bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in the expression of pseudogenes including AKR1B10P1, RP11-465B22.3, WASH8P, and NPM1P25 as a model for predicting hepatocellular carcinoma patient survival
Authors: Firouzi-Farsani Khatereh , Dehghani-Samani Mina , Gerami Razieh , Moosavi Reihaneh Sadat , Gerami Marzieh , Mahdevar Mohammad 
Published: May 2022

Abstract
Introduction: The goal of this study was to look at changes in pseudogene genes level as oncogenes and tumor suppressors in hepatocellular carcinoma (HCC) by large-scale analysis and to develop a survival prediction model based on their expression.Methods: The cancer genome data were applied to evaluate the expression alternations of all pseudogene in HCC and their correlation with patients' prognosis. Also, a risk model was computed based on the expression of pseudogenes and their predictive power in patient mortality rates. The co-expression network and RT-qPCR method were utilized to discover pathways related and confirmed the outcomes, respectively.Results: The results revealed that 12 pseudogenes were down-regulated in HCC, and their increased expression was associated with good prognosis. Also, 11 pseudogenes were overexpressed and associated with patients' poor prognoses. The multivariate Cox regression test indicated that overexpression of AKR1B10P1, RP11-465B22.3, WASH8P, and downregulation of NPM1P25 could predict the survival rate of patients independent of clinical parameters. The risk score model based on mentioned pseudogenes could considerably distinguish patients based on their fatality rate. Also, the co-expression network shown that the identified pseudogene genes can play a role in fatty acid metabolism, proliferation, and mTOR. RT-qPCR results also showed that the expression level of WASH8P was significantly increased in cancer specimens compared to normal.Conclusion: Our results revealed that change expression of AKR1B10P1, RP11-465B22.3, WASH8P, and NPM1P25 was independently associated with prognosis and the patient mortality risk model based on these four pseudogenes can reasonably predict the survival rate of patients.
Comparing critically-ill ARDS patients with versus without COVID-19: Prospective analysis of 690 patients
Authors: Algethamy Haifa M , Aboudeif Mohammed M , Alhandi Moatz O , Majrashi Fahd Y , Hakami Shrooq H , Jan. Midhat A , Kabli Hanan A , Alhomrani Mohammed H , White Kevin P. 
Published: May 2022

Abstract
BACKGROUND: Few studies have directly and prospectively compared ICU patients with acute respiratory distress syndrome (1) caused by COVID-19 versus other causes, almost all previously-published studies retrospective and employing historical non-COVID cases. This study aimed to identify patient characteristics and predictors of mortality associated with COVID-related ARDS.METHODS: We performed a Prospective cohort study. Consecutive ARDS patients with versus without confirmed COVID-19 admitted to a single ICU of a major tertiary-care hospital from March-December 2020 were included. Data were collected and both bivariate and multivariable analysis performed on COVID-19 status, demographics; morphometrics; comorbidities; presenting symptoms; admission general health status (APACHE-II); respiratory and laboratory tests at admission, within 24 hours of admission, and pre-intubation; treatments administered; and outcomes. Data capture was almost 100%.RESULTS: Numerous clinical differences were detected between n=160 patients with versus n=530 patients without COVID-19. Most notably, COVID-19 patients were generally older and heavier, much more frequently presented with fevers/chills, dyspnoea, cough, anosmia/ageusia, and sore throat — and had worse outcomes, including over a two-fold rate of mortality and five-fold rate of survivors requiring prolonged supplemental oxygen. The presenting symptom dyad of fevers and/or chills and dyspnoea was 93.0% sensitive and 63.4% specific for COVID-related ARDS. A baseline APACHE-II Score ≥17 and requiring mechanical ventilation was 94.4% sensitive and 70.5% specific for mortality. All 37 COVID patients with an APACHE-II score >30 died, versus survival among non-COVID patients with APACHE-II scores up to 40.CONCLUSION: In one of the first large studies to directly compare contemporary populations of COVID-19 and non-COVID ICU patients with ARDS, employing multi-variable analysis, numerous differences in patient characteristics, presentation, and outcomes were detected.
Development and verification of a nomogram for the prediction of coronary heart disease in the Chinese Guangxi Zhuang population
Authors: Meng Yumin , Chen Chengxia , Jiang Zhiyuan , Chen Kequan , Ouyang Jun , Wang Hui , Huang Jiangnan 
Published: May 2022

Abstract
Objective: The purpose of this study was to explore the independent risk factors involved in coronary heart disease (CHD), and to develop and verify a fibrinogen-based nomogram to predict its risk in the Chinese Zhuang population in Guangxi Province. Methods: Patients who underwent coronary angiography at the First Affiliated Hospital of Guangxi Medical University from January 2018 to November 2019 were included, and randomly divided into a training set and a validation set at a ratio of 7:3. After multivariate logistic regression analysis, the nomogram for the prediction of CHD was constructed. Receiver operating characteristic (ROC) curves, calibration curves and decision curve analyses (DCA) were used to evaluate the discriminatory ability of the model, and its calibration and its use as a model. Results: Multivariate logistic regression showed that males (OR = 2.22, 95% CI (1.37-3.58); P = 0.001), smoking (OR = 1.71, 95% CI (1.11-2.62); P = 0.014), hypertension (OR = 9.79, 95% CI (5.67-16.86); P < 0.001), diabetes (OR=6.32, 95%CI (2.98-13.41)); P<0.001), fibrinogen (OR = 1.74, 95% CI (1.39-2.18); P < 0.001) and triglycerides (OR = 1.43, 95% CI (1.10-1.86); P = 0.007) were independent predictors of CHD. We then use these seven risk factors to construct and predict the nomogram. Our patients’ population was 480 with 205 patients randomly assigned to the training set and verification set respectively. The AUC of the nomogram in the training and validation sets were 0.837 and 0.889. The sensitivity and specificity in the validation set were 87.7% and 80.4%. However, the training set was 79.9% and 77.7%, respectively. These results indicate that the model predicts very well the presence of CHD. In addition, the calibration curve from the validation set shows a strong consistent performance from the nomogram model, and at the same time, DCA also showed excellent results from the nomogram. Conclusions: This study found that gender (men), age, smoking, hypertension, diabetes, fibrinogen, and triglycerides were all independent risk factors for CHD. Moreover, a novel method based on a fibrinogen nomogram was developed and validated to predict the risk of CHD in the Guangxi Zhuang population. These findings help medics to assess the risk of CHD, and can be easily used for its early diagnosis and improved screening in patients at high risk of CHD
The nutrient preferences of rice and wheat influence fluoranthene uptake
Authors: Xu Yuanzhou , Xiao Zhuoliang , Zhang Xinyue , Zhao Chenyu , Li Yunyun , Che Ting , Li Yajuan , Zang Xiayun , Jiang Shuyi , Li Huixin , Xu Li , Hu Feng 
Published: May 2022

Abstract
Applications of the key plant nutrient nitrogen (N) increase the uptake and accumulation of pollutants such as polycyclic aromatic hydrocarbons (PAHs). However, it is unclear how a plant’s preference for a particular form of N in the soil affects its uptake and accumulation of PAHs. In this study, we investigated the physiological mechanisms involved in fluoranthene (Flu) uptake by rice (Oryza sativa L.) and wheat (Triticum aestivum L.) and examined how these mechanisms are affected by different forms of N treatment under an equivalent N supply. Both N form and plant species affected plant Flu uptake. Rice accumulated more Flu than wheat under an equivalent N supply, while the transfer coefficient of Flu in wheat was higher than that in rice. Flu accumulation in rice and wheat was positively correlated with plant root morphology parameters, and the transfer coefficient was positively correlated with transpiration. Of the treatments examined, ammonium (NH4+-N)-treated rice and nitrate (NO3−-N)-treated wheat accumulated the most Flu at equivalent N supply. Flu accumulation was positively correlated with plant growth, total nitrogen N content, total protein content, and antioxidant enzyme activities. Based on a partial least squares path model (PLS-PM) analysis, total plant N was the main factor influencing Flu uptake by rice and wheat treated with different forms of N. Overall, ammonium-preferring rice and nitrate-preferring wheat had the highest nutrient content in their preferred N forms, which also promoted Flu uptake. Therefore, regulating the form of N applied to the soil could be a suitable strategy to improve the safety of agricultural products.
Hybrid Enhancement-Based Prototypical Networks for Few-Shot Relation Classification
Authors: Wang Lei , Qu Jianfeng , Xu Tianyu , Li Zhixu , Chen Wei , Xu Jiajie , Zhao Lei 
Published: May 2022

Abstract
Few-shot relation classification is to recognize the semantic relation between an entity pair with very few samples. Prototypical network has proven to be a simple yet effective few-shot learning method for relation extraction. However, under the condition of data scarcity, the relation prototypes we achieve are usually biased compared to the real ones computed from all samples within a relation class. To alleviate this issue, we propose hybrid enhancement-based prototypical networks. In particular, our model contains three main enhancement modules: 1) a query-guided prototype enhancement module using rich interactive information between the support instances and the query instance as guidance to obtain more accurate prototype representations; 2) a query enhancement module to diminish the distribution gap between the query set and the support set; 3) a support enhancement module adopting a pseudo-label strategy to expand the scale of available data. On basis of these modules, we further design a novel prototype attention fusion mechanism to fuse information and compute discriminative relation prototypes for classification. In this way, we hope to obtain unbiased representations closer to our expected prototypes by improving the available data scale and data utilization efficiency. Extensive experimental results on the widely-used FewRel dataset demonstrate the superiority of our proposed model.
Cardiac toxicity in patients with lung cancer receiving thoracic radiotherapy and immunotherapy
Authors: Son Christine , Moey Melissa Y.Y. , Walker Paul R. , Naqash Abdul R. , Peach M. Sean , Ju Andrew 
Published: May 2022

Abstract
BackgroundImmune checkpoint inhibitors (ICIs) are used in the treatment of locally advanced and metastatic lung cancer. ICIs can lead to severe immunogenic related cardiotoxicities. The cardiotoxic profile of these agents when combined with thoracic radiotherapy is not well-defined. Here, we assessed the risk of cardiotoxicity in ICI-treated lung cancer patients with or without cardiac radiation from thoracic radiotherapy. Methods Retrospective data was collected on Stage III-IV lung cancer patients who received ICIs between 2015 and 2018. All cardiotoxicities associated with ICI were assessed by cardiologists and medical oncologists in correlation with the timing of RT in relation to ICI and the mean RT heart dose. RT was delivered between cycles of immunotherapy for patients who received RT concurrently with ICI. Multivariate analysis on the rate of cardiac events/cardiotoxicity in relation to radiotherapy timing and heart dose was performed on multiple logistic regression including the Framingham risk score and steroid use prior to ICI therapy.ResultsOf 194 ICI-treated patients evaluated, 66 (34.02%) and 128 (65.98%) had Stage III and IV SCLC or NSCLC, respectively, the median age was 64 years (range, 36-88), and 42.47% were female. Within the total cohort, 55.2% (n=107/194) patients had received thoracic RT at a median dose of 60.4 Gy (range, 15-75). Cardiotoxicities such as non-ST elevated myocardial infarction and new onset supraventricular tachycardias were observed in 13 (12.2%) of those who had thoracic RT versus 9 (10.3%) who did not (p=0.87). There were 38 patients who received RT concurrently with ICI and did not develop any cardiotoxicity whereas cardiotoxicity was observed in 14.1% (n=22/156) of those who did not receive concurrent RT (univariate, p=0.030; multivariate, p=0.055). There were no significant differences in the mean heart RT dose, Framingham risk score, and steroid treatment between patients that received concurrent RT with ICI versus non-concurrent RT/ICI.ConclusionICI-related cardiotoxicities were not significantly associated with patients who received concurrent thoracic radiotherapy. Univariate analysis suggests a potential cardioprotective effect of thoracic RT with ICI’s, which may be due to modulation of the immune response through reduction of lymphocytes involved in autoimmune processes.
Laparoscopy in high-risk emergency general surgery reduces intensive care stay, length of stay and mortality
Authors: Wilson Iain , Rahman Saqib , Pucher Philip , Mercer Stuart 
Published: May 2022

Abstract
Purpose
Emergency general surgery patients undergoing laparoscopic surgery are at reduced risk of mortality and may require reduced length of critical care stay. This study investigated the effect of laparoscopy on high-risk patients’ post-operative care requirements.
Methods
Data were retrieved for all patients entered into the NELA database between 2013 and 2018. Only high-risk surgical patients (P-POSSUM predicted mortality risk of ≥ 5%) were included. Patients undergoing laparoscopic and open emergency general surgical procedures were compared using a propensity score weighting approach. Outcome measures included total length of critical care (level 3) stay, overall length of stay and inpatient mortality.
Results
66,517 high-risk patients received emergency major abdominal surgery. A laparoscopic procedure was attempted in 6998 (10.5%), of these the procedure was competed laparoscopically in 3492 (49.9%) and converted to open in 3506 (50.1%). Following inverse probability treatment weighting adjustment for patient disease and treatment characteristics, high-risk patients undergoing laparoscopic surgery had a shorter median ICU stay (1 day vs 2 days p < 0.001), overall hospital length of stay (11 days vs 14 days p < 0.001) and a lower inpatient mortality (16.0% vs 18.8%, p < 0.001). They were also less likely to have a prolonged ICU stay with an OR of 0.78 (95% CI 0.74–0.83, p < 0.001).
Conclusion
The results of this study suggest that in patients at high risk of post-operative mortality, laparoscopic emergency bowel surgery leads to a reduced length of critical care stay, overall length of stay and inpatient mortality compared to traditional laparotomy.
International Scientific Co-Publications in Europe
Authors: Leogrande Angelo , Costantiello Alberto , Laureti Lucio , Matarrese Marco Maria 
Published: May 2022

Abstract
The determinants of “International Scientific Co-Publications” in Europe are analyzed in the following article. Data from the European Innovation Scoreboard-EIS of the European Union for 36 countries in the period 2010-2019 were used. The data were analyzed using Panel Data with Fixed Effects, Panel Data with Random Effects, Pooled OLS, WLS, Dynamic Panel. The results show that the variable “International Scientific Co-Publication” is negatively associated with “Employment Share Manufacturing”, “Intellectual Assets”, “Turnover Share Large Enterprises”, “Linkages” and positively associated with “SMEs innovating in house”, “Trademark Applications”, “Human Resources”, “Public-private co-publications”, “Attractive Research Systems”, “Government procurement of advanced technology products”, “Turnover Share SMEs”. Then, a clustering analysis is realized with the algorithm k-Means. The Silhouette Coefficient and the Elbow Method are confronted to optimize the k-Means algorithm. The results show that the Elbow method is more efficient than the Silhouette coefficient in identifying the optimal number of clusters corresponding to k = 4 with the k-Means algorithm. A network analysis was then carried out using the “Manhattan Distance”. The analysis shows the presence of 9 network structures of which 5 are complex i.e., with a number of linkages greater than 3, and 4 are basic i.e. consist of a single link between two countries. Furthermore, we confront eight different machine learning algorithms to predict the future level of “International Scientific Co-Publications”. We found that the best algorithm in performing prediction with original data is the Tree Ensemble Regression. The predicted value of “International Scientific Co-Publication” is expected to growth by 0.61%.
Delayed vs early enteral feeding after repair of congenital recto-vestibular fistula
Authors: Kurdi Mazin , Mokhtar Ahmed , Elkholy Mahoud , El-wassia Heidi , Bamehriz Maha , Khirallah Mohammad 
Published: May 2022

Abstract
purpose: To study the effect of delayed vs early enteral feeding on the occurrence of perineal wound infection (PWI) after repair of congenital recto vestibular fistula.methods: Fifty-five infants with recto-vestibular fistula were included. They were managed by single stage anterior sagittal anorectoplasty (ASARP)at an age ≥ 3 months. Groups A and B included infants who started oral intake on the 6th and 2nd postoperative days respectively. Group A infants were kept on peripheral parenteral nutrition (PPN) during the fasting period. Results: Superficial wound infection occurred in three cases in group A while it developed in seven cases in group B. Deep perineal infection occurred in two and five cases in group A and group B respectively. The mean hospital stay was 8 days in group A vs 13 days in group B when PWI developed. Conclusion: Delayed enteral feeding with PPN keeps the perineal wound more dry and less contaminated with stool. This promoted proper and fast healing with lower incidence of PWI. Also, PPN compensates the catabolic effects of both surgical trauma and fasting during the postoperative period and ensures maintenance of normal levels of essential nutrients that allow for proper healing.
Role of Echocardiography in the Assessment of Cardiac Involvement in Takayasu Arteritis
Authors: Fu Jiarong , Liu Jinfeng , Li Xiaoming , Wu Shan , Yu Huimei , Zhang Chun 
Published: May 2022

Abstract
The aim of this study is to investigate echocardiographic features of patients with cardiac involvement and evaluate the value of echocardiography in Takayasu arteritis (TA). This retrospective study compared the clinical manifestations and echocardiographic parameters of 127 TA patients with and without cardiac involvement and further explored the relationship between pulmonary hypertension (PH) and echocardiographic parameters. Clinical, imaging and laboratory results of the TA patients were obtained from hospital files. In our study, 68 patients (53.54%) had cardiac involvement. Valvular abnormalities were found in 55 (80.88%) patients in the heart involvement group, coronary artery abnormalities in 10 (14.71%), myocardial abnormalities in 18 (26.47%) and heart failure in 10 patients (14.71%), respectively. Among TA patients with cardiac involvement, PH was detected in 11 patients (16.18%) with echocardiographic assessment. Compared to the control group, both the TA patients with cardiac involvement associated with and without PH presented with the significantly differences of echocardiographic parameters regarding LAD, IVST, LVPWT, LVEDD, LVESD, LVEF, LV mass, LV mass/BSA, MPAD and E peak (P < 0.05). Compared the echocardiographic parameters between the patients with and without PH of TA patients with cardiac involvement, the differences were of no statistical significance (P > 0.05). Cardiac involvement is not infrequent in TA patients and it should be carefully evaluated. Echocardiography plays a vital role in the assessment of cardiac involvement in TA which is helpful for diagnosis and management of TA.
HER2 expression in peritoneal dissemination of high-grade serous ovarian carcinoma: a comparative study of immunohistochemical reactivity using four HER2 antibodies
Authors: Yeo Min-Kyung , Kim Sup , Yoo Heon Jong , Suh Kwang-Sun , Kim Kyung-Hee 
Published: May 2022

Abstract
Objective
Most high-grade serous ovarian carcinomas (HGSOCs) involving the peritoneum are highly aggressive. Epidermal growth factor receptor 2 (HER2) is aberrantly activated and a therapeutic target in a variety of solid cancers. However, the role of HER2 in HGSOC is still controversial. The HER2 status of a tumor is based on cytoplasmic membrane staining of an intracellular domain (ICD)-specific HER2 antibody. In this study, we compared four anti-HER2 antibodies in an immunohistochemical study of HGSOC with peritoneal dissemination.
Methods
HER2 expression was assessed in peritoneal disseminated HGSOC specimens from 38 patients by immunohistochemistry using four different anti-HER2 antibodies [an ICD antibody (clone A0485), an extracellular domain (ECD) antibody (clone SP3), and two antibodies recognizing HER2 phosphorylated at tyrosine 877 or 1248 (pHER2Y877 and pHER2Y1248)]. HER2 gene amplification was accessed by chromogenic in situ hybridization (CISH).
Results
The antibodies showed HER2 positivity as follows: 31.6 % of cases (12/38) with A0485, 26.3 % (10/38) with SP3, 7.9 % (3/38) with pHER2Y877, and 21.1% (8/38) with pHER2Y1248. Fifteen of 38 (39.5 %) cases were positive with at least one of the four HER2 antibodies, and two cases tested positive with all four antibodies. Differences in the HER2 expression using the pHER2Y877 assay and the A0485 or SP3 assay were observed (p = 0.012 and p = 0.039, respectively). HER2 gene amplification was detected in 3/19 cases.
Conclusion
All four HER2 antibodies could be used for patient selection for anti-HER2 therapies. These findings raise the possibility of anti-HER2 therapeutic strategies for HGSOC with peritoneal dissemination.
In Silico Identification of Non-cross-reactive Epitopes for Monkeypox Cell Surface-Binding Protein
Authors: Gao Andrew , Gao Sarah 
Published: May 2022

Abstract
Smallpox, a disease caused by the Variola virus, was eradicated after global vaccination efforts. Recently, the monkeypox virus (MPV) has been spreading worldwide and is becoming a significant concern. The cell surface-binding protein E8L is found on MPV virion membranes and is essential for virion attachment to host cells, potentially making it an attractive vaccine target. In this study, E8L was investigated to assess its viability as a vaccine target and identify epitopes. BLAST analysis showed that the MPV Zaire-96-I-16 strain E8L amino acid sequence exhibits 38.2% percent identity with the human enzyme carbonic anhydrase III (CA3). Multiple sequence alignment and Expasy Translate were used to identify the corresponding E8L amino acid sequence of the May 2022 Massachusetts MPV case draft genome. The Massachusetts MPV E8L sequence was identical to the Zaire strain E8L sequence except for a single residue. Peptide Match software was used to identify pentapeptide subunits of E8L that are not found within the human proteome, thus addressing concerns about cross-reactivity with human proteins (such as CA3) and improving antigen specificity. Overall, 28 such pentapeptides were identified. The Immune Epitope Database was queried for experimentally-characterized epitopes/antigens containing these 28 pentapeptides, yielding 21 matching epitopes, demonstrating that some of these pentapeptides can evoke immune responses. This study identified human-foreign pentapeptides within E8L which could be explored to find viable epitopes for MPV vaccines. While existing vaccines confer protection against MPV, the risk of vaccine escape (as seen with SARS-CoV-2) suggests that additional vaccines should be investigated.