In Silico Design and Synthesis of Antifungal Peptides Guided by Quantitative Antifungal Activity.

Antifungal peptides (AFPs) are emerging as promising candidates for advanced antifungal therapies because of their broad-spectrum efficacy and reduced resistance development. In silico design of AFPs, however, remains challenging, due to the lack of an efficient and well-validated quantitative assessment of antifungal activity. This study introduced an AFP design approach that leverages an innovative quantitative metric, named the antifungal index (AFI), through a three-step process, i.e., segmentation, single-point mutation, and global multipoint optimization. An exhaustive search of 100 putative AFP sequences indicated that random modifications without guidance only have a 5.97-20.24% chance of enhancing antifungal activity. Analysis of the search results revealed that (1) N-terminus truncation is more effective in enhancing antifungal activity than the modifications at the C-terminus or both ends, (2) introducing the amino acids within the 10-60% sequence region that enhance aromaticity and hydrophobicity are more effective in increasing antifungal efficacy, and (3) incorporating alanine, cysteine, and phenylalanine during multiple point mutations has a synergistic effect on enhancing antifungal activity. Subsequently, 28 designed peptides were synthesized and tested against four typical fungal strains. The success rate for developing promising AFPs, with a minimal inhibitory concentration of ≤5.00 µM, was an impressive 82.14%. The predictive and design tool is accessible at https://antifungipept.chemoinfolab.com.

Electronic structures and quantum capacitance of twisted bilayer graphene with defects based on three-band tight-binding model.

Twisted bilayer graphene (tBLG) with C vacancies would greatly improve the density of states (DOS) around the Fermi level (EF) and quantum capacitance; however, the single-band tight-binding model only considering pz orbitals cannot accurately capture the low-energy physics of tBLG with C vacancies. In this work, a three-band tight-binding model containing three p orbitals of C atoms is proposed to explore the modulation mechanism of C vacancies on the DOS and quantum capacitance of tBLG. We first obtain the hopping integral parameters of the three-band tight-binding model, and then explore the electronic structures and the quantum capacitance of tBLG at a twisting angle of θ = 1.47° under different C vacancy concentrations. The impurity states contributed by C atoms with dangling bonds located around the EF and the interlayer hopping interaction could induce band splitting of the impurity states. Therefore, compared with the quantum capacitance of pristine tBLG (∼18.82 µF cm-2) at zero bias, the quantum capacitance is improved to ∼172.76 µF cm-2 at zero bias, and the working window with relatively large quantum capacitance in the low-voltage range is broadened in tBLG with C vacancies due to the enhanced DOS around the EF. Moreover, the quantum capacitance of tBLG is further increased at zero bias with an increase of the C vacancy concentration induced by more impurity states. These findings not only provide a suitable multi-band tight-binding model to describe tBLG with C vacancies but also offer theoretical insight for designing electrode candidates for low-power consumption devices with improved quantum capacitance.

Determination of organic acids for predicting sourness intensity of tea beverage by liquid chromatography-tandem mass spectrometry and chemometrics methods.

The contents of organic acids (OAs) in tea beverage and their relationship with taste intensity have not been fully understood. In this work, a rapid (10 min for a single run) and sensitive (limits of quantification: 0.0044-0.4486 µg/mL) method was developed and validated for the simultaneous determination of 17 OAs in four types of tea, based on liquid chromatography-tandem mass spectrometry with multiple reaction monitoring mode. The contents of 17 OAs in 96 tea samples were measured at levels between 0.01 and 11.80 g/kg (dried weight). Quinic acid, citric acid, and malic acid were determined as the major OAs in green, black, and raw pu-erh teas, while oxalic acid and tartaric acid exhibited the highest contents in ripe pu-erh tea. Taking the OAs composition as input features, a partial least squares regression model was proposed to predict the sourness intensity of tea beverages. The model achieved a root-mean-square error of 0.58 and a coefficient of determination of 0.84 for the testing set. The proposed model provides a theoretical way to evaluate the sensory quality of tea infusion based on its chemical composition.

Mesenchymal stem cells, as glioma exosomal immunosuppressive signal multipliers, enhance MDSCs immunosuppressive activity through the miR-21/SP1/DNMT1 positive feedback loop.

BACKGROUND: The immunosuppressive microenvironment in glioma induces immunotherapy resistance and is associated with poor prognosis. Glioma-associated mesenchymal stem cells (GA-MSCs) play an important role in the formation of the immunosuppressive microenvironment, but the mechanism is still not clear. RESULTS: We found that GA-MSCs promoted the expression of CD73, an ectonucleotidase that drives immunosuppressive microenvironment maintenance by generating adenosine, on myeloid-derived suppressor cells (MDSCs) through immunosuppressive exosomal miR-21 signaling. This process was similar to the immunosuppressive signaling mediated by glioma exosomal miR-21 but more intense. Further study showed that the miR-21/SP1/DNMT1 positive feedback loop in MSCs triggered by glioma exosomal CD44 upregulated MSC exosomal miR-21 expression, amplifying the glioma exosomal immunosuppressive signal. Modified dendritic cell-derived exosomes (Dex) carrying miR-21 inhibitors could target GA-MSCs and reduce CD73 expression on MDSCs, synergizing with anti-PD-1 monoclonal antibody (mAb). CONCLUSIONS: Overall, this work reveals the critical role of MSCs in the glioma microenvironment as signal multipliers to enhance immunosuppressive signaling of glioma exosomes, and disrupting the positive feedback loop in MSCs with modified Dex could improve PD-1 blockade therapy.

Effects of provisioning on the activity budget and foraging strategies of black-and-white snub-nosed monkeys (Rhinopithecus bieti) in the Baima Snow Mountain Nature Reserve, Yunnan, China.

Provisioning can significantly affect the ranging patterns, foraging strategies, and time budget of wild primates. In this study, we document for the first time, the effects of provisioning on the activity budget and foraging effort in an Asian colobine. Over 3-years, we used an instantaneous scanning method at 10-min intervals to collect data on the activity budget of a semiprovisioned breeding band (SPB) of black-and-white snub-nosed monkeys (Rhinopithecus bieti) (42-70 individuals) at Xiangguqing (Tacheng), Yunnan, China. We then compared the effects of provisioning in our study band with published data on a sympatric wild nonprovisioned breeding band (NPB) of R. bieti (ca. 360 monkeys) at the same field site. The SPB spent 25.6% of their daytime feeding, 17.1% traveling, 46.9% resting, and 10.3% socializing. In comparison, the NPB devoted more time to feeding (34.9%) and socializing (14.1%), less time to resting (31.3%), and was characterized by a greater foraging effort (1.74 versus 0.96, foraging effort = (feeding + traveling)/resting; see Methods). There was no difference between bands in the proportion of their activity budget devoted to traveling (15.7% vs. 17.1%). In addition, the SPB exhibited a more consistent activity budget and foraging effort across all seasons of the year compared to the NPB. These findings suggest that the distribution, availability, and productivity of naturally occurring feeding sites is a major determinant of the behavioral strategies and activity budget of R. bieti. Finally, a comparison of our results with data on six nonprovisioned R. bieti bands indicates that caution must be raised in meta-analyses or intraspecific comparisons of primate behavioral ecology that contain data generated from both provisioned and nonprovisioned groups.

Volatile flavour identification and odour complexity of radix Angelicae sinensis by electronic nose, integrated gas chromatography-mass spectrometry/olfactometry and comprehensive two-dimensional gas chromatography-time-of-flight-mass spectrometry.

INTRODUCTION: Radix Angelicae sinensis (Danggui, DG) is known as one of the typical traditional Chinese medicines. DG material consists of a variety of volatile substances, polysaccharides, organic acids, ceramides, amino acids, vitamins, microelements, among others, and thus has been used for medicinal and edible purposes in a long history. The fragrance is of importance to assessing the DG material quality. OBJECTIVES: This study was to determine volatile flavour compositions of DG materials and to reveal the odour complexity. MATERIAL AND METHODS: Electronic nose (E-nose), integrated gas chromatography-mass spectrometry/olfactometry (GC-MS/O) and comprehensive two-dimensional gas chromatography-time-of-flight-mass spectrometry (GC × GC-TOF-MS), combined with solid-phase micro-extraction (SPME), were mainly used to address the flavour complexity of DG materials. RESULTS: Using the E-nose sensor responses, a total of 105 batches of DG samples cultivated in six provinces of China were categorised according to their odour differentiations, and a principal component analysis (PCA) model was established for evaluating the sample quality through a combination of Hotelling's T2 and Q-residual values in a statistical quantitative sense. By the GC-MS/O and GC × GC-TOF-MS analyses, 196 volatile flavour compounds were identified, 51 odour-active areas discerned and 39 odourants determined. It was terpenes and aromatics of the flavour compounds that mainly contributed to the odour attributes of DG herb. CONCLUSION: The SPME-GC × GC-TOF-MS method was the first time employed to analyse the volatile flavours of DG materials, and thus made a breakthrough in determining 196 flavour compounds, much more than those in any previous report. The work also made a significant step forward to link the flavour compositions and odour complexity of radix Angelicae sinensis by E-nose and GC-MS/O techniques. It not only provided a statistical PCA model that did not depend on any predetermined compositions or sensory properties for, but also a comprehensive insight into the quality evaluation of DG materials.

m6A Modification-mediated GRAP Regulates Vascular Remodeling in Hypoxic Pulmonary Hypertension.

Pulmonary arterial hypertension (PAH) is characterized by pulmonary vascular remodeling induced by human pulmonary arterial smooth muscle cell (HPASMC) proliferation, migration, and apoptosis resistance. m6A (N6-methyladenosine) is the most prevalent RNA posttranscriptional modification in eukaryotic cells. However, its role in PAH remains elusive. We designed this study to investigate whether m6A modification and its effector proteins play a role in pulmonary vascular resistance. Lung samples were used to profile m6A concentrations in control subjects and patients with PAH. Bioinformatics analysis, real-time PCR, immunohistochemistry, and Western blotting were used to determine the role of m6A effectors in PAH. The biological effects of GRAP modified by m6A were investigated using in vitro and in vivo models. Furthermore, RIP-PCR was used to assess the writers and readers of GRAP. In this study, we revealed that m6A-modified GRAP mRNA was upregulated in PAH lung samples, cHx/Su-induced mouse models, and hypoxia-stimulated HPASMCs; however, GRAP mRNA and protein were abnormally downregulated. Functionally, overexpression of GRAP drastically alleviated the proliferative and invasive ability of PAH HPASMCs through inhibition of the Ras/ERK signaling pathway in vitro and in vivo. In addition, METTL14 (methyltransferase-like 14) and the m6A binding protein YTHDF2 were significantly increased in PAH. Moreover, we found that m6A-modified GRAP mRNA was recognized by YTHDF2 to mediate the degradation. GRAP expression was consistently negatively correlated with METTL14 and YTHDF2 in vivo and in vitro. Taken together, for the first time, our findings highlight the function and therapeutic target value of GRAP and extend our understanding of the importance of RNA epigenetics in PAH.

EWSR1-induced circNEIL3 promotes glioma progression and exosome-mediated macrophage immunosuppressive polarization via stabilizing IGF2BP3.

BACKGROUND: Gliomas are the most common malignant primary brain tumours with a highly immunosuppressive tumour microenvironment (TME) and poor prognosis. Circular RNAs (circRNA), a newly found type of endogenous noncoding RNA, characterized by high stability, abundance, conservation, have been shown to play an important role in the pathophysiological processes and TME remodelling of various tumours. METHODS: CircRNA sequencing analysis was performed to explore circRNA expression profiles in normal and glioma tissues. The biological function of a novel circRNA, namely, circNEIL3, in glioma development was confirmed both in vitro and in vivo. Mechanistically, RNA pull-down, mass spectrum, RNA immunoprecipitation (RIP), luciferase reporter, and co-immunoprecipitation assays were conducted. RESULTS: We identified circNEIL3, which could be cyclized by EWS RNA-binding protein 1(EWSR1), to be upregulated in glioma tissues and to correlate positively with glioma malignant progression. Functionally, we confirmed that circNEIL3 promotes tumorigenesis and carcinogenic progression of glioma in vitro and in vivo. Mechanistically, circNEIL3 stabilizes IGF2BP3 (insulin-like growth factor 2 mRNA binding protein 3) protein, a known oncogenic protein, by preventing HECTD4-mediated ubiquitination. Moreover, circNEIL3 overexpression glioma cells drives macrophage infiltration into the tumour microenvironment (TME). Finally, circNEIL3 is packaged into exosomes by hnRNPA2B1 and transmitted to infiltrated tumour associated macrophages (TAMs), enabling them to acquire immunosuppressive properties by stabilizing IGF2BP3 and in turn promoting glioma progression. CONCLUSIONS: This work reveals that circNEIL3 plays a nonnegligible multifaceted role in promoting gliomagenesis, malignant progression and macrophage tumour-promoting phenotypes polarization, highlighting that circNEIL3 is a potential prognostic biomarker and therapeutic target in glioma.

miR-3184-3p enriched in cerebrospinal fluid exosomes contributes to progression of glioma and promotes M2-like macrophage polarization.

Liquid biopsy is a novel strategy for tumour diagnosis. The contents of cerebrospinal fluid (CSF) exosomes could reflect glioma status, hence sampling exosomes from CSF is a means of liquid biopsy for glioma. However, few studies have focused on the function of microRNAs in CSF exosomes. In this study, we found that miR-3184-3p was enriched in CSF exosomes in glioma patients and was downregulated after tumour resection. We found that miR-3184 facilitates glioma progression in two ways. On the one hand, miR-3184 directly promotes proliferation, migration, and invasion while inhibiting apoptosis in glioma. On the other hand, miR-3184 in glioma-derived exosomes polarizes macrophages to an M2-like phenotype, which further aggravates tumour progression. Overall, the current findings uncovered a new mechanism and highlighted the significant role of miR-3184 in glioma progression. Furthermore, exosomal miR-3184 could be a considerable factor with potential applications in glioma diagnosis and treatment in the future.

Pancancer landscape analysis of the thymosin family identified TMSB10 as a potential prognostic biomarker and immunotherapy target in glioma.

BACKGROUND: Thymosin family genes (TMSs), biologically important peptides with diverse intracellular and extracellular functions, have been shown to promote the progression of multiple cancers. However, multiomics characterization of TMSs and their role in human cancer prognosis has not been systematically performed. METHODS: We performed a comprehensive analysis of TMSs and thymosin ß10 (TMSB10) using multiomics data from more than 10,000 tumor samples of 33 cancer types from The Cancer Genome Atlas (TCGA). We used single-sample gene set enrichment analysis (ssGSEA) and the gene set variation analysis (GSVA) algorithm to investigate the differences in tumor microenvironment (TME) cell infiltration and functional annotation for individual tumor samples, respectively. The role of TMSB10 in the malignant progression of glioma, the promotion of macrophage infiltration,and immunosuppressive polarization, and the combination drug efficacy were assessed via biological function assays. RESULTS: We comprehensively assessed genomic mutations, expression dysregulation, prognosis and immunotherapeutic response across 33 human cancer samples and showed that TMSB10 is specifically overexpressed in almost all types of cancer tissues. Further pan-cancer analysis showed that TMSB10 is closely related to the biological function, immune regulation and prognosis of glioma. Similar results were also found in several public glioma cohorts and our Qilu local cohort. Further integration with other biological experiments revealed the key roles of TMSB10 in the malignant progression of glioma, the promotion of macrophage infiltration and immunosuppressive polarization. We also identified multiple drugs targeting cells with high TMSB10 expression and validated that knockdown of TMSB10 improved the efficacy of selumetinib (a MEK1/2 inhibitor approved by the FDA for the treatment of neurofibromatosis-associated tumors) and anti-PD1 treatment in glioma. CONCLUSION: These results indicate that TMSB10 holds promise as a novel prognostic marker and therapeutic target, providing a theoretical basis for the development of more effective and targeted clinical treatment strategies for glioma patients.

Characteristics of cathepsin members and expression responses to poly I:C challenge in Pacific cod (Gadus macrocephalus).

Cathepsins are major lysosomal enzymes that participate in necessary physiological processes, including protein degradation, tissue differentiation, and innate or adaptive immune responses. According to their proteolytic activity, vertebrate cathepsins are classified as cysteine proteases (cathepsins B, C, F, H, K, L, O, S, V, W, and X or Z), aspartic proteases (cathepsin D and E), and serine proteases (cathepsin A and G). Several cathepsins were reported in teleosts, however, no cathepsin gene has been identified from Pacific cod so far. In the present study, a total of 13 cathepsin genes were identified for Pacific cod. The evolutionary path of each cathepsin gene was demonstrated via analysis of phylogenetic trees, multiple alignments, conserved domains, motif compositions, and tertiary structures. Tissue distribution analysis showed that all cathepsin genes were ubiquitously expressed in eight healthy tissues but they exhibited diverse levels of expression. Several cathepsin genes were found to be highly expressed in the kidney, spleen, head kidney and liver, whereas low or modest levels were detected in the gills, skin, intestines, and heart. Temporal-specific expression of cathepsins in early developmental stages of Pacific cod were also conducted. CTSK, S, F, and Z were highly expressed at 1 dph and 5 dph and decreased later, while CTSL, L1, and L.1 transcript levels gradually increased in a time-dependent manner. Additionally, the expression profiles of cathepsin genes in Pacific cod were evaluated in the spleen and liver after poly I:C challenge. The results indicated that all cathepsin genes were significantly upregulated upon poly I:C stimulation, suggesting that they play key roles in antiviral immune responses in Pacific cod. Our findings establish a foundation for future exploration of the molecular mechanisms of cathepsins in modulating antiviral immunity in Pacific cod.

Exosomal miR-1246 from glioma patient body fluids drives the differentiation and activation of myeloid-derived suppressor cells.

Glioma is a heterogeneous cellular environment in which immune cells play critical roles in tumor progression. Myeloid-derived suppressor cells (MDSCs) contribute to the formation of the immunosuppressive microenvironment of glioma; however, how glioma cells interact with MDSCs and how this interaction affects the function of other immune cells are unclear. Glioma cells can systemically communicate with immune cells via the secretion of exosomes, which contain microRNAs (miRNAs). Leveraging miRNA sequencing of exosomes, we identified enrichment of miR-1246 in glioma-derived exosomes and exosomes isolated from the cerebrospinal fluid (CSF) of glioma patients. We demonstrated that miR-1246 drives the differentiation and activation of MDSCs in a dual specificity phosphatase 3 (DUSP3)/extracellular signal­regulated kinase (ERK)-dependent manner. In addition, postoperative CSF exosomal miR-1246 expression was found to be associated with the glioma recurrence rate. Hypoxia, a well-recognized feature of the glioblastoma microenvironment, increased miR-1246 levels in glioma-derived exosomes by enhancing miR-1246 transcription and selective packaging via upregulation of POU class 5 homeobox 1 (POU5F1) and heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1). Importantly, we identified a mechanism of 2-methoxyestradiol, a microtubule inhibitor currently undergoing clinical trials for glioblastoma. 2-Methoxyestradiol suppresses MDSC activation by inhibiting hypoxia-driven exosomal miR-1246 expression in glioma cells and PD-L1 expression in MDSCs.

Effects of sepiolite and biochar on the photosynthetic and antioxidant systems of pakchoi under Cd and atrazine stress.

Sepiolite and biochar effectively immobilize Cd and atrazine in vegetable soils. This study further investigated the effects of sepiolite and biochar on the photosynthetic and antioxidative defence systems of pakchoi under Cd and atrazine stress. The results showed that after adding sepiolite and biochar to contaminated soil, the chlorophyll content was restored and the photosynthetic rate increased, whereas the soluble sugar content of pakchoi decreased. In the antioxidant system of the plants, the activities of peroxidase, ascorbate peroxidase, and superoxide dismutase decreased, while the activity of catalase increased. The content of malondialdehyde, glutathione, and O2·- increased, but the content of H2O2 decreased. In general, remediation materials reduced the bioavailability of Cd and atrazine, reduced the stress on pakchoi, and restored and improved the rate of photosynthesis and function of antioxidants.

Comparative transcriptomic analysis reveals the gene expression profiles in the liver and spleen of Japanese pufferfish (Takifugu rubripes) in response to Vibrio harveyi infection.

Japanese pufferfish (Takifugu rubripes) is one of the main marine aquatic fish species cultured in Asia due to its high nutritional value. In recent years, disease caused by Vibrio harveyi infections have led to serious mortality in Japanese pufferfish industry. To understand the complex molecular mechanisms between V. harveyi and Japanese pufferfish, we performed a transcriptome analysis of liver and spleen samples from Japanese pufferfish at 1 and 2 day post-infection. Between-group comparisons revealed 922 genes that were significantly differentially expressed. The altered genes emphasized the function in several immune related pathways including MAPK signaling pathway, JAK-STAT signaling pathway, toll-like receptor signaling pathway, cytokine-cytokine receptor interaction and lysosomal pathway. The data generated in this study provided insight into the responses of Japanese pufferfish against V. harveyi at the transcriptome level, promoting our comprehensive understanding of immune responses for aquatic animal against V. harveyi.

Molecular characterization and expression analysis of galectins in Japanese pufferfish (Takifugu rubripes) in response to Vibrio harveyi infection.

Galectins are a family of proteins with conserved carbohydrate recognition domains (CRDs) that bind to specific glycans, including the glycans on the surface of pathogens, and therefore play a role in cytokine secretion, cell activation, migration, adhesion and apoptosis. Currently, galectins have been extensively studied in mammalian species but rarely studied in teleost fish species. In this study, a total of 12 galectin genes were characterized to understand the molecular mechanisms of galectin function in Japanese pufferfish (Takifugu rubripes). Phylogenetic analyses and syntenic analyses confirmed their correct annotation and suggested the strongest relationships to tetraodon. Furthermore, expression analyses were conducted in healthy tissues of Japanese pufferfish and after infection with Vibrio harveyi in the intestine, liver and spleen. The results showed that galectin genes were widely expressed in all examined tissues; however, most of the galectin genes were highly expressed in mucosal tissues (skin, gill and intestine). Moreover, majority of the galectin genes were significantly regulated after V. harveyi infection in the intestine, liver and spleen, suggesting that galectins were involved in the immune response to V. harveyi infection in Japanese pufferfish. This study established the foundation for future studies of galectin gene functions.

Identification of a Combined RNA Prognostic Signature in Adenocarcinoma of the Lung.

BACKGROUND Adenocarcinoma of the lung is a type of non-small cell lung cancer (NSCLC). Clinical outcome is associated with tumor grade, stage, and subtype. This study aimed to identify RNA expression profiles, including long noncoding RNA (lncRNA), microRNA (miRNA), and mRNA, associated with clinical outcome in adenocarcinoma of the lung using bioinformatics data. MATERIAL AND METHODS The miRNA and mRNA expression profiles were downloaded from The Cancer Genome Atlas (TCGA) database, and lncRNA expression profiles were downloaded from The Atlas of Noncoding RNAs in Cancer (TANRIC) database. The independent dataset, the Gene Expression Omnibus (GEO) accession dataset, GSE81089, was used. RNA expression profiles were used to identify comprehensive prognostic RNA signatures based on patient survival time. RESULTS From 7,704 lncRNAs, 787 miRNAs, and 28,937 mRNAs of 449 patients, four joint RNA molecular signatures were identified, including RP11-909N17.2, RP11-14N7.2 (lncRNAs), MIR139 (miRNA), KLHDC8B (mRNA). The random forest (RF) classifier was used to test the prediction ability of patient survival risk and showed a good predictive accuracy of 71% and also showed a significant difference in overall survival (log-rank P=0.0002; HR, 3.54; 95% CI, 1.74-7.19). The combined RNA signature also showed good performance in the identification of patient survival in the validation and independent datasets. CONCLUSIONS This study identified four RNA sequences as a prognostic molecular signature in adenocarcinoma of the lung, which may also provide an increased understanding of the molecular mechanisms underlying the pathogenesis of this malignancy.

Effects of spatio-temporal landscape patterns on land surface temperature: a case study of Xi'an city, China.

A city is a mixed ecosystem of nature, economy, and society and is simultaneously transforming natural areas and adapting to nature. Urbanization causes the population to expand rapidly, leading to rapid expansions of scale. Consequently, the proportions of impermeable surfaces (ISs) and greenspaces (GSs) change drastically, which has a considerable influence on the urban thermal environment. The aim of this study was to research the effects of spatio-temporal landscape patterns on land surface temperature (LST) and between GS and IS in the city of Xi'an using the urban-rural gradient, the moving split-window algorithm (MSA), multiple grid resolutions, and landscape metrics based on three-phase Landsat data. The results showed that there was a significantly positively correlated with IS density and significantly negatively correlated with the GS density from the urban center to rural areas. Over the past 25 years, the main urban area of Xi'an has expanded by nearly 6.2 times its initial size. The correlation between IS density and LST increased with increasing grid size, and the correlation between GS density and LST increased with decreasing grid size. Thus, LST is highly sensitive to the ISs and GSs at particular grid sizes. The correlation coefficients of the ISs and GSs with LST increased with decreasing grid size during 1992-2016. Hence, the LST was less sensitive to IS and the GS densities in conjunction with larger grid sizes. The class area (CA) and the landscape shape index (LSI) of the ISs were significantly positively correlated with the LST, whereas the CA and largest patch index (LPI) of the GSs were negatively correlated with the LST. The LST of the ISs in 1992, 2006, and 2016 were 1.6, 1.8, and 3.9 °C higher, respectively, than those of the GSs, indicating that GSs are important to lowering urban LSTs. Therefore, the government and urban planning departments should consider optimizing the spatial patterns of ISs and GSs to fully exploit the cooling effect of optimally configured GSs, which would be conducive to the sustainable development of the urban ecological environment.

Low-content quantification in powders using Raman spectroscopy: a facile chemometric approach to sub 0.1% limits of detection.

A robust and accurate analytical methodology for low-content (<0.1%) quantification in the solid-state using Raman spectroscopy, subsampling, and chemometrics was demonstrated using a piracetam-proline model. The method involved a 5-step process: collection of a relatively large number of spectra (8410) from each sample by Raman mapping, meticulous data pretreatment to remove spectral artifacts, use of a 0-100% concentration range partial least-squares (PLS) regression model to estimate concentration at each pixel, use of a more accurate, reduced concentration range PLS model to calculate analyte concentration at each pixel, and finally statistical analysis of all 8000+ concentration predictions to produce an accurate overall sample concentration. The relative prediction accuracy was ∼2.4% for a 0.05-1.0% concentration range, and the limit of detection was comparable to high performance liquid chromatography (0.03% versus 0.041%). For data pretreatment, we developed a unique cosmic ray removal method and used an automated baseline correction method, neither of which required subjective user intervention and thus were fully automatable. The method is applicable to systems which cannot be easily analyzed chromatographically, such as hydrate, polymorph, or solvate contamination.

Comprehensive, quantitative bioprocess productivity monitoring using fluorescence EEM spectroscopy and chemometrics.

This study demonstrates the application of fluorescence excitation-emission matrix (EEM) spectroscopy to the quantitative predictive analysis of recombinant glycoprotein production cultured in a Chinese hamster ovary (CHO) cell fed-batch process. The method relies on the fact that EEM spectra of complex solutions are very sensitive to compositional change. As the cultivation progressed, changes in the emission properties of various key fluorophores (e.g., tyrosine, tryptophan, and the glycoprotein product) showed significant differences, and this was used to follow culture progress via multiple curve resolution alternating least squares (MCR-ALS). MCR-ALS clearly showed the increase in the unique dityrosine emission from the product glycoprotein as the process progressed, thus provided a qualitative tool for process monitoring. For the quantitative predictive modelling of process performance, the EEM data was first subjected to variable selection and then using the most informative variables, partial least-squares (PLS) regression was implemented for glycoprotein yield prediction. Accurate predictions with relative errors of between 2.3 and 4.6% were obtained for samples extracted from the 100 to 5000 L scale bioreactors. This study shows that the combination of EEM spectroscopy and chemometric methods of evaluation provides a convenient method for monitoring at-line or off-line the productivity of industrial fed-batch mammalian cell culture processes from the small to large scale. This method has applicability to the advancement of process consistency, early problem detection, and quality-by-design (QbD) practices.

DiseaseMeth: a human disease methylation database.

DNA methylation is an important epigenetic modification for genomic regulation in higher organisms that plays a crucial role in the initiation and progression of diseases. The integration and mining of DNA methylation data by methylation-specific PCR and genome-wide profiling technology could greatly assist the discovery of novel candidate disease biomarkers. However, this is difficult without a comprehensive DNA methylation repository of human diseases. Therefore, we have developed DiseaseMeth, a human disease methylation database (http://bioinfo.hrbmu.edu.cn/diseasemeth). Its focus is the efficient storage and statistical analysis of DNA methylation data sets from various diseases. Experimental information from over 14,000 entries and 175 high-throughput data sets from a wide number of sources have been collected and incorporated into DiseaseMeth. The latest release incorporates the gene-centric methylation data of 72 human diseases from a variety of technologies and platforms. To facilitate data extraction, DiseaseMeth supports multiple search options such as gene ID and disease name. DiseaseMeth provides integrated gene methylation data based on cross-data set analysis for disease and normal samples. These can be used for in-depth identification of differentially methylated genes and the investigation of gene-disease relationship.