bluuebunny/crossref_metadata_2025 huggingface dataset:
Quality control recommendations for RNASeq using FFPE samples based on pre-sequencing lab metrics and post-sequencing bioinformatics metrics
Authors: Liu Yuanhang , Bhagwate Aditya , Winham Stacey J , Stephens Melissa T , Harker Brent W , McDonough Samantha J , Stallings-Mann Melody L , Heinzen Ethan P , Vierkant Robert A , Hoskin Tanya L , Frost Marlene , Carter Jodi M , Pfrender Michael E. , Littlepage Laurie , Radisky Derek C , Cunningham Julie M , Degnim Amy C , Wang Chen
Published: March 2022

BackgroundFormalin-fixed, paraffin-embedded (FFPE) tissues have many advantages for identification of risk biomarkers, including wide availability and potential for extended follow-up endpoints. However, RNA derived from archival FFPE samples has limited quality. Here we identified parameters that determine which FFPE samples have the potential for successful RNA extraction, library preparation, and generation of usable RNAseq data.MethodsWe optimized library preparation protocols designed for use with FFPE samples using seven FFPE and Fresh Frozen replicate pairs, and tested optimized protocols using a study set of 130 FFPE biopsies from women with benign breast disease. Metrics from RNA extraction and preparation procedures were collected and compared with bioinformatics sequencing summary statistics. Finally, a decision tree model was built to learn the relationship between pre-sequencing lab metrics and qc pass/fail status as determined by bioinformatics metrics.ResultsSamples that failed bioinformatics qc tended to have low median sample-wise correlation within the cohort (Spearman correlation < 0.75), low number of reads mapped to gene regions (< 25 million), or low number of detectable genes (11,400 # of detected genes with CPM > 2). The median RNA concentration and pre-capture library Qubit values for qc failed samples were 18.7 ng/ul and 1.68 ng/ul respectively, which were significantly lower than those of qc pass samples (40.8 ng/ul and 5.58 ng/ul). We built a decision tree model based on input RNA concentration, input library qubit values, and achieved an F score of 0.803 in predicting QC status (pass/fail) of FFPE samples. ConclusionsWe provide a bioinformatics quality control recommendation for FFPE samples from breast tissue by evaluating bioinformatic and sample metrics. Our results suggest a minimum concentration of 25 ng/ul FFPE-extracted RNA for library preparation and 1.8 ng/ul pre-capture library output to achieve adequate RNA-seq data for downstream bioinformatics analysis.
Responses and tolerance mechanisms of K. paniculate seedlings under lead stress: physiological indicators, morphological distribution, enrichment effects and microstructure
Authors: Chen Yonghua , Xie Tianzhi , Su Rongkui , Yao Haisong , Du Lu , Liu Jun
Published: March 2022

Phytoremediation could be an alternative strategy for lead (Pb) contamination, The physiological mechanisms of plant resistance to Pd contamination are of less concern. In this study, Different concentrations of Pb solutions were added to explore the growth of Koelreuteria paniculate (Sapindaceae). physiology and microstructure of K. paniculate were determined. The results showed that plant growth increased up to 123.8% and 112.7% relative to the control group when the lead concentration was 200 and 400 mg/L. In all treatments, most of the Pb accumulation reached 81.31%-86.69% in the roots and slightly lower concentrations in the above-ground leaves than in the stems. Transmission electron microscopy (TEM) showed that Pb accumulates in the inactive metabolic parts (cell walls and vesicles) in roots and stems, which may be the main mechanism for plants to reduce Pb biotoxicity. In addition, by Fourier transform infrared spectroscopy (FTIR), Pb stress increased the content of intracellular -OH and -COOH functional groups, including compounds such as organic acids, polysaccharides and proteins that bind to Pb, attenuating the toxicity to plants and enhancing their adaptation and tolerance to heavy metals.
Two SKAP2 modular organizations differently recognize SRC kinases depending on their activation status and localization
Authors: Levillayer Laurine , Cassonnet Patricia , Declercq Marion , Santos Mélanie Dos , Lebreton Louis , Danezi Katerina , Demeret Caroline , Sakuntabhai Anavaj , Jacob Yves , Bureau Jean-François
Published: March 2022

Background: The activation of SRC kinases by trans-phosphorylation raises the question of their interplay. This work addresses this question by studying the interactions of SRC kinases with the SRC Kinase Adaptor Phosphoprotein 2 (SKAP2) by combining a luciferase complementation assay and extensive site-directed mutagenesis. Results: SKAP2 interacts with SRC kinases through two different module organizations that have different affinities for the activated and non-activated kinase conformations. The DIM domain of SKAP2 is necessary and sufficient to bind to most activated SRC kinases. A second SKAP2 module organization for binding to SRC kinases at their steady state is composed of the DIM and SH3 domains as well as the linker located between the PH and the SH3 domains. Classical binding sites of the PH and SH3 domains and the tyrosines located inside linkers modulate these interactions. Analysis of HCK mutants supports this model and shows the role of two residues, Y390 and K7, on its degradation following activation. Conclusion: In this article, we show that SKAP2 have a modular architecture composed of 2 domains and one interdomain to interact with SRC kinases, which binding capacity of each module depends on their localization and activation. This work opens new perspectives on how activation of SRC kinases occurs, which could have new and interesting therapeutic consequences.
The Impact of Covid-19 Pandemic on Child Abuse and Neglect
Authors: Lupariello Francesco , Mattioda Giuliana , Lauria Barbara , Aguzzi Sonia , Castagno Emanuele , Bondone Claudia , Vella Giancarlo Di
Published: March 2022

Purpose - Child abuse and neglect (CAN) is a worldwide issue due to its biological, psychological, and social effects. Research in this field is particularly useful to understand CAN aspects which are still unknown and to define updated intervention strategies. Until now, there are no clear indications about the possible effects determined by the SARS-CoV-2 pandemic on CAN. For these reasons, the authors of the present manuscript propose a study in which they compared quantitative and qualitative variables of pre-pandemic and pandemic cases evaluated at an Italian ambulatory specialized in diagnosis and management of CAN. The main aims were to: define if there was a reduction or an increase of cases referred for CAN during SARS-CoV-2 pandemic; evaluate if there were statistically significant differences of variables’ distributions between pre-pandemic and pandemic periods. Methods - The study included children 0 - 18 years of age who were referred to the specialized ambulatory during the first 13 months of the SARS-COV-2 pandemic in Italy: March 2020 - March 2021. As control group (Group B - GB), the authors chose children 0 - 18 years of age evaluated by the healthcare professionals of the same ambulatory from March 2018 to March 2019. Ages and main qualitative variables were compared between the two samples throughout statistical tests. Results - The analysis yielded no statistical differences for age distributions and for the most part of qualitative variables. The study pointed out a reduction of the distribution of the number of cases. Conclusions - In this study, the comparison of frequencies’ distribution of the most part of variables between pre and post pandemic samples did not differ. The most important result of the present analysis is that in the pandemic period the volume of observed CAN cases decreased. This allows us to confirm the indications of the scientific literature. We cannot exclude that the decrease was due to a negative impact of the pandemic on the child protection system. The afore-mentioned data will be useful to program corrective interventions, also for future pandemic and disasters.
Alterations in Mitochondria-Associated Endoplasmic Reticulum Membranes Under Oxidative Stress in R28 Cells
Authors: Yang Yuting , Wu Jihong , Lu Wei , Dai Yiqin , Zhang Youjia , Sun Xinghuai
Published: March 2022

This study aimed to investigate alterations in mitochondria-associated endoplasmic reticulum membranes (MAMs) under oxidative stress conditions in R28 retinal precursor cells. Hydrogen peroxide (H2O2) and hypoxia (0.2% oxygen) were used to induce oxidative stress in R28 cells. Cell viability, reactive oxygen species (ROS) levels, mitochondrial membrane potential, mitochondrial calcium concentration, MAMs, and autophagy were evaluated. Mitofusin-2 (MFN2), a protein that plays a role in the structural regulation of MAMs, was either upregulated or downregulated in R28 cells to further explore the potential role of MFN2 in modulating MAMs. Oxidative stress not only modulated MAMs but also induced mitochondrial membrane potential (MMP) and increased mitochondrial calcium concentration. H2O2 and hypoxia also induced oxidative stress-associated autophagy in R28 cells. Additionally, autophagy inhibition increased MAM signaling. MFN2 silencing increased MAM expression and induced MMP collapse under normal conditions, whereas MFN2 upregulation rescued hypoxia-induced MAM alterations and alleviated MMP collapse. However, Mfn2 overexpression further enhanced H2O2-induced MAMs and failed to rescue MMP collapse. Our study indicates that MAMs possibly serve as a membrane source for oxidative stress-associated autophagy in R28 cells. MFN2 appears to play a negative role in maintaining MAM biogenesis under hypoxic conditions; however, its role in H2O2-associated MAM dysfunction remains unclear.
A Nonextensive View on the COVID-19 in the World
Authors: Liu Yang , Yu Chen-Yue , Shen Ke-Ming
Published: March 2022

This paper deals with a general Susceptible-Infectious-Removed (SIR) model for the coronavirus disease 2019 (COVID-19) within a non-extensive view. A time-dependent SIR model was modified when particularly regarding control and mitigation measures in response to the societal impacts of epidemics and pandemics. We validated all the theoretical results by fitting the derived q-distributions with data from the COVID-19 pandemic in the world. It was found that not all the changeable fit parameters are independent, some of which shared common properties, a result corroborated by our model prediction. Our modified SIR model was proved to be effective in fitting the COVID-19 epidemic distributions. The relative non-extensive parameter was strongly connected with the freedom of systems, which thus threw a light upon the prevention and treatment of disease next in the world.
Deep Learning for MYC binding site recognition
Authors: Fioresi R. , Demurtas P. , Perini G.
Published: March 2022

Motivation: The definition of the genome distribution of the Myc transcription factor is extremely important since it may help predict its transcriptional activity particularly in the context of cancer. Myc is among the most powerful oncogenes involved in the occurrence and development of more than 80% of different types of pediatric and adult cancers. Myc regulates thousands of genes which can be in part different, depending on the type of tissues and tumours. Myc distribution along the genome has been determined experimentally through chromatin immunoprecipitation This approach, although powerful, is very time consuming and cannot be routinely applied to tumours of individual patients. Thus, it becomes of paramount importance to develop in-silico tools that can effectively and rapidly predict its distribution on a given cell genome. New advanced computational tools (DeeperBind) can then be successfully employed to determine the function of Myc in a specific tumour, and may help to devise new directions and approaches to experiments first and personalized and more effective therapeutic treatments for a single patient later on. Results: The use of DeeperBind with DeepRAM on Colab platform can effectively predict the binding sites for the MYC factor with an accuracy above 0.96 AUC, when trained with multiple cell lines. The analysis of the filters in DeeperBind trained models shows, besides the consensus sequence CACGTG classically associated to the MYC factor, also the other consensus sequences G/C box or TGGGA, respectively bound by the SP1 and MIZ-1 transcription factors, which are known to mediate the MYC repressive response. Overall, our findings suggest a stronger sinergy between the machine learning tools as DeeperBind and biological experiments, which may reduce the time consuming experiments by providing a direction to guide them.
Activation of Swell1 in microglia suppresses neuroinflammation and reduces brain damage in ischemic stroke
Authors: Chen Baoyi , Xie Cong , Shi Tengrui , Yue Shiqin , Li Weiping , Huang Guodong , Zhang Yuan , Liu Wenlan
Published: March 2022

Background
Neuroinflammation and immune responses mediated by microglia are associated with brain injury after ischemic stroke, and it is novel that Cl− movement and Cl-sensitive signal pathways have been shown to be implicated in the survival and switch of inflammation patterns of immune cells. Swell1, one of the components of Volume-regulated Cl− currents (VRAC) is considered to be the main channels mediating Cl− efflux from nerves cells. However, the role of Swell11 in ischemia-induced inflammation and the effect of Swell1 on the inflammation patterns switch of microglia remain unknown.
Methods
Whole-cell patch clamp recordings was used to examine Swell1-mediated VRAC in BV2 cells. In vivo and vitro studies comparing EGFP and Swell1 conditional knock-in mice were performed to determine the role of microglia Swell1 on inflammation and brain injury after ischemic stroke. In vitro experiments to further explored the mechanism of microglia Swell1 in regulating neuroinflammation.
Results
Our data showed that knockdown or overexpression of Swell1 in cultured BV2 cells inhibited or increased hypotonic-activated Cl− currents, respectively, and these changes were completely blocked by the VRAC inhibitor DCPIB. Swell1 conditional knock-in mice promoted microglial survival in the lesion region, leading to reductions in neural cell apoptosis, infarction size and neurological deficits following transient middle cerebral artery occlusion (tMCAO). Using gene manipulating technique and pharmacological inhibitors, we further revealed that Swell1 opening led to SGK1 (a Cl−-sensitive kinase)-mediated activation of FOXO3a/CREB as well as WNK1 (another Cl−-sensitive kinase)-mediated SPAK/OSR1-CCCs activation, which promoted microglial survival and M2 polarization, thereby attenuating inflammation and ischemic brain injury.
Conclusion
Our results demonstrated that Swell1 is an essential component of microglia VRAC and its activation protects against ischemic brain injury through promoting microglial survival and M2 polarization, which provides new a new orientation for the treatment of ischemic stroke and other neurological diseases associated with inflammation.
Discrimination between earthquakes and quarry blasts in the Aswan region, southern Egypt using P-wave source spectra
Authors: Saadalla Hamada , Mossa Hesham , Hayashida Takumi
Published: March 2022

We analyzed 3,069 seismic signals from 413 events (112 explosions and 301 shallow earthquakes, depths < 5 km) recorded by the Aswan seismic sub-network in southern Egypt from 2010 to 2021 to discriminate between shallow earthquakes and quarrying activity. We investigated the spectral properties and related source parameters (e.g., seismic moment and corner frequency) using the estimated P-wave source spectra for both earthquakes and quarry blasts. The analysis showed that the P-wave source spectra of shallow earthquakes have higher corner frequencies (8.8–23 Hz) than quarry blasts (1.0–2.6 Hz) within the same magnitude range. The source spectra of quarry blasts exhibited significant misfits with the omega-square model and had steeper falloffs at high frequencies. The selected quarry blasts have a narrow seismic moment range, from 2.03⋅1011 to 1.35⋅1012 Nm. Our results demonstrate that the evaluation of misfit of P-wave spectra from the omega-square source model based on spectral amplitude characteristics of high and low frequency bands is the most reliable discriminant method in the routine data analysis of the target area.
Effect of Tear Derived Exosomes on Corneal Epithelial Cells During Diabetic Keraropathy
Authors: Li X , Wang S , Liu Y , Wang J , Zhu R , Jin X , Zhang H
Published: March 2022

Background: As reliable intercellular transporters, exosomes for the diagnosis and function of various disease are fully explored. Also, exosomes extracted from tear film have been used as indictors for various eye disease, even systemic disease due to the easy and non-invasive collection nature with microRNAs variation. However, there still no reports focus the change and function of on exosomes and exosomal microRNAs during diabetes ocular dysfunction.Methods: Paired diabetes and health tear film-derived exosomes were collected by test strips and identified according standard regimens. Different expression microRNAs were profiled by microarray. The function of exosomes to cornea epithelium was detected by cornea wound model in vivo and cell viability and migration assay in vitro. Bioinformatics analysis, including GO and KEGG were conducted to explore the potential biological signaling pathway.Results: We confirmed diabetic tear film derived exosomes contribute to delay cornea wound healing and aggravate diabetic dry eye-like syndrome. Total 12 differential expression microRNAs were confirmed compared with paired controls, may participate in glycosphingolipid biosynthesis; mucin type O-Glycan biosynthesis; Ras signaling pathway; AMPK signaling pathway; bacterial invasion of epithelial cells; ErbB signaling pathway; cGMP-PKG signaling pathwayConclusion: This study provides evidence that diabetic tear film derived exosomes can affect the ocular surface health during diabetes, while healthy exosomes have no similar effects. Thus, the different expression of microRNAs existed in the exosomes from diabetes and healthy volunteer may be the reason of different function.
SARS-CoV 2 accessory protein 7b forms homotetramers in detergent
Authors: Torres Jaume , Surya Wahyu , Queralt-Martin Maria , Mu Yuguang , Aguilella Vicente M.
Published: March 2022

A global pandemic is underway caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The SARS-CoV-2 genome, like its predecessor SARS-CoV, contains open reading frames that encode accessory proteins involved in virus-host interactions active during infection and which likely contribute to pathogenesis. One of these accessory proteins is 7b (p7b), with only 44 and 43 residues in SARS-CoV and SAR-CoV-2, respectively. It has one predicted transmembrane domain fully conserved, which suggests a functional role, whereas most variability is contained in the predicted cytoplasmic C-terminus. In SARS-CoV, 7b protein is expressed in infected cells where the transmembrane domain was necessary and sufficient for Golgi localization. Also, anti-p7b antibodies have been found in the sera of SARS-CoV convalescent patients. In the present study, we have investigated the hypothesis that SARS-2 7b protein forms oligomers with ion channel activity. We show that 7b protein is almost completely α-helical in both SARS viruses and has a single transmembrane domain. In SDS, p7b forms various oligomers, from monomers to tetramers, but only monomers when exposed to reductants DTT or TCEP. Combination of SDS gel electrophoresis and and analytical ultracentrifugation (AUC) in both equilibrium and velocity modes suggests a dimer-tetramer equilibrium, and an equilibrium between monomeric, dimeric and tetrameric forms in the presence of reductant. Inclusion of pentamers or higher oligomers in the SARS-2 7b model worsened the fits. Although sensitivity to reductants suggests the involvement of disulfide-linked dimers, the presence of disulfide bonds was not essential to form tetramers. A preliminary model of this association was generated with Alpha-Fold, which was exposed to a molecular dynamics simulation in presence of a model lipid membrane. However, neither of the two models provide any evident pathway for ions. To confirm this, SARS-2 p7b was studied using Planar Bilayer Electrophysiology. Addition of p7b produced occasional membrane permeabilization that is not consistent with bona fide ion channels made of a tetrameric assembly of α-helices.
Depolarization time and extracellular glutamate levels aggravate ultra-early brain injury after subarachnoid hemorrhage
Authors: Murai Satoshi , Hishikawa Tomohito , Takeda Yoshimasa , Okura Yasuko , Fushimi Miki , Kawase Hirokazu , Takahashi Yu , Kidani Naoya , Haruma Jun , Hiramatsu Masafumi , Sugiu Kenji , Morimatsu Hiroshi , Date Isao
Published: March 2022

Early brain injury after aneurysmal subarachnoid hemorrhage (SAH) worsens the neurological outcome. We hypothesize that a longer duration of depolarization and excessive release of glutamate aggravate neurological outcomes after SAH, and that brain hypothermia can accelerate repolarization and inhibit the excessive release of extracellular glutamate and subsequent neuronal damage. So, we investigated the influence of depolarization time and extracellular glutamate levels on the neurological outcome in the ultra-early phase of SAH using a rat injection model as Experiment 1 and then evaluated the efficacy of brain hypothermia targeting ultra-early brain injury as Experiment 2. Dynamic changes in membrane potentials, intracranial pressure, cerebral perfusion pressure, cerebral blood flow, and extracellular glutamate levels were observed within 30 min after SAH. A prolonged duration of depolarization correlated with peak extracellular glutamate levels, and these two factors worsened the neuronal injury. Under brain hypothermia using pharyngeal cooling after SAH, cerebral perfusion pressure in the hypothermia group recovered earlier than that in the normothermia group. Extracellular glutamate levels in the hypothermia group were significantly lower than those in the normothermia group. The early induction of brain hypothermia could facilitate faster recovery of cerebral perfusion pressure, repolarization, and the inhibition of excessive glutamate release, which would prevent ultra-early brain injury following SAH.
Diagnostic Concordance Between Multiplex PCR FilmArray® Pneumonia Panel and Culture in Patients with COVID-19 Pneumonia Admitted to Intensive Care Units: The Experience of the Third Wave in Eight Hospitals in Colombia.
Authors: Molina Francisco José , Botero Luz Elena , Isaza Juan Pablo , Cano Luz Elena , López Lucelly , Tamayo Leidy , Torres Antoni
Published: March 2022

BackgroundDetection of co-infections is important to initiate appropriate antimicrobial therapy. Molecular diagnostic testing identifies pathogens at a greater rate than conventional microbiology. We assessed both bacterial co-infections identified in culture or multiplex PCR FilmArray® Pneumonia Panel (FA-PNEU) in patients infected with SARS-CoV-2 in ICU and the concordance between these techniques.MethodsProspective study of patients with SARS-CoV-2 who were hospitalized for no more than 48 hours, in mechanical ventilation no longer than 24 hours in 8 ICUs in Medellín, Colombia. We studied mini-bronchoalveolar lavage or endotracheal aspirate samples processed in conventional culture and FA-PNEU. Co-infection was defined as the identification of a respiratory pathogen using FA-PNEU or cultures.ResultsOf 110 patients who underwent both methods, FA-PNEU and culture-positive samples comprised 24.54% vs 17.27%, respectively. 18 samples were positive for both techniques, 82 were negative, one was culture-positive with negative FA-PNEU, and 9 were FA-PNEU-positive with negative culture. The two bacteria most frequently detected by FA-PNEU were Staphylococcus aureus (37.5%) and Streptococcus agalactiae (20%) and by culture were Staphylococcus aureus (34.78%) and Klebsiella pneumoniae (26.08%). The overall concordance was 90.1% and by microorganism it was between 92.7% and 100%. Positive predictive values (PPV) were between 50% and 100%, being lower for Enterobacter cloacae and Staphylococcus aureus. Negative predictive values (NPV) were high (between 99.1% and 100%); MecA/C/MREJ had a specificity of 94.55% and a NPV of 100%.ConclusionsThe overall concordance was 90.1%, and it was between 92.7% and 100% by microorganisms. The positive qualitative agreement was between 50% and 100%, with a very high NPV.
Predictive Value of Neutrophil-To-Lymphocyte Ratio for Distant Metastasis in Gastric Cancer Patients
Authors: Zhang Xin , Wang Xuan , Li Wenxing , Sun Tuanhe , Diao Dongmei , Dang Chengxue
Published: March 2022

Purpose
We aim to investigate the clinical significance of NLR in predicting gastric cancer (GC) metastasis.
Methods
Clinical data from 1,667 consecutive GC patients were retrospectively analyzed. The cut-off was calculated from the receiver operating characteristics (ROC) curve with the maximal Youden index. Prediction probability was obtained by binary logistic regression of GC markers (CEA, CA19-9 and CA72-4) with (P1) or without NLR (P2). Diagnostic efficacy of indicators as well as prediction probability was estimated and compared by ROC analysis. Clinicopathological parameters including inflammatory markers were evaluated for distant metastasis using multiple logistic regression analysis.
Results
The optimal cut-off for NLR was 2.91 with 55% sensitivity and 73.4% specificity. P2 had significantly higher efficacy than P1 for peritoneal metastasis (P = 0.013), osseous metastasis (P = 0.017) and hepatic metastasis (P < 0.001). In multiple logistic regression analysis, age (OR: 0.68, 95% CI: 0.547–0.844), NLR (OR: 2.858, 95% CI: 2.295–3.559), CEA (OR: 2.108, 95% CI: 1.671–2.661), CA19-9 (OR: 1.844, 95% CI: 1.466–2.32), CA72-4 (OR: 2.348, 95% CI: 1.851–2.978) were found to be significantly associated with GC metastasis.
Conclusion
NLR was a risk factor of GC metastasis. Combining CEA, CA19-9, CA72-4 and NLR could better predict metastases in GC.
Short-Term Prediction of Ammonia Levels In Geese Houses Based On Combined Feature Selector and Random Forest
Authors: Huang Jiande , Guo Jianjun , Wu Huilin , Zhang Xinglong , Liu Shuangyin , Hassan Shahbaz Gul
Published: March 2022

Ammonia concentration (NH3) is a dominant source of environmental pollution in geese housing and profoundly affects the healthy growth of geese. Accurately forecasting NH3 and analyzing its change trends in geese houses is crucial for the survival of geese. To improve the prediction accuracy of NH3, we propose a novel forecasting model by the combination of feature selector (CFS) and random forest (RF). The developed model integrated two modules. First, combining mutual information (MI) and relief-F, we propose CFS quantify the importance values of each feature and eliminate the low-relation or unrelated features. Second, we built a random forest model and used the K-fold cross-validation grid search algorithm (CVGS) to obtain the RF hyper-parameters to predict NH3. The simulation results show that the prediction accuracy was improved when feature selection after quantification based on the CFS was used. The mean square error (MSE), root mean square error (RMSE) and mean absolute percent error (MAPE) for the proposed model were 0.5072, 0.6583, 2.88%, respectively. The NH3 prediction model based on CFS-GS-RF exhibited best prediction accuracy, and generalization performance compared with other parallel forecasting models and is a suitable and useful tool for predicting NH3 in geese houses.
Assessing the effect of selenium on cyclin D1 level and nuclear factor kappa b activity in NIH/3T3 fibroblast cells at 2100 MHz electromagnetic field exposure
Authors: Ergun Dilek Duzgun , Ozsobaci Nural Pastaci , Yilmaz Tuba , Ozcelik Dervis , Kalkan Mustafa Tunaya
Published: March 2022

Purpose: Although there are various studies on the biological effects of the 2100 MHz electromagnetic field (EMF), which is among the mobile phone frequencies, there are conflicting results in the literature on this subject. Materials and Methods: The present study was designed to assess the effect of 200 nM selenium (Se) on cell viability% [trypan blue], cell cycle biomarker [cyclin D1] and the transcription factor [nuclear factor kappa b (NF-κB)] in NIH/3T3 fibroblast cells exposed to 2100 MHz mobile phone frequency. Cells were divided to following groups: Control, sham control, 2100 MHz EMF, and 200 nM Se + 2100 MHz EMF for 2 h. And we measurement cell viability%, cyclin D1 level and NF-κB activity. Results and Conclusions: While of cell viability% decreased in 2100 MHz EMF group compared to control group, cell viability% increased in 200 nM Se + 2100 MHz EMF group compared to 2100 MHz EMF. It was also shown that while cyclin D1 level and NF-κB activity increased significantly in the 2100 MHz EMF group compared to the control group, the same parameters decreased in the 200 nM Se + 2100 MHz EMF group compared to the 2100 MHz EMF group. Although future studies will be required to investigate the biological effects of EMF emitted by mobile phones, our results provide insight into the molecular mechanisms underlying selenium's protective function and efficacy against 2100 MHz EMF exposure.
RBM47 is a Critical Regulator of Mouse Embryonic Stem Cell Differentiation
Authors: Shivalingappa Pavan Kumar Mysuru , Singh Divya Kumari , Sharma Vaishali , Arora Vivek , Shiras Anjali , Bapat Sharmila
Published: March 2022

RNA-binding proteins (RBPs) are pivotal for regulating gene expression as they are involved in each step of RNA metabolism. Several RBPs are essential for viable growth and development in mammals. RNA-binding motif 47 (RBM47) is an RRM-containing RBP whose role in mammalian embryonic development is poorly understood, yet deemed to be essential since its loss in mouse embryos leads to perinatal lethality. In this study, we attempted to elucidate the significance of RBM47 cell-fate decisions of mouse embryonic stem cells (mESCs). Downregulation of Rbm47 did not affect mESC maintenance and the cell cycle but perturbed the expression of primitive endoderm (PrE) markers. The PrE misregulation, however, could be reversed by either FGFR or MEK inhibitor suggesting an implication of RBM47 in regulating FGF-ERK signaling. Further, lineage-specific differentiation experiments revealed that Rbm47 is essential for neuroectodermal and endodermal differentiation. Taken together, our study thereby assigns a hitherto unknown role(s) to RBM47 in a subtle regulation of mESC differentiation.
Impact of COVID-19 on University Students’ Quality of life and mental health in Greece: A Cross-sectional study
Authors: Tsami Faidra Foteini , Kanellopoulou Aimilia , Alexopoulou-Prounia Loukia , Tsapara Aggeliki , Katsadoros Kiriakos , Alexopoulos Panos , Vantarakis Apostolos
Published: March 2022

COVID-19 pandemic has highlighted an increasing deterioration of university students’ quality of life and mental health. We conducted a cross-sectional study using an online interview survey on students at public universities in Greece to better understand the effects of the pandemic on their quality of life and mental health. Three tools were used (WHOQOL-BREF, IES-R, and HADS).1.266 university students from public Greek Universities participated in the study. We observed that 55,8% had a score lower than 50 in the psychological domain and 52,3% in the social domain of WHOQOL-BREF. Additionally, 46.6% of the respondents had a score of 37+ on the IES-R questionnaire, 45% of the respondents had abnormal results regarding anxiety and 33.6% had abnormal results regarding depression on the HADS questionnaire. Due to the long duration of the pandemic and measures such as lockdown and stay-at-home orders, the COVID-19 pandemic brings negative impacts on the quality of life and wellbeing of students. The findings of our study highlight the urgent need to develop interventions and strategies to address the quality of life and mental health consequences of university students.
The treatment of Qibai Pingfei Capsule on chronic obstructive pulmonary disease may be mediated by Th17 / Treg balance and gut-lung axis microbiota
Authors: Jia Yu , He Tiantian , Wu Di , Tong Jiabing , Zhu Jie , Li Zegeng , Dong Jingcheng
Published: March 2022

Background: Chronic obstructive pulmonary disease (COPD), a prevalent, progressive respiratory disease, has become the third leading cause of death globally. Increasing evidence suggests that intestinal and pulmonary microbiota dysbiosis is associated with COPD. Researchers have shown that T helper (Th) 17/regulatory T (Treg) imbalance is involved in COPD. Qibai Pingfei Capsule (QBPF) is a traditional Chinese medicine used to treat COPD clinically in China. However, the effects of QBPF intervention on the Th17/Treg balance and microbiota in the gut and lung are still poorly understood. Methods: This study divided the rats into three groups (n=8): control, model, and QBPF group. After establishing the model of COPD for four weeks and administration of QBPF for two weeks, Th17 cells, Treg cells, their associated cytokines, transcription factors, and intestinal and pulmonary microbiota of rats were analyzed. Furthermore, the correlations between intestinal and pulmonary microbiota and between bacterial genera and pulmonary function and immune function were measured. Results: The results revealed that QBPF could improve pulmonary function and contribute to the new balance of Th17/Treg in COPD rats. Meanwhile, QBPF treatment could regulate the composition of intestinal and pulmonary microbiota and improve community structure in COPD rats, suppressing the relative abundance of Coprococcus_2 , Prevotella_9 , and Blautia in the gut and Mycoplasma in the lung, but accumulating the relative abundance of Prevotellaceae_UCG_003 in the gut and Rikenellaceae_RC9_gut_group in the lung. Additionally, gut–lung axis was confirmed by the significant correlations between the intestinal and pulmonary microbiota. Functional analysis of microbiota showed amino acid metabolism was altered in COPD rats in the gut and lung. Spearman correlation analysis further enriched the relationship between the microbiota in the gut and lung and pulmonary function and immune function in COPD model rats. Conclusions: Our study indicated that the therapeutic effects of QBPF may be achieved by maintaining the immune cell balance and regulating the gut-lung axis microbiota, providing references to explore the potential biomarkers of COPD and the possible mechanism of QBPF to treat COPD.
Comparison the clinical efficacy and quality of life between uncut Roux-en-Y and Billroth II with Braun anastomosis in laparoscopic distal gastrectomy for gastric cancer patients
Authors: Gao Sen , Zhang Yunfeng , Bao Wenzhong , Tang Dawei , Yang Renbao , LI liang
Published: March 2022

Purpose:To compare the clinical efficacy and quality of life between uncut Roux-en-Y and Billroth II with Braun anastomosis in laparoscopic distal gastrectomy for gastric cancer patients. Method:A retrospective cohort study was performed. clinical data of 200 patients whounderwent laparoscopic distal gastrectomy at the Department of Gastrointestinal Surgery of the Second People's Hospital of Hefei from January 2018 to January 2021 were collected. Of the 200 patients,100 underwent uncut Roux-en-Y anastomosis and 100 underwent Billroth II with Braun anastomosis. The general data, intraoperative and postoperative conditions, complications, and endoscopic evaluation 1-year postoperative were compared. Besides, the quality of life of two groups was also compared using the Chinese version of the European Organization For Research and Treatment of Cancer (EORTC) quality of life questionnaire-Core 30 (QLQ-C30) and quality of life questionnaire-stomach 22 (QLQ -STO22).Results: There were no significant differences in characteristics between the two groups ( P>0.05). All the 200 patients successfully underwent laparoscopic distal gastrectomy without intraoperative complications, conversion to open surgery or perioperative death. There were no significant differences between two groups in operative time, intraoperative blood loss, postoperative complications, time to flatus,time to liquid diet and postoperative hospital stay (P>0.05). Endoscopic evaluation was conducted 1-year postoperative .Compared to Billroth II with Braun group, the uncut Roux-en-Y group had a significantly lower incidences of gastric stasis [(18.6%,16/86) vs. (32.8%,27/82), χ2 =3.76, P=0.042], gastritis [11.6% (10/86) vs.30.5% (25/82), χ2=9.053, P=0.003] and bile reflux [1.2% (1/86) vs. 25.6% (21/82), χ2=22.044, P<0.001], and the differences were statistically significant. The EORTC questionnaire was performed 1-year postoperative, there were no significant differences in the scores of QLQ-C30 scale between the two groups (P>0.05), while the scores of QLQ-STO22 compared to the Billroth II with Braun group, the uncut Roux-en-Y group had a lower pain score (median:8.3 vs 16.7, P=0.029) and reflux score (median: 0 vs5.6, P=0.012), and the differences were statistically significant (P<0.05), indicating milder symptoms. Conclusion: Both the two anastomosis are safe and reliable in laparoscopic distal gastrectomy for gastric cancer , compare to the Billroth II with Braun anastomosis , the uncut Roux-en-Y anastomosis can reduce the incidences of gastric stasis, gastritis and bile reflux, and improve the quality of life
Immersive ultraviolet disinfection of E. coli and MS2 phage on woven cotton textiles
Authors: MacIsaac Sean , Mullin Toni J , Munoz Sebastian , Ontiveros C. Carolina , Gagnon Graham A.
Published: March 2022

Immersive ultraviolet disinfection provides a chemical-free technology for safer textiles, surfaces, and public spaces by inactivating communicable pathogens. This study examined immersive UV disinfection, using a disinfection cabinet, of E. coli and MS2 that was inoculated on white cotton T-shirts. The impact that porous materials have on UV disinfection is poorly understood with the majority of previous surface disinfection research focusing on hard, smooth surfaces. Several approaches were used in this study to characterize the light dynamics within the disinfection cabinet including colorimetric dosimetry coupons, biodosimetry, and spectroradiometry. Micro and macro geometry of porous surfaces are important factors to consider when using immersive UV technologies. Physical shading of emitted UV light within the disinfection cabinet and physical properties of a porous material, such as the woven pattern of cotton, both contribute to UV disinfection efficiency. This work identified that light distribution is crucial for immersive UV technologies as areas of T-shirts which were misaligned with UV lamp illuminance were not adequately disinfected. Other inoculated areas achieved upwards of 1-log reductions values for MS2 and upwards of 2-log reductions for E. coli.
Infectious diseases in rising riding-horse and donkey milk industry: First detection of Neospora sp. antibodies in donkeys in Turkey
Authors: Baydar Ersoy , Aydogdu Ugur , Utuk Armagan Erdem , Kaya Feyyaz , Timurkan Ozkan , Erol Ufuk , Babur Cahit
Published: March 2022

The present study was aimed to investigate the prevalence of some protozoa (B. caballi, T. equi, T. gondii, Neospora sp.) and viral agents (equine influenza, equine viral arteritis, equine herpesviruses) of equids in Balikesir and its surroundings, in Turkey. Plasma and serum samples were collected from 66 horses and 96 donkeys. Babesia caballi, T. equi, Neospora sp. antibodies were detected with c-ELISA while T. gondii antibodies with the Sabin Feldman Dye test. Viral agents were detected by using the PCR technique. The prevalence rates of the protozoa in horses were 12.12% for B. caballi, 34.84% for T. equi, 9.09% for T. gondii, and 10.6% for Neospora sp. respectively. The molecular prevalence of the viral agents was detected as 3.03% for equine influenza virus, and 6.06% for equine herpesvirus 5. Equine viral arteritis virus and other herpesviruses (1,2 and 4) were not detected (0%) in any of the samples. However, the rates of seropositivities in donkeys were B. caballi 1.69%, T. equi 71.87%, T. gondii 90.62%, Neospora sp. 23.95%, equine influenza virus 1.04%, equine viral arteritis virus 0%, equine herpesvirus-5 3.12%, and other herpesviruses 0%. The results indicated that T. equi was more prevalent than B. caballi in both species. This study is important about being is the first study in Turkey that reported the existence of anti-Neospora sp. antibodies in donkeys, and the seroprevalence of T. gondii west side of the country in horses and donkeys.
Exploring Alternative Financing Models and Early Access Schemes for Orphan Drugs: a Belgian Case Study
Authors: Abdallah Khadidja , Claes Kathleen , Huys Isabelle , Follon Lennert , Calis Charlotte , Simoens Steven
Published: March 2022

Background: Although some countries have made specific adjustments in their healthcare system to accommodate often-expensive orphan drugs, availability of these orphan drugs is still not evident. This study investigates alternative financing models and early access schemes for orphan drugs in the context of the Belgian healthcare system. Methods: Three focus group discussions were held with a panel of eleven experts from the Belgian Drug Reimbursement Committee, the Colleges for Orphan Drugs, the pharmaceutical industry, physicians, ethicists and pharmacists. Retrieved data were pseudonymised, analysed and coded according to the Qualitative Analysis Guide of Leuven.Results: Experts disfavoured an insulated orphan drug fund as well as private insurance, as isolation of a separate budget and a mostly profit-driven mechanism, respectively, would contradict the Belgian fundamental principle of solidarity. Moreover, an insulated fund could potentially reproduce the same budgetary constraints as the general reimbursement system albeit on a smaller scale. As the Special Solidarity Fund is intended for urgent care and exclusively accommodates eligible to the criteria, its design would not allow general financing of orphan drugs. Overall, implementation of an alternative financing model was not endorsed, instead, suggestions to improve the current reimbursement system were preferred; increased collaboration and transparency, robust and quality real-world evidence but also digitalization of data were elements mentioned. Alleviating administrative burden and simplifying the admission process for compassionate use program/medical need program and early treatment reimbursement should be prioritized to facilitate early access. Furthermore, a legal framework for off-label use could stimulate proper adoption. Efforts on collaboration of expertise centres and coordination of orphan drug databases across Europe could foster a robust data network to support orphan drug availability in individual countries. Conclusions: This research reveals that reassessing current financing models and early access schemes by eliminating inadequacies, may be more conducive than establishing alternative systems to increase availability of orphan drugs in Belgium. Other jurisdictions may rely on this information to review their own models of early access and financing and cultivate a more sustainable delivery of orphan drugs.
Urine CD163 is a Promising Biomarker for the Diagnosis and Evaluation of Lupus Nephritis
Authors: Huang Yun Ju , Lin Chiung-Hung , Huang-Yu Yang , Luo Shue-Fen , Kuo Chang-Fu
Published: March 2022

Objectives
Urine soluble CD163 (usCD163) is released from alternatively activated macrophages involved in the resolution of inflammation in glomeruli, and plays an important role in glomerulonephritis. This study explored the role of usCD163 in patients with systemic lupus erythematosus (SLE).
Methods
usCD163 concentrations were measured cross-sectionally in 261 SLE patients. Clinical and laboratory data were collected, and SLE disease activity scores were calculated to assess the correlation with usCD163.
Results
SLE patients with high usCD163 levels tended to be younger, with a higher hospital admission rate, higher prednisolone dose, lower estimated glomerular filtration rate, higher urine protein creatinine ratio (UPCR), more pyuria and hematuria, higher levels of inflammatory markers, higher rates of anemia, neutropenia, and lymphopenia, lower complement 3 (C3) levels, higher anti-double stranded DNA antibody (anti-dsDNA Ab) levels, and higher disease activity scores (p < 0.05). usCD163 levels were significantly higher in patients with active lupus nephritis (LN) than in those with extrarenal or inactive SLE, and correlated with UPCR, disease activity, and anti-dsDNA Ab levels. SLE patients with high usCD163 levels tended to have a higher chronic kidney disease stage.
Conclusion
The usCD163 level correlates with the severity of LN and disease activity in renal SLE.
Association of hemoglobin levels with bone mineral density in the thoracic and lumbar spine for adults over 18 years of age: a cross-sectional study
Authors: Liu En Qi , Hou Xin Zheng , Liu Si Qi , Han Jing , Lv Hao
Published: March 2022

Aim:The overall object of this study is to find out the association between hemoglobin (HGB) and bone mineral density (BMD) in the lumbar and thoracic spine among adults over the age of 18.Methods:The current cross-sectional study used the non-institutionalised US population from the National Health and Nutrition Survey (NHANES) as the sample source. A multiple linear regression model and smoothed curve fitting were used to show the assessment of the relationship between hemoglobin and bone mineral density in the lumbar and thoracic spine, with analysis of subgroups according to gender and race.Results:After accounting for relevant confounders, HGB was negatively associated with bone mineral density in multiple regression models. In subgroup analyses stratified by sex or race, however, the relationship between HGB and thoracic spine BMD was only found in women and Mexican-Americans, and the association with lumbar spine BMD was present in males and females, Mexican-American and Non-Hispanic White. Among participants in other races and those whose race was not reported, the relationship between HGB with BMD in the lumbar spine and the thoracic spine showed an inverted U-shaped curve (turning point: HGB 11.9 g/dL).Conclusion: HGB was negatively associated with BMD in the lumbar spine and BMD in the thoracic spine. However, this significant correlation varies by gender and race.
Full-length ITS Amplicon Sequencing of Feline Gut Mycobiome of Malaysian Local Breeds Using Nanopore Flongle
Authors: Tay Darren Dean , Siew Shing Wei , Kamal Shamrulazhar Shamzir , Razali Mohd Najib , Ahmad Hajar Fauzan
Published: March 2022

The gut mycobiome exhibits major influence on the gastrointestinal health and disease but received less attention due to low abundance. This study characterises the fungal community and compares the microbial diversity between indoor and outdoor cats. Genomic DNA was extracted and sequenced by targeting the full-length internal transcribed spacer (ITS) region using Flongle flow cell on MinION™ sequencing platform. Results show the Ascomycota and Peniophorella were numerous in indoor cats, whereas the Basidiomycota and Pichia were abundant in outdoor cats. Peniophorella formed the core mycobiome in both feline populations. Furthermore, alpha (p-value = 0.0207) and beta diversities results (p-value = 0.009) showed significant differences between the two groups. Overall, indoor cats have greater amounts of Peniophorella, whereas outdoor cats have higher Trichosporon and unclassified Sordariaceae. The study also suggests that keeping a cat indoors or left as a stray will affect their respective gut mycobiome.