bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimal water allocation based on agricultural and environmental water value
Authors: Hatamkhani Amir , Moridi Ali 
Published: October 2021

Abstract
Despite the significant role of wetlands in maintaining a healthy ecosystem and providing various ecosystem services, they are under threat due to human activities and agriculture use. The fact that the economic value of ecosystem services is not considered in hydro-economic models and integrated water resources management is a key issue that affects the ecosystem and its degradation. the economic value of ecosystem services provides a quantitative and important basis for the reasonable management of water resources. Given that supplying the agriculture and environmental demands conflict with each other, achieving a balance between these goals is very important. So, in this study, a simulation-optimization (WEAP-PSO) approach is employed for optimal planning at the basin and designing environmental flow based on wetland ecosystem services. The objective function of the problem is considered to be the total economic value of the river, which includes the economic value of the agricultural sector and the economic value of the wetland ecosystem services. The decision variables of the problem are considered as, the cultivation area of agricultural units and environmental flow of Kani Barazan wetland. The results show that considering these two objectives together, in addition to sustainable development, causes the highest economic efficiency in the basin.
ARBic: An All-Round Biclustering Algorithm for Analyzing Gene Expression Data
Authors: Liu Xiangyu , Su Zhengchang , Li Guojun 
Published: October 2021

Abstract
Background: Identifying significant biclusters of genes with specific expression patterns is an effective approach to reveal functionally correlated genes in gene expression data. However, existing algorithms are limited to finding either broad or narrow biclusters but both due to failure of balancing between effectiveness and efficiency. Methods: We developed a new algorithm ARBic which can accurately identify any meaningful biclusters of shape no matter broad or narrow in a large scale gene expression data matrix, even when the values in the biclusters to be identified have the same distribution as that the background data has. ARBic is developed by integrating column-based and row-based strategies into biclustering procedure. The column-based strategy borrowed from ReBic, a recently published biclustering tool, prefers to narrow bicluters. The row-based strategy newly designed in this article by repeatedly finding a longest path in a specific directed graph prefers to broader ones. Result and Conclusion: When tested and compared to other seven salient biclustering algorithms on simulated datasets, ARBic achieved recovery, relevance and f1-scores 29% higher than the second best algorithm. Furthermore, ARBic substantially outperforms all of them on real datasets and robusts to noises, shapes of biclusters and types of datasets.Code: https://github.com/holyzews/ARBicData: https://doi.org/10.5281/zenodo.5121018
Discriminators of Pseudoprogression and True Progression in High-Grade Gliomas: A Systematic Review and Meta-Analysis
Authors: Taylor Christopher Stephen , Ekert Justyna O. , Sefcikova Viktoria , Fersht Naomi , Samandouras George 
Published: October 2021

Abstract
BackgroundHigh-grade gliomas remain the most common primary brain tumour with limited treatments options and early recurrence rates following adjuvant treatments. However, differentiating true tumour progression (TTP) from treatment-related effects or pseudoprogression (PsP), may critically influence subsequent management options. Structural MRI is routinely employed to evaluate treatment responses, but misdiagnosis of TTP or PsP may lead to continuation of ineffective or premature cessation of effective treatments, respectively. MethodsA systematic review and meta-analysis were conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) method. The entirety of the Embase and MEDLINE databases were searched for methods differentiating PsP and TTP, and studies were selected using pre-specified eligibility criteria. The sensitivity and specificity of included studies were summarised in a forest plot. Three of the identified methods were assessed in a separate subgroup meta-analysis.ResultsTwenty-six studies assessing seven distinct neuroimaging methods in 1145 patients were included in the systematic review. 18F-fluoroethyltyrosine PET (FET PET) and amide proton transfer-weighted MRI (APTw-MRI) showed high diagnostic accuracy, but results were based on single low-powered studies. The highest performing methods in the subgroup analysis were DWI (AUC = 0.95 [0.92 – 0.96]) and DSC-pMRI (AUC = 0.94 [0.91 – 0.95]), compared to DCE-pMRI (AUC = 0.90 [0.87 – 0.93]).ConclusionsBoth DWI and DSC-pMRI performed with high sensitivity and specificity for differentiating PsP from TTP. Considering the technical parameters and feasibility of each identified method, DSC-pMRI was found to be the most promising technique.
Biweekly Oxaliplatin Plus S1 (SOX) As First Line Therapy For Advanced Or Metastatic Gastric Or Gastroesophageal Junction (G/GEJ) Caner In Chinese Elderly Patients: An Open-Label, Single-Arm, Phase 2 Study.
Authors: Jiang Zhichao , Zhou Aiping , Sun Yongkun , Zhang Wen 
Published: October 2021

Abstract
Background: SOX (oxaliplatin and S1 every 3 weeks) is one of the most common used first line chemotherapy for advanced or metastatic G/GEJ cancer in Asia, but with significant hematological and neurological toxicity. In China, the majority of gastric cancer patients are the middle-aged and elderly with dissatisfactory tolerance to 3-weekly chemotherapy. Therefore, we aimed to assess efficacy and safety of biweekly SOX as first line treatment in patients 60 years old or older with advanced G/GEJ cancer in a single arm phase 2 study. Methods: Oxaliplatin was administered intravenously on day 1 at 85 mg/m2. S-1 was given at 80, 100, 120 mg/day depending on body surface area of <1.25 m2, 1.25 to <1.5 m2, or ≥1.5 m2 two times daily on days 1-10, every 2 weeks. Eligible patients were aged 60 years old or older with histological or cytological diagnosis of advanced G/GEJ adenocarcinoma, had measurable disease according to the RECIST v 1.1 without previous treatment. The primary endpoint was objective response rate (ORR), and the secondary endpoints included progression free survival (PFS), overall survival (OS), disease control rate (DCR), duration of response (DOR) and safety. Results: Between May 2016 and Sep 2018, 42 patients were enrolled. Median follow-up time was 43.6 months. ORR and DCR were 52.4% and 85.7%, respectively. Median PFS was 4.6 months (95%CI 2.486-6.714). Median OS was 11.1 months (95%CI 8.001-14.199). The most common treatment-related adverse events (TRAEs) of any grade were thrombocytopenia (59.5%), neutropenia (57.1%), appetite loss (57.1%) and nausea (54.8%). Only two patients respectively suffered from grade 3 treatment-related neutropenia (1 patient, [2.4%]) and diarrhea (1 patient, [2.4%]). No other grade 3 or worse TRAEs occurred. Conclusions: First line biweekly SOX showed promising PFS and OS with a remarkable tolerance in advanced G/GEJ cancer patients 60 years old or older preliminary worth further evaluation.Trial registration: ClinicalTrials.gov ID: NCT04694404 (5/1/2021). This study was approved by the Ethical Committee of National Cancer Center/ National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, (17-048/1303).
Computed Tomography Characterization of Emphysema in Combined Pulmonary Fibrosis and Emphysema (CPFE) and its Correlation with Lung Cancer with Comparison to Chronic Obstructive Pulmanory Disease (COPD)
Authors: Qiu Jianxing , Nie Ligong , Xiong Yan 
Published: October 2021

Abstract
Purpose: To investigate imaging features of emphysema on high-resolution computed tomography (HRCT) in combined pulmonary fibrosis and emphysema (CPFE) and its correlation with lung cancer, with comparison to chronic obstructive pulmonary disease (COPD). Methods: 160 consecutive patients (80 CPFE and 80 COPD ) were analyzed retrospectively. The HRCT imaging features of the two groups were compared, and the correlation between factors underlying CPFE and the occurrence of lung cancer was analyzed. Results: We found paraseptal emphysema to be the more common form of emphysema in CPFE (38.75%), with an incidence statistically higher than that of COPD (χ²=14.462, p=0.001). The extent of emphysema in each lung lobe in the CPFE group was statistically less than that in the COPD group (p<0.01). Homogeneous emphysema was common in both the CPFE (73.8%) and COPD groups (52.5%), and it showed a higher incidence in CPEF group (χ²=7.760, p=0.004). Homogeneous emphysema also showed significantly high correlation to lung cancer (χ²=9.298, p=0.004). The incidence of lung cancer in the CPFE group (20%) was higher than that in the COPD group (8.8%) (χ²=4.113, p=0.035). There was a linear relationship between the incidence of lung cancer and the degree of pulmonary interstitial fibrosis and years of smoking in CPFE patients (χ²=6.679, p=0.01* ,b=0.148). Conclusion: Different emphysema features showed between CPFE and COPD, and CPFE showed higher incidence of lung cancer. Homogenous emphysema, severity of damage caused by interstitial fibrosis and the number of smoking years have high relationship with incidence of lung cancer in CPFE.
A novel single-cell RNA-sequencing platform and its applicability connecting genotype to phenotype in ageing-disease
Authors: Shomroni Orr , Sitte Maren , Schmidt Julia , Parbin Sabnam , Ludewig Fabian , Yigit Gökhan , Zelarayan Laura Cecilia , Streckfuss-Bömeke Katrin , Wollnik Bernd , Salinas Gabriela 
Published: October 2021

Abstract
Advances in single cell multi-omics analysis such as the ability of a genotype to show phenotypic diversity lead to a comprehensive understanding of cellular events in human diseases. The cardinal feature to access this information is the technology used for single-cell isolation, barcoding, and sequencing. While numerous platforms have been reported for single-cell RNA-sequencing, technical enhancements are needed in terms of highly purified single cell selection, cell documentation or limitations in cell sizing and chemistry. In this study, we present a novel high-throughput platform using a full-length RNA-sequencing approach that offers substantial technical improvements of all parameters. We applied this platform to dermal fibroblasts derived from six patients with different segmental progeria syndromes and defined phenotype-associated pathway signatures and variant-associated expression modifiers. These results validate the applicability of our platform to highlight genotype–expression relationships for molecular phenotyping in ageing disorders.
Dysgeusia Due to Zinc Deficiency After Pancreaticoduodenectomy Requiring Continuous Intravenous Zinc Supplementation: a Case Report and Literature Review
Authors: Hata Hironobu , Ota Yojiro , Uesaka Katsuhiko , Yamazaki Yutaka , Murata Tsubasa , Murai Chika , Yoshikawa Kazuhito , Imamachi Kenji , Yurikusa Takashi , Kitagawa Yoshimasa 
Published: October 2021

Abstract
Background: Zinc is mainly absorbed in the duodenum and proximal jejunum, which are removed during pancreaticoduodenectomy (PD). Little is known about the adverse oral events and skin disorders caused by zinc deficiency after PD. Herein, we reviewed studies regarding the development of zinc deficiency after PD and presented the case of a patient with zinc deficiency after PD, who required home intravenous zinc replacement.Case presentation: A 73-year-old woman with glossitis, taste disorder, and acrodermatitis enteropathica-like eruption on her fingers presented to the Division of Dentistry and Oral Surgery 69 days after PD. Her serum zinc level markedly decreased to 30 μg/dL. Oral zinc administration was inadequate to treat hypozincemia after PD; therefore, multi-trace elements were injected intravenously under readmission. Her serum zinc levels recovered, and the lesions gradually improved. Furthermore, a central venous port was implanted to maintain normal serum zinc levels, and she continued self-injecting zinc at home.Conclusion: Zinc deficiency after PD rarely occurs. The clinical oncologist community, including dentists responsible for the oral care of cancer patients, should be aware of dysgeusia associated with zinc deficiency after cancer surgery, as well as that induced by chemotherapy or head and neck radiation therapy.
Evaluation of a Method Combining Physical Experiment and Data Insertion For the Assessment of PET-CT Systems
Authors: Maronnier Quentin , Courbon Frédéric , Caselles Olivier 
Published: October 2021

Abstract
Background: To evaluate and compare Positron Emission Tomography (PET) devices among them, tests are performed on phantoms that generally consist in simple geometrical objects, fillable with radiotracers. On one hand, those tests bring a control over the experiment through the operator preparation but on the other hand, they are limited in terms of reproducibility, repeatability and are time-consuming, in particular, if several replications are required. To overcome these restrictions, we designed a method combining physical experiment and data insertion that aims to avoid experimental repetitions while testing multiple configurations for the performance evaluation of PET scanners.Methods: Based on the National Electrical Manufacturers Association Image Quality standard, four experiments, with different spheres-to-background ratios: 2:1, 4:1, 6:1 and 8:1, were performed. An additional acquisition was done with a radioactive background and no activity within the spheres. It was created as a baseline to artificially simulate the radioactive spheres and reproduce initial experiments. Standard sphere set was replaced by smaller target sizes (4, 5, 6, 8, 10 and 13 mm) to match current detectability performance of PET scanners. Images were reconstructed following standard guidelines, i.e. using OSEM algorithm, and an additional BPL reconstruction was performed. We visually compared experimental and simulated images. We measured the activity concentration values into the spheres to calculate the mean and maximum recovery coefficient (RCmean and RCmax ) which we used in a quantitative analysis.Results: No significant visual discrepancies were identified between experimental and simulated series. Mann-Whitney U tests comparing simulated and experimental distributions showed no statistical differences for both RCmean (P value = 0.611) and RCmax (P value = 0.720). Spearman tests revealed high correlation for RCmean (ρ = 0.974, P value < 0.001) and RCmax (ρ = 0.974, P value < 0.001) between both datasets. According to Bland-Altman plots, we highlighted slight shifts in RCmean and RCmax of respectively 2.1 ± 16.9 % and 3.3 ± 22.3 %.Conclusions: The method produced realistic results compared to experimental data. Known synthesized information fused with original data allows full exploration of the system's capabilities while avoiding the limitations associated with repeated experiments.
ACACIAS Project: Physiological and Subjective Effects of High-fidelity Simulation During Delivery of Bad News in Oncology
Authors: Deluche Elise , Salle Henri , Leobon Sophie , Facchini-Joguet Teeva , Troussel Alexandre , Caire Francois , Fourcade Laurent , Taibi Abdelkader 
Published: October 2021

Abstract
Background: Delivering bad news is difficult and requires specific training, but this training can be accomplished through high-fidelity simulation (HFS). This prospective study was conducted to objectively evaluate the emotional impact of HFS as an effective tool to develop clinical proficiency.Methods: This prospective feasibility study was conducted from January 2021 to May 2021. Students received a 1- or 2-day training course. The emotional impact of the intervention was evaluated by self-questionnaire and by an Affect-tag wristband that analysed Emotional power (EP), Emotional density (ED), and Cognitive load (CL).Results: The study population included 46 students with a median age of 25 years (range 21–34 years). Participants were emotionally and effectively involved in the HFS training without being completely overpowered by emotions, which may be an inherent feature of the training format. Students who participated twice improved their EP (p < 0.001) and decreased their ED (p = 0.005). CL remained stable (p = 0.751). The mean time of the first and second training increased (1:41 vs. 2:16, p = 0.02). Skills improved as assessed by self-questionnaires and by outsiders (actor/nurse).Conclusion: HFS is a good method for this type of training, considering the emotional impact. Training in delivering bad news was improved through objective practice and self-assessment by participants.
Modeling and Analysis of Unbalanced Magnetic Pull in Synchronous Motorized Spindle Considering Magneto-thermal Coupling
Authors: feng wei , Zhang Kun , Liu Zongyao , Liu Baoguo , Zhang Huijuan , Mei Junwei , Wu Luji 
Published: October 2021

Abstract
The unbalanced magnetic pull (UMP) is one of the main vibration sources of the motorized spindle. A calculation model of UMP in a synchronous motorized spindle considering the magneto-thermal coupling is proposed in this paper. The finite element analysis models of the electromagnetic field and the temperature field of a motorized spindle are first established. Then a two-way coupling analysis method considering the effect of temperature variations on electromagnetic material properties of the motor is proposed. An experiment is conducted to verify the efficiency of this method. The thermal deformations of the spindle are calculated and used to analyze the air-gap variations between rotor and stator of the built-in motor. The 3D finite element electromagnetic model is adopted to calculate the UMP in the motorized spindle. The analysis results show that the eccentricity caused by thermal deformation can generate large UMP in the motorized spindle.
Prognostic signature for hepatocellular carcinoma based on 4 pyroptosis-related genes
Authors: Zhong Yuanbin 
Published: October 2021

Abstract
Background

Hepatocellular carcinoma (HCC) is a cancer with a poor prognosis. Many recent studies have suggested that pyroptosis is important in tumour progression. However, the role of pyroptosis-related genes (PRGs) in HCC remains unclear.
Materials and methods

We identified differentially expressed PRGs in tumours versus normal tissues. Through univariate, LASSO, and multivariate Cox regression analyses, a prognostic PRG signature was established. The signature effectiveness was evaluated by time-dependent receiver operating characteristic (ROC) curve and Kaplan–Meier (KM) survival analysis. The signature was validated in the ICGC (LIRI-JP) cohort. In addition, single-sample gene enrichment analysis (ssGSEA) showed the infiltration of major immune cell types and the activity of common immune pathways in different subgroups.
Results

Twenty-nine pyroptosis-related DEGs from The Cancer Genome Atlas-Liver Hepatocellular Carcinoma (TCGA-LIHC) dataset were detected, and four genes (CTSV, CXCL8, MKI67 and PRF1) among them were selected to construct a prognostic signature. Then, the patients were divided into high- and low-risk groups. The pyroptosis-related signature was significantly associated with overall survival (OS). In addition, the patients in the high-risk group had lower levels of immune infiltration.
Conclusion

The prognostic signature for HCC based on 4 pyroptosis-related genes has reliable prognostic and predictive value for HCC patients.
Interplay of Meaning between Verbal and Visual Texts in a Japanese Children’s Book
Authors: Puspitasari Dewi 
Published: October 2021

This research aimed to interpret the meaning of aspects in the verbal and visual texts to identify whether these two texts created interplay. It was intended to understand the meaning conveyed by the writer and illustrator in a Japanese children’s book entitled ‘Kuroino’ (Little Shadow). This research used the approaches for verbal text analysis by Halliday about Systemic Functional Linguistics (SFL) and visual text analysis by Kress and van Leeuwen about Visual Grammar (VG). The research method was descriptive qualitative by explaining two data types: clauses in the Japanese language and images in the storybook. The data analysis of every aspect in the three metafunctions of language and the three metafunctions of images show the meaning that completes each other. In the analysis of ideational meaning, interpersonal meaning, and textual meaning, the writer narrates the friendship and adventure of ‘Kuroino’ (the Black) and Watashi (I). Meanwhile, in the analysis of representational meaning, interactive meaning, and compositional meaning, the illustrator describes two characters in a book entitled ‘Kuroino’ as the focuses in some pictures. Besides, the illustrator describes the background in detail as if he invites the reader to participate in the adventure of these two characters. Although verbal and visual texts describe a story from two different perspectives, in ‘Kuroino’, these texts collaborate to create a message in the story with synergy and meaning to be easily understood by the readers by maintaining the entertainment aspect in a story narrated.
Research Status, Synthesis and Clinical Application of Recently
Marketed and Clinical BCR-ABL Inhibitors
Authors: Xu Xiao-Liang , Cao Yu-Jing , Zhang Wen , Rao Guo-Wu 
Published: October 2021

:
Tyrosine kinases expressed by BCR-ABL fusion genes can cause changes in
cell proliferation, adhesion, and survival properties, which are the main causes of chronic
myelogenous leukemia (CML). Inhibiting the activity of BCR-ABL tyrosine kinase has
become one of the effective methods for the treatment of chronic myelogenous leukemia.
Initially, imatinib was the first small molecule of BCR-ABL tyrosine kinases inhibitors
(TKIs) for the effective treatment of chronic myelogenous leukemia. Later, due to the
emergence of various BCR-ABL mutations, especially T315I mutation, imatinib developed
strong resistance. The second-generation kinase inhibitors dasatinib and nilotinib
were able to overcome most of the mutation resistance but not T315I mutations. Therefore,
in order to further overcome the problem of drug resistance, new types of KTIs such
as flumatinib and radotinib have been developed, providing more options for clinical
treatment. Some new drugs have entered clinical trials. In this review, two new BCRABL
inhibitors (flumatinib and radotinib) and five new BCR-ABL inhibitors have been
introduced into the clinical market in recent years. We reviewed their research status, synthesis
methods, and clinical applications.