bluuebunny/crossref_metadata_2025_split huggingface dataset:
Feasibility of Serial Neurocognitive Assessment Using Cogstate During and After Therapy for Childhood Leukemia
Authors: Cole Peter D. , Kim Soo Young , Li Yuelin , Schembri Adrian , Kelly Kara M , Sulis Maria-Luisa , Vrooman Lynda M. , Welch Jennifer J.G. , Ramjan Sameera , Silverman Lewis B. , Sands Stephen A. 
Published: June 2022

Abstract
Purpose: Neurocognitive impairment is frequently observed among survivors of childhood acute lymphoblastic leukemia (ALL) within the domains of attention, working memory, processing speed, executive functioning and learning and memory. However, few studies have characterized the trajectory of treatment-induced changes in neurocognitive function beginning in the first months of treatment, to test whether early changes predict impairment among survivors. If correct, we hypothesize that those children who are most susceptible to early impairment would be ideal subjects for clinical trials testing interventions designed to protect against treatment-related neurocognitive decline. Methods: In this pilot study, we prospectively assessed neurocognitive functioning (attention, working memory, executive function, visual learning, and processing speed), using the Cogstate computerized battery at six time points during the 2 years of chemotherapy and 1 year post treatment enrolled on or as per Dana-Farber Cancer Institute ALL Consortium protocol 11-001; NCT01574274. Results: 43 patients with ALL consented to serial neurocognitive testing. Of the 31 participants who remained on study through the final time point, one year after completion of chemotherapy, 28 (90%) completed at least five of six planned Cogstate testing timepoints. Performance and completion checks indicated a high tolerability (≥88%) for all subtests. One year after completion of treatment, 10 of 29 patients (34%) exhibited neurocognitive function more than 2 sd below age-matched norms on one or more Cogstate subtests. Conclusions: Serial collection of neurocognitive data (within a month of diagnosis with ALL, during therapy and one year post treatment) is feasible and informative for evaluating treatment-related neurocognitive impairment.
Comprehensive analysis of candidate signatures of long non-coding RNA LINC01116 and related protein-coding genes in patients with hepatocellular carcinoma
Authors: Wang Xiang-Kun , Luo Kai , Yu Long , Wang Hong-Lei , Zhang Xu-Dong , Li Ren-Feng 
Published: June 2022

Abstract
Background
Hepatocellular carcinoma (HCC) is a long-term malignancy that causes high morbidities and mortalities worldwide. Notably, long non-coding RNAs (LncRNAs) have been identified as candidate targets for malignancy treatments.
Methods
LncRNA LINC01116 and its Pearson-correlated genes (PCGs) were identified and analyzed in HCC patients. The diagnostic and prognostic value of the lncRNA was evaluated using data from The Cancer Genome Atlas (TCGA). Further, we explored the target drugs of LINC01116 for clinical application. Relationships between immune infiltration and PCGs, methylation and PCGs were explored. The diagnostic potentials were then validated by real time-PCR and Oncomine cohorts.
Results
LINC01116 and the PCG OLFML2B are differentially and highly expressed in tumor tissues (both P ≤ 0.050). We found that LINC01116, TMSB15A, PLAU, OLFML2B, and MRC2 have diagnostic potentials (all AUC ≥ 0.700, all P ≤ 0.050) while LINC01116 and TMSB15A have prognostic significance (both adjusted P ≤ 0.050). LINC01116 was enriched in the vascular endothelial growth factor (VEGF) receptor signaling pathway, mesenchyme morphogenesis, etc.. After that, candidate target drugs with potential clinical significance were identified: Thiamine, Cromolyn, Rilmenidine, Chlorhexidine, Sulindac_sulfone, Chloropyrazine, and Meprylcaine. Analysis of immune infiltration revealed that MRC2, OLFML2B, PLAU, and TMSB15A are negatively associated with the purity but positively associated with the specific cell types (all P < 0.050). Analysis of promoter methylation demonstrated that MRC2, OLFML2B, and PLAU have differential and high methylation levels in primary tumors (all P < 0.050). Validation results of the differential expressions and diagnostic potential of LINC01116 (RT-PCR) and OLFML2B (RT-PCR and Oncomine) were consistent with those obtained in the TCGA cohort (all P < 0.050, all AUC > 0.700).
Conclusions
Differentially expressed LINC01116 could be a candidate diagnostic and an independent prognostic signature in HCC. Besides, its target drugs may work for HCC therapy via the VEGF receptor signaling pathway. Differentially expressed OLFML2B could be a diagnostic signature involved in HCC via immune infiltrates.
Exosomal circRNA-miRNA Expression profile from plasma in Alzheimer’s Disease Patients by Bioinformatics and Integrative Analysis
Authors: Besli Nail , Sarikamis Bahar , Cakmak Rabia Kalkan , Kilic Ulkan 
Published: June 2022

Abstract
Alzheimer's disease (AD) is an age-dependent neurodegenerative ailment globally. Compelling evidence suggests the function of exosomal non-coding RNAs has been associated with the progression of AD but whose exosomal-linked non-coding RNAs mediated regulatory mechanisms are broadly unlit. This study, therefore, set out with the aim of exploring the exosomal circRNA-miRNA networks in the plasma of AD patients. Data of 3 samples from each group (healthy, mild cognitive impairment (MCI), and AD) were fetched from ArrayExpress. The MCI and AD groups were compared with the healthy group by screening for differentially expressed miRNAs (DEmiRs) and circRNAs (DEcircRs) in plasma exosomes. Subsequently, common DEmiRs and DEcircRs for both MCI and AD groups were evaluated to identify gene ontologies, pathways, and networks. Lastly, the analysis of the PPI (protein–protein interaction) network and hub genes selection were performed. A total of common 19 (7 upregulated and 12 downregulated) DEmiRs and 24 DEcircRs were identified. It was predicted 4559 target genes for upregulated DemiRs, while 6504 target genes for downregulated DEmiRs and most of the target genes were associated with the PI3K-Akt pathway and that they were mostly regulated by hsa-mir-615-3p, hsa-mir-196a-5p, hsa-let-7c-5p, hsa-let-205-5p, hsa-mir-185-3p, hsa-mir-185-5p, hsa-mir-374a-5p, hsa-mir-374a-3p. Also, 9 hub genes (CCNE2, CCND1, CDK6, ACTB, MAPK1, AKT1, GSK3B, IGF1R, HSP90AA) were uncovered as the genes most associated with AD by a PPI network using Cytoscape plug-in cytohubba. Our outcomes exhibit a new outlook on a possible exosomal-linked miRNA-circRNA network in the pathogenesis of AD.
Designing of peptide based multi-epitope vaccine construct against gallbladder cancer using immunoinformatics and computational approaches
Authors: Dar Mukhtar Ahmad , Kumar Pawan , Kumar Prakash , Shrivastava Ashish , Dar Muneer Ahmad , Singh Ashutosh , Chauhan Richa , Velayutham Ravichandiran , Dhingra Sameer 
Published: June 2022

Abstract
Gallbladder cancer (GBC) is an aggressive and difficult to treat biliary tract carcinoma characterised by late presentation, poor prognosis, and a survival rate of <1 year. GBC is difficult to treat and the current treatments have yielded dismal outcomes. The aim of this study was to design a multi-epitope vaccine candidate against GBC using reverse vaccinology and immunoinformatics tools. Epitopes from three antigenic proteins (NT5E, ANPEP and MME) were used for designing the epitope vaccine. CTL, HTL and B-cell epitopes were predicted and screened on the basis of immunogenicity, antigenicity, allergenicity, toxicity and IFN-γ inducing properties. The selected epitopes were connected using linkers and suitable adjuvant for designing final vaccine construct. The physicochemical properties were analysed followed by 2D and 3D structure generation, refinement and validation. The binding affinity of vaccine construct with immune receptors (TLR2, 3 and 4) was assessed through molecular docking. The stability of the docked vaccine-receptor complexes were evaluated using 100ns MD simulations. The epitope vaccine showed an adequate antibody and cell mediated immune responses through in-silco immune simulation. Our vaccine construct demonstrated good solubility, stability, antigenicity, non-allergenicity and non-toxicity with potential to elicit strong immune responses. However, further experimental research is needed to validate the safety and efficacy of the designed vaccine.
Presence of schistosome eggs in lymph nodes predict unfavorable prognosis in colorectal cancer patients
Authors: Pan Weiyu , Guo Jiaojiao , Li Jiali , Su Jieakesu , Zhang Xiaolei , Liu Jia , Xu Chen , Hou Yingyong 
Published: June 2022

Abstract
Aim: The purpose of this study was to investigate the prognostic significance of schistosome eggs location in schistosomal colorectal cancer (SCRC). Methods: Two hundred and one cases of SCRC were retrospectively analyzed. Patient demographics, clinicopathological parameters and survival rates were analyzed.Results: There were 120 males and 81 females, the median age was 71 years (range, 44-91). All patients were followed, and the median time was 3.85 years (range, 0.08-6.30). The 5-year disease free survival (DFS) and overall survival (OS) were 60.3% and 70.7% respectively. There were 104 patients with PS1 (presence site 1, eggs deposited in the mucosa) and 97 patients with PS2 (presence site 2, eggs deposited in the muscularis propria or throughout the full thickness of the intestinal wall), 184 patients presented with eggs in cutting edges and 98 patients in lymph nodes (LNs). Hepatic schistosomiasis was found in 28.9% of patients by imaging modalities and correlated to patients with PS2 (P < 0.001) and LNs’ eggs (P < 0.001). Survival analysis showed that eggs in LNs associated with worse DFS (P = 0.001) or marginal worse OS (P = 0.067) in stage III-IV SCRC, not in stage I-II SCRC. Multivariate analysis revealed perineural invasion was an independent prognostic factor for DFS and OS (P < 0.001, 0.027, respectively), histology grade was an independent prognostic factor for OS (P = 0.001). Conclusion: Schistosome eggs’ presence in LNs could predict poor prognosis in advanced SCRC. Deeper egg deposition, and LNs’ eggs, are associated with hepatic schistosomiasis.
Long noncoding RNA ASH1L-AS1 promotes glycolysis and cisplatin resistance in ovarian cancer cells via its regulation on EZH2-mediated CNRIP1 methylation
Authors: Sun Xiao-Fei , Wang Yu , Yin Li-Li , Song Gui-Yu , Yang Qing 
Published: June 2022

Abstract
The authors have requested that this preprint be removed from Research Square.
An investigation of the effects of PVP stabilizing agent on ZnO nanoparticles morphology, crystalline growth, and optical properties
Authors: Seoudi Roshdi , Al-Salem Lulua , Said Doaa 
Published: June 2022

Abstract
Polyvinylpyrrolidone (PVP) was successfully used as a capping reagent in an aqueous solution to prepare zinc oxide semiconductor nanoparticles (ZnONPs). Transmission electron microscopy (TEM), X-ray diffraction (XRD), Fourier transform infrared (FTIR), and UV-visible spectroscopy were used to determine the effects of PVP concentrations on the morphology, crystallinity, and spectroscopic properties of (ZnONPs). TEM results showed ZnONPs in various shapes (spherical, cubic, hexagonal) and sizes (40 nm-70 nm). PVP concentrations had a significant effect on crystal sizes, full width at half maximum, and X-ray diffraction results of ZnONPs. As confirmed by FTIR spectroscopy, a chemical group of C=O in PVP is electrostatically bound to ZnONPs. A UV-vis spectroscopy experiment was performed in the range of wavelengths (300 nm - 800nm), an energy gap study was conducted based on Tauc's relation, and an Urbach energy calculation was conducted. In addition to improving morphology and crystalline growth, PVP concentrations contributed to improvements in optical properties, which are beneficial for the practical application of ZnONPs.
Mitochondria respiratory complexes and supercomplexes co-exist simultaneously in mammalian cells
Authors: Enriquez Jose , Martín-García Elena , Cabrera Jose Luis , Benica Cristiane , Cantarero Verónica Labrador , Herrero Diego , Diaz Francisca , Andilla Jordi , Loza-Alvarez Pablo , Moraes Carlos , Sánchez-Cabo Fátima , Caiolfa Valeria R. 
Published: June 2022

Abstract
The mitochondrial electron transport chain was understood as four respiratory complexes (RCs) independently moving in the mitochondrial inner membrane and electrons transferred between them by CoQ and cytochrome c1,2. The disruption of the mitochondrial membranes with mild detergents followed by blue native electrophoresis (BNGE), allowed visualization of RCs as independent entities, but also associated forming a variety of supercomplexes (SCs)1,3. This led to the proposal that RCs are not moving free entities but instead they super-assembly into structures, called supercomplexes (SCs) or respirasomes3. The use of detergents raised concerns on the existence of either free RCs or SCs in the cellular context4, and does not allow determining the relevance of additional SCs. To address this controversy, it was proposed the plasticity model that considered that both RCs and SCs co-existed in a dynamic organization1,5,6. Over the last 20 years the reality of respiratory supercomplexes was confirmed by functional3,6–8, genetic6,9 and structural10–15 studies. However, the co-existence of free RCs and SCs is still unanswered. We applied multi-color Stimulated Emission Depletion (STED) microscopy in whole cells in a panel of cell lines: mtDNA depleted cells (p0), complex III (CYTbM) or complex IV (COX10KO) depleted cell lines and their isogenic controls. We demonstrate the co-existence of RCs and SCs in large cell areas. Our observations support the plasticity organization model of the mitochondrial respiratory chain were RCs and SCs co-exist and reveal an unexpected heterogeneous distribution of RCs and SCs within mitochondria in-situ.
A GIS-based Simulation and Visualization Tool for the Assessment of Gully Erosion Processes
Authors: Omran Adel , Schröder Dietrich , Sommer Christian , Hochschild Volker , Maerker Michael 
Published: June 2022

Abstract
Gully erosion is known to affect soil productivity, limit land use, and to pose threats on infrastructure in many parts of the world. Gully erosion has been largely neglected because it is difficult to model and visualize its effects. Many gullies grow rapidly to large sizes, making effective control technically difficult and often too expensive. To assess the susceptibility of soils and substrates to gully erosion, the triggering factors must be identified and analyzed. For this study, a simulation of gully development over time was implemented in Python based on the topographic characteristics of the test watershed, soil properties, and measured runoff. The full simulation GIS was tested on a gully in the KwaThunzi region, South Africa. The results are very promising and allow a 2D/3D visualization of the time series of gully evolution.
Goreisan alleviates cerebral oedema by inhibiting aquaporin 4 function: In vivo study using an established mouse model of cerebral oedema
Authors: Shimizu Tomofumi , Matsumoto Chinami , Kido Toshitaka , Murakami Kazuhito , Isohama Yoichiro 
Published: June 2022

Abstract
BackgroundLow atmospheric pressure triggers weather-related illnesses, such as headaches. Although many individuals are affected by weather-related illnesses, only a few therapeutic drugs are available. In Japan, goreisan (GRS) is traditionally used to relieve headaches; however, its mechanism of action is unclear. Therefore, we investigated the mechanism of action of GRS against headaches, focusing on water dynamics.MethodsWe used a well-established mouse model of cerebral oedema to evaluate the effects of GRS on related symptoms and brain water content. The mouse model was subjected to magnetic resonance imaging (MRI) using 17O-labelled water (H217O) to assess water dynamics in the brain. The effect of GRS on water permeability through aquaporin 4 (AQP4) was examined in vitro to elucidate its mechanism of action.ResultsGRS inhibited the loss of righting reflex and survival in the mouse model by ameliorating the increase in brain water content. In the same mouse model, MRI evaluation of water dynamics using H217O-derived signal changes showed that GRS reduced the maximum signal intensity change in the cortex and the areas under the curve in the cortex and lateral ventricle. Evaluation of water permeability in Xenopus laevis oocytes expressing AQP4 showed that GRS inhibited water permeability by suppressing AQP4 function. ConclusionsGRS inhibits cerebral oedema and related symptoms partly by inhibiting AQP4 water permeability. These findings provide insights into the alleviating effects of GRS on headaches caused by cerebral oedema. This study could serve as a basis to develop novel therapeutic agents for treating weather-related illnesses.
Dairy intake in relation to metabolic health status in overweight and obese adolescents
Authors: Tirani Shahnaz Amani , Mirzaei Saeideh , Asadi Ali , Akhlaghi Masoumeh , Saneei Parvane 
Published: June 2022

Abstract
There was a lack of evidence on the association between dairy intake and metabolic health status in overweight/obese adolescents. This study aimed to evaluate the association between dairy intake and metabolic health status in overweight/obese Iranian adolescents. Overweight/obese adolescents (n= 203; 101 boys and 102 girls) (aged 12-18 years) selected by a multistage cluster random sampling method have participated in this cross-sectional study. Dietary intake was assessed using a validated 147-item food frequency questionnaire. Anthropometric indices, blood pressure, fasting glucose, insulin, and lipid profiles were measured. Participants were categorized to metabolically healthy obese (MHO) and metabolically unhealthy obese (MUO) according to International Diabetes Federation (IDF) criteria and a combination of IDF with Homeostasis Model Assessment Insulin Resistance (HOMA-IR) criteria. The frequency of MUO based on IDF, and IDF/HOMA-IR definitions was 38.9% and 33.0%, respectively. In fully-adjusted model, participants in the highest tertile of dairy intake had 61% lower odds of MUO based on IDF criteria (OR: 0.39, 95%CI: 0.15-0.99). Higher dairy intake was associated with a non-significant lower risk of MUO according to IDF/HOMA-IR definition in the maximally-adjusted model (OR: 0.44, 95%CI: 0.17-1.16). Stratifies analysis by sex and body mass index revealed that the association was stronger in girls and overweight subjects. However, in boys and obese adolescents, the association was insignificant. This community-based cross-sectional study revealed that higher intake of dairy was associated with a significant lower odd of MUO among Iranian adolescents, especially in girls and overweight subjects. Further large-scale prospective studies are necessary to confirm these results.
IGF2BP3 Mediates the mRNA Degradation of NF1 to Promote Triple-Negative Breast Cancer Progress via an m6A-Dependent Manner
Authors: Ding Qiang , Zhang Xu , Shi Liang , Sun Handong , Wang Zi-Wen , Xu Feng , wei Ji-Fu 
Published: June 2022

Abstract
N6-methyladenosine (m6A) is the most abundant reversible modification of eukaryotic mRNA. Emerging evidence has supported that m6A plays a vital role in tumorigenesis. As a crucial reader, IGF2BP3 usually mediates the stabilization of mRNAs in an m6A-dependent manner. However, the functions and m6A mechanism of IGF2BP3 have not been reported in triple-negative breast cancer (TNBC). Here we showed that IGF2BP3 was highly expressed in TNBC tissues and cell lines and was associated with poor prognosis. TET3-mediated IGF2BP3 promoter hypomethylation leads to upregulation of IGF2BP3 expression in TNBC. Knocking down IGF2BP3 markedly inhibited the proliferation and increased the apoptosis of TNBC in vitro and in vivo. Intersection co-assays revealed that IGF2BP3 decreased NF1 stabilization in an m6A-dependent manner. NF1 expression was negatively correlated with IGF2BP3, and knockdown of NF1 could rescue the phenotypes of IGF2BP3 knockdown cells partially in vitro and in vivo. Mechanistically, m6A reader IGF2BP3 promoted proliferation and inhibited the apoptosis of TNBC by destabilizing NF1 mRNA in an m6A-dependent manner. TET3-mediated IGF2BP3 promoter hypomethylation leads to upregulation of IGF2BP3 expression in TNBC. It suggested that IGF2BP3 has the potential to be the target for TNBC treatment.
Magnetic compression technique for ureterovesical anastomosis: An experimental study in rabbits
Authors: An Yingfeng , Zhang Miaomiao , Xu Shuqin , Deng Bo , Shi Aihua , Lyu Yi , Yan Xiaopeng 
Published: June 2022

Abstract
This study aimed to explore the feasibility of the magnetic compression technique (MCT) for ureterovesical anastomosis in a rabbit model with ureteral obstruction. The distal ureteral obstruction model using female New Zealand rabbits was induced by ligating the distal end of the right ureter with silk thread for four weeks. A pair of cylindrical NdFeB magnets (daughter magnet and parent magnet) with a hole in the center was used for the ureterovesical anastomosis. The daughter magnet and the parent magnet were respectively placed close to the obstruction site through the dilated proximal ureter and urethra, and then the daughter-parent magnets pair was attracted together automatically. Postoperative X-rays were taken to confirm the position of the magnets. The anastomotic stoma specimens were obtained two weeks postoperatively, and the anastomotic stoma formation was observed by the naked eye and histological staining. The operation time and the anastomotic burst pressure were measured. The ureter was significantly dilated in the fourth week after ligation, which satisfied the placement of the daughter magnet. The ureterovesical magnet placements were successfully performed in ten experimental rabbits, with an operation time of 36.5 ± 6.09 min. The parent and daughter magnets attracted each other well and were subsequently removed through the urethra two weeks postoperatively, resulting in the establishment of ureterovesical anastomosis. The anastomotic burst pressure was 147.5 ± 14.59 mmHg. Gross specimens and histological examination of the anastomotic stoma showed that the anastomotic stoma healed well. MCT is feasible and simple for ureterovesical anastomosis.