Ab initio investigation of the crystallization mechanism of cadmium selenide

Cadmium selenide (CdSe) is an inorganic semiconductor with unique optical and electronic properties that made it useful in various applications, including solar cells, light-emitting diodes, and biofluorescent tagging. In order to synthesize high-quality crystals and subsequently integrate them into devices, it is crucial to understand the atomic scale crystallization mechanism of CdSe. Unfortunately, such studies are still absent in the literature.To overcome this limitation, we employed an enhanced sampling-accelerated active learning approach to construct a deep neural potential with ab initio accuracy for studying the crystallization of CdSe.Our brute-force molecular dynamics simulations revealed that a spherical-like nucleus formed spontaneously and stochastically, resulting in a stacking disordered structure where the competition between hexagonal wurtzite and cubic zinc blende polymorphs is temperature-dependent. We found that pure hexagonal crystal can only be obtained approximately above 1430 K, which is 35 K below its melting temperature. We observed that the solidification dynamics of Cd and Se atoms were distinct due to their different diffusion coefficients. The solidification process was initiated by lower mobile Se atoms forming tetrahedral frameworks, followed by Cd atoms occupying these tetrahedral centers and settling down until the third-shell neighbor of Se atoms sited on their lattice positions. Therefore, the medium-range ordering of Se atoms governs the crystallization process of CdSe. Our findings indicate that understanding the complex dynamical process is the key to comprehending the crystallization mechanism of compounds like CdSe, and can shed lights in the synthesis of high-quality crystals.Comment: 25 pages, 7 figure

Elucidating the anti-hypertensive mechanisms of Uncaria rhynchophylla-Alisma plantago-aquatica L: an integrated network pharmacology, cluster analysis, and molecular docking approach

Background: With the increasing global prevalence of hypertension, a condition that can severely affect multiple organs, there is a growing need for effective treatment options. Uncaria rhynchophylla-Alisma plantago-aquatica L. (UR-AP) is a traditional drug pair used for treating hypertension based on the liver-kidney synergy concept. However, the detailed molecular mechanisms underlying its efficacy remain unclear.Methods: This study utilized an integrative approach combining network pharmacology, cluster analysis, and molecular docking to uncover the bioactive components and targets of UR-AP in the treatment of hypertension. Initially, we extracted data from public databases to identify these components and targets. A Protein-Protein Interaction (PPI) network was constructed, followed by enrichment analysis to pinpoint the bioactive components, core targets, and pivotal pathways. Cluster analysis helped in identifying key sub-networks and hypothesizing primary targets. Furthermore, molecular docking was conducted to validate the interaction between the core targets and major bioactive components, thus confirming their potential efficacy in hypertension treatment.Results: Network pharmacological analysis identified 58 bioactive compounds in UR-AP, notably quercetin, kaempferol, beta-sitosterol (from Uncaria rhynchophylla), and Alisol B, alisol B 23-acetate (from Alisma plantago-aquatica L.), as pivotal bioactives. We pinpointed 143 targets common to both UR-AP and hypertension, highlighting MAPK1, IL6, AKT1, VEGFA, EGFR, and TP53 as central targets involved in key pathways like diastolic and endothelial function, anti-atherosclerosis, AGE-RAGE signaling, and calcium signaling. Cluster analysis emphasized IL6, TNF, AKT1, and VEGFA’s roles in atherosclerosis and inflammation. Molecular docking confirmed strong interactions between these targets and UR-AP’s main bioactives, underscoring their therapeutic potential.Conclusion: This research delineates UR-AP’s pharmacological profile in hypertension treatment, linking traditional medicine with modern pharmacology. It highlights key bioactive components and their interactions with principal targets, suggesting UR-AP’s potential as a novel therapeutic option for hypertension. The evidence from molecular docking studies supports these interactions, indicating the relevance of these components in affecting hypertension pathways. However, the study acknowledges its limitations, including the reliance on in silico analyses and the need for in vivo validation. These findings pave the way for future clinical research, aiming to integrate traditional medicine insights with contemporary scientific approaches for developing innovative hypertension therapies

Pathogenic spectrum and risk factors of peritoneal dialysis-associated peritonitis: a single-center retrospective study

Abstract The present study aimed to explore the pathogenic spectrum and risk factors of peritoneal dialysis-associated peritonitis (Peritoneal dialysis associated peritonitis, PDAP) in Yongzhou, Hunan, China. The clinical and epidemiological data on regular peritoneal dialysis (Peritoneal dialysis, PD) between January 2016 and December 2020 in Yongzhou were collected for retrospective analysis. The related factors of peritonitis were evaluated by single-factor analysis, while risk factors of refractory PDAP were evaluated by multivariate logistic regression analysis.172/331 172 (51.9%) patients developed peritonitis. The risk factors of PDAP in PD patients included high C-reactive protein (C-reactive protein, CRP), low albumin(Albumin, ALB), low hemoglobin (Hemoglobin, Hb), low educational level (junior high school or lower), preference of spicy food, irregular diet, low annual household income, unfavorable fluid exchange conditions, unstable employment (including working as a farmer), and unfavorable humidity conditions (P < 0.05). 63/172 (36.6%) PDAP patients were intractable cases with a pathogenic bacteria positive rate of 74.60% in the peritoneal dialysate cultures, and 109/172 patients were non-intractable cases with a pathogenic bacteria positive rate of 53.21%. Gram-positive bacteria (G+) were detected in most of the dialysate cultures, with Staphylococcus epidermidis (S. epidermidis) as the most common type, while Escherichia coli (E. coli) was the most common Gram-negative bacteria (G-). Gram-positive bacteria were sensitive to vancomycin and linezolid, while G- bacteria were sensitive to imipenem and amikacin. Lifestyle, educational level, and environmental factors are the major contributors to PDAP in PD patients. Fungal and multi-bacterial infections are the major causes of death; PD is stopped for such patients

A Unified Assessment Approach for Urban Infrastructure Sustainability and Resilience

The concepts of sustainability and resilience have become very popular in the field of urban infrastructure. This paper reviews previous research on sustainability and resilience of urban infrastructure. The concepts of urban infrastructure’s sustainability and resilience are compared from the perspectives of dimensions, properties, goals, and methodologies. The paper systematically assesses the sustainability and resilience of urban infrastructure by using the concept of the grade point average (GPA). The GPA of urban infrastructure’s sustainability and resilience (urban infrastructure SR-GPA) is proposed as a unified concept. The assessment index system of urban infrastructure SR-GPA is constructed from five dimensions including demand, status, influence, resource, and measure. The analytic network process (ANP) is used to assess urban infrastructure SR-GPA considering the interaction between the indexes. The ANP structure model of urban infrastructure SR-GPA is established based on the assessment method and index system. The Harbin subway SR-GPA is selected as an empirical study to test the applicability of the proposed assessment method. The results show that the assessment indexes have different impacts on urban infrastructure SR-GPA. The Harbin subway SR-GPA is in a low level and can be upgraded through increasing construction investment, allocating resources efficiently, and considering resilience in the whole life cycle

Genomic Evidence Reveals the Extreme Diversity and Wide Distribution of the Arsenic-Related Genes in <i>Burkholderiales</i>

<div><p>So far, numerous genes have been found to associate with various strategies to resist and transform the toxic metalloid arsenic (here, we denote these genes as “arsenic-related genes”). However, our knowledge of the distribution, redundancies and organization of these genes in bacteria is still limited. In this study, we analyzed the 188 <i>Burkholderiales</i> genomes and found that 95% genomes harbored arsenic-related genes, with an average of 6.6 genes per genome. The results indicated: a) compared to a low frequency of distribution for <i>aio</i> (arsenite oxidase) (12 strains), <i>arr</i> (arsenate respiratory reductase) (1 strain) and <i>arsM</i> (arsenite methytransferase)-like genes (4 strains), the <i>ars</i> (arsenic resistance system)-like genes were identified in 174 strains including 1,051 genes; b) 2/3 <i>ars</i>-like genes were clustered as <i>ars</i> operon and displayed a high diversity of gene organizations (68 forms) which may suggest the rapid movement and evolution for <i>ars-</i>like genes in bacterial genomes; c) the arsenite efflux system was dominant with ACR3 form rather than ArsB in <i>Burkholderiales</i>; d) only a few numbers of <i>arsM</i> and <i>arrAB</i> are found indicating neither As III biomethylation nor AsV respiration is the primary mechanism in <i>Burkholderiales</i> members; (e) the <i>aio-like</i> gene is mostly flanked with <i>ars-like</i> genes and phosphate transport system, implying the close functional relatedness between arsenic and phosphorus metabolisms. On average, the number of arsenic-related genes per genome of strains isolated from arsenic-rich environments is more than four times higher than the strains from other environments. Compared with human, plant and animal pathogens, the environmental strains possess a larger average number of arsenic-related genes, which indicates that habitat is likely a key driver for bacterial arsenic resistance.</p></div

Four major metabolic strategies for arsenic resistance and transformation were found in microbes.

<p>a) cytoplasmic AsV reduction by ArsC and As III extrusion by ArsB or ACR3; b) periplasmic AsV reduction under anaerobic conditions by ArrAB; c) As III oxidation by AioAB and AsV extrusion through a phosphate transporter system; d) As III methylation to the gaseous compound As(CH)3 by ArsM. The gene organizations representative of these four processes are shown in the pale blue box, and the corresponding functions of the genes are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092236#pone-0092236-t001" target="_blank">Table 1</a>.</p

Habitat impacts the distribution of arsenic-related genes in <i>Burkholderiales</i>.

<p>The scatter distribution of the number of arsenic-related genes per genome grouped by the isolation sources. The isolation sources included human (H), plant (P), animal (Z), rhizosphere or root nodules (R), soil (S), sediment (D) and wastewater or sludge (W) (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092236#pone.0092236.s003" target="_blank">Table S1</a>).</p

Arsenic-related genes involved in bacterial arsenic resistance and transformation.

<p>Note: <i>ars</i>, cytoplasmic AsV reduction; <i>arr</i>, periplasmic AsV reduction; <i>aio</i>, arsenite oxidation; <i>arsM</i>, arsenite methylation.</p

Multiple organizations of the <i>aio</i> gene cluster and flanking sequences were detected in arsenite-oxidizing bacteria in <i>Burkholderiales</i>.

<p>Multiple organizations of the <i>aio</i> gene cluster and flanking sequences were detected in arsenite-oxidizing bacteria in <i>Burkholderiales</i>.</p

Diversity of organizations of the arsenate-resistance operon (<i>ars</i>) cluster in the 161 <i>Burkholderiales</i> genomes.

<p>Diversity of organizations of the arsenate-resistance operon (<i>ars</i>) cluster in the 161 <i>Burkholderiales</i> genomes.</p