bluuebunny/crossref_metadata_2025_split huggingface dataset:
GOLM1 promotes epithelial-mesenchymal transition by activating TGFβ1/Smad2 signaling in prostate cancer
Authors: Qin Xuke , Liu Lin , Li Yanze , Chen Hui , Weng Xiaodong 
Published: July 2022

Abstract
Background
Prostate cancer (PCa) is the one of the most commonly diagnosed cancer in men in worldwide. Epithelial-mesenchymal transition (EMT) is considered to play a crucial role in the development of the metastatic castration resistant prostate cancer (CRPC), which caused the majority of the death cases in prostate cancer. Golgi membrane protein 1 (GOLM1) is highly expressed in PCa and has been identified as a driver factor for EMT in various cancers. However, its biological functions and underlying mechanisms remain ambiguous in PCa.
Method
GOLM1 expression level of PCa was detected by Western blot and immunohistochemistry (IHC) analyses. To investigate GOLM1 functions in cancer cells, we overexpressed and knocked down GOLM1 in different prostate cancaer cell lines. Transwell assay and wound healing assay were used to determine the role of GOLM1 in cell Epithelial-mesenchymal transition, such as migration and invasion abilities. TGF-β1/Smad2 signaling pathway downstream of GOLM1 was detected by Western blot and Transwell assay.
Result
GOLM1 expression is up-regulated in PCa and correlated with worse prognosis. GOLM1 promotes the abilities of migration and invasion in PCa cell lines (DU145 and LNCaP). Furthermore, TGF-β1/Smad2 signaling is positively regulated by GOLM1 to facilitate EMT in PCa, whereas this role can be restored by TGF-β1 after GOLM1 knockdown or be abrogated by p-Smad inhibitor SB431542.
Conclusion
GOLM1 acts as a critical oncogene by promoting PCa cell EMT process. And GOLM1 is able to play oncogenic functions through activating TGF-β1/Smad2 signaling pathway. Therefore, GOLM1 has the potential to be a biomarker for PCa diagnosis and to predict prognosis of PCa patients. It is of great significance to seek effective and specific inhibitor of GOLM1 for PCa treatment as well.
A multi-level approach to study the metabolic effects of chronic exposure to Aldrin in prostate cancer cells
Authors: Bedia Carmen , Dalmau Nuria , Nielsen Lars K. , Tauler Romà , de Mas Igor Marín 
Published: July 2022

Abstract
Despite numerous studies support a dose-effect relation between Endocrine disruptors (EDs) and tumor progression and malignancy, the effects of chronic exposure to non-lethal concentrations of EDs in cancer remains unknown. Previous studies demonstrated induction of the malignant phenotype in DU145 prostate cancer (PCa) cells after chronic exposure to Aldrin (an ED). However, the mechanisms underlying this process remain limited. Here, two complementary computational approaches to investigate the molecular processes involved in the observed malignancy acquisition in Pca are applied. Firstly, the metabolic reprogramming associated to the chronic exposure to Aldrin in DU145 cells was studied by integrating transcriptomics and metabolomics via constraint-based metabolic modeling. Secondly, Gene Set Enrichment Analysis was applied to determine: i) altered regulatory pathways and ii) correlation of changes in the transcriptomic profile between the DU145 Aldrin-exposed cells and tumor progression in different tumor types.The experimentally validated predictions unveiled a dis-regulation in metabolic and regulatory pathways, modifying the triacylglyceride/cholesterol ratio in Aldrin-exposed cells, which is associated with the malignant phenotype reported in Aldrin-exposed cells.This approach can be applied to study the molecular mechanisms triggered by the chronic exposure to sub-lethal concentration of other pollutants ina variety of diseases with potential clinical and environmental applications.
Structural interventions that affect racial inequities and their impact on population health outcomes: a systematic review
Authors: Clark Emily , Cranston Emily , Polin Tionné , Ndumbe-Eyoh Sume , MacDonald Danielle , Betker Claire , Dobbins Maureen 
Published: July 2022

Abstract
Structural racism is the historical and ongoing reinforcement of racism within society due to discriminatory systems and inequitable distribution of key resources. Racism, embedded within institutional structures, processes and values, perpetuates historical injustices and restricts access to structural factors that directly impact health, such as housing, education and employment. Due to the complex and pervasive nature of structural racism, interventions that act at the structural level, rather than the individual level, are necessary to improve racial health equity. This systematic review was conducted to evaluate the effects of structural-level interventions on determinants of health and health outcomes for racialized populations. A total of 28 articles are included in this review, analyzing interventions such as supplemental income programs, minimum wage policies, nutrition safeguard programs, immigration-related policies, and reproductive and family-based policies. Most studies were quasi-experimental or natural experiments. Findings of studies were largely mixed, although there were clear benefits to policies that improve socioeconomic status and opportunities, and demonstrable harms from policies that restrict access to abortion or immigration. Overall, research on the effects of structural-level interventions to address health inequities is lacking, and the evidence base would benefit from well-designed studies on upstream policy interventions that effect the structural determinants of health and health inequities and improve daily living conditions.
Design and analysis of a high-performance terahertz photoconductive modulator enhanced by photonic crystal cavity
Authors: Alihosseini Faramarz , Heshmatpanah Zahra , Zandi Hesam 
Published: July 2022

Abstract
We propose and design a high-speed and high-performance optically controlled terahertz (THz) intensity modulator based on the free carrier modulation of a GaAs semiconductor. The device comprises a photonic crystal cavity-waveguide coupling structure for operation in the THz region. This modulator benefits from the strong interaction between the THz wave and the photoconductive substance to obtain a deep modulation with GHz speed, even with a low external optical power. The finite element method was used to calculate the most important properties of the modulator, such as the modulation depth, insertion loss, and modulation rate. The proposed modulator also demonstrated external optical power-dependent characteristics. The results indicate that the THz intensity can be modulated at a switching frequency of 1 GHz with high modulation depths of 83% and 90.3% under the continuous wave laser pumping of 50 W/cm2 and 80 W/cm2 respectively. In addition, this modulator exhibits efficient performance under the same pumping power with a switching frequency of up to 3 GHz. The device exhibited higher modulation depths with higher laser power intensities. The outstanding properties of the proposed structure are promising for the development of modulators and switches in THz communication systems.
Quantifying mixing in arbitrary fluid domains: A Pade approximation approach
Authors: Anderson Thomas , Bonnet Marc , Veerapaneni Shravan 
Published: July 2022

Abstract
We consider the model problem of mixing of passive tracers by an incompressible viscous fluid. Addressing questions of optimal control in realistic geometric settings or alternatively the design of fluid-confining geometries that successfully effect mixing requires a meaningful norm in which to quantify mixing that is also suitable for easy and efficient computation (as is needed e.g.\ for use in gradient-based optimization methods). We use the physically-inspired reasonable surrogate of a negative index Sobolev norm over the complex fluid mixing domain $\Omega$, a task which could be seen as computationally expensive since it requires the computation of an eigenbasis for $L^2(\Omega)$ by definition. Instead, we compute a representant of the scalar concentration field in an appropriate Sobolev space in order to obtain an equivalent definition of the Sobolev surrogate norm. The representant, in turn, can be computed to high-order accuracy by a Pad\'e approximation to certain fractional pseudo-differential operators, which naturally leads to a sequence of elliptic problems with an inhomogeneity related to snapshots of the time-varying concentration field. Fast and accurate potential theoretic methods are used to efficiently solve these problems, with rapid per-snapshot mix-norm computation made possible by recent advances in numerical methods for volume potentials. We couple the methodology to existing solvers for Stokes and advection equations to obtain a unified framework for simulating and quantifying mixing in arbitrary fluid domains. We provide numerical results demonstrating the convergence of the new approach as the approximation order is increased.
Multi-agent simulation model updating and forecasting for the evaluation of COVID-19 transmission
Authors: Castro Brenno Moura , Reis Marcelo de Miranda , Salles Ronaldo Moreira 
Published: July 2022

Abstract
Agent-based models have been an emerging approach in epidemiological modelling, specifically in investigating the COVID-19 virus. However, there are challenges to its validation due to the absence of real data on specific socio-economic and cognitive aspects. Therefore, this work aims to present a strategy for updating, verifying and validating these models based on applying the particle swarm optimization algorithm to better model a real case. For such application, this work also presents a new framework based on multi-agents that allows estimating the evolution of the pandemic, predicting hospital resources, and estimating adaptive population immunization and population density in specific areas. Evaluation metrics such as the data's Shape Factor (SF), Mean Square Error (RMSE), and statistical and sensitivity analyses of the responses obtained were applied for comparison with the real data. The Brazilian municipality of Passa Vinte, located in the State of Minas Gerais (MG), was used as a case study. The model was updated in cumulative cases until the 365th day of the pandemic. The results obtained in the statistical and sensitivity analysis showed similar patterns around the actual data up to the 500th day of the pandemic. Their mean values ​​of SF and RMSE were 0.96 and 7.22, respectively, showing good predictability and consistency, serving as an adequate tool for decision-making in health policies.
Overlapping pathogenic de novo CNVs in neurodevelopmental disorders and congenital anomalies impacting constraint genes regulating early development
Authors: Shabestari Seyed Ali Safizadeh , Nassir Nasna , Sopariwala Samana , Karimov Islam , Tambi Richa , Zehra Binte , Kosaji Noor , Akter Hosneara , Berdiev Bakhrom K. , Uddin Mohammed 
Published: July 2022

Abstract
Neurodevelopmental disorders (NDDs) and congenital anomalies (CAs) are a collection of rare disorders with complex etiology. In this study, we investigated the less understood genomic overlap of copy number variants (CNVs) in two large cohorts of NDD and CA patients to identify de novo CNVs and candidate genes associated to both NDD and CA phenotypes. We analyzed clinical microarray CNV data from 10,620 NDD and 3,176 CA cases annotated using Horizon platform of GenomeArc Analytics and then applied rigorous downstream analysis to evaluate overlapping genes from NDD and CA CNVs. Out of 154 patients (NDD and CA cases), we extracted genes from overlapping 217 pathogenic de novo CNVs (47.3% (80/169) of NDD and 64.6% (31/48) CA cases) and performed constraint gene analysis. 79 constraint genes (10.1% non-OMIM entries) were found to have significantly enriched genomic overlap within rare de novo pathogenic deletions (P-value = 0.01, OR = 1.58) and 45 constraint genes (13.3% non-OMIM entries) within rare de novo pathogenic duplications (P-value = 0.01, OR = 1.97). Analysis of spatiotemporal transcriptome demonstrated both pathogenic deletion and duplication genes to be highly expressed during the prenatal stage in human developmental brain (P-value = 4.95 X 10− 6). From the list of overlapping genes, EHMT1, an interesting known NDD gene encompassed de novo pathogenic CNVs from both NDD and CA patients, whereas FAM189A1, and FSTL5 are new candidate genes from non-OMIM entries. In summary, we have identified constraint overlapping genes from CNVs in NDD and CA patients that have the potential to play a vital role in common disease etiology.
Escape and precipitation of planetary ions at Mercury under different solar wind conditions
Authors: Aizawa Sae , André Nicolas , Persson Moa , Modolo Ronan , Raines Jim M. , Leblanc Francois , Chaufray Jean-Yves , Nenon Quentin , Murakami Go 
Published: July 2022

Abstract
The escape and precipitation of planetary ions at Mercury under different solar wind conditions have been examined using a global hybrid simulation. The combination of Mercury’s weak intrinsic magnetic field and solar wind conditions at Mercury’s location results in the formation of a relatively small magnetosphere compared to that of Earth. Its magnetosphere is strongly compressed and may disappear when solar wind conditions are extreme. Under these circumstances, the solar wind can directly interact with the thickest part of the exosphere and surface and the escape of planetary ions is expected to be enhanced. By focusing on the dynamic pressure and interplanetary magnetic field dependence, three different solar wind conditions are used in this study. Under the extreme solar wind conditions, planetary protons shows the highest escape rates while planetary sodium ions show the smallest, indicating that the distribution of the sodium ions around the planet is controlled by the size of the magnetosphere. As the Larmor radius of planetary sodium ions is larger than that of planetary protons, they cannot escape and instead precipitate onto the surface during extreme solar wind conditions, when the dayside magnetosphere is well compressed. The precipitation maps of the solar wind protons, planetary protons, and planetary sodium ions) show that the flux from planetary plasmas is sometimes higher than the flux of solar wind plasmas, suggesting that the precipitation of planetary plasmas are probably a non-negligible source of the space weathering of Mercury’s surface, in particular during extreme solar wind conditions.
Effect of Entamoeba histolytica infection on gut microbial diversity and composition in diarrhoeal patients from New Delhi
Authors: Iyer Lakshmi Rani , Chandel Nisha , Verma Anil Kumar , Thakur Vivek , Paul Jaishree , Mandal Ashish Kumar , Bhattacharya Alok 
Published: July 2022

Abstract
During amoebiasis, colonization of the gut by Entamoeba histolytica can lead to alterations of the host microbiota. In this study we have compared the gut microbiota of patients of amoebiasis with healthy controls using 16S rRNA gene variable regions, (V1-V3) and (V3-V5) of the bacterial genome. From this 16S rRNA gene amplicon data one paired end and two single end data sets were selected and compared by the number of OTUs obtained, sequence count and diversity analysis. Our results showed that the V1-V3- paired end data set gave the maximum number of OTUs in comparison to the two single end data sets studied. The amoebiasis patient samples showed a significant drop in richness in the alpha diversity measurements and lower intra group similarity compared to the healthy controls. Bacteria of genus Prevotella, Sutterella and Collinsella were more abundant in healthy controls whereas Escherichia, Klebsiella and Ruminococcus were more abundant in the E. histolytica positive patients. All the healthy controls harboured bacteria belonging to Faecalibacterium, Prevotella, Ruminococcus, Subdoligranulum and Escherichia genera while all the E. histolytica positive patients samples contained genus Enterobacter.
Altered basal forebrain function during whole-brain network activity at pre- and early-plaque stages of Alzheimer’s disease in TgF344-AD rats
Authors: Berg Monica van den , Adhikari Mohit , Verschuuren Marlies , Pintelon Isabel , Vasilkovska Tamara , Audekerke Johan Van , Missault Stephan , Heymans Loran , Ponsaerts Peter , De Vos Winnok H. , Linden Annemie Van der , Keliris Georgios A. , Verhoye Marleen 
Published: July 2022

Abstract
Background: Imbalanced synaptic transmission appears to be an early driver in Alzheimer’s Disease (AD) leading to brain network alterations. Early detection of altered synaptic transmission and insight into mechanisms causing early synaptic alterations would be valuable treatment strategies. This study aimed to investigate how whole-brain networks are influenced at pre- and early-plague stages of AD and if these manifestations are associated with concomitant cellular and synaptic deficits. Methods: To this end, we used an established AD rat model (TgF344-AD) and employed resting state functional MRI and quasi-periodic pattern (QPP) analysis, a method to detect recurrent spatiotemporal motifs of brain activity, in parallel with state-of-the-art immunohistochemistry in selected brain regions. Results: At the pre‑plaque stage, QPPs in TgF344-AD rats showed decreased activity of the basal forebrain (BFB) and the default-mode like network. Histological analyses revealed increased astrocyte abundance restricted to the BFB, in the absence of amyloid plaques, tauopathy and alterations in number of cholinergic, gaba-ergic and glutamatergic synapses. During the early-plaque stage, when mild amyloid-beta (Aβ) accumulation was observed in the cortex and hippocampus, QPPs in the TgF344-AD rats normalized suggesting the activation of compensatory mechanisms during this early disease progression period. Interestingly, astrogliosis observed in the BFB at the early-plaque stage was absent at the early-plaque stage. In wild-type rats, at both time-points, peak activity in the BFB preceded peak activity in other brain regions – indicating its modulatory role during QPPs. However, this pattern was eliminated in TgF344-AD suggesting that alterations in BFB-directed neuromodulation have a pronounced impact in network function in AD. Conclusions: This study demonstrates the value of rsfMRI and advanced network analysis methods to detect early alterations in BFB function in AD, which could aid early diagnosis and intervention in AD. Restoring the global synaptic transmission by modulating astrogliosis in the BFB might be a promising therapeutic strategy to restore brain network function and delay the onset of symptoms in AD.
Development and Validation of the Nomograms for Prognostic analysis in Patients With extremity Synovial Sarcoma
Authors: Li Bo , He Zhiwen , Lin Mingchao , Yu Fan , Zhou Song 
Published: July 2022

Abstract
Background
Extremity Synovial Sarcoma (SS) is a rare and highly malignant disease with a poor prognosis. This study aimed to determine the main factors affecting the prognosis and survival of patients with extremity SS and predict the overall survival (OS) and cancer-specific survival (CSS) by establishing a predictive model.
Methods
The Surveillance, Epidemiology, and End Results (SEER) database was used to screen patients who were diagnosed with extremity SS from 2004 to 2015. Univariate and multivariate Cox regression analyses were used to identify the clinical risk factors, and a prognostic nomogram was established to predict the 5- and 10-years OS and CSS.
Results
A total of 811 patients with extremity SS were divided into training cohort (n = 406) and validation cohort (n = 405) cohorts. Based on the results of data analysis, we found that age, sex, primary site, chemotherapy, surgery, Radiation and SEER stage were independent risk factors for OS and CSS in patients with extremity SS and used them to construct the prognostic nomogram. In the training cohort, the C-indexes of the nomogram were 0.752 (95% CI: 0.717–0.787) and 0.772 (95% CI: 0.735–0.809) for predicting OS and CSS, respectively. In the validation cohort, the corresponding C-indexes were 0.754(95% CI: 0.719–0.789) and 0.779 (95% CI: 0.742–0.816), respectively. The results of the calibration curves of OS and CSS in the training and validation cohorts proved that the 5-year and 10-year survival time were consistent with the survival time predicted by the nomogram.
Conclusions
age, sex, primary site, chemotherapy, surgery, Radiation and SEER stage were independent prognostic risk factors in patients with extremity SS. Compared with the SEER stage model, our nomogram model that we established had more advantages.
Plant growth-promoting properties of the phosphate-solubilizing red yeast Rhodosporidium paludigenum, with fine-tuning capabilities
Authors: Chen Yi-Ru , Kuo Chih-Yen , Fu Shih-Fen , Chou Jui-Yu 
Published: July 2022

Abstract
Phosphorus (P) is one of the essential elements that are necessary for plant development and growth. However, the availability of soluble forms of P for plants in the soils is limited, because a large proportion of it is bound to soil constituents. Thus, the concentration of P available to plants at any time is very low and, moreover, its availability depends on the soil pH. As a solution, phosphate-solubilizing microorganisms (PSMs) are employed that render inorganic P available to plants in soluble form. Thus far, research into PSMs has been insufficient, and only few such organisms have been considered for exploitation as microbial fertilizer strains. The characteristics of plant growth promotion with the plant-PSMs coculture system remain to be elucidated. In the current study, we report on the isolate Rhodosporidium paludigenum JYC100 that exhibits good performance for solubilizing calcium phosphate. We found that it can be regulated by the amount of soluble phosphate. Furthermore, R. paludigenum JYC100 promotes plant growth under specific conditions (P deficiency, but with insoluble phosphate) in different media and soil pots. In contrast, the yeast Aureobasidium pullulans JYC JYC104 exhibited weak phosphate-solubilizing capacities and no plant growth-promoting ability. Compared to control plants, the biomass, shoot height, and cellular inorganic P content of plants increased in plants cocultivated with R. paludigenum JYC100. In addition, histochemical GUS and qRT-PCR assays of phosphate starvation-induced (PSI) genes showed that the expression of these PSI genes is decreased in the plants cocultured with R. paludigenum JYC100. These findings reflect the unique ability of R. paludigenum JYC100 to convert insoluble P compounds to plant-available P, thereby leading to growth promotion. Our study results highlight the use of yeasts as potential substitutes for inorganic phosphate fertilizers to meet the P demands of plants, which may eventually improve yields in sustainable agricultures.