An Improved Focused Crawler: Using Web Page Classification and Link Priority Evaluation

A focused crawler is topic-specific and aims selectively to collect web pages that are relevant to a given topic from the Internet. However, the performance of the current focused crawling can easily suffer the impact of the environments of web pages and multiple topic web pages. In the crawling process, a highly relevant region may be ignored owing to the low overall relevance of that page, and anchor text or link-context may misguide crawlers. In order to solve these problems, this paper proposes a new focused crawler. First, we build a web page classifier based on improved term weighting approach (ITFIDF), in order to gain highly relevant web pages. In addition, this paper introduces an evaluation approach of the link, link priority evaluation (LPE), which combines web page content block partition algorithm and the strategy of joint feature evaluation (JFE), to better judge the relevance between URLs on the web page and the given topic. The experimental results demonstrate that the classifier using ITFIDF outperforms TFIDF, and our focused crawler is superior to other focused crawlers based on breadth-first, best-first, anchor text only, link-context only, and content block partition in terms of harvest rate and target recall. In conclusion, our methods are significant and effective for focused crawler

Prodromal dementia with lewy bodies and recurrent panic attacks as the first symptom : a case report

La demencia de inicio psiquiátrico con cuerpos de Lewy (DLB) puede incluir síntomas de depresión, alucinaciones, ansiedad y apatía. Aquí, reportamos un paciente con DLB con ataques de pánico recurrentes como su primer síntoma 5 años antes de un diagnóstico de base biológica de probable DCL. Proporcionamos una descripción ampliada de la presentación clínica y curso de DCL de inicio psiquiátrico a demencia en una mujer de 83 años. Este caso ilustra el diagnóstico erróneo común de DLB y la demora en tener un diagnóstico clínico y evaluación de biomarcadores para el diagnóstico estructurado. Con una descripción detallada de la clínica. presentación de este caso, las estrategias de tratamiento empírico y las perspectivas del paciente, Nuestro objetivo es concienciar a los médicos sobre los ataques de pánico dentro de la DCL de inicio psiquiátrico. Palabras clave: demencia con cuerpos de Lewy, ataques de pánico, reporte de caso, demencia prodrómica con cuerpos de Lewy, síntomas neuropsiquiátricosQ2Q2Psychiatric-onset dementia with Lewy bodies (DLB) might include symptoms of depression, hallucinations, anxiety, and apathy. Here, we report a patient with DLB with recurrent panic attacks as her first symptom 5 years before a biological-based diagnosis of probable DLB. We provide an extended description of the clinical presentation and course from psychiatric-onset DLB to dementia in an 83-year-old woman. This case illustrates the commonmisdiagnosis of DLB and the delay of having a detailed clinical and biomarker assessment for structured diagnosis. With a detailed description of the clinical presentation of this case, the empirical treatment strategies, and the patient perspectives, we aim to make clinicians aware of panic attacks within the psychiatric-onset DLB. Keywords: dementia with Lewy bodies, panic attacks, case report, prodromal dementia with Lewy bodies, neuropsychiatric symptomshttps://orcid.org/ 0000-0001-5832-0603https://scholar.google.es/citations?hl=es&user=MrICwaMAAAAJhttps://scienti.minciencias.gov.co/cvlac/visualizador/generarCurriculoCv.do?cod_rh=0001429659Revista Nacional - Indexad

Lineage tracing for multiple lung cancer by spatiotemporal heterogeneity using a multi-omics analysis method integrating genomic, transcriptomic, and immune-related features

IntroductionThe distinction between multiple primary lung cancer (MPLC) and intrapulmonary metastasis (IPM) holds clinical significance in staging, therapeutic intervention, and prognosis assessment for multiple lung cancer. Lineage tracing by clinicopathologic features alone remains a clinical challenge; thus, we aimed to develop a multi-omics analysis method delineating spatiotemporal heterogeneity based on tumor genomic profiling.MethodsBetween 2012 and 2022, 11 specimens were collected from two patients diagnosed with multiple lung cancer (LU1 and LU2) with synchronous/metachronous tumors. A novel multi-omics analysis method based on whole-exome sequencing, transcriptome sequencing (RNA-Seq), and tumor neoantigen prediction was developed to define the lineage. Traditional clinicopathologic reviews and an imaging-based algorithm were performed to verify the results.ResultsSeven tissue biopsies were collected from LU1. The multi-omics analysis method demonstrated that three synchronous tumors observed in 2018 (LU1B/C/D) had strong molecular heterogeneity, various RNA expression and immune microenvironment characteristics, and unique neoantigens. These results suggested that LU1B, LU1C, and LU1D were MPLC, consistent with traditional lineage tracing approaches. The high mutational landscape similarity score (75.1%), similar RNA expression features, and considerable shared neoantigens (n = 241) revealed the IPM relationship between LU1F and LU1G which were two samples detected simultaneously in 2021. Although the multi-omics analysis method aligned with the imaging-based algorithm, pathology and clinicopathologic approaches suggested MPLC owing to different histological types of LU1F/G. Moreover, controversial lineage or misclassification of LU2’s synchronous/metachronous samples (LU2B/D and LU2C/E) traced by traditional approaches might be corrected by the multi-omics analysis method. Spatiotemporal heterogeneity profiled by the multi-omics analysis method suggested that LU2D possibly had the same lineage as LU2B (similarity score, 12.9%; shared neoantigens, n = 71); gefitinib treatment and EGFR, TP53, and RB1 mutations suggested the possibility that LU2E might result from histology transformation of LU2C despite the lack of LU2C biopsy and its histology. By contrast, histological interpretation was indeterminate for LU2D, and LU2E was defined as a primary or progression lesion of LU2C by histological, clinicopathologic, or imaging-based approaches.ConclusionThis novel multi-omics analysis method improves the accuracy of lineage tracing by tracking the spatiotemporal heterogeneity of serial samples. Further validation is required for its clinical application in accurate diagnosis, disease management, and improving prognosis

Identification of microtubule-associated biomarkers in diffuse large B-cell lymphoma and prognosis prediction

Background: Diffuse large B-cell lymphoma (DLBCL) is a genetically heterogeneous disease with a complicated prognosis. Even though various prognostic evaluations have been applied currently, they usually only use the clinical factors that overlook the molecular underlying DLBCL progression. Therefore, more accurate prognostic assessment needs further exploration. In the present study, we constructed a novel prognostic model based on microtubule associated genes (MAGs).Methods: A total of 33 normal controls and 1360 DLBCL samples containing gene-expression from the Gene Expression Omnibus (GEO) database were included. Subsequently, the univariate Cox, the least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analysis were used to select the best prognosis related genes into the MAGs model. To validate the model, Kaplan-Meier curve, and nomogram were analyzed.Results: A risk score model based on fourteen candidate MAGs (CCDC78, CD300LG, CTAG2, DYNLL2, MAPKAPK2, MREG, NME8, PGK2, RALBP1, SIGLEC1, SLC1A1, SLC39A12, TMEM63A, and WRAP73) was established. The K-M curve presented that the high-risk patients had a significantly inferior overall survival (OS) time compared to low-risk patients in training and validation datasets. Furthermore, knocking-out TMEM63A, a key gene belonging to the MAGs model, inhibited cell proliferation noticeably.Conclusion: The novel MAGs prognostic model has a well predictive capability, which may as a supplement for the current assessments. Furthermore, candidate TMEM63A gene has therapeutic target potentially in DLBCL

Assessing the Accuracy of Landsat-MODIS NDVI Fusion with Limited Input Data: A Strategy for Base Data Selection

Despite its wide applications, the spatiotemporal fusion of coarse- and fine-resolution satellite images is limited primarily to the availability of clear-sky fine-resolution images, which are commonly scarce due to unfavorable weather, and such a limitation might cause errors in spatiotemporal fusion. Thus, the effective use of limited fine-resolution images, while critical, remains challenging. To address this issue, in this paper we propose a new phenological similarity strategy (PSS) to select the optimal combination of image pairs for a prediction date. The PSS considers the temporal proximity and phenological similarity between the base and prediction images and computes a weight for identifying the optimal combination of image pairs. Using the PSS, we further evaluate the influence of input data on the fusion accuracy by varying the number and temporal distribution of input images. The results show that the PSS (mean R = 0.827 and 0.760) outperforms the nearest date (mean R = 0.786 and 0.742) and highest correlation (mean R = 0.821 and 0.727) strategies in both the enhanced spatial and temporal adaptive reflectance fusion model (ESTARFM) and the linear mixing growth model (LMGM), respectively, for fusing Landsat 8 OLI and MODIS NDVI datasets. Furthermore, base images adequately covering different growth stages yield better predictability than simply increasing the number of base images

Fundamental Reaction Pathway for Peptide Metabolism by Proteasome: Insights from First-Principles Quantum Mechanical/Molecular Mechanical Free Energy Calculations

Proteasome is the major component of the crucial non-lysosomal protein degradation pathway in the cells, but the detailed reaction pathway is unclear. In this study, first-principles quantum mechanical/molecular mechanical free energy calculations have been performed to explore, for the first time, possible reaction pathways for proteasomal proteolysis/hydrolysis of a representative peptide, succinyl-leucyl-leucyl-valyl-tyrosyl-7-amino-4-methylcoumarin (Suc-LLVY-AMC). The computational results reveal that the most favorable reaction pathway consists of six steps. The first is a water-assisted proton transfer within proteasome, activating Thr1-O^γ. The second is a nucleophilic attack on the carbonyl carbon of a Tyr residue of substrate by the negatively charged Thr1-O^γ, followed by the dissociation of the amine AMC (third step). The fourth step is a nucleophilic attack on the carbonyl carbon of the Tyr residue of substrate by a water molecule, accompanied by a proton transfer from the water molecule to Thr1-N^z. Then, Suc-LLVY is dissociated (fifth step), and Thr1 is regenerated <i>via</i> a direct proton transfer from Thr1-N^z to Thr1-O^γ. According to the calculated energetic results, the overall reaction energy barrier of the proteasomal hydrolysis is associated with the transition state (TS3^b) for the third step involving a water-assisted proton transfer. The determined most favorable reaction pathway and the rate-determining step have provided a reasonable interpretation of the reported experimental observations concerning the substituent and isotopic effects on the kinetics. The calculated overall free energy barrier of 18.2 kcal/mol is close to the experimentally derived activation free energy of ∼18.3–19.4 kcal/mol, suggesting that the computational results are reasonable

Fundamental Reaction Pathway and Free Energy Profile for Inhibition of Proteasome by Epoxomicin

First-principles quantum mechanical/molecular mechanical free energy calculations have been performed to provide the first detailed computational study on the possible mechanisms for reaction of proteasome with a representative peptide inhibitor, Epoxomicin (EPX). The calculated results reveal that the most favorable reaction pathway consists of five steps. The first is a proton transfer process, activating Thr1-O^γ directly by Thr1-N^z to form a zwitterionic intermediate. The next step is nucleophilic attack on the carbonyl carbon of EPX by the negatively charged Thr1-O^γ atom, followed by a proton transfer from Thr1-N^z to the carbonyl oxygen of EPX (third step). Then, Thr1-N^z attacks on the carbon of the epoxide group of EPX, accompanied by the epoxide ring-opening (S_N2 nucleophilic substitution) such that a zwitterionic morpholino ring is formed between residue Thr1 and EPX. Finally, the product of morpholino ring is generated via another proton transfer. Noteworthy, Thr1-O^γ can be activated directly by Thr1-N^z to form the zwitterionic intermediate (with a free energy barrier of only 9.9 kcal/mol), and water cannot assist the rate-determining step, which is remarkably different from the previous perception that a water molecule should mediate the activation process. The fourth reaction step has the highest free energy barrier (23.6 kcal/mol) which is reasonably close to the activation free energy (∼21–22 kcal/mol) derived from experimental kinetic data. The obtained novel mechanistic insights should be valuable for not only future rational design of more efficient proteasome inhibitors but also understanding the general reaction mechanism of proteasome with a peptide or protein

Rapid Estimation of Decameter FPAR from Sentinel-2 Imagery on the Google Earth Engine

As a direct indicator of vegetation photosynthesis, the fraction of absorbed photosynthetically active radiation (FPAR) serves as a critical input in a series of land surface models. While existing satellite FPAR products are generally at coarse resolutions ranging from 250 m to 1 km, operational FPAR products at fine resolution are urgently needed in studying land surface processes at the plot scale. However, existing methods for estimating fine-resolution FPAR were mainly designed for Landsat data, and few studies have attempted to develop algorithms for Sentinel-2 data. In particular, the operational estimation of decameter FPAR has a higher requirement for the algorithms in terms of generalizability, efficiency, accuracy, and adaptability to Sentinel-2 data. In this paper, we developed a retrieval chain on the Google Earth Engine (GEE) platform to estimate FPAR by learning the relationship between MODIS FPAR and Sentinel-2 surface reflectance. Scale-consistent multilinear models were used to model the relationship between MODIS FPAR and Sentinel-2 surface reflectance, and the model coefficients were regressed from the selected training samples. To account for the spectral and spatial characteristics of the Sentinel-2 data, we designed criteria for selecting training samples and compared different band combinations. Three strategies for band combination were used: (1) green, red, and near infrared (NIR) bands at 10 m resolution (i.e., three bands); (2) green, red, NIR, and red edge (RE) 1, RE2, and RE3 bands at 20 m resolution (i.e., five bands); and (3) green, red, NIR, RE1, RE2, RE3, shortwave infrared1 (SWIR1) and SWIR2 bands at 20 m resolution (i.e., eight bands). Meanwhile, the official Sentinel Application Platform (SNAP) method has also been implemented to estimate the Sentinel FPAR at 10 m and 20 m resolutions for comparison. Both methods were applied to the western Guanzhong area, Shaanxi Province, China, for FPAR estimation of all cloud-free Sentinel-2 images in 2021. The results show that the scaling-based method using five bands at 20 m resolution was the most accurate compared to the in situ measurements (RMSE = 0.076 and R&sup2; = 0.626), which outperformed the SNAP method at 10 m and 20 m resolutions and the scaling-based method using other strategies. The results of the scaling-based method using all three strategies were highly consistent with the MODIS FPAR product, while the SNAP method systematically underestimated FPAR values compared to the MODIS FPAR products. The proposed method is more ready-to-use and more efficient than SNAP software. Considering that the service of the MODIS sensor is overdue, the proposed method can be extended to alternatives to MODIS products, such as VIIRS and Sentinel-3 data