bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and verification of feature biomarkers associated with immune cells in neonatal sepsis
Authors: Liao Weiqiang , Xiao Huimin , He Jinning , Huang Lili , Liao Yanxia , Qin Jiaohong , Yang Qiuping , Qu Liuhong , Ma Fei , Li Sitao 
Published: September 2022

Abstract
Background: Neonatal sepsis (NS), a life-threatening condition, is characterized by organ dysfunction and is the most common cause of neonatal death. However, the pathogenesis of NS is unclear and the clinical inflammatory markers currently used are not ideal for diagnosis of NS. Thus, exploring the link between immune responses in NS pathogenesis, elucidating the molecular mechanisms involved, and identifying potential therapeutic targets is of great significance in clinical practice. Herein, we study aimed to explore immune-related genes in NS and identify potential diagnostic biomarkers. Datasets for patients with NS and healthy controls were downloaded from the GEO database; GSE69686 and GSE25504 were used as the analysis and validation datasets, respectively. Differentially expressed genes (DEGs) were identified and Gene set enrichment analysis (GSEA) was performed to determine their biological functions. Composition of immune cells was determined and immune-related genes (IRGs) between the two clusters were identified and their metabolic pathways were determined. Key genes with correlation coefficient > 0.5 and p < 0.05 were selected as screening biomarkers. Logistic regression models were constructed based on the selected biomarkers, and the diagnostic models were validated.
Results: Fifty-two DEGs were identified, and GSEA indicated involvement in acute inflammatory response, bacterial detection, and regulation of macrophage activation. Most infiltrating immune cells, including activated CD8+ T cells, were significantly different in patients with NS compared to the healthy controls. Fifty-four IRGs were identified, and GSEA indicated involvement in immune response and macrophage activation and regulation of T cell activation. Diagnostic models of DEGs containing five genes (PROS1, TDRD9, RETN, LOC728401, and METTL7B) and IRG with one gene (NSUN7) constructed using LASSO algorithm were validated using the GPL6947 and GPL13667 subset datasets, respectively. The IRG model outperformed the DEG model. Additionally, statistical analysis suggested that risk scores may be related to gestational age and birth weight, regardless of sex.
Conclusions: We identified six IRGs as potential diagnostic biomarkers for NS and developed diagnostic models for NS. Our findings provide a new perspective for future research on NS pathogenesis.
Comparison of Serum Levels of Cell Adhesion Molecules (E-selectin, P-selectin, Icam-1, Vcam-1, Lrg-1) in Placental İnvasi̇on and Adhesion Anomalies With Patients With Vaginal Delivery and Former Cesarerean
Authors: Ersuz Rutkay , Karapınar Oya Soylu , Doğan Serdar 
Published: September 2022

Abstract
Objective: The effect of cell adhesion molecules on placental location and adhesion anomalies was investigated.
Materials and Methods: Patients between March 2020 and September 2021 were included in the study. While 56 patients aged 18-50 years, out of 153 cases formed the placental adhesion and/or localization anomaly group, 55 cases without placental adhesion anomaly (placental invasion anomaly and/or previa pathology) constituted the cesarean section group and 42 cases constituted the vaginal birth control group. Demographic characteristics and histories of 153 patients were questioned. I-CAM-1, V-CAM-1, E-Selectin, P-Selectin, LRG-1 levels were studied.
Results: There were significant differences in E-Selectin, P-Selectin, ICAM-1 and LRG-1 values between the groups (p<0.05).
There was a significant difference between the NVD and PP groups in terms of E-Selectin (p=0.038). In terms of P-Selectin, there was a significant difference between the C/S and PP groups (p=001). P-Selectin was higher in the PP group. There was a significant difference between the NVD, C/S group (p=0.041) and the NVD, PP group (p=0.013) in terms of ICAM-1, but there was no significant difference between the C/S and PP groups. In terms of LRG-1, there was a significant difference between all 3 groups (p<0.05).
Conclusions: In our study, all adhesion molecules except V-CAM-1 were found to be significantly higher in the PP group. E-Selectin and LRG-1 adhesion molecules were found to be significantly higher even in C/S patients compared to normal delivery. As a result; these adhesion molecules can be studied as a marker in PP patients.
Volumetric evaluation of orbital fractures treated by titanium mesh
Authors: MOURA Lucas Borin , JÜRGENS Philipp Christian , MARQUES Nathalia Caetano , CARVALHO Pedro Henrique de Azambuja , GABRIELLI Marisa Aparecida Cabrini , SPIN-NETO Rubens , PEREIRA-FILHO Valfrido Antonio 
Published: September 2022

Abstract
Purpose: Orbital fractures are high prevalent and result in volumetric changes which may result in clinical impairment as enophthalmos and diplopia. This study aims to evaluate orbital volume and anteroposterior eyeball position in orbital fractures treated by titanium mesh.
Methods: This multicenter study evaluated 60 postoperative CT scans of unilateral orbital fractures treated using titanium mesh. Orbital defects were classified according to the extension and involved regions, and the orbital volumes were analyzed by two methods, image sectioning (IS) and computerized segmentation (CS). The eyeball position was obtained from the axial slice in the mid orbit region. Differences up to 8.0% (volume) and 2.0 mm (eyeball position) were considered normal.
Results: Most of defects were class II (n=25) and class III (n=26). Volumetric differences between unaffected and reconstructed orbit ranged from -7.15% to 10.46% (mean: -0.15%), and from -6.32% to 9.69% (mean: -0.01%) in IS and CS method, respectively. In both methods, two reconstructions were greater than anatomical differences, however there was no statistical differences between the orbits in both methods, IS (p=0.852) and CS (p=0.987). Anteroposterior eyeball position ranged from -0.9 mm to 1.8 mm. The correlation between defect classification, eyeball position and IS or CS, were not positive.
Conclusion: In conclusion, regardless of the extent of the orbital defect or evaluation method, fractures treated by titanium mesh reestablished adequately the orbital volume.
Development and assessment of a novel core biopsy-based prediction model for pathological complete response to neoadjuvant chemotherapy in breast cancer
Authors: Lan Ailin , Chen Junru , Li Chao , Jin Yudi , Wu Yinan , Dai Yuran , Jiang Linshan , Li Han , Peng Yang , Liu Shengchun 
Published: September 2022

Abstract
Purpose
Pathological complete response (pCR), the goal of NAC, is considered a surrogate for favorable outcomes in breast cancer (BC) patients administrated neoadjuvant chemotherapy (NAC). This study aimed to develop and assess a novel nomogram model for predicting the probability of pCR based on the core biopsy.
Methods
It was a retrospective study involving 769 BC patients administrated NAC between January 2012 and December 2017. After converting continuous variables to categorical variables, variables entering the model were sequentially identified by univariate analysis, multicollinearity test, and binary logistic regression analysis, and then a nomogram model was developed. The performance of the model was assessed concerning its discrimination, accuracy, and clinical utility. Internal validation was performed by the Bootstrap method.
Results
The optimal predictive threshold for estrogen receptor (ER), progesterone receptor (PR), Ki67, and p53 were 22.5% (95%CI: 0.603-0.718), 6.5% (95%CI: 0.578-0.693), 32.5% (95%CI: 0.610-0.731), and 37.5% (95%CI: 0.586-0.716), respectively (all P <0.001). Five variables were selected to develop the model, clinical T staging (cT), clinical nodal status (cN), ER status, Ki67 status, and p53 status (all P ≤0.001). The nomogram showed good discrimination with the area under the curve (AUC) of 0.804 (95% CI: 0.756-0.853; P <0.001) and good calibration. Decision curve analysis (DCA) showed that the model had practical clinical value.
Conclusion
This study constructed a novel nomogram model based on cT, cN, ER status, Ki67 status, and p53 status, which could be applied to personalize the prediction of pCR in BC patients treated with NAC.
Common and uncommon CT findings in CVID related GL-ILD: correlations with clinical parameters, therapeutic decisions and potential implications in the differential diagnosis
Authors: Scarpa Riccardo , Landini Nicholas , Cinetto Francesco , Milito Cinzia , Gianese Sabrina , Soccodato Valentina , Buso Helena , Garzi Giulia , Carrabba Maria , Messina Emanuele , Panebianco Valeria , Morana Giovanni , Lougaris Vassilios , Catalano Carlo , Bondioni Maria Pia 
Published: September 2022

Abstract
Purpose
To investigate common and uncommon CT findings in GL-ILD that may be also helpful in differential diagnosis, i.e. with sarcoidosis. To compare CT features with functional and immunological parameters. To look for radiological and non-radiological elements that may be predictive of GL-ILD therapy.
Methods
We retrospectively described CT features of 38 GL-ILD patients before any specific therapy. Correlations with functional and immunological features were computed. A logistic regression was performed to find a model associated with subsequent GL-ILD therapeutic decisions.
Results
Most common CT alterations were: bronchiectasis, non-perilymphatic nodules, consolidations, GGO, bands and enlarged mediastinal lymphnodes without calcification. GL-ILD was usually predominant in lower fields.
Fibrotic ILD, GGO, reticulations and bronchiectasis were associated with decreased lung performance (p<0.05). Fibrosis, GGO and bronchiectasis were associated with low IgA levels at diagnosis, whereas high CD4+ T cells percentage was related to GGO (p<0.05).
20/38 patients underwent GL-ILD therapy after CT. A multivariate model combining MZ B cells percentage, IgA at diagnosis, CT evidence of lower field consolidations and mediastinal lymphnodes enlargement showed a good discriminatory capacity with regards to GL-ILD treatment (AUC=0.91).
Conclusions
Most common CT findings in GL-ILD before treatment were small nodules with a non-perilymphatic distribution, consolidations, GGO, bands and bronchiectasis. GL-ILD was usually prevalent in lower fields. A lower fields involvement with non-perylimphatic nodules and a non-traction bronchiectasis pattern could suggest GL-ILD instead of sarcoidosis. MZ B cells percentage, IgA at diagnosis, lower field consolidations and mediastinal lymphnodes enlargement were predictive of a specific GL-ILD therapy.
Analysis of telomere length and the relationship with neurocognitive functions in euthymic bipolar disorder: a cross-sectional pilot study
Authors: Zeng Ziwen , Cai Luyao , Wan Chao , Yang Haichen , Yang Xi 
Published: September 2022

Abstract
Background: Telomere shortening has been considered a potential biological marker related to disease susceptibility and aging in psychiatric disorders. However, the relationship between telomere length and bipolar disorder (BD-I and BD-II) is uncertain. Moreover, whether telomere shortening is an independent factor of cognitive impairment in BD patients is still inconclusive.
Methods: We explore telomere length and cognitive function in patients with bipolar disorder and the relationship between them. We enrolled three groups (35 patients with euthymic BD-I, 18 with euthymic BD-II, and 37 healthy controls). Telomere length was measured by fluorescent quantitative polymerase chain reaction (q-PCR), and cognitive function was evaluated by the MATRICS Consensus Cognitive Battery (MCCB). SPSS 24.0 was used for statistical analysis.
Results: The telomere length of euthymic patients with BD-I and BD-II was shorter than that of healthy controls. Telomere length was not significantly different between BD-I and BD-II. Patients with BD-I and BD-II showed poor cognitive function compared to healthy controls. In the three groups, no correlation was detected with telomere length orcognitive function. The duration of illness (DI) was negatively correlated with reasoning and problem solving in BD-I. Nevertheless, the duration of untreated illness (DUI) showed a negative correlation with visual learning performance.
Conclusions: This study provides preliminary evidence that shortenedtelomere length is a potential biomarker for BD-I and BD-II. However, the cognitive deficit in BD has no correlation with shortened telomere length.
Global extreme wave estimates and their sensitivity to the analysed data period and data sources
Authors: AMAROUCHE Khalid , AKPINAR Adem , KAMRANZAD Bahareh , KHAMES Ghollame-Ellah-Yacine 
Published: September 2022

Abstract

In the lack of wave measuring buoys operating over extended periods, the use of wave hindcast data or satellite observations is indispensable for estimating global extreme wave heights. However, the results may depend on the analysed wind wave sources and the length of the analysed period. The sensitivity of the estimated extreme significant wave heights (SWH) to the analysed data sources and periods is investigated in this study. Global extreme wave heights are estimated using ECMWF Reanalysis v5 data (ERA5), global wave hindcast developed based on Simulating WAves Nearshore forced by the Japanese 55-year Reanalysis (SWAN-JRA55), satellite altimeter observations, and long-term wave buoy measurements. Both Annual Maximum fitting to the Generalized Extreme Value Distribution (AM-GEV) and Peaks Over Threshold fitted to the Generalized Pareto Distribution (POT-GPD) models are used. The results show that the global extreme SWH estimates considerably depend on the analysed data sources. The relative differences observed between the analysed data sources are > 20% in large part of the world. Thus, by increasing the analysed data periods, the relative differences in extreme SWH are mainly lower, but they can reach 30% and are more important using AM-GEV. Besides, by comparing the extreme values from reanalysis and hindcast wave data to those from long-term wave measurements, underestimations of up to 2 m are observed for a return period of 100 years in the North-West Atlantic and North-East Pacific.
Classes of Mormordicoside with potent and selective tumor cell growth inhibitory activity: prediction of Pyruvate kinase muscle isozyme 2 (PKM 2) and Anti-apoptotic Myeloid leukemia 1 (MCL1) inhibitor through machine learning.
Authors: Ibisanmi Tope Abraham , Aribisala Jamiu O , Odjegba Peace Ifeoma , Ademuyiwa Damilola , Akinmusere Ayomide Gbenga , Ajayi Faith Ibukunoluwa 
Published: September 2022

Abstract

Background
The difficulty in treating cancer resides in the ability to target abnormal proliferation while protecting normal proliferation, a feat that necessitates a thorough comprehension of both the normal and malignant mechanisms that promote cell growth and proliferation. Targeting cell death signaling pathways such as glycolytic and mitochondrial apoptosis is hallmark of many cancers the aim in which this research is ready to evaluate.
Methods
Atomistic molecular dynamics simulation of top hits after molecular docking and ADMET profiling of the ligands were performed for main protease-hit complexes.
Results
Docking scores of ligands used against PKM2 ranges from – 9.36 to – 12.1 kcal/mol, wherein, Mormordicoside-F2 had the highest score (-12.1kcal/mol) performing better than the FDA approved drug Benserazide(-7kcal/mol). Likewise, the scores ranged between – 8.51 and – 12.05kcal/mol for Anti-apoptotic Myeloid leukemia 1 (MCL-1), with Mormordicoside-F1 being the highest ranked compound performing better than the FDA approved drug Venetoclax(-8.6 kcal/mol). The RMSD plots obtained depicted stable trajectories with consistent and minor fluctuations implying that the protein (PKM2 and MCL1) backbone underwent minor structural perturbations. In addition, several significant peaks of increased fluctuations (RMSF) were also observed, indicating their increased interaction potential implying that the ligands could adapt effectively in the binding pocket of the protein. SASA analysis results shows that ligands used retained inside their shallow binding pocket. The phylogenetic tree obtained implies likelihood of reoccurring result of the Insilco profiling.
Conclusion
This research unveils that Mormordicoside F1 shows acceptable stability with Anti-apoptotic Myeloid leukemia 1 (MCL-1), likewise Mormordicoside F2 against PKM2. These hits may offer a more advantageous repurposing alternative.
CT-based machine learning radiomics predict CCR5 expression level and survival in ovarian cancer
Authors: Wan Sheng , Zhou Tianfan , Che Ronghua , Li Ying , Peng Jing , Wu Yuelin , Gu Shengyi , Cheng Jiejun , Hua Xiaolin 
Published: September 2022

Abstract
Objective
We aimed to evaluate the prognostic value of C-C motif chemokine receptor type 5 (CCR5) expression level for patients with ovarian cancer and to establish a radiomic model that can predict CCR5 expression level using The Cancer Imaging Archive (TCIA) and The Cancer Genome Atlas (TCGA) database.
Methods
A total of 343 cases of ovarian cancer from the TCGA were used for the gene-based prognostic analysis. 57 cases had preoperative computed tomography (CT) images stored in TCIA with genomic data in TCGA were used for radiomic feature extraction and model construction. 89 cases with both TCGA and TCIA clinical data were used for radiomic model evaluation.
Results
CCR5 was identified as a differentially expressed prognosis-related gene in tumor and normal sample, which were involved in the regulation of immune response and tumor invasion and metastasis. Four optimal radiomic features were selected to predict overall survival. The performance of the radiomic model for predicting the CCR5 expression level with 10-fold cross- validation achieved Area Under Curve (AUCs) of 0.770 and of 0.726, respectively, in the training and validation sets. A predictive nomogram was generated based on the total risk score of each patient, the AUCs of the time-dependent receiver operating characteristic (ROC) curve of the model was 0.8, 0.673 and 0.792 for 1-year, 3-year and 5-year, respectively. Along with clinical features, important imaging biomarkers could improve the overall survival accuracy of the prediction model.
Conclusion
The expression levels of CCR5 can affect the prognosis of patients with ovarian cancer. CT-based radiomics could serve as a new tool for prognosis prediction.
A Comparison between the da Vinci Xi Endowrist Stapler and a conventional Laparoscopic Stapler in Rectal Transection: A Randomized Controlled Trial
Authors: Teo Nan Zun , Ngu James Chi-Yong 
Published: September 2022

Abstract
PURPOSE
Distal rectal transection following robotic total mesorectal excision (TME) for rectal cancer can be challenging especially in the deep and narrow pelvis. This can be performed transabdominally using either a robotic stapler (RS) or laparoscopic stapler (LS). We compared the operative outcomes and ergonomic differences between RS and LS after robotic TME.
METHODS
We performed a single center randomized controlled trial. 40 patients with rectal or rectosigmoid cancer who were planned for elective robotic rectal surgery were randomized to either RS (N = 20) or LS (n = 20). Primary outcome was the number of stapler cartridges required to completely transect the rectum. Secondary end points included technical ease and efficacy of stapler use, completeness of the staple line, staple line bleeds, and clinically significant anastomotic leaks.
RESULTS
The mean number of stapler cartridges expended was similar between RS and LS (1.75 versus 2.05, p=0.082). While significantly less stapler adjustments were required in the RS group (1.55 versus 2.75, p = 0.014), complete rectal transection took a comparable amount of time (p=0.149). There were no differences in integrity of staple line, staple line bleeding and anastomotic leaks. Results from the user experience survey showed that RS scored better for control, engagement, visualization and overall experience. Experience with firing and disengagement was similar between both groups.
CONCLUSION
The RS was more ergonomic than the LS. While this complemented the use of robotics in rectal surgery, it did not result in a significant reduction in the number of stapler cartridges required for rectal transection.
KIAA1429 regulates the expression of RAB27B in a m6A YTHDF1 axis-dependent manner and promotes the progression of chronic myeloid leukemia, serving as a potential therapeutic target
Authors: Yao Fangyi , Zhong Fangmin , Jiang Junyao , Cheng Ying , Xu Shuai , Liu Jing , Lin Jin , Zhang Jing , Li Shuqi , Li Meiyong , Xu Yanmei , Huang Bo , Wang Xiaozhong 
Published: September 2022

AbstractBackground:Chronic myeloid leukemia (CML) is one of the most common adult leukemias. The considerable negative changes in its acute phase and the adverse drug effects could lead to poor prognosis. N6-methyladenine (m6A) modification plays an important regulatory role in physiological and pathological processes. KIAA1429 is an important m6A regulator, but the biological role of KIAA1429 in CML is still unclear.Methods:RT-qPCR and Western blot were used to analyze the differential expression of KIAA1429 in CML clinical samples and cell lines. CCK-8, EdU staining, flow cytometry, Transwellassay, cellular morphology evaluation, and liquid chromatography-mass spectrometry (LC-MS) were further implemented to assess the changes in the biological functions of CML cell lines with KIAA1429 knockdown or overexpression. In addition, subcutaneous tumorigenesis experiment in nude mice was performed forin vivofunction assessment. The combination of MeRIP-seq and mRNA-seq predicted that RAB27B is a downstream target gene of KIAA1429. RIP-qPCR, RNA stability analysis, SELECT, and “rescue” experiments were then conducted to explore the mechanisms underlying the regulation of KIAA1429/m6A/YTHDF1 axis on RAB27B. Finally, the inhibitory effects of rucaparib on KIAA1429 and CML were exploredin vitroandin vivo.Results:The m6A and KIAA1429 expression was significantly upregulated in patients with blast phase CML. KIAA1429 was found to regulate the total level of RNA m6A modification in the CML cells and to promote the malignant biological behaviors of CML cells, including proliferation, migration, and imatinib resistance. Inhibiting KIAA1429 in CML cells regulated the stability of RAB27B mRNA through the m6A/YTHDF1 axis, consequently inhibiting CML proliferation and drug efflux, and ultimately increasing cell sensitivity to imatinib. Rucaparib suppressed the expression of KIAA1429 and CML cell proliferation, and promoted cell apoptosis. The combined use of rucaparib and imatinib enhanced the sensitivity of CML cells to imatinib. Rucaparib inhibited the tumorigenesis capability of CML cellsin vivo.Conclusions:Elevated KIAA1429 expression in the blast phase of CML enhanced the stability of RAB27B mRNA through the m6A/YTHDF1 axis to upregulate RAB27B expression, and thus promoting CML progression. Therefore, rucaparib exerts inhibitory effects on KIAA1429 expression and CML progression.