3D spherical-cap fitting procedure for (truncated) sessile nano- and micro-droplets & -bubbles

In the study of nanobubbles, nanodroplets or nanolenses immobilised on a substrate, a cross-section of a spherical-cap is widely applied to extract geometrical information from atomic force microscopy (AFM) topographic images. In this paper, we have developed a comprehensive 3D spherical cap fitting procedure (3D-SCFP) to extract morphologic characteristics of complete or truncated spherical caps from AFM images. Our procedure integrates several advanced digital image analysis techniques to construct a 3D spherical cap model, from which the geometrical parameters of the nanostructures are extracted automatically by a simple algorithm. The procedure takes into account all valid data points in the construction of the 3D spherical cap model to achieve high fidelity in morphology analysis. We compare our 3D fitting procedure with the commonly used 2D cross-sectional profile fitting method to determine the contact angle of a complete spherical cap and a truncated spherical cap. The results from 3D-SCFP are consistent and accurate, while 2D fitting is unavoidably arbitrary in selection of the cross-section and has a much lower number of data points on which the fitting can be based, which in addition is biased to the top of the spherical cap. We expect that the developed 3D spherical-cap fitting procedure will find many applications in imaging analysis.Comment: 23 pages, 7 figure

Accurate and Efficient Calculation of Three-Dimensional Cost Distance

Cost distance is one of the fundamental functions in geographical information systems (GISs). 3D cost distance function makes the analysis of movement in 3D frictions possible. In this paper, we propose an algorithm and efficient data structures to accurately calculate the cost distance in discrete 3D space. Specifically, Dijkstra’s algorithm is used to calculate the least cost between initial voxels and all the other voxels in 3D space. During the calculation, unnecessary bends along the travel path are constantly corrected to retain the accurate least cost. Our results show that the proposed algorithm can generate true Euclidean distance in homogeneous frictions and can provide more accurate least cost in heterogeneous frictions than that provided by several existing methods. Furthermore, the proposed data structures, i.e., a heap combined with a hash table, significantly improve the algorithm’s efficiency. The algorithm and data structures have been verified via several applications including planning the shortest drone delivery path in an urban environment, generating volumetric viewshed, and calculating the minimum hydraulic resistance

Rethinking solar photovoltaic parameter estimation: global optimality analysis and a simple efficient differential evolution method

Accurate, fast, and reliable parameter estimation is crucial for modeling, control, and optimization of solar photovoltaic (PV) systems. In this paper, we focus on the two most widely used benchmark datasets and try to answer (i) whether the global minimum in terms of root mean square error (RMSE) has already been reached; and (ii) whether a significantly simpler metaheuristic, in contrast to currently sophisticated ones, is capable of identifying PV parameters with comparable performance, e.g., attaining the same RMSE. We address the former using an interval analysis based branch and bound algorithm and certify the global minimum rigorously for the single diode model (SDM) as well as locating a fairly tight upper bound for the double diode model (DDM) on both datasets. These obtained values will serve as useful references for metaheuristic methods, since none of them can guarantee or recognize the global minimum even if they have literally discovered it. However, this algorithm is excessively slow and unsuitable for time-sensitive applications (despite the great insights on RMSE that it yields). Regarding the second question, extensive examination and comparison reveal that, perhaps surprisingly, a classic and remarkably simple differential evolution (DE) algorithm can consistently achieve the certified global minimum for the SDM and obtain the best known result for the DDM on both datasets. Thanks to its extreme simplicity, the DE algorithm takes only a fraction of the running time required by other contemporary metaheuristics and is thus preferable in real-time scenarios. This unusual (and certainly notable) finding also indicates that the employment of increasingly complicated metaheuristics might possibly be somewhat overkill for regular PV parameter estimation. Finally, we discuss the implications of these results and suggest promising directions for future development.Comment: v2, see source code at https://github.com/ShuhuaGao/rePVes

Genetic diversity and differentiation of three populations of Penaeus monodon Fabricus

【英文摘要】 Genetic diversity of two wild Penaeus monodon populations sampled from the coastal waters of Qinglan (Hainan Province of China,HN) and Malaysia (KD),and the F1 generation of a Thailand broodstock population (CP) were examined by vertical polyacrylamide gel electrophoresis. Of 21 loci encoded by ten enzymes,11 were polymorphic. The mean proportions of polymorphic loci of HN,KD and CP were 36.36%,45.45% and 50.00%,with the average heterozygosities of 0.135,0.181 and 0.191,and the effective numbers of alleles ..The National Natural Science Foundation of China under contract No.30471322

Clinical significance and biological function of interferon regulatory factor 1 in non-small cell lung cancer

The clinical application and biological function of interferon regulatory factor 1 (IRF1) in non-small cell lung cancer (NSCLC) patients undergoing chemoimmunotherapy remain elusive. The aim of this study was to investigate the predictive and prognostic significance of IRF1 in NSCLC patients. We employed the cBioPortal database to predict frequency changes in IRF1 and explore its target genes. Bioinformatic methods were utilized to analyze the relationship between IRF1 and immune regulatory factors. Retrospective analysis of clinical samples was conducted to assess the predictive and prognostic value of IRF1 in chemoimmunotherapy. Additionally, A549 cells with varying IRF1 expression levels were constructed to investigate its effects on NSCLC cells, while animal experiments were performed to study the role of IRF1 in vivo. Our findings revealed that the primary mutation of IRF1 is deep deletion and it exhibits a close association with immune regulatory factors. KRAS and TP53 are among the target genes of IRF1, with interferon and IL-2 being the predominantly affected pathways. Clinically, IRF1 levels significantly correlate with the efficacy of chemoimmunotherapy. Patients with high IRF1 levels exhibited a median progression-free survival (mPFS) of 9.5 months, whereas those with low IRF1 levels had a shorter mPFS of 5.8 months. IRF1 levels positively correlate with PD-L1 distribution and circulating IL-2 levels. IL-2 enhances the biological function of IRF1 and recapitulates its role in vivo in the knockdown group. Therefore, IRF1 may possess predictive and prognostic value for chemoimmunotherapy in NSCLC patients through the regulation of the IL-2 inflammatory pathway

Comprehensive Bibliometric Analysis of the Kynurenine Pathway in Mood Disorders: Focus on Gut Microbiota Research

Background: Emerging evidence implicates the dysregulated kynurenine pathway (KP), an immune-inflammatory pathway, in the pathophysiology of mood disorders (MD), including depression and bipolar disorder characterized by a low-grade chronic pro-inflammatory state. The metabolites of the KP, an important part of the microbiota-gut-brain axis, serve as immune system modulators linking the gut microbiota (GM) with the host central nervous system.Aim: This bibliometric analysis aimed to provide a first glimpse into the KP in MD, with a focus on GM research in this field, to guide future research and promote the development of this field.Methods: Publications relating to the KP in MD between the years 2000 and 2020 were retrieved from the Scopus and Web of Science Core Collection (WoSCC), and analyzed in CiteSpace (5.7 R5W), biblioshiny (using R-Studio), and VOSviewer (1.6.16).Results: In total, 1,064 and 948 documents were extracted from the Scopus and WoSCC databases, respectively. The publications have shown rapid growth since 2006, partly owing to the largest research hotspot appearing since then, “quinolinic acid.” All the top five most relevant journals were in the neuropsychiatry field, such as Brain Behavior and Immunity. The United States and Innsbruck Medical University were the most influential country and institute, respectively. Journal co-citation analysis showed a strong tendency toward co-citation of research in the psychiatry field. Reference co-citation analysis revealed that the top four most important research focuses were “kynurenine pathway,” “psychoneuroimmunology,” “indoleamine 2,3-dioxygenase,” and “proinflammatory cytokines,” and the most recent focus was “gut-brain axis,” thus indicating the role of the KP in bridging the GM and the host immune system, and together reflecting the field’s research foundations. Overlap analysis between the thematic map of keywords and the keyword burst analysis revealed that the topics “Alzheimer’s disease,” “prefrontal cortex,” and “acid,” were research frontiers.Conclusion: This comprehensive bibliometric study provides an updated perspective on research associated with the KP in MD, with a focus on the current status of GM research in this field. This perspective may benefit researchers in choosing suitable journals and collaborators, and aid in the further understanding of the field’s hotspots and frontiers, thus facilitating future research

Genome-wide association studies and CRISPR/Cas9-mediated gene editing identify regulatory variants influencing eyebrow thickness in humans

Hair plays an important role in primates and is clearly subject to adaptive selection. While humans have lost most facial hair, eyebrows are a notable exception. Eyebrow thickness is heritable and widely believed to be subject to sexual selection. Nevertheless, few genomic studies have explored its genetic basis. Here, we performed a genome-wide scan for eyebrow thickness in 2961 Han Chinese. We identified two new loci of genome-wide significance, at 3q26.33 near SOX2 (rs1345417: P = 6.51×10−10) and at 5q13.2 near FOXD1 (rs12651896: P = 1.73×10−8). We further replicated our findings in the Uyghurs, a population from China characterized by East Asian-European admixture (N = 721), the CANDELA cohort from five Latin American countries (N = 2301), and the Rotterdam Study cohort of Dutch Europeans (N = 4411). A meta-analysis combining the full GWAS results from the three cohorts of full or partial Asian descent (Han Chinese, Uyghur and Latin Americans, N = 5983) highlighted a third signal of genome-wide significance at 2q12.3 (rs1866188: P = 5.81×10−11) near EDAR. We performed fine-mapping and prioritized four variants for further experimental verification. CRISPR/Cas9-mediated gene editing provided evidence that rs1345417 and rs12651896 affect the transcriptional activity of the nearby SOX2 and FOXD1 genes, which are both involved in hair development. Finally, suitable statistical analyses revealed that none of the associated variants showed clear signals of selection in any of the populations tested. Contrary to popular speculation, we found no evidence that eyebrow thickness is subject to strong selective pressure

Estrogen protects neuronal cells from amyloid beta-induced apoptosis via regulation of mitochondrial proteins and function

BACKGROUND: Neurodegeneration in Alzheimer's disease is associated with increased apoptosis and parallels increased levels of amyloid beta, which can induce neuronal apoptosis. Estrogen exposure prior to neurotoxic insult of hippocampal neurons promotes neuronal defence and survival against neurodegenerative insults including amyloid beta. Although all underlying molecular mechanisms of amyloid beta neurotoxicity remain undetermined, mitochondrial dysfunction, including altered calcium homeostasis and Bcl-2 expression, are involved in neurodegenerative vulnerability. RESULTS: In this study, we investigated the mechanism of 17β-estradiol-induced prevention of amyloid beta-induced apoptosis of rat hippocampal neuronal cultures. Estradiol treatment prior to amyloid beta exposure significantly reduced the number of apoptotic neurons and the associated rise in resting intracellular calcium levels. Amyloid beta exposure provoked down regulation of a key antiapoptotic protein, Bcl-2, and resulted in mitochondrial translocation of Bax, a protein known to promote cell death, and subsequent release of cytochrome c. E(2 )pretreatment inhibited the amyloid beta-induced decrease in Bcl-2 expression, translocation of Bax to the mitochondria and subsequent release of cytochrome c. Further implicating the mitochondria as a target of estradiol action, in vivo estradiol treatment enhanced the respiratory function of whole brain mitochondria. In addition, estradiol pretreatment protected isolated mitochondria against calcium-induced loss of respiratory function. CONCLUSION: Therefore, we propose that estradiol pretreatment protects against amyloid beta neurotoxicity by limiting mitochondrial dysfunction via activation of antiapoptotic mechanisms

Population Genetic Structure of Peninsular Malaysia Malay Sub-Ethnic Groups

Patterns of modern human population structure are helpful in understanding the history of human migration and admixture. We conducted a study on genetic structure of the Malay population in Malaysia, using 54,794 genome-wide single nucleotide polymorphism genotype data generated in four Malay sub-ethnic groups in peninsular Malaysia (Melayu Kelantan, Melayu Minang, Melayu Jawa and Melayu Bugis). To the best of our knowledge this is the first study conducted on these four Malay sub-ethnic groups and the analysis of genotype data of these four groups were compiled together with 11 other populations' genotype data from Indonesia, China, India, Africa and indigenous populations in Peninsular Malaysia obtained from the Pan-Asian SNP database. The phylogeny of populations showed that all of the four Malay sub-ethnic groups are separated into at least three different clusters. The Melayu Jawa, Melayu Bugis and Melayu Minang have a very close genetic relationship with Indonesian populations indicating a common ancestral history, while the Melayu Kelantan formed a distinct group on the tree indicating that they are genetically different from the other Malay sub-ethnic groups. We have detected genetic structuring among the Malay populations and this could possibly be accounted for by their different historical origins. Our results provide information of the genetic differentiation between these populations and a valuable insight into the origins of the Malay sub-ethnic groups in Peninsular Malaysia