bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of novel natural drug candidates against BRAF mutated carcinoma; An integrative in-silico structure-based pharmacophore modeling and virtual screening process
Authors: Dain Md Opo F. A. , Alsaiari Ahad Amer , Rahman Molla Mohammad Habibur , Ahmed Sumon Md Afsar , Yaghmour Khaled A. , Ahammad Foysal , Mohammad Farhan , Simal-Gandara Jesus
Published: October 2022

The BRAF gene is responsible for transferring signals from outside of the cell to inside of the nucleus by converting a protein namely B-Raf through the RAS/MAPK pathway. This pathway contribute to cell division, proliferation, migration, and apoptotic cell death of human and animal. Mutation in this gene may cause the development of several cancers, including lung, skin, colon, and neuroblastoma. Currently, a few available drugs are being used that has developed by targeting the BRAF mutated protein, and due to the toxic side effects, patients suffer a lot during their treatment. Therefore this study aimed to identify potentially lead compounds that can target and block the expression of BRAF and subsequently inhibit the cancer. The hits were generated through the pharmacophore model-based virtual screening, molecular docking, pharmacohore model validation, ADME (absorption, distribution, metabolism, and excretion) analysis molecular dynamics (MD) simulation to find more suitable candidate against the overexpress BRAF gene. The pharmacophore based screening initially identified 14 k possible hits from online database which were further screened by ligand scout advance software to get hit compound. Based on molecular docking score of ZINC70454679 (-10.6 kcal/mol), ZINC253500968 (-9.4 kcal/mol), ZINC106887736 (-8.6 kcal/mol), and ZINC107434492 (-8.1 kcal/mol), pharmacophore feature and toxicity evaluation, we selected four possible lead compounds. The dynamic simulation with Schrodinger Maestro software was used to determine the stability of the potential lead candidates with target protein (PDB ID: 5VAM). The results showed that the newly obtained four compounds were more stable than the control ligand (Pub Chem ID: 90408826). The current results showed that the ZINC70454679, ZINC253500968, ZINC106887736, and ZINC107434492 compounds may be able to work against several cancers through targeting the BRAF overexpressed gene. To develop a novel drug candidate, however the evaluation of the web lab based experimental work are necessary to evaluate the efficiency of the each compound against the BRAF target gene.
The diagnosis of leptospirosis complicated by pulmonary tuberculosis complemented by metagenomic next-generation sequencing: A case report
Authors: Shi Jichan , Wu Wenjie , Wu Kang , Ni Chaorong , He Guiqing , Zheng Shilin , Cheng Fang , Yi Yaxing , Ren Ruotong , Jiang Xiangao
Published: October 2022

Leptospirosis is a zoonotic infection caused by the pathogenic Leptospira. Leptospirosis is transmitted mainly through contact with contaminated rivers, lakes, or animals carrying Leptospira. Human leptospirosis has a wide range of non-specific clinical manifestations ranging from fever, hypotension, and myalgia to multi-organ dysfunction, which severely hampers the timely clinical diagnosis and treatment of leptospirosis. Therefore, there is an urgent clinical need for an efficient strategy/method that can be used for the accurate diagnosis of leptospirosis, especially in critically ill patients. Here, we report a case of a 75-year-old male patient with clinical presentation of fever, cough, and diarrhea. Initial laboratory tests and a computed tomography (CT) scan of the chest suggested only tuberculosis. The patient was finally diagnosed with pulmonary tuberculosis (PTB) combined with leptospirosis by sputum Xpert MTB RIF, epidemiological investigations, and delayed serological testing. Furthermore, through metagenomic next-generation sequencing (mNGS) of clinical samples of cerebrospinal fluid (CSF), urine, plasma and sputum, the causative pathogens were identified as Mycobacterium tuberculosis complex and Leptospira spp. With specific treatment for both leptospirosis and tuberculosis, and associated supportive care (e.g., hemodialysis), the patient showed a good prognosis. This case report suggests that mNGS can generate a useful complement to conventional pathogenic diagnostic methods through more detailed etiological screening (i.e., at the level of species or species complex).
Measuring embodied conceptualizations of pitch in singing performances: Insights from an OpenPose study
Authors: Prové Valentijn
Published: October 2022

People conceptualize auditory pitch as vertical space: low and high pitch correspond to low and high space, respectively. The strength of this cross-modal correspondence, however, seems to vary across different cultural contexts and a debate on the different factors underlying this variation is currently taking place. According to one hypothesis, pitch mappings are semantically mediated. For instance, the use of conventional metaphors such as “falling” or “rising” melodies strengthens a pitch-height mapping to the detriment of other possible mappings (e.g., pitch as bright/dark color or small/big size). Hence, entrenched pitch terms shape specific conceptualizations. The deterministic role of language is called into question by the hypothesis that different pitch mappings share a less constraining conceptual basis. As such, conceptual primitives may be concretizedad hocinto specific domains so that more local variation is possible. This claim is supported, for instance, by the finding that musicians use language-congruent (conventional) and language-incongruent (ad hoc) mappings interchangeably. The present paper substantiates this observation by investigating the head movements of musically trained and untrained speakers of Dutch in a melody reproduction task, as embodied instantiations of a vertical conceptualization of pitch. The OpenPose algorithm was used to track the movement trajectories in detail. The results show that untrained participants systematically made language-congruent movements, while trained participants showed more diverse behaviors, including language-incongruent movements. The difference between the two groups could not be attributed to the level of accuracy in the singing performances. In sum, this study argues for a joint consideration of more entrenched (e.g., linguistic metaphors) and more context-dependent (e.g., musical training and task) factors in accounting for variability in pitch representations.
Mitigation strategies for participant non-attendance in VR remote collaborative experiments
Authors: Bovo Riccardo , Giunchi Daniele , Costanza Enrico , Steed Anthony , Heinis Thomas
Published: October 2022

COVID-19 led to the temporary closure of many HCI research facilities disrupting many ongoing user studies. While some studies could easily move online, this has proven problematic for virtual reality (VR) studies. The main challenge of remote VR study is the recruitment of participants who have access to specialized hardware such as head-mounted displays. This challenge is exacerbated in collaborative VR studies, where multiple participants need to be available and remotely connect to the study simultaneously. We identify the latter as the worst-case scenario regarding resource wastage and frustration. Across two collaborative user studies, we identified the personal connection between the experimenter and the participant as a critical factor in reducing non-attendance. We compare three recruitment strategies that we have iteratively developed based on our recent experiences. We introduce a metric to quantify the cost for each recruitment strategy, and we show that our final strategy achieves the best metric score. Our work is valuable for HCI researchers recruiting participants for collaborative VR remote studies, but it can be easily extended to every remote experiment scenario.
Genetic diversity and population structure of the antimalarial plant Cryptolepis sanguinolenta in Ghana
Authors: Amissah Jacqueline Naalamle , Hadziabdic Denita , Boggess Sarah L. , Trigiano Robert N.
Published: October 2022

Cryptolepis sanguinolenta is an important medicinal plant used in the treatment of malaria in Ghana. Overharvesting, destruction of entire plant populations and poor seed viability have resulted in a substantial decrease in wild populations thereby threatening its long-term potential and survivability. In this study, fifteen polymorphic microsatellite loci were used to evaluate the genetic diversity and population structure of 179 C. sanguinolenta individuals among eight subpopulations in Ghana. The subpopulations were separated by a distance of 8.3 – 233.3 km. Our results indicated relatively high levels of genetic diversity (Ho= 0.41; He=0.61) and high gene flow (Nm=7.06), an indication of greater stability and adaptability within the ecosystem, limited genetic differentiation (mean FST=0.05; highest FST=0.1), which suggested insignificant differentiation among the subpopulations. The high levels of gene flow resulting from the wind-dispersed seeds might have contributed to the limited genetic differentiation among the subpopulations. The Bayesian cluster analysis revealed the presence of a population structure (K=2). A lack of isolation by distance (r=0.012; P=0.34) indicated an increase in the genetic similarity among the subpopulations as the geographic distance between them decreased. This study described the genetic diversity and population structure in the current C. sanguinolenta accessions and laid a foundation for future breeding efforts.
Impact of technical aspects of vein of Marshall ethanol infusion on mitral isthmus block for persistent atrial fibrillation ablation
Authors: Kong Lingcong , Shuang Tian , Li Zheng , Zou Zhiguo , Pu Jun , Wang Xin-Hua
Published: October 2022

Aims

Ethanol infusion into the VOM (EIVOM) adjunctive to radiofrequency catheter ablation (RFCA) was a novel approach facilitating mitral isthmus (MIth) block for persistent atrial fibrillation (PeAF); However, there were remarkable disparities in its technical aspects. This study aimed to evaluate the impact of EIVOM technical aspects on acute MIth block.

Methods

Eighty consecutive patients (63 males, average age 66.4 ± 8.6 years) undergoing de novo PeAF ablation were assigned to different groups. The procedural parameters in “EIVOM first” (n = 13) or “RFCA first” (n = 13) as well as small dose ([SD], ≤4 ml, n = 26) or big dose ([BD], >4 ml, n = 54) approaches were analyzed to identify the predictors for acute MIth block.

Results

Compared with the “EIVOM first” approach, the “RFCA first” approach was associated with longer procedural and MIth ablation time (134 ± 27 min vs. 112 ± 17 min; 14.9 ± 5.5 min vs. 9.3 ± 5.1 min, both P < 0.05, respectively), but with comparable success of MIth block. The ethanol dose was 6.3 ± 1.5 ml in BD group vs. 3.1 ± 1.0 ml in SD group (P < 0.001) and was correlated significantly with the size of Δlow voltage area (r = 0.66, P < 0.001). The success of MIth block was 92.6% in BD group vs. 73.1% in SD group, P = 0.03. The ethanol dose >5.75 ml independently predicted successful MIth block (OR: 0.428, 95% CI: 0.219–0.839, P = 0.01).

Conclusions

Despite the comparable effectiveness on MIth block, the “EIVOM first” approach was associated with shorter procedural and MIth ablation time than the “RFCA first” approach. The ethanol dose in EIVOM was an independent predictor for MIth block.
Using artificial intelligence in the development of diagnostic models of coronary artery disease with imaging markers: A scoping review
Authors: Wang Xiao , Wang Junfeng , Wang Wenjun , Zhu Mingxiang , Guo Hua , Ding Junyu , Sun Jin , Zhu Di , Duan Yongjie , Chen Xu , Zhang Peifang , Wu Zhenzhou , He Kunlun
Published: October 2022

Background

Coronary artery disease (CAD) is a progressive disease of the blood vessels supplying the heart, which leads to coronary artery stenosis or obstruction and is life-threatening. Early diagnosis of CAD is essential for timely intervention. Imaging tests are widely used in diagnosing CAD, and artificial intelligence (AI) technology is used to shed light on the development of new imaging diagnostic markers.

Objective

We aim to investigate and summarize how AI algorithms are used in the development of diagnostic models of CAD with imaging markers.

Methods

This scoping review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) guideline. Eligible articles were searched in PubMed and Embase. Based on the predefined included criteria, articles on coronary heart disease were selected for this scoping review. Data extraction was independently conducted by two reviewers, and a narrative synthesis approach was used in the analysis.

Results

A total of 46 articles were included in the scoping review. The most common types of imaging methods complemented by AI included single-photon emission computed tomography (15/46, 32.6%) and coronary computed tomography angiography (15/46, 32.6%). Deep learning (DL) (41/46, 89.2%) algorithms were used more often than machine learning algorithms (5/46, 10.8%). The models yielded good model performance in terms of accuracy, sensitivity, specificity, and AUC. However, most of the primary studies used a relatively small sample (n < 500) in model development, and only few studies (4/46, 8.7%) carried out external validation of the AI model.

Conclusion

As non-invasive diagnostic methods, imaging markers integrated with AI have exhibited considerable potential in the diagnosis of CAD. External validation of model performance and evaluation of clinical use aid in the confirmation of the added value of markers in practice.

Systematic review registration

[https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42022306638], identifier [CRD42022306638].
Natural history and clinical significance of aortic focal intimal flaps
Authors: Maas Austin , van Bakel Pieter A. J. , Ahmed Yunus , Patel Himanshu J. , Burris Nicholas S.
Published: October 2022

Objective

Focal intimal flaps (FIF) are a variety of defects of the aorta that result in a short, flap-like projection into the lumen, and are often encountered in asymptomatic patients undergoing computed tomography angiography (CTA) surveillance for aortic aneurysm, but the natural history and clinical significance of such lesions has not yet been studied.

Methods

We retrospectively identified patients with an asymptomatic FIF and available imaging follow-up (>1 year). FIF was defined as flap-like intimal irregularity < 4 cm in length involving the thoracic aorta (TA), abdominal aorta (AA) or common iliac arteries (CIA). FIF characteristics included length and circumferential extent as well as the presence and size (width and depth) of associated penetrating aortic ulcers (PAUs). Patient characteristics, adverse events and history of surgical repair was determined by chart review. FIFs and associated PAUs were assessed for progression by comparing baseline and follow-up CTA studies.

Results

A total of 84 FIFs were identified in 77 patients. Average age was 69.2 ± 10.1 years, and 81% were male (81%). Common co-morbidities included: hypertension (78%), hyperlipidemia (68%), smoking (60%), coronary artery disease (41%), aortic aneurysm (34%), type II diabetes mellitus (27%) and prior cardiovascular surgery (25%). FIFs were most commonly located in the abdominal aorta (n= 50, 60%). Nearly all FIFs were associated with local atherosclerotic plaque (93%). Mean follow-up interval was 3.5 ± 2.6 years (259 cumulative follow-up years). Change in FIF length and local aortic diameter over follow-up were 0.7 ± 2.3 mm and 0.8 ± 1.1 mm, respectively. Nearly half (47%) of FIFs were associated with penetrating aortic ulcers (PAU) with baseline depth of 7.3 mm (IQR: 6.1–10.2) and change in depth of 0.5 ± 1.4 mm. Only 12% of FIFs and 0% of associated PAUs demonstrated growth (≥3 mm) at follow-up. No acute pathology developed in the location of FIFs and no aortic interventions were performed specifically to treat FIFs.

Conclusion

Focal intimal flaps identified in asymptomatic patients with aortic disease were co-localized with atherosclerotic plaque and PAUs, and demonstrated indolent behavior, not leading to significant growth or acute aortic events, supporting a conservative management approach.
Secular trends and determinants of influenza vaccination uptake among patients with cardiovascular disease in Korea: Analysis using a nationwide database
Authors: Kim Min , Yang Bumhee , Gu Seonhye , Kim Eung-Gook , Kim So Rae , Oh Kyeong Seok , Yoon Woong-Su , Bae Dae-Hwan , Lee Ju Hee , Kim Sang Min , Choi Woong Gil , Bae Jang-Whan , Hwang Kyung-Kuk , Kim Dong-Woon , Cho Myeong-Chan , Lee Hyun , Lee Dae-In
Published: October 2022

Background

Influenza vaccination reduces cardiovascular events in patients with cardiovascular disease (CVD). Identifying the factors that affect influenza vaccination uptake can help improve the prognosis in patients with CVD. This study aimed to evaluate the secular trends of influenza vaccination uptake and factors associated with lack of vaccination in individuals with CVD.

Materials and methods

We analyzed the annual trends and factors associated with influenza vaccination among 3,264 patients with CVD, included from the Korea National Health and Nutrition Examination Survey which reflect the health and nutritional status of the nationwide population of Korea conducted between 2007/2008 and 2018/2019. We used a stratified, multistage sampling method.

Results

The influenza vaccination rate was greater in patients with CVD (53–74%) than in those without CVD (28–40%). Multivariable logistic regression analysis showed that age <50 years [odds ratio (OR), 16.22; 95% confidence interval (CI), 7.72–34.07], 50–64 years (OR, 6.71; 95% CI, 4.37–10.28), male sex (OR, 1.45; 95% CI, 1.14–1.65), and asthma (OR, 0.45; 95% CI, 0.22–0.92) were independently associated with a lack of influenza vaccination. Among patients aged <65 years, smoking (OR, 2.30; 95% CI, 1.31–4.04), college graduation status (OR, 1.81; 95% CI, 1.16–2.82), and hypertension (OR, 0.70; 95% CI, 0.51–0.95) were independently associated with influenza vaccination. For individuals aged 65years, there was no significant determinant of lack of vaccination.

Conclusion

In patients with CVD, a continuous increase in the secular trend of influenza vaccination was demonstrated in Korea. Young age, male sex, and non-asthma status were independently associated with lack of influenza vaccination uptake.
Spotlight on very-low-density lipoprotein as a driver of cardiometabolic disorders: Implications for disease progression and mechanistic insights
Authors: Lee Hsiang-Chun , Akhmedov Alexander , Chen Chu-Huang
Published: October 2022

Very-low-density lipoprotein (VLDL) is the only lipoprotein containing apolipoprotein B that is secreted from the liver, where VLDL is assembled from apolipoproteins, cholesterol, and triglycerides. The primary function of VLDL is to transport cholesterol and other lipids to organs and cells for utilization. Apart from its role in normal biologic processes, VLDL is also known to contribute to the development of atherosclerotic cardiovascular disease. Large VLDL particles, which are subclassified according to their size by nuclear magnetic resonance spectrometry, are significantly correlated not only with atherosclerosis, but also with insulin resistance and diabetes incidence. VLDL can also be subclassified according to surface electrical charge by using anion-exchange chromatography. The most electronegative VLDL subclass is highly cytotoxic to endothelial cells and may contribute to coronary heart disease. In addition, electronegative VLDL contributes to the development of atrial remodeling, especially in patients with metabolic syndrome, which is an established risk factor for atrial fibrillation. In this review, we focus on the VLDL subclasses that are associated with apolipoprotein alterations and are involved in cardiometabolic disease. The postprandial enhancement of VLDL’s pathogenicity is a critical medical issue, especially in patients with metabolic syndrome. Therefore, the significance of the postprandial modification of VLDL’s chemical and functional properties is extensively discussed.
How artificial intelligence enables modeling and simulation of biological networks to accelerate drug discovery
Authors: DiNuzzo Mauro
Published: October 2022

The pharmaceutical industry suffered a significant decline of innovation in the last few decades, whose simple reason is complex biology. Artificial intelligence (AI) promises to make the entire drug discovery and development process more efficient. Here I consider the potential benefits of using AI to deepen our mechanistic understanding of disease by leveraging data and knowledge for modeling and simulation of genome-scale biological networks. I outline recent developments that are moving the field forward and I identify several overarching challenges for advancing the state of the art towards the successful integration of AI with modeling and simulation in drug discovery.
Modelled sensitivity of Monte San Lorenzo ice cap, Patagonian Andes, to past and present climate
Authors: Martin Julian , Davies Bethan J. , Jones Richard , Thorndycraft Varyl
Published: October 2022

Sparse measurements of glacier mass balance, velocity and ice thickness in Patagonia challenge our ability to understand glacier sensitivity to climate change and relate past glacier fluctuations to palaeoclimate change. Small ice caps, such as Monte San Lorenzo, have short response times and high climate sensitivity, making well-dated moraines in their glacier foregrounds an important tool for exploring glacier response to rapid changes in palaeoclimate. Here, the Parallel Ice Sheet Model (PISM) is used to model ice flow across a domain centred on the Monte San Lorenzo ice cap. Ice-flow parameters are calibrated to match present-day ice extent, velocity and thickness. Our aim is, firstly, to quantify present-day physical glacier properties, and ice cap dynamics and sensitivities, and secondarily, to evaluate the controls on the deglaciation of the ice cap within the context of the Southern Hemisphere palaeoclimate system during the Last Glacial-Interglacial Transition (LGIT). The simulated present-day ice cap shows high surface mass flux, with ablation at outlet glacier tongues up to 18 m w. e. a−1, accumulation at the highest elevations of up to 5.5 m w. e. a−1 and a simulated Equilibrium Line Altitude (ELA) of 1750–2000 m asl. The ice cap is more sensitive to changes in precipitation relative to changes in temperature. We provide envelopes with likely ranges of palaeotemperature and palaeoprecipitation for glacial advances to moraines formed during the Last Glacial-Interglacial Transition and Holocene. Our numerical model predicts that cooling and an increase in precipitation is required to force glacial advance to mapped moraine limits at 12.1 ka (2°C cooler, 50% more precipitation), 5.6 ka (0°C cooler, 50% more precipitation) and 0.2 ka (1°C cooler, 25% more precipitation). Our modelling results thus provide insights into the present-day mass balance, thermal regime and velocity of the ice cap, explores the sensitivities of this ice cap to various model and climatic parameters, and provide palaeoclimatic envelopes for readvances during the LGIT and Holocene in Patagonia.
Programmatic assessment design choices in nine programs in higher education
Authors: Baartman Liesbeth , van Schilt-Mol Tamara , van der Vleuten Cees
Published: October 2022

In programmatic assessment (PA), an arrangement of different assessment methods is deliberately designed across the entire curriculum, combined and planned to support both robust decision-making and student learning. In health sciences education, evidence about the merits and pitfalls of PA is emerging. Although there is consensus about the theoretical principles of PA, programs make diverse design choices based on these principles to implement PA in practice, fitting their own contexts. We therefore need a better understanding of how the PA principles are implemented across contexts—within and beyond health sciences education. In this study, interviews were conducted with teachers/curriculum designers representing nine different programs in diverse professional domains. Research questions focused on: (1) design choices made, (2) whether these design choices adhere to PA principles, (3) student and teacher experiences in practice, and (4) context-specific differences between the programs. A wide range of design choices were reported, largely adhering to PA principles but differing across cases due to contextual alignment. Design choices reported by almost all programs include a backbone of learning outcomes, data-points connected to this backbone in a longitudinal design allowing uptake of feedback, intermediate reflective meetings, and decision-making based on a multitude of data-points made by a committee and involving multi-stage procedures. Contextual design choices were made aligning the design to the professional domain and practical feasibility. Further research is needed in particular with regard to intermediate-stakes decisions.
“Listen when I come to the table”: Reimagining education with and for Black elementary-aged youth and their mothers
Authors: Duane Addison , Mims Lauren C.
Published: October 2022

Much of the literature regarding Black youth experiences in schools considers the effects of racism and takes up inquiry through deficit views. Yet, to understand how to shift the system of schooling to provide equitable, liberatory learning experiences, it is critical to center Black children’s voices and perspectives. In the current study, we partnered with eleven Black elementary youth and their mothers to explore their dreams for re-imagining schools. We identified four themes related to school improvement from a child-centered, abolitionist lens. Our findings highlight the need to increase opportunities for youth voice in scholarship and practice, and join existing conversations that see education as the practice of liberation and freedom.
Fatty acid metabolism-related genes in bronchoalveolar lavage fluid unveil prognostic and immune infiltration in idiopathic pulmonary fibrosis
Authors: Lyu Yin , Guo Chen , Zhang Hao
Published: October 2022

Background

Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive condition with an unfavorable prognosis. A recent study has demonstrated that IPF patients exhibit characteristic alterations in the fatty acid metabolism in their lungs, suggesting an association with IPF pathogenesis. Therefore, in this study, we have explored whether the gene signature associated with fatty acid metabolism could be used as a reliable biological marker for predicting the survival of IPF patients.

Methods

Data on the fatty acid metabolism-related genes (FAMRGs) were extracted from databases like Kyoto Encyclopedia of Genes and Genomes (KEGG), Hallmark, and Reactome pathway. The GSE70866 dataset with information on IPF patients was retrieved from the Gene Expression Omnibus (GEO). Next, the consensus clustering method was used to identify novel molecular subgroups. Gene Set Enrichment Analysis (GSEA) was performed to understand the mechanisms involved. The Cell-type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT) algorithm was used to evaluate the level of immune cell infiltration in the identified subgroups based on gene expression signatures of immune cells. Finally, the Least Absolute Shrinkage and Selection Operator (LASSO) regression and multivariate Cox regression analysis were performed to develop a prognostic risk model.

Results

The gene expression signature associated with fatty acid metabolism was used to create two subgroups with significantly different prognoses. GSEA reveals that immune-related pathways were significantly altered between the two subgroups, and the two subgroups had different metabolic characteristics. High infiltration of immune cells, mainly activated NK cells, monocytes, and activated mast cells, was observed in the subgroup with a poor prognosis. A risk model based on FAMRGs had an excellent ability to predict the prognosis of IPF. The nomogram constructed using the clinical features and the risk model could accurately predict the prognosis of IPF patients.

Conclusion

The fatty acid metabolism-related gene expression signature could be used as a potential biological marker for predicting clinical outcomes and the level of infiltration of immune cells. This could eventually enhance the accuracy of the treatment of IPF patients.
Key hepatic signatures of human and mouse nonalcoholic steatohepatitis: A transcriptome–proteome data meta-analysis
Authors: Pyo Jeong Joo , Choi Yongsoo
Published: October 2022

Background

Despite the global prevalence of nonalcoholic fatty liver disease (NAFLD), its pathophysiology remains unclear. In this study, we established highly confident nonalcoholic steatohepatitis (NASH) gene signatures and evaluated the pathological mechanisms underlying NASH through a systematic meta-analysis of transcriptome and proteome datasets obtained from NASH patients and mouse models.

Methods

We analyzed NASH transcriptome datasets from 539 patients and 99 mice. A whole-liver tissue proteome dataset was used to confirm the protein level dysregulation of NASH signatures significant in both humans and mice.

Results

In total, 254 human and 1,917 mouse NASH gene signatures were established. Up-regulated genes of 254 human signatures were associated with inflammation, steatosis, apoptosis, and extracellular matrix organization, whereas down-regulated genes were associated with response to metal ions and lipid and amino acid metabolism. When different mouse models were compared against humans, models with high fat and high fructose diet most closely resembled the genetic features of human NAFLD. Cross-species analysis revealed 66 genes that were concordantly dysregulated between human and mouse NASH. Among these, 14 genes were further validated to be dysregulated at the protein level. The resulting 14 genes included some of the well-established NASH associated genes and a promising NASH drug target. Functional enrichment analysis revealed that dysregulation of amino acid metabolism was the most significant hepatic perturbation in both human and mouse NASH.

Conclusions

We established the most comprehensive hepatic gene signatures for NASH in humans and mice to date. To the best of our knowledge, this is the first study to collectively analyze the common signatures between human and mouse NASH on a transcriptome–proteome scale.
The radiative flow of the thin-film Maxwell hybrid nanofluids on an inclined plane in a porous space
Authors: Gul Taza , Mukhtar Safyan , Alghamdi Wajdi , Tag Eldin Elsayed , Yassen Mansour F. , Guedri Kamel
Published: October 2022

Due to their accelerated rate of heat transfer, nanofluids are of immense interest. This work analyzes an innovative concept of hybrid nanoemulsion with an optimized design under the chemical radiative flow and its thermophysical properties. We are able to achieve great aspects of the flow with the assistance of the sheet’s permeable texture and inclined surface. Furthermore, the effects of thermal conductivity mix convection, chemical reaction, and thermal radiations on velocity, temperature, and concentration fields are also investigated. After converting the fundamental equations to ordinary differential equations with the use of similarity transportation, the problem is then solved analytically with the HAM technique. To investigate key attributes and parameters, a hybrid nanofluid with Ag and Al2O3 nanoparticles as well as Al2O3 for conventional nanofluids with the base solvent water is taken. To illustrate the effects of chemical radiative and mix convection on the thin-film flow, numerous graphs, charts, and tables are shown. Calculations and reviews are performed for reduced friction coefficient, heat, and mass transportation. According to this study, hybrid nanofluids have a higher heat-transfer rate than nanofluids when exposed to thermal radiation and at the appropriate surface angle of inclination. Due to ϕAl2O3, ϕAg,S, Rd, the temperature increases, but velocity has the opposite effect. This investigation’s innovative findings will promote the study of condensed nanostructures and nanomaterials.
Spatial distribution and risk identification of arsenic contamination in water and soil through GIS-based interpolation techniques in Jianghan Plain, Central China
Authors: Xiao Tianyun , Muhammad Akhtar Malik , Pan Xiao , Wang Yu , Guangming Hu , Tang Zhonghua
Published: October 2022

Arsenic is considered a poison because of its seriously toxic effects on the human body; elevated concentrations of arsenic in drinking water have been reported in different parts of the world. Investigating the arsenic distributions in soil, surface water (SW), and groundwater (GW) is an interesting topic of research, along with probing its correlations with local factors of the ecosystem and other hydrogeochemical parameters. This study mainly aims to investigate the impacts of various factors on elevated arsenic concentrations in water and soil. The following factors are assessed for their relationship to the propagation of arsenic in Jianghan Plain, which is the study area: population density, pumping rate, rain, land use, surface elevation, water level, and heavy metal contamination. The arsenic contamination potential prediction map and categories were developed using GIS-based techniques, such as ordinary kriging and quantile methods. Then, the “raster calculator” tool was applied to verify the impacts of the abovementioned factors on arsenic concentration. Eighty-four single-factor, bi-factor, and multi-factor models were established to investigate the effective combinations among the factors. Land use and pumping rate were identified from the soil through an equal frequency tool, whereas water population density and pumping rate were obtained with high matching percentages. The arsenic concentrations varied in the ranges of 0.0001–0.1582 mg/L in GW, 0.0003–0.05926 mg/L in SW, and 1.820–46.620 mg/kg in soil sediment. The single factors showed the best equal frequency of arsenic concentration in water for population density (68.62%) and in soil for land use (65.57%) and pumping (63.66%). Statistical calculations with percentage frequency factors also depicted a positive trend. Arsenic was reported to have high correlations with Fe in GW (r2 = 0.4193), with EC in SW (r2 = 0.4817), and with Cu in soil (r2 = 0.623). It is observed that the alkaline behaviors of water bodies are associated with arsenic mobility. Elevated arsenic values were observed in grids along surface flows with high anthropogenic activities and urbanization. Additionally, low concentrations of Fe depicted reduced activities in aquifer systems. Filtering drinking water as well as controlling the suspected sources and factors affecting concentrations of arsenic in the three phases are options for reducing the health risks of the local populations.
Effect of precipitation on synthetic aperture radar hurricane wind field retrieval
Authors: Guo Chaogang , Ai Weihua , Hu Shensen , Du Xiaoyong , Chen Nan
Published: October 2022

C-band synthetic aperture radar (SAR) with all-weather observation capability is gradually being used for the high-resolution observation of hurricane. The extreme wind speed in hurricanes is retrieved by combining the co- and cross-polarized SAR signals. However, the heavy precipitation associated with hurricanes will seriously affect the retrieval of SAR sea surface wind speed. In this study, the effects of precipitation-related parameters and phenomena on wind speed retrieval under strong hurricane conditions were examined by using the data from co-located global precipitation measurement Dual-frequency Precipitation Radar, SAR on Sentinel-1 and Radarsat-2, and stepped frequency microwave radiometer. The results show that precipitation will increase the retrieval error of wind speed, and the effect of convective precipitation is more obvious than that of stratiform precipitation. When the wind speed is less than 30 m/s and the rain rate is less than 20 mm/h, the distribution of the melting layer has no obvious effect on SAR wind speed retrieval. Rain cells are mainly the product of convective precipitation and can also be produced when the storm top height is very low. An increase in the vertical-horizontal (VH) polarized normalized radar cross section (NRCS) in rain cells is usually greater than that of the vertical-vertical (VV) polarized NRCS because the sensitivity of the VH signal in a hurricane area is usually greater than that of the VV signal. When the rain rate is low, the difference between the retrieved wind speed inside and outside the rain cells is within the error range of hurricane wind speed retrieval. When the rain rate is further increased, the difference will exceed 10 m/s.
Carbon dioxide fluxes of cyanobacterial crusts and underlying soil under different precipitation patterns in the Ulan Buh Desert, China
Authors: Wang Lili , Gao Ying , Cao Xiaoming , Lu Weiwei
Published: October 2022

Cyanobacterial crusts, sensitive to changes in the moisture content, are widely distributed in the Ulan Buh Desert. Changes in precipitation patterns due to global climate change are expected to influence the carbon emission and photosynthetic carbon fixation of soil in areas covered with cyanobacterial crusts. We assessed how changes in precipitation amount and frequency affect carbon processes of Cyanobacterial Crusts. Taking average precipitation amount and frequency in August during the past 30 years as control, we established nine precipitation patterns (three amounts × three frequencies). The net carbon flux (NCF) and dark respiration rate (DRR) of cyanobacterial crusts and underlying soil were investigated. Precipitation could stimulate NCF and DRR immediately. With increasing water application times, the peak values of NCF, DRR and 12 h cumulative carbon emissions gradually decreased. Both precipitation amount and frequency significantly affected cumulative carbon emissions but without an interactive effect. Under the same frequency, cumulative carbon emissions increased with increasing precipitation amounts. Under the same total precipitation amount, cumulative carbon emissions caused by high-frequency events were the highest, followed by those of low-frequency precipitation and the control. However, such changes, against the background of a changing global climate, will result in increased carbon emissions of cyanobacterial crusts and underlying Soil, suggesting that cyanobacteria should be considered in projections of the future carbon budget.
Male intrasexual aggression and partial dominance of females over males in vervet monkeys
Authors: Saccà Tommaso , Gort Gerrit , van de Waal Erica , Hemelrijk Charlotte K.
Published: October 2022

Females dominate a subset of the males in a minority of mammalian species despite male-biased sexual dimorphism. How this may arise is suggested by a computational model, DomWorld. The model represents male-biased sexual dimorphism through the males’ greater initial dominance and higher intensity of aggression, meaning that fights initiated by males have a greater impact than those by females. The model shows that female dominance over males increases with a greater proportion of males in the group. This happens because when males are involved in a larger fraction of fights this results in greater hierarchical differentiation (i.e., steepness). This causes rank overlap between the sexes (i.e., partial female dominance). We test the validity of these processes in vervet monkeys (Cercopithecus pygerythrus), a primate species with partial female dominance. We confirm that the proportion of males in the group is significantly positively correlated with the degree of dominance by females over males and with the steepness of the hierarchy among males exclusively, but not with the steepness of the hierarchy among all adults of the group. The steepness in male hierarchies correlated positively with female dominance over males in these groups. We show that steeper hierarchies among vervet males resulted from male-to-male fights being a larger proportion of the fights among all adults of the group. We conclude that the higher frequency of male intrasexual aggression favors female dominance in vervet monkeys. We also show that females received coalitionary support when they were in conflict with a male, mainly from other females, and that this favors female dominance in this species, but this does not explain why partial female dominance increased with the proportion of males in the group. We advocate further investigation of the influence of male intrasexual aggression on the degree of female dominance over males in other species with partial female dominance.
Historical declines in parrotfish on Belizean coral reefs linked to shifts in reef exploitation following European colonization
Authors: Muraoka Wendy T. , Cramer Katie L. , O’Dea Aaron , Zhao Jian-xin , Leonard Nicole D. , Norris Richard D.
Published: October 2022

Humans have utilized the Mesoamerican Reef (MAR) for millennia but the effects of prehistorical and historical fishing on this ecosystem remain understudied. To assess the long-term coupling of reef ecosystem and human dynamics in this region, we tracked trends in the structure and functioning of lagoonal reefs within the Belizean portion of the MAR using fish teeth fossils and sediment accumulation rates within reef sediment cores. We then paired this with a timeline of demographic and cultural changes in this region’s human populations. The ∼1,300-year timeline encompassed in the core record shows that declines in the relative abundance and accumulation rate of teeth from parrotfish, a key reef herbivore, occurred at all three reef sites and began between ∼1500 and 1800 AD depending on site and metric of abundance. A causality analysis showed that parrotfish relative abundance had a positive causal effect on reef accretion rates, a proxy of coral growth, reconfirming the important role of these fish in reef ecosystem functioning. The timing of initial declines in parrotfish teeth occurred during a time of relatively low human population density in Belize. However, declines were synchronous with cultural and demographic upheaval resulting from European colonization of the New World. The more recent declines at these sites (∼1800 AD) occurred in tandem with increased subsistence fishing on reefs by multiple immigrant groups, a pattern that was likely necessitated by the establishment of an import economy controlled by a small group of land-owning European elites. These long-term trends from the paleoecological record reveal that current parrotfish abundances in central Belize are well below their pre-European contact peaks and that increased fishing pressure on parrotfish post-contact has likely caused a decline in reef accretion rates. The origins of reef degradation in the Belizean portion of the MAR began hundreds of years before the onset of modern declines resulting from the combined effects of local human disturbances and climate change.
A novel mixed-integer programming approach for the aircraft landing problem
Authors: Rogovs Sergejs , Nikitina Viktoriya , Gerdts Matthias
Published: October 2022

Due to the upward trend in the aviation industry, the existing approaches for air traffic control need to be improved to achieve efficient schedules. This paper deals with the aircraft landing problem, which consists of determining a landing time for each aircraft within the radar range of an airport and allocating it to a runway. We propose an exact solution approach that involves mixed-integer linear programming. The objective is hereby to minimize the sum of weighted deviations from the target landing times under consideration of different safety, efficiency and fairness constraints. Despite of the problem’s NP-hardness, our method exhibits low execution times thanks to a modified modeling strategy and provides near-optimal results. Numerical experiments prove efficiency of the approach for different large airports.
Sensors securing sustainable digital urban logistics—A practitioner’s perspective
Authors: Knapskog Marianne , Browne Michael
Published: October 2022

The transport of goods, equipment and waste to, from, in and through urban areas (urban logistics) are essential for the economic vitality of the city but at the same time make urban environmental and social targets more difficult to achieve The European Green Deal and the UN Sustainability Goals also challenge the ways of addressing planning and management. At the same time Covid 19 has led to new challenges for urban logistics together with changes in consumer purchasing and travel patterns. Digitalisation offers new ways of collecting data and providing input to planning and modelling of urban logistics that might alleviate these challenges. This article addresses how digitalisation and especially sensors can contribute to new forms of data for analysis and play a role in developing sustainable digital urban logistics measures and plans through data collection and sharing. The research contains empirical insights from a survey and workshop in Norway. The results from the survey show that sensors are the digital solution that practitioners see as most useful for urban transport. This is supported by results from the workshop supporting a sensor scenario. When it comes to the digitalisation process, the practitioners expect that the different levels of government will facilitate digitalisation of urban logistics and most practitioners have the opinion that all levels of government should do more to facilitate new solutions Testing should take place as collaboration between private and public actors. Due to Covid 19 the government level is seen to have an important role for exchange of information and advice, and for giving economic incentives and support, rather than providing law and regulatory changes or the reorganisation of public services. The local level is considered to have an especially important role for digitalisation including data for modelling, planning or public procurement procedures. The article addresses these questions by reference to the partnerships for freight transport in London and Gothenburg. This article adds insights for planning practitioners into how sensors will challenge as well as provide new possibilities, to suggest new paths for planning and modelling urban logistics and an amplified role for freight partnerships.