bluuebunny/crossref_metadata_2025_split huggingface dataset:
LncRNA RP11-59J16.2 Aggravates Apoptosis and Increases Tau Phosphorylation via Inhibiting MCM2 On The AD SH-SY5Y Cell Model Induced By Aβ.
Authors: Guan Fulin , Gao Qichang , Gu Jiaao , Dai Xinghua , Li Lei , Bao Rui 
Published: November 2021

Abstract
ObjectiveAlzheimer's disease (AD) is a degenerative disease of central nervous system with unclear pathogenesis, accounting for 60% - 70% of dementia cases. It is necessary to study the pathogenesis and therapeutic prospect of AD. LncRNAs have been found to play an important role in the development of AD. This study aims to explore the role of differentially expressed lncRNAs in AD patients' serum in the pathogenesis of AD.MethodsIn this study, serum microarray analysis was performed in AD patients and healthy controls to establish lncRNAs and mRNA expression profiles. The biological processes and key pathways were identified by GO analysis and KEGG pathway analysis. A protein-protein interaction network was analyzed and constructed by using String database. SH-SY5Y cells were treated with Aβ 1-42 to establish AD cell model. The expression of RP11-59J16.2 and MCM2 was detected by qRT-PCR. The mRNA binding sites and target genes of RP11-59J16.2 were predicted by bioinformatics analysis. Dual luciferase reporter gene analysis verified the targeting effect of RP11-59J16.2 on MCM2. Inhibition of RP11-59J16.2 or overexpression of MCM2, CCK-8 and flow cytometry were used to detect cell viability and apoptosis and Western Blot was used to detect the expression of p-Tau.ResultsDifferential expression of lncRNAs and mRNAs was screened by microarray data, and high expression of RP11-59J16.2 and low expression of MCM2 were detected in serum of AD patients. GO analysis and KEGG pathway analysis revealed that G1/S transition of mitotic cell cycle may be involved in the development of AD. The mRNA binding sites and target genes of RP11-59J16.2 were predicted by bioinformatics analysis. Dual luciferase reporter gene analysis, qRT-PCR and Western Blot were used to verify the targeted regulation of RP11-59J16.2 on MCM2. The expression of RP11-59J16.2 was increased and that of MCM2 was decreased in SH-SY5Y cells treated with Aβ1-42. CCK-8 assay and Annexin V FITC/PI apoptosis assay kit results showed that RP11-59J16.2 could reduce cell viability, aggravate apoptosis and increase Tau phosphorylation in AD cell model by inhibiting MCM2.ConclusionThrough gene microarray and bioinformatics analysis, high differentially expressed lncRNAs RP11-59J16.2 and low expressed mRNA MCM2 in AD patients were screened. By using bioinformatics prediction and dual luciferase reporter gene analysis, it was confirmed that RP11-59J16.2 could target MCM2 regulation. SH-SY5Y cells were treated with Aβ1-42 to construct AD cell model. Overexpression or inhibition of RP11-59J16.2 or MCM2, we found that RP11-59J16.2 could promote neuronal apoptosis and increase Tau phosphorylation by regulating MCM2 in vitro. Thus, RP11-59J16.2 might be a potential target molecule for the prediction, diagnosis and treatment of AD.
Smart Cotton Functionalized With Self-Implanted Palladium Nanopanicles: Full Ultraviolet Shielding Potency
Authors: Emam Hossam E. , Zaghloul Saad , Ahmed Hanan B. 
Published: November 2021

Abstract
Unique technique is currently demonstrated for preparation of ultraviolet protective cotton fabrics with full shielding effect, via self-implantation of palladium nanopanciles. Palladium (Pd) nanopanciles were in-situ immobilized within native & cationized cotton using two different concentrations of palladium precursor (20 & 60 mM) under strong acidic (pH 2) and basic (pH 11.5) media. Cationization (50% and 100%) of cotton fabrics was performed in order to increase the accessibility of fabric for controllable implantation of palladium nanopanciles. Size distribution of palladium nanopanciles in supernatant solution was estimated via Transmission electron microscopy to be 3.2 nm. The estimated data showed that the sample prepared with the highest cationization percent and highest concentration of palladium precursor in strong alkaline medium exhibited the highest yellowness index, color strength and excellent ultraviolet shielding effects. The yellowness index was significantly increased from 15.67 for cationized cotton to 74.99 for the sample prepared with the highest cationization percent and highest concentration of Pd+2 in alkaline medium (Pd-CC (100)4). Tensile strength was insignificantly decreased from 93.2 MPa for cationized cotton to 84.5 MPa for Pd-CC (100)4. Ultraviolet shielding effect was superiorly enhanced with implantation of palladium nanopanciles. The UV protection factor (UPF) was also excellency increased from 1.3 (insufficient) for native cotton to 256.6 (excellent) for Pd-CC (100)4.
Ploidy Mosaics - Does Endopolyploidy in Explants Affects the Cytogenetic Stability of Orchids Regenerated From PLBs?
Authors: Fritsche Yohan , Ornellas Thiago Sanches , Stefenon Valdir Marcos , Guerra Miguel Pedro 
Published: November 2021

Abstract
The induction and regeneration of protocorm-like bodies (PLBs) is a morphogenetic pathway widely used for orchid micropropagation. As endopolyploidy, i.e., the coexistence of cells with different ploidy levels, is a common feature in orchid tissues, a natural question arises when using somatic tissues as explants for orchid micropropagation: does endopolyploidy in explants affect the cytogenetic stability of regenerated plantlets? To answer this question, Epidendrum fulgens was used as a model plant, and flow cytometry (FC) was used to analyze endopolyploidy in pollinia, petals, labella, leaf bases, leaf tips, root tips, protocorms bases and protocorms apexes, which were subsequently used as explants for PLB induction and plant regeneration. The ploidy screening showed contrasting ploidy patterns in the samples. Endopolyploidy was detected in all tissues, with C-values ranging from 1C to 16C. Protocorm bases and root tips presented the highest proportion of endopolyploidy, while petals and protocorm apexes showed the lowest proportion. Flower parts presented high oxidation for PLB induction and pollinia failed to produce PLB or callus. The highest induction rate was observed at 10 µM TDZ, with 92%, 22%, and 0.92% for protocorm bases, leaves, and root tips, respectively. Plantlets were more easily regenerated from PLBs induced from protocorm bases than from leaves and roots. Doubled ploidy levels were registered in a proportion of 11% and 33% for PLB-regenerated plantlets obtained from protocorm bases and leaf bases, respectively, which was not directly associated with the proportion of endopolyploid cells or cycle value of explants.
RNA-sequencing and Mathematical Modeling Identify Suite of Light-sensitive Circadian Genes in an Orb-web Weaving Spider
Authors: Toporikova Natalia , Cheng Wenduo , Qian Leyuan , Mah Andrew , Clarke Thomas , Jones Thomas C. , Moore Darrell , Ayoub Nadia A. 
Published: November 2021

Abstract
BackgroundMost organisms rely on a molecular circadian clock to orchestrate a wide range of physiological processes to match the 24-hour day. These molecular clocks are typically based on a negative feedback loop among a small set of proteins that govern the circadian output. Light or other environmental conditions can reset the circadian clock, but true circadian behaviors continue to cycle even in constant darkness, with an intrinsic period called the free-running period (FRP). Spiders have unusual FRPs, with some species having extremely short FRP (e.g. 18 hours for trashline orb weaver), and many having highly variable FRPs (intraspecific variation of up to 10 hours). In the absence of any genetic model of circadian rhythms in spiders, we developed a mathematical model to optimize experimental conditions for identifying circadian genes that also respond to light cues. ResultsOur mathematical model involved a single gene that encodes a protein that inhibits its own transcription. In our model, light degrades the circadian transcript, which allows a broad range of FRPs to be entrained to a 24-hour day. Our model predicted that exposing spiders to a pulse of light in the middle of the night would cause a pattern of expression between two later time points that was opposite the pattern exhibited by spiders who did not receive a pulse of light. RNA-sequencing of four groups of adult female orb weaving spiders, Metazygia wittfeldae, under these experimental conditions resulted in 528 significantly differentially expressed (DE) transcripts between the two collection times or between the light pulse and no light pulse. Consistent with our model, we found a cluster of transcripts with the flipped pattern of expression between the two collection times, dependent on the application of light.ConclusionsOur DE transcripts represent the first genetic evidence for circadian output in spiders. Furthermore, those transcripts with a flipped pattern of expression represent prime candidates for light-sensitive circadian genes, which may be involved in entraining the circadian clock to light. Functions of these genes varied from growth and development to reproduction to gene regulation, consistent with other circadian systems.
Construction of a Prognostic m6A-related lncRNA Signature to Predict Immunotherapy and Chemotherapy Response in Hepatocellular Carcinoma
Authors: Zou Yiping , Chen Zhihong , Han Hongwei , Lou Qi , Zhang Yuanpeng , Chen Zhenrong , Ma Zuyi , Jin Haosheng , Shi Ning 
Published: November 2021

Abstract
Hepatocellular carcinoma (HCC) is one of the main causes of cancer-related deaths worldwide. N6-methyladenosine (m6A) and long noncoding RNA (lncRNA) are two common modifications that affect tumor development and play vital roles in the prognosis of HCC. Therefore, we comprehensively analyzed transcriptome data from the Cancer Genome Atlas (TCGA) and identified lncRNAs related to m6A regulators. Univariate, LASSO, and multivariate Cox regression analyses were used to build a prognostic model. Patients were then divided into low- and high-risk groups according to the optimal cut-off point. The prognosis value of the novel model was evaluated using Kaplan-Meier analysis and the receiver operating characteristic curve. Besides, mutation and immune profiles together with immune checkpoint expressions were further explored to identify the difference in somatic alteration and tumor immune landscape between the two groups. Additionally, a better response to conventional chemotherapy and immunotherapy was found in patients with the high-risk group, but they were more resistant to sorafenib. The m6A-related lncRNAs model might be used to predict the prognosis and drug responses in patients with HCC.
Coordination and Equilibrium Selection in Games: The Role of Local Effects
Authors: Raducha Tomasz , Miguel Maxi San 
Published: November 2021

Abstract
We study the role of local effects and finite size effects in reaching coordination and in equilibrium selection in two-player coordination games. We investigate three update rules – the replicator dynamics (RD), the best response (BR), and the unconditional imitation (UI). For the pure coordination game with two equivalent strategies we find a transition from a disordered state to coordination for a critical value of connectivity. The transition is system-size-independent for the BR and RD update rules. For the IU it is system-size-dependent, but coordination can always be reached below the connectivity of a complete graph. We also consider the general coordination game which covers a range of games, such as the stag hunt. For these games there is a payoff-dominant strategy and a risk-dominant strategy with associated states of equilibrium coordination. We analyse equilibrium selection analytically and numerically. For the RD and BR update rules mean-field predictions agree with simulations and the risk-dominant strategy is evolutionary favoured independently of local effects. When players use the unconditional imitation, however, we observe coordination in the payoff-dominant strategy. Surprisingly, the selection of pay-off dominant equilibrium only occurs below a critical value of the network connectivity and disappears in complete graphs. As we show, it is a combination of local effects and update rule that allows for coordination on the payoff-dominant strategy.
Human In Silico Trials for Parametric Computational Fluid Dynamics Investigation of Cerebrospinal Fluid Drug Delivery: Impact of Injection Location, Injection Protocol, and Physiology
Authors: Khani Mohammadreza , Burla Goutham Kumar Reddy , Sass Lucas R. , Arters Ostin N. , Xing Tao , Wu Haiming , Martin Bryn 
Published: November 2021

Abstract
BackgroundIntrathecal drug delivery has a significant role in pain management and CNS disease therapeutics. A fluid-physics based tool to assist clinicians in choosing specific drug doses to the spine or brain may help improve treatment schedules. MethodsThis study applied computational fluid dynamics (CFD) and in vitro model verification to assess intrathecal drug delivery in an anatomically realistic model of the human CSF system. Key parameters analyzed included the role of a) injection location including lumbar puncture (LP), cisterna magna (CM) and intracerebroventricular (ICV), b) LP injection rate, injection volume, and flush volume, c) physiologic factors including cardiac-induced and deep respiration-induced CSF stroke volume increase. Simulations were conducted for 3-hours post-injection and used to quantify spatial-temporal tracer concentration, regional area under the curve (AUC), time to maximum concentration (T max ), and maximum concentration (C max ), for each case. ResultsCM and ICV increased AUC to brain regions by ~2 logs compared to all other simulations. A 3X increase in bolus volume and addition of a 5 mL flush both increased intracranial AUC to the brain up to 2X compared to a baseline 5 mL LP injection. In contrast, a 5X increase in bolus rate (25 mL/min) did not improve tracer exposure to the brain. An increase in cardiac and respiratory CSF movement improved tracer spread to the brain, basal cistern, and cerebellum up to ~2 logs compared to the baseline LP injection. ConclusionThe computational modeling approach provides ability to conduct in silico trials representative of CSF injection protocols. Taken together, the findings indicate a strong potential for delivery protocols to be optimized to reach a target region(s) of the spine and/or brain with a needed therapeutic dose. Parametric modification of bolus rate/volume and flush volume was found to have impact on tracer distribution; albeit to a smaller degree than injection location, with CM and ICV injections resulting in greater therapeutic dose to brain regions compared to LP. CSF stroke volume and frequency both played an important role and may potentially have a greater impact than the modest changes in LP injection protocols analyzed such as bolus rate, volume, and flush.
SEMA6A/RhoA/YAP Axis Mediates Tumor-Stroma Interactions and Prevents Response to Dual BRAF/MEK Inhibition in BRAF-Mutant Melanoma
Authors: Loria Rossella , Laquintana Valentina , Scalera Stefano , Fraioli Rocco , Caprara Valentina , Falcone Italia , Bazzichetto Chiara , Martile Marta Di , Rosanò Laura , Bufalo Donatella Del , Bossi Gianluca , Sperduti Isabella , Terrenato Irene , Visca Paolo , Soddu Silvia , Milella Michele , Ciliberto Gennaro , Falcioni Rita , Ferraresi Virginia , Bon Giulia 
Published: November 2021

Abstract
Background: Despite the promise of dual BRAF/MEK inhibition as a therapy for BRAF-mutant (BRAF-mut) melanoma, heterogeneous responses have been observed in patients, thus predictors of benefit from therapy are needed. We have previously identified semaphorin 6A (SEMA6A) as a BRAF-mut-associated protein involved in actin cytoskeleton remodeling. The purpose of the present study is to dissect the role of SEMA6A in the biology of BRAF-mut melanoma, and to explore its predictive potential towards dual BRAF/MEK inhibition.Methods: SEMA6A expression was assessed by immunohistochemistry in melanoma cohort RECI1 (N=112) and its prognostic potential was investigated in BRAF-mut melanoma patients from DFCI and TCGA datasets (N=258). The molecular mechanisms regulated by SEMA6A to sustain tumor aggressiveness and targeted therapy resistance were investigated in vitro by using BRAF-mut and BRAF-wt melanoma cell lines, an inducible SEMA6A silencing cell model and a microenvironment-mimicking fibroblasts-coculturing model. Finally, SEMA6A prediction of benefit from dual BRAF/MEK inhibition was investigated in melanoma cohort RECI2 (N=14).Results: Our results indicate higher protein expression of SEMA6A in BRAF-mut compared with BRAF-wt melanoma patients and show that SEMA6A is a prognostic indicator in BRAF-mut melanoma from TCGA and DFCI patients cohorts. In BRAF-mut melanoma cells, SEMA6A coordinates actin cytoskeleton remodeling by the RhoA-dependent activation of YAP and dual BRAF/MEK inhibition by dabrafenib+trametinib induces SEMA6A/RhoA/YAP axis. In microenvironment-mimicking co-culture condition, fibroblasts confer to melanoma cells a proliferative stimulus and protect them from targeted therapies, whereas SEMA6A depletion rescues the efficacy of dual BRAF/MEK inhibition. Finally, in BRAF-mut melanoma patients treated with dabrafenib+trametinib, high SEMA6A predicts shorter recurrence-free interval. Conclusions: Overall, our results indicate that SEMA6A contributes to microenvironment-coordinated evasion of melanoma cells from dual BRAF/MEK inhibition and it might be a good candidate predictor of short-term benefit from dual BRAF/MEK inhibition.
Cooling of cultured water can resist heart failure caused by collagen deposition and necrosis of cardiac fibers under chronic heat stress in sturgeon
Authors: Zhang Chaoyang , Zhang Miao , Xu Zihan , Li Datian , Gong Quan , Huang Xiaoli , Wu Jiayun , He Zhi , Du Xiaogang , Chen Defang , Jiang Jun , Du Jun , Yang Shiyong 
Published: November 2021

Abstract
Background

Chronic heat stress (CHS) may threaten the survival of cultivated and wild sturgeon by jeopardizing heart function.
Methods

Therefore, we established a heart damage model for the Siberian sturgeon (Acipenser baerii) using varying degrees of CHS (24°C and 28°C) to explore its effect on the heart structure and function, and their mutual relationship.
Results

Our research showed that CHS caused systemic heart failure in A. baerii, clinically manifested as severely irregular ventricles, increased myocardial fibrotic in the interstitium of cardiomyocytes, and myocardial necrosis. Echocardiographic imaging of A. baerii revealed an accelerated heart rate, incomplete ventricular contraction, decreased cardiac output, and significantly reduced pumping efficiency under CHS. Generally, the contractility of the heart decreased and the afterload increased under CHS, which is typical of high-resistance and low-output heart failure. However, cooling of cultured water (20°C) can offset the adverse effects of partial or total CHS on tissue structure and function.
Conclusion

Our results systematically characterized the relationship between the effects of CHS on the heart structure and heart function in sturgeon. This work provides a preliminary reference for future summer breeding pond management and protection of sturgeon.
Oecophylla Smaragdina (Hymenoptera: Formacidae) and Odontotermes sp. (Isoptera: Termitidae) a Potential Source of Antioxodant: The Two Most Preferred Edible Insects of Arunachal Pradesh, India
Authors: Raza Mohsin , Tukshipa Sonam Drema , Chakravorty Jharna 
Published: November 2021

Abstract
Antioxidant potential of weaver ant Oecophylla smaragdina (adult & brood) and termite odontotermes sp, the two common species of insects used as food by tribes of Arunachal Pradesh and elsewhere in India. Our findings highlight the antioxidant potential of these two insects. DPPH scavenging activity IC50 (µg/ml) ranged from 59.559 (ant adult) to 66.30 (termite). Termite species scored higher ABTS scavenging activity (IC50: µg/ml), Ferric reducing power (TPEE µg/g) and phenols (mg GAE/g) (18.70, 36.60 and 626.92) than weaver ant adult (52.57, 211.21 and 369.69) and ant brood (33.34, 114.32, 486.04). On the other hand, ant adult scored higher flavonoid (mg RTE/g) (663.4) than its brood (387.2) and termite species (58.0). Ant brood contained substantial amounts of phenols and flavonoid, comparatively higher than phenols of ant adult and flavonoid of termite. These two insects may serve as an ideal dietary food supplement for handling oxidative stress and as replacement for some conventional food products. However, further study is needed to find out the bio-active compound at individual species level.
Causes of different goiter rates with the same iodine deficiency among the pastoral and agricultural populations of Tibet: A geographical comparison
Authors: Xu Jing , Liu Shichuan , Ma Wei , Li Xiuwei , Guo Min , Cao Xiaoxiao , Gu Yunyou , Wang Haiyan , Wang Jianqiang , Zhang Ying , Zhuang Guangxiu , Liu Liejun 
Published: November 2021

Abstract
Background
The residents of both the agricultural and pastoral areas of Tibet share the same iodine deficiency and iodine nutrition, but the rate of thyroid goiter was significantly higher in the agricultural areas than in the pastoral areas. This project sought to determine why the populations in the iodine-deficient pastoral areas show a lower rate of thyroid goiter.
Methods
Food frequency questionnaires (FFQs) and 24 h history recalls were adopted to investigate the dietary patterns of the residents of the agricultural and pastoral areas. Meat and milk samples were collected to measure their inorganic iodine, total iodine and thyroid hormone contents using ICP-MS, AsIII-Ce4+ catalytic spectrophotometry and the Siemens’ chemiluminescence method, respectively. The intake of protein, and the microelements, selenium and iron, was calculated according to their content in the food.
Results
The per capita daily intake of meat, dairy, and cereal in the pastoral areas was 116.7, 216.7, and 433.3 g, respectively, which are significantly higher than those in the agricultural areas (50.0, 72.2, and 375.0 g, respectively) (p < 0.05). The content of thyroid hormone in dried beef and milk in the pastoral areas was 62.6 and 13.5 µg/kg, respectively, which was significantly higher than those in the agricultural areas (25.1 and 4.1 µg/kg, respectively) (p < 0.05). The daily intake of thyroid hormone, protein and microelements, selenium and iron from foods by the residents of the pastoral areas were 10.5 µg, 99.6 g, 30.0 µg and 15.8 mg respectively, which was significantly higher than those in the agricultural areas (1.79 µg, 56.5 g, 23.8 µg and 13.2 mg, respectively) (p < 0.05).
Conclusions
The significantly high intake of the food-borne thyroid hormone by the residents of the pastoral area could be the main reason the residents in the pastoral areas show a lower rate of thyroid goiter than those in the agricultural area. Moreover, the relatively high intake of protein and trace elements, selenium and iron by residents in the pastoral area could be another important factor for reducing the goiter rates.