bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of cloud and precipitation processes in regional and global models with ULTIMATE (ULTra-sIte for Measuring Atmosphere of Tokyo metropolitan Environment): A case study using the dual-polarization Doppler weather radars
Authors: Satoh Masaki , Matsugishi Shuhei , Roh Woosub , Ikuta Yasutaka , Kuba Naomi , Seiki Tatsuya , Hashino Tempei , Okamoto Hajime 
Published: March 2022

Abstract
We describe a collaborative analysis study involving numerical models and observation data for the Tokyo metropolitan area, called the ULTIMATE (ULTra-sIte for Measuring Atmosphere of Tokyo Metropolitan Environment) project. It evaluates cloud microphysics schemes of numerical models using extensive observation data for the Tokyo area. We have access to a variety of remote sensing and in-situ data for the Tokyo area for operational and research purposes, particularly by enhancing observations for ground validation of the EarthCARE satellite, which is set to launch in 2023. This study focuses on using the dual-polarization Doppler weather radar, operated by the Japan Meteorological Agency. In terms of numerical models, we use and compare multi-models with various cloud microphysics schemes, including a global non-hydrostatic model, NICAM (Non-hydrostatic Icosahedral Atmospheric Model), and the regional model of the Japan Meteorological Agency, ASUCA (A System based on a Unified Concept for Atmosphere), together with a regional model, SCALE (Scalable Computing for Advanced Library and Environment) developed by RIKEN. In particular, because NICAM can be used as both a global and a regional model, we can immediately test the improved scheme on a global scale for its effect on climatology and the evaluation of climate sensitivity.This paper introduces the methodology for evaluating numerical models by the dual-polarization radar using the observation simulator and compares numerical model results with observations. We found discrepancies in the signals of rain and graupel between the observation and the simulations. In future studies, we will use the present results to improve the cloud microphysics scheme, which will be tested on a global model.
A deep learning-based self-adapting ensemble method for segmentation in gynecological brachytherapy
Authors: Li Zhen , Zhu Qingyuan , Zhang Lihua , Yang Xiaojing , Li Zhaobin , Fu Jie 
Published: March 2022

Abstract
Purpose: Fast and accurate outlining of the organs at risk (OARs) and high-risk clinical tumor volume (HRCTV) is especially important in high-dose-rate brachytherapy (HDR-BT) due to the highly time-intensive online treatment planning process and the high dose gradient around the HRCTV. This study aims to apply a self-configured ensemble method for fast and reproducible auto-segmentation of OARs and HRCTVs in gynecological cancer.Materials and methods: We applied nnU-Net (no new U-Net), an automatically adapted deep convolutional neural network based on U-Net, to segment the OARs and HRCTV in gynecological cancer. In nnU-Net, three architectures, including 2D U-Net, 3D U-Net and 3D-Cascade U-Net, were trained and finally ensembled. 207 cases were randomly chosen for training, and 30 for testing. Quantitative evaluation used well-established image segmentation metrics, including Dice Similarity Coefficient (DSC), 95% Hausdorff distance (HD95%), and Average Surface Distance (ASD). Qualitative analysis of automated segmentation results was performed visually by two radiation oncologists. Dosimetric evaluation was performed by comparing the dose-volume parameters of both predicted segmentation and human contouring.Results: nnU-Net obtained high qualitative and quantitative segmentation accuracy on the test dataset, and performed better than previously reported methods in the bladder and rectum segmentation. In quantitative evaluation, 3D-Cascade achieved the best performance in the bladder (DSC: 0.936±0.051, HD95%: 3.503±1.956, ASD: 0.944±0.503), rectum (DSC: 0.831±0.074, HD95%: 7.579±5.857, ASD: 3.6±3.485), and HRCTV (DSC: 0.836±0.07, HD95%: 7.42±5.023, ASD: 2.094±1.311). According to the qualitative evaluation, over 90% of the test data set had no or minor visually detectable errors in segmentation. Conclusion: This work demonstrated nnU-Net’s superiority in segmenting OARs and HRCTV in gynecological brachytherapy, among which 3D-Cascade shows the highest accuracy in segmentation across different applicators and patient anatomy.
Implementation of portable head CT imaging in patients with severe acute brain injury in a French ICU: a prospective before-after design pilot study
Authors: Launey Yoann , Mycinski Clément , Eugène François , Bellec Elise , Serpolay Hubert , Ferré Jean-Christophe , Seguin Philippe , Gauvrit Jean-Yves 
Published: March 2022

Abstract
Head-CT-scanning is a cornerstone procedure during the management of patients admitted for acute brain injury (ABI) in intensive care unit (ICU). But intrahospital transfer for these procedure may cause severe adverse events potentially worsening the brain injuries. Portable head-CT (pCTH) may facilitate pCTH performance in safer conditions for the patients avoiding transfer out of the ICU. To evaluate the safety and the time duration required to use a portable head CT (pCTH) scanner in the intensive care unit (ICU) in the French healthcare system in ICU patients admitted for acute brain injury.We prospectively included all ICU-patients admitted for severe ABI over a 2-year period following before-after design. As the main outcome, we compared the time required to perform a scan with pCTH to that with conventional head CT (cCTH) and reported adverse events. In total, forty-five patients were included (25 in the pCTH group and 21 in the cCTH group). The median (interquartile) time required to perform a scan with pCTH was 28 (23-48) minutes compared to 30 (25-36) minutes with cCTH (p=0.825). The duration time required to perform a pCTH was similar to that with cCTH in an ICU of the French healthcare system without increasing adverse events.
Barriers and facilitators of consistent condom use among adolescents and young adults in South Africa: A cross-sectional survey
Authors: Ajayi Anthony Idowu , Omonaiye Olumuyiwa , Nwogwugwu Charlotte 
Published: March 2022

Abstract
BackgroundPrevious studies have examined consistent condom use correlates in South Africa, focusing on sociodemographic factors, HIV risk perceptions, relationship conflict, multiple sexual partners, and masculinity. However, the effect of family financial support, HIV testing, partner communication and self-efficacy for HIV prevention is less studied. We drew from a cross-sectional survey to address this gap and highlight the key barriers and facilitators of consistent condom use among young people. Methods We analysed data obtained from 631 unmarried sexually active male and females students selected using stratified sampling from a university in Eastern Cape Province of South Africa. Consistent condom use was defined as regular use of condoms in all sexual encounters in the past year. We used an open-ended question to probe the reasons for inconsistent condom use. Adjusted and unadjusted regression analysis were fitted to examine factors associated with consistent condom use. ResultsThe prevalence of consistent condom use was 39.3% (CI: 35.5%-43.2%), with no significant gender and age differences. After adjusting for relevant covariates, living with foster parents (AOR; 1.80 95% CI; 1.09-2.97), adequate family financial support (AOR; 2.49 95% CI; 1.71-3.62), partner knew status (AOR; 1.91 95% CI; 1.09-3.37) and feeling confident in one's ability to prevent HIV (AOR; 1.77 95% CI; 1.09-2.86) were associated with increased odds of consistent condom use. However, self-report of low condom self-efficacy (AOR; 0.58 95% CI; 0.40-0.85) and alcohol use (AOR; 0.83 95% CI; 0.58-1.19) were associated with lower odds of consistent condom use. Young people who inconsistently used condoms reiterated that sex is often unplanned and condoms are not always available. The desire for maximum pleasure, partner's objection, trust, and use of hormonal contraceptives were further reasons others inconsistently use condoms.Conclusions Inconsistent condom use remains a challenge among unmarried sexually active young people in South Africa. Education of young people on the need for partner communication about HIV, HIV testing uptake, and condom use should happen more rigorously in school and through the media to improve their consistent use of condoms.
Recurrent exon-deleting activating mutations in AHR act as drivers of urinary tract cancer
Authors: Vlaar Judith , Borgman Anouska , Kalkhoven Eric , Westland Denise , Besselink Nicolle , Shale Charles , Faltas Bishoy , Priestley Peter , Kuijk Ewart , Cuppen Edwin 
Published: March 2022

Abstract
Bladder cancer has a high recurrence rate and low survival of advanced stage patients. Few genetic drivers of bladder cancer have thus far been identified. We performed in-depth structural variant analysis on whole-genome sequencing data of 206 metastasized urinary tract cancers. In ˜10% of the patients, we identified recurrent in-frame deletions of exons 8 and 9 in the aryl hydrocarbon receptor gene (AHRΔe8-9), which codes for a ligand-activated transcription factor. Pan-cancer analyses show that AHRΔe8-9 is highly specific to urinary tract cancer and mutually exclusive with other bladder cancer drivers. In AHRΔe8-9 the ligand-binding domain is disrupted and we show that this results in ligand-independent AHR-pathway activation. In bladder organoids, AHRΔe8-9 induces a transformed phenotype that is characterized by upregulation of AHR target genes, downregulation of differentiation markers and upregulation of genes associated with stemness and urothelial cancer. Furthermore, AHRΔe8-9 expression results in anchorage independent growth of bladder organoids, indicating tumorigenic potential. DNA-binding deficient AHRΔe8-9 fails to induce transformation, suggesting a role for AHR target genes in the acquisition of the oncogenic phenotype. In conclusion, we show that AHRΔe8-9 is a novel driver of urinary tract cancer and that the AHR pathway could be an interesting therapeutic target.
Research Status and Development Trends of Network Pharmacology in Chinese Medicine
Authors: Wang Hanye , Cui Xiuming , Liu Yuan 
Published: March 2022

Abstract
Background: The increasing demand for Chinese medicine resources has piqued the scientific community’s interest in modernizing the Chinese medicine industry. However, traditional Chinese medicine (TCM) is based on the "multiple targets and multiple components" treatment modality and involves unique treatment methods, such as "same disease with different treatments" and "treating different diseases with same method." Hence, it is difficult to elucidate the mechanisms of TCM formulations. Network pharmacology enables the analysis of the characteristics of "multiple components, multiple targets, and multiple pathways," which is consistent with the overall characteristics of TCM. Hence, network pharmacology analysis can be used to examine the active ingredients, mechanism of action, and compatibility rules of TCM, consequently providing a scientific basis for the theories of TCM. Results: Network pharmacology is a new pharmacological research method that can quickly predict the pharmacological action mechanism of TCMs. Compared with traditional pharmacological research, this method does not require complicated TCM extraction and long-term experimental verification, is fast and efficient, but has certain errors. Combined with multi-omics methods, it can reduce the error while shortening the experiment time, and it can be used in the analysis of the mechanism of action and compatibility of TCM quickly and efficiently. In addition, the application of this method in reverse pharmacology is helpful for the development of new Chinese medicines for specific diseases. In our article, we briefly summarize the commonly used databases and software and calculation methods, and pay more attention to the combination of multi-omics and TCM. At the same time, we also summarize the mechanism of single prescription, compound prescriptions, "same disease with different treatments and treating different diseases with the same method" in TCM, reverse pharmacology of TCM.Conclusions: Network pharmacology has unique advantages to active ingredients, compatibility rules, and mechanisms of action explorations of TCMs. Using network pharmacology to clarify the mechanism of TCM can enhance the global acceptance of TCM products and promote the modernization and international development of the TCM industry, as well as providing a scientific basis for the law of compatibility of TCM.
Ocular manifestations of early-onset combined methylmalonic acidemia and mutations in MMCHC gene
Authors: Zhong Qionglei , Wang Shaoli , Li Yueping , Zhang Wei , Xue Caihong 
Published: March 2022

Abstract
Purpose: Combined MMA is related with retinopathy and optic neuropathy. We aimed to find the relationship of genotypes, the levels of metabolites and ocular damages in combined MMA.Methods: We retrospectively analyzed the ocular manifestations, gene tests and levels of organic acid metabolism in seven patients with early-onset combined MMA. Results: Seven patients aged 2 to 7 years old, revealed different gene mutations. Two patients with remarkable retinal degenerations had mutations in MMCHC gene, which were one heterozygous for c.567dupT p.Ile190Tyrfs*13, c.658_660del p.Lys220del, the other one with c.482G>A, p. R161Q, c.567dupT, p. I190Yfs*13 genotypes. Four patients present normal fundus, in whom one was homozygous for c.609G>A, p. W203X, the second one was heterozygous for c.609G>A, p. W203X, c.626dupT p.Thr210Aspfs*35, the third one with c.567dup, p.I190Yfs*13, c.606-641delins CTT, p.W203-R214delinsF, the last one with c.609G>A, p. Trp203*, c.615C>A, p. Tyr205*genotypes. There was one patient who was heterozygous for c.609G>A, p. Trp203*, c.615C>A, p. Tyr205* revealed light color of optic nerve but normal VEP. Elevated level of plasma homocysteine and normal levels of MMA concentrations and its metabolites revealed in two patients with remarkable retinal degenerations, whereas the levels of plasma homocysteine, MMA and its metabolites were normal in five patients without retinal disease.Conclusions: The mutations detected may be related to retinopathy and optic neuropathy in children with combined MMA. Metabolite levels may also affect the clinical manifestations.
Smart Film Based on Polylactic Acid, Modified with Polyaniline/ZnO/CuO: Investigation of Physicochemical Properties and its use of Intelligent Packaging of Orange Juice
Authors: Abdolsattari Parisa , Rezazadeh-Bari Mahmoud , Pirsa Sajad 
Published: March 2022

Abstract
In this study, a biodegradable/conducting film based on polylactic acid (PLA) modified with polyaniline, zinc oxide and copper oxide (PLA/PAn/CuO/ZnO) was prepared. The effect of polyaniline, zinc oxide and copper oxide on the electrical, physicochemical, antioxidant and antimicrobial properties of polylactic acid films by different techniques such as SEM, FTIR, TGA, etc. were investigated. Electricity conductive films were used for intelligent packaging of orange juice. The chemical and microbial properties of orange juice and the electrical conductivity of packaging films during storage time (56 days) were investigated. The results showed that the effect of polyaniline, zinc oxide and copper oxide greatly increased the antioxidant and antimicrobial properties of polylactic acid film. Polyaniline gave the film good electrical conductivity, but zinc oxide and copper oxide had no significant effect on it. The active film used to package the orange juice increased the chemical and microbial viability of the orange juice. The electrical resistance of the conductive films used for packaging increased over time and a significant mathematical relationship was established between storage time and changes in electrical resistance, which was used to estimate the shelf life and expiration date of orange juice. Examination of the performance of the films showed that these films with an accuracy of over 90% have the ability to estimate the storage time of orange juice. Electricity conductive/antimicrobial/antioxidant film based on polylactic acid as an active and intelligent film has the ability to increase the shelf life and detect spoilage of orange juice.
A novel intergenic region ALK fusion is targetable by alectinib in a non-small cell lung cancer patient with brain metastasis
Authors: Qian Chunfa , Cheng Wanwan , Zhang Haitao , Meng Qi , Yin Jiani C. , Fang Shencun 
Published: March 2022

Abstract
ALK rearrangement defines a unique non-small cell lung cancer (NSCLC) molecular subtype, of which the patients could potentially benefit from anti-ALK therapies. So far, the outcomes of the canonical EML-ALK patients subjected to ALK inhibitors are well established. However, given the increasing complexity of ALK fusion partners, as detected by high-throughput sequencing, the responses of those with rare ALK fusion events remain to be explored. Here, we report a lung adenocarcinoma patient with brain metastasis harboring an ARHGAP5 downstream intergenic region (IGR) ALK fusion, as detected by using DNA-based next-generation sequencing (NGS), who experienced a partial response to alectinib treatment. While whole transcriptome RNA sequencing (RNA-seq) failed to identify potential ALK fusion transcripts, subsequent targeted deep RNA-seq revealed the expression of EML4-ALK transcripts in the tumor tissue. Given the increasingly application of the ALK-TKIs, it is extremely crucial to define the patients who could be suitable for this treatment in clinic. The present case has provided supporting evidence that non-canonical ALK rearrangements on the genomic level are often functionally relevant and targetable by ALK-TKI, particularly in cases with sub-optimal quantity and quality for RNA validation.
Primary undifferentiated pleomorphic sarcoma of the rectum: A case report and review of the literature
Authors: Kodera Keita , Hoshino Masato , Takahashi Sumika , Hidaka Suguru , Kogo Momoko , Hashizume Ryosuke , Imakita Tomonori , Ishiyama Mamoru , Ogawa Masaichi , Eto Ken 
Published: March 2022

Abstract
Background: Undifferentiated pleomorphic sarcoma (UPS) is a malignant soft tissue tumor that has been reclassified from malignant fibrous histiocytoma with the development of the pathological diagnosis. It principally occurs in the extremities, but rarely occurs in the rectum. We herein report a rare case of UPS arising in the rectum.Case presentation: A 85-year-old woman was referred to our hospital with a complaint of anal pain, which had persisted for several months. Computed tomography (CT) showed a 53×58×75 mm mass on the left side of the rectum. Colonoscopy revealed a submucosal elevation in the rectum without any exposure of the tumor to the surface. Contrast-enhanced CT and magnetic resonance imaging revealed an 80-mm-mass that originated in the rectal muscular propria, and we suspected a gastrointestinal stromal tumor. No lymph node metastasis or distant metastasis was observed. We performed a laparoscopic Hartmann's operation. Intraoperatively, severe adhesion around the tumor caused tumor injury and right ureteral dissection. Thus, laparoscopic right ureteral anastomosis and ureteral stenting were additionally performed. The operation time was 6 hours and 3 minutes, and the estimated blood loss was small. The patient was discharged without complications 25 days after surgery. A pathological examination showed that the tumor was composed of highly heterogeneous cells with no specific differentiation traits, leading to a diagnosis of UPS. Contrast-enhanced CT performed 2 months after surgery showed bilateral pelvic lymph node enlargement, which indicated recurrence. Considering the patient's age, we performed radiotherapy (50 Gy/25 Fr targeting the pelvic region). At present, 16 months have passed since the completion of radiotherapy, Contrast-enhanced CT shows that the recurrent lymph nodes have disappeared and no new distant metastasis has been observed. Conclusions: We reported a case of UPS arising in the rectum. The surgical procedure and indication of preoperative therapy should be carefully selected because complete removal of the tumor is desirable in UPS.
The Acid Sphingomyelinase Inhibitor Amitriptyline Ameliorates TNF-α-induced Endothelial Dysfunction via the MAPK Signaling Pathway
Authors: Ji Yang , Chen Jing , Pang LiHua , Chen Changnong , Ye Jinhao , Liu Hao , Chen Huanzhen , Zhang Songhui , Liu Shaojun , Liu Benrong , cheng chuanfang , Liu Shiming , Zhong Yun 
Published: March 2022

Abstract
Purpose
Inflammation associated endothelial cell (ECs) dysfunction is key to atherosclerotic disease. The soluble endo-lysosomal protein, acid sphingomyelinase (ASMase) plays a crucial role in atherosclerosis. However, the mechanism by which ASMase regulates the inflammatory reaction in ECs remains unknown. Numerous studies have demonstrated that in addition to the antidepressant effects, amitriptyline can also effectively inhibit ASMase. Thus, the aim of this study was to investigate whether the effects of amitriptyline protect against inflammation in TNF-α-induced ECs.
Methods
HUVEC were pre-incubated with 2.5 µM amitriptyline (1 h) and subjected to 23 h TNF-α (20 ng/ml). EdU, tube formation, transwell and monocyte adhesion assay were performed to investigate the endothelium function. Vascular tone measurement was used to detected endothelial-dependent relaxation in mice. Protein levels of ICAM-1, VCAM-1, MCP-1, MAPK and NF-κB were detected using western blot.
Results
We demonstrated that preconditioning with the amitriptyline down-regulated TNF-α-induced expression of proinflammatory proteins including ICAM-1, VCAM-1, and MCP-1 in ECs, as well as the secretion of sICAM-1 and sVCAM-1. Additionally, we demonstrated that amitriptyline suppressed TNF-α-induced MAPK phosphorylation as well as the activity of NF-κ B in HUVEC. Results also indicated that with treatment of TNF-α, the aorta of ASMase−/− mice showed elevated endothelial-dependent relaxation compared to wild-type counterparts.
Conclusion
These results suggest that the AMI reduces endothelial inflammation, consequently improving vascular endothelial function. This study showed that amitriptyline might protect ECs from TNF-α-induced inflammation. Thus, identification of amitriptyline as a potential strategy to reverse endothelial function is of importance to preventing vascular diseases.
New Binary and Ternary Quasi-Cyclic Codes with Good Properties
Authors: Akre Dev , Aydin Nuh , Harrington Matthew , Pandey Saurav 
Published: March 2022

Abstract
One of the most important and challenging problems in coding theory is to construct codes with best possible parameters and properties. The class of quasi-cyclic (QC) codes is known to be fertile to produce such codes. Focusing on QC codes over the binary field, we have found 113 binary QC codes that are new among the class of QC codes using an implementation of a fast cyclic partitioning algorithm and the highly effective ASR algorithm. Moreover, these codes have the following additional properties: a) they have the same parameters as best known linear codes, and b) many of the have additional desired properties such as being reversible, LCD, self-orthogonal or dual-containing. Additionally, we present an algorithm for the generation of new codes from QC codes using ConstructionX, and introduce 33 new record breaking linear codes over GF(2), GF(3) and GF(5) produced from this method.