bluuebunny/crossref_metadata_2025_split huggingface dataset:
The association of gene expressions of MAP3K7, NF2, STK3 and STK4 therewith Quantum Resonance Magnetic Analyzer (QRMA) in COVID-19 patients
Authors: Abdolyousefi Ehsan Nabi , Kahkesh Samaneh , Saadi Mahdiyar Iravani , Nabi Mehran 
Published: June 2023

Abstract
Objectives
COVID-19 is initiated by coronavirus infections and it can principally damage the cell’s function of the lung. Assessment of some important genes may capability more operational administration in patients. Therefore, in the recent study, we investigated mRNA and protein expression of MAP3K7, NF2, STK3 and STK4 in virus-infected patients compared with the control group. In addition, we used Quantum Resonance Magnetic Analyzer (QRMA) in order to analyze blood lipids, basic physical quality, lung function and immune system which are divided into twenty-five different variables in patients compared to healthy individuals.
Materials and Methods
The statistical population was divided into two different groups: patients and healthy individuals. The Expression of the mRNA level of objective genes was assessed with the SYBR Green Real-time Polymerase Chain Reaction method. The protein level expression of target genes was calculated by Enzyme-linked Immunosorbent Assay. Furthermore, in this study, we use QRMA to analyze some quantities such as blood lipids, basic physical quality, lung function and immune system in patients compared to healthy individuals. Statistical analyses were accomplished with SPSS software (version, 18) and Graph-Pad Prism software (Graph-Pad Prism, version 8.0.1).
Results
The mRNA and protein expressions level of NF2, MAP3K7, STK3 and STK4 genes in the group of patients decreased significantly compared to healthy individuals. The evaluation of blood lipids, basic physical quality, lung function and immune system in the study by QRMA showed that the Arterial oxygen content Paco2, low-density lipoprotein-C, tonsil immune index and immunoglobulin index were significantly higher in patients group compared to healthy individuals. In contrast, the amount of High-density lipoprotein-C, bone marrow index, respiratory immune index and gastrointestinal immune index were significantly lower in patients group compared to healthy individuals.
Conclusions
Compared to healthy individuals, the amount of mRNA and protein expressed by NF2, MAP3K7, STK3 and STK4 genes was reduced in COVID-19 patients. In truth, these genes have some critical function in some cellular and sub-cellular pathways. Accordingly, when the expression of genes decreased maybe it can increase the influence of coronavirus. Various mechanisms are involved in COVID-19, the increasing of the amount of the arterial oxygen content Paco2, low-density lipoprotein-C, tonsil immune index, immunoglobulin index and decreasing the amount of the High-density lipoprotein-C, bone marrow index, respiratory immune index and gastrointestinal immune index in COVID-19 patients, can be involved in the effects of coronavirus. Therefore, a deep perception of the relationship between these objective genes and QRMA therewith pathogenesis of COVID-19 infections in a larger population with longer supplements is required.
PROVISION OF FEEDBACK USING THE “4C/ID” MODEL FOR “Program Internsip Dokter Indonesia (PIDI)” ASSISTING PHYSICIANS: a mixed method research
Authors: Latief Shofiyah , Suhoyo Yoyo , Rahayu Gandes Retno , Royani Ida , Rahma Marliyanti Nur , Aisyah Windy Nur , Kartika Andy Visi , - Widyandana , Arguni Eggi , Utami Dian Fahmi 
Published: June 2023

Abstract
Objectives
The need of effective feedback is important to gain clinical performance improvement of new doctor. Evaluation carried out by the Komite Internsip Dokter Indonesia (KIDI) with the Asosiasi Institusi Pendidikan Kedokteran Indonesia (AIPKI) shows 38% of selected health care are not showing a maximum result in terms of giving feedback (less than 3 on a Likert scale). Thus, we would like to examine the impact of training on giving feedback using the "4C/ID" model on assisting physicians of the Program Internsip Dokter Indonesia (PIDI).
Methods
Mixed method study was employed. Structurized feedback using “4C/ID” model were trained to 14th assisting physicians from 3 hospital and 11 primary health care at Makassar, Gowa, and Maros. Questionnaire, Pre- and post-test, and check-lists were used to collect qualitative data followed by Kirckpatrick evaluation. Focus group discussions were organized twice to collect qualitative data and followed by an inductive thematic analysis.
Results
Kirkpatrick evaluation showed improvement of knowledge and skill on assisting physicians of PIDI after training on giving feedback using the "4C/ID" model. First FGD inductive thematic analysis offered 4 themes with 2 additional themes after the 2nd. All 6th themes were complimentary to quantitative data.
Conclusions
Training on giving feedback using the "4C/ID" model has a positive influence on knowledge and skill of assisting physicians of PIDI.
The application of epiphenotyping approaches to DNA methylation array studies of the human placenta
Authors: Khan Almas , Inkster Amy M , Peñaherrera Maria S , King Suzanne , Kildea Sue , Oberlander Tim F , Olson David M , Vaillancourt Cathy , Brain Ursula , Beraldo Ella O , Beristain Alexander G , Clifton Vicki L , Gobbo Giulia F Del , Lam Wan L , Metz Gerlinde AS , Ng Jane WY , Price E Magda , Schuetz Johanna M , Yuan Victor , Portales-Casamar Élodie , Robinson Wendy P 
Published: June 2023

Abstract
Background: Genome-wide DNA methylation (DNAme) profiling of the placenta with Illumina Infinium Methylation bead arrays is often used to explore the connections between in utero exposures, placental pathology, and fetal development. However, many technical and biological factors can lead to signals of DNAme variation between samples and between cohorts, and understanding and accounting for these factors is essential to ensure meaningful and replicable data analysis. Recently, “epiphenotyping” approaches have been developed whereby DNAme data can be used to impute information about phenotypic variables such as gestational age, sex, cell composition, and ancestry. These epiphenotypes offer avenues to compare phenotypic data across cohorts, and to understand how phenotypic variables relate to DNAme variability. However, the relationships between placental epiphenotyping variables and other technical and biological variables, and their application to downstream epigenome analyses, have not been well studied.
Results: Using DNAme data from 204 placentas across three cohorts, we applied the PlaNET R package to estimate epiphenotypes gestational age, ancestry, and cell composition in these samples. PlaNET ancestry estimates were highly correlated with independent polymorphic ancestry informative markers, and epigenetic gestational age, on average, was estimated within 4 days of reported gestational age, underscoring the accuracy of these tools. Cell composition estimates varied both within and between cohorts, but reassuringly were robust to placental processing time. Interestingly, the ratio of cytotrophoblast to syncytiotrophoblast proportion decreased with increasing gestational age, and differed slightly by both maternal ethnicity (lower in white vs. non-white) and genetic ancestry (lower in higher probability European ancestry). The cohort of origin and cytotrophoblast proportion were the largest drivers of DNAme variation in this dataset, based on their associations with the first principal component.
Conclusions: This work confirms that cohort, array (technical) batch, cell type proportion, self-reported ethnicity, genetic ancestry, and biological sex are important variables to consider in any analyses of Illumina DNAme data. Further, we demonstrate that estimating epiphenotype variables from the DNAme data itself, when possible, provides both an independent check of clinically-obtained data and can provide a robust approach to compare variables across different datasets.
Simulation of the sedimentary characteristics of braided deltas in a Paleogene salty lake, Qaidam Basin, China
Authors: Xiaojun Zhang , Yingchun Gou , Shiming Zhang , Juerong Fu , Pu Wang , Liangyu Wu 
Published: June 2023

Abstract
In recent years, oil reservoirs have been discovered in the large-scale delta sedimentary system of a salty lake in the Lower Ganchaigou Formation (E31) and the Lower Youshashan Formation (N21) in the western part of the Qaidam Basin. This discovery represented the start of an oil and gas exploration breakthrough in the Qaidam Basin. In this study, a braided delta deposition model of the salty lake was developed, and the regular patterns of sand accumulation from three source areas of Alar, Niubiziliang, and Tiemulike were investigated. These areas were then selected as sedimentary prototypes to conduct physical simulation experiments to examine large flume deposition, dynamic braided delta deposition processes, and models of sand accumulation. The results showed that the braided delta had sedimentary characteristics of a small delta front, with a large delta plain, underwater distribution channels, and a mouth bar in a saltwater environment. The lake salinity controlled the grain size, thickness, regularity of the spatial distribution, and particle transport distance, as well as the scale of development for the underwater distribution channels and the mouth bar. Due to the dynamic complexity of the lake inputs caused by the vertical stratification of salinity, the braided branch channels of the braided delta plain and the mouth bar of the braided delta front may hold good reservoirs.
Environmental regulation, Energy consumption structure and industrial pollution emissions
Authors: chen fangli , shao mimi , chen weitong , wang furu 
Published: June 2023

Abstract
China has become the world's largest carbon emitter due to its high-investment, low-efficiency development model. It is urgent to reduce industrial pollution emissions. This study analyzes the impact of environmental regulation intensity and energy consumption structure on industrial SO2 pollution emissions by establishing a fixed-effect regression model based on panel data from 2009 to 2018 in China. The results show that the overall environmental regulation intensity in China has a significant negative effect on industrial pollution emissions. In other words, increasing the level of environmental regulation is conducive to reducing industrial pollution emissions. The proportion of coal consumption in the overall national energy consumption structure has a positive correlation with the concentration of industrial pollution emissions. Due to the differences in economic development and industrial foundation, the pollution emissions effect shows significant heterogeneity in the eastern and western regions of China under the constraint of environmental regulation. Based on these conclusions, this article proposes policy recommendations from four aspects: strengthening environmental regulation, improving energy consumption structure, promoting industrial structure adjustment and upgrading, and improving the foreign investment access system.
Molecular phylogenetic analyses identify the process of speciation of endemic willow species in the Japanese Archipelago
Authors: Kikuchi Satoshi , Setsuko Suzuki , Nagamitsu Teruyoshi , Suzuki Wajiro 
Published: June 2023

Abstract
Here we examine the evolutionary history of Salix in Japan, and in particular the subg. Vetrix/Chamaetia complex. To do so, we performed molecular phylogenetic analyses covering all available native species, using multilocus datasets of low-copy nuclear genes and chloroplast sequences. Using phylogenetic network analysis and divergence time estimation, we identified three major lineages within Japanese subg. Vetrix, confirmed the polyphyly of subg. Chamaetia, and further resolved the taxonomic status of various taxa at the section to species levels. Moreover, this study also highlighted the speciation processes for many endemic species. These include S. hukaoana, a novel monotypic section of Hukaoana that distinctly shows ancient divergence and not hybrid speciation, and S. miyabeana (sect. Helix), which shows evidence of genomic and morphological differentiation from subsp. miyabeanavia intersectional hybridization and introgression with the sympatric species S. schwerinii (sect. Viminella). Finally, we also identified local endemics classified into sect. Hastatae(i.e., S. rupifraga, S. shiraii, and S. japonica) which show evidence of radiative speciation from a single lineage descended from S. vulpina(sect. Cinerella).
Racially Fair Pupillometry Measurements for RGB Smartphone Cameras using the Far Red Spectrum
Authors: Barry Colin , Wang Edward 
Published: June 2023

Abstract
Pupillometry is a measurement of pupil dilation commonly performed as part of neurological assessments. Prior work have demonstrated the potential for pupillometry in screening or diagnosing a number of neurological disorders including Alzheimer's Disease, Schizophrenia, and Traumatic Brain Injury. Unfortunately, the expense and inaccessibility of specialized pupilometers that image in the near infrared spectrum limit the measurement to high resource clinics or institutions. Ideally, this measurement could be available via ubiquitous devices like smartphones or tablets with integrated visible spectrum imaging systems. In the visible spectrum of RGB cameras, the melanin in the iris absorbs light such that it is difficult to distinguish the pupil aperature that appears black. In this paper, we propose a novel pupillometry technique to enable smartphone RGB cameras to effectively differentiate the pupil from the iris. The proposed system utilizes a 630nm long-pass filter to image in the red to far red spectrum, where the melanin in the iris reflects light to appear brighter in constrast to the dark pupil. Using a convolutional neural network, the proposed system measures pupil diameter as it dynamically changes in a frame by frame video. Comparing across 4 different smartphone models, the pupil-iris contrast of N=12 participants increases by an average of 451% with the proposed system. In a validation study of N=11 participants comparing the relative pupil change in the proposed system to a Neuroptics PLR-3000 Pupillometer during a pupillary light response test, the prototype system acheived a mean absolute error of 2.4%.
Ovarian serous borderline tumors with recurrent or extraovarian lesions: a Japanese, retrospective, multi-institutional, population-based study
Authors: Baba Tsukasa , Koshiyama Masafumi , Kagabu Masahiro , Mikami Yoshiki , Minamiguchi Sachiko , Moritani Suzuko , Ishikawa Mitsuya , Okamoto Aikou , Terao Yasuhisa , Nakanishi Toru , Katabuchi Hidetaka , Tokunaga Hideki , Satoh Toyomi , Konishi Ikuo , Yaegashi Nobuo 
Published: June 2023

Abstract
Background
Ovarian serous borderline tumors (SBT) are typically unilateral and are primarily treated using hysterectomy and bilateral salpingooophorectomy (SO). However, most young patients prefer fertility-sparing surgeries (FSS) with tumorectomy or unilateral SO. Micropapillary morphology and invasive implants have been designated as histopathological risk indicators for recurrence or metastasis, but their clinical impact remains controversial because of limitations like diagnostic inconsistency and incomplete surgical staging.
Methods
A nationwide multi-institutional population-based retrospective surveillance was conducted with a thorough central pathology review to reveal the clinical features of SBT. Of 313 SBT patients enrolled in the Japanese Society of Clinical Oncology's Surveillance of Gynecologic Rare Tumors, 289 patient records were reviewed for clinical outcomes. The glass slides of patients at stage II–IV or with recurrence or death were reevaluated by three gynecological pathologists.
Result
The 10-year overall and progression free survival (PFS) rates were 98.6% and 92.3%. A recurrence of 77.0% was observed in the contralateral ovary within a few years. Patients aged ≤ 35 years underwent FSS more frequently and relapsed more (p<.001). A clinic-pathological analysis revealed diagnosis during pregnancy, FSS, and treatment at non-university institutes as well as advanced stage and large diameter were independent risk factors of recurrence. Among patients having pathologically-confirmed SBTs, PFS was not influenced by the presence of micropapillary pattern or invasive implants.
Conclusion
The recurrence rate was lower in this cohort than previous reports, but the clinical impacts of incomplete resection and misclassification of the tumor were still significant on the treatment of SBT.
Type III interferon inhibits bladder cancer progression by reprogramming macrophage-mediated phagocytosis and orchestrating effective immune responses
Authors: Wang Bo , Zhou Bingkun , Chen Junyu , Sun Xi , Yang Wenjuan , Yang Tenghao , Yu Hao , Chen Peng , Chen Ke , Huang Xiaodong , Fan Xinxiang , He Wang , Huang Jian , Lin Tianxin 
Published: June 2023

Abstract
Background
Interferons (IFNs) are essential for activating an effective immune response and play a central role in immunotherapy-mediated immune cell reactivation for tumor regression. Type III IFN (λ), related to type I IFN (α), plays a crucial role in infections, autoimmunity, and cancer. However, the direct effects of IFN-λ on the tumor immune microenvironment have not been thoroughly investigated.
Methods
We used mouse MB49 bladder tumor models, constructed a retroviral vector expressing mouse IFN-λ3, and transduced tumor cells to evaluate the antitumor action of IFN-λ3 in immune-proficient tumors and T cell-deficient tumors. Furthermore, human bladder cancer samples (Cohort 1, n = 15) were used for IHC and mIF analysis to assess the expression pattern of IFN-λ3 in human bladder cancer and correlate it with immune cells’ infiltration. IHC analysis was performed in neoadjuvant immunotherapy cohort (Cohort 2, n = 20) to assess the correlation between IFN-λ3 expression and the pathologic complete response rate.
Results
In immune-proficient tumors, ectopic Ifnl3 expression in tumor cells significantly increased the infiltration of cytotoxic CD8+ T cells, Th1 cells, natural killer cells, M1-like macrophages, and dendritic cells. Transcriptomic analyses revealed significant upregulation of many genes associated with effective immune response, including lymphocyte recruitment, activation, and phagocytosis, consistent with increased antitumor immune infiltrates and tumor inhibition. Furthermore, IFN-λ3 activity sensitized immune-proficient tumors to anti-PD-1/PD-L1 blockade. In T cell-deficient tumors, increased Ly6G–Ly6C+I-A/I-E+ phagocytic macrophages still enhanced tumor cell phagocytosis in Ifnl3 over-expressing tumors. IFN-λ3 is expressed by tumor and stromal cells in human bladder cancer, and high IFN-λ3 expression was positively associated with effector immune infiltrates and the efficacy of immune checkpoint blockade therapy.
Conclusions
Our study indicated that IFN-λ3 enables macrophage-mediated phagocytosis and antitumor immune responses and suggests a rationale for using Type III IFN as a predictive biomarker and potential immunotherapeutic candidate for bladder cancer.
How National Health Insurance Coverage Policy Changed the Use of Lenvatinib for Adult Patients with Advanced Hepatocellular Carcinoma: A Retrospective Cohort Analysis with Real World Big Data
Authors: Liu Yanyan , Bao Yuwen , Huang Yaxin , Zhang Mengdie , Xin Li 
Published: June 2023

Abstract
Background
To establish a long-term mechanism to control the cost burden of drugs, the Chinese government organized seven rounds of price negotiations for the national reimbursement drug list (NRDL) from 2016 to the end of 2022. The study aimed to evaluate the impact of the National Health Insurance Coverage (NHIC) policy on the use of lenvatinib as the first-line treatment for advanced hepatocellular carcinoma (HCC) within a specific medical insurance region from the micro perspective of individual patient characteristics.
Methods
The data of HCC patients that received lenvatinib from September 2019 to August 2022 was retrieved from the Medical and Health Big Data Center and longitudinally analyzed. Chi-square statistics and binary logistic regression analysis were used to compare the differences in the categorical variables. Interrupted time-series (ITS) regression analysis was performed to evaluate the changes in the utilization of lenvatinib over 36 months. Multiple linear regression was used to analyze the impact of receiving lenvatinib on the total hospitalization expenses of hospitalized patients with advanced HCC.
Results
A total of 12,857 patients with advanced HCC were included in this study. The usage rate of lenvatinib increased from 6.09–15.05% over 36 months (P < 0.001). By controlling the other factors, consistent with this, the probability of patients with advanced HCC receiving lenvatinib increased by 2.8-fold after the implementation of the NHIC policy (OR = 2.800,95% CI:2.465–3.180, P < 0.001. Older, residency in rural areas, lack of fixed income, treatment at hospitals below the tertiary level, and coverage by urban-rural residents’ basic medical insurance (URRBMI) were risk factors for the use of lenvatinib among patients with advanced HCC (P < 0.05). After the implementation of the NHIC policy, the total hospitalization expenses increased (Beta=-0.039, P < 0.001). However, compared to patients who received lenvatinib, the total hospitalization expenses were higher for those who did not receive the drug (33549.83 ± 36738.35 vs. 24893.28 ± 29123.74, Beta = 0.059, P < 0.001).
Conclusions
The NHIC policy has significantly increased the utilization of lenvatinib. In addition, we speculate that establishing multi-level medical insurance systems for economically disadvantaged patients would be beneficial in improving the effectiveness of the NHIC policy in the real world.
Denoising watermarked images using Bidirectional Recurrent Convolutional Neural Networks
Authors: Agarwal Pragya , Kumar Somesh , Yadav Chandra Shekhar 
Published: June 2023

Abstract
Recurrent Neural Networks are being widely used for examining and learning sequential motion as well as stationary data, like video, audio, speech, images, etc. In this paper, a Bidirectional convolutional Recurrent Neural Network is being used, for the purpose of image denoising for watermarked images. A Bidirectional network has two parallel channels and can store and memorize information from both forward and backward directions. Because of the information taken from an extended time zone, it can learn and predict more accurate results and can model better visual-temporal dependency. Moreover, instead of considering a fully connected recurrent neural network from input to hidden layer, a weight-sharing convolutional neural network is employed, which is less costly and that’s why the model can become more computationally efficient. The input for this denoising technique is a watermarked image, which is overall the greatest challenge. There are many other existing image and video denoising methods, based on Convolutional Neural Networks, Recurrent Neural Networks, and some other traditional methods. But none of them is able to denoise a watermarked image/video effectively, because they consider the inserted watermark as a sequence of noise and try to destroy it. In this paper, the performances of RNN and CNN based techniques are analyzed and compared with the proposed image denoising technique, which is based on BRCNN. It has been observed experimentally that the proposed technique’s accuracy rate is much more (95 percent) than its counterpart techniques RNN and CNN (89 percent and 67 percent respectively). Moreover, the time taken for removing noise is less (9.35 Seconds) as compared to RNN based techniques (15.29 seconds) and CNN-based techniques (12.67 seconds).