bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physiological and biochemical responses of strawberry crown and leaf tissues to freezing stress
Authors: Zareei Elnaz , Karami Farhad , Gholami Mansour , Ershadi Ahmad , Avestan Saber , Aryal Rishi , Gohari Gholamreza , Farooq Muhammad 
Published: November 2021

Abstract
Background
In northern Iran and other cold regions, winter freezing injury and resultant yield instability are major limitations to strawberry production. However, there is scarcity of information on the physiological and biochemical responses of strawberry cultivars to freezing stress. This study aimed to investigate the physiological and biochemical responses of strawberry cultivars (Tennessee Beauty, Blakemore, Kurdistan, Queen Elisa, Chandler, Krasnyy Bereg, and Yalova) to different freezing temperature treatments (− 5, − 10, − 15, − 20, and − 25 °C) under controlled conditions.

Results
All measured physiological and biochemical features were significantly affected by the interaction effect between low temperatures and cultivars. Tennessee Beauty showed the highest RWC at − 25 °C. The highest Fv/Fm was observed in Queen Elisa. Krasnyy Bereg had the least freezing injury (FI) in crown and leaf, while Yalova and Chandler showed the highest crown and leaf FI, respectively. At − 20 to − 25 °C, the highest carbohydrates contents of crown and leaf were noted in Blakemore and Krasnyy Bereg cultivars, respectively. The Yalova showed the highest protein content in both crown and leaf tissues at − 25 °C. The Tennessee Beauty and Blackmore cultivars showed the highest proline in crowns and leaves at − 15 °C, respectively. The highest ThioBarbituric Acid Reactive Substances (TBARS) contents in the crown and leaf were observed in Kurdistan and Queen Elisa, respectively. Queen Elisa and Krasnyy Bereg cultivars showed SOD and POD peaks in the crown at − 15 °C, respectively.

Conclusion
Freezing stress was characterized by decreased Fv/Fm and RWC, and increased FI, TBARS, total carbohydrates, total proteins, proline content, and antioxidant enzyme activity. The extent of changes in above mentioned traits was cultivar dependent. FI and TBARS were the best traits among destructive parameters for evaluating freezing tolerance. Moreover, maximum quantum yield of PSII (Fv/Fm index), as non-destructive parameters, showed a significant efficiency in rapid assessment for screening of freezing tolerant strawberry cultivars. The cultivars Krasnyy Bereg, Queen Elisa, and Kurdistan were the most tolerant cultivars to freezing stress. These cultivars can be used as parents in breeding programs to develop new freezing tolerant cultivars.
Application of BASNEF model in students training regarding cutaneous leishmaniasis prevention behaviors: a school-based quasi experimental study
Authors: Alizadeh Gholamreza , Shahnazi Hossein , Hassanzadeh Akbar 
Published: November 2021

Abstract
Background
Cutaneous leishmaniasis (CL) is endemic in 98 countries, and 350 million people are at risk of the disease worldwide. In endemic areas, conducting educational interventions is necessary to change preventive behaviors of CL. This study aimed to investigate the effect of an educational intervention based on the BASNEF model on CL preventive behavior in students.

Methods
The present quasi-experimental study examined 80 students living in endemic areas of leishmaniasis in Isfahan province, Iran based on the BASNEF model. The required data were collected twice before and two months after the educational intervention based on a questionnaire whose validity and reliability had been already proven in other studies. The intervention was performed in three educational sessions for the students in the intervention group and 1 educational session for teachers and parents. Data were analyzed by SPSS (VER26) using the chi-square test, independent t-test, analysis of covariance (ANCOVA), and Paired t-test.

Results
After intervention, the mean scores of Knowledge (P < 0.001), attitude (P = 0.02), subjective norms (P = 0.04), behavioral intention (P < 0.001), and behavior (P = 0.02) indicated significant differences between the intervention and control groups, but an increase in mean scores of enabling factors was not significant (P = 0. 93).

Conclusions
Providing students with the educational intervention based on the BASNEF model improve their ability to the extent that they transmit these educations to their family members, which would be effective in preventing and controlling CL in leishmaniasis-prone areas.

Trial registration

Name: Iranian Registry of Clinical Trials. Registration number: IRCT20201024049131N1. Registration date: 2020–11-20. Registration timing: prospective.
Impact of time of flight and point spread function on quantitative parameters of lung lesions in 18F-FDG PET/CT
Authors: Huang Kemin , Feng Yanlin , Liang Weitang , Li Lin 
Published: November 2021

Abstract
Background
Image reconstruction algorithm is one of the important factors affecting the quantitative parameters of PET/CT. The purpose of this study was to investigate the effects of time of flight (TOF) and point spread function (PSF) on quantitative parameters of lung lesions in 18F-FDG PET/CT.

Methods
This retrospective study evaluated 60 lung lesions in 39 patients who had undergone 18F-fluoro-deoxy-glucose (FDG) PET/CT. All lesions larger than 10 mm in diameter were included in the study. The PET data were reconstructed with a baseline ordered-subsets expectation–maximization (OSEM) algorithm, OSEM + PSF, OSEM + TOF and OSEM + TOF + PSF respectively. The differences of maximum standard uptake value (SUVmax), mean standard uptake value (SUVmean), metabolic tumor volume (MTV), total lesion glycolysis (TLG)and signal to noise ratio (SNR)were compared among different reconstruction algorithms.

Results
Compared with OSEM reconstruction, using OSEM + TOF + PSF increased SUVmean and SUVmax by 23.73% and 22.71% respectively, and SNR increased by 70.18%, MTV decreased by 23.84% (p < 0.01). The percentage difference was significantly higher in smaller lesions (diameter 10–22 mm) than in larger lesions (diameter 23–44 mm), and significantly higher in low contrast lesions (SNR ≤ 15.31) than in high contrast lesions (SNR > 15.31). The difference of TLG among various reconstruction algorithms is relatively small, the highest value is − 6.48% of OSEM + TOF + PSF, and the lowest value is 0.81% of OSEM + TOF.

Conclusion
TOF and PSF significantly affected the quantitative parameters of lung lesions in 18F-FDG PET/CT. OSEM + TOF + PSF can significantly increased SUVmax, SUVmean and SNR, and significantly reduce MTV, especially in small lesions and low contrast lesions. TLG can be relatively stable in different reconstruction algorithms.
Relationship of shear wave elastography anisotropy with tumor stem cells and epithelial-mesenchymal transition in breast cancer
Authors: Leng Xiaoling , Japaer Rexida , Zhang Haijian , Yeerlan Mila , Ma Fucheng , Ding Jianbing 
Published: November 2021

AbstractBackgroundThis study is to examine the feasibility of shear wave elastography (SWE) anisotropy in assessing the prognosis of breast cancer.MethodsWe enrolled 119 breast cancer patients from January 2017 to October 2019. SWE was performed before operation. Emax (maximum elasticity value), Emean (average elasticity value), Esd (standard deviation of the lesion elasticity value), Eratio (elasticity value of adipose tissue), anisotropy coefficient and difference were recorded. After operation, we collected clinical pathological data, and performed immunohistochemistry and real-time PCR tests on CD44, CD24, E-cadherin, β-catenin, vimentin and N-cadherin. Finally, we analyzed the correlation among parameters of SWE, anisotropy and clinicopathology, and markers of CSCs (cancer stem cells) and EMT (epithelial-mesenchymal transition).ResultsEmax, Emean and Esd of the cross section were higher than those of the longitudinal section. Breast cancer with a higher elastic modulus was often accompanied by a hyperechoic halo, which was manifested as mixed echo and post-echo attenuation, and was accompanied by a higher BI-RADS (breast imaging reporting and data system) classification. When breast cancer had hyperechoic halo and weakened posterior echo, SWE of the lesion showed more obvious anisotropy. In addition, larger diameter of the longitudinal section indicated higher stiffness of the cross section. Correlation analysis showed that E-cadherin was negatively correlated with SWE in longitudinal section. CD44, N-cadherin, β-catenin were positively correlated with SWE in longitudinal and cross sections. Vimentin and CD24 had no correlation with SWE parameters.ConclusionSWE of breast cancer is anisotropic. The cross-sectional SWE is better than the longitudinal SWE, Emax is better than Emean, the anisotropy of SWE is better than SWE, and the anisotropy factor is better than the anisotropy difference.
X-ray repair cross-complementing protein 1 (XRCC1) loss promotes β-lapachone –induced apoptosis in pancreatic cancer cells
Authors: Zheng Yansong , Zhang Hengce , Guo Yueting , Chen Yuan , Chen Hanglong , Liu Yingchun 
Published: November 2021

Abstract
Background
β-lapachone (β-lap), the NQO1 bioactivatable drug, is thought to be a promising anticancer agent. However, the toxic side effects of β-lap limit the drug use, highlighting the need for a thorough understanding of β-lap’s mechanism of action. β-lap undergoes NQO1-dependent futile redox cycling, generating massive ROS and oxidative DNA lesions, leading to cell death. Thus, base excision repair (BER) pathway is an important resistance factor. XRCC1, a scaffolding component, plays a critical role in BER.

Methods
We knocked down XRCC1 expression by using pLVX-shXRCC1 in the MiaPaCa2 cells and BxPC3 cells and evaluated β-lap-induced DNA lesions by γH2AX foci formation and alkaline comet assay. The cell death induced by XRCC1 knockdown + β-lap treatment was analysed by relative survival, flow cytometry and Western blotting analysis.

Results
We found that knockdown of XRCC1 significantly increased β-lap-induced DNA double-strand breaks, comet tail lengths and cell death in PDA cells. Furthermore, we observed combining XRCC1 knockdown with β-lap treatment switched programmed necrosis with β-lap monotherapy to caspase-dependent apoptosis.

Conclusions
These results indicate that XRCC1 is involved in the repair of β-lap-induced DNA damage, and XRCC1 loss amplifies sensitivity to β-lap, suggesting targeting key components in BER pathways may have the potential to expand use and efficacy of β-lap for gene-based therapy.
NME6 is a phosphotransfer-inactive, monomeric NME/NDPK family member and functions in complexes at the interface of mitochondrial inner membrane and matrix
Authors: Proust Bastien , Radić Martina , Vidaček Nikolina Škrobot , Cottet Cécile , Attia Stéphane , Lamarche Frédéric , Ačkar Lucija , Mikulčić Vlatka Godinić , Tokarska-Schlattner Malgorzata , Ćetković Helena , Schlattner Uwe , Bosnar Maja Herak 
Published: November 2021

Abstract
Background
NME6 is a member of the nucleoside diphosphate kinase (NDPK/NME/Nm23) family which has key roles in nucleotide homeostasis, signal transduction, membrane remodeling and metastasis suppression. The well-studied NME1-NME4 proteins are hexameric and catalyze, via a phospho-histidine intermediate, the transfer of the terminal phosphate from (d)NTPs to (d)NDPs (NDP kinase) or proteins (protein histidine kinase). For the NME6, a gene/protein that emerged early in eukaryotic evolution, only scarce and partially inconsistent data are available. Here we aim to clarify and extend our knowledge on the human NME6.

Results
We show that NME6 is mostly expressed as a 186 amino acid protein, but that a second albeit much less abundant isoform exists. The recombinant NME6 remains monomeric, and does not assemble into homo-oligomers or hetero-oligomers with NME1-NME4. Consequently, NME6 is unable to catalyze phosphotransfer: it does not generate the phospho-histidine intermediate, and no NDPK activity can be detected. In cells, we could resolve and extend existing contradictory reports by localizing NME6 within mitochondria, largely associated with the mitochondrial inner membrane and matrix space. Overexpressing NME6 reduces ADP-stimulated mitochondrial respiration and complex III abundance, thus linking NME6 to dysfunctional oxidative phosphorylation. However, it did not alter mitochondrial membrane potential, mass, or network characteristics. Our screen for NME6 protein partners revealed its association with NME4 and OPA1, but a direct interaction was observed only with RCC1L, a protein involved in mitochondrial ribosome assembly and mitochondrial translation, and identified as essential for oxidative phosphorylation.

Conclusions
NME6, RCC1L and mitoribosomes localize together at the inner membrane/matrix space where NME6, in concert with RCC1L, may be involved in regulation of the mitochondrial translation of essential oxidative phosphorylation subunits. Our findings suggest new functions for NME6, independent of the classical phosphotransfer activity associated with NME proteins.
Novel Circulating Hypermethylated RASSF1A ddPCR for Liquid Biopsies in Patients With Pediatric Solid Tumors
Authors: van Zogchel Lieke M. J. , Lak Nathalie S. M. , Verhagen Onno J. H. M. , Tissoudali Ahmed , Gussmalla Nuru Mohammed , Gelineau Nina U. , Zappeij-Kannengieter Lily , Javadi Ahmad , Zijtregtop Eline A. M. , Merks Johannes H. M. , van den Heuvel-Eibrink Marry , Schouten-van Meeteren Antoinette Y. N. , Stutterheim Janine , van der Schoot C. Ellen , Tytgat Godelieve A. M. 
Published: November 2021

PURPOSELiquid biopsies can be used to investigate tumor-derived DNA, circulating in the cell-free DNA (cfDNA) pool in blood. We aimed to develop a droplet digital polymerase chain reaction (ddPCR) assay detecting hypermethylation of tumor suppressor gene RASSF1A as a simple standard test to detect various pediatric tumor types in small volume blood samples and to evaluate this test for monitoring treatment response of patients with high-risk neuroblastoma.METHODSWe developed a ddPCR assay to sensitively detect tumor-derived hypermethylated RASSF1A DNA in liquid biopsies. We tested this assay in plasma of 96 patients with neuroblastoma, renal tumors, rhabdomyosarcoma, or Hodgkin lymphoma at diagnosis and in cerebrospinal fluid of four patients with brain tumors. We evaluated the presence of hypermethylated RASSF1A in plasma samples during treatment and follow-up in 47 patients with neuroblastoma treated according to high-risk protocol and correlated results with blood mRNA–based and bone marrow mRNA–based minimal residual disease detection and clinical outcomes.RESULTSThe total cfDNA level was significantly higher in patients with metastatic neuroblastoma and nephroblastoma compared with healthy adult and pediatric controls. Hypermethylated RASSF1A was present in 41 of 42 patients with metastatic neuroblastoma and in all patients with nephroblastoma, with the median percentage of 69% and 21% of total RASSF1A, respectively. Hypermethylated RASSF1A levels decreased during therapy and recurred at relapse.CONCLUSIONOur findings demonstrate the value of ddPCR-based detection of hypermethylated RASSF1A as a circulating molecular tumor marker in neuroblastoma. Our preliminary investigation of RASSF1A hypermethylation detection in circulating cfDNA of other pediatric tumor entities demonstrates potential as a pan-tumor marker, but requires investigation in larger cohorts to evaluate its use and limitations.
Germline Testing Data Validate Inferences of Mutational Status for Variants Detected From Tumor-Only Sequencing
Authors: Jalloul Nahed , Gomy Israel , Stokes Samantha , Gusev Alexander , Johnson Bruce E. , Lindeman Neal I. , Macconaill Laura , Ganesan Shridar , Garber Judy E. , Khiabanian Hossein 
Published: November 2021

PURPOSEPathogenic germline variants (PGVs) in cancer susceptibility genes are usually identified through germline testing of DNA from blood or saliva: their detection can affect treatment options and potential risk-reduction strategies for patient relatives. PGV can also be identified in tumor sequencing assays, which, when performed without patient-matched normal specimens, render determination of variants' germline or somatic origin critical.METHODSTumor-only sequencing data from 1,608 patients were retrospectively analyzed to infer germline versus somatic status of variants using an information-theoretic, gene-independent approach. Loss of heterozygosity was also determined. Predicted mutational models were compared with clinical germline testing results. Statistical measures were computed to evaluate performance.RESULTSTumor-only sequencing detected 3,988 variants across 70 cancer susceptibility genes for which germline testing data were available. We imputed germline versus somatic status for > 75% of all detected variants, with a sensitivity of 65%, specificity of 88%, and overall accuracy of 86% for pathogenic variants. False omission rate was 3%, signifying minimal error in misclassifying true PGV. A higher portion of PGV in known hereditary tumor suppressors were found to be retained with loss of heterozygosity in the tumor specimens (72%) compared with variants of uncertain significance (58%).CONCLUSIONAnalyzing tumor-only data in the context of specimens' tumor cell content allows precise, systematic exclusion of somatic variants and suggests a balance between type 1 and 2 errors for identification of patients with candidate PGV for standard germline testing. Although technical or systematic errors in measuring variant allele frequency could result in incorrect inference, misestimation of specimen purity could result in inferring somatic variants as germline in somatically mutated tumor suppressor genes. A user-friendly bioinformatics application facilitates objective analysis of tumor-only data in clinical settings.
WBC-based segmentation and classification on microscopic images: a minor improvement
Authors: Lam Xin-Hui , Ng Kok-Why , Yoong Yih-Jian , Ng Seng-Beng 
Published: November 2021

Introduction White blood cells (WBCs) are immunity cells which fight against viruses and bacteria in the human body. Microscope images of captured WBCs for processing and analysis are important to interpret the body condition. At present, there is no robust automated method to segment and classify WBCs images with high accuracy. This paper aims to improve on WBCs image segmentation and classification method. Methods A triple thresholding method was proposed to segment the WBCs; meanwhile, a convolutional neural network (CNN)-based binary classification model that adopts transfer learning technique was proposed to detect and classify WBCs as a healthy or a malignant. The input dataset of this research work is the Acute Lymphoblastic Leukemia Image Database (ALL-IDB). The process first converts the captured microscope images into HSV format for obtaining the H component. Otsu thresholding is applied to segment the WBC area. A 13 × 13 kernel with two iterations was used to apply morphological opening on image to ameliorate output results. Collected cell masks were used to detect the contour of each cell on the original image. To classify WBCs into a healthy or a malignant category, characteristics and conditions of WBCs are to be examined. A transfer learning technique and pre-trained InceptionV3 model were employed to extract the features from the images for classification. Results The proposed WBCs segmentation method yields 90.45% accuracy, 83.81% of the structural similarity index, 76.25% of the dice similarity coefficient, and is computationally efficient. The accuracy of fine-tuned classifier model for training, validation and test sets are 93.27%, 92.31% and 96.15% respectively. The obtained results are high in accuracy and precision are over 96% and with lower loss value. Discussion Triple thresholding outperforms K-means clustering in segmenting smaller dataset. Pre-trained InceptionV3 model and transfer learning improve the flexibility and ability of classifier.
Does COVID-19 infection change the need for future surgical interventions? An exploratory analysis.
Authors: Welk Blayne , Richard Lucie 
Published: November 2021

Background: It is unknown whether recovery from coronavirus disease 2019 (COVID-19) infection leads to an increased need for common surgical procedures. Our objective was to conduct an exploratory analysis of surgical procedures performed after a documented COVID-19 infection. Methods: We conducted a retrospective cohort study using routinely collected data from the province of Ontario, Canada. We identified individuals with a positive COVID-19 test between February 1 2020 and May 31 2020, and matched them 1:2 with individuals who had a negative COVID-19 test during the same period. We used physician billing codes to identify the ten most frequent surgical procedures in the COVID-19 cohort. An at-risk period 30 days after the first positive COVID-19 swab (or matched index date in the control group) until November 30 2020 was used. Cox proportional hazard models (adjusted for important baseline differences) are reported with hazard ratios (HR) and 95% confidence intervals. Results: After exclusions and matching, we had 19,143 people in the COVID-19 cohort, and 38,286 people in the control cohort. The top ten surgical procedures were hand/wrist fracture fixation, cesarean-section, ureteral stent placement, cholecystectomy, treatment of an upper tract urinary stone, hysterectomy, femur fracture repair, hip replacement, transurethral prostatectomy, and appendectomy. There was a significantly reduced hazard of requiring upper tract renal stone surgery (adjusted hazard ratio [aHR] 0.50, 95% confidence interval [CI] 0.29-0.87) or ureteral stent placement (aHR 0.54, 95%CI 0.36-0.82), or undergoing a cholecystectomy (aHR 0.43, 95%CI 0.26-0.71) among those with a prior positive COVID-19 test. Conclusions: After a COVID-19 infection there is not an increased risk of needing several common surgical procedures. There appears to be a reduced risk of renal stone disease treatment and ureteral stent placement, and a reduced risk of cholecystectomy, however understanding the reasons for this will require further study.