bluuebunny/crossref_metadata_2025_split huggingface dataset:
Escherichia coli cells are primed for survival before lethal antibiotic stress
Authors: Hossain Tahmina , Singh Abhyudai , Butzin Nicholas 
Published: December 2022

Abstract
Non-genetic factors can cause significant fluctuations in gene expression levels. Regardless of growing in a stable environment, this fluctuation leads to cell-to-cell variability in an isogenic population. This phenotypic heterogeneity allows a tiny subset of bacterial cells in a population, referred to as persister cells, to tolerate long-term lethal antibiotic effects by entering into a non-dividing, metabolically altered state. One fundamental question is whether this heterogeneous persister population is due to a pre-existing genetic mutation or a result of a transiently-primed reversible cell state. To explore this, we tested clonal populations starting from a single cell using a modified Luria–Delbrück fluctuation test. Through we kept the conditions the same, the diversity in persistence level among clones was relatively consistent: varying from ~ 60–100 and ~ 40–70 fold for ampicillin (Amp) and apramycin (Apr), respectively. Then we divided and diluted each clone to observe whether the same clone had comparable persister levels for more than one generation. Replicates had similar persister levels even when clones were divided, diluted by 1:20, and allowed to grow for ~ 5 generations. This result explicitly shows a cellular memory passed on for generations and eventually lost when cells are diluted to 1:100 and regrown (> 7 generations). Our result demonstrates 1) the existence of a small population prepared for stress ("primed cells") resulting in higher persister numbers, 2) the primed memory state is reproducible and transient, passed down for generations but eventually lost, and 3) a heterogeneous persister population is a result of a transiently-primed reversible cell state and not due to a pre-existing genetic mutation.
Virtual Screening–Molecular Docking–Activity Evaluation of Ailanthus altissima (Mill.) Swingle Bark in the Treatment of Ulcerative Colitis
Authors: Ma Shanbo , Liu Lun , Li Xiang , Xie Yan-hua , Shi Xiao-peng , Wang Si-wang 
Published: December 2022

Abstract
Background:The dried bark of Ailanthus altissima (Mill.) Swingle(BAA),which is a traditional Chinese medicine,is widely used in Chinese folklore for the treatment of ulcerative colitis.Consequently, the objective of this study was to explore the therapeutic basis of BAA for the treatment of ulcerative colitis (UC) based on Virtual Screening–Molecular Docking–Activity Evaluation technology.
Methods:By searching the Traditional Chinese Medicine (TCM) Systems Pharmacology (TCMSP) Database and Analysis Platform, 89 compounds from the chemical components of BAA were obtained. Then, after preliminarily screening the compounds based on Lipinski’s rule of five and other relevant conditions, the AutoDock Vina molecular docking software was used to evaluate the affinity of the compounds to UC-related target proteins and their binding modes by scoring function to identify the best candidate compounds.Additionally,Further verification of the compound's properties was achieved through in vitro experiments.
Results: Twenty-two compounds obtained from the secondary screening were molecularly docked with UC-related target proteins (IL-1R, TLR, EGFR, TGFR, and Wnt) using AutoDock Vina. The free energy of the highest scoring compounds binding to the active cavity of human IL-1R, TLR, EGFR, TGFR, and Wnt proteins was −8.7, −8.0, −9.2, −7.7, and −8.5 kcal/mol, respectively. Potential compounds, dehydrocrebanine, ailanthone, and kaempferol, were obtained by scoring function and docking mode analysis. Furthermore, the potential compound ailanthone (1, 3, and 10 μM) was found to have no significant effect on cell proliferation, while ailanthone (10 μM) reduced the level of proinflammatory factors caused by lipopolysaccharide (LPS).
Conclusion:Among the active components of BAA, ailanthone plays a major role in its anti-inflammatory properties . The present study shows that ailanthone has advantages in cell proliferation and inhibition of inflammation, but further animal research is needed to confirm the pharmaceutical potential thereof in the future.
Clinical profile of strabismus at University of Gondar Tertiary Eye Care and Training Center-North West Ethiopia: A cross sectional study
Authors: Moges Solomon Tekewe , Ayele Fisseha Admassu , Dawud Teshager Wondale 
Published: December 2022

Abstract
Background: Strabismus has been defined as an intermittent or constant misalignment of the visual axes. Several studies have reported that strabismus affects about 1-6 % of the population across the world. This study aimed to assess the clinical profile of strabismus patients at the University of Gondar (UOG) tertiary eye care and training center.
Material and Methods: A hospital-based cross-sectional study was conducted from April to October 2021 on all consecutive strabismus patients attending at UOG tertiary eye care and training center. Interviewer-administered questionnaires and clinical examinations were performed by residents and pediatric ophthalmologist for data collection.
Results: A total of 258 strabismus patients with a median age of 8 (SD ±17.64) years old were enrolled in this study of whom 60.1% were esotropia (ET) and 32.6% were exotropia (XT). Accommodative-ET (AET) 46 (17.8%), constant type of XT 38 (14.7%), infantile ET 36 (14.0%) and acquired non-AET 34 (13.3%) were common sub-variants of strabismus. Having inferior oblique over action IOOA (AOR=7.6: 95% CI: 2.77 - 20.83) and being hyperopic in the left eye (AOR=8: 95% CI: 2.55-25) were significant factors associated with ET.
Conclusion: Esotropia was the most common type of deviation accounting for more than half of the strabismus patients. Having IOOA and being hyperopic on the left eye were significant factors associated with ET.
Toosendanin induces apoptosis in Oral Squamous Cell Carcinoma cells through inhibition of p-STAT3 and inhibits tumor growth in a OSCC-PDX model
Authors: Wu Ye , He Shaohai , Wang Tao , Chen Lingling , Zheng Dali , Lin Lisong 
Published: December 2022

Abstract
BACKGROUND
Toosendanin (TSN) has been found to inhibit the proliferation of different types of tumor cell lines. However, there is no data on the role of TSN in oral squamous cell carcinoma (OSCC). The purpose of this study was to evaluate the effects of TSN on OSCC cells in vitro, and to verify its effects on oral squamous cell carcinoma in vivo in a patient-derived xenograft (PDX) model.
METHODS
The effect of TSN on OSCC cells was investigated by cytotoxicity assays and flow cytometry. The expression of proteins was detected by Western blotting. An OSCC PDX model was constructed to further study the role of TSN in regulating the function of oral squamous cell carcinoma.
RESULTS
The cell viability of CAL-27 and HN-6 cells decreased gradually when the concentration of TSN increased from 0.025µM and 0.05µM to 0.1µM, and the apoptosis rate increased. Compared with the control group, the cytotoxic effect of TSN on CAL-27 and HN-6 cells was enhanced in a dose-dependent manner, and it could inhibit proliferation and induce apoptosis at lower doses. TSN can also induce apoptosis by inducing cell cycle arrest and regulating the expression of proteins such as STAT3. After successfully constructing an OSCC-PDX model with high pathological homology to the primary tumor and treated with intraperitoneal injection of TSN, The results showed that TSN could significantly reduce the tumor size of PDX model mice without obvious toxicity.
CONCLUSIONS
The in vivo experiments showed that TSN has a significant inhibitory effect on tumor growth, suggesting that it may be a promising drug for the treatment of oral squamous cell carcinoma. TSN may be an effective potential anticancer drug for the treatment of oral squamous cell carcinoma.
Identification of mitophagy-associated proteins (MAPs) profile as potential plasma biomarkers of idiopathic Parkinson’s disease
Authors: Wang Wen-Wen , He Hai-Jun , Xiong Xi , Qian Shuangjie , Ye Qianqian , Feng Feifei , Zhou Shuoting , Xie Chenglong 
Published: December 2022

Abstract
It is noteworthy that despite many efforts to screen biochemical plasma markers for PD diagnosis, there is still not an accepted and validated surrogate biomarker. To decipher the role of the mitophagy-associated proteins (MAPs) in idiopathic PD subjects and investigate whether the diagnosis is related to MAP levels and whether the levels predict motor and cognitive progression. This prospective study totally enrolled 150 PD patients. 71 age-matched controls (CN) alongside 41 PDs in two cohorts: modeling cohort (cohort 1), including 121 PD, 52 CN, and 29 PDs; validated cohort (cohort 2), including 29 PD, 19 CN, and 12 PDs. The MAPs (PINK1, Parkin, PGAM5, BNIP3, and p-TBK1) and a-synuclein-related proteins (ASPs: total a-synuclein, phosphorylated a-synuclein, and a-synuclein oligomer) levels were measured using an electrochemiluminescence immunoassay. MAPs are elevated in the plasma of PD patients. The PINK1, Parkin, and PGAM5 displayed the top three measurable increase trends in amplitude compared to BNIP3 and p-TBK1. Moreover, the AUCs of PINK1, PGAM5, and Parkin were ranked the top three MAP candidates in diagnosis accuracy for PD from CN, but the MAPs hard to differentiate the PD from PDs. In addition, Plasma PINK1 positively correlated with total UPDRS, UPDRS part III, and H-Y stage, with no significant correlations with HAMA, HAMD, and RBD scores. As expected, higher plasma PINK1-Parkin levels and prominent diagnostic accuracy in A-synuclein (+) subjects than in A-synuclein (-) subjects. These results uncover that plasma MAPs (PINK1, Parkin, and PGAM5) may be potentially useful target biomarkers for PD diagnosis. Studies on larger cohorts would be required to test whether elevated plasma MAP levels are related to PD risk or prediction.
Genetic characteristics and phylogenetic analysis of Leishmania infecting sandflies and humans based on the kDNA and ITS2 gene dataset in the new focus of Cutaneous Leishmaniasis in Shiraz, south of Iran
Authors: shahabi saeed , Sarkari Bahador , Dabaghmanesh Sorna , Asgari Qasem , Azizi Kourosh 
Published: December 2022

Abstract
Objective
Cutaneous leishmaniasis is a neglected tropical disease with an incidence of one million people annually worldwide. Iran has many important fuci for this disease which Leishmania major and L. tropica cause. However, this study aimed to investigate Zoonotic and environmental factors in the spread of leishmaniasis in the city of Shiraz, southern Iran with a phylogenetic inference of Leishmania by examining the infection of patients and vectors with Leishmania parasite based on molecular datasets of kDNA and ITS2 genes.
Methods
Sand flies were caught using sticky paper traps indoors (bedrooms, bathrooms, storage rooms, etc.) and outdoors. Twenty samples of human lesions were also examined. Leishmania infection was evaluated by PCR of kinetoplast (k) DNA. Subsequently, parasite species identification was confirmed by PCR and DNA sequencing of the 18S ribosomal RNA internal transcribed spacer two (ITS2) gene.
Results
All Phylogenetic reconstruction based on Bayesian, UPGMA, and Neighbor-Joining methods revealed sequences of Leishmania parasites infecting patients and sand-fly species were clustered into two main monophyletic clades of L. major and L. tropica. The overall infection rate of sand flies (pools) with Leishmania DNA was 72.5%, and the Mean diversity within L. major clade was 0.01.
Conclusions
A new focus on ACL and ZCL is reported in the tourist city of Shiraz. Human interference in the environment, such as habitat destruction, housing in orchards and foothills, and other health factors, have caused the emergence of both diseases in this area which need to be considered for a survival health program.
A treatment-refractory and aggressive MDS-MLD with multiple highly complex chromosome 5 intrachromosomal rearrangements: a case report
Authors: Sasi Ramakrishnan , Senft Jamie , Spruill Michelle , Barua Subit , Dougaparsad Sam , Vos Jeffrey A. , Perrotta Peter L. 
Published: December 2022

Abstract
Background
A patient with a myelodysplastic neoplasm exhibited a karyotype with multiple complex chromosome 5 rearrangements. This patient appeared to have a catastrophic cytogenetic event that manifested as a treatment-refractory aggressive form of disease, which lead to patient demise within one year. Both the clinical presentation and disease course were unusual based on the medical history and morphologic findings. Such cases of Myelodysplastic Syndrome with Multilineage Dysplasia (MDS-MLD) with complex abnormalities are not reported in the literature.
Case presentation
The patient was a 62-year-old female who presented with pancytopenia and dyspnea. The morphologic appearance of the peripheral blood smear and bone marrow biopsy, along with flow cytometric findings, favored the diagnosis of MDS-MLD unclassifiable. Myelodysplastic syndrome (MDS) with multilineage dysplasia (MDS-MLD), is an MDS characterized by one or more cytopenias and dysplastic changes in two or more of the myeloid lineages (i.e., erythroid, granulocytic, and megakaryocytic). The bone marrow, in particular, showed prominent dysplasia, including the presence of atypical megakaryocytes with small hypolobated morphology reminiscent of those typically seen in MDS with isolated 5q deletion. Cytogenetic analysis, including interphase and metaphase FISH, karyotype and SNP chromosomal microarray were performed, as well as DNA sequencing studies. Cytogenetic analysis showed a very complex karyotype featuring multiple 5q intrachromosomal rearrangements including a pericentric inversion with multiple interspersed deletions and monosomy 7. FISH studies showed a partial deletion of the PDGFRβ gene, and SNP chromosomal microarray and targeted panel-based sequencing identified biallelic loss of function of the TP53 gene. Based on the pathologic findings, the patient was treated for MDS but did not respond to either lenalidomide or azacitidine.
Conclusion
The genetic changes described, in particular, the complex intrachromosomal rearrangements of chromosome 5, suggest the occurrence of a sudden catastrophic event that led to an aggressive course in the patient’s disease. Conventional karyotyping, metaphase and interphase FISH, SNP chromosomal microarray and NGS helped to identify the complex genetic changes seen in this case. This highlights the importance of utilizing a multimodality approach to fully characterize complex chromosomal events that may significantly impact disease progression, treatment and survival.
A new prognostic model related to tumor microenvironment in colon adenocarcinoma
Authors: Yuan Jianxu , Jiang Qing , Wang Jiawu , Hua Zhengzhao , Yu Shengjie 
Published: December 2022

Abstract
Background: Researches have shown that tumor microenvironment (TME) can regulate the proliferation and metastasis of solid tumors, and has an important impact on the immunotherapy of solid tumors. Based on the transcriptome data of colon adenocarcinoma (COAD), we studied the prognostic role of TME related genes, established and verified the prognostic model of TME related signatures.
Methods: We Obtained relevant data from TCGA (the Cancer Genome Atlas) to calculate TME related genes which expressed differentially in distinct tissues. Then, we employed NMF (nonnegative matrix factorization) clustering method to get different clusters. Univariate Cox regression and Lasso regression analysis were used to screen genes with prognostic significance, the prognosis model and corresponding nomogram were completed according to the risk genes. Finally, the ROC (Receiver operating characteristic) and the DCA (Decision curve analysis) curves were used for internal and external verification.
Results: Our research obtained a gene panel consisting of 15 TME related genes (FOXD1, FSCN1, PRAME, SOX12, ATP6V1C2, EPHB4, CD36, BANK1, NOL3, DPP7, FAM24B, AEN, CCNF, PSRC1 and F2RL2). The established model clearly showed the survival time of patients in different risk groups based on the former genes. Kaplan Meier survival analysis showed that the survival time of high-risk group was significantly shorter than that of low-risk group. The ROC curve’s value of AUC with this prognostic signature was basically over 0.65. In addition, we further validated the model with GSE39582 from GEO (the Gene Expression Omnibus) database. Univariate analysis and multivariate Cox regression analysis proved that the risk score we established in this study was an independent risk factor affecting the prognosis of COAD patients.
Conclusion: The signature set we established could more accurately and effectively evaluate the prognosis of colon cancer patients. And the analysis of TME could also provide new opportunities for the diagnosis, treatment and prognosis of patients with COAD.
A Lagrange-type interpolation method nearly free of oscillations
Authors: Ysern Bernardo de la Calle , Sastre Pedro Galán del 
Published: December 2022

Abstract
This work is concerned with the interpolation of a function f when using a low number of interpolation points, as required by several schemes intended to solve PDEs numerically. The function f is assumed to have a jump or a steep derivative, and our goal is to minimize the oscillations produced by the Gibbs phenomenon while preserving the approximation properties for smoother functions. This is achieved by interpolating the transform ḟˆ=g ᴼf using Lagrange polynomials, where g is a rational transformation chosen by minimizing a suitable functional depending on the values of f. The mapping g is monotonic and constructed to posses boundary layers that remove the Gibbs phenomenon. No previous knowledge of the location of the jump is required. The extension to functions of several variables is straightforward, of which we provide several examples.
MSC Classification: 65D05 , 65D15
The potential role of microRNA-155 in Neurodegenerative diseases with a focus on Alzheimer's disease
Authors: Rasmi Yousef , Shokati Ameneh , Rahimi Atefeh , Aziz Shiva Golizadeh-Ghaleh , Farnamian Yeganeh , Hassan Amber , Alipour Shahriar 
Published: December 2022

Abstract
Neurodegenerative diseases (NDD) are caused by the destruction of nerve cells in the central nervous system and are severely debilitating. The incidence of NDDs increases, and they are expected to become more prevalent with life expectancy. Depending on the number of neurons involved, there are various types of NDDs, and one of the most common NDDs is Alzheimer's disease (AD). Due to the lack of treatment, NDDs had become a significant neurobiology challenge. Therefore, identifying accurate, early, and non-invasive biomarkers of NDDs, are an unmet challenge. The growing importance of microRNAs (miRNAs) in biology has led scientists to investigate their potential relevance to neurodegeneration to identify novel therapeutic targets. Recent discoveries have found the role of miRNAs in many model organisms during aging and have revealed potential miRNA biomarkers of NDDs. Among the various miRNAs, the data confirm that miR-155 as so-called inflamma-miR, a potent activator of inflammation, is the fundamental miR in the pathogenesis of autoimmune diseases because it influences myeloid cell polarization to a phenotypic and functional proinflammatory form. miR-155 dysregulation also plays an essential role in many human cancers, hematological malignancies, and responses to viral infections. Here, we discuss this new field of miR-155 related to NDDs, focusing on AD and prospects.
577 nm yellow laser source using external pumping
Authors: Chayran Great , Jambunathan Venkatesan , Smrz Martin , Mocek Tomas 
Published: December 2022

Abstract
We demonstrated a 577 nm yellow laser source with a proper combination of Raman medium and frequency doubling medium, pumped externally. Cryogenic Yb:YAG oscillator acts as an external pump source and it generates 1.2 mJ energy at 1KHz emitting around 1029 nm. Using Raman resonator with Ba(NO3)2 as Raman medium, SRS around 1153.4 was generated. Finally, 577 nm yellow laser was generated using the frequency doubling medium LBO. A maximum average output power of 65 mW with a pulse duration of 18 ns at 1 KHz was achieved.
Congenital Diaphragmatic Hernia, Predictors of Survival and Adverse Outcomes
Authors: Aljuaid Nemer , Ghahmdi Nawaf Al , ALI KAMAL , Ghazwani Abadi , Alshreedah Saad , Alsaif Abdurhman , Alsaif Saif , Ali Kamal 
Published: December 2022

Abstract
Objective: To examine prenatal and postnatal predictors of survival in infants with Congenital Diaphragmatic Hernia (CDH).
Method: Six- years retrospective review of all cases of CDH born at King Abdulaziz Medical City , Riyadh, Kingdom of Saudi Arabia .
Results: Twenty-seven infants (67.5%) survived to discharge. Non-survivors had a higher best , mean and highest OI (P<0.001) in day 1 compared to survivors. Best (AUC = 0.917), mean (AUC=0.945) and highest (AUC=0.923) OI in day 1 were all highly predictive of mortality.
There was a significant correlation between the preoperative OI and time to surgery (TTS) (rS =0.462, P=0.017) and the length of hospital stay (LOS) (rS =0.458, P=0.019). Mean day 1 OI had a significant correlation with the duration of ventilation (DOV) (rS =0.549, P=0.004) and the TTS (rS =0.526, P=0.007) and the LOS (rS =0.497, P=0.012). Best and highest day 1 OI also correlated significantly with DOV, TTS and LOS.
Conclusion: Our CDH survival rates of 67.5% are comparable to those of other international studies despite the lack of ECMO utilization and antenatal interventions. First day oxygenation indices were excellent predictors of survival and have a significant correlation with the DOV, LOS and TTS in infants with CDH.
Privatization, Mixed Duopoly and Quality Differentiation with Excess Burden
Authors: Choi Kangsik 
Published: December 2022

Abstract
Incorporating the excess burden of taxation into a mixed duopoly to evaluate privatization, we analyze competition of the public and private firms producing goods of different qualities between Cournot and Bertrand competition. When the only private firm offers a high quality, (i) under both Bertrand and Cournot competition, it is desirable to choose privatization if the the excess burden of taxation is sufficiently large, and vice versa; however, (ii) if the excess burden of taxation is intermediate, it is desirable to choose reversely with regard to the policy of privatization between Bertrand and Cournot competition. On the other hand, when the only public firm offers a high quality, (i) under Cournot competition, it is always desirable to choose mixed duopoly rather than privatization; (ii) under Bertrand competition, it is desirable to choose mixed duopoly if the excess burden of taxation is sufficiently large, and vice versa.
JEL Classification: D43, L13, M21.
GNN-based Passenger Request Prediction
Authors: Makhdomi Aqsa Ashraf , Gillani Iqra Altaf 
Published: December 2022

Abstract
Passenger request prediction is essential for operations planning, control, and management in ride-sharing platforms. While the demand prediction problem has been studied extensively, the Origin-Destination (OD) flow prediction of passengers has received less attention from the research community. This paper develops a Graph Neural Network framework along with the Attention Mechanism to predict the OD flow of passengers. The proposed framework exploits various linear and non-linear dependencies that arise among requests originating from different locations and captures the repetition pattern and the contextual data of that place. Moreover, the optimal size of the grid cell that covers the road network and preserves the complexity and accuracy of the model is determined. Extensive simulations are conducted to examine the characteristics of our proposed approach and its various components. The results show the superior performance of our proposed model compared to the existing baselines.