bluuebunny/crossref_metadata_2025_split huggingface dataset:
Time is precious for a scientist: Harmonization and standardization of manuscript submission to journals
Authors: YILMAZ Huriye ERBAK , YILMAZ Murat 
Published: April 2022

Abstract
Background
Preparation and submission of a manuscript per the specific instructions of every publisher is time consuming for not only authors but also for reviewers and authors as well. This condition constitutes an obstacle for scientific development as well. In this aim, description of uniform criteria representing contents of paper submission as well as practical principles for manuscript preparation and submission will be useful both to save time and to reinforce spread of scientific information.
Methods
A cross-sectional study was performed by collection of relevant data from journal sites, publishers’ instructions for authors, online submission resources and experiences of journal editors, authors, and reviewers.
Results
The instructions for authors for submission of a manuscript differ remarkably per various journals. These variations include formats of cover letter, title page, abstract, references, as well as manuscript font type and size. The word limit for the abstract and manuscript as well as figure and page arrangements is highly variable between journals. There are no uniform and standards for the conflicts of interest and author contribution forms per the publishers.
Conclusion
It is necessary to establish standard guidelines for facilitation and harmonization of manuscript preparation and submission to journals. The lack of a standard template for submission of manuscripts to journals leads to waste of time and decreased motivation for authors. We suggest that reaching such a consensus on a standard module for preparation and submission of manuscripts for all journals will be useful for both saving time and maintenance of sustainability in publishing.
Bacterial Community Composition and Diversity Changes Across an Agricultural Intensity Gradient
Authors: Mason Alexander Robert George , Cavagnaro Timothy , Guerin Greg , Lowe Andrew 
Published: April 2022

Abstract
Ecological impacts associated with agricultural land use change are evident via the direct replacement of natural communities with managed production systems. These impacts are extensively studied, but the implications for soil biology and belowground diversity remain poorly understood. Due to their contribution to soil systems and ability to survive under harsh and changing conditions, soil bacteria are a good candidate to highlight belowground ecological community dynamics. Here, we use soil physicochemical assessment and 16S rDNA sequencing to investigate soil bacterial community assemblage across an agricultural intensity gradient in a semi-arid mixed-use agricultural landscape. We collected and assessed soil samples from distinct land use systems including remnant vegetation, old pasture, recently established vineyards and old vineyards and recently revegetated areas. We found that land use systems differed in soil physicochemical characteristics (specifically nitrogen and phosphorus) likely influenced by agricultural inputs and plant functional diversity. Land use and management practises were also linked to a shift in the soil microbiome, such that distinct bacterial communities were associated with specific land use systems. Counter to expectations, highest bacterial diversity was observed in the most intensively modified agricultural systems (vineyards). These systems were also broadly linked with a beneficial bacterial community shift (in the context of soil and plant health). The community composition of recently revegeted areas was also more similar to remnant habitat suggesting that bacterial community composition can respond quickly to above ground changes. Collectively, results suggest that while vineyard agriculture may reduce aboveground plant diversity, it can increase belowground bacterial diversity. We propose that this is in-part due to disturbance associated with the vineyard agricultural systems. These findings highlight the need to further explore practices influencing soil biological components in agricultural systems, and the potential to develop microbiome-based strategies to enhance soil health and agricultural productivity.
Research on Key Algorithms of the Lung CAD System Based on Deep Feature Fusion and MKL-SVM-IPSO Recognition
Authors: Li Yang , Zheng Hewei , Huang Xiaoyu , Chang Jiayue , Hou Debiao , Lu Huimin 
Published: April 2022

Abstract
Lung CAD system can provide auxiliary third-party opinions for doctors, improve the accuracy of lung nodule recognition. The selection and fusion of nodule features and the advancement of recognition algorithms are crucial improving lung CAD systems. Based on the HDL model, this paper mainly focuses on the three key algorithms of feature extraction, feature fusion and nodule recognition of lung CAD system. First, CBAM is embedded in VGG16 and VGG19 to construct feature extraction models AE-VGG16 and AE-VGG19. So that the network can focus more on the key points in nodule description. Characteristic information. Then, feature dimensionality reduction based on PCA and feature fusion based on CCA are sequentially performed on the extracted depth features to obtain low-dimensional fusion features. Finally, the fusion features are input into the proposed MKL-SVM-IPSO model based on the improved Particle Swarm Optimization algorithm to speed up the training speed, get the global optimal parameter group. The public dataset LUNA16 was selected for the experiment. The results show that the accuracy of lung nodule recognition of the proposed lung CAD system can reach 99.56%, and the sensitivity and F1-score can reach 99.3% and 0.9965, respectively, which can reduce the possibility of false detection and missed detection of nodules.
Clinical features of Herpes Simplex Virus Reactivation after Microvascular Decompression for Trigeminal Neuralgia: Experience of 200 patients and a literature review
Authors: Kikuchi Asami , Ishizaki Sumiko , Yokosako Suguru , Kubota Yuichi , Kasuya Hidetoshi 
Published: April 2022

Abstract
Background and Objective: Herpes simplex virus (HSV) reactivation occasionally develops in the early postoperative period after microvascular decompression (MVD) for trigeminal neuralgia (TN). Therefore, the present study investigated the clinical features of this phenomenon. Methods: The study cohort comprised 200 patients with 125 (63%) women aged between 17 and 90 years (median age, 66 years) who underwent MVD for TN between January 2010 and December 2020. Characteristics were compared between patients with and without HSV reactivation and clinical features were analyzed. Results: Twenty patients had HSV reactivation: herpes labialis in 18; herpes zoster (final diagnosis) in 2. A multivariate analysis revealed independent correlations between postoperative HV reactivation and a previous history of herpes labialis (OR:6.32, p=0.0003) and re-operation for recurrent or persistent pain (OR:5.06, p=0.0211). No significant differences were observed in pain relief, postoperative facial numbness, or BNI Pain Intensity/Facial Numbness Scores in the last follow-up between patients with and without HSV reactivation. HSV reactivation manifested at a median of the 4th postoperative day (1-10 days) and its location was not related to the preoperative distribution of facial pain. All patients were treated with local acyclovir and were completely cured within 1-2 weeks. Conclusions: HSV reactivation occurred in 10% of patients after MVD including 1% of herpes zoster. A previous history of herpes labialis and re-operation were identified as risk factors for reactivation. Symptoms were completely cured by antiviral drugs within 1-2 weeks. It is important to note that cases of herpes zoster may be confused with cases of herpes simplex virus after MVD.
LncRNA FAM83H-AS1 promotes malignant progression of pancreatic ductal adenocarcinoma by stabilizing FAM83H mRNA to protect β-catenin from degradation
Authors: Qin renyi , Zhou Min , Pan Shutao , Qin Tingting , Zhao Chunle , Yin Taoyuan , Gao Yang , Liu Yuhui , Zhang Zhenxiong , Shi Yongkang , Bai Yu , Gong Jun , Guo Xingjun , Wang Min 
Published: April 2022

Abstract
Background: Pancreatic cancer was prone to metastasis, which leaded to the poor survival and low quality of life. Here, we found that FAM83H-AS1 was highly correlated with metastasis of pancreatic cancer and further explored the functions and mechanisms involving in the malignant progression of pancreatic cancer. Method: We profiled and analyzed the aberrant expression of lncRNA (long non-coding RNA) in TCGA database and screened FAM83H-AS1 most effective in promoting the migration of pancreatic cancer cells. Firstly, the expression level of FAM83H-AS1 in serum, tissues and cells were detected by RT-qPCR, and the distribution of it in pancreatic cancer cells was tested by FISH and nuclear/cytosol fractionation RT-qPCR. Next, a series of functional assays were conducted to elucidate the relationship between FAM83H-AS1 and pancreatic cancer in vivo and vitro. The regulation relationship between FAM83H-AS1 and FAM83H was verified by protein and RNA degradation assays respectively. A series of Co-immunoprecipitation assays was utilized to explore the potential mechanism of FAM83H and β-catenin. Rescue assays were used to illustrate the regulation axis of FAM83H-AS1/FAM83H/ Wnt/β-catenin in pancreatic cancer.Results: FAM83H-AS1 was highly expressed in cancer tissues and serum of PDAC patients, and was correlated with poorer survival. FAM83H-AS1, as an oncogene, promoted the proliferation, invasion and metastasis of PDAC cells by functional assays and bioinformatics analysis. FAM83H, the homologous gene of FAM83H-AS1, also manifested the same biological behaviour as FAM83H-AS1 in PDAC. Also, FAM83H-AS1 protected FAM83H mRNA from degradation and FAM83H directly bound β-catenin. Mechanically, FAM83H-AS1 facilitated the expression of FAM83H by stabilizing its mRNA and promoted FAM83H to decrease the ubiquitylation of β-catenin, which activated the effect genes of Wnt/β-catenin signalling.Conclusions: This study revealed the function of FAM83H-AS1 involving in the progression of PDAC, and might provide a new prognostic indicator and therapy target for PDAC.
Prognostic value and antitumor immune response elicited by FAT3 and LRP1B co-mutation in endometrial cancer
Authors: Jiang Zhansheng , Zhu Mingyu , Zhang Lu , Cui Haiyan , Wang Hao , Zhai Baochao , Jiang Richeng , Yang Yanfang 
Published: April 2022

Abstract
FAT3 and LRP1B, two tumor suppressor genes with high mutation frequency in multiple cancer types, have been linked to prognosis and prediction of immunotherapy response in a few previous studies, but their clinical significance in endometrial cancer (EC) has been relatively poorly studied. In this study, based on a cohort of 502 EC samples, we performed a comprehensive analysis of its multidimensional data types including genomic, transcriptomic, and clinical information. We observed that the incidences of FAT3 and LRP1B mutations in EC patients were 19.52% and 19.32%, respectively, and there was a tendency for co-occurrence between mutations of these two genes, with a co-mutation frequency of 11.16%. FAT3 and LRP1B co-mutation was not only associated with age, weight, tumor type, and new neoplasm event, but also defined a dataset with prominently increased mutational burden, decreased tumor aneuploidy, and specially enriched in microsatellite instability high (MSI-H). Furthermore, the co-mutation subgroup manifested increased expression of cytotoxic T-cell markers, effector cytokines, and immune checkpoints, especially exclusive upregulation of PD-L1 levels and higher PD-L1+/CD8A+ proportion. Further analysis focused on lymphocyte infiltration and pathway enrichment explored the immune cell composition of the microenvironment and underlying molecular mechanisms affecting tumor development. More strikingly, EC patients with FAT3 and LRP1B co-mutation possessed significantly prolonged progression free survival (PFS) and overall survival (OS). In conclusion, this research provides evidence that FAT3 and LRP1B co-mutation may serve as a potential prognostic and predictive biomarker of antitumor immunity activation in endometrial cancer.
Stunting does not randomly occur in Indonesia: A spatial analysis
Authors: Sipahutar Tiopan , Eryando Tris , Budhiharsana Meiwita Paulina , Siregar Kemal N. , Aidi Muhammad Nur , Utari Diah Mulyawati , Rahmaniati Martya , Hendarwan Harimat , Minarto Minarto 
Published: April 2022

Abstract
Background
Indonesia is a vast country that is still struggling to reduce its prevalence of stunting. Thus, identifying priority areas is urgent. In determining areas to prioritize, one needs to consider geographical issues, particularly the correlation among areas. This study aimed to discover whether stunting prevalence in Indonesia occurs randomly or in clusters and, if it occurs in clusters, which areas are the hotspots.
Method
This ecological study used aggregate data from the Basic Health Research Report of Indonesia 2018 and the Poverty Data and Information Report from the Central Bureau of Statistics 2018. We analysed 514 districts/cities across 34 provinces on seven major Indonesian islands. We used the Euclidean distance method to determine stunting hotspots. A Moran’s I test was used to identify autocorrelation, while a Moran scatter plot was used to identify stunting hotspots, particularly those in the high–high quadrant.
Result
Autocorrelation was found among districts/cities in Sumatera, Java, Sulawesi, and Bali Nusa Tenggara Timur (NTT) and Nusa Tenggara Barat (NTB), resulting in 135 districts/cities identified as stunting hotspots on four major islands.
Conclusion
Autocorrelation proves that stunting in Indonesia does not occur randomly.
Not just species recording: what is the role for volunteers in supporting assessment of habitat?
Authors: Barnes A. E. , Pocock M. J. O. , Jones G. , Newton N. , Robinson R. A. 
Published: April 2022

Abstract
Reversing the global biodiversity crisis requires not only conservation and management of species, but the habitats in which they live. However, while there is a long history of biodiversity recording, especially in Europe, information on habitats is less frequently recorded meaning knowledge of their extent and quality is generally poor. In part, this is because recording of the sometimes complex features that differentiate habitats has traditionally been done by trained professionals at a limited number of sites. However, both Earth Observation methods and citizen scientists provide opportunities to expand the range and scale of habitat recording. We provide a framework for determining how citizen scientists, particularly those that are already collecting biodiversity data, can contribute to monitoring of habitats and discuss the opportunities and challenges associated with this. We illustrate the application of our framework with reference to existing habitat recording by biodiversity recorders in the UK, both to assess the extent/quality of existing habitat, but also as a tool for validating Earth Observation data.
Deep Neural Features for Document Image Analysis
Authors: Mondal Ajoy , Jawahar C. V. 
Published: April 2022

Abstract
Recent studies show that the deep Convolutional Neural Networks (CNN)s have performed impressively well on various document image analysis tasks. Possibly, there is a limited systematic study to know why deep cnns perform so well for document image analysis tasks. In this paper, we explore a multi-layered Deconvolutional Network (deconvnet) to visualize and analyze learned features by cnns for various document image analysis tasks. The deconvnet projects the learned feature activation of a layer back into the input pixel space for visualizing features. We create one new dataset: Indic-Script, and use two existing datasets: DOCFigure and RVL-CDIP for visualizing learned features by the cnns for Indic script classification, document figure classification , and document image classification tasks, respectively. Experimental results conclude that (i) the initial layers of the network learn more generic features like vertical, horizontal, circular, diagonal edges, etc, (ii) higher layers learn class-specific features — Layer4-Layer6 learn features corresponding to a character of a word, Layer7-Layer9 learn features related to words, and Layer10-Layer12 learn features connected to text presents in the document. We hope that this paper helps the readers to interpret the network’s insight, motivating them to design new networks for various document analysis tasks.
Quinacrine inhibits cMET-mediated metastasis and angiogenesis in breast cancer stem cells
Authors: Das Biswajit , Sethy Chinmayee , Chatterjee Subhajit , Dash Somya Ranjan , Sinha Saptarshi , Paul Subarno , Goutam Kunal , Kundu Chanakya Nath 
Published: April 2022

Abstract
A trans-membrane receptor, mesenchymal-epithelial transition factor (cMET), is responsible for cancer metastasis and angiogenesis. A very little is known about the role of cMET in cancer stem cells (CSCs). Quinacrine (QC), a bioactive agent, has shown anti-CSCs activity. Here, the role of QC in deregulation of cMET-mediated metastasis and angiogenesis has been systematically evaluated in vitro in highly-metastatic-breast-CSCs (mBCSCs), ex vivo in patient-derived-breast-cancer-stem-cells (PDBCSCs) and in vivo in xenograft mice model systems. Cell proliferation, migration, invasion and representative metastasis markers were upregulated in cMET-overexpressed cells and QC exposure inhibited these processes in both mBCSCs and PDBCSCs. Interestingly, metastasis was inhibited after silencing of cMET and very less significant alteration of the process was noted in QC-treated cMET-silenced cells. Increased in vascularization, and cell-cell tube formation, and enhanced MMP2 and MMP9 enzymatic activities were noted after cMET-overexpression but these processes got reversed after cMET knockdown. In addition, QC inhibited angiogenesis after cMET-overexpression, but failed to change in cMET-silenced cells. Reduction of tumor volume and decreased expression of metastatic and angiogenic markers were also noted in xenograft mice after QC treatment. Furthermore, QC inhibited cMET activity by de-phosphorylation of its tyrosine residues (Y1234 and Y1356) and downregulation of its downstream cascade.
Cost-Effectiveness of a Shorter Four-Month Tuberculosis Treatment Regimen in India
Authors: Muniyandi Malaisamy , Karikalan Nagarajan , Velayutham Banurekha , Rajsekar Kavitha , Padmapriyadarsini Chandrasekaran 
Published: April 2022

Abstract
Globally efforts are underway to shorten the existing 6-month tuberculosis (TB) treatment regimen for drug-sensitive patients, which would be equally effective and safe. At present, there is a lack of evidence on the cost implications of a shorter 4-month TB regimen in India. This economic modeling study was conducted in the Indian context with a high TB burden. We used a hybrid economic model comprising of a decision tree and Markov analytics. The study estimated the incremental costs, life-years (LYs), and quality adjusted life years (QALYs) gained by the introduction of a Moxifloxacin-based shorter 4-month treatment regimen for pulmonary TB patients. The outcomes are expressed in incremental cost-effectiveness ratios (ICERs) per QALYs gained. The cost per case to be treated under the 4-month regimen was $145.94 whereas for the 6-month regimen it was $150.39. A shorter 4-month TB regimen was cost-saving with $4.62 per LY and $5.29 per QALY. One-way sensitive analysis revealed that the cost of the drugs for the 4-month regimen, hospitalization cost for adverse drug reaction, and human resources incurred for the 6-month regimen had a higher influence on the ICER. The short-course first-line 4-month TB treatment regimen was found to be cost-saving to both patients and National TB Elimination Programme in India.
Relationship between neuromuscular profile and total volume of resisted sprint training in male professional soccer players
Authors: Grazioli Rafael , Loturco Irineu , Veeck Filipe , Radaelli Regis , Teodoro Juliana L. , Garcia-tabar Ibai , Inácio Martinho , Pinto Ronei S. , Cadore Eduardo L. 
Published: April 2022

Abstract
Purpose: This 11-week study aimed to correlate the neuromuscular profile and the total volume of resisted sprint training (RST) under different velocity loss (VL) magnitudes in male professional soccer players. Methods: Seventeen soccer players (age 25.8±4.3 years; height 180.0±8.6 cm; weight 77.7±9.7 kg) were randomly allocated into two training groups, who trained at distinct percentages of VL: 10% of VL (G10, n=8) or 20% of VL (G20, n=9). The velocity-based sled training consisted of 20m resisted sprints executed with a progressive loading increase (45% to 65% of body-mass). Sprint times (10m and 20m), vertical jump height (countermovement jump [CMJ] and squat jump [SJ]), knee flexion and extension peak torque, as well as isometric rate of torque development, and lower-limb lean mass were correlated with the total volume of RST performed by G10 and G20 groups. Results: The G10 performed 31% less repetitions and total RST distance than G20 (p<0.05). Significant negative Pearson’s correlations (large-to-very large) were observed between total volume performed by G10 and CMJ height (r=-0.85, p=0.016) as well as SJ height (r=-0.90, p= 0.005), and knee extension concentric peak torque (r=-0.70, p=0.05). No further correlation was found (p>0.05). Conclusions: When lower magnitudes of VL were used during training sessions (10%), the stronger and more powerful players performed lower volume of RST. Interestingly, this relationship is not confirmed when higher magnitudes of VL (20%) are prescribed (greater fatigue incidence).