bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel necroptosis-related gene index for predicting prognosis and a cold tumor immune microenvironment in stomach adenocarcinoma
Authors: Khan Muhammad , Lin Jie , Wang Baiyao , Chen Chengcong , Huang Zhong , Tian Yunhong , Yuan Yawei , Bu Junguo 
Published: October 2022

BackgroundGastric cancer (GC) represents a major global clinical problem with very limited therapeutic options and poor prognosis. Necroptosis, a recently discovered inflammatory form of cell death, has been implicated in carcinogenesis and inducing necroptosis has also been considered as a therapeutic strategy.ObjectiveWe aim to evaluate the role of this pathway in gastric cancer development, prognosis and immune aspects of its tumor microenvironment.Methods and resultsIn this study, we evaluated the gene expression of 55 necroptosis-related genes (NRGs) that were identified via carrying out a comprehensive review of the medical literature. Necroptosis pathway was deregulated in gastric cancer samples (n=375) as compared to adjacent normal tissues (n=32) obtained from the “The Cancer Genome Atlas (TCGA)”. Based on the expression of these NRGs, two molecular subtypes were obtained through consensus clustering that also showed significant prognostic difference. Differentially expressed genes between these two clusters were retrieved and subjected to prognostic evaluation via univariate cox regression analysis and LASSO cox regression analysis. A 13-gene risk signature, termed as necroptosis-related genes prognostic index (NRGPI), was constructed that comprehensively differentiated the gastric cancer patients into high- and low-risk subgroups. The prognostic significance of NRGPI was validated in the GEO cohort (GSE84437: n=408). The NRGPI-high subgroup was characterized by upregulation of 10 genes (CYTL1, PLCL1, CGB5, CNTN1, GRP, APOD, CST6, GPX3, FCN1, SERPINE1) and downregulation of 3 genes (EFNA3, E2F2, SOX14). Further dissection of these two risk groups by differential gene expression analysis indicated involvement of signaling pathways associated with cancer cell progression and immune suppression such as WNT and TGF-β signaling pathway. Para-inflammation and type-II interferon pathways were activated in NRGPI-high patients with an increased infiltration of Tregs and M2 macrophage indicating an exhausted immune phenotype of the tumor microenvironment. These molecular characteristics were mainly driven by the eight NRGPI oncogenes (CYTL1, PLCL1, CNTN1, GRP, APOD, GPX3, FCN1, SERPINE1) as validated in the gastric cancer cell lines and clinical samples. NRGPI-high patients showed sensitivity to a number of targeted agents, in particular, the tyrosine kinase inhibitors.ConclusionsNecroptosis appears to play a critical role in the development of gastric cancer, prognosis and shaping of its tumor immune microenvironment. NRGPI can be used as a promising prognostic biomarker to identify gastric cancer patients with a cold tumor immune microenvironment and poor prognosis who may response to selected molecular targeted therapy.
Accuracy of CCL20 expression level as a liquid biopsy-based diagnostic biomarker for ovarian carcinoma
Authors: Sakares Watchara , Wongkhattiya Wannaporn , Vichayachaipat Ponlawat , Chaiwut Chompunoot , Yodsurang Varalee , Nutthachote Pattiya 
Published: October 2022

ObjectiveThe study aimed to investigate the potentiality of chemokines, including MCP-1, CCL15, CCL20, and CXCL14, as biomarkers for differential diagnosis between benign tumors and ovarian cancer (OC).MethodsA cross-sectional study was conducted in women aged &gt;18 years who had adnexal masses treated with elective surgery at the HRH Maha Chakri Sirindhorn Medical Center, Srinakharinwirot University, between 2020 and 2021. The preoperative MCP-1, CCL15, CCL20, and CXCL14 serum levels were measured using a sandwich enzyme-linked immunosorbent assay. Preoperative diagnosis was defined according to the risk of malignancy index. The histological diagnosis and cancer subtype were confirmed using pathological specimens.ResultsNinety-eight participants were preoperatively diagnosed with malignant tumors. The pathological diagnosis confirmed OC in 33 patients and disclosed 27 misdiagnosed cases, of which endometriotic cyst was the most common (44.44%). CCL20 and CA125 serum levels were significantly higher in the patients with cancer than in those with benign. In addition, CCL20 level could differentiate between benign and early-stage malignancy. Furthermore, only CCL20 levels could distinguish endometriotic cysts from OC, whereas CA125 levels could not. Concordant with the serum protein level, the increased mRNA level of CCL20 was observed in ovarian cancers comparing with that in benign tissues. We found that CCL20 levels could differentiate between benign tumors and OC with 60.61% sensitivity and 75.44% specificity at the optimal cutoff value of 38.79 pg/ml. Finally, the logistic regression model integrating CCL20, CA125, and menopause status promoted diagnostic accuracy by increasing the specificity to 91.23%.ConclusionsOur study revealed the potential usefulness of CCL20 level as a biomarker for diagnosing early-stage OC with endometriosis differentiation. We recommend further studies to confirm the accuracy of CCL20 levels with the current diagnosis in a large patient sample.
Development and validation of a scatter-corrected CBCT image-guided method for cervical cancer brachytherapy
Authors: Wu Ailin , Cui Hehe , Jiang Xiao , Yan Bing , Wu Aidong , Liu Yunqin , Zhu Lei 
Published: October 2022

Background and purposeMultiple patient transfers have a nonnegligible impact on the accuracy of dose delivery for cervical cancer brachytherapy. We consider using on-site cone-beam CT (CBCT) to resolve this problem. However, CBCT clinical applications are limited due to inadequate image quality. This paper implements a scatter correction method using planning CT (pCT) prior to obtaining high-quality CBCT images and evaluates the dose calculation accuracy of CBCT-guided brachytherapy for cervical cancer.Materials and methodsThe CBCT of a self-developed female pelvis phantom and five patients was first corrected using empirical uniform scatter correction in the projection domain and further corrected in the image domain. In both phantom and patient studies, the CBCT image quality before and after scatter correction was evaluated with registered pCT (rCT). Model-based dose calculation was performed using the commercial package Acuros®BV. The dose distributions of rCT-based plans and corrected CBCT-based plans in the phantom and patients were compared using 3D local gamma analysis. A statistical analysis of the differences in dosimetric parameters of five patients was also performed.ResultsIn both phantom and patient studies, the HU error of selected ROIs was reduced to less than 15 HU. Using the dose distribution of the rCT-based plan as the baseline, the γ pass rate (2%, 2 mm) of the corrected CBCT-based plan in phantom and patients all exceeded 98% and 93%, respectively, with the threshold dose set to 3, 6, 9, and 12 Gy. The average percentage deviation (APD) of D90 of HRCTV and D2cc of OARs was less than 1% between rCT-based and corrected CBCT-based plans.ConclusionScatter correction using a pCT prior can effectively improve the CBCT image quality and CBCT-based cervical brachytherapy dose calculation accuracy, indicating promising prospects in both simplified brachytherapy processes and accurate brachytherapy dose delivery.
Nomograms for predicting the prognosis of patients with penoscrotal extramammary Paget’s disease: A retrospective study in the SEER database and two medical centers
Authors: Song Le-Bin , Zhou Xiang , Luan Jiao-Chen , Wang Hao-Yang , Cao Xue-Chen , Lu Jia-Wei , Zheng Yu-Jie , Wu Xin-Feng , Lu Yan 
Published: October 2022

BackgroundExtramammary Paget’ s disease (EMPD) is a rare cutaneous malignant tumor, and the prognostic factors associated with penoscrotal EMPD remains unclear. The purpose of this study is to investigate prognostic factors and construct nomograms to predict the outcome of patients with EMPD located in the penis or scrotum.MethodsFrom the Surveillance, Epidemiology and End Results (SEER) database, we extracted 95 patients with primary EMPD located in the penis or scrotum as the training cohort. Forty-nine penoscrotal EMPD patients were included from two medical centers as the external validation cohort. Univariate and multivariate Cox regression model were applied to investigating risk factors of cancer-specific survival (CSS) and overall survival (OS). Based on the results of multivariate Cox regression analysis, the nomograms were constructed for predicting CSS and OS of patients with penoscrotal EMPD. The concordance index (C-index), receiver operating characteristic (ROC) curves and calibration curves were applied to evaluate the practicability and accuracy of the nomograms.ResultsIn the training cohort, multivariate Cox regression analysis showed that marital status and tumor stage were independent factors of CSS, and marital status, tumor stage and surgery are associated with OS independently in patients with penoscrotal EMPD. Based on these results, we developed nomograms to predict CSS and OS respectively. The C-index values were 0.778 for CSS, and 0.668 for OS in the training set, which displayed the good discriminations. In the external validation set, the C-index values were 0.945 for CSS, and 0.703 for OS. The areas under the curve (AUC) values of nomogram predicting 1-, 3-, and 5-year CSS were 0.815, 0.833, and 0.861 respectively, and 0.839, 0.654, and 0.667 for nomogram predicting 1-, 3-, and 5-year OS respectively. In the validation set, the AUC values of nomogram predicting 1-, 3-, and 5-year CSS were 0.944, 0.896, and 0.896 respectively, and 0.777, 0.762 and 0.692 for nomogram predicting 1-, 3-, and 5-year OS respectively. Additionally, the internal calibration curves also proved that our nomograms have good accuracy.ConclusionsBy incorporating marital status, tumor stage and/or surgery, our nomograms can efficiently predict CSS and OS of patients with penoscrotal EMPD.
An exploratory study of CT radiomics using differential network feature selection for WHO/ISUP grading and progression-free survival prediction of clear cell renal cell carcinoma
Authors: Yin Fu , Zhang Haijie , Qi Anqi , Zhu Zexuan , Yang Liyang , Wen Ge , Xie Weixin 
Published: October 2022

ObjectivesTo explore the feasibility of predicting the World Health Organization/International Society of Urological Pathology (WHO/ISUP) grade and progression-free survival (PFS) of clear cell renal cell cancer (ccRCC) using the radiomics features (RFs) based on the differential network feature selection (FS) method using the maximum-entropy probability model (MEPM).Methods175 ccRCC patients were divided into a training set (125) and a test set (50). The non-contrast phase (NCP), cortico-medullary phase, nephrographic phase, excretory phase phases, and all-phase WHO/ISUP grade prediction models were constructed based on a new differential network FS method using the MEPM. The diagnostic performance of the best phase model was compared with the other state-of-the-art machine learning models and the clinical models. The RFs of the best phase model were used for survival analysis and visualized using risk scores and nomograms. The performance of the above models was tested in both cross-validated and independent validation and checked by the Hosmer-Lemeshow test.ResultsThe NCP RFs model was the best phase model, with an AUC of 0.89 in the test set, and performed superior to other machine learning models and the clinical models (all p &lt;0.05). Kaplan-Meier survival analysis, univariate and multivariate cox regression results, and risk score analyses showed the NCP RFs could predict PFS well (almost all p &lt; 0.05). The nomogram model incorporated the best two RFs and showed good discrimination, a C-index of 0.71 and 0.69 in the training and test set, and good calibration.ConclusionThe NCP CT-based RFs selected by differential network FS could predict the WHO/ISUP grade and PFS of RCC.
DNA methylation topology differentiates between normal and malignant in cell models, resected human tissues, and exfoliated sputum cells of lung epithelium
Authors: Tajbakhsh Jian , Mortazavi Fariborz , Gupta Nirdesh K. 
Published: October 2022

BackgroundGlobal DNA hypomethylation is a prominent feature of cancer cells including lung cancer, that has not been widely explored towards cancer diagnosis. In this study we assess the comparative distribution of global DNA methylation in normal cells versus cancer cells in various specimen models.MethodsWe used in situ immunofluorescence labeling of overall 5-methylcytosine (5mC) and covisualization of global DNA (gDNA) by 4’,6-diamidino-2-phenylindole (DAPI), confocal microscopy and 3D image analysis to derive 5mC/DAPI colocalization patterns in human cell lines (BEAS-2B, A549, H157) and upper respiratory epithelial cells derived from various sources (i.e., sputum from healthy and cancer patients, and resected tissues from normal parenchyma and lung tumors).ResultsBy introducing 5mC/DAPI colocalization index as a metric we could distinguish between normal epithelial cells and aberrantly hypomethylated cancer cells. Cultured lung cancer cells (H157 and A549) had significantly lower indices compared to normal cells (BEAS-2B). Furthermore, we were able to identify such extensively hypomethylated low-index cells in tumor tissues and the matching sputum from cancer patients. In contrast, the indices of cells derived from sputum of healthy individuals had more similarity to epithelial cells of normal parenchyma and the phenotypically normal BEAS-2B cells.ConclusionsThe results suggest that 5mC topology using high-resolution image cytometry shows potential for identifying hypomethylated cancerous cells in human tissues and amongst normal cells in matching sputum, which may render a valuable surrogate for biopsied tissues. This promising feature deserves further validation in more comprehensive studies.
Rabbit manure compost as a peat substitute for compound growing media: Proportioning optimization according to physiochemical characteristics and seedling effects
Authors: Li Rangling , Hao Hongyun , Yang Chengcai , Wang Liangju , Wang Hongying 
Published: October 2022

A large amount of rabbit manure is produced with the development of the rabbit industry, which will cause environmental pollution without proper treatment. Rabbit manure compost may be suitable for seedling cultivation, considering its low moisture, low heavy metal, high lignocellulose, and good fertilizer effect. In this study, a pre-proportioning test of growing media was conducted to optimize the ratio of perlite and vermiculite with peat/rabbit manure compost according to their physicochemical properties. Then, based on the results of the first proportioning optimization, the mixing ratio of rabbit manure compost and peat was further optimized using a bioassay. In this bioassay, salt-tolerant calendula (Calendula officinalis L.) and salt-intolerant cucumber (Cucumis sativus L.) were selected as test plants. The seedling effects (e.g., seedling emergence percentage, plant growth parameters, plant biomass, and nutrient effects) were evaluated. It was shown in the results that the rabbit manure compound growing media could be used for the seedlings, and suitable seedling performance was obtained with the increase of the total porosity (5.0%–61.2%), organic matter content (8.3%–39.9%), and nutrient elements from the rabbit manure compost. From the perspective of seedling emergence, there was no significant difference between rabbit manure compound media and peat treatment, in which the highest emergence percentages were &gt;90%. At the same time, the nutrient performance of plant aboveground was significantly increased in rabbit manure compound growing media compared to peat treatment. In particular, the contents of P and Mg were increased by 31%–141.4% and 80.4%–107.8% for calendula and by 82.6%–117.4% and 35.1%–67.6% for cucumber, respectively. It was indicated in the two-step optimization that the rabbit manure compost proportion of 30%–50% (that is, 60%–100% instead of peat) was more suitable. Additionally, the greenhouse gas emission could be reduced by using rabbit manure compost replacing peat, and the greenhouse gas emission reduction potential would be 3.65 × 105–4.06 × 108 kg CO2-equivalent/year in China, which has important ecological significance.
Learning to see after early and extended blindness: A scoping review
Authors: May Eloise , Arach Proscovia , Kishiki Elizabeth , Geneau Robert , Maehara Goro , Sukhai Mahadeo , Hamm Lisa M. 
Published: October 2022

PurposeIf an individual has been blind since birth due to a treatable eye condition, ocular treatment is urgent. Even a brief period of visual deprivation can alter the development of the visual system. The goal of our structured scoping review was to understand how we might better support children with delayed access to ocular treatment for blinding conditions.MethodWe searched MEDLINE, Embase and Global Health for peer-reviewed publications that described the impact of early (within the first year) and extended (lasting at least 2 years) bilateral visual deprivation.ResultsOf 551 reports independently screened by two authors, 42 studies met our inclusion criteria. Synthesizing extracted data revealed several trends. The data suggests persistent deficits in visual acuity, contrast sensitivity, global motion, and visual-motor integration, and suspected concerns for understanding complex objects and faces. There is evidence for resilience in color perception, understanding of simple shapes, discriminating between a face and non-face, and the perception of biological motion. There is currently insufficient data about specific (re)habilitation strategies to update low vision services, but there are several insights to guide future research in this domain.ConclusionThis summary will help guide the research and services provision to help children learn to see after early and extended blindness.
Using of the Recombinant ORF2 and ORF3 Polypeptides of the 3rd Genotype of the Hepatitis Virus E in the Development of an Enzyme Immunoassay Test System for the Serodiagnosis of Class G Immunoglobulins
Authors: Жаворонок С.В. , Задора И.С. , Давыдов В.В. , Анисько Л.А. , Рогачева Т.А. , Алаторцева Г.И. , Лухверчик Л.Н. , Нестеренко Л.Н. , Зверев В.В. , Симирский В.В. , Щербань А.И. , Щука Н.В. , Мытько Ю.А. 
Published: October 2022

В статье приведены результаты использования в качестве иммобилизированных антигенов рекомбинантных полипептидов, содержащих белковые продукты открытых рамок считывания генов ORF2 и ORF3 вируса гепатита Е (ВГЕ) 3-го генотипа (разработаны и предоставлены ФГБНУ «Научно-исследовательский институт вакцин и сывороток им. И.И. Мечникова», Москва, Россия), разведенных в карбонатно-бикарбонатном буфере до рабочей концентрации 2 и 0,25 мкг/мл соответственно. Установлено, что иммуносорбент одинаково хорошо взаимодействует с иммуноферментными конъюгатами тест-систем Вектогеп Е-IgG («Вектор-Бест», Новосибирск) и «ДС-ИФА-АНТИ-HEV-G» (НПО «Диагностические системы», РФ), что может использоваться для адаптации тест-систем ИФА в зависимости от целей исследования. Для оценки показателей внутрисерийной воспроизводимости были исследованы одна низко- и две высокопозитивные по содержанию анти-ВГЕ IgG сыворотки пациентов в нескольких повторах. Показатели коэффициента вариации не превышали рекомендуемую величину в 10%. При этом более специфичной в отношении низкопозитивных по анти-ВГЕ IgG сывороток крови людей является комбинация ORF2 и ORF3 2,0 и 0,25 мкг/мл и конъюгата тест-системы «ДС-ИФА-АНТИ-HEV-G», что определяет ее преимущественное использование в дальнейшем.
The article presents the results of using recombinant polypeptides containing protein products of the open reading frames of the ORF2 and ORF3 genes of the hepatitis E virus (HЕV) of the 3rd genotype as immobilized antigens (developed and provided by FSBSI "Scientific Research Institute of Vaccines and Serums I.I. Mechnikov", Moscow, Russian), diluted in a carbonate-bicarbonate buffer to a working concentration of 2 and 0.25 μg/ml. It was found the immunosorbent interact equally well with enzyme immunoassay conjugates of the Vectohep E-IgG test systems (Vector-Best, Novosibirsk) and DS-ELISA-ANTI-HEV-G (NPO Diagnostic Systems, RF), which can be used for adaptation ELISA test systems in depending on the objectives of the study. To assess the indicators of in-series reproducibility, one low- and two high-positive anti-HЕV IgG sera of patients in several repeats were studied. The coefficient of variation when using the immunosorbent did not exceed the recommended value of 10%. At the same time, the combination of ORF2 and ORF3 2.0 μg/ml and 0.25 μg/ml with the conjugate DS-ELISA-ANTI-HEV-G is more specific for low-positive anti-HЕV IgG human blood sera, which determines its preferential use in the future.
COVID-19 Associated Invasive Pulmonary Aspergillosis: Problems of Diagnosis and Treatment (clinical cases, literature review)
Authors: Матиевская Н.В. , Прокопчик Н.И. , Данилевич Н.А. , Валентюкевич В.В. , Полудень Н.В. , Смоленская Д.С. 
Published: October 2022

Представлен обзор литературы по современным методам диагностики и лечения инвазивного аспергиллеза легких, ассоциированного с COVID-19. Описаны 3 клинических случая инвазивного аспергиллеза легких у пациентов с тяжелой инфекцией COVID-19, 2 из которых были подтверждены на аутопсии.
A review of the literature on modern methods of diagnosis and treatment of invasive pulmonary aspergillosis associated with COVID-19 is presented. 3 clinical cases of the invasive pulmonary aspergillosis in patients with severe COVID-19 are presented, 2 of which were confirmed at autopsy.
Laju Korosi Atmosferik Baja Konstruksi di Area Pabrik PT. Karya Tanah Subur
Authors: Supardi Joli , Susanto Herdi 
Published: October 2022

Abstract Environmental pollution that can cause atmospheric corrosion is the exhaust gas (exhaust fumes) generated from operating the palm oil industry. This atmospheric corrosion will reduce the volume and material mass of a machine component, so that if it reaches certain conditions the strength of the material will result in failure of industrial machine components. The corrosion rate of the construction steel can be measured using the weight loss method according to the ASTM G-50 standard and the ASTM G-1 standard. The research was conducted for one year and data collection was taken every month, the research location was at PT Agro Sinergi Nusantara Batee Puteh. The results of the study, the highest corrosion rate occurred in strip steel reaching 0.57 mpy in October and the lowest corrosion rate occurred for angled steel in September and cylindrical steel in May with a corrosion rate of 0.06 mpy. Keywords— atmospheric corrosion, ASTM G-50, ASTM G-1, PT. KTS