bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neurogenic locus notch homolog protein 1 (Notch1) SNP informatics coupled with Intrinsically Disordered Region and Post Translational Modifications reveals the complex structural crosstalk of Lung Adenocarcinoma (LUAD)
Authors: John Pearl , Sudandiradoss C 
Published: August 2024

Abstract

Lung adenocarcinoma (LUAD) is the foremost histological subtype among the lung cancer which is a fundamental root cause in the cancer mortality rate. Prominent documented modifications in lung cancer are notable rates of mutational and cross talking of the signalling pathways. Here we are seeking insight into addressing the structural and functional role of NOTCH1 and associated SNPs in LUAD progression. Our previous study established that NOTCH1 as prognostic marker having a notable high expression in the LUAD and cross talking of Epithelial Mesenchymal Transition (EMT) signalling even though it is down regulated. With the aid of insilico tools the deleterious SNPs were predicted and designated. The highlighted deleterious mutations were characterized through Molecular Docking and dynamics simulations (MDS) studies. The sequential SNP analysis in NOTCH1 resulted in 43 deleterious SNPs and 13 SNPs resulted deleterious and damaging effect. The structural based analysis results three stabilizing SNPs such as S1464I, A1705V and T1602I in the conserved and functional domain of NOTCH1. In addition, 1660–2555 sequence locations were identified as the Intrinsically Disordered Region (IDR) with a score of above 0.5 in the NOTCH1. Moreover the Post Translational Modification (PTM) analysis revealed two key PTM modifications such as o-linked glycosylation and Phosphothreonine within the IDR region which are functional as well as the conserved domains and the most essential role for the LUAD progression. The outcome of our research reflects a potential backdrop of deleterious SNPs of NOTCH1 in LUAD progression through the crosstalk of the Epithelial Mesenchymal Transition signalling.
Non-thermal shelf-life extension of fresh Hummus by High Hydrostatic Pressure and refrigeration
Authors: Shahein Mohammad , Albawarshi Yanal , Al-khamaiseh Ashraf , El-Eswed Bassam , Kanaan Omar , Majdalawi Majdi 
Published: August 2024

Abstract

Consumers are interested in fresher and minimally processed ready to eat foods, therefore this work aimed to investigate the efficacy of the of HHP of 600MPa for 6 minutes against Listeria monocytogenes, Salmonella enterica, and Escherichia coli O157:H7 in fresh hummus samples, and to study the significance of the combined treatment of HHP and refrigeration on the shelf life of Hummus samples. Results showed that a treatment of HHP at 600MPa for 6 minutes was able to achieve more than 5 log reductions of the tested pathogens, and about 4 logs for aerobic plate count (APC) and Yeast and Mold (YM), respectively. Moreover, pathogens remained undetectable during the period of refrigerated storage for 1 year, while APC and YM were increased to log 2.32 and <1 log, respectively. After 52 weeks of refrigerated storage, HHP treated samples showed no significant differences in respect to sensorial properties of hummus samples and remained microbiologically within the “High quality” standards according to the microbiological criteria of ready to eat foods.
Optimization of Sparse Phenotyping Strategies in Multi-Environmental Trials in Maize
Authors: Mothukuri Srinivasa Reddy , Beyene Yoseph , Gültas Mehmet , Burgueno Juan , Griebel Stefanie 
Published: August 2024

Abstract

The phenotyping needs to be optimized and aims to achieve desired precision at low costs because selection decisions are mainly based on multi-environmental trials. Optimization of sparse phenotyping is possible in plant breeding by applying relationship measurements and genomic prediction. Our research utilized genomic data and relationship measurements between the training (full testing genotypes) and testing set (sparse testing genotypes) to optimize the allocation of genotypes to subsets in sparse testing. Different sparse phenotyping designs were mimicked based on the percentage (%) of lines in the full set, the number of partially tested lines, the number of tested environments, balanced and unbalanced methods for allocating the lines among the environments. The eight relationship measurements were utilized to calculate the relatedness between full and sparse set genotypes. The results demonstrate that balanced and allocating 50% of lines to the full set designs have shown a higher Pearson correlation in terms of accuracy measurements than assigning the 30% of lines to the full set and balanced sparse methods. By reducing untested environments per sparse set, results enhance the accuracy of measurements. The relationship measurements exhibit a low significant Pearson correlation ranging from 0.20 to 0.31 using the accuracy measurements in sparse phenotyping experiments. The positive Pearson correlation shows that the maximization of the accuracy measurements can be helpful to the optimization of the line allocation on sparse phenotyping designs.
The Neurocognitive Burden of Onchocerciasis-associated Epilepsy in an onchocerciasis-endemic zone in Cameroon: a case-control study
Authors: Njohjam Mundih Noelar 
Published: August 2024

Abstract

Background
A specific form of epilepsy called onchocerciasis-associated epilepsy (OAE) is common in onchocerciasis-endemic communities. Data on the prevalence and pattern of neurocognitive impairment caused by OAE is sparse in Africa. This aim of this study was to determine the spectrum and severity neurocognitive impairment among patients with OAE in two onchocerciasis-endemic communities.
Methods
A case-control study was conducted in two rural villages in an onchocerciasis-endemic zone in the central region of Cameroon. Based on diagnostic criteria established in other studies, we diagnosed patients with onchocerciasis-associated epilepsy and matched by age, sex, and educational level to controls. Neurocognitive functions were assessed using the Montreal Cognitive Assessment Test, Frontal Assessment Battery, International HIV Dementia Scale, Dubois’ Five Words Tests and Isaac Set’s tests. Data were analyzed using SPSS software version 19. The threshold for statistical significance was set at P < 0.05.
Results
The study included fifty people with OAE and fifty healthy controls. The mean age for the cases was 26.3 years, and for the controls, it was 26.4 years. Cases were more impaired cognitively than the controls, 96% for the cases vs. 78% for the controls (P = 0.007, OR;7.7). The main cognitive functions affected were memory (86% of cases Vs 30% of controls, P < 0.001, OR = 34.4), verbal fluency (80% of cases Vs 42% of controls, P < 0.001, OR = 15.6), attention, and executive functions (80% of cases as against 42% of controls, P < 0.001). The main factors associated with poorer neurocognitive outcomes were longer duration of epilepsy (P < 0.001), frequent seizures (P < 0.001), low educational level (P = 0.027), generalized tonic-clonic seizures (P < 0.001) and early age of onset of epilepsy (0.001)
Conclusion
Onchocerciasis-associated epilepsy causes severe neurocognitive impairment in those affected. The need to eliminate onchocerciasis and, hence, reduce the prevalence of OAE has never been more imperative.
Clinical Efficacy of Pocketing Air-Visco Expanding Detachment Deep Lamellar Keratoplasty for Keratoconus with Scars after Acute Hydrops
Authors: Binghong Wang , tian Tian , Wenjia Xie , Luyi Ying , Yuanfang Zhu , Wenya Qiu 
Published: August 2024

Abstract

Background
To analyze the clinical efficacy of PAVED (Pocketing Air-Visco Expanding Detachment) deep anterior lamellar keratoplasty (DALK) for the treatment of keratoconus with scarring after acute hydrops
Methods
50 eyes from 50 patients with keratoconus who developed scarring after acute hydrops and who underwent PAVED DALK from 2011 to 2021 were included. Patients with irrelevant ocular diseases or surgical history were excluded. Patients who underwent DALK with either femtosecond laser-assisted or manual trephination techniques were followed-up for at least one year. Preoperative corneal characteristics, refractive status, and endothelial cell counts, as well as postoperative vision, refractive status, endothelial cell counts, and complications, were recorded and compared between different surgery groups.
Results
Intraoperative findings revealed that in 28 eyes (56.00%), the scarred stroma was mildly adherent to Descemet's membrane (DM), which could be easily separated, and the DM could be fully exposed. In 12 eyes (24.00%), there was significant adhesion, which required careful multiangle and multiround pushing to achieve complete separation, revealing 1-4 mm long microfissures within the DM scar. In 9 eyes (18.00%), the adhesion was tight, separation was not feasible, and a large fissure was observed within the scar, leaving an extremely thin layer of residual stroma. The last recorded uncorrected visual acuity (UCVA) was 0.46±0.24 (logMAR), and the best-corrected visual acuity (BCVA) was 0.21±0.13 (logMAR), with 16 eyes achieving ≥0.8 and 40 eyes achieving ≥0.5. There was a statistically significant difference in postoperative BCVA (logMAR) (P value = 0.04), with the femtosecond laser group having a BCVA of 0.16±0.11 and the manual trephination group having a BCVA of 0.24±0.14.
Conclusions
Keratoconus with scarring after acute hydrops involving the deep stroma and DM can be effectively treated with PAVED DLK because of the advantage at exposing the DM in most patients. For patients who have DM microfissures or an extremely thin layer of residual stroma, the postoperative vision is generally well restored with few complications. Femtosecond laser assistance not only has limited risk of DM rupture, but also manifests better postoperative best-corrected visual acuity compared to manual trephination.
The expression of transcription factor WRINKLED1 of Dunaliella parva promotes the accumulation of lipids in Auxenochlorella protothecoides
Authors: Wu Han , Qiu Yanhong , Feng Xiaoyun , Zhang Yibo , Xue Yongchang , Xue Weiwei , Liu Changbin B. 
Published: August 2024

Abstract

WRINKLED1 (WRI1) is a member of the APETALA2 (AP2)/EREBP (ethylene response element binding protein) transcription factor family and has been shown to be one of the important transcription regulators involved in the oil biosynthesis pathway. To investigate the role of WRI1 in the regulation of oil synthesis in Auxenochlorella protothecoides (A. protothecoides), the wri1 gene, cloned from Dunaliella parva (D. parva), was introduced and expressed in A. protothecoides. We discovered that the oil content of the genetically modified algae strain (A. protothecoides-Dpwri1) increased by 38.3% compared to the wild strain. The transcriptome analysis revealed that the expression of Dpwri1 in A. protothecoides up-regulated the expression of glucose-6-phosphate isomerase (GPI), 3-phosphoglyceraldehyde dehydrogenase (GAPDH), phosphoenolpyruvate carboxykinase (PEPCK), diacylglycerol acyltransferase (DGAT), which involved in glycolytic pathway and triglyceride synthesis pathway respectively, resulting in the flow of carbon to the synthesis of lipids. In addition, the expression of acyl-CoA oxidase (ACOX) and acetyl-CoA acetyltransferase 1(ACAT1) were down-regulated, which is beneficial to the accumulation of lipids in cells. This study reveals the important role of the exogenous WRI1 transcription factor in regulating the accumulation of lipids in A. protothecoides, which is of guiding significance for the construction of high-yield oil-producing strains.
Chitosan-Coated Probiotic Nanoparticles Mitigate Acrylamide-Induced Toxicity in the Drosophila Model
Authors: Kumar Swetha Senthil , Mohideen Sahabudeen Sheik 
Published: August 2024

Abstract

The novelty of this study lies in the development of an effective therapeutic agent using natural components—specifically, low molecular weight chitosan and L. fermentum—utilizing the Drosophila model. The design and formulation of chitosan-coated probiotic nanoparticles (CSP NPs) aim to enhance the bioavailability of probiotics in the gut, thereby improving their efficacy against ACR-induced toxicity. Nanoencapsulation, a vital domain of the medical nanotechnology field plays a key role in targeted drug delivery, bioavailability, multi-drug load delivery systems and synergistic treatment options. Chitosan, known for its non-toxic nature, offers additional benefits such as anti-inflammatory properties and immune system stimulation. Lactobacillus fermentum, incorporated for its cholesterol-lowering and potent immunomodulatory effects, also plays a significant role in influencing behavioural and developmental mechanisms in Drosophila. The synergistic effect of chitosan and L. fermentum ensures the stability and sustained release of microbial load and its secondary metabolites, facilitating prolonged exposure in the gut. This slow-release mechanism allows for an extended duration of action, effectively combating the detrimental effects of process-induced toxins like acrylamide. By optimizing bioavailability through nanoencapsulation, this study demonstrated the efficiency of the formulation in rescuing ACR-induced behavioural and biochemical deficits.
Effect of Graded Inclusion of Black Soldier Fly (Hermetia Illucens, Linnaeus, 1758) Meal in Diets for Gilthead Seabream (Sparus Aurata, Linnaeus, 1758) on Gut Microbiome and Liver Morphology.
Authors: Basili Marco , Randazzo Basilio , Caccamo Letteria , Guicciardi Stefano , Meola Martina , Perdichizzi Anna , Quero Grazia Marina , Maricchiolo Giulia 
Published: August 2024

Abstract

Over the last decades, insect meal has received great attention for finfish diets, due to its nutritional composition and low ecological footprint. In the present study, four experimental diets were formulated in which black soldier fly (Hermetia illucens) meal (HI) was used to replace 0 (HI0), 25 (HI25), 35 (HI35) and 50 (HI50) percent of fish meal. The experimental diets were administered to gilthead seabream (Sparus aurata) in a 131-day feeding trial in an open recirculating system. At the end of the experiment a remarkable change in gut microbiota composition related to HI inclusion was observed, with a preponderance of Nitrospirota in HI0 and HI25 and of Chloroflexi in HI35 and HI50 groups. Predictive analysis on bacterial metabolic pathways showed a clear separation between HI0-HI25 and HI35-HI50 groups. The microbiota shifts observed suggest a pivotal role of HI in inducing a bacterial-mediated physiological response in this fish species, probably due to chitin content and the fatty acid profile of this ingredient. Liver histology showed a higher hepatocyte size in fish from HI50 group, while a marginal adaptive response was observed in HI25 group. Overall, 50% HI dietary inclusion is not recommended, since possible alteration in lipid deposition, particularly at hepatic level, were highlighted in this fish species.
In-hospital Outcomes of early Versus Late Transcatheter Closure of Patent Ductus Arteriosus in Preterm Infants
Authors: Elsisy Mohamed , Nicholson George , Stephens Elizabeth , Sreeniva Gayathri , Gupta Arpit 
Published: August 2024

Abstract

Background
Transcatheter closure of patent ductus arteriosus (PDA) in small, premature infants is increasingly performed in the contemporary practice. Data regarding optimal timing of PDA closure are scarce. We therefore decided to compare morbidity and mortality of early and late device closure in preterm infants.
Methods
Hospitalizations of 166,583 newborn infants diagnosed with PDA were identified from the Kids’ Inpatient Database (KID) in 2009, 2012, 2016, and 2019. Of these, 299 preterm infants (gestational age (GA) ≤32 weeks, birth weight <1500 grams) underwent percutaneous PDA closure. Characteristics and peri-procedural outcomes were compared between early (≤ 30 days) (n=120) and late PDA closure (>30 days) (n=179).
Results
Mean age (±standard deviation) for early PDA closure was 18.6 days ± 7 and 67.3 days ± 36.5 in late PDA closure. Co-morbidities including respiratory distress syndrome/bronchopulmonary dysplasia, heart failure and pulmonary hypertension were comparable between the two groups. There was no difference in mortality or referral for surgical ligation between early and late closure. Post-procedural vascular complications were low, but higher in patients with early PDA closure (3.3% vs 0%; p=0.025). Length of hospital stay was longer in late PDA closure group (121.1 days ± 51.7 vs 81.5 days ± 48.8; p=<0.01).
Conclusion
Preterm or very low birth weight infants may benefit from early percutaneous PDA closure as it is associated with a shorter hospital LOS. There was no difference in in-hospital mortality or major periprocedural complications between early and late PDA closure, except vascular complications that were higher with early PDA closure.
Integrated Spatial Multi-Omics Analysis Reveals Novel Immunoinflammatory CD8+ T Cells Associated with Tertiary Lymphoid Structure and Immunotherapy Response in Colorectal Cancer
Authors: Huang Yuan , Cheng Ranyang , Hu Nan , Lou Kaiyu , Xu Xuemei , Huang Bin , Yang Qinyu , Chen Lijie , Li Tingting , Xiao Zhiyuan , Wang Shuyang , Ye Yaping , Jiao Hongli 
Published: August 2024

Abstract

Background: Based on the spatial distribution of immune cells, tumors are classified into three immunophenotypes: immune-inflamed, immune-excluded and immune-desert, among which the immune-inflamed phenotype exhibits favorable prognosis, high immunotherapy response rate, and abundant CD8+ T cells infiltration. However, there is no existing study elucidating the distinctive features of CD8+ T cells under the background of immune-inflamed in colorectal cancer (CRC).
Methods: Bulk RNA sequencing (bulk RNA-seq), single cell RNA sequencing (scRNA-seq), spatial transcriptomics RNA sequencing (stRNA-seq) and pathomics were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). Integrated spatial multi-omics, combined with immunofluorescence (IF) revealed immune-inflamed related CD8+ CXCL13+ proliferative T cells as a novel component in tertiary lymphoid structure (TLS). A prognostic model related to CD8+ CXCL13+ proliferative T cell was established, with verifications performed internally and externally.
Results: Our research distinguished three immunophenotypes in CRC and revealed immune-inflamed related CD8+ CXCL13+ proliferative T cells were characterized by exhaustion features, proliferative ability and effector functions. Remarkably, CD8+ CXCL13+ proliferative T cells were predominantly located within TLS, thus likely marking TLS and contributing to TLS formation. The specifically decreased ETS1 transcriptional activity in immune-inflamed related CD8+ T cells and ETS1 mRNA peaking at terminal differentiation indicated ETS1's key role in developing exhaustion. Finally, the CD8+T related prognostic model can serve as a powerful prognostic index to optimize risk stratification and provide new insights for individualized immunotherapy treatment of CRC.
Conclusion: These findings revealed that immune-inflamed related CD8+ CXCL13+ proliferative T cells, predominantly located within TLS, might serve as potential biomarkers for TLS presence, immunotherapy response, and prognosis in CRC. Besides, targeting the ETS1-terminal exhaustion axis was highlighted for enhancing the efficacy of immunotherapy for CRC. Our research provides new insights into the determinants affecting TLS and ICI responsiveness.
Electrically Spectral-Switchable Longwave Quantum Cascade Lasers beyond λ~10 μm
Authors: Niu Shan , Sun Yongqiang , Cheng FengMin , Zhuo Ning , Zhai Shenqiang , Sun Ruixuan , Lu Xiyu , Liu Fengqi , Lu Quanyong , Zhang Jinchuan 
Published: August 2024

Abstract

A spectral-switchable longwave quantum cascade laser design emitting at 10.5 μm is reported. The active region features a multi-miniband transition design for broad and multi-band operations. Spectral-switchability between λ~8.59-9.67 μm and 10.20-10.68 μm is achieved from a Littrow external cavity device by varying the voltages. The maximum peak power at room temperature and continuous wave power at 298 K is 1.4 W and 0.32 W, respectively. This multi-spectra switchable laser source would be ideal for selective multi-gas sensing and spectroscopy.
Crowdsourced reviews reveal substantial disparities in public perceptions of parking
Authors: Li Lingyao , Hu Songhua , Dinh Ly , Hemphill Libby 
Published: August 2024

Abstract

Due to increased reliance on private vehicles and growing travel demand, parking remains a longstanding urban challenge globally. Quantifying parking perceptions is paramount as it enables decision-makers to identify problematic areas and make informed decisions on parking management. This study introduces a cost-effective and widely accessible data source, crowdsourced online reviews, to investigate public perceptions of parking across the U.S. Specifically, we examine 4,987,483 parking-related reviews for 1,129,460 points of interest (POIs) across 911 core-based statistical areas (CBSAs) sourced from Google Maps. We employ the Bidirectional Encoder Representations from Transformers (BERT) model to classify the parking sentiment and conduct regression analyses to explore its relationships with socio-spatial factors. Findings reveal significant variations in parking sentiment across POI types and CBSAs, with \textit{Restaurants} showing the most negative. Regression results further indicate that denser urban areas with higher proportions of African Americans and Hispanics and lower socioeconomic status are more likely to exhibit negative parking sentiment. Interestingly, an opposite relationship between parking supply and sentiment is observed, indicating increasing supply does not necessarily improve parking experiences. Finally, our textual analysis identifies keywords associated with positive or negative sentiments and highlights disparities between urban and rural areas. Overall, this study demonstrates the potential of a novel data source and methodological framework in measuring parking sentiment, offering valuable insights that help identify hyperlocal parking issues and guide targeted parking management strategies.
4-Methylthiazole Triggers Apoptosis and Mitochondrial Disruption in HL-60 Cells
Authors: Meriç Neslihan , Kar Ezgi , Kar Fatih 
Published: August 2024

Abstract

Thiazole derivatives are gaining prominence in cancer research due to their potent anti-cancer effects and multifaceted biological activities. Notably, in leukemia research, these compounds are studied for their ability to induce apoptosis, disrupt mitochondrial membrane potential (MMP), and modulate cell signaling pathways. This study focuses on 4-Methylthiazole's effectiveness in inducing apoptosis in HL-60 leukemia cells. It significantly disrupts MMP, activates caspase-3, and promotes cytochrome c release, which are key indicators of apoptosis (**** p < 0.0001, *** p < 0.001, ** p < 0.01, * p < 0.05). Additionally, 4-Methylthiazole reduces CD45 and CD123 surface markers, altering the phenotypic characteristics of leukemia cells (**** p < 0.0001). A high-dose treatment with 4-Methylthiazole significantly increases ROS levels, pointing to elevated oxidative stress and intracellular free radicals, contributing to its cytotoxic effects (*p < 0.05). The study also observed a significant rise in TNF-α levels post-treatment, indicating a pro-inflammatory response that may further inhibit leukemia cell viability. While IL-6 levels remained unchanged, a dose-dependent decrease in IL-10 levels was noted, suggesting a reduction in immunosuppressive conditions within the tumor microenvironment (*p < 0.05). Overall, 4-Methylthiazole targets leukemia cells through multiple apoptotic mechanisms and modifies the immune landscape of the tumor microenvironment, enhancing its therapeutic potential. This study highlights the need for further clinical investigation to fully exploit the potential of thiazole derivatives in leukemia treatment.