested by 312 participants to screen items and test reliability and validity. The analysis included internal consistency, content validity, and construct validity. The Strengthening the Reporting of Observation studies in Epidemiology (STROBE) checklist was used as the reporting guideline for this study. FINDINGS: The final Discharge Readiness Scale for Cataract surgery consists of 21 items in five dimensions: cognition of discharge readiness, personal status, mastery of health education knowledge, coping capacity, and social support. Five common factors were extracted from the exploratory factor analysis, and they explained 70.12% of the total variance. All of the indexes of the confirmatory factor analysis were within the theoretical allowable range. The Cronbach's α of the total scale was 0.903, and the scale-level content validity index/average variance extracted was 0.99. CONCLUSIONS: The Discharge Readiness Scale for Cataract surgery, evaluated by nurses, has good reliability and validity and can be used to determine the discharge readiness of cataract patients undergoing day surgery.

Alloying-Induced Synthesis of Amorphous PdZnS Hollow Spheres as Enhanced Oxygen Reduction Catalysts.

Amorphous alloys have multiple advantages in electrocatalysis, yet the isotropic nature makes their syntheses a great obstacle in application. In this work, it is shown that the Zn2+ can interfere with the crystallization of Pd-base structures to form amorphous alloy materials. By simply adjusting the Zn2+ content, unique PdZnS amorphous hollow spheres (AHS) with various compositions and degrees of crystallinity can be obtained through a facile one-pot wet chemical method. Owing to both the amorphous nature and hollow morphologies, the PdZnS AHSs possess appealing activities and stabilities as oxygen reduction catalysts. Typically, the Pd20 ZnS10 AHSs exhibit the highest half-wave potential (E1/2 ) of 0.940 V (vs reversible hydrogen electrode), and such E1/2 only negatively shifts 25 mV after 60 000 cycles.

Robust deep learning-based PET prognostic imaging biomarker for DLBCL patients: a multicenter study.

OBJECTIVE: To develop and independently externally validate robust prognostic imaging biomarkers distilled from PET images using deep learning techniques for precise survival prediction in patients with diffuse large B cell lymphoma (DLBCL). METHODS: A total of 684 DLBCL patients from three independent medical centers were included in this retrospective study. Deep learning scores (DLS) were generated from PET images using deep convolutional neural network architecture known as VGG19 and DenseNet121. These DLSs were utilized to predict progression-free survival (PFS) and overall survival (OS). Furthermore, multiparametric models were designed based on results from the Cox proportional hazards model and assessed through calibration curves, concordance index (C-index), and decision curve analysis (DCA) in the training and validation cohorts. RESULTS: The DLSPFS and DLSOS exhibited significant associations with PFS and OS, respectively (P<0.05) in the training and validation cohorts. The multiparametric models that incorporated DLSs demonstrated superior efficacy in predicting PFS (C-index: 0.866) and OS (C-index: 0.835) compared to competing models in training cohorts. In external validation cohorts, the C-indices for PFS and OS were 0.760 and. 0.770 and 0.748 and 0.766, respectively, indicating the reliable validity of the multiparametric models. The calibration curves displayed good consistency, and the decision curve analysis (DCA) confirmed that the multiparametric models offered more net clinical benefits. CONCLUSIONS: The DLSs were identified as robust prognostic imaging biomarkers for survival in DLBCL patients. Moreover, the multiparametric models developed in this study exhibited promising potential in accurately stratifying patients based on their survival risk.

Leaked Mitochondrial C1QBP Inhibits Activation of the DNA Sensor cGAS.

Cytosolic DNA from pathogens activates the DNA sensor cyclic GMP-AMP (cGAMP) synthase (cGAS) that produces the second messenger, cGAMP. cGAMP triggers a signal cascade leading to type I IFN expression. Host DNA is normally restricted in the cellular compartments of the nucleus and mitochondria. Recent studies have shown that DNA virus infection triggers mitochondrial stress, leading to the release of mitochondrial DNA to the cytosol and activation of cGAS; however, the regulatory mechanism of mitochondrial DNA-mediated cGAS activation is not well elucidated. In this study, we analyzed cGAS protein interactome in mouse RAW264.7 macrophages and found that cGAS interacted with C1QBP. C1QBP predominantly localized in the mitochondria and leaked into the cytosol during DNA virus infection. The leaked C1QBP bound the NTase domain of cGAS and inhibited cGAS enzymatic activity in cells and in vitro. Overexpression of the cytosolic form of C1QBP inhibited cytosolic DNA-elicited innate immune responses and promoted HSV-1 infection. By contrast, deficiency of C1QBP led to the elevated innate immune responses and impaired HSV-1 infection. Taken together, our study suggests that C1QBP is a novel cGAS inhibitor hidden in the mitochondria.

Exploiting total internal reflection geometry for deep broadband terahertz modulation using a GaAs Schottky diode with integrated subwavelength metal microslits.

We developed a GaAs Schottky diode with integrated periodic subwavelength metal microslits with total internal reflection (TIR) geometry to achieve deep broadband THz modulation at high frequency with low insertion loss. The non-resonant electric field enhancement effect in the subwavelength microslits intensifies the evanescent wave in TIR, which increases broadband absorbance of THz light signals by free carriers in the GaAs Schottky diode. Devices with various microslit spatial periods and gap widths were fabricated and measured. Among the devices, that with a microslit period of 10 µm and gap width of 2 µm produced ∼70% modulation depth at frequencies of 0.2 to 1.2 THz, while in the range of 0.25 to 0.4 THz, ∼90% modulation depth was achieved. By encapsulating the device in high refractive index material, ∼100% modulation depth was achieved in the range of 0.4 to 0.6 THz, the 3 dB bandwidth operational frequency was ∼160 kHz, and the insertion loss introduced by the device was less than 8 dB, which is much lower than existing metasurface-based THz modulators. In general, our first-generation device has improved modulation depth, operational bandwidth, insertion loss, and operational frequency. Optimization of the metal microslits, TIR geometry, and doped layer could further improve the performance of our design.

Enhanced sensitivity of dilute aqueous adrenaline solution with an asymmetric hexagonal ring structure in the terahertz frequencies.

Quantitative detection of neurotransmitters in aqueous environment is crucial for the early diagnosis of many neurological disorders. Terahertz waves, as a non-contact and non-labeling tool, have demonstrated large potentials in quantitative biosensing. Although the detection of trace-amount analyte has been achieved with terahertz metamaterials in the recent decades, most studies have been focused on dried samples. Here, a hexagonal asymmetric metamaterial sensor was designed and fabricated for aqueous solution sensing with terahertz waves in the reflection geometry. An absorption enhancement of 43 was determined from the simulation. Dilute adrenaline solutions ranging from 30 µM to 0.6 mM were measured on our sensor using a commercial terahertz time-domain spectroscopy system, and the effective absorption was found to be linearly correlated with the concentration (R2 = 0.81). Furthermore, we found that as the concentration becomes higher (>0.6 mM), a non-linear relationship starts to take place, which confirmed the previous theory on the extended solvation shell that can be probed on the picosecond scale. Our sensor, without the need of high-power and stable terahertz sources, has enabled the detection of subtle absorption changes induced by the solvation dynamics.

Temperature-Dependent Terahertz Spectra of Isonicotinamide in the Form I Studied Using the Quasi-Harmonic Approximation.

Anharmonicity of molecular vibrational motions is closely associated with the thermal property of crystals. However, the origin of anharmonicity is still not fully understood. Low-frequency vibrations, which are usually defined in the terahertz (THz) range, show excellent sensitivity to anharmonicity. In this work, anharmonicity of isonicotinamide in the form I was investigated by using temperature-dependent terahertz time-domain spectroscopy and the quasi-harmonic approximation (QHA) approach at PBE-D3 and PBE-MBD levels. Both DFT calculations suggest the variation of π-π stacking conformation dominates in the thermal expansion of the unit cell. Frequency shifts of the modes in THz range obtained by QHA approach are found to be qualitatively consistent with experimental observations, demonstrating QHA approach is a useful tool for the interpretation of frequency shifts of modes induced by temperature.

HClO-triggered interventional probe enabled early detection and intervention of atherosclerosis.

Foam cell formation and further accumulation in the subendothelial space of the vascular wall is a hallmark of early atherosclerosis (AS). Targeting foam cell formation can be a promising approach for the early detection and prevention of AS. However, only a few studies have actually examined foam cells in vivo, and most methods combined nanotechnology with angiography, which is complex and could cause further damage to the endothelium. Herein, based on methylene blue, a biosafe NIR dye approved by the FDA, an interventional probe (HMB-NA@Mp) triggered by hypochlorous acid (HClO) was designed for imaging foam cells easily, safely, and effectively in the early stage of AS. Here, encapsulation of the probe by foam cells targeted platelet membrane (Mp) increased probe targeting and reduced toxicity. Cell and animal experimental results showed that the probe could accumulate at the lesion site and significantly enhance fluorescence in the early AS model group. Remarkably, at the same time, it could also release the metabolite niacin, which played a role in inhibiting atherosclerosis. Thus, HMB-NA@Mp is expected to be a powerful means for the early detection and timely intervention of early AS in the absence of clinical symptoms.

Integrative Predictive Models of Computed Tomography Texture Parameters and Hematological Parameters for Lymph Node Metastasis in Lung Adenocarcinomas.

OBJECTIVES: The aims of the study were to integrate characteristics of computed tomography (CT), texture, and hematological parameters and to establish predictive models for lymph node (LN) metastasis in lung adenocarcinoma. METHODS: A total of 207 lung adenocarcinoma cases with confirmed postoperative pathology and preoperative CT scans between February 2017 and April 2019 were included in this retrospective study. All patients were divided into training and 2 validation cohorts chronologically in the ratio of 3:1:1. The χ2 test or Fisher exact test were used for categorical variables. The Shapiro-Wilk test and Mann-Whitney U test were used for continuous variables. Logistic regression and machine learning algorithm models based on CT characteristics, texture, and hematological parameters were used to predict LN metastasis. The performance of the multivariate models was evaluated using a receiver operating characteristic curve; prediction performance was evaluated in the validation cohorts. Decision curve analysis confirmed its clinical utility. RESULTS: Logistic regression analysis demonstrated that pleural thickening (P = 0.013), percentile 25th (P = 0.033), entropy gray-level co-occurrence matrix 10 (P = 0.019), red blood cell distribution width (P = 0.012), and lymphocyte-to-monocyte ratio (P = 0.049) were independent risk factors associated with LN metastasis. The area under the curve of the predictive model established using the previously mentioned 5 independent risk factors was 0.929 in the receiver operating characteristic analysis. The highest area under the curve was obtained in the training cohort (0.777 using Naive Bayes algorithm). CONCLUSIONS: Integrative predictive models of CT characteristics, texture, and hematological parameters could predict LN metastasis in lung adenocarcinomas. These findings may provide a reference for clinical decision making.

Solid-State Thermal Memory of Temperature-Responsive Polymer Induced by Hydrogen Bonds.

Memory is an essential element for a computer to process information, which is integrated by logical circuits. Like electronic computing, thermal information can also be stored and read out by a thermal memory. Here, we show that a phase-changing polymer with hysteretic thermal transport properties can be experimentally processed into thermal memories at room temperature. We used a temperature-responsive and reversible polymer synthesized with melamine (M) and 6,7-dimethoxy-2,4[1H,3H]-quinazolinedione (Q) as a model system to demonstrate the manipulation of thermal transport at a molecular level. Fourier transform infrared spectroscopy and differential scanning calorimetry measurements indicate that this hysteretic behavior is based on the interaction of hydrogen bonds at high (317 K) and low (297 K) temperatures. This work demonstrates a controllable phonon transport process through the manipulation of hydrogen bonds, and thus it has potential applications in thermal memories.

Deep THz modulation at Fabry-Perot resonances using graphene in periodic microslits.

Potential applications of terahertz (THz) radiation are constantly being investigated for high-speed communication due to its large bandwidth. For example, frequency hopping communication technology would benefit from the large bandwidth. To attach the information to the carrier wave, THz modulators with deep and stable modulation at different frequencies are crucial, yet are still lacking. Here a THz modulator, designed by integrating a non-resonant field enhancement effect of periodic metal microslits to assist a Fabry-Perot resonance structure (MS-FP) is proposed and demonstrated. New equations are developed to describe the superior performance of the novel design. The >95% modulation depth is achieved by a SiO2/Si gated graphene device at 14 Fabry-Perot resonant frequencies across 1.4 THz bandwidth, outperforming the recently reported 75% modulation depth THz modulator with a similar Fabry-Perot structure.

Low-frequency vibrational spectroscopy: a new tool for revealing crystalline magnetic structures in iron phosphate crystals.

In this report, the strong-dependence of low-frequency (terahertz) vibrational dynamics on weak and long-range forces in crystals is leveraged to determine the bulk magnetic configuration of iron phosphate - a promising material for cathodes in lithium ion batteries. We demonstrate that terahertz time-domain spectroscopy - coupled with quantum mechanical simulations - can discern between various spin configurations in FePO4. Furthermore, the results of this work unambiguously show that the well-accepted space group symmetry for FePO4 is incorrect, and the low-frequency spectroscopic measurements provide a clearer picture of the correct structure over the gold-standard of X-ray diffraction. This work opens the door for characterizing, predicting, and interpreting crystalline magnetic ordering using low-frequency vibrational spectroscopy.

The Chinese Spiritual Coping Scale: Development and Initial Psychometric Evaluation.

The aim of the study was to develop and psychometrically evaluate the Chinese Spiritual Coping Scale. The items in the questionnaire were written according to the study's theoretical conception and literature research. A sample of 415 participants with or without religious beliefs was used for exploratory factor analyses to select the items. In addition, another sample of 207 participants was used to cross-validate the factor structure and examine the internal consistency. The results supported the four-factor structure of the Chinese Spiritual Coping Scale (17 items, four dimensions: Mystical Experience, Moral Practice, Meaning Exploration, and Transcendent Attitude). The analyses demonstrated adequate internal consistency and construct validity. The overall psychometric evaluation of the Spiritual Coping Scale suggested that this could be a promising measure of spiritual coping for Chinese individuals.

RepLong: de novo repeat identification using long read sequencing data.

Motivation: The identification of repetitive elements is important in genome assembly and phylogenetic analyses. The existing de novo repeat identification methods exploiting the use of short reads are impotent in identifying long repeats. Since long reads are more likely to cover repeat regions completely, using long reads is more favorable for recognizing long repeats. Results: In this study, we propose a novel de novo repeat elements identification method namely RepLong based on PacBio long reads. Given that the reads mapped to the repeat regions are highly overlapped with each other, the identification of repeat elements is equivalent to the discovery of consensus overlaps between reads, which can be further cast into a community detection problem in the network of read overlaps. In RepLong, we first construct a network of read overlaps based on pair-wise alignment of the reads, where each vertex indicates a read and an edge indicates a substantial overlap between the corresponding two reads. Secondly, the communities whose intra connectivity is greater than the inter connectivity are extracted based on network modularity optimization. Finally, representative reads in each community are extracted to form the repeat library. Comparison studies on Drosophila melanogaster and human long read sequencing data with genome-based and short-read-based methods demonstrate the efficiency of RepLong in identifying long repeats. RepLong can handle lower coverage data and serve as a complementary solution to the existing methods to promote the repeat identification performance on long-read sequencing data. Availability and implementation: The software of RepLong is freely available at https://github.com/ruiguo-bio/replong. Contact: ywsun@szu.edu.cn or zhuzx@szu.edu.cn. Supplementary information: Supplementary data are available at Bioinformatics online.

Selective in vivo metabolic cell-labeling-mediated cancer targeting.

Distinguishing cancer cells from normal cells through surface receptors is vital for cancer diagnosis and targeted therapy. Metabolic glycoengineering of unnatural sugars provides a powerful tool to manually introduce chemical receptors onto the cell surface; however, cancer-selective labeling still remains a great challenge. Herein we report the design of sugars that can selectively label cancer cells both in vitro and in vivo. Specifically, we inhibit the cell-labeling activity of tetraacetyl-N-azidoacetylmannosamine (Ac4ManAz) by converting its anomeric acetyl group to a caged ether bond that can be selectively cleaved by cancer-overexpressed enzymes and thus enables the overexpression of azido groups on the surface of cancer cells. Histone deacetylase and cathepsin L-responsive acetylated azidomannosamine, one such enzymatically activatable Ac4ManAz analog developed, mediated cancer-selective labeling in vivo, which enhanced tumor accumulation of a dibenzocyclooctyne-doxorubicin conjugate via click chemistry and enabled targeted therapy against LS174T colon cancer, MDA-MB-231 triple-negative breast cancer and 4T1 metastatic breast cancer in mice.

Once daily oral extended-release hydrocodone as analgesia following tibial plateau leveling osteotomy in dogs.

OBJECTIVE: To determine the efficacy of oral extended-release hydrocodone compared with oral firocoxib for analgesia following tibial plateau leveling osteotomy surgery in dogs in a hospital setting. STUDY DESIGN: Prospective, randomized, blinded, clinical trial. ANIMALS: Thirty-six client-owned dogs weighing 25-43 kg with unilateral hindlimb lameness and cranial cruciate ligament rupture. METHODS: Dogs were assigned to 1 of 2 groups (n = 18/group). Group 1 received hydrocodone 3 mg/kg orally every 24 hours, and group 2 received firocoxib 5 mg/kg orally every 24 hours. Both hydrocodone and firocoxib (according to group assignment) were provided as preemptive analgesia 10 hours before induction to anesthesia and then every 24 hours for the remainder of the study period The level of analgesia was compared between treatments on the basis of a modified Glasgow Composite Pain Score (mGCPS) in each dog, the number of dogs requiring rescue analgesia (hydromorphone 0.05 mg/kg subcutaneously), pressure platform stance data, and number of adverse events. RESULTS: Nine of 18 dogs that received hydrocodone and 2/18 dogs that received firocoxib had an mGCPS ≥6 (P = .02). Two dogs had an mGCPS ≥6 three times, and 1 had an mGCPS ≥6 two times; all 3 of these dogs were in the hydrocodone group. Average postoperative peak pressure placed on the affected limb was lower in dogs that received hydrocodone (P = .01). Regurgitation and decreased appetite were more common in the dogs that received hydrocodone. CONCLUSION: Dogs that were treated with hydrocodone exhibited higher pain scores and lower limb function than dogs treated with firocoxib under the conditions of our study. CLINICAL SIGNIFICANCE: Our results do not provide evidence to justify the administration of extended-release hydrocodone at 3 mg/kg orally every 24 hours rather than firocoxib at 5 mg/kg orally every 24 hours in dogs undergoing tibial plateau leveling osteotomy.

LW-FQZip 2: a parallelized reference-based compression of FASTQ files.

BACKGROUND: The rapid progress of high-throughput DNA sequencing techniques has dramatically reduced the costs of whole genome sequencing, which leads to revolutionary advances in gene industry. The explosively increasing volume of raw data outpaces the decreasing disk cost and the storage of huge sequencing data has become a bottleneck of downstream analyses. Data compression is considered as a solution to reduce the dependency on storage. Efficient sequencing data compression methods are highly demanded. RESULTS: In this article, we present a lossless reference-based compression method namely LW-FQZip 2 targeted at FASTQ files. LW-FQZip 2 is improved from LW-FQZip 1 by introducing more efficient coding scheme and parallelism. Particularly, LW-FQZip 2 is equipped with a light-weight mapping model, bitwise prediction by partial matching model, arithmetic coding, and multi-threading parallelism. LW-FQZip 2 is evaluated on both short-read and long-read data generated from various sequencing platforms. The experimental results show that LW-FQZip 2 is able to obtain promising compression ratios at reasonable time and memory space costs. CONCLUSIONS: The competence enables LW-FQZip 2 to serve as a candidate tool for archival or space-sensitive applications of high-throughput DNA sequencing data. LW-FQZip 2 is freely available at http://csse.szu.edu.cn/staff/zhuzx/LWFQZip2 and https://github.com/Zhuzxlab/LW-FQZip2 .