Exploring the nexus of urban form, transport, environment and health in large-scale urban studies: A state-of-the-art scoping review.

BACKGROUND: As the world becomes increasingly urbanised, there is recognition that public and planetary health relies upon a ubiquitous transition to sustainable cities. Disentanglement of the complex pathways of urban design, environmental exposures, and health, and the magnitude of these associations, remains a challenge. A state-of-the-art account of large-scale urban health studies is required to shape future research priorities and equity- and evidence-informed policies. OBJECTIVES: The purpose of this review was to synthesise evidence from large-scale urban studies focused on the interaction between urban form, transport, environmental exposures, and health. This review sought to determine common methodologies applied, limitations, and future opportunities for improved research practice. METHODS: Based on a literature search, 2958 articles were reviewed that covered three themes of: urban form; urban environmental health; and urban indicators. Studies were prioritised for inclusion that analysed at least 90 cities to ensure broad geographic representation and generalisability. Of the initially identified studies, following expert consultation and exclusion criteria, 66 were included. RESULTS: The complexity of the urban ecosystem on health was evidenced from the context dependent effects of urban form variables on environmental exposures and health. Compact city designs were generally advantageous for reducing harmful environmental exposure and promoting health, with some exceptions. Methodological heterogeneity was indicative of key urban research challenges; notable limitations included exposure and health data at varied spatial scales and resolutions, limited availability of local-level sociodemographic data, and the lack of consensus on robust methodologies that encompass best research practice. CONCLUSION: Future urban environmental health research for evidence-informed urban planning and policies requires a multi-faceted approach. Advances in geospatial and AI-driven techniques and urban indicators offer promising developments; however, there remains a wider call for increased data availability at local-levels, transparent and robust methodologies of large-scale urban studies, and greater exploration of urban health vulnerabilities and inequities.

Commentary: A road map for future data-driven urban planning and environmental health research.

Recent advances in data science and urban environmental health research utilise large-scale databases (100s-1000s of cities) to explore the complex interplay of urban characteristics such as city form and size, climate, mobility, exposure, and environmental health impacts. Cities are still hotspots of air pollution and noise, suffer urban heat island effects and lack of green space, which leads to disease and mortality burdens preventable with better knowledge. Better understanding through harmonising and analysing data in large numbers of cities is essential to identifying the most effective means of disease prevention and understanding context dependencies important for policy.

Acinetobacter baumannii: An overview of emerging multidrug-resistant pathogen.

The emergence of infections caused by Acinetobacter baumannii, a multidrug-resistant bacterium, has been a concern worldwide. This bacterium is an important hospitalacquired pathogen that causes several diseases including ventilator-associated pneumonia, bloodstream infections, and meningitis. This study aimed to determine antibioticresistant mechanisms in the pathogenesis of A. baumannii and the alternative treatment strategies against it. The combined actions of outer membrane protein A, formation of a biofilm on biotic and abiotic surfaces, phospholipases C and D, metal homeostatic system, lipopolysaccharides, and verotoxins are relevant for virulence and pathogenesis. A. baumannii resists the broad-spectrum antibiotics by its mechanisms of resistance, such as ß-lactamases, efflux pump, aminoglycoside modifying enzymes, permeability changes, and alternation of targets. In an attempt to overcome the resistance mechanisms, plant-derived compounds and a combination of the antibiotics and the plant phytocompounds have been focused. Nanoparticles synthesised with the plant extract have been studied extensively. Furthermore, we projected modern methods, including multi-omics analysis, to study insight into mechanisms of actions of antibiotics. The information suggested that the potential antibiotic mechanisms of A. baumannii could lead to an alternative treatment against A. baumannii infections.

An updated Axiom buffalo genotyping array map and mapping of cattle quantitative trait loci to the new water buffalo reference genome assembly.

The objectives of this study were to provide the buffalo research community with an updated SNP map for the Axiom Buffalo Genotyping (ABG) array with genomic positions for SNP currently unmapped and to map all cattle QTL from the CattleQTLdb onto the buffalo reference assembly. To update the ABG array map, all SNP probe sequences from the ABG array were re-aligned against the UOA_WB_1 assembly. With the new map, the number of mapped markers increased by approximately 10% and went from 106 778 to 116 708, which reduced the average marker spacing by approximately 2 kb. A comparison of results between signatures of autozygosity study using the ABG and the new map showed that, when the additional markers were used there was an increase in the autozygosity peaks and additional peaks in BBU5 and BBU11 could be identified. After sequence alignment and quality control, 64 650 (UMD3.1) and 76 530 (ARS_UCD1.2) cattle QTL were mapped onto the buffalo genome. The mapping of the bovine QTL database onto the buffalo genome should be useful for genome-wide association studies in buffalo and, given the high homology between the two species, the positions of cattle QTL on the buffalo genome can serve as a stepping stone towards a water buffalo QTL database.

Clinical manifestations and outcomes of COVID-19 in the paediatric population: a systematic review.

OBJECTIVE: Coronavirus disease 2019 (COVID-19), the respiratory illness caused by severe acute respiratory syndrome coronavirus 2, has affected hundreds of thousands of people. We aim to report the distribution of cases, prevalence, and clinical, radiological, and laboratory signs and outcomes of COVID-19 in paediatric patients. Moreover, we intend to evaluate neonatal clinical outcomes. Hence, our age range of interest is 0 to 19 years. METHODS: A systematic literature review was conducted using the Medline database to identify papers published between 1 December 2019 and 9 April 2020 on COVID-19. RESULTS: The search identified 27 relevant scientific papers and letters. The review showed that the prevalence of COVID-19 in the paediatric population accounts for a small percentage of patients, whose clinical signs and symptoms are often milder than those of adults. Despite better prognosis and low mortality in children, the disease can progress to severe pneumonia in some cases, especially in the presence of co-morbidities. Children are likely to become a hidden source of infection because of their atypical presentation, and they may play a role in community transmission, leading to unfavourable outcomes. There is little evidence about intrauterine vertical transmission. As no vaccine or specific antiviral is currently available, management plans include supportive treatment. CONCLUSION: As compared with that in adults, the presentation of COVID-19 in children is mild and has a better prognosis. Sufficient evidence regarding the probability of intrauterine vertical transmission could not be found, and further studies need to be conducted to establish this relationship.

Clinical and functional outcomes following platelet rich plasma in the management of knee osteoarthritis: A case series in a tertiary care hospital.

OBJECTIVE: To clinically assess the efficacy of Platelet rich Plasma (PRP) in improving the functional movement in knee osteoarthritis. METHODS: This prospective case series, on 89 patients, was studied in Sindh Rangers Hospital, Karachi, Pakistan from 1st October 2018 to 31st March 2019. The analysis involved all patients aged 30-65 years diagnosed with grade 1, 2 and 3 arthritis. PRP was administered in three doses one month apart, and patients were evaluated for outcome measures after the third month of the third dose of PRP. To measure functional improvement in knee osteoarthritis, the range of motion (ROM), McMaster University Osteoarthritis index (WOMAC), Western Ontario, and Visual analogue scale (VAS) were used. RESULTS: PRP was infused into 89 patients, with a mean age of 61.24±8.92 years. The average pre-treatment WOMAC score was 37.0 ±2.9, and it was lowered to 18.8± 5.2 after PRP (p<0.02). The pre-treatment VAS was 8.42 ±0.84, and it was reduced to 4.91±2.12, indicating mild to moderate pain. Our PRP therapy was appreciated by 63 (70.07%) patients, while 17 (19.1%) were only partly satisfied. However, 9 (10.1%) patients were dissatisfied. CONCLUSIONS: The results of this case series showed that the use of PRP injections for treating osteoarthritis (grade 1 to 3) proved to be successful in terms of improving functional outcomes and reducing pain intensity.

Using artificial intelligence techniques for COVID-19 genome analysis.

The genome of the novel coronavirus (COVID-19) disease was first sequenced in January 2020, approximately a month after its emergence in Wuhan, capital of Hubei province, China. COVID-19 genome sequencing is critical to understanding the virus behavior, its origin, how fast it mutates, and for the development of drugs/vaccines and effective preventive strategies. This paper investigates the use of artificial intelligence techniques to learn interesting information from COVID-19 genome sequences. Sequential pattern mining (SPM) is first applied on a computer-understandable corpus of COVID-19 genome sequences to see if interesting hidden patterns can be found, which reveal frequent patterns of nucleotide bases and their relationships with each other. Second, sequence prediction models are applied to the corpus to evaluate if nucleotide base(s) can be predicted from previous ones. Third, for mutation analysis in genome sequences, an algorithm is designed to find the locations in the genome sequences where the nucleotide bases are changed and to calculate the mutation rate. Obtained results suggest that SPM and mutation analysis techniques can reveal interesting information and patterns in COVID-19 genome sequences to examine the evolution and variations in COVID-19 strains respectively.

Genomic heritability and genome-wide association analysis of anti-Müllerian hormone in Holstein dairy heifers.

Anti-Müllerian hormone (AMH) is an ovarian growth factor that plays an important role in regulation of ovarian follicle growth. The objectives of this study were to estimate the genomic heritability of AMH and identify genomic regions associated with AMH production in a genome-wide association (GWA) analysis. Concentrations of AMH were determined in 2,905 dairy Holstein heifers genotyped using the Zoetis medium density panel (Zoetis Inclusions, Kalamazoo, MI) with 54,519 single nucleotide polymorphism (SNP) markers remaining after standard genotype quality control edits. A linear mixed model was used to model the random effects of sampling day and genomics on the logarithm of AMH. The genomic heritability (± standard error of the mean) of AMH was estimated to be 0.36 ± 0.03. Our GWA analysis inferred significant associations between AMH and 11 SNP markers on chromosome 11 and 1 SNP marker on chromosome 20. Annotated genes with significant associations were identified using the Ensembl genome database (version 88) of the cow genome (version UMD 3.1; https://www.ensembl.org/biomart). Gene set enrichment analysis revealed that 2 gene ontology (GO) terms were significantly enriched in the list of candidate genes: G-protein coupled receptor signaling pathway (GO:0007186) and the detection of chemical stimulus involved in sensory perception (GO:0050907). The estimated high heritability and previously established associations between AMH and ovarian follicular reserve, fertility, longevity, and superovulatory response in cattle implies that AMH could be used as a biomarker for genetic improvement of reproductive potential.

18F-FDG PET-CT imaging versus bone marrow biopsy in pediatric Hodgkin's lymphoma: a quantitative assessment of marrow uptake and novel insights into clinical implications of marrow involvement.

OBJECTIVE: To evaluate whether positron emission tomography/computed tomography using fluorine-18 fluoro-deoxyglucose (18F-FDG PET-CT) predicts bone marrow involvement (BMI) in pediatric Hodgkin's lymphoma (pHL) with sufficient accuracy to supplant routine staging bone marrow biopsy (BMB), and to assess the clinical importance of marrow disease by comparing the prognosis of stage IV HL with BMI versus that without BMI. METHODS: Data were retrospectively analyzed for all cases of pHL between July 2010 and June 2015 referred for staging 18F-FDG PET-CT scan and BMB. The reference standard was BMB. Stage IV patients were divided into three groups to compare their progression-free and overall survival: PET+ BMB-, PET+ BMB+, and PET- BMB-. RESULTS: Of the 784 patients, 83.3% were male and 16.7% female, with age ranging from 2 to 18 years (mean 10.3 years). Among the total cases, 104 (13.3%) had BMI; of these, 100 were detected by PET imaging and 58 by BMB. BMB and 18F-FDG PET/CT scans were concordant for BMI detection in 728 patients (93%): positive concordance in 54 and negative in 674. Of the 56 discordant cases, four had a false-negative PET scans and were upstaged by BMB, 46 with focal uptake were PET/CT-positive and BMB-negative (not obtained from active sites), and six with diffuse uptake were false-positive on PET due to paraneoplastic marrow activation. The sensitivity, specificity, PPV, and NPV of PET for identifying BMI was 93.6, 94, 53, and 99.4% respectively. On quantitative assessment, mean iBM-SUVmax of bilateral iliac crests was significantly higher in those with BMI versus those without (p < 0.05). CONCLUSIONS: 18F-FDG PET-CT imaging is more sensitive than BMB for BMI detection in pHL staging. BMB should be limited to those with normal marrow uptake in the presence of poor risk factors or those with diffusely increased uptake to exclude marrow involvement in the background of reactive marrow.

Musculoskeletal Spect-Ct: A Pictorial Review.

SPECT-CT being a hybrid imaging scanner provides molecular and anatomical imaging in one go as a one stop shop. The addition of correlative CT scan to the planar skeletal scintigraphy gives better localization of the lesion, its characterization and attenuation correction as well. We present a brief overview of our institutional experience with hybrid SPECT-CT, as an adjunct to planar skeletal scintigraphy. SPECT-CT imaging improves the diagnostic yield and specificity of planar skeletal scintigraphy.

Biologics in spine arthrodesis.

Spine fusion is a tool used in the treatment of spine trauma, tumors, and degenerative disorders. Poor outcomes related to failure of fusion, however, have directed the interests of practitioners and scientists to spinal biologics that may impact fusion at the cellular level. These biologics are used to achieve successful arthrodesis in the treatment of symptomatic deformity or instability. Historically, autologous bone grafting, including iliac crest bong graft harvesting, had represented the gold standard in spinal arthrodesis. However, due to concerns over potential harvest site complications, supply limitations, and associated morbidity, surgeons have turned to other bone graft options known for their osteogenic, osteoinductive, and/or osteoconductive properties. Current bone graft selection includes autograft, allograft, demineralized bone matrix, ceramics, mesenchymal stem cells, and recombinant human bone morphogenetic protein. Each pose their respective advantages and disadvantages and are the focus of ongoing research investigating the safety and efficacy of their use in the setting of spinal fusion. Rh-BMP2 has been plagued by issues of widespread off-label use, controversial indications, and a wide range of adverse effects. The risks associated with high concentrations of exogenous growth factors have led to investigational efforts into nanotechnology and its application in spinal arthrodesis through the binding of endogenous growth factors. Bone graft selection remains critical to successful fusion and favorable patient outcomes, and orthopaedic surgeons must be educated on the utility and limitations of various biologics in the setting of spine arthrodesis.

Retrospective Analysis of Thoracolumbar Junction Injuries Using the Thoracolumbar Injury Severity and Classification Score, American Spinal Injury Association Class, Injury Severity Score, Age, Sex, and Length of Hospitalization.

STUDY DESIGN: Retrospective review of patient cohort. OBJECTIVE: Our goal was to assess the validity of the Thoracolumbar Injury Classification and Severity (TLICS) score system by comparing the TLICS system to prior management of thoracolumbar injuries at our institution between January 1, 2006 to March 31, 2011. SUMMARY OF BACKGROUND DATA: TLICS was introduced in 2005 to classify and assign treatment recommendations for injuries based on 3 axes: mechanism of injury, integrity of the posterior ligamentous complex, and neurological status. METHODS: We retrospectively obtained and analyzed patient data regarding thoracolumbar junction injuries at a major academic medical center servicing level I trauma. In addition, we compared the American Spinal Injury Association (ASIA) class at time of injury to last follow-up to determine if there was any change in neurological status after intervention. We also compared sex, injury severity score (ISS), length of hospitalization, and age between nonoperatively and operatively treated patients. RESULTS: Included in our study were 201 patients (70% male and 30% female). We found the TLICS system agreed with prior thoracolumbar junction injury management at our institution 98% of the time in nonoperatively treated patients and 78% of the time in operatively treated patients. Age, sex, and ISS were not statistically significant factors in patients who were treated operatively versus nonoperatively, however, there was a trend towards higher ISS in operatively treated patients. Average TLICS score between nonoperative and operative groups was 1.56 and 4.8, respectively, and was a statistically significant difference. There was no statistically significant difference in ASIA class improvement between operative and nonoperative treatment, however, this is likely because of having only 20 patients in this subcohort. Of note, about 50% of the 17 operatively treated patients had improvement in ASIA class. CONCLUSIONS: Our data suggest that TLICS is a valuable tool in a spine surgeon's armamentarium in treating thoracolumbar junction injuries. Some surgeons might be more likely to operate on thoracolumbar junction injuries that should be treated nonoperatively according to the TLICS score. As with all classification schemes, the TLICS system should be used in conjunction with sound clinical judgment.

Evaluation and treatment of spinal metastatic disease.

With the increased survival of oncologic patients, evaluation and management of patients with spinal metastasis is crucial to reducing morbidity and maximizing function. In this chapter, we present some guidelines for the initial systematic evaluation of patients with spinal lesions, as well as the risks, benefits, and alternatives to nonoperative and operative management of metastatic spinal disease, and the overall survival of these patients.

SPM4GAC: SPM based approach for genome analysis and classification of macromolecules.

Genome sequence analysis and classification play critical roles in properly understanding an organism's main characteristics, functionalities, and changing (evolving) nature. However, the rapid expansion of genomic data makes genome sequence analysis and classification a challenging task due to the high computational requirements, proper management, and understanding of genomic data. Recently proposed models yielded promising results for the task of genome sequence classification. Nevertheless, these models often ignore the sequential nature of nucleotides, which is crucial for revealing their underlying structure and function. To address this limitation, we present SPM4GAC, a sequential pattern mining (SPM)-based framework to analyze and classify the macromolecule genome sequences of viruses. First, a large dataset containing the genome sequences of various RNA viruses is developed and transformed into a suitable format. On the transformed dataset, algorithms for SPM are used to identify frequent sequential patterns of nucleotide bases. The obtained frequent sequential patterns of bases are then used as features to classify different viruses. Ten classifiers are employed, and their performance is assessed by using several evaluation measures. Finally, a performance comparison of SPM4GAC with state-of-the-art methods for genome sequence classification/detection reveals that SPM4GAC performs better than those methods.

Source Attribution of Health Burdens From Ambient PM2.5, O3, and NO2 Exposure for Assessment of South Korean National Emission Control Scenarios by 2050.

We quantify anthropogenic sources of health burdens associated with ambient air pollution exposure in South Korea and forecast future health burdens using domestic emission control scenarios by 2050 provided by the United Nations Environment Programme (UNEP). Our health burden estimation framework uses GEOS-Chem simulations, satellite-derived NO2, and ground-based observations of PM2.5, O3, and NO2. We estimate 19,000, 3,300, and 8,500 premature deaths owing to long-term exposure to PM2.5, O3, and NO2, respectively, and 23,000 NO2-associated childhood asthma incidences in 2016. Next, we calculate anthropogenic emission contributions to these four health burdens from each species and grid cell using adjoint sensitivity analysis. Domestic sources account for 56%, 38%, 87%, and 88% of marginal emission contributions to the PM2.5-, O3-, and NO2-associated premature deaths and the NO2-associated childhood asthma incidences, respectively. We project health burdens to 2050 using UNEP domestic emission scenarios (Baseline and Mitigation) and population forecasts from Statistics Korea. Because of population aging alone, there are 41,000, 10,000, and 20,000 more premature deaths associated with PM2.5, O3, and NO2 exposure, respectively, and 9,000 fewer childhood asthma incidences associated with NO2. The Mitigation scenario doubles the NO2-associated health benefits over the Baseline scenario, preventing 24,000 premature deaths and 13,000 childhood asthma incidences by 2050. It also slightly reduces PM2.5- and O3-associated premature deaths by 9.9% and 7.0%, unlike the Baseline scenario where these pollutants increase. Furthermore, we examine foreign emission impacts from nine SSP/RCP-based scenarios, highlighting the need for international cooperation to reduce PM2.5 and O3 pollution.

FSP4HSP: Frequent sequential patterns for the improved classification of heat shock proteins, their families, and sub-types.

Heat shock proteins (HSPs) from different families and sub-types play a vital role in the folding and unfolding of proteins, in maintaining cellular health, and in preventing serious disorders. Previous computational methods for HSP classification have yielded promising performance. However, most of the existing methods rely heavily on amino acid composition features and still face challenges related to interpretability and accuracy. To overcome these issues, we introduce a novel frequent sequential pattern (FSP)-based analysis and classification method for the classification of HSPs, their families, and sub-types. The proposed method is called FSP4HSP, which stands for "FSP for HSP". It identifies FSPs of amino acids (FSPAAs) and utilizes them for analysis and classification. Besides FSPAAs, sequential rules among amino acids are also discovered. Both binary and multi-class classification scenarios are considered, with the utilization of eight integer-based and four string-based classifiers. The incorporation of FSPAAs in the classification/prediction task enhances the interpretability of FSP4HSP and a comprehensive performance comparison using various evaluation measures demonstrates that it surpasses existing methods for the classification/recognition of HSPs.

Prevalence of Incidental Findings and Assessment of Maxillary Sinus Pathologies and Dental Diseases Using Cone-Beam Computed Tomography (CBCT) in the Tamil Nadu Population: A Retrospective Study.

Background Cone-beam computed tomography (CBCT), a cross-sectional imaging technique, is valuable for clinical diagnosis and creating effective treatment plans. CBCT can precisely examine the connection between the maxillary sinuses and the maxillary root apices. Oral radiologists must be aware of all potential incidental findings and should be diligent in thoroughly identifying and assessing possible underlying diseases. Aim To determine the prevalence of incidental maxillary sinus pathologies and their relationship to dental diseases. Materials and methods In the present retrospective study, CBCT scans from 300 subjects (encompassing 600 right and left maxillary sinuses), aged 18 to 70, were gathered from various CBCT centers to represent the Tamil Nadu population. The CBCT images were analyzed using proprietary software, which provided both a panoramic reconstruction view and multiplanar reformation modules, including axial, sagittal, and coronal slices. The entire sample size was classified as follows: Group 1, age groups of 18 to 25 years; Group 2, age groups of 26 to 35 years; Group 3, age groups of 36 to 45 years; Group 4, age groups of 46 to 55 years; Group 5, age groups of 56 to 65 years; Group 6, age groups of 66 to 70 years. The prevalence of incidental maxillary sinus findings was analyzed, and their relationship with periapical abscess, periapical granuloma, periapical cyst, and breach was assessed. Results There was a prevalence of 52.05% of cases that had incidental maxillary sinus findings. Among them, 53.43% were males and 50.65% were females. Maxillary sinus pathologies were more common in individuals between 46 and 55 years, i.e., Group 4. In 300 datasets, the frequency of incidental maxillary sinus findings on the right is 21.33%, on the left is 24%, in both is 6.67%, and absent in 48% of the cases. Mucosal thickening was observed in 30% of cases with a periapical abscess, 19.52% with a periapical granuloma, 25% with a periapical cyst, and 51.79% with a breach. Polypoidal mucosal thickening was present in 32.50% of cases with a periapical abscess, 13.79% with a periapical granuloma, 50% with a periapical cyst, and 23.21% with a breach. Opacification occurred in 37.50% of cases with a periapical abscess, 20.69% with a periapical granuloma, 25% with a periapical cyst, and 25% with a breach. Conclusion Dental professionals should have a bird's-eye view in treating chronic odontogenic infections close to the maxillary sinus. Early diagnosis and prompt treatment of odontogenic infections help prevent maxillary sinus pathologies.

Autocrine CCL2, CXCL4, CXCL9 and CXCL10 signal in retinal endothelial cells and are enhanced in diabetic retinopathy.

This study aimed at examining the presence and role of chemokines (angiogenic CCL2/MCP-1 and angiostatic CXCL4/PF-4, CXCL9/Mig, CXCL10/IP-10) in proliferative diabetic retinopathy (PDR). Regulated chemokine production in human retinal microvascular cells (HRMEC) and chemokine levels in vitreous samples from 40 PDR and 29 non-diabetic patients were analyzed. MCP-1, PF-4, Mig, IP-10 and VEGF levels in vitreous fluid from PDR patients were significantly higher than in controls. Except for IP-10, cytokine levels were significantly higher in PDR with active neovascularization and PDR without traction retinal detachment (TRD) than those in inactive PDR, PDR with TRD and control subjects. Exploratory regression analysis identified associations between higher levels of IP-10 and inactive PDR and PDR with TRD. VEGF levels correlated positively with MCP-1 and IP-10. Significant positive correlations were observed between MCP-1 and IP-10 levels. In line with these clinical findings Western blot analysis revealed increased PF-4 expression in diabetic rat retinas. HRMEC produced MCP-1, Mig and IP-10 after stimulation with IFN-γ, IL-1ß or lipopolysaccharide. IFN-γ synergistically enhanced Mig and IP-10 production in response to IL-1ß or lipopolysaccharide. MCP-1 was produced by HRMEC in response to VEGF treatment and activated HRMEC via the ERK and Akt/PKB pathway. On the other hand, phosphorylation of ERK induced by VEGF and MCP-1 was inhibited by PF-4, Mig and IP-10. In accordance with inhibition of angiogenic signal transduction pathways, PF-4 inhibited in vitro migration of HRMEC. Thus, regulatory roles for chemokines in PDR were demonstrated. In particular, IP-10 might be associated with the resolution of active PDR and the development of TRD.

PSAC-PDB: Analysis and classification of protein structures.

This paper presents a novel framework, called PSAC-PDB, for analyzing and classifying protein structures from the Protein Data Bank (PDB). PSAC-PDB first finds, analyze and identifies protein structures in PDB that are similar to a protein structure of interest using a protein structure comparison tool. Second, the amino acids (AA) sequences of identified protein structures (obtained from PDB), their aligned amino acids (AAA) and aligned secondary structure elements (ASSE) (obtained by structural alignment), and frequent AA (FAA) patterns (discovered by sequential pattern mining), are used for the reliable detection/classification of protein structures. Eleven classifiers are used and their performance is compared using six evaluation metrics. Results show that three classifiers perform well on overall, and that FAA patterns can be used to efficiently classify protein structures in place of providing the whole AA sequences, AAA or ASSE. Furthermore, better classification results are obtained using AAA of protein structures rather than AA sequences. PSAC-PDB also performed better than state-of-the-art approaches for SARS-CoV-2 genome sequences classification.

Sources of PM2.5-Associated Health Risks in Europe and Corresponding Emission-Induced Changes During 2005-2015.

We present a newly developed approach to characterize the sources of fine particulate matter (PM2.5)-related premature deaths in Europe using the chemical transport model GEOS-Chem and its adjoint. The contributions of emissions from each individual country, species, and sector are quantified and mapped out at km scale. In 2015, total PM2.5-related premature death is estimated to be 449,813 (257,846-722,138) in Europe, 59.0% of which were contributed by domestic anthropogenic emissions. The anthropogenic emissions of nitrogen oxides, ammonia, and organic carbon contributed most to the PM2.5-related health damages, making up 29.6%, 23.2%, and 16.8%, respectively of all domestic anthropogenic contributions. Residential, agricultural, and ground transport emissions are calculated to be the largest three sectoral sources of PM2.5-related health risks, accounting for 23.5%, 23.0%, and 19.4%, respectively, of total anthropogenic contributions within Europe. After excluding the influence of extra-regional sources, we find eastern European countries suffered from more premature deaths than their emissions caused; in contrast, the emissions from some central and western European regions contributed premature deaths exceeding three times the number of deaths that occurred locally. During 2005-2015, the first decade of PM2.5 regulation in Europe, emission controls reduced PM2.5-related health damages in nearly all European countries, resulting in 63,538 (46,092-91,082) fewer PM2.5-related premature deaths. However, our calculation suggests that efforts to reduce air pollution from key sectors in some countries can be offset by the lag in control of emissions in others. International cooperation is therefore vitally important for tackling air pollution and reducing corresponding detrimental effects on public health.