Automated Detection and Characterization of Cracks on Concrete using Laser Scanning

Accurate crack detection and characterization on concrete are essential for the maintenance, safety, and serviceability of various infrastructures. In this paper, an innovative approach was developed to automatically measure the cracks from 3D point clouds collected by a phase-shift terrestrial laser scanner (TLS) (FARO Focus3D S120). The approach integrates several techniques to characterize the cracks, which include the deviation on point normal determined using k-nearest neighbor (kNN) and principal components analysis (PCA) algorithms to identify the cracks, and principal axes and curve skeletons of cracks to determine the projected and real dimensions of cracks, respectively. The coordinate transformation was then performed to estimate the projected dimensions of cracks. Curve skeletons and cross sections of cracks were extracted to represent the real dimensions. Two cases of surface cracks were used to validate the developed approach. Because of the differences in definitions of the crack dimension in the three methods and due to the curve shape of the crack, the width and depth of cracks obtained from the cross-section method and manual measurement were close but slightly smaller than those measured by the projection algorithm; whereas the length of cracks determined by the curve-skeletons method was slightly larger than those obtained by the manual measurement and projection method. The real dimension of a crack has good agreements with real situations when compared with the results of the manual measurement and projection method

A Novel Blind Separation Method in Magnetic Resonance Images

A novel global search algorithm based method is proposed to separate MR images blindly in this paper. The key point of the method is the formulation of the new matrix which forms a generalized permutation of the original mixing matrix. Since the lowest entropy is closely associated with the smooth degree of source images, blind image separation can be formulated to an entropy minimization problem by using the property that most of neighbor pixels are smooth. A new dataset can be obtained by multiplying the mixed matrix by the inverse of the new matrix. Thus, the search technique is used to searching for the lowest entropy values of the new data. Accordingly, the separation weight vector associated with the lowest entropy values can be obtained. Compared with the conventional independent component analysis (ICA), the original signals in the proposed algorithm are not required to be independent. Simulation results on MR images are employed to further show the advantages of the proposed method

Distance-Decay Relationship for Biological Wastewater Treatment Plants.

UnlabelledPatterns in the spatial distribution of organisms provide important information about mechanisms underlying biodiversity and the complexity of ecosystems. One of the most well-documented spatial patterns is the distance-decay relationship, which is a universal biogeographic pattern observed repeatedly for plant and animal communities, particularly for microorganisms in natural ecosystems such as soil, ocean, and salt marsh sediment. However, it is uncertain whether the microorganisms exhibit a distance-decay pattern in engineered ecosystems. Therefore, we measured the distance-decay relationship across various microbial functional and phylogenetic groups in 26 biological wastewater treatment plants (WWTPs) in China using a functional gene array (GeoChip 4.2). We found that microbial communities of activated sludge in WWTPs exhibited a significant but very weak distance-decay relationship. The taxon-area z values for different functional and phylogenetic groups were <0.0065, which is about 1 to 2 orders of magnitude lower than those observed in microbial communities elsewhere. Variation-partitioning analysis (VPA) showed that the relationships were driven by both environmental heterogeneity and geographic distance. Collectively, these results provided new insights into the spatial scaling of microbial communities in engineering ecosystems and highlighted the importance of environmental heterogeneity and geographic distance in shaping biogeographic patterns.ImportanceDetermining the distance-decay relationship of microbial biodiversity is important but challenging in microbial ecology. All studies to date are based on natural environments; thus, it remains unclear whether there is such a relationship in an engineered ecosystem. The present study shows that there is a very weak distance-decay relationship in an engineered ecosystem (WWTPs) at the regional-to-continental scale. This study makes fundamental contributions to a mechanistic, predictive understanding of microbial biogeography

Downramp-assisted underdense photocathode electron bunch generation in plasma wakefield accelerators

It is shown that the requirements for high quality electron bunch generation and trapping from an underdense photocathode in plasma wakefield accelerators can be substantially relaxed through localizing it on a plasma density downramp. This depresses the phase velocity of the accelerating electric field until the generated electrons are in phase, allowing for trapping in shallow trapping potentials. As a consequence the underdense photocathode technique is applicable by a much larger number of accelerator facilities. Furthermore, dark current generation is effectively suppressed.Comment: 4 pages, 3 figure

The interaction between different types of activated RAW 264.7 cells and macrophage inflammatory protein-1 alpha

<p>Abstract</p> <p>Background</p> <p>Two major ways of macrophage (MΦ) activation can occur in radiation-induced pulmonary injury (RPI): classical and alternative MΦ activation, which play important roles in the pathogenesis of RPI. MΦ can produce chemokine MΦ inflammatory protein-1α (MIP-1α), while MIP-1α can recruit MΦ. The difference in the chemotactic ability of MIP-1α toward distinct activated MΦ is unclear. We speculated that there has been important interaction of MIP-1α with different activated MΦ, which might contribute to the pathogenesis of RPI.</p> <p>Methods</p> <p>Classically and alternatively activated MΦ were produced by stimulating murine MΦ cell line RAW 264.7 cells with three different stimuli (LPS, IL-4 and IL-13); Then we used recombinant MIP-1α to attract two types of activated MΦ. In addition, we measured the ability of two types of activated MΦ to produce MIP-1α at the protein or mRNA level.</p> <p>Results</p> <p>Chemotactic ability of recombinant MIP-1α toward IL-13-treated MΦ was the strongest, was moderate for IL-4-treated MΦ, and was weakest for LPS-stimulated MΦ (p < 0.01). The ability of LPS-stimulated MΦ to secrete MIP-1α was significantly stronger than that of IL-4-treated or IL-13-treated MΦ (p < 0.01). The ability of LPS-stimulated MΦ to express MIP-1α mRNA also was stronger than that of IL-4- or IL-13-stimulated MΦ (p < 0.01).</p> <p>Conclusions</p> <p>The chemotactic ability of MIP-1α toward alternatively activated MΦ (M2) was significantly greater than that for classically activated MΦ (M1). Meanwhile, both at the mRNA and protein level, the capacity of M1 to produce MIP-1α is better than that of M2. Thus, chemokine MIP-1α may play an important role in modulating the transition from radiation pneumonitis to pulmonary fibrosis <it>in vivo</it>, through the different chemotactic affinity for M1 and M2.</p

Obesity and clinical outcomes in COVID-19 patients without comorbidities, a post-hoc analysis from ORCHID trial

ObjectiveLarge body of studies described individuals with obesity experiencing a worse prognosis in COVID-19. However, the effects of obesity on the prognosis of COVID-19 in patients without comorbidities have not been studied. Therefore, the current study aimed to provide evidence of the relationship between obesity and clinical outcomes in COVID-19 patients without comorbidities.MethodsA total of 116 hospitalized COVID-19 patients without comorbidities from the ORCHID study (Patients with COVID-19 from the Outcomes Related to COVID-19 Treated with Hydroxychloroquine among Inpatients with Symptomatic Disease) were included. Obesity is defined as a BMI of ≥30 kg/m2. A Cox regression analysis was used to estimate the hazard ratio (HR) for discharge and death after 28 days.ResultsThe percentage of obesity in COVID-19 patients without comorbidities was 54.3% (63/116). Discharge at 28 days occurred in 56/63 (84.2%) obese and 51/53 (92.2%) non-obese COVID-19 patients without comorbidities. Four (3.4%) COVID-19 patients without any comorbidities died within 28 days, among whom 2/63 (3.2%) were obese and 2/53 (3.8%) were non-obese. Multivariate Cox regression analyses showed that obesity was independently associated with a decreased rate of 28-day discharge (adjusted HR: 0.55, 95% CI: 0.35–0.83) but was not significantly associated with 28-day death (adjusted HR: 0.94, 95% CI: 0.18–7.06) in COVID-19 patients without any comorbidities.ConclusionsObesity was independently linked to prolonged hospital length of stay in COVID-19 without any comorbidity. Larger prospective trials are required to assess the role of obesity in COVID-19 related deaths

Image-guided interstitial brachytherapy for recurrent cervical cancer after radiotherapy: A single institution experience

PurposeThe aim of this study is to evaluate the efficacy and toxicity of image-guided high-dose rate (HDR) interstitial brachytherapy (ISBT) for the reirradiation of cervical cancer within a previously irradiated area.Methods and materialsTwenty-three consecutive patients with cervical cancer were reirradiated with curative intent using brachytherapy (BT) with or without external beam irradiation. The median biologically equivalent dose in 2-Gy fractions (EQD2) for reirradiation was 64.0 Gy (range: 31.3–95.1 Gy), and the median cumulative EQD2 (for primary treatment and reirradiation) was 152.4 Gy (range: 97.8–200.9 Gy). The average clinical target volume was 82.9 cm3 (range: 26.9–208.3 cm3), and the median treatment-free interval (TFI) was 13 months (range: 3–93 months).ResultsThe median follow-up time was 19 months (range: 2–59 months). The complete response rate after reirradiation was 56.5%. The 1-, 2- 3-, and 4-year post-relapse survival (PRS) rates were 65.2%, 43.5%, 33.8%, and 27.1%, respectively. The median reirradiation EQD2 D2cc of rectum and bladder was 39.5 Gy (range = 14.6–96.2 Gy) and 52.1 Gy (range = 29.1–114.2 Gy). The median cumulative EQD2 D2cc of rectum and bladder was 115.0 Gy (range = 84.4–189.3 Gy) and 130.5 Gy (range = 95.5–173.5 Gy). During follow-up, nine (39.1%) patients had experienced grade 3 or 4 late toxicities. Grade ≥3 rectal toxicity occurred in three patients (13.0%). Grade ≥3 urinary toxicity occurred in five patients (21.7%). One patient (4.3%) had both grade ≥3 urinary and rectal toxicity. Tumor volume, TFI, tumor invasion organ number, and local control were significant prognostic factors adversely affecting OS.ConclusionsFor recurrent cervical cancer after radiotherapy, reirradiation of HDR-ISBT is feasible, even if the local tumor invasion is large, with a good chance of survival and acceptable side effects

HHMD: the human histone modification database

Histone modifications play important roles in chromatin remodeling, gene transcriptional regulation, stem cell maintenance and differentiation. Alterations in histone modifications may be linked to human diseases especially cancer. Histone modifications including methylation, acetylation and ubiquitylation probed by ChIP-seq, ChIP-chip and qChIP have become widely available. Mining and integration of histone modification data can be beneficial to novel biological discoveries. There has been no comprehensive data repository that is exclusive for human histone modifications. Therefore, we developed a relatively comprehensive database for human histone modifications. Human Histone Modification Database (HHMD, http://bioinfo.hrbmu.edu.cn/hhmd) focuses on the storage and integration of histone modification datasets that were obtained from laboratory experiments. The latest release of HHMD incorporates 43 location-specific histone modifications in human. To facilitate data extraction, flexible search options are built in HHMD. It can be searched by histone modification, gene ID, functional categories, chromosome location and cancer name. HHMD also includes a user-friendly visualization tool named HisModView, by which genome-wide histone modification map can be shown. HisModView facilitates the acquisition and visualization of histone modifications. The database also has manually curated information of histone modification dysregulation in nine human cancers

CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes

CpG islands (CGIs) are CpG-rich regions compared to CpG-depleted bulk DNA of mammalian genomes and are generally regarded as the epigenetic regulatory regions in association with unmethylation, promoter activity and histone modifications. Accurate identification of CpG islands with epigenetic regulatory function in bulk genomes is of wide interest. Here, the common features of functional CGIs are identified using an average mutual information method to differentiate functional CGIs from the remaining CGIs. A new approach (CpG mutual information, CpG_MI) was further explored to identify functional CGIs based on the cumulative mutual information of physical distances between two neighboring CpGs. Compared to current approaches, CpG_MI achieved the highest prediction accuracy. This approach also identified new functional CGIs overlapping with gene promoter regions which were missed by other algorithms. Nearly all CGIs identified by CpG_MI overlapped with histone modification marks. CpG_MI could also be used to identify potential functional CGIs in other mammalian genomes, as the CpG dinucleotide contents and cumulative mutual information distributions are almost the same among six mammalian genomes in our analysis. It is a reliable quantitative tool for the identification of functional CGIs from bulk genomes and helps in understanding the relationships between genomic functional elements and epigenomic modifications